hai Jiao

Transcription

hai Jiao

1 Bo
ook of Programme and Abstract for TACC2008
8 Shangh
hai Jiao
o Tong Univers
sity
Shanghai Jiao Tong Univeersity (SJTU),, formerly th
he Nang Yangg Public Scho
ool, founded in 1896 by Mr. SH
HENG Xuanhuai, is a key u
university of C
China. Among the famous f
and outstanding alumni are JIANG Zemin
n, the Secrettary General of CPC and the President of th
he People's R
Republic of Ch
hina, and WA
ANG Daohan, ZOU
U Taofen, LU Dingyi, MAO Yisheng, QIA
AN Xuesen, CA
AI Er, WANG An, etc. Today SJTU h
has 16 schoo
ols and 80 insstitutes. In ad
ddition, SJTU has also sett up the Graduatee Schools and Schools for Continuing Education. Up U till now SJJTU has 74 Masteers degree prrograms, 42 P
Ph.D. program
ms and 8 natiional key discciplines and 5
5 national keyy laboratories and national engineering research cen
nters. SJTU has assembled a large number of o
well‐known w
teeachers and lecturers, including somee faamous scienttists and proffessors. Todayy SJTU has 14
4 Academicians
A
of Academ
mia Science and a
of Chinaa Academy A
of Engineering E
aand 1, 200 professors and
d associate proffessors. Today there are 18,,000 studen
nts in SJTU
U, in
ncluding 14
4,000 undeergraduates and 4000
0 postgraduates
p
s and Ph. D. sstudents, 4,00
00 continuingg sttudents and over 290 fo
oreign students. Students frrom SJTU have h
achieveed top prize
es in various competitions. SJTU is un
ndergoing rap
pid developm
ment and grow
wth. Now, it has five campuses, th
he Xuhui, thee Minhang, the t Qibao, th
he Shangzhong Road and the Fahu
uazheng Road
d. Over the past decade, tthe area of caampuses from 40 ha to 175 ha. SJTU has built the new campus in Minhang M
District, Shanghai. The new n
campuss has an areea of 297 accre. The completion o
of the constru
uction of Min
nhang Campu
us is the new starting point and neew hope in the t history of o developmeent of Shangghai Jiao Tong Universsity. SJTU has been actively involved in
n the exchan
nge and coop
peration with other co
ountries. Up till now, SJTU
U has establisshSed relation
ns with moree than 60 univversities abro
oad as well as a large numb
ber of foreign
n research insstitutions and
d corporations. SJTU has in
nvited more tthan 100 fam
mous scientists, including thee Nobel prizee winners an
nd physicists Yang Zhenn
ning, Li Zhenggdao and Ding Zaozhongg. SJTU sends excellent teaachers and sttudents abroaad every year to give lecttures, to stud
dy or to atten
nd internatio
onal academicc conferences. SJTU is maaking great efforts e
to approach the world w
first‐raate standard of institutio
ons of higher learning at th
he beginning in the 21st century. 2
2 Book of Programme and Abstract for TACC2008 Theory and Applications of Computational Chemistry TACC2008 Programme and Abstract September 23 – 27, 2008 Shanghai, China 3 Table of Contents Shanghai Jiao Tong University.............................................................................................................. 2
Table of Contents ................................................................................................................................. I
Greeting Message ................................................................................................................................ II
List of Sponsors and Media Partners...................................................................................................III
Organizing Committee ........................................................................................................................ V
Conference Hall Plan ......................................................................................................................... VI
Programme .......................................................................................................................................... 1
Timetable ............................................................................................................................................. 3
Timetable - Keynote and Plenary ................................................................................................... 3
Timetable - Invited Talk and Oral Session ...................................................................................... 6
1.
Electronic Structure ........................................................................................................ 6
2.
Statistical Mechanics and Multi-scale Issues .................................................................... 8
3.
Bioformatics and Biochemistry ...................................................................................... 10
4.
Materials and Nano ...................................................................................................... 12
5.
Cheminformatics and Drug Design ............................................................................... 14
6.
Chemical Modelling for a Sustainable Environment ....................................................... 16
Timetable - Poster Sessions 01 (Sep. 24th Evening) ........................................................................ 17
Timetable - Poster Sessions 02 (Sep. 26th Evening) ........................................................................ 21
Abstracts ............................................................................................................................................ 26
Keynote & Plenary ...................................................................................................................... 26
Abstract - Invited and Oral Presentation ...................................................................................... 54
1.
Electronic Structure ...................................................................................................... 54
2.
Statistical Mechanics and Multiscale Issues ................................................................... 75
3.
Bioformatics and Biochemistry ...................................................................................... 95
4.
Materials and Nano .................................................................................................... 114
5.
Cheminformatics and Drug Design ............................................................................. 136
6.
Chemical Modelling for a Sustainable Environment..................................................... 150
Poster ....................................................................................................................................... 163
List of participants (Alphabetic order) ............................................................................................... 286
Additional Informations ................................................................................................................... 301
International Association of Scientists in the Interdisciplinary Areas(IASIA) .............................. 301
IASIA Membership Application Form ....................................................................................... 302
I Book of Programme and Abstract for TACC2008 Greeting Message Dear friends:
On behalf of the Shanghai Jiaotong University and International Association of Scientists in the Interdisplinary
Areas(IASIA) I would like to welcome you all to Shanghai to attend the the international conference on the Theory
and Applications of Computational Chemistry(TACC 2008). Indeed, it provides us an excellent opportunity to get
together with some most prominent scientists in the world, to name a couple of them, Prof. Rudy Marcus, the 1992
Nobel Prize Laureate in Chemistry and Prof. Martim Karplus of Harvard University.
Since the first applications of computer in chemistry in the early 1960's, "computational chemistry" has evolved
today to be at the vanguard of most advances in chemistry, material science, physics, geology, biology and
medicine. Its impact on chemistry can be noted from the fact that within four decades of its existence, five of the
top ten most highly cited publications in 125 years of JACS are related to computational chemistry. Apart from
technical advances in computers and algorithms, the phenomenal impact of computational chemistry is also due to
the dedicated and sustained efforts of a large number of individuals. In this regard, we felt that it would be befitting
to organize a symposium "Theory and Applications of Computational Chemistry" in 2008 gathering nearly all of
the world's leading exponents of computational chemistry. This event also follows previous successful TACC
conferences, for example, 2004 TACC conference in Korea.
2008 is a special year for China, we have successfully hosted the 29th Olympics Game. We feel confident that we
are able to work with scientists in the world to achieve excellence on theory and application of computational
chemistry. This great country of colure and history now experiences greatest opportunity to advance our sciences
and technology to a new level. Your visit and presence at TACC 2008 means a great deals to us.
Shanghai Jiao Tong University is one of the oldest universities in China. The University, through its century-long
history, has nurtured large numbers of outstanding figures and made significant contributions to the thriving and
prosperity of the nation and the development of science and technology. Its famous alumni include JIANG Zemin
and QIAN Xuesen. Of all the academicians of China's Academy of Sciences and Academy of Engineering, more
than 200 are the alumni of Jiao Tong University. It is a honor to have you with us when we are implement a grand
blueprint for future development and determined to make continued efforts to build itself into a first class university
in the world.
Hopefully you fully enjoy your stay in Shanghai and have a wonderful conference!
Sincerely,
Dongqing Wei, Ph.D.
Professor of Theoretical Chemistry and Bioinformatics
Conference Chairman:
Wei, Dongqing (Shanghai Jiao Tong University)
Peslherbe, Gilles H. (Concordia University, Canada)
Hynes, James T. (ENS, Paris/University of Colorado)
II Book of Programme and Abstract for TACC2008 List of Sponsors and Media Partners Cosponsors ‐ Organizations Shanghai Jiao Tong University
http://www.sjtu.edu.cn/english/index/index.htm
International Association of Scientists in the
Interdisciplinary Areas(IASIA)
http://interdisciplinarysciences.org/EnglishNew
National Science Foudation of China(NSFC)
http://www.nsfc.gov.cn/nsfc2008/index.htm
Chinese Chemical Society
http://www.ccs.ac.cn/
Canadian Hongcam International Trade Corp
http://www.hongcam.com.cn/
Tri-I Biotech, Inc.
http://www.tri-ibiotech.com.cn/
Shanghai Center for Bioinformation Technology
(SCBIT)
http://scbit.org/eng/index.php
Cosponsors – Journals Interdisciplinary Sciences (An International
Journal)
http://www.springer.com/life+sci/bioinformatics/jour
nal/12539
III Book of Programme and Abstract for TACC2008 Journal of
Physical Chemistry and Chemical Physics
http://www.rsc.org/Publishing/Journals/CP/index.asp
Acta Physico-Chimica Sinica
http://www.whxb.pku.edu.cn/enindex.asp
Journal of Molecular Graphics and Modelling
http://www.elsevier.nl/locate/jmolgraph
Molecular Simulation
http://www.tandf.co.uk/journals/titles/08927022.asp
Media Partners www.bioon.com
http://www.bioon.com/
www.goingtomeet.com
http://www.meeting.edu.cn/
http://www.chemistry.or.jp/index-e.html
http://www.chemistry.or.jp/index-e.html
http://www.sciencenet.cn/
http://www.sciencenet.cn/
Special Acknowledgement
TACC2008 is financially Supported by K.C.Wong Education Foundation Hong Kong
IV Book of Programme and Abstract for TACC2008 Organizing Committee Conference Chairman Conference Co-chairmen
Wei, Dongqing (Shanghai Jiao Tong University) Peslherbe, Gilles H. (Concordia University, Canada) Hynes, James T. (ENS, Paris/University of Colorado) Local Organizing Committee
Chairman
Li, Yixue (Shanghai Jiao Tong University)
Members(alphabetic order)
Fang, Decai (Beijing Normal University)
Fang, Weihai (Beijing Normal University)
Han, Keli (Dalian Institute of Chemical Physics)
Jiang, Hualiang (Shanghai Institute of Materia Medica, SIMM, CAS)
Lai, Luhua (Beijing University)
Li, Shuhua (Nanjin University)
Li, Xiangyuan (Sichuan University)
Liu, Wenjian (Beijing University)
Shuai, Zhigang (Institute of Chemistry, CAS)
Sun, Huai (Shanghai Jiao Tong University)
Wei, Dongqing (Shanghai Jiao Tong University)
Wu, Wei (Xiamen University)
Yang, Jinlong (University of Science and Technology)
International Advisory Committee
Chairman
Prof. Salahub, Dennis (University of Calgary)
Members(alphabetic order)
Brooks III, Charles (Scripps Institute)
Blum, Lesser (University of Puerto Rico)
Chou, Kuo-Chen (Gordon Life Science Institute)
Gao, Jiali (University of Minnesota)
Guo, Hong (University of Tennessee)
Kim, Kwan (Pohang University of Science and Technology)
Klein, Michael (University of Pennsylvania)
Luo, Xincai (Astrazeneca)
Patey, Gren (University of British Columbia)
Peslherbe, Gilles (Concordia University)
Rossky, Peter (University of Texas at Austin)
Roux, Benoit (Cornell University)
Yang, Weitao (Duke University)
Zhang, John (New York University)
V Bo
8 Confere
ence Halll Plan Placce for sess
sions
Registering
Prefunction Area 1
P
Keynote & Plenary
ES (Electronnic structure)
SM (Statisticcal Mechanicss and Multi-sscale Issues)
BIO (Bioform
matics and Biiochemistry)
➊ New Cenntury Hall
➊ New Cenntury Hall
➊ New Ceentury Hall
➊ New Ceentury Hall
MN (Materiaals and Nano))
CD (Cheminnformatics andd Drug Desiggn)
EV (Chemicaal Modelling for a Sustainnable Environnment)
Poster Sessioons
➑ Virtue Hall / ➐Generrosity Hall
➏ Harmonyy Hall
➍ Honour Hall
H
➊New Cenntury Hall
V
VI Book of Programme and Abstract for TACC2008 Programme Timetable of TACC2008, Sep. 23 – 27, Shanghai, China
Time
Event
Full Day
22
Monday
Hongcam’s Supplier workshop
New Century Hall
Evening
20:15 – 22:10
Hongcam’s Supplier workshop
New Century Hall
08:00 – 08:30
Opening Ceremony
New Century Hall
08:30 – 11:50
Friday
27
Saturday
2. Plenary Sessions: P23-01, P23-02
Plenary Sessions: P23-03, P23-04
New Century Hall
14:00 – 18:05
Evening
19:00 – 21:00
Morning
08:00 – 11:50
New Century Hall
Afternoon
14:00 – 18:05
Parallel Sessions
* (See below)
Evening
19:00 – 21:00
Morning
08:00 – 11:50
Afternoon
14:00 – 18:05
Plenary Session: P25-03, P25-04
New Century Hall
Evening
19:00 – 21:00
Banquet
New Century Hall
Morning
08:00 – 11:50
New Century Hall
Afternoon
14:00 – 18:05
Parallel Sessions
* (See below)
Evening
19:00 – 21:00
Poster Session 02
New Century Hall
Morning
08:00 – 11:50
Parallel Sessions
* (See below)
Afternoon
14:00 – 18:05
Parallel Sessions
* (See below)
Evening
19:00 – 21:00
-------
25
26
1. Keynote lecture: Rudy Marcus;
Afternoon
Wednesday
Thursday
Prefunction Area 1
16:30 – 18:00
23
24
Registration
Afternoon
Morning
Tuesday
Location
SYBYL8.0，new software new targets,
Tri- Biotech, Inc.
Poster Session 01
Author’s Workshop (simultaneous)
1. Keynote lecture: Martin Karplus
2. Plenary Session: P25-01, P25-02
New Century Hall
New Century Hall
New Century Hall
New Century Hall
Place for parallel sessions:
ES (Electronic structure)
New Century Hall – 1
SM (Statistical Mechanics and Multi-scale Issues)
BIO (Bioformatics and Biochemistry)
MN (Materials and Nano)
Virtue Hall / Generosity Hall
CD (Cheminformatics and Drug Design)
Harmony Hall
EV (Chemical Modelling for a Sustainable Environment)
Honour Hall
1 Book of Programme and Abstract for TACC2008 Hongcam’s Supplier workshop Time: September 22, 2008 (Register Day) Location: New Century Hall Timetable: Section 1 16:30‐18:00 1. 16:30‐16:50 HyperChem and the Future of Molecular Modeling by Neil S. Ostlund. 2. 16:50‐17:10 Dawning’s Solution in Computional Chemistry by Chongshan Zhao 3. 17:10‐17:40 GRIP docking: A Simple and Fast Docking Method by Subhash Ajmani, PhD 4. 17:40‐18:00 The MOLCAS package: A platform for application and development of ab inito methods. By Roland Lindh Section 2 20:15‐22:10 Topic: Introducing ADF2008 seminar (The Amsterdam Density Functional program) 1. 20:15‐21:05 Historical overview of ADF and applications in spectroscopy and reaction chemistry by Prof. E.J. Baerends (Vrije Universiteit Amsterdam) 21:05‐21:20 Coffee break 2. 21:20‐21:55 New features in ADF2008 and short GUI demonstration by Dr. S.J.A. van Gisbergen (CEO of Scientific Computing & Modelling) 21:55‐22:10 Questions and Answers 2 Book of Programme and Abstract for TACC2008 Timetable Timetable – Keynote and Plenary Sep. 23 Tuesday
Keynot & Plenary P23-01, Chair: Wei, Dongqing
8:00 – 8:30
Opening Ceremony
Keynote Lecture
8:30 – 9:10
Rudy Marcus
Abst. No.
Experiment-motivated theoretical studies of reaction rates:’on water’ organic
reactions, isotope fractionation and single-molecule fluctuations
Plenary Lectures
9:10 – 9:40
Patey, Gren
9:40 – 10:10
Salahub, Dennis
Abst. No.
Structural and Dynamical Properties of Ionic Liquids: Influences of Ion Size Disparity
and Charge Location
Quantum mechanics and molecular mechanics: could they/should they play a key
role in systems biology? What’s possible? What’s not?
10:10 – 10:20
KN001
PL024
PL002
Coffee Break
Plenary Lecture P23-02, Chair: Patey, Gren
10:20 – 10:50
Blum, Lesser
10:50 – 11:20
Yang, Weitao
11:20 – 11:50
Hirst, Jonathan D.
A New Analytical Theory For Real Electrolytes: The Extended Soft Binding Mean
Spherical Approximation (ESBIMSA.)
Ab Initio QM/MM Minimum Free Energy Path for Chemical Reactions in Enzymes and
in Solution
Computing spectroscopic observables from protein simulations
11:50 – 14:00
PL003
PL004
PL005
Lunch
Plenary Lecture P23-03, Chair: Peslherbe, Gilles
14:00 – 14:25
Helgaker, Trvgue
New techniques of self-consistent field theory
PL034
14:25 – 14:50
Clementi, Enrico
From Atomic and Molecular Orbitals to Chemical Orbitals.
PL007
14:50 – 15:15
Van der Avoird
Ab initio intermolecular force fields spectroscopically validated: state of the art
PL008
15:15 – 15:40
Friesner, Richard A.
High Resolution Modeling of Protein Structure and Protein-Ligand Interactions
PL009
15:40 – 15:50
Coffee Break
Plenary Lecture P23-04, Chair: Salahub, Dennis
16:00 – 16:25
Gerber, Benny
16:25 – 16:50
Brooks, Bemard
16:50 – 17:15
Frenking, Gernot
17:15 – 17:40
Bryant, Stephen
17:40 – 18:05
Werner,
Hans-Joachim
Anharmonic Vibrations of Biological Molecules:
Quantum Algorithms and Spectroscopic Applications
Multi-scale Methods for Macromolecular Systems in Computational Biophysics
Direct Estimate of Conjugation, Hyperconjugation and Aromaticity with the EDA
Method
PL010
PL011
PL026
PubChem and the NIH Molecular Libraries Project
PL013
Recent advances in local and explicit electron correlation methods
PL014
3 Book of Programme and Abstract for TACC2008 Sep. 24 Wednesday
Plenary Lecture P24-01, Chair: Amalendu Chandra
8:00 – 8:25
Wei, Dong-Qing
Structure Bioinformatics, TCM Databases, and Personalized Drug Design
PL015
8:25 – 8:50
Parrinello, Michelle
Large Scale Motions in Proteins
PL016
Computer simulation of biomolecular systems: where do we stand ?
PL017
Systematic Coarse-graining of Biomolecular Systems
PL018
8:50 – 9:15
9:15 – 9:40
Van Gunsteren,
Wilfred F.
Voth, Gregory A.
9:40 – 9:50
Coffee Break
Plenary Lecture P24-02, Chair: Yang, Weitao
Accurate interaction energies of building blocks of biomacromolecules: quantum
9:50 – 10:15
Hobza, Pavel
10:15 – 10:40
Smith, Jeremy
Computer Simulation of Protein Dynamics
PL020
10:40 – 11:05
Thiel, Walter
QM/MM Studies of Enzymes
PL021
11:05 – 11:30
Iñaki Tuñón
11:30 – 11:55
Whangbo, Mike.H
chemical study
Dynamical Effects in Enzyme Catalysis. An Analysis of the Chalcone Isomerase
Catalyzed Reaction
Effects of Spin-Orbit coupling on Magnetic Properties of Discrete and Extended
Magnetic Systems
PL019
PL022
PL023
Sep. 25 Thursday
Keynote and Plenary Lecture P25-01, Chair: Guo, Hong
Keynote Lecture
8:00 – 8:40
Karplus, Martin
How Biomolecular Motors Work: Insights from Simulations
KN002
Plenary Lectures
8:40 – 9:10
Li, Yixue
9:10 – 9:35
Wang, Alex
9:35 – 10:00
Bagchi, Biman
Functional classification of small molecules by gene expression module based
similarity search
Orbital-Corrected Orbital-Free Density Functional Theory
Anomalous Dynamics of Water in Bulk Liquid and in Hydration Layer of Proteins and
DNA
10:00 – 10:10
PL001
PL025
PL040
Coffee Break
Plenary Lecture P25-02, Chair: Gao Jiali
10:10 – 10:35
Guo, Hong
10:35 – 11:00
Luzar, Alenka
11:00 – 11:25
Kato, Shigeki
11:25 – 11:50
Roos, Björn
11:50 – 12:15
Patel, Sandeep
Narrowing the gap in understanding protein structure and function through computer
simulations
Nanoscale 4nergetic in electric field
Free Energy Surfaces and Dynamics of Chemical Reactions in Solution and
Biological Systems
Multiconfigurational Quantum Chemistry – the state of the art
Non-Additive Electrostatic Force Fields for Biomolecules: Development and
Application of Charge Equilibration Models
PL027
PL028
PL029
PL030
PL031
4 Book of Programme and Abstract for TACC2008 Plenary Lecture P25-03, Chair: Yang, Weitao
Quantum Conductance of Subnanowires, Negative Differential Resistance of
14:00 – 14:25
Kim, Kwang S.
14:25 – 14:50
Hase, William L.
Direct Dynamics Simulations of Post-Transition State Dynamics
PL033
14:50 – 15:15
Liu, Wenjian
New Generation Relativistic Electronic Structure Theory
PL006
15:15 – 15:40
Hirata, Fumio
Molecular Recognition Realized by the Statistical Mechanics Theory of Liquids
PL035
Molecular Wires, and Super-gnetoresistance of Graphene Nanoribbon Devices
15:40 – 15:50
PL032
Coffee Break
Plenary Lecture P25-04, Chair: Hirst, Jonathan
16:00 – 16:25
Hirao, Kimihiko
16:25 – 16:50
Piecuch, Piotr
16:50 – 17:15
Pulay, Peter
17:15 – 17:40
17:40 – 18:05
Towards Linear-Scaling Hybrid DFT
Renormalized Coupled-Cluster Methods: Theoretical Foundations and Extension to
Open-Shell and Large Systems
Raghavachari,
Krisahnan
PL036
PL037
Efficient ab initio Monte Carlo simulations of molecules in solution
PL038
QM ⁄ QM Electronic Embedding Models for Materials Chemistry
PL039
Mukamel, Shaul
PL012
Sep. 26 Friday
Plenary Lecture P26-01, Chair: Liu, Wenjian
8:00 – 8:25
Kim, Hyung
Chemical Reactions in Room-Temperature Ionic Liquids
PL041
8:25 – 8:50
Ohmine, Iwao
Water Dynamics; Fluctuations, Phase-Transitions and Reactions
PL042
8:50 – 9:15
Tobias, Doug
Simulation Studies of Heterogeneous Atmospheric Chemical Processes
PL043
9:15 – 9:40
Szalewicz Krzysztof
Recent progress in theory of intermolecular forces
PL044
9:40 – 9:50
Coffee Break
Plenary Lecture P26-02, Chair: Kim, Hyung
Importance and Application of “Computational Resources for Drug Discovery”
9:50 – 10:15
Raghava, Gajendra
10:15 – 10:40
Cui, Qiang
O, Proton(s), Where Art Thou?
PL046
10:40 – 11:05
Ernzerhof, Matthias
Simple models for the description of molecular conductors
PL047
11:05 – 11:30
Burghardt, Irene
11:30 – 11:55
Pomes, Regis
Plateform
Ultrafast Electronic Processes at Organic Semiconductor Junctions: A
Molecular-Level, Quantum-Dynamical Perspective
Theoretical Studies of Proton Translocation in Membrane Proteins
PL045
PL048
PL049
5 Book of Programme and Abstract for TACC2008 Timetable – Invited Talk and Oral Session 1.
Electronic Structure Sep. 24 Wednesday – Electronic Structure
Oral session O24-ES01, Chair: Bian,Wensheng
New Developments in Computationally Efficient Generalized Van Vleck Perturbation
14:00 – 14:20
Hoffmann, Mark
14:20 – 14:40
Li, Shuhua
14:40 – 15:00
Allen, Wesley
15:00 – 15:20
Kallay, Mihaly
Theory and applications of perturbative coupled-cluster methods.
IN-ES004
15:20 – 15:40
Van Gisbergen, Stan
New developments in the Amsterdam Density Functional (ADF) program suite
IN-ES005
Theory
Block correlated coupled cluster theory for bond breaking potential energy surfaces
Methodological Advances in State-Specific Multireference Coupled Cluster Theory.
Applications to Benzynes, Antiaromatics, Novel Carbenes, and Benchmark Systems
15:40 – 16:00
IN-ES001
IN-ES002
IN-ES003
Coffee Break
Oral session O24-ES02, Chair: Gerber, Benny
16:00 – 16:20
Garcia-Cervera,
A Linear Scaling Subspace Iteration Algorithm with Optimally Localized Wave
Carlos J
Functions for Kohn-Sham Density-Functional Theory
16:20 – 16:40
Jacek Korchowiec
16:40 – 17:00
Bian,Wensheng
17:00 – 17:20
Varandas, Antonio
17:20 – 17:40
HADA, Masahiko
Elongation cutoff technique: an efficient sparse matrix algebra approach to linear
scaling
A scheme with combination of methods: Highly efficient quantum calculations of
acetylene-vinylidene isomerization in full-dimensionalitya
Toward High-Accuracy Ab Initio Potentials At Low Cost
An Endeavor at Constructing an Accurate Two-Component Relativistic Method for
Heavy and Super-Heavy Elements
IN-ES006
OR-ES007
IN-ES008
IN-ES009
IN-ES010
Sep. 26 Friday – Electronic Structure
Oral session O26-ES03, Chair: Ramasami,Ponnadurai
14:00 – 14:20
Crawford, Daniel
Chiroptical Response and Local Correlation
14:20 – 14:40
Cortona, Pietro
14:40 – 15:00
Filatov, Michael
Static Electron Correlation in Molecules: Spin-restricted Density Functional Approach
IN-ES013
15:00 – 15:20
Geerlings, Paul
Conceptual DFT : Redox Reactions Revisited
IN-ES014
15:20 – 15:40
Goerling, Andreas
Solving longstanding problems in DFT with orbital-dependent functionals
IN-ES015
New correlation 6nergetic6 in DFT: theory and New correlation 6nergetic6 in DFT:
theory and tests
15:40 – 16:00
IN-ES011
IN-ES012
Coffee Break
Oral session O26-ES04, Chair: Geerlings, Paul
Wesolowski,
Localized electronic excitations in condensed phase from orbital-free embedding
Tomasz
calculations
16:20 – 16:40
Stavros C. Farantos
Interpreting Molecular Vibrational Spectra By Periodic Orbits
OR-ES017
16:40 – 17:00
Lindh, Roland
New developments of the Cholesky Decomposition technique in Quantum Chemistry
IN-ES018
17:00 – 17:20
Althorpe,Stuart C
Quantum dynamics at conical intersections
IN-ES019
16:00 – 16:20
IN-ES016
6 Book of Programme and Abstract for TACC2008 17:20 – 17:40
Baerends, Evert Jan
Excitation energies with time-dependent density matrix functional theory
IN-ES024
Sep. 27 Saturday- Electronic Structure
Oral session O27-ES01, Chair:
8:00 – 8:20
Hirata, So
8:20 – 8:40
Hoggan, Philip
8:40 – 9:00
Kobayashi, Masato
9:00 – 9:20
Sun, Zhigang
9:20 – 9:40
Chan, Garnet
Xu, Xin
Toward exact numerical solutions of the nonrelativistic Schrödinger equation of
polyatomic molecules
Sturmian exponential type orbitals and geminals for structure, properties and electron
correlation
Divide-and-conquer electronic structure method: Extension to post-HF correlation
theories
New Development of Tri-atomic State‐to‐state Reaction Scattering Calculation Using
Time‐dependent Wave Packet Method
Ab-initio Density Matrix Renormalization Group and Tensor Network wavefunctions
9:40 – 10:00
IN-ES021
IN-ES022
IN-ES023
OR-ES020
IN-ES025
Coffee Break
Oral session O27-ES02, Chair: Li, Shuhua
10:00 – 10:20
Moszynski, Robert
10:20 – 10:40
Glushkov,Alexander
10:40 – 11:00
Cremer, Dieter
11:00 – 11:20
Rassolov,Vitaly
11:20 – 11:40
Chen, Feiwu
Relativistic and qed treatment of long-range resonant interactions between like atoms
Relativistic quantum chemistry of heavy elements, hadronic atoms and heavy ions
collisions
Relativistic Methods Based on the Regular Approximation and the Normalized
limination of the Small Component Application to Mercury Bonding
Stable long-time semiclassical description of zero-point energy in high-dimensional
molecular systems
IN-ES026
OR-ES027
IN-ES028
IN-ES029
IN-ES030
Oral session O27-ES03, Chair: Hoggan,Philip
14:00 – 14:20
Wu, Wei
14:20 – 14:40
Eliav, Ephraim
14:40 – 15:00
Lischka, Hans
15:00 – 15:20
Nakata, Maho
15:20 – 15:40
Yañez, Manuel
VBPT2: A Valence Bond Method that Incorporates Perturbation Theory
Benchmark calculations of exited states in heavy elements compounds: new
strategies and results
Why multireference approaches: biradicals, excited states and nonadiabatic
photodynamics
The Reduced Density Matrix Method: Application Of T20 N-representability Condition
and Development of Highly Accurate Solver
Resonance Assisted Hydrogen Bonds: myth or reality?
15:40 – 16:00
IN-ES031
IN-ES032
IN-ES033
IN-ES034
IN-ES035
Coffee Break
Oral session O27-ES04, Chair: Wei, Wu
16:00 – 16:20
Coogan,Anthony
Proposal of a Communications Theory of Quantum Mechanics.
OR-ES036
16:20 – 16:40
Kong, Jing
Faster DFT with mrXC
IN-ES037
16:40 – 17:00
Xu, Xin
Extending the applicability of B3LYP
IN-ES038
17:00 – 17:20
Yao, Shuwen
Local Reactivity Index Deduced from Mocular Orbitals works in Reactivity Prediction
OR-ES039
17:20 – 17:40
Lin, I-Chun
Improving the predictions of noncovalent interactions in DFT with atom-centered
potentials
IN-ES040
7 Book of Programme and Abstract for TACC2008 2.
Statistical Mechanics and Multiscale Issues Sep. 24 Wednesday – Statistical Mechanics and Multi-scale Issues
Oral session O24-SM01, Chair: Sun, Huai
14:00 – 14:20
Podeszwa,Rafal
14:20 – 14:40
Bichoutskaia, Elena
14:40 – 15:00
Dupuis, Michel
15:00 – 15:20
Elstner, Marcus
15:20 – 15:40
Guenza,Marina
Accurate First Principles Intermolecular Potentials in Modeling of Molecular Crystals
Multiscale 8nergeti of carbon based nanomaterials: fundamentals and applications to
nanoelectronics
Proton Transport in Polymeric Membranes: Insights from Atomistic Simulations and
Electronic Structure Computations
Investigation of proton transfer events and optical properties of the light driven proton
pump Bacteriorhodopsin using multi-scale QM/MM methods
Structural and Dynamical Coarse Graining of Macromolecular Systems
15:40 – 16:00
IN-SM011
IN-SM002
IN-SM003
IN-SM004
IN-SM005
Coffee Break
Oral session O24-SM02, Chair: Wesolowski, Tomasz A.
The Mixed Quantum Classical Molecular Dynamics Study of Diatomic Molecule
16:00 – 16:20
Li, Shenmin
16:20 – 16:40
Shigeta, Yasuteru
Quantum Dynamics in terms of Cumulant
OR-SM007
16:40 – 17:00
Ten-no, Seiichiro
Accurate QM/MM hierarchies for 8nergetic and enzymes
IN-SM008
17:00 – 17:20
Martyna,Glenn J
17:20 – 17:40
Pittner, Jiri
Vibrational Frequency Shifts in Nano-Confined Solvent
Using novel methodology, parallel algorithms and computer simulation to probe
biophysical, materials and chemical systems
Efficient techniques for non-adiabatic molecular dynamics
IN-SM006
IN-SM009
IN-SM010
Sep. 26 Friday – Statistical Mechanics and Multi-scale Issues
Oral session O26-SM03, Chair: Yu, Yangxin
14:00 – 14:20
Gao, Yiqin
14:20 – 14:40
Kalia, Rajiv
14:40 – 15:00
Ma, Jianpeng
15:00 – 15:20
Hou, Zhonghuai
15:20 – 15:40
Naidoo, Kevin J.
Integrated Temperature enhanced Sampling (ITS) method Simulation Results on
water/air Interfaces
Multimillion-to-billion atom molecular dynamics simulations of shear deformation,
fracture and nanoindentation in silica glass
Novel Empirical Potential Functions and Monte Carlo Sampling Techniques
Nonlinear Dynamics and Nonequilibrium Thermodynamics in Mesoscopic chemical
Systems
Developing a Reliable Semi-Empirical QM/MD Treatment of Carbohydrates for
investigating Multidimensional Reaction Surfaces
15:40 – 16:00
IN-SM001
IN-SM012
IN-SM013
IN-SM014
IN-SM015
Coffee Break
Oral session O26-SM04, Chair: Rajiv K. Kalia
16:00 – 16:20
Lee, Sangyoub
16:20 – 16:40
Karttunen, Mikko
Theory of Non-Markovian Rate Processes
Dynamics and self-assembly of peptides and lipid-like molecules. New paradigm for
lipid diffusion
IN-SM016
IN-SM017
17:00 – 17:20
17:20 – 17:40
Nakai, Hiromi
Kobryn,
Alexander
E.
Yamazaki, Takeshi
Acceleration of SCF convergence in ab initio direct molecular dynamics simulations
IN-SM018
Molecular theory of slip boundary conditions in nanofluidics
OR-SM019
Multiple Scale Modeling of Supramolecular Architectures in Solution by 3D molecular
theory of solvation
OR-SM020
Sep. 27 Saturday – Statistical Mechanics and Multi-scale Issues
Oral session O27-SM01, Chair: Podeszwa,Rafal
8:00 – 8:20
Klamt, Andreas
8:20 – 8:40
Rayez, Jean-Claude
COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics
On simple semi-classical tools to improve the capability of
IN-SM021
classical mechanics to
describe molecular scattering processes
8:40 – 9:00
9:00 – 9:20
IN-SM022
IN-SM023
Porter, Richard
The Quantum Field Theory of Molecular Ensembles
OR-SM024
9:20 – 9:40
9:40 – 10:00
Coffee Break
Oral session O27-SM02, Chair: Porter, Richard
Dynamics of single-file water chains inside nanoscale channels: physics, biological
10:00 – 10:20
Fang, Haiping
10:20 – 10:40
Mark, Alan E.
10:40 – 11:00
Gavrilenko, Vladimir
11:00 – 11:20
Praprotnik,Matej
Adaptive Resolution Molecular Dynamics Simulation
IN-SM029
11:20 – 11:40
Julius Su
Simulation of large-scale excited electron dynamics
OR-SM030
significance and applications
Simulating self-organization in Biomolecular systems
IN-SM026
IN-SM027
Optical Properties of Molecular Aggregates and Conjugated Polymers from First
Principles
IN-SM028
Oral session O27-SM03, Chair: Fang, Haiping
14:00 – 14:20
Li, Yigui
14:20 – 14:40
Yu, Yang-Xin
14:40 – 15:00
Li, Xuejin
15:00 – 15:20
CHAN, Kwong-Yu
15:20 – 15:40
Piquemal,Jean-Philip
15:40 – 16:00
Study on Non-primitive Mean Spherical Approximation (MSA) to Real Aqueous
Electrolyte Solutions
Molecular Dynamics Simulation on the Structural and Thermodynamic Properties of
DNA-Electrolyte Solutions
Dissipative Particle Dynamics Simulations of Shapes Transformations of Membrane
Vesicles from Amphiphilic Triblock Copolymers
Probing
Dynamics
and
Impedance
of
Inhomogeneous
Electrolytes
with
Alternating-Current Non-Eequilibrium Molecular Dynamics (AC-NEMD) Simulations
Progress towards quantitative molecular 9nergeti: development of new generation
force fields.
IN-SM031
OR-SM032
OR-SM033
IN-SM034
OR-SM035
Coffee Break
Oral session O27-SM04, Chair: CHAN, Kwong-Yu
16:00 – 16:20
Christ, Clara D.
Multiple free energies from a single simulation: Extending enveloping distribution
sampling to non-overlapping phase-space distributions
OR-SM036
9 Book of Programme and Abstract for TACC2008 Molecular Simulation of Solubility and Diffusion of Water in Polymer Electrolyte
16:20 – 16:40
Sun, Huai
16:40 – 17:00
Wang, Renxiao
IN-SM038
17:00 – 17:20
Gagliardi, Laura
IN-SM039
17:20 – 17:40
Görling, Andreas
IN-SM040
3.
Membranes
IN-SM037
Bioformatics and Biochemistry Sep. 24 Wednesday – Bioformatics and Biochemistry
Oral session O24-BIO01, Chair: Zhang, John
14:00 – 14:20
Gao, Jiali
14:20 – 14:40
Jansen, Georg
14:40 – 15:00
Holthausen, Max C.
15:00 – 15:20
Shurki, Avital
15:20 – 15:40
Sherrill, David
Combined QM/MM studies of enzymatic reactions
Stacking interactions in DNA from the combined density functional theory and
symmetry-adapted perturbation theory approach
Bioinorganic Models for Dinuclear Copper Proteins: Aliphatic and Aromatic
Hydroxylation from a Quantum Chemical Point of View
Hybrid ab initio Valence Bond / Molecular Mechanics (VB/MM), A New Method for
Calculating Biochemical Systems
Noncovalent Interactions in Extended Systems
15:40 – 16:00
IN-BIO001
IN-BIO002
IN-BIO003
IN-BIO004
IN-BIO005
Coffee Break
Oral session O24-BIO02, Chair: Sherrill, David
16:00 – 16:20
Lambert,
Jean-François
Amino acids organisation at inorganic oxides interfaces
IN-BIO006
Dissociation of Charged Protein Complexes in the Gas Phase
IN-BIO007
16:20 – 16:40
Thachuk, Mark
16:40 – 17:00
Smith, Brian
17:00 – 17:20
Xu, Jiancong
17:20 – 17:40
Gräter, Frauke
How nature designed protein mechanical response
IN-BIO010
17:40 – 18:00
Chen, Su-Shing
Interaction dynamics at different levels: proteins, ligands and ion-channels
IN-BIO030
Modelling interactions between proteins and peptides: applications in the study of
pain and toxins.
Insights into the Association and Interaction of Cohesin-dockerin Complex in
Cellulosome Assembly
IN-BIO008
OR-BIO009
Sep. 26 Friday – Bioformatics and Biochemistry
Oral session O26-BIO03, Chair: Smith Brian
14:00 – 14:20
Marrink,
Siewert-Jan
Fascinating Vesicles
IN-BIO011
Molecular Theory and Simulation for Biochemical Reactions in Crowded Environment
OR-BIO012
14:20 – 14:40
Jiang,Jianwen
14:40 – 15:00
Gieger, Christian
15:00 – 15:20
Rothstein,Stuart M
Do point mutations evoke disperse entropic changes throughout a protein domain?
IN-BIO014
15:20 – 15:40
Paci,Emanuele
Forcing proteins to unfold: simulation, theory and experiment.
IN-BIO015
A genome-wide association study reveals SLC2A9 as a major gene for uric acid
levels
IN-BIO013
Coffee Break
Oral session O26-BIO04, Chair: Chen, Haifeng
16:00 – 16:20
Lazaridis , Themis
Insights from implicit solvent models: coiled-coils and protein-membrane interactions
IN-BIO016
16:20 – 16:40
Liu, Qi
Inferring transcriptional regulatory network from ChIP-chip and knock-out data
OR-BIO017
16:40 – 17:00
Moliner, Vicent
Theoretical design of new biological catalysts
OR-BIO018
17:00 – 17:20
Wang, Wen
Origin and Evolution of Genetic Novelties
IN-BIO019
A Novel Proton Transfer through Peptide Groups in Proteins
IN-BIO020
17:20
- 17:40
Kamiya,
Katsumasa
Sep. 27 Saturday – Bioformatics and Biochemistry
Oral session O27-BIO01, Chair: Chen, Su-shing
8:00 – 8:20
Stewart, James
Calculation of Accurate Protein Geometries using PM6 and X-ray structures
IN-BIO021
8:20 – 8:40
Gwaltney, Steven
Substrate Specificity in Carboxylesterate Binding
OR-BIO022
8:40 – 9:00
Yang, Wei
9:00 – 9:20
Abad, Enrique
A novel rate theory approach to transport in ion channels
OR-BIO024
9:20 – 9:40
Tanaka, Shigenori
Applications of the Fragment Molecular Orbital Method to Biomolecular Systems
IN-BIO025
IN-BIO023
9:40 – 10:00
Coffee Break
Oral session O27-BIO02, Chair: Shigenori Tanaka
10:00 – 10:20
10:20 – 10:40
Reuter,Nathalie
Shubhra
Ghosh
Dastidar
10:40 – 11:00
Dashti, Hesam T.
11:00 – 11:20
Stacklies, Wolfram
11:20 – 11:40
Kaupp, Martin
Human Neutrophil Elastase and Proteinase 3: so similar yet so different
IN-BIO026
Interrupting the MDM2-p53 interface with high affinity: Computational studies
OR-BIO027
Applying Recurrent Artificial Neural Networks to Conventional Motif Discovery
Problem
Force propagation from molecular dynamics simulations reveals sparse
mechanical network in proteins
Computation of EPR Parameters for Transition Metal Complexes and Metalloenzyme
Sites
OR-BIO028
OR-BIO029
IN- BIO030
Oral session O27-BIO03, Chair: Gwaltney, Steven
14:00 – 14:20
Huang,Xur
14:20 – 14:40
Shen, Yong
Computational Exploration of Conformational Transition Pathway in the Allosteric
Process of Calcium-induced Recoverin
A QM/MM Investigation of the Catalytic Mechanism of the Ferrochelatase
OR-BIO031
OR-BIO032
Measuring the impact of genomic sequence variations on gene structure variations
14:40 – 15:00
Wei, Chaochun
and its application to the association study of genomic sequences and their disease
IN-BIO013
susceptibility
15:00 – 15:20
Chen, Haifeng
Insight into the Misfolding Mechanism of Amyloid Fibril
OR-BIO034
15:20 – 15:40
Wang, Cunxin
Study on protein-protein interaction and recognition by molecular docking
OR-BIO035
Coffee Break
Oral session O27-BIO04, Chair: Han, Keli
16:00 – 16:20
A QM/MM Study of the First Proton Transfer in the Catalytic Cycle of Cytochrome
16:20 – 16:40
Wang, Dongqi
16:40 – 17:00
Wang, Zhuo
17:00 – 17:20
Duan, Yong
IN-BIO039
17:20 – 17:40
Carloni, Paolo
IN-BIO040
17:40 – 18:00
Song, Youtao
4.
P450cam and Its Mutant D251N
Exploring photosynthesis evolution by comparative analysis of metabolic networks
between chloroplasts and photosynthetic bacteria
Structural and Dynamic Properties of a New Highly Amyloidogenic Chicken
Cystatin Mutant I108T
OR-BIO037
OR-BIO038
IN-BIO041
Materials and Nano
Sep. 24 Wednesday – Materials and Nano
Oral session O24-MAT01, Chair: Yang, Jinlong
14:00 – 14:20
Jiang, De-en
Properties of p-electrons in nanographenes
IN-MN001
14:20 – 14:40
Broer, Ria
The State of Transition Metals in Transition Metal Oxides
IN-MN002
14:40 – 15:00
Groß, Axel
Structure-reactivity relationship for nanostructured bimetallic surfaces
IN-MN003
15:00 – 15:20
Sakaki, Shigeyoshi.
15:20 – 15:40
Rost, Jan Michael
Bonding Nature and Reaction Behavior of Transition Metal Complexes: Theoretical
Study with Post-Hartree-Fock method
Rare gas clusters under illumination of short and intense pulses with VUV and X-ray
frequencies
15:40 – 16:00
IN-MN004
IN-MN005
Coffee Break
Oral session O24-MAT02, Chair: Zwanziger, Josef W.
16:00 – 16:20
Yang, Jinlong
First-principles design of low-dimensional nanomaterials for spintronics
IN-MN006
16:20 – 16:40
Naumkin,Fedor
Gold shells shaped by carbon cores: From an Au18 cage to a C10Au18 aurocarbon
IN-MN007
16:40 – 17:00
Neuhauser,Daniel
Nanopolaritonics and friction
IN-MN008
17:00 – 17:20
Chen,Zhongfang
Computational Explorations of Low-Dimensional Nanomaterials
IN-MN009
17:20 – 17:40
Yang, Zhongzhi
Developing ABEEM fluctuating charge force field for proteins
IN-SM025
Sep. 26 Friday – Materials and Nano
Oral session O26-MAT03, Chair: Naumkin,Fedor
14:00 – 14:20
IN-MN011
14:20 – 14:40
Nikolay V. Sokolov
The General Properties Of Nanoparticles Distributions
OR-MN012
14:40 – 15:00
Zwanziger, Josef W.
Materials Properties from DFT in the Projector Augmented Wave Formalism
OR-MN013
Minot, Christian
15:20 – 15:40
Huang, Jingsong
Adsorption electropositive atoms with an odd number of electrons (H, K, Au) on a
perfect TiO2(110) surface
Universal Model for Nanoporous Carbon Supercapacitors
OR-MN014
OR-MN015
Oral session O26-MAT04, Chair: Huang, Jingsong
16:00 – 16:20
Yan, Likai
A Theoretical Study on the Nonlinear Optical Properties of π-Conjugated Porphyrin
Arrays
16:20 – 16:40
IN-MN017
16:40 – 17:00
Ozcan, Ozlem
17:00 – 17:20
Nguyen, Ngoc Ha
17:20 – 17:40
OR-MN016
Linking Stability Studies to the Preferential Growth of ZnO
Periodic Density Functional Theory Study of The oxidative Dehdrogenation of
n-butane on the (001) Surface of V2O5
TACHIBANA,
Regional DFT – Electronic Stress Tensor Study of Aluminium Nanostructures for
Akitomo
Hydrogen Storage
OR-MN018
OR-MN019
IN-MN020
Sep. 27 Saturday- Materials and Nano
Oral session O27-MAT01, Chair: Li, Zhenyu
8:00 – 8:20
Zhao, Jijun
Electronic properties and aromaticity of medium-sized boron cage clusters
IN-MN021
8:20 – 8:40
Bolesta, Alexey
Molecular dynamics simulations of mechanical deformation in metallic thin films
IN-MN022
8:40 – 9:00
IN-MN023
9:00 – 9:20
Shu, Yuan-jie
9:20 – 9:40
Pyykkö, Pekka
Theoretical studies on the structure design and property evaluation of imidazole and
pyrazole compounds
The metallophilic attraction: The current situation
9:40 – 10:00
IN-MN024
IN-MN025
Coffee Break
Oral session O27-MAT02, Chair: Zhao, Jijun
10:00 – 10:20
Csaszar, Attila
10:20 – 10:40
Moreau, Philippe
10:40 – 11:00
11:00 – 11:20
11:20 – 11:40
Vyboishchikov,
Sergei F.
Pacchioni,
Gianfranco
Chen, Xuebo
First-principles rovibrational spectroscopy
Comparison simulation/experiment in the Low Energy-Loss region: application to
lithium battery materials.
IN-MN026
IN-MN027
Theoretical studies of weak Si···H interactions
OR-MN028
Ultra-thin oxide films: new materials with unprecedented properties
IN-MN029
Quantum Chemical Modeling of a Light-Driven Three Strokes Molecular Engine and
Its Application in biological Nanocavities
OR-MN030
Oral session O27-MAT03, Chair: Jiang De-en
14:00 – 14:20
Li, Zhenyu
14:20 – 14:40
Golovneva,Elena I
14:40 – 15:00
Liu, Boping
15:00 – 15:20
Wang, Jinlan
Electric field effects on electronic structures of BN nanotubes with defects or molecule
intercalations
The investigation of nano-dimensional alloys thermodynamic properties
Theoretical Studies on Bis(triphenylsilyl)chromate—as a Homogeneous Model of
Phillips Cr/Silica Catalysts for Ethylene Polymerization
Structure and Magnetic Properties of TM-Ligand Clusters and wires
OR-MN031
IN-MN032
OR-MN033
IN-MN034
Wang, Lu
First-principles study of water clusters confined in nonpolar cavities modeled by
carbon fullerenes
15:40 – 16:00
OR-MN035
Coffee Break
Oral session O27-MAT04, Chair: Chen, Xuebo
16:00 – 16:20
Rupnik, Kresimir
IN-MN036
16:20 – 16:40
Chen, Xiangrong
IN-MN037
16:40 – 17:00
Russo, Nino
IN-MN038
17:00 – 17:20
Yuan, Bo
IN-MN039
17:20
- 17:40
IN-MN040
5.Cheminformatics and Drug Design Sep. 24 Wednesday – Cheminformatics and Drug Design
Oral session O24-CHEM01, Chair: Chen, Xiaowu
14:00 – 14:20
Ajmani, Subhash
G-QSAR: A Novel Group Based QSAR Method
IN-CD001
14:20 – 14:40
Merz, Ken
A Quantum of Common Sense in Crystallography
IN-CD002
14:40 – 15:00
Zipse, Hendrik
Thermochemical Aspects of Radical Reactions
IN-CD003
15:00 – 15:20
Ji, Lin
Delayed Coupling adjusted calcium signaling in a noise perturbed system
OR-CD041
15:20 – 15:40
Umeyama, Hideaki
A new docking and screening method using a new operator based upon
bio-informatics
15:40 – 16:00
IN-CD005
Coffee Break
Oral session O24-CHEM02, Chair: Zipse, Hendrik
16:00 – 16:20
Stahl, Gunther
16:20 – 16:40
Chen, Xiaowu
16:40 – 17:00
Chao, Ito
17:00 – 17:20
17:20 – 17:40
Bickelhaupt,
Matthias
Beteringhe, Adrian
Topomer CoMFA – a new method in Lead Optimization
Novel Interaction Between Influenza Neuraminidase and Oseltamivir and Its
implication on Virtual Screening and Drug Discovery
IN-CD006
IN-CD007
Theoretical design of organic molecules with small internal reorganization energies
IN-CD008
Origin of Reaction Barriers and Rational Design in Chemistry
IN-CD009
Study of the ligand – biological receptor interactions for Co(II), Cu(II) and Zn(II)
complexes with oxicam derivatives using “Molecular Docking” and QSAR procedures
OR-CD010
Sep. 26 Friday – Cheminformatics and Drug Design
Oral session O26-CHEM03, Chair: Ostlund, Neil S.
14:00 – 14:20
Shoeib,Tamer
14:20 – 14:40
Adrian Beteringhe
14:40 – 15:00
Meihua Tu
A Structural and Free Energy Analysis of Ag+ Complexes to Five Small Peptides
Study of the ligand – biological receptor interactions for Co(II), Cu(II) and Zn(II)
complexes with oxicam derivatives using “Molecular Docking” and QSAR procedures
Enhancing Ligand Binding Affinity Predictions by Retraining Docking Scores with
QSAR Models
OR-CD011
OR-CD012
OR-CD013
Dunbrack, Roland
15:20 – 15:40
Shen, Jian
Statistical analysis of protein structures: electron density, conformational analysis,
and protein-protein interfaces
An optimized method for structure-based ligand optimization
15:40 – 16:00
IN-BIO036
OR-CD015
Coffee Break
Oral session O26-CHEM04, Chair: Steve Bryant
16:00 – 16:20
Michielin, Olivier
16:20 – 16:40
Gao, Junhui
16:40 – 17:00
Wang, Qiantao
17:00 – 17:20
Yin, Shuangye
17:20 – 17:40
Wang, Yanli
Using EADock, a new docking program based on the CHARMM force field, to design
inhibitors of important cancer protein targets
A method for building virtual combinatorial chemical library
Towards accurate protein-ligand docking: Implementation of a combined quantum
mechanical (QM) and polarizable molecular mechanical (Mmpol) model
Force Field based Scoring Function and Molecular Dynamics Refinement for Virtual
Drug Screening
PubChem: NIH’s public repository for biological test results
IN-CD016
OR-CD017
OR-CD018
OR-CD019
IN-CD020
Sep. 27 Saturday – Cheminformatics and Drug Design
Oral session O27-CHEM01, Chair: Wang, Yanli
8:00 – 8:20
Ostlund, Neil S.
HyperProtein –a New Bioinformatics Program
OR-CD021
8:20 – 8:40
Cao, Zhiwei
In silico platform for mechanistic study of Traditional Chinese Medicine
IN-CD022
8:40 – 9:00
Wang, Yi-Fei
9:00 – 9:20
Smith, David
9:20 – 9:40
Yu, Chin-hui
IN-CD023
Computational Investigations of Enzyme Mechanisms: An Application to the
B12-Independent Glycerol Dehydratase
Controlling the Formation of Low Barrier Hydrogen Bonds
9:40 – 10:00
IN-CD024
IN-CD025
Coffee Break
Oral session O27-CHEM02, Chair: Chen, Xiaowu
Quantum Mechanical and Experimental Study of Anomerization Pathways of
10:00 – 10:20
Satoh, Hiroko
10:20 – 10:40
Lian, Peng
10:40 – 11:00
Zhou, Zhigang
11:00 – 11:20
Yan, Tianying
A Multistate Empirical Valence Bond (MS-EVB) Model for Proton Transfer in Imidazole
OR-CD029
11:20 – 11:40
Yokojima, Satoshi
Ab initio NMR chemical shift calculations using fragment molecular orbitals
IN-CD030
Pyranosides
Study on Interaction between DNA and POU Cooperating with HMG by Molecular
Dynamics Simulation
New Antiviral Compound Discovery and Design through Computational Screening and
Scaffold Replacement against Dengue Virus E Protein
IN-CD026
OR-CD027
OR-CD028
Oral session O27-CHEM03, Chair: Yan, Tianying
14:00 – 14:20
Zhou, Zhiyong
Improved Protein Long Loop Structure Prediction
OR-CD031
14:20 – 14:40
Hannongbua, Supa
IN-CD032
14:40 – 15:00
Kurnikova, Maria
IN-CD033
15:00 – 15:20
Lilienfeld, Anatole
IN-CD034
Lim, Carmay
IN-CD035
15:40 – 16:00
Coffee Break
Oral session O27-CHEM04, Chair: Zhou, Zhiyong
16:00 – 16:20
Nilsson, Lennart
Activity in the Thioredoxin Family: Structure, Dynamics and Electrostatics
16:20 – 16:40
IN-CD036
IN-CD037
16:40 – 17:00
Pirzadeh, Payman
IN-CD038
17:00 – 17:20
Wan, Jian
IN-CD039
17:20
Xie, Lu
IN-CD040
- 17:40
5.
Chemical Modelling for a Sustainable Environment
Sep. 24 Wednesday – Chemical Modelling for a Sustainable Environment
Oral session O24-ENV01, Chair: Hirst Jonathan
Role of Extracellular Domains in Modulating Ion Permeation through the Nicotinic
14:00 – 14:20
Cheng, Xiaolin
14:20 – 14:40
Jarzecki, Andrzej
14:40 – 15:00
Chandra, Amalendu
15:00 – 15:20
Wang, Hailong
15:20 – 15:40
Nikolay V. Sokolov
Receptor Channel
Lead Toxicity: Quantum-Mechanical Exploration of Lead Poisoned Zinc Fingers
Hydrogen bond fluctuations and vibrational spectral diffusion in normal and
supercritical water
Molecular dynamics study of cation 16nergetic16s through nicotinic acetylcholine
receptor channel.
Modeling in environmental chemistry with the aid of generalization to pafnutii l.
Tchebycheff’s (chebyshev’s) inequality
15:40 – 16:00
IN-EV001
IN-EV002
IN-EV007
IN-EV004
OR-EV005
Coffee Break
Oral session O24-ENV02, Chair: Chandra, Amalendu
16:00 – 16:20
16:20 – 16:40
Evaluation of Phase Transition Temperatures of Phosphatidylcholine Lipids based on
Goursot, Annick
DFT Born-Oppenheimer Dynamics of monomers
Rotational Barriers, Energy differences and Thermodynamics Parameters of Furfural,
Ramasami,
2-Furoylfluoride and their Sulfur and Selenium Analogues: DFT Study in the Gas and
Ponnadurai
16:40 – 17:00
Halstead, S. J.
17:00 – 17:20
Sprik, Michiel
17:20 – 17:40
Yarovsky, Irene
IN-EV006
OR-EV003
Solution Phases
A Molecular Dynamics Study of the anomalous pKW in near-critical and supercritical
water
Vertical electron binding energy and oxidation free energy of the aqueous hydroxide
anion.
Design of New Materials by Computer Simulations: Light Metal Nanostructures for
Hydrogen Storage
OR-EV008
IN-EV009
IN-EV010
Sep. 26 Friday – Chemical Modelling for a Sustainable Environment
Oral session O26-ENV03, Chair: Sprik, Michiel
14:00 – 14:25
Zahedi,Gholamreza
Supercritical carbon dioxide extraction of nimbin from neem seeds- an optimization
study
OR-EV011
14:50 – 15:15
IN-EV012
Sabolovic, Jasmina
Development Of Molecular Mechanics (MM) Force Fields For Modelling Of Copper(II)
Amino Acid Complexes In Different Environments
15:15 – 15:40
IN-EV013
OR-EV014
15:40 – 16:00
Coffee Break
16:00 – 16:25
Skala, Lubomir
IN-EV016
16:25 – 16:50
Martin, Gershom
IN-EV017
16:50 – 17:10
Gori-Giorgi, Paola
IN-EV018
Sep. 27 Saturday – Chemical Modelling for a Sustainable Environment
Oral session O27-ENV01, Chair:
Jiang Jianwen
Exploring the structure characters of the protic ionic liquids in different solvents: a
9:00 – 9:25
Li, Haoran
9:25 – 9:50
Michael Probst
H6 (hexahydrogen) cation revisited
OR-ENV022
9:50 – 10:15
Zhu, Jianjun
Solvent Dynamics Effect in Condensed-Phase Electron-Transfer Reactions
IN’-ENV023
theoretical investigation
10:15 – 10:25
OR-ENV021
Coffee Break
Oral session O27-ENV02, Chair: Cui Qian
From s-block to Transition Metal Species: Quantitative Modeling via the correlation
10:25 – 10:50
Wilson, Angela
10:50 – 11:15
Xu,Yisheng
Theoretical study of OH formation from ozonolysis of Limonene
OR-ENV025
11:15 – 11:40
Allen, Wesley
Mechanisms of Hydrocarbon Oxidation, Pyrolysis, and Soot Formation
IN-ENV026
consistent Composite Approach (ccCA)
IN-ENV024
Oral session O27-ENV03, Chair:Zhu, Jianjun
14:00 – 14:25
Lemke, Kono H.
14:25 – 14:50
Plowright, Richard
14:50 – 15:15
Rong, Zimei
Structure, Stability and Distribution of Neutral Water Clusters in high-Temperature
low-Density Fluids
Sporadic Metal Layers: Ion- Molecule chemistry of Metal cations and its implications
for the upper atmosphere
Displacement Matrix Elements of Deng-Fan Potential for Modelling Molecular
Vibrations
OR-ENV027
OR-ENV028
OR-ENV029
Timetable – Poster Sessions 01 (Sep. 24th Evening) Poster Session01 – Sep. 24 Evening 19:00 – 21:00
Peng, Wei-Tou
Phenalenyl-Based Three-Component Systems for Remote Control of Hydrogen Bonds
PO-001
Kuang, Zhifeng
Computatinal Design Of Multifunctional Peptides For Detection Of Chemical Agents
PO-002
Du, Xiuquan
Prediction of protein-protein interaction sites using Granularity computing of quotient space theory
PO-003
Liao, Rong-Zhen
Theoretical Investigation of the Reaction Mechanism of the Dinuclear Zinc Enzyme Dihydroorotase
PO-004
17 Book of Programme and Abstract for TACC2008 Liu, Huanxiang
A new proposed mechanism of ATP hydrolysis in nature
PO-005
Pu, Min
Theoretical Study on the Structure of 4,4’-Azobenzene Sulphonate and Layered Double Hydroxide
PO-006
Pu, Min
Theoretical Study on the Mechanism of Catalytic Synthesis of Ethyl Tertiary Butyl Ether over Zeolite
PO-007
Ji-guo Su
Protein folding core revealed by Elastic Network Model
PO-008
Chen, Qilong
Modeling and analysis the tertiary structures of the SOX4 mutants encoded proteins of lung cancer
tissues based on Pdb-Viewer and MATLAB
Songa, Mee
Effect of micropore volume on the hydrogen adsorption into the aluminophosphate molecular sieves:
Kyung
GCMC simulation
Ji, Lin
Delayed coupling adjusted calcium signaling in a noise perturbed system
Zhang, Zhuoyong
Zhou, Zhongfu
Chen, Xi
Zhao, Guang-Jiu
QSAR Studies of Hallucinogenic Phenylalkylamines by Using Neural Network and Support Vector
Machine Approaches
Design and Computational Investigations of Molecular Quasicrystals
First 18nergetic calculation on the binding modes and critical 18nergetic constants of Aluminum
chelators
Theoretical Study of the Electronic Excited-State Hydrogen Bonding Dynamics and Its Important Roles on
Photochemistry and Photobiophysics
PO-009
PO-010
PO-011
PO-012
PO-013
PO-014
PO-015
Chen, Jingwen
Application Perspectives in the KOA Predicting Models: Validation, Application Domain and Algorithm
PO-016
Liu, Xin
Unique Reactivity of Confined Metal Overlayers on Si(111)
PO-017
Hakima
Decomposition Mechanism Studies of Energetic Molecules Using HOMO and LUMO Orbital Energy
Abou-Rachid
Driven Molecular Dynamics
Bhat,Savithri
Comparitive Studies On Gelation Behaviour Of Spider, Silkworm And Husk Proteins
PO-019
Dae Dong Sung
Strcture and Energy of The Aminolysis of Alkylsulfinyl Halides
PO-020
Shu-Bai Li
Lei, zhong
Li, Weikun
Zhao, Shu-Lei
Wang, Lijuan
4-Hydroxyphenylacetic acid: inhibition of monophenolase and activation of diphenolase of mushroom
(Agaricus bisporus) tyrosinase
DFT Calculations on CrO+ as a Model System for Ethylene Polymerization over Phillips Catalyst
Different Reactivities of TiO2 polymorphs: Comparative DFT calculations of water and formic acid
adsorption at anatase and brookite TiO2 surfaces
First-Principles Calculations of the Surface Properties of TiO2/CeO2 Mixed Oxide
Molecular Modelling Study on Selective Flotation Mechanism of Sodium Chloride Particle with
Dodecylmorpholine
PO-018
PO-021
PO-022
PO-023
PO-024
PO-025
Liu,Zhen
Mechanism of Ethylene Dimerization on CrOH+ Studied by Density Functional Theory (DFT) Method
PO-026
Shahnaz Sheykh
Evaluation On The Structural As Selective Electrodes For Removing Trace Metal Ions By Some
Shoaie
Compounds As Selective Sensors With Using Semi-Empirical Calculations
Yin, Fuchang
Hydrophobic Matching in mixed DMPC/DDPC lipid bilayers
PO-029
Pouneh Ebrahimi
Prediction of Gas Chromatographic Retention Time of Iodobenzenes using MLR
PO-030
Pouneh Ebrahimi
Modeling of Retention time for some Iodobenzenes on DB-5 Stationary Phase using ANN-MLR
PO-031
Yao Jinhuan
DFT Study of Electric Field Effect on Carbon Monoxide Adsorption on Pt(111) Surface
PO-032
PO-028
18 Book of Programme and Abstract for TACC2008 He, Zhitao
Design a RPR-based Negotiation Mechanism for E-Marketplaces
PO-033
Li, Wenlan
Studies on the Chemical Constituents of “JinKuiShenQi Pills” Metabolized in Vivo
PO-034
Li, Wenlan
Biotransformation of Paeonol and Study on Relationship Between it and Cytochrome P450
PO-035
Wang, Xiaolin
Monolayer and Multilayer Compact Film Formations on Different Substrates by Physical Deposition
PO-036
Wang, Chang-long
Comprehensive Evaluation System Uncertainty on Durability of Concrete Structure
PO-037
Qin , Yi
The Analysis of the Eutrophic Status in the Largest Lake in Changshu City
PO-038
Shaopeng Li
Datta, Dipayan
Development of Algorithms for the Direct Complete Active Space Self-Consistent Field (CASSCF) Method
and the Direct Restricted Active Space Self-Consistent Field (RASSCF) Method
An Explicitly Spin-free Compact Open-shell Coupled Cluster Theory Using a Multi-reference Combinatoric
Exponential Ansatz: Formal Development and Applications
PO-039
PO-040
Bhabani S. Mallik
Vibrational spectral diffusion in aqueous solutions
PO-041
Arindam Bankura
Migration of protonic defects in confined aqueous systems
PO-042
Li, Jun
Software Development and Application to Estimate Melting Points
PO-043
Chen, Junxian
Theoretical Study on the Proton Transfers of Non-fluorinated Polymers for Fuel Cells
PO-044
Yu Liu
Open-Shell Local Coupled Cluster Theory
PO-045
Yoshida,Norio
Miyata, Tatsuhiko
QM/MM Method Combined with Reference Interaction Site Model Theory to investigate the electronic
structure and 19nergetic structure of proteins.
Combination of Molecular Dynamics Method and 3D-RISM Theory for Conformational Sampling of
Flexible Molecules in Solution
PO-046
PO-047
Xiong, Ying
Theoretical investigation on the thermal decomposition mechanisms of some high nitrogen s-tetrazines
PO-048
Chang, Yu-Chang
A Theoretical Study on the Air-Stability of n-Channel Organic Field-Effect Transistors
PO-049
Hsu, Chao-Ping
Electronic coupling in ground and excited state molecules
PO-050
PO-051
Wu, Rongliang
Tan, Shuai-Xia
Qiao, Baofu
Chernykh,
I.G.
Molecular Dynamics Simulations of the Adsorption and Crystallization of Long Alkanes on PE(110) and
Amorphous Carbon Surfaces
Real-time Investigation and Determination of Diffusion Coefficient for Drug in Hydrogels using Electronic
Speckle Pattern Interferometry
PO-052
PO-053
Dynamics of Hydrogen bonds in Ionic Liquids
PO-054
Reacting media models building optimization
PO-055
Noorbatcha,
Quantum Chemical Quantitative Structure Activity Studies of Anticancer Activity of Aldohexose
Ibrahim Ali
chloroethylnitrosourea Analogs
M. E. Zeynali
The role of diffusion in catalyst design for dehydrogenation of diethylbenzene to divinylbenzene
PO-057
A. V. Moradi
DFT study of O2 Adsorption on (100) Chromium surface
PO-058
Chemisorption of Oxygen Molecule on Vanadium-Surface Nanocluster by Quantum Mechanics Studies
PO-059
Baei,Mohammad
Taghi
E. Vessally
Mono-heteroatom effects on singlet-triplet energy gaps of divalent five-membered ring XC3H3C (X=CH,
N, P and As)
PO-056
PO-060
19 Book of Programme and Abstract for TACC2008 E. Vessally
Dabiri, Fedyeh
Farsani,R.Eslami
Electronic effects in norbornadiene-quadricyclane system for maximizing the solar energy storage: DFT
calculations
Aromaticity in BN-containing Heterocycles
Fourier Transform Infrared Study on Types of Commercial and Special Acrylic Fibers in the Fabrication of
Carbon Fibers
PO-061
PO-063
PO-065
Tan, Hepan
Structural Flexibility and Rigidity Analysis of HIV-1 gp120
PO-066
Korchowiec, Jacek
Interaction of Sugar-Based Amphiphilic 14-Member Macrocycles with Metal Ions
PO-067
Makowski, Marcin
Elongation-MP2 formalism – implementation and efficiency
PO-068
Zhu, Chao-Hua
Asymmetric bio-sulfoxidation to synthesize I-pantoprazole by mushroom tyrosinase
PO-069
Zhang, Houyu
A density functional theory study on blue-emitting iridium complexes with different ancillary ligands
PO-070
Gu, Xin
Electronic structures and spectroscopic properties of phosphorescent iridium(III) complexes with
phenylpyrazole ligands by a density functional theory study
PO-071
Zhang, Chunxiao
Research on the various factors influencing the Moisture Absorption of Sodium Polyacrylate
PO-072
Wang, Hongyan
Simulation and modeling of interior water-endurance property of polyacrylate latex films
PO-073
Zhao,Yong-Wu
Statistical Mechanics of Semiflexible Polymer
PO-074
Lyoo,Junho
Computational Method of Analyzing Secondary Structure of Protein, Based on IR Spectroscopy
PO-076
Tian, Guocai
Molecular Dynamics Simulation on the Spectrum and Dynamics of H2O in Ionic Liquids
PO-077
Mori,Toshifumi
Theoretical study of the Grignard reagents in solution
PO-078
Kosugi, Takahiro
Ju-Young Kim
Ho-Sung Kim
Change of flexibility upon binding with the substrate in psychrophilic
and mesophilic enzymes
Structures and 20nergetic of Gly–(H2O)5 : Thermodynamic and kinetic stabilities
Structures and electronic spectra of CdSe – Cys complexes: DFT Study of a Simple Peptide-coated
Nanocluster
PO-079
PO-081
PO-082
Suk Im
Solvent – mediated tautomerization of protonated nicotine
PO-083
Oh, Young-Ho
Efficiency of Bulky Protic Solvent for SN2 Reaction
PO-084
Shurki, Avital
The Coordination Number of Cu(I) within CopperChaperones
PO-085
The eSOC System and Drug Discovery
PO-086
Pan, Kai
An implementation of Substructure Search in Chemical DataBase Management System
PO-087
Sun, Huarong
A personalized DB tool for Bio- and Chemoinformatics
PO-088
Liangying Luo,
Ruisheng Zhang*
Bi,Shuping
Bi,Shuping
Chen, Shuang Ma,
Jing
Yi Liao
DFT Study on the Hydration Structure of Monomeric Aluminum (III)-Water Complexes and the
Deprotonation Effect
Density Functional Theory Study on the Interaction between Chloride and Al (III)-water Complexes
PO-091
PO-092
Charge-transport Properties of Metal and Nonmetallic Phthalocyanine Iodides. Effects of Packing,
Dopant, Central Metal, and Core
PO-093
Modification
Solvent and Stacking Effects on the Electronic Structures of Alkynylgold Triphenylphosphine Oligomers
PO-094
20 Book of Programme and Abstract for TACC2008 Li, Hui
Fragmentation-based QM/MM Simulations of Solution Conformations of Macromolecules
PO-095
Lu, Xiancai
Swelling behaviors and interlayer structure of K- and Cs-smectites: a molecular dynamic simulation study
PO-096
Miao, Qiang
Characterizing potential infection virus for its host: Nucleotide sequence pattern analysis
PO-097
Miao, Qiang
Zipf’s Power Law and k-word distribution in Human genome cDNA
PO-098
Li, Ruifang
Shu Wang
A New Target for Synthesis: Theoretical Prediction for the Reaction between Boron Nitride Nanotube and
Dichlorocarbene
Structure of the Liquid-Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics
Study
PO-099
PO-100
Li, Shu
Molecular Dynamics Simulation of LiTFSI
PO-101
Zhen, Cao
The Solvation Structure of Ethanol around Fullerene C60
PO-102
Miskufova, Martina
Hoda Abdel-Aal
Learn on the fly technique combined with QM/MM approach: Defects in semiconductors at finite
temperature
PO-209
Molecular Modelling of Alginate Oligosaccharides in the EPS Matrix
PO-210
Hainam Do
Phase Equilibria Of Mixtures Of Non-Polar Molecules: CO2, CH4, C2H6, and CO2 + CH4
PO-211
Luo,Yi
Mechanistic Investigation of Methyltrioxorhenium-Catalyzed Olefin Cyclization
PO-212
Zeng, Zhiping
The mechanism of formation of the α-hydrophosphonate: a theoretical study
PO-218
Wu, Yu
The Role of Molecular Conformation in the Eleetronic Transport Properties of BPE Molecular Junction
PO-219
Jalili, Seifollah
Study of Hydrogen Adsorption on Ti Dopped BC3 Nanotubes using DFT methods
PO-224
Bettley
Frimurer, Thomas
MaJianYi
Feng, Changjun
Hu, Guang
Xu, Yu
Site-Directed Drug DiscoveryÒ. A knowledge-based efficient approach for hit and lead generation to 7TM
receptors.
Making use of full molecular symmetry in relativistic electronic structure calculations
Research on the IAI of substituted aromatic compounds with Topological Indices and artificial neural
network
Tangled of Extended Goldberg polyhedral
TheoreticTheoretical Modeling of the two new mono-epoxylignans derived from the fruits of Forsythia
suspensa Vahl
PO-225
PO-226
PO-228
PO-229
PO-230
Timetable ‐ Poster Sessions 02 (Sep. 26th Evening) Poster Session02 - Sep. 26 Evening 19:00 - 21:00
Huang, Xinchuan
Accurate Quartic Force Fields for CCH- and NH2-
PO-103
Cheng, Ru Jen
Spin Distribution in Low-Spin Iron(III) Porphyrin Complexes with Different Electronic Structures
PO-104
Huang, Niu
Tying Protein Druggability Prediction with Fragment-based Virtual Screening
PO-105
Ying-chieh Sun
A Docking Study of PDK1 Inhibitor Ligands
PO-106
P. K. D. Dawson
Theoretical Studies of Nucleophilic Substitution Reactions of Iodonium Salts
PO-107
21 Book of Programme and Abstract for TACC2008 You, Wei
Classification of DNA Sequences Basing on the Dinucleotide Compositions
PO-108
You, Wei
Similarity Analysis of DNA Sequences Using “Molecular Connectivity Indices” Method
PO-109
Gao, Hongze
Su, Zhongmin
Zhang,Zhengquan
Theoretical Characterization photophysical and charge-transport properties of hole-blocking
material-TAZ
Theoretical study of two-dimensional nonlinear optical responses in donor-acceptor substituted
difunctionalization hexamolybdates
The research of radar absorbing structures made of glass/carbon fibers/epoxy composites filled with
carbon nanotubes
Huang, Jingsong
Crystal Packing of TCNQ Anion π-radicals Governed by Intermolecular Covalent π−π Bonding
Glushkov,
Monte-Carlo Quantum Chemistry of Biomolecules: Energy and Structural Properties of Biogene Amines
Alexander
and Account for Laser and Neutron Capture Effects
Yamasaki, Hideki
Theoretical investigation on the chemical origin of the interaction between the special pair in the
photosynthetic reaction center
PO-110
PO-111
PO-112
PO-113
PO-114
PO-115
Gomez,Sidonis
Retarding the aging process
PO-116
Cheng, Lan
Four component relativistic theory for NMR parameters
PO -119
Ge, Hao
Waiting Cycle Times and Generalized Haldane Equality in the Steady-State Cycle Kinetics
PO-120
Allouche, Alain
Quantum modeling of hydrogen interaction with beryllium (0001).
PO-121
Anupriya Kumar
Kim, Woo Youn
Photo-excitation and photo-ionization dynamics of water photolysis and excited state dynamics of
pyrrole-water complexes
Quantum Conductance of Subnanowires, Negative Differential Resistance of Molecular Wires, and
Super-Magnetoresistance of Graphene Nanoribbon Devices
PO-122
PO-123
Wang, Shihao
Chiral induction: The transfer of chirality from chiral solutes and surfaces to achiral solvents
PO-125
Sonawane,Lalit V.
Docking studies of few substituted 5-benzyl-2, 4-thiazolidinedione with PPAR-γ for antidiabetic activity
PO-126
Zahedi,Gholamreza
Imai, Takashi
Ikuo Fukuda
Sheikhshoaei, Iran
Sheikhshoaei, Iran
Li, Baiqing
Li, Ying
Dynamic modeling and simulation of heavy paraffin dehydrogenation reactor for selective olefin
production in Linear Alkyl Benzene (LAB) production plant
Molecular thermodynamics of trifluoroethanol-induced helix formation: Analyses of the solvation
structure and free energy by the 3D-RISM theory
Evaluation of Electrostatic Interaction by Charge-Neutralizing principle in Molecular Dynamics Method
The Structural Property Investigation For Some Two And Three Dentate Schiff Base Ligands By
Semi-Empirical Calculations
A Theoretical Investigation On The Nonlinear Optical (NLO) Property Of Four P- Conjugated Salen
Based Compounds
Optimal dynamics discrimination of similar quantum systems
Effect of Surfactant Molecule Structure on the Foam Stability Characterized by Molecular Dynamic
Simulations
PO-127
PO-128
PO-129
PO-130
PO-131
PO-132
PO-133
Zhuo, Shuping
Evidence of high-pressure Rh2O3 phase in rhodium/gamma-Al2O3 catalytic system
PO-134
DING, Yaping
Analysis of Blend Spectra of Nitrophenol Isomers with Doolittle Multivariate Calibration
PO-135
Lu, Wen-Cong
Subcellular Location Predicting by Using AdaBoost
PO-136
Niu, Bing
Predicting toxic action mechanisms of phenols using AdaBoost Learner
PO-137
22 Book of Programme and Abstract for TACC2008 Che, Xinsheng
Emulation and Simulation of Dynamic Weighting Signal
PO-138
Tai, Da Lin,Quan
Molecular dynamic studies on the gated loop domain of the imidazolonepropionase
PO-139
Carsten Baldauf
Investigations on the cleavage of the von Willebrand factor by ADAMTS13
PO-140
Cheng, Shanmei
How sequence determines elasticity of disordered proteins
PO-141
Xia, Fei
Hydrolysis of Peptide Bonds under Stress: A QM/MM Study
PO-142
Xiao, Senbo
Force distribution explains toughness of silk-like crystalline units
PO-143
Pu, Xuemei
Solvent Effects on Isolated Formamide and its Monohydrated Complex: Observations from PCM Study
PO-144
Zhou, Ge
Chewook Lee
Hong, Jooyeon
Li,Qingyu
Li,Wencheng
Rayez,
Jean-Claude
Ha, Yong-Quan
Qi, Qi;
Sun, Yueming
Molecular Dynamics Simulations to Determine the Effect of Temperatures and Salt in Aqueous Solution
on the Structures of Polyacrylamide
Exploring the Molecular Interaction in Ab aggregation by MD Simulation
PO-145
PO-146
Theoretical approaches on the role of secondary structure propensity in oligomerization process of
amyloid beta peptide
Judging Isomeric Compound Based on Elementary Operations on a Matrix
PO-147
PO-148
Prediction of key residues and interactions in the dimmer structure of small heat shock protein HtpX-3 in
thermophilic archaeon Sulfolobus solfataricus
PO-149
Atomistic modelling of soot particles and of their interaction with surrounding molecules
PO-150
Density Functional Theory Study of forming diradicals on the Gilch polymerization
PO-151
Molecular Structure, electronic, and optical properties study of new naphthalimides
PO-152
Shen, Yong
A Dual Functional Inhibitor Mediating Transcriptional Activation against AP-1 and NF-kB: 3D-QSAR and
Zheng, Kangcheng
Molecular Docking Analyses
Wang, Dongqi
Tracking the Folding/Unfolding Equilibrium of Mixed a/b- Peptides in Solution by MD Simulations
PO-155
Tang, Sishi
Exploring Protein Energy Landscapes with Molecular DynamicsSimulation
PO-157
A novel scoring schema for protein identification by using tandem mass spectrometry data
PO-159
Tu, Yuan
Metabonomics Analysis of Human Plasma on Gastric Cancer UsingPattern Recognition
PO-160
Xu, Xiaomin
The new development about peptide elution time prediction
PO-161
Yang, Chiming
A holistic carbon-atom cybernetics in the emergence of genetic information and heredity
PO-162
Zheng, Haoping
Ab initio calculation of electronic structure of protein in solution
PO-163
Fang, Hong
High-pressure thermodynamic study of Ir by first principle calculation
PO-164
Zhao, Pu
Prediction of MHC-binding peptides, using different data representations
PO-165
Shu, Chen
Li, Tonghua
Ihsan Shehadi
John P. Graham
Cheng, Jun
Theoretical study of the molecular properties and chemical reactivity of flavonoids related to their
antioxidant activity
Theoretical Investigations of the Structure, Bonding and Electrochemistry of
2S2 itrosyl Complexes of
Iron and Cobalt
A density Function Theory Study of the a-Olefin Selectivity in Fischer-Tropsch Synthesis
PO-153
PO-166
PO-167
PO-168
23 Book of Programme and Abstract for TACC2008 Tussupbayev,
DFT study of C–H bond activation and C–C coupling in a binuclear ruthenium complex
PO-169
Li, Haiyan
Small-world network approach to identify nucleus residues of small proteins
PO-170
Wang, Jihua
An Analysis of the Avian Influenza Virus Using Z-Curve Method
PO-171
Wang, Jihua
Unfolding Study of small Protein in the Physical Property Space
PO-172
Amir Assadi
Construction of empirical topologies from Infomax Gene Networks based on mRNA microarray data
PO-173
Song Yuanqiang
First principle study of the oxygen vacancy in fluorite CeO2
PO-174
Li,Yuanxun
The Influences of Vanadium on TiV Alloy Performances
PO-175
Samat
Li,Yuanxun
Xue, Ying
Xue, Ying
Guo,Zhen
Delgado, Alina
Agramonte
Aquino, A. J. A.
The Thermal Stability and Degradation Kinetics of Rod-shaped Polyaniline-Barium Ferrite
Nanocomposites
The interfacial structure of self-assembled switchable peptide surfactants
The effect of Polyethylene Glycol (PEG) Spacers on the Conformational Properties of Small Peptides: A
Molecular Dynamics Study
Intrinsic Reaction Coordinate Analysis of Activation of CH4 by Molybdenum atoms: Density Functional
Study of Crossing Seams of Potential Energy Surfaces
In silico prediction of escape mutants of the HIV-1 protease
The role of hydrogen bonds and cation-bridges on the thermodynamic stability of humic acids: modeling
study
PO-176
PO-177
PO-178
PO-179
PO-181
PO-182
Shen, Yao
Targeting type II fatty acid synthetic pathway---design of new antibiotics
PO-183
Lu, Tongtong
Theoretical study on the structures and absorption spectra of protonated phthalocyanine
PO-186
Abolfazl Semnani
Interaction Between 1,3,5–trithiane And Iodine Monobromide in Halomethane Sotutions
PO-187
Zhang, ShuPing
detection of carbofuran with immobilized acetylcholinesterase based on carbon nanotubes modified
electrode
PO-188
Gora,Urszula
Excitation Energy Calculations with R12 Corrections
PO-189
Ardalan,Adel
Applying Recurrent Artificial Neural Networks to Conventional Motif Discovery Problem
PO-190
Tari, Shervin
Designing Three layer Architecture Software for prediction of fluctuations pathways Using Computational
Mohammadi
methods to formulate the signaling pathway models
Zhang, He
A Structure Knowledge-based Method for Protein Thermostability Prediction and Design
PO-192
Naumkin, Fedor Y.
Unusual structural and electronic features of small CnAlm clusters
PO-193
Xiaoxia Ge
Molecular Dynamics Study of Antibiotic Binding to the Ribosome
PO-194
The First Principle Calculation on Composites of TiB2/Cu and Doped Series
PO-196
Zhang, Min
Quantum Chemical Calculation of Maleic Anhydride Ring-opening Reaction
PO-197
Pei-Qiang Huang*;
A computational exploration of substitute effects on the trans-diastereoselective triethylsilane reduction
Xin Lu*
of maliminium
Xie, Hujun
Exploring the Reaction Mechanism of Carbon Monoxide Dehydrogenase: Insights from QM Calculations
MIN Xin-min,
LAN Dongxai
base on ODE and biological Networks
PO-191
PO-198
PO-199
24 Book of Programme and Abstract for TACC2008 Wang,Hai-Xia
Tetrafluoroborate Ionic Liquid
PO-200
Li,Chengyun
Genome-wide analysis of microsatellite sequence in seven filamentous fungi
PO-201
Hu, Xingbang
Explore the structure-reactivity relation of ionic liquid supported acetylacetone catalysts
PO-202
Feng, Xiujuan
Research on ammonia nitrogen pollution forecast Based on RBP neural network model
PO-203
Vijayan, Ranjit
Mu, Yuguang
Chen, Qi
Modulatory ion binding sites in the ligand binding domain of glutamate receptors of the kainate subtype:
dynamics and thermodynamics
Hybrid Hamiltonian Replica Exchange molecular dynamics simulation method employing the
Poisson–Boltzmann model
Evolutionary changes of chloroplast metabolic structure enable stable photosynthetic rates under
environments which can cause high rates of mutation
PO-204
PO-205
PO-206
Dai, Cong-Ying
Theoretical Study of Optical Stability of Pyoluteorin(Plt)
PO-207
Wang, Xi-Jun
Multiscale Simulations of Shock and Thermal Decomposition of Energetic Materials
PO-208
Hou, Xin-Chi
Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Lipase catalysis
reactions
PO-213
Li Fang-Zhen
A simplified tether model for bio-molecular motor transporting cargo
PO-214
Gu, Hui
Preliminary study of the function of phosphorothioation of DNA in bacteria
PO-215
Tang, Bei
Molecular Dynamics of the Rab5a A30P Polymorphism and its Affect on Active Site
PO-216
Yan, Li-Wei
The role of charge seperation of dipole in the ferroelectric liquid crystal phases
PO-217
Li, Jue
Preliminary Studies OF Cytochrame P450 and Metobolizing Mechanism of CYP2E1
PO-220
Yu, Shuhao
The Application of ANN to QSAR and ADME/T
PO-221
Wang, Jingfang
Molecular Dynamics Simulations of Protein Tyrosine Phosphatase 1B: From the Active Site to the
Second Phosphatyrosine Binding Site
PO-222
Zhang, Tao
Database of the Cytochrome P450 SNPs and Their Catalytic Activity
PO-223
Yu, Yao
Fingerprint and its application in similarity search
PO-227
Safa, Fariba
Theoretical Studies on Butene Isomerization Catalyzed by 4-H proton of 1-Ethyl-3-Methyl-Imidazolium
Prediction of Gas Chromatographic Retention Indices of Some Saturated Alcohols on Different
Stationary Phases Using Novel Atom-Type-Based Topological Descriptor
PO-064
25 Book of Programme and Abstract for TACC2008 Abstracts Keynote & Plenary KN-001
Experiment-motivated theoretical studies of reaction rates: 'on water' organic reactions, isotope fractionation and
single-molecule fluctuations
Rudolph A. Marcus
Noyes Laboratory of Chemical Physics, California Institute of Technology
MC 127-72, Pasadena CA 91125
Much of theoretical chemistry has involved equations and their application to experiments, Debye, Debye-Hückel, TST,
Kramers, LCAO, RRKM, among others. In fortunate circumstances one can, as in a theory of electron transfer reactions,
relate different experiments to each other without adjustable parameters, as well as make predictions. A major focus more
recently has been on computations for individual systems, on the specific rather than on the generic. The computations
have permitted the treatment of certain experiments in a detailed fashion not possible earlier. In some cases computations
served as numerical experiments yielding new insights, as in an analysis of classical and quantum trajectories in the
literature of a simple H+H2 reaction, leading to the coining of a new term, vibrational adiabaticity.1
Recent formulations of theory in the analytic/computational domain will be described, using several of the following
examples: mass-independent isotope effect in ozone formation,2 catalysis of certain organic on-water reactions,3
intermittent fluorescence of nanoparticles,4 single-molecule properties of proteins,5 temperature independence of the H/D
kinetic isotope effect for some enzymes operating under their natural conditions,6 and an abnormal Arrhenius
pre-exponential factor for a thermophilic enzyme operating below its “break-point” temperature.6
It will be interesting to see how the interplay between experiment, analytic theory and computation develops in future
theoretical chemistry. The emphasis in this talk will be on puzzles that arise from experiments, puzzles in search of a
theory.
1. RAM J.Chem.Phys. 43,1598 (1965)
2. Y.Q. Gao & RAM J.Chem.Phys. 116,137 (2002) and 127,Art.No. 244318 (2007)
3. Y. Jung & RAM J.Am.Chem.Soc. 129,5492 (2007)
4. J. Tang & RAM, J.Chem.Phys. 123,Art.No.05470 (2005); P. Frantsuzov & RAM Phys.Rev.B 72,155321 (2005).
5. M. K. Prakash & RAM, Proc.Nat.Acad.Sci.USA 104,15982 (2007) and J.Phys.Chem.B 112,399 (2008)
6. RAM, in “Quantum Tunneling in Enzyme Catalyzed Reactions,” R. Allemann and N.S. Scutton, ed. (to be published
2009)
KN-002
How Biomolecular Motors Work: Insights from Simulations
Martin Karplus
Department of Chemistry & Chemical Biology, Harvard University
Cambridge, Massachusetts 02138, U.S.A.
and
26 Book of Programme and Abstract for TACC2008 Laboratoire de Chimie Biophysique, ISIS
Université Louis Pasteur, 67000 Strasbourg France
Cells are a collection of machines with a wide range of functions. To understand their mechanisms, a synergistic
combination of experiments and computer simulations is required. A description of some underlying concepts concerning
the proteins involved in such machines and their motions will be presented. An important element is that the
conformational changes that are required for machine function are built into the structure by evolution. To illustrate the
ideas, some specific biomolecular machines and how they work will be described.
PL-001
Functional classification of small molecules by gene expression module based similarity search
Li Yixue
School of Life Seicence and Technology, Shanghai Jiao Tong University, Shanghai, China 200240
The use of selective chemical interventions to investigate biological processes is a general method in biomedical
researches and drug discovery. In these kinds of studies fingerprinting cellular responses to chemical interventions
based on gene expression experiments made significant approaches for deciphering relationships among small molecules
and gene functions. A plenty of libraries of gene expression profiling corresponding to selected small molecules and
diverse chemical treatments were produced. According to these types of data some algorithms were provided to classify
those chemical probes. The major methods of them were to do similarity comparison among chemical interventions
resulted gene expression profiling. However, these existing methods lay more emphasize on global comparison ignoring
noises and margin affections, which is insufficient under certain queries and also hard to uncover the underlying
mechanisms that lead to the similarity of two molecules, though the whole information of the expressed profiling was
used. Here a new approach was presented to perform functional classification of small molecules by gene expression
module based similarity search. Using Kolmogorov-Smirnov statistic a score matrix was constructed according to the
modulization properties of gene expression profiling for the similarity search and classification of small molecules.
Through the modulization of the cellular fingerprinting induced by chemical interventions this method can reduce noises
and margin effects of gene expression experiments and directly correlate small molecules with gene function modules.
Furthermore, case studies showed that our methodology was much sensitive and provided more reasonable and abundant
search results comparing with the old methods.
PL-002
“Quantum mechanics and molecular mechanics: could they/should they play a key role in systems biology?
What’s possible? What’s not?”
Dennis R. Salahub
Department of Chemistry
IBI - Institute for Biocomplexity and Informatics
ISEEE – Institute for Sustainable Energy, Environment and Economy
University of Calgary
[email protected]
The lecture will review the still emerging field of systems biology from the perspective of computational biology, on the
one hand, and bioinformatics, on the other. I will describe the state-of-the-art of atomistic multi-scale approaches
including those that use quantum mechanics to describe chemical reactions and give a few results for nano-bio systems
that are now being calculated using Density Functional Theory (DFT). Although modern DFT is fast, it is still not fast
27 Book of Programme and Abstract for TACC2008 enough for applications in biology so we are paying attention to so-called reactive force fields (ReaxFF) which try to
capture the essence of quantum mechanical calculations through parametrization against DFT calculations on full
chemical reaction paths. I will then summarize recent results on protein production regulated by genetic networks that
incorporate the main steps in the transcription and translation processes. The Gillespie (Kinetic Monte Carlo) algorithm
is used to solve the (effective) chemical master equation. The seminar will finish with our first (baby-step) attempts to
look at the mechanism of transcription involving metallo-proteins with Mg ions in the active site. The project uses both
DFT and the ReaxFF force field. We hope, in the fullness of time, to be able to feed calculated information on reaction
rates into a stochastic algorithm and, hence, have the behavior of the regulatory network guided by the underlying
atomistic and electronic mechanisms.
Recently, Born Oppenheimer Molecular Dynamics simulations have been performed for an isolated lipid molecule. A
sharp phase transition associated with conformational kinks in the hydrocarbon tails has been located very near to the
observed transition temperature for lipid bilayers, indicating that lipid “melting” is fundamentally a single-molecule
process.
PL-003
A New Analytical Theory For Real Electrolytes: The Extended
Soft Binding Mean Spherical Approximation (ESBIMSA).
L. Bluma,b, M. Ariasb, and D.V. Perez Velozb
a
Department of Mathematics, Hill Center, Busch Campus, Rutgers University, Piscataway, N.J. 08854
b
Department of Physics, P.O. Box 23343, University of Puerto Rico, Rio Piedras, PR00931.
Explaining biology still represents a major scientific challenge because there is a delicate but exacting interplay between
electrostatics and structure: A recent example that was studied by Th. Lazaridis and M. Karplus [1] is protein folding at
the interface of a charged membrane. The Poisson-Boltzmann theory has been the source of much interesting theoretical
work, and is still being used in the simplified linear form ( the Debye- Hueckel (DHT) theory) or in various flavors of
non linear theories. We show here that there are new simple screening parameter theories that are amazingly accurate and
that should be useful. The DHT is a one screening parameter κ theory, that is easy to handle, if not really accurate in its
predictions. A major improvement of the DHT is the MSA (mean spherical approximation) in which all ions are treated
as hard spheres, which is accurate even for concentrated solutions, with a new screening parameter Г. The molecular
solvent model of Wei and Blum [2] has also a simple analytical solution in terms of two lengths Γ, λ, where λ is a
polarization parameter to account for dielectric response and polarizability effects. In recent times we have been able to
extend the nonlinear results to a binary electrolyte: This is the ESBIMSA which is a combination of the extended soft
mean spherical approximation ESMSA[3] and the binding mean spherical approximation BIMSA [4] which uses
Wertheim’s theory of associating fluids. In our current version of the ESBIMSA a single screening parameter Γ is
computed solving a nonlinear equation, where the hard cores are included to all orders , so that the exact full association
Debye − Hueckel limiting laws are satisfied (no other theory does that). For the contact pair correlation function we use
the accurate exponential approximation.
[1] T. Lazaridis, J. Phys. Chem. B2006 110, 1464;T. Lazaridis and M. Karplus, Biophys. Chem. 2003 100, 367;
[2] D.Q Wei and L.Blum, J. Chem. Phys. 1987 87, 555,2999.
[3] L.Blum and M. Arias, Mol. Phys. 2006,104, 3801
[4] O.Bernard and L.Blum, J. Chem. Phys. 1996 104, 4746
PL-004
28 Book of Programme and Abstract for TACC2008 Ab Initio QM/MM Minimum Free Energy Path for Chemical Reactions in Enzymes and in Solution
Weitao Yang
Department of Chemistry, Duke University
Development of methods for first-principles QM/MM free energy calculations for chemical reactions in solution and in
enzyme will be presented. The first method is our QM/MM-FE approach which provides a very efficient and accurate
approximation to reaction free energy assuming the independent dynamics of the QM and MM subsystems.
The
independent dynamics assumption in QM/MM-FE can be removed by the reaction path potential (RPP) approach which
is an analytical energy expression of the combined QM/MM potential energy along the minimum energy path. The
recent development of quantum mechanics/molecular mechanics minimum free energy path (QM/MM-MFEP) eliminates
the dependence on local conformations of the protein/solvent environment, leading to significant enhancement in
accuracy and stability.
The efficient implementation the QM/MM-MFEP method and applications for enzyme and
solution reactions will be featured.
References
1.
Y. Zhang, T. Lee, and W. T. Yang, “A pseudo-bond approach to combining quantum mechanical and molecualr
mechanical methods,” J. Chem. Phys., vol. 110, pp. 46–54, 1999.
2.
Y. Zhang, H. Liu, and W. T. Yang, “Free energy calculation on enzyme reactions with an efficient iterative
procedure to determine minimum energy paths on a combined ab initio qm/mm potential energy surface,” J. Chem. Phys.,
vol. 112, pp. 3483–3492, 2000.
3.
Z. Lu and W. T. Yang, “Reaction path potential for complex systems derived from ab initioqm/mm calculations,” J.
Chem. Phys., vol. 121, pp. 89–100, 2004.
4.
H. Hu, Z. Y. Lu, and W. T. Yang, “Qm/mm minimum free-energy path: Methodology and application to
triosephosphate isomerase,” Journal of Chemical Theory and Computation, vol. 3, pp. 390–406, Mar-Apr 2007.
5.
H. Hu and W. T. Yang, “Free energies of chemical reactions in solution and in enzymes with ab initio QM/MM
methods,” Annual Review of Physical Chemistry, vol. 59, p. 573–601, 2008.
6.
H. Hu, A. Boone, and W. T. Yang, “Mechanism of omp decarboxylation in orotidine 5’-monophosphate
decarboxylase,” Journal of American Chemical Society, 2008. in press.
7.
J. M. Parks, H. Hu, J. Rudolph, and W. T. Yang, “Mechanism of cdc25b phosphatase with the small molecule
substrate p-nitrophenyl phosphate from qm/mm-mfep calculations,” Journal of American Chemical Society, 2008.
submitted.
PL-005
Computing spectroscopic observables from protein simulations
Jonathan D. Hirst
School of Chemistry, University of Nottingham, University of Nottingham,
Nottingham NG7 2RD, United Kingdom
Biomolecular simulations allow us to probe many different aspects of proteins, from their folding to their biological
function. One particularly exciting experimental approach to protein folding is fast time-resolved spectroscopy, both in
the infra-red and ultra-violet regions of the electromagnetic spectrum, the latter via time-resolved electronic circula
dichroism spectroscopy. These spectroscopic methods offer resolution on a nanosecond (or faster) timescale, but they do
not provide the spatial resolution of techniques like X-ray crystallography or NMR. I will describe some of our research
[1-4] aimed at underpinning fast timescale spectroscopic studies of protein folding by coupling molecular dynamics
simulations to calculations of spectroscopy. I will discuss the inter-play between molecular dynamics simulation and
experimental data with reference to a case study [3] on the structure and dynamics of a three-helix bundle: the ubiquitin
29 Book of Programme and Abstract for TACC2008 binding domain of the protein p62. And I will also describe recent calculations on charge-transfer transitions in the
vacuum-ultraviolet of protein circular dichroism spectra [1,3].
[1] M.T. Oakley, J.D. Hirst, J. Am. Chem. Soc. 2006, 128, 12414.
[2] T. La Cour Jansen, A.G. Dijkstra, T.M. Watson, J.D. Hirst, J. Knoester, J., J. Chem. Phys. 2006, 125, 044312.
[3] C.-L. Evans, J.E. Long, T.R.A. Gallagher, J.D. Hirst, M.S. Searle, Proteins: Structure, Function & Bioinformatics,
2008, 71, 227.
[4] B.M. Bulheller, A.J. Miles, B.A. Wallace, J.D. Hirst, J. Phys. Chem. B, 2008, 112, 1866.
PL-006
New Generation Relativistic Electronic Structure Theory
Wenjian Liu
Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking
University, Beijing 100871, P. R. China
Any quantum chemical or physical calculation should be concerned with two issues: the choice of Hamiltonian and then
the choice of method for correlating the motion of the particles. And it is clear that, any ‘good’ theory for a certain class
of problem must fulfill all the three criteria:
1.
Simple. The true physics and the underlying laws are all simple and beautiful, e.g., the Newton equation, the
Maxwell equation, the Schrödinger equation (SE), the Dirac equation (DE), as well as the mass-energy relationship
(E=mc2), to name just a few.
2.
Accurate. One should get the right answer for the right reason, without relying on error compensation.
3.
Efficient. For the same accuracy, the cheaper the better. Reversely, given the same efficiency, the more accurate the
better.
Up to date, most quantum chemical and physical calculations have been based on the SE. Such calculations have turned
out to be very successful in analyzing experiments. However, it must be realized that the SE describes an artificial world
in which light travels at infinite speed. Instead, only the DE built upon the special theory of relativity represents our real
world. Since all experiments are carried out in the real world, in principle only the DE can validate and predict
experiments. As a matter of fact, the SE can faithfully be applied only to the ground states of systems composed of light
elements, say, up to Z=36. According to the above criteria, the SE is not a ‘good’ theory. On the other hand, the DE is
also not a ‘good’ theory because it tends to overshoot chemistry and ordinary physics: Its negative energy solutions have
nothing to do with chemistry and ordinary physics. To get a ‘good’ theory, the following four questions have to be
addressed. If the point of departure is the DE, (Q1) can we find an exact two-component (2C), electron-only theory? (Q2)
can the computational effort of the DE be reduced down to that of a 2C counterpart? If the point of departure is the SE,
(Q3) can we find an optimal scalar relativistic equation that is as simple as the SE? Finally, starting from the midpoint of
the DE and SE, (Q4) can we find an equation that can seamlessly fuse the two equations such that heavy and light
elements in the system can be treated differently?
All the four questions have nicely been answered, based on the simple idea of “from atoms to molecule” [1-3] rather than
on mathematical tricks. It can now be claimed that relativity in chemistry has been solved, 80 years after Dirac though.
1.
W. Kutzelnigg and W. Liu, J. Chem. Phys. 123, 241102 (2005).
2.
W. Liu and D. Peng, J. Chem. Phys. 125, 044102 (2006).
3.
D. Peng, W. Liu, Y. Xiao, and L. Cheng, J. Chem. Phys. 127, 104106 (2007).
30 Book of Programme and Abstract for TACC2008 PL-007
From Atomic and Molecular Orbitals to Chemical Orbitals.
Enrico Clementi
Via Carloni, 38, I-22100, Como, Italy
Giorgina Corongiu
Dipartimento di Scienze Chimiche ed Ambientali, Università dell’Insubria
Via Lucini 3, I-22100, Como, Italy
The variational combination of the Hartree-Fock, HF, with the Heitler-London, HL, methods, yielding the
Hartree-Fock-Heitler-London, HF-HL, method is analyzed for diatomic hydrides and homonuclear molecules of the
first and second row atoms [1-5], and for preliminary computations on H20.
The correlation energy correction needed in HF and HL computations is reduced in the HF-HL method to its dynamic
component, since the non-dynamical correlation is accounted by explicitly considering near degeneracy and state
crossing [1,2]. The dynamical correlation is computed 1) via expansion with selected Multi-Configuration of HF and HL
functions [2] and 2) by including ionic structures, which account for the molecular extra correlation energy yielding
correctly the binding energy [3-5]. The atomic dynamic correlation components of the total molecular correlation are
accounted via the Coulomb hole density functional. With the latter the computed total and binding energies for all
internuclear separations are in good agreement with laboratory data [3-5]. Improved computations relative to those
presently published are reported [7].
A recently proposed one-electron function, the Chemical Orbital, CO, and the corresponding determinantal wave
function, the Chemical Orbital wave function, ΨCO [6] is discussed. We show that ΨCO can be decomposed into a HF-HL
like function with covalent and ionic components, designated “adjoined HF-HL function”. The HF-HL, HF, and HL
wave functions are derivable as special cases of the ΨCO wave function. A single “adjoined HF-HL function” can
realistically represent molecular systems from the united atom, to equilibrium distances, to dissociation; a linear
expansion of
very few
“adjoined HF-HL
functions” yields accurate non-relativistic energies. Preliminary test
computations with “adjoined HF-HL function” are presented for the ground state of the H2 and LiH .
The topics above mentioned are discussed in detail in a recent paper [8].
[1] Corongiu, G., Int. J. Quantum Chem. 2005, 105, 831.
[2] Corongiu, G.,
J. Phys. Chem. A, 2006, 110, 11584.
[3] Clementi, E. and Corongiu, G., Theor. Chem. Acc. 2007, 107, 214.
[4] Corongiu, G.,
J. Phys. Chem. A, 2007, 111,5333.
[5] Corongiu, G.,
J. Phys. Chem. A, 2007,111,13611..
[6] Clementi, E. and Corongiu, G., Int. J. Quantum Chem., 2008, DOI:10.1002.
[7] Corongiu, G., to be published.
[8] Clementi, E. and Corongiu, G., Hua Xue Ton Bao, 2008, in press.
PL-008
Ab initio intermolecular force fields spectroscopically validated: state of the art
Krzysztof Szalewicz(a) and Ad van der Avoird(b)*;
31 Book of Programme and Abstract for TACC2008 (a) Department of Physics and Astronomy, University of Delaware Newark, DE 19716, USA
(b)Theoretical Chemistry, Institute for Molecules and Materials Radboud University, Nijmegen, The Netherlands
In this talk a review will be given of the state of the art in obtaining intermolecular potential surfaces from ab initio
electronic structure calculations, by different methods. The reliability of the resulting force fields can be critically tested
in computations of the bound levels and spectra of Van der Waals complexes and comparison of the computed spectra
with experimental high-resolution spectra. Such complexes, bound by hydrogen bonding or by dispersion forces, are
floppy. They exhibit large amplitude vibrations, internal rotations, and tunneling motions, and the spectra are extremely
sensitive to the shape of the anharmonic wells in the potential and to the barriers between these wells. Special methods
based on molecular scattering theory are devised to compute the spectra of these complexes from a given potential with
sufficient accuracy.
This will be illustrated by showing the latest information on the pair and many-body potential of water, the application of
some new potentials to the vibration-rotation tunneling (VRT) spectra of normal and perdeuterated water dimers and
trimers, and the importance of this knowledge to establish the role of many-body forces in determining the intriguing
properties of liquid water [1].
[1] R. Bukowski, K. Szalewicz, G. C. Groenenboom, and A. van der Avoird, Science 315, 1249 (2007)
* E-mail: [email protected]
PL-009
High Resolution Modeling of Protein Structure and Protein-Ligand Interactions
Richard A. Friesner
Department of Chemistry, Columbia University, 3000 Broadway, MC 3110
New York, NY, 10027
We will discuss novel sampling algorithms and scoring functions designed to provide high resolution prediction of local
structures in protein active sites (loop, side chains, protein-ligand complexes), and to predict protein-ligand binding
affinities. The specific focus will include methods for induced fit docking, empirical scoring functions for protein-ligand
interactions, structural refinement via continuum solvation models, and a molecular dynamics method for determining
the chemical potential of water molecules in the active site.
Large data sets, primarily containing interesting
pharmaceutical targets, are used to evaluate the utility of the various methods.
PL-010
Anharmonic Vibrations of Biological Molecules: Quantum Algorithms and Spectroscopic Applications
R.B. Gerber
Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
and
Department of Chemistry, University of California, Irvine, CA 92697, U.S.A.
Progress is described on algorithms that greatly accelerate calculations of anharmonic vibrational energy levels and
wavefunctions of large molecules. The new algorithms use variants of the Vibrational Self-Consistent Field (VSCF)
approach, and lead to much improved scaling of the effort with N, the number of vibrational modes. The results make
possible calculations of adequate accuracy for systems as large as tetra-peptides and beyond. Applications are provided.
32 Book of Programme and Abstract for TACC2008 Several examples of applications to spectroscopy of biological molecules are presented, where the methods play a
useful role in the interpretation of experimental data. For proton-bound dimers of amino acids, comparison with
experiment helps determine structure, and elucidates the role of coupling between modes in different parts of the
spectrum. For the chromophore of the Photoactive Yellow Protein (PYP), the results establish properties of the potential
surface for the intermediate state of the photocycle.
Future prospects and directions in the field are authored.
PL-011
Multi-scale Methods for Macromolecular Systems in Computational Biophysics
Bernard R. Brooks
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda,
Maryland, USA.
This presentation focuses on our recent efforts to develop multi-scale macromolecular modeling methods and to apply
them to problems of biological significance. One objective in developing multi-scale modeling techniques is to be able to
include multiple scale representations within a single study. By combining scales, you can examine properties that would
be difficult or too costly to examine with a single model. Examples are presented from the following models:
Grid based map objects (EMAP)
Coarse-grained models using elastic network models (ENM) and Langevin network models (LNM)
Coarse-grained models using Hydrophibic/Hydrophibic/Neutral models (BLN)
Atomic models using a classical force field (CHARMM, Amber,…)
Models employing a quantum mechanical subsystem (CHARMM/Q-Chem,…)
Examples of methods employing these models include:
Structural analysis via single particle electron tomography
Protein-protein docking with grid based methods
Vibrational free energy partitioning and subsystem analysis
Structure and dynamics of lipid bilayers
Examining protein folding in confinement
Rapid exploration of conformational space for peptides
Examining reaction profiles using QM/MM methods
1. X. Wu and B. R. Brooks, “Modeling of Macromolecular assemblies with map objects,” Proceedings of the 2007
International Conference on Bioinformatics and Computational Biology Vol. II: 411-417 (2007)
2. J. L. S. Milne, X. W. Wu, M. J. Borgnia, J. S. Lengyel, B. R. Brooks, D. Shi, R. N. Perham and S. Subramaniam.
"Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes
using cryoelectron microscopy," J. Biol. Chem., 281 (7): 4364-4370 (2006)
3. J. B. Klauda, B. R. Brooks and R. W. Pastor. "Dynamical motions of lipids and a finite size effect in simulations of
bilayers," Journal of Chemical Physics, 125 (14): (2006)
4. H. L. Woodcock, M. Hodoscek, A. T. B. Gilbert, P. M. W. Gill, H. F. Schaefer and B. R. Brooks. "Interfacing Qchem
and CHARMM to perform QM/MM reaction path calculations," Journal of Computational Chemistry, 28 (9): 1485-1502
(2007)
5. H. L. Woodcock, M. Hodoscek and B. R. Brooks. "Exploring SCC-DFTB paths for mapping QM/MM reaction
mechanisms," Journal of Physical Chemistry a, 111 (26): 5720-5728 (2007)
6. X. Wu and B.R. Brooks, “Self-guided Langevin dynamics simulation method,” Chem. Phys. Letter 381, 512-518
(2003).
33 Book of Programme and Abstract for TACC2008 7. X. Wu, Y. Zhen, B.R. Brooks, and Y.A. Su, “The local maximum clustering method and its application in microarray
gene expression data analysis,” EURASIP JASP 1, 53-63 (2004).
8. W. J. Zheng and B. R. Brooks, “Identification of dynamical correlations within the myosin motor domain by the
normal mode analysis of an elastic network model,” J. Mol. Biol., 346 (3): 745-759 (2005)
9. G. Stan, B. R. Brooks, G. H. Lorimer and D. Thirumalai. "Identifying natural substrates for chaperonins using a
sequence-based approach," Protein Sci, 14 (1): 193-201 (2005)
10.G. Stan, B. R. Brooks, G. H. Lorimer and D. Thirumalai. "Residues in substrate proteins that interact with GroEL in
the capture process are buried in the native state," Proc. Natl. Acad. Sci. U. S. A., 103 (12): 4433-4438 (2006)
11. J. B. Klauda, N. Kucerka, B. R. Brooks, R. W. Pastor and J. F. Nagle. "Simulation-based methods for interpreting
X-ray data from lipid bilayers," Biophys. J., 90 (8): 2796-2807 (2006)
12. G. Stan, G. H. Lorimer, D. Thirumalai and B. R. Brooks. "Coupling between allosteric transitions in GroEL and
assisted folding of a substrate protein," Proc. Natl. Acad. Sci. U. S. A., 104 (21): 8803-8808 (2007)
13. B. T. Miller, W. J. Zheng, R. M. Venable, R. W. Pastor and B. R. Brooks. “Langevin network model of myosin,” J.
Phys. Chem. B, 94 (8): 6274-6281 (2008)
PL-012
Mukamel, Shaul
PL-013
PubChem and the NIH Molecular Libraries Project
Bryant, Stephen
PL-014
Recent advances in local explicit electron correlation methods
Hans-Joachim Werner
Institute for Theoretical Chemistry, University of Stuttgart,
Pfaffenwaldring 55, D-70569 Stuttgart, Germany
The lecture will review recent developments of explicitly correlated methods, in particular new explicitly correlated
coupled-cluster methods for closed- and open-shell systems. Applications of these methods to predictions of reaction
enthalpies, ionization potentials, electron affinities, as well as binding energies of molecular clusters will demonstrate
that these high-level methods can now be routinely applied. Using triple-zeta basis sets results that are very close to the
basis set limit are obtained at moderate cost. By combining explicitly correlated methods with local approximations
nearly linear scaling of the computational cost with molecular size can be achieved, and explicitly correlated LMP2
calculations for reactions of biochemical interest involving molecules with up to 80 atoms and 200 correlated electrons
will be presented
PL-015
Structure Bioinformatics, TCM Databases, and Personalized Drug Design
JF Wang1,2, T Zhang1, J. He1, YQ Zhong1,2, XJ Wang1, Dong-Qing Wei1*
1
College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
2
Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Science, Chinese Academy of
Science, Shanghai 200031, China
34 Book of Programme and Abstract for TACC2008 Structure bioinformatics tools have been developed to generate 3D structure from sequences of novel genes[1-3]. It
allows us pursue structure based drug design. Applications were made to drug design for SARS, H5N1 and HIV. A
octapeptide AVLQSGFR designed by us was synthesized and its antiviral potential against SARS coronavirus (BJ-01)
was assessed, which demonstrates that AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus
compared with other compounds reported so far(EC50 is 2.7×10-2mg/L, and its selectivity index is more than 3704),
while no detectable toxicity on Vero cells under the condition of experimental concentration is observed.
We have developed a methodology that efficiently locates feature sequences(FS) of HA gene, which is visually
identifiable in the gene finger print. This FS is only found in H5N1 not in any other influenza viruses. The FS is a 30 bp
gene segment consists of main “a” and “g”, which can be used to explain the high pathogenecity of the virus and its
evolution. A homology model[4] of H5N1 NA is built according to the X-ray protein structure of NA complexed with
DANA (2, 3-didehydro-2-deoxy-N-acetylneuraminic acid) (PDB code: 1F8B). We find that the residues in the active site
of NA family are highly conserved in H5N1 NA. However, a partially lipophilic pocket composed by Ala246, Thr247
and lipophilic parts of Glu276 and Arg224 in NA 1F8B, becomes a hydrophilic pocket because the lipophilic residues
Ala246 and Thr247 are replaced by hydrophilic residue Ser246 and Thr247 in H5N1 NA. On other hand, two hydrophilic
residues Asn346 and Asn347 of 1F8B are replaced by two lipophilic residues Ala346 and Tyr347, and a new lipophilic
pocket is formed in H5N1 NA. These changes not only spoil the original lipophilic environment but also change the
complement interaction between H5N1 NA and docked ligands. This may be related to the drug resistance of H5N1
influenza virus for many existing NA inhibitors.
We have built an effective component Database of the Traditional Chinese Medicine(TCMD), which contains 3-D
structures of 9127 different compounds from various sources of traditional Chinese medicines.
The database is
screened with various cheminformatics tools, many promising molecules were obtained, for example, agaritine was
singled out through similarity search and molecular docking method. Agaritine, a Chinese herbal medicine, has been
known as an antiviral and anticancer medicine, but no anti-HIV effect of it has been reported before. After further
modification of agaritine and docking study of its derivatives, we got an in-depth molecular insights of the binding
interaction and thus proposed the binding mechanism and drug candidates. In our another study of peptide inhibitor to
HIV Pr, we found a tetrapeptide QNC-THR-PHM-RHS binding tightly with the target enzyme by performing flexible
molecular alignment with the natural substrate and molecular docking to the protease. Thereby we calculated the atom
electric charge distribution of different peptides complexed with HIV Pr and made comparisons between different
peptides using quantum mechanics (QM) method. Results of the computation indicates that there should be a
modification to the –CO=NH– group between P1 and P1` to avoid possible cleverage by the protease. And the modified
tetrpeptide has been testified by our QSAR (Quantitative Structure Activity Relationship) model. We built a QSAR
model of HIV protease peptidomimetic inhibitors by incorporating artificial intelligence technique and rational selection
of molecular descriptors. The structure of the optimum Artificial Neural Networks (ANN) achieving the highest
Pearson’s-R coefficient was determined to demonstrate correlations between molecular properties and anti-HIV
bioactivity, which is advantageous over the methods of Partial Least Squares (PLS) and Genetic Algorithms (GA).
Among the considered 192 molecular descriptors, non-covalent interactions such as hydrophobicity, shape and hydrogen
bonding describe well the antiviral activity of the HIV Pr compounds. And another interesting finding is the significance
of lipophilicity and relationship to HIV-1 associated hyperlipidemia and lipodystrophy syndrome, which may be quite
helpful in future anti-HIV inhibitor design.
Cytochrome P450s are considered as the most important enzymes responsible for the phase I drug metabolism[5,6]. By
now, there are over 7700 distinct CYP sequence which can be found in the NCBI database. For their metabolizing more
than 90% known drugs, CYP1, 2 and 3 families are of the most importance. In the current study, the three-dimensional
(3D) structure of CYP2E1 has been development by homology modeling methods using the crystal structure of CYP2C5
as a guide. Then, a series assessment has been carried out on the computational 3D structure. After a short molecular
35 Book of Programme and Abstract for TACC2008 dynamics, 12 known drugs have been docked to the optimized computational 3D structure using AutoDock. To
investigate the interactions of CYP2E1 with substrates, 8ns MD simulations were subsequently carried out. And it is
found that Leu368 is of most importance for the interactions of CYP2E1 with substrates. It can provide hydrophobic
molecular surface to stabilize corresponding substrates. In addition, Ile115, Phe298 and Val364 are in charge of
stabilizing some special substrates. All these findings accord with the results obtained from photo-affinity labeling
studies, and will be very useful for conducting mutagenesis studies, providing useful information for drug metabolism
and personalization of drug treatments, as well as stimulating novel strategies for finding desired personalized drugs.
Keywords: Structure Bioinformatics, Computer Aided Drug Design, Traditional Chinese Databases, SARS, HIV, H5N1.
References
1.
Suzanne Sirois, Rui Zhang, Weina Gao, Hui Gao, Yun Li and Dong-Qing Wei*, “Discovery of Potent
anti-SARS-CoV MPro inhibitors”, Current Computer Aided Drug Design, 3, 341-352(2007).
2.
William Kem, Ferenc Soti, Susan LeFrancois, Kristin Wildeboer, Kelly MacDougall, Dong-Qing Wei, Kuo-Chen
Chou and Hugo R. Arias, “The Nemertine Toxin Anabaseine and its Derivative DMXBA (GTS-21): Chemical and
Pharmacological Properties”, Marine Drugs 4, 55-273(2006).
3.
Kuo-Chen Chou, Dong-Qing Wei, Qi-Shi Du, Suzanne Sirois, Wei-Zhu Zhong, Progress in Drug Development
against SARS, Current Medicinal Chemistry, 13, 3263-3270(2006).
4.
DQ Wei, QS Du, H Sun, KC Chou, BBRC, 344 (2006) 1048–1055
5.
Cheng-Cheng Zhang, Jing-Fang Wang, DQ Wei et al. , Structure of cytochrome P450s and personalized drug,
Current Med. Chem. (In press)
6.
Jing-Fang Wang, Cheng-Cheng Zhang, DQ Wei et al., Molecular Modeling of CYP Proteins and Its Implication for
Personal Drug Design.
“Automation in Genomics and Proteomics: An Engineering Case-Based Approach”
to be
published by Wiley Publishing, a text book for Harvard and MIT students
PL-016
Large Scale Motions in Proteins
Michele Parrinello
Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, 6900 Lugano,
Switzerland
Simulating conformational changes in proteins is of great importance and molecular dynamics simulations are expected
to play a major role. However, such simulations are hampered by the very short time they can run. Here we present a
complex strategy for alleviating this problem. We characterize the structure of proteins by a number of collective
variables or order parameters and calculate the associated free energy surface. In particular we present two efficient
methods for exploring this surface, one being well-tempered metadynamics and the other a path-based method. With the
help of these methods, very long time scale phenomena can be simulated.
PL-017
Computer simulation of biomolecular systems: where do we stand ?
Wilfred F. van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH 8093 Zurich, Switzerland
Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and
biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement
36 Book of Programme and Abstract for TACC2008 by experimental means, computer simulation can complement experiment by providing not only averages, but also
distributions and time series of any definable – observable or non-observable – quantity, for example conformational
distributions or interactions between parts of molecular systems. Present day biomolecular modelling is limited in its
application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble
(sampling) problem, and 4) the experimental problem. These four problems will be discussed and illustrated by practical
examples. Perspectives will be outlined for pushing forward the limitations of molecular modelling.
Angew. Chem. Int. Ed. 45 (2006) 4064 – 4092
J. Comput. Chem. 29 (2007) 157 – 166
J. Biomol. NMR 39 (2007) 265 – 273
www.igc.ethz.ch
PL-018
Systematic Coarse-graining of Biomolecular Systems
Gregory A. Voth
[email protected]
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah
A multiscale theoretical and computational methodology will be presented for characterizing biomolecular systems and
assemblies across multiple length- and timescales. The approach provides a connection between all-atom molecular
dynamics, mesoscopic models, and near continuum-scale mechanics. At the heart of the methodology is the multiscale
coarse-graining method for systematically deriving coarsegrained models from atomistic-scale forces. Applications will
be given for membranes, peptides, and proteins. Recent advances for coarse-graining large protein complexes and
membrane proteins will also be described if time allows.
PL-019
Accurate interaction energies of building blocks of biomacromolecules: quantum chemical study
Pavel Hobza
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
166 10 Prague 6, Czech Republic
[email protected]
Structures and stabilization energies of noncovalently bound molecular clusters playing a role in biodisciplines are
investigated. Specifically, we consider H-bonded and stacked structures of DNA base pairs and amino acid pairs in a gas
phase as well as in an environment. Structure of pairs is either optimized or is taken from experiment. Benchmark
stabilization energies of complexes studied are determined as the Complete Basis Set (CBS) limit of the CCSD(T)
calculations and various constructions of these energies are discussed. The role of CCSDT and CCSD(TQ) levels is also
considered. Resulting stabilization energies of H-bonded and stacked pairs are very large, much larger than considered
before. This is especially
true about stacked DNA base pairs and amino acid pairs. It is expected that these energies
are highly accurate and differ from the real numbers by less than 0.5 kcal/mol. Stabilization energy of stacked structures
originates exclusively in London dispersion energy and only high-level wave function and density functional theories can
be applied. Electrostatic energy is responsible for the orientation of the cluster and bringing subsystems closer together.
The partitioning of the total interaction energy to the components is performed by using the DFT-SAPT method and the
role of electrostatic and dispersion energies in stabilizing staked and H-bonded structures is discussed. The use of
density functional theories including the recently introduced hybrid meta GGA functionals is briefly considered and
37 Book of Programme and Abstract for TACC2008 successes and failures of these procedures is mentioned. It is shown that stability of DNA double helix is mainly due to
stacking interactions of nucleic acid bases while H-bonding is playing the role in molecular recognition. The unique role
of dispersion energy is stressed.
PL-020
Computer Simulation of Protein Dynamics
Jeremy C. Smith
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
Recent results will be presented combining neutron scattering with computer simulation to bring about new insight into
protein dynamics and protein-protein and protein-ligand interactions. Phenomena driving peptide folding will be
explored. Computational approaches to understanding complex conformational transitions will be outlined.
1.
F. NOE, I. HORENKO, C. SCHÜTTE and J.C.SMITH. J Chem Phys 126 (15):155102 (2007).
2.
D.R. NUTT and J.C.SMITH. J Chem Theo Comput 3(4) 1550-1560 (2007).
3.
S. KOPPOLE, J.C. SMITH and S. FISCHER, Structure 15 (7): 825-837 (2007).
4.
K. MORITSUGU and J.C. SMITH.. Biophys J 93(10):3460-3469 (2007).
I.
DAIDONE, M. ULMSCHNEIDER, A. DI NOLA, A. AMADEI and J.C. SMITH. Proc Natl Acad Sci (U.S.A.)
104 39 15230-15235 (2007).
5.
L. MEINHOLD, F. MERZEL and J.C. SMITH. Phys Rev Letts 99 (13):138101 (2007).
6.
L. MEINHOLD, J.C. SMITH., A. KITAO and A.H. ZEWAIL. Proc Natl Acad
Sci (U.S.A.) 104 44 17261-17265
(2007).
7.
K. VOLTZ, J. TRYLSKA, V. TOZZINI, V. KURKAL-SIEBERT, J.C. SMITH and J. LANGOWSKI. J Comp
Chem. 29(9):1429-39 (2008).
8.
L MEINHOLD, D. CLEMENT, M. TEHEI, R. DANIEL, J.L. FINNEY & J.C. SMITH. Biophys J94(12):4812-8
(2008).
9.
V. KURKAL-SIEBERT, R. AGARWAL & J.C. SMITH. Phys Rev Letts. 100 13 138102 (2008).
10. M. KRISHNAN, V. KURKAL-SIEBERT & J.C. SMITH. J Phys Chem B. 112(17):5522-33 (2008).
11. T. NEUSIUS, I. DAIDONE, I.M. SOKOLOV & J.C. SMITH. Phys Rev Letts. 100 18 188103 (2008).
PL-021
QM/MM Studies of Enzymes
Walter Thiel
Max-Planck-Institut für Kohlenforschung,
Kaiser-Wilhelm-Platz 1, D-45470 Mülheim, Germany
In recent years, it has become possible to model chemical reactions in large biomolecules using combined quantum
mechanical / molecular mechanical (QM/MM) methods. After a general outline of the theoretical background and the
chosen strategy [1], the lecture will describe some of our recent work on biocatalysis by enzymes, in particular
p-hydroxybenzoate hydroxylase (PHBH) [2,3] and cytochrome P450cam [4-8]. In the case of PHBH, the focus will be on
methodological advances in QM/MM approaches, particularly with regard to the accuracy that can be reached, while
P450cam will serve as an example of the chemical insights and the improved mechanistic understanding that can be
provided by QM/MM calculations.
1.
H. M. Senn, W. Thiel, Top. Curr. Chem. 2007, 268, 173-290.
H. M. Senn, S. Thiel, W. Thiel, J. Chem. Theory Comput. 2005, 1, 494-505.
3.
R. Mata, H.-J. Werner, S. Thiel, W. Thiel, J. Chem. Phys. 2008, 128, 025104.
4.
J. C. Schöneboom, H. Lin, S. Cohen, S. Shaik, W. Thiel, J. Am. Chem. Soc. 2004, 126, 4017-4034.
5.
J. C. Schöneboom, F. Neese, W. Thiel, J. Am. Chem. Soc. 2005, 127, 5840-5853.
6.
J. Zheng, D. Wang, W. Thiel, S. Shaik, J. Am. Chem. Soc. 2006, 127, 13204-13215.
A.
Altun, S. Shaik, W. Thiel, J. Am. Chem. Soc. 2007, 129, 8978-8987.
7.
D. Wang, J. Zheng, S. Shaik, W. Thiel, J. Phys. Chem. B 2008, 112, 5126-5138.
PL-022
Dynamical Effects in Enzyme Catalysis. An Analysis of the Chalcone Isomerase Catalyzed Reaction
Iñaki Tuñón,a Javier J. Ruiz-Pernía,a Vicente Moliner,b James T. Hynes,c Maite Roca,d
a
Departamento de Química Física. Universidad de Valencia, SPAIN
b
c
Departamento de Química Física y Analítica. Universidad Jaume I, Castellón, SPAIN
Département de Chimie. Ecole Normale Supérieure. Paris, FRANCE
and Department of Chemistry and Biochemistry. University of Colorado, USA
d
Department of Chemistry. University of Southern California, USA
Dynamical effects have recently received considerable attention as a possible source of catalysis in enzymatic reactions.
The essence of the idea is that the internal motions of the protein could be significantly coupled to the reaction coordinate
that defines the internal changes in the chemical system providing thus important deviations with respect to the
equilibrium picture. In this contribution we show that Grote-Hynes theory provides an excellent theoretical tool to
quantify departures from Transition State Theory due to the use of simplified reaction coordinates to describe the free
energy profile of the process. The application of this theory requires of the evaluation of the friction kernel in the
transition state obtained from the averaged forces exerted on a distinguished reaction coordinate by the remaining degrees
of freedom of the system. Using the Generalized Langevin Equation it is then possible to estimate the transmission
coefficient of the reaction and thus compare the contribution of ‘dynamical effects’ to the reaction rate in solution and in
the enzyme.1,2 We have recently applied Grote-Hynes theory to the analysis of the Michael addition reaction catalyzed
by Chalcone Isomerase leading from 6’-deoxychalcone to the corresponding flavanone.3 Catalysis is explained in terms
of a very significant difference in the evolving solvation pattern of the nucleophilic oxygen in water and in the enzyme.
While in the former medium this atom suffers an important desolvation, the enzyme provides -through variations in the
distances with some residues and water molecules- an essentially constant electric field on this atom along the reaction
progress. Grote-Hynes theory provides transmission coefficients in excellent agreement with the Molecular Dynamics
estimations. These are quite similar in both media, making then a negligible contribution to catalysis.4 Within the context
of this theory, analysis of the friction spectrum together with normal mode analysis is used to identify those motions
-both of the substrate and the environment- strongly coupled to the reaction coordinate and to classify them as
dynamically active or inactive.
(1) Roca, M.; Moliner, V.; Tuñón, I.; Hynes, J. T., J. Am. Chem. Soc. 2006, 128, 6186.
(2) Castillo, R.; Roca, M.; Soriano, A.; Moliner, V.; Tuñón, I.; J. Phys. Chem. B 2008, 112, 529.
(3) Ruiz-Pernía, J. J.; Silla, E.; Tuñón, I. J. Am. Chem. Soc. 2007, 129, 9117-9124.
(4) Ruiz-Pernía, J. J.; Tuñón, I.; Moliner, V Hynes, J. T.; Roca, M., J. Am. Chem. Soc. ASAP.
PL-023
Effects of Spin-Orbit coupling on Magnetic Properties of Discrete and Extended Magnetic Systems
D. Daia, H. J. Xiangb and M.-H. Whangboc
39 Book of Programme and Abstract for TACC2008 a
Duke Clinical Research Institute, Durham, North Carolina 27705, USA
b
National Renewable Energy Laboratory, Golden, Colorado 80401, USA
c
Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
In accounting for the magnetic properties of discrete and extended compounds with unpaired spins, it is crucial to know
the nature of their ground and low-lying excited states. The nature of these magnetic states can be strongly affected by
spin-orbit coupling. In this talk we will survey quantum mechanical descriptions on how these states are affected by
spin-orbit coupling and attempt to provide a conceptual framework with which to think about spin-orbit coupling and its
applications [1]. It is hoped that this brief review will stimulate further discussions on how to think about spin orbit
coupling and its applications.
[1] D. Dai, H. J. Xiang and M.-H. Whangbo, J. Comput. Chem. 2008, in press.
PL-024
Structural and Dynamical Properties of Ionic Liquids: Inuences of Ion Size Disparity and Charge Location
G. N. Patey and H.V. Spohr
Department of Chemistry, University of British Columbia, Vancouver BC
Canada, V6T 1Z1
Ionic liquids range from molten salts, consisting of simple inorganic ions, to room temperature ionic liquids, which are
composed of large organic cations, for example quaternary amines, imidazoles or other heterocyclic molecules and
organic or inorganic anions. Room temperature ionic liquids are of importance for two reasons. Firstly, they have very
different properties than common organic solvents and therefore are used as alternate solvents in chemical reactions.
Secondly, they have the advantage of flexibility, because the solvent properties can be adjusted by altering the nature of
the ionic constituents. Tuning can also be achieved by changing the composition of ionic liquid mixtures. However, it
remains difficult to predict ionic liquid properties from the molecular structure of the ions. Our objective is to find and
separate the ionic features that govern the liquid properties. In contrast to many simulation studies of ionic liquids, which
employ all atom models, we focus on simpler model systems in order to isolate the influences of different molecular
traits. Room temperature ionic liquids are often composed of ions that are very different in size, moreover, the charge of
at least one of the ions is often \located" away from the center of mass. The influences of varying the ion size disparity
and charge location on the liquid structure, the diffusion constants, the shear viscosity, and the electrical conductivity are
determined by molecular dynamics simulations. It is shown that charge location is of particular importance, having
significant effects on both structural and dynamical properties of ionic liquids. Some comparisons with experiment will
be discussed.
PL-025
Orbital-Corrected Orbital-Free Density Functional Theory
Yan Alexander Wang
Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada [email protected]
Density functional theory (DFT) has been firmly established as one of the most widely used first-principles quantum
mechanical methods in many fields. Each of the two ways of solving the DFT problem, i.e., the traditional orbital-based
Kohn-Sham (KS) and the orbital-free (OF) [1] schemes, has its own strengths and weaknesses. We have developed a new
implementation of DFT, namely orbital-corrected OF-DFT (OO-DFT) [2], which coalesces the advantages and avoids
the drawbacks of OF-DFT and KS-DFT and allows systems within different chemical bonding environment to be studied
40 Book of Programme and Abstract for TACC2008 at a much lower cost than the traditional self-consistent KS-DFT method. For the cubic-diamond Si and the
face-centered-cubic Ag systems, OO-DFT accomplishes the accuracy comparable to fully self-consistent KS-DFT with at
most two non-self-consistent iterations [2] via accurately evaluating the total electronic energy before reaching the full
self-consistency [2-6]. Furthermore, OO-DFT can achieve linear scaling by employing currently available linear-scaling
KS-DFT algorithms and may provide a powerful tool to treat large systems of thousands of atoms within different
chemical bonding environment much more efficiently than other currently available linear-scaling DFT methods. Our
work also provides a new impetus to further improve OF-DFT method currently available in the literature.
1.
“Orbital-Free Kinetic-Energy Density Functional Theory,” Y. A. Wang and E. A. Carter, in Theoretical Methods in
Condensed Phase Chemistry, edited by S. D. Schwartz (Kluwer, Dordrecht, 2000), p. 117-184.
2.
“Orbital-Corrected Orbital-Free Density Functional Theory,” B. Zhou and Y. A. Wang, J. Chem. Phys. 124, 081107
(2006). (Communication)
3.
“An Accurate Total Energy Density Functional,” B. Zhou and Y. A. Wang, Int. J. Quantum Chem. 107, 2995-3000
(2007).
4.
“Total Energy Evaluation in the Strutinsky Shell Correction Method,” B. Zhou and Y. A. Wang, J. Chem. Phys. 127,
064101 (2007).
5.
“Accelerating the Convergence of the Total Energy Evaluation in Density Functional Theory Calculations,” B.
Zhou and Y. A. Wang, J. Chem. Phys. 128, 084101 (2008).
6.
“Perturbative Total Energy Evaluation in SCF Iterations: Tests on Molecular Systems,” Y. A. Zhang and Y. A.
Wang, Int. J. Quantum Chem. (submitted).
PL-026
Direct Estimate of Conjugation, Hyperconjugation and Aromaticity with the EDA Method
Gernot Frenking
Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, D-35043 Marburg, Germany.
Email: [email protected]
The concept of π electron delocalization via double bonds which are separated by one single bond is an important
bonding model in chemistry. Conjugative interactions play a major role in explaining geometries and reactivities of
unsaturated molecules particularly in organic chemistry. While the latter effects are observable quantities, π conjugation
itself is a virtual quantity which cannot be measured directly.
A special class of
π conjugated species are aromatic
compounds which exhibit a particular stability if the number of π electrons in the cyclic system follows the 4n+2 rule.
Even saturated compounds may become stabilized by the interaction of π orbitals which is termed hyperconjugation.
Numerous desriptors have been sugegsted in the past for estimating the strength of conjugation, hyperconjugation and
aromaticity. In the context of analyzing the nature of the chemical bond using an energy decomposition analysis (EDA)1
we found that the strength of the intrinsic π orbital interactions correlates very well with experimental quantities which
have been suggested as indicators for π conjugation, such as Hammet constants and 13C NMR chemical shifts. The EDA
calues for ΔEπ
are very useful for directly estimating the strength of conjugation, hyperconjugation and aromaticity
without using external reference values.2
1. (a) A. Krapp, F. M. Bickelhaupt, G. Frenking, Chem. Eur. J., ASAP. (b) M. Lein and G. Frenking, Theory and
Applications of Computational Chemistry: The First 40 Years, p. 291, C.E. Dykstra, G. Frenking, K.S. Kim, G.E.
Scuseria (Eds), Elsevier, Amsterdam, 2005. (b) Krapp, A.; Bickelhaupt, F. M.; Frenking, G. Chem. Eur. J. 2006 12,
9196. (c) A. Kovács, C. Esterhuysen, G. Frenking, Chem. Eur. J. 2005, 11, 1813. (d) Frenking, G.; Wichmann, K.;
Fröhlich, N.; Loschen, C.; Lein, M.; Frunzke, J.; Rayón, V.M. Coord. Chem. Rev. 2003, 238-239, 55.
41 Book of Programme and Abstract for TACC2008 2. (a) D. Cappel, S. Tüllmann, A. Krapp, G. Frenking, Angew. Chem. 2005,117, 3683; Angew. Chem. Int. Ed. Engl. 2005,
44, 3617. (b) . I. Fernández and G. Frenking, J. Org. Chem., 2006, 71, 2251. (c) I. Fernández and G. Frenking,
Chem.
Eur. J. 2006, 12, 3617. (d) I. Fernández and G. Frenking, Chem. Commun. 2006, 5030. (e) I. Fernández and G. Frenking,
Faraday Disc. 2007, 135, 403. I. Fernández and G. Frenking, Chem. Eur. J.
2007, 13, 5873.
PL-027
Narrowing the gap in understanding protein structure and function through
computer simulations
Hong Guo
Dept. of Biochem. Cell. & Mol. Biol., University of Tennessee, Knoxville, TN, USA
The results of quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy
simulations on different enzymes are discussed. It is demonstrated how computer simulations may lead to new insights
into biological structure and function. One type of enzymes to be discussed is protein lysine methyltransferases (PKMTs).
PKMTs play an important role in writing epigenetic code of histone lysine methylation which can lead to distinct
downstream events in the regulation of chromatin structure and gene expression. The biological consequences of the
lysine methylation may differ depending on whether the lysine residue is mono-, dior tri-methylated. Therefore, the
ability of different protein lysine methyltransferases (PKMTs) to generate different methylation states for lysine (i.e.,
product specificity) adds more complexity to the histone code and provides an additional layer of regulatory control. We
demonstrate that it may be possible to apply QM/MM free energy simulations to generate a triplet code for interpretation
and prediction of how epigenetic marks of histone lysine methylation are written by HKMTs. The second type of
enzymes to be discussed is serine-carboxyl peptidases (sedolisins) which was recently characterized but is poorly
understood. It is suggested from the simulations on kumamolisin-As (a member of this family) that unlike classical serine
peptidases the members of this sedolisin family may stabilize the tetrahedral intermediates primarily through a general
acid-base mechanism. Another interesting discovery from the simulations is the existence of dynamic substrate-assisted
catalysis (DSAC) which may have a general implication for catalysis and specificity.
[1] Guo, H-B. and Guo, H. Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 8797-8802.
[2] Xu, Q., Guo, H-B., Wlodawer, A., and Guo, H. J. Am. Chem. Soc., 2006, 128, 5994-5995.
[3] Guo, H-B., Wlodawer, A., and Guo, H. J. Am. Chem. Soc., 2005, 127, 15662-15663.
[4] Guo, H-B., Rao, N., Xu, Q., and Guo, H. J. Am. Chem. Soc., 2005, 127, 3191-3197.
[5] Xu, Q., Guo, H-B., Wlodawer, A., Nakayama, T., and Guo, H. Biochem., 2007, 46,3784-3792.
PL-028
Nanoscale solvation in electric field
Alenka Luzar,
Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, [email protected]
As accessible experimental length scales become shorter, the modification of interfacial properties of water using electric
field must come to grips with novel effects existing at the nanoscale. I will survey some of our recent progress we have
made in understanding these effects using molecular simulations. The results are potentially relevant to surface
manipulation in nanofluidics, as well as for basic understanding of field charge effects that modulate local hydrophilicity
of engineered and biophysical surfaces (supported by US National Science Foundation).
PL-029
42 Book of Programme and Abstract for TACC2008 Free Energy Surfaces and Dynamics of Chemical Reactions
in Solution and Biological Systems
Shigeki Kato
Department of Chemistry, Graduate School of Science,
Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
Chemical reaction under solvent or protein environment is an important issue of theoretical chemistry. Although
reactions in gas phase are described in terms of the potential energy surfaces, free energy surfaces obtained after
thermally averaging solvent or protein degrees of freedom are conveniently utilized for ondensed phase reactions. For
reactions involving the surface crossing between different electronic states such as electron transfer and photochemical
reactions, the nonequilibrium solvation effect coming from thermal fluctuation of solvent orientation plays critical role.
In order to describe such effect, we chose the electrostatic potentials acting on the solute atomic sites as the solvation
coordinates and defined the linear response free energy surfaces (LRFEs) as the function of solute nuclear coordinates
and salvation ones.
We calculated the free energy surfaces for proton coupled electron transfer reaction of ubiquinol complex and
photochemical process of adenine in solution employing RISMSCF method and discussed the importance of
nonequilibrium solvation effect in describing these processes. We also devised a method to calculate the reaction paths
on the free energy surface with QM/MM method and applied to locate the transition state for enzymatic reactions as well
as reactions in solution.
1. T. Yamamoto and S. Kato, J. Chem. Phys., 126, 224514 (2007).
2. S. Yamazaki and S. Kato, J. Amer. Chem. Soc., 129, 2901 (2007).
3. M. Higashi, S. Hayashi and S. Kato, J. Chem. Phys., 126, 144503 (2007), Chem. Phys. Lett., 437, 293 (2007).
PL-030
Multiconfigurational Quantum Chemistry - the state of the art
Björn Roos
Department of Theoretical Chemistry, Chemical Center, P.O.B. 124, S-221 00 Lund, Sweden
E-mail: [email protected]
The lecture will discuss the multiconfigurational approach in quantum chemistry, in particular the CASSCF and CASPT2
methods. Recent developments in the technology today allows larger molecules to be studied. A Cholesky decomposition
of the two-electron integral matrix has drastically reduced the computer resources (in time and disk space) that are
needed to perform CASSCF/CASPT2 calculations, thus allowing much larger basis sets to be used. The new technology
will be illustrated in calculations on transition metal complexes and other heavy element compounds.
PL-031
Non-Additive Electrostatic Force Fields for Biomolecules:
Development and Application of Charge Equilibration Models
Sandeep Patel
University of Delaware, Department of Chemistry and Biochemistry
Newark, Delaware 19716, USA
43 Book of Programme and Abstract for TACC2008 Integral membrane proteins such as ion channels are now the subjects of intense theoretical and experimental study due
to the prevalence of these molecules in normal human function. From a modeling perspective, molecular dynamics
simulations have provided atomic-level information related to the structure-function in such systems. For accurate
modeling of these systems, well-tuned, physics-based interaction models, or force fields, for proteins and lipid
membranes are needed. The next generation of classical force fields strives to incorporate electrostatic polarization, and
among the several approaches being pursued, the charge equilibration methods show promise as a viable, efficient
approach for accounting for electrostatic non-additive effects. In this work, we present a revised CHARMM force field
for lipids based on the charge equilibration model for incorporating polarization effects into molecular dynamics
simulations. The model addresses deficiencies in the dihedral, electrostatic, and Lennard-Jones (van der Waals)
parameters. The revised force field has been applied to molecular dynamics simulations of
higher alkanes ranging from hexane to pentadecane. Finally, we will discuss extension of the alkane force field for
application to lipid bilayer simulations.
Application of the revised polarizable force field to DMPC bilayers demonstrates sound performance with respect to
predicted surface area per headgroup and local chain dynamics as represented by deuterium order parameters. We will
discuss DMPC membrane properties using existing nonpolarizable models contrasted with the newly developed
polarizable force field.
PL-032
Woo Youn Kim and Kwang S. Kim*
Center for Superfunctional Materials, Dept. of Chemistry, Pohang University of Science and Technology, San 31,
Hyojadong, Namgu, Pohang 790-784, Korea
*E-mail: [email protected]
Based on first principles theory, we have investigated metallic nanowires. We discuss the thinning process of silver
nanowires (NW) [1] and the design of linear single atomic chains which is stabilized by the charge-transfer-driven
alloying process [2]. The pathway of thinning process for transient silver NWs is discussed. The unambiguous
identification of the structure of a NW is made with the study of conductance (G) vis-a-vis transient NW structure. The
puzzling experimental observation of fractionally quantized G values is explained.
We also discuss the negative differential resistance (NDR) of molecular electronic devices with carbon nanotube (CNT)
electrodes [3-5]. We find that in the presence of an applied field, metallic CNTs can form asymmetric couplings even if
symmetric structures are employed.
We also discuss a novel spin-valve device based on carbon-based systems [6]. In particular, we predict that graphen
nanpribbon devices can be used as key components of a magnetoresistive random access memory [7]. The magnetic
resistance of the proposed spin-valve device shows millions %, as compared to the present highest value (a few
hundreds %). The origin of the extraordinary behavior is explained. The device is able to play a role as a spin filter which
selectively transmits near 100% spin-polarized current. The domain wall formation energies for both collinear and
non-collinear types of spin waves were investigated. The non-collinear spin states were fully taken into account in a
self-consistent manner with the non-equilibrium Green’s function approach by using the Postrans program package [4].
The study of the cases for the non-collinear type domain wall is the first fully self-consistent ab initio results for
transmission calculations.
44 Book of Programme and Abstract for TACC2008 [1] D. Cheng, et al., Phys. Rev. Lett. 96, 096104 (2006).
[2] Y. C. Choi, et al., Phys. Rev. Lett. 98, 076101 (2007).
[3] W. Y. Kim, S. K. Kwon, and K. S. Kim, Phys. Rev. B 76, 033425 (2007).
[4] W. Y. Kim and K. S. Kim, J. Comput. Chem. 29, 1073 (2008).
[5] W. Y. Kim, Y. C. Choi, and K. S. Kim, J. Materials Chem. (in press).
[6] M. Diefenbach and K. S. Kim, Angew. Chem. Int. Ed. 46, 7640 (2007).
[7] W. Y. Kim and K. S. Kim, Nature Nanotech. (in press).
PL-033
Direct Dynamics Simulations of Post-Transition State Dynamics
William L. Hase
Department of Chemistry and Biochemistry, Texas Tech University
Lubbock, Texas 79409-1061, United States of America
Many chemical reactions have a potential energy surface (PES) with a rate-controlling transition state (TS), whose
properties, when inserted into transition state theory (TST), give an accurate reaction rate constant.1 Attributes of the
chemical reaction, such as branching between different product channels and reaction pathways2-4 and partitioning of the
available energy to reaction products,5-7 are determined by features of the PES after crossing the rate-controlling TS, and
not TST.
To contemplate the possible complexity of these post-transition state dynamics,8 consider standing at a high
energy rate-controlling transition state and gazing towards the reaction products and observing a ‘rough’
multi-dimensional landscape, with multiple potential energy minima, reaction pathways, low energy barriers, etc.
connecting the transition state to multiple product channels.
Given the range of possible dynamics resulting from the
variety of these PES features, there is considerable interest in determining the actual post-transition state dynamics for
chemical reactions. In this presentation, recent direct dynamics simulations of the post-transition state dynamics for the
F- + CH3OOH9 and Cl- + CH3I10 reactions will be discussed.
1. J. I. Steinfeld, J. S. Francisco, and W. L. Hase, Chemical Kinetics and Dynamics, 2nd ed. (Princeton Hall, Upper Saddle
River, NJ, 1998).
2. W. L. Hase, Acc. Chem. Res. 1998, 31, 659.
3. D. J. Mann and W. L. Hase, J. Am. Chem. Soc. 2002, 124, 3208.
4. L. Sun, K. Song, and W. L. Hase, Science 2002, 296, 875.
5. W. L. Hase and K. C. Bhalla, J. Chem. Phys. 1981 75, 2807.
6. W. L. Hase, D. G. Buckowski, and K. N. Swamy, J. Chem. Phys. 1983, 87, 2754.
7. G. H. Peslherbe and W. L. Hase, J. Chem. Phys. 1996, 104, 7882.
8. G. Vayner, S. V. Addepalli, K. Song, and W. L. Hase, J. Chem. Phys. 2006, 125, 014317.
9. J. G. López, G. Vayner, U. Lourderaj, S. V. Addepalli, S. Kato, W. A. deJong, T. L. Windus, and W. L. Hase, J. Am.
Chem. Soc. 2007, 111, 10292.
10. J. Mikosch, S. Trippel, C. Eichhorn, R. Otto, U. Lourderaj, J. X. Zhang, W. L. Hase, M. Weidemüller, and R. Wester,
Science 2008, 319, 183.
PL-034
45 Book of Programme and Abstract for TACC2008 New Techniques of Self-Consistent Field Theory
S. Coriania,b, T. Helgakerb, S. Høstc, T. Kjærgaardc, B. Jansikc, P. Jørgensenc,
J. Olsenc, S. Reineb, P. Salekd and E. Tellgrenb
a
Department of Chemistry, University of Trieste, Italy;
b
c
Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Norway;
The Lundbeck Foundation Center for Theoretical Chemistry, Department of Chemistry, University of Aarhus, Denmark;
d
Dept. Theor. Chem., Royal Institute of Technology, Stockholm, Sweden
Recent developments in Hartree–Fock and Kohn–Sham self-consistent field theories are reviewed, with emphasis on
techniques for large systems. Using an exponential parameterization of the density matrix [1], it is shown how the energy
may be efficiently minimized using a diagonalization-free quasi-Newton method that combines the separate
diagonalization and DIIS steps of standard SCF optimizations into a single concerted step that makes full use of the
second-order information generated during the minimization [1,2]. It is also shown how a density-matrix starting guess
containing all the essentials features of molecular bonding may be generated, significantly reducing optimization cost.
The calculation of the exchange contribution to Fock and Kohn–Sham matrices is briefly discussed [3]. Developments in
the calculation of molecular properties are considered [4,5].
[1] Linear-scaling implementation of molecular electronic self-consistent field theory, P. Salek et al., J. Chem. Phys. 126,
114110 (2007)
[2] A ground-state direct optimization scheme for the Kohn–Sham energy, S. Høst et al., Phys. Chem. Chem. Phys. 2008,
10.1039/b807639a.
[3] Variational and robust density fitting of four-center two-electron integrals in local metrics, S. Reine et al., J. Chem.
Phys. in press
[4] Linear-scaling implementation of molecular response theory in SCF electronic-structure theory, S. Coriani et al., J.
Chem. Phys.. 126, 154108 (2007)
[5] HF and KS response theory in a second-quantization AO formalism suitable for linear scaling, T.Kjærgaard et al., J.
Chem. Phys. in press
PL-035
Molecular Recognition Realized by the Statistical Mechanics Theory of Liquids
Fumio Hirata
Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
Few years ago, we have succeeded to “probe” water molecules bound in a cavity of a protein by means of the
statistical mechanics of molecular liquids, or the RISM/3D-RISM theory. [1,2] This is the first finding in the history of
the statistical mechanics to show that the theory is applicable to such fluids in an extremely inhomogeneous field in
atomic scale. On the other hand, the finding implies that we got a powerful machinery in our hand to clarify the
“molecular recognition” which is the most fundamental process in living cells. It will become a “bridgehead” in our
theoretical challenge on life phenomena.
In the succeeding applications of the method, we have focused on a variety of molecular processes in bio-systems, in
which the molecular recognition plays an essential role: the selective ion-binding by protein, an enzymatic reaction,
water channels (aquaporin), the preferential binding of inert gas by protein, and the pressure denaturation of protein.
[3-7]
46 Book of Programme and Abstract for TACC2008 In the talk, I will present our recent studies on the topics stated above, focusing especially on the possibility of ion
permeation through aquaporins.
References
[1] T. Imai, et. al., J. Am. Chem. Soc. ), 127 (44), 15334 (2005).
[2] F. Hirata, ed., Molecular Theory of Solvation, Springer-Kluwer, 2003.
[3] N. Yoshida,et.al., J. Am. Chem. Soc. , 128 (37), 12042 (2006) .
[4] T. Ima, et. al., J. Phys. Chem. B, 111, 11585 (2007).
[5] S.
Phonphanphanee, et. al., J. Am. Chem. Soc. [6] , 130, 1540 (2008).
[6] T. Imai, et. al., Protein Science. 16, 1927 (2007)
[7] Y. Ikuta, et. al., submitted to Chem. Phys. Lett.
PL-036
Towards Linear-Scaling Hybrid DFT
Takahito Nakajima, Takao Tsuneda, and Kimihiko Hirao
Department of Applied Chemistry, School of Engineering,
University of Tokyo, Japan 113-8656
DFT is one of the most widely used methods in computational chemistry due to the extremely favorable balance of
efficiency versus accuracy in estimating electron correlation.
Recently, there has been considerable interest toward the
new hybrid functionals based on the long-range correction (LC) scheme [1-3]. In the LC scheme, the exchange functional
is partitioned with respect to the interelectronic separation into long-range and short-range parts using a standard error
function. Only the short-range part is retained, while the long-range part is replaced with an exact orbital expression
using Hartree-Fock (HF) exchange integrals. The LC approach was shown to clearly solve many of the problems which
conventional DFT confronted.
We have developed and implemented a new Coulomb
Coulomb (GFC) method [4-5].
method for DFT, called the Gaussian and finite element
The electrostatic potential V(r) is expanded in an auxiliary basis of Gaussians and
finite-element functions and V(r) is found by solution of the Poisson equation. The linear scaling is achieved using
conjugate-gradient and fast multipole methods. The GFC method is highly effective for both 1D and compact 3D
molecules.
[1] H. Iikura, T. Tsuneda, T. Yanai, and K. Hirao, J. Chem. Phys. 2001, 115, 3540.
[2] Y. Tawada, T. Tsuneda, S. Yanagisawa, T. Yanai, and K. Hirao, J. Chem. Phys. 2004, 120, 8425.
[3] J.-W. Song, T. Hirosawa, T. Tsuneda, and K. Hirao, J. Chem. Phys. 2007, 126, 154105.
[4] Y.Kurashige, T. Nakajima and K.Hirao, J.Chem.Phys., 2007, 126, 144106.
[5] M.Watson, Y.Kurashige, T. Nakajima and K.Hirao, J.Chem.Phys.,2008, 128, 054105.
PL-037
Renormalized Coupled-Cluster Methods:
Theoretical Foundations and Extension to Open-Shell and Large Systems
Piotr Piecuch,a,b Wei Li,a Jeffrey R. Gour,a and Marta Włoch,a,c
a
Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
b
Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
c
Department of Chemistry, Michigan Technological University, Houghton, Michigan, USA
47 Book of Programme and Abstract for TACC2008 The renormalized coupled-cluster methods [1-3], such as CR-CCSD(T), CR-CCSD(TQ), and the recent size extensive
formulation of CR-CCSD(T), termed CR-CC(2,3), which are all derived from the asymmetric energy expressions that
define the method of moments of coupled-cluster equations [1,2(a,b),3(b)] and which are available in the GAMESS
package, represent a new generation of single-reference approaches that eliminate the failures of conventional
coupled-cluster approximations, such as CCSD(T), whenever non-dynamical correlation effects become more significant.
We will show that the relatively inexpensive renormalized coupled-cluster methods provide an accurate and balanced
description of reaction pathways involving bond breaking, radicals, and biradicals, singlet-triplet gaps in biradical and
magnetic systems, and excited states dominated by one- and two-electron transitions, enabling one to address interesting
mechanistic problems in organic and bioinorganic chemistries, and photochemistry, where other methods that one can
afford encounter difficulties. We will describe the extension of the CR-CC(2,3) approach to open-shell systems [3] and
the most recent development of the CR-CC(2,3) and other coupled-cluster methods for large molecular systems with
hundreds of atoms [4] through the use of the linear scaling parallel and vectorized algorithms employing the local
correlation ansatz termed ‘cluster-in-molecule’ [5].
[1] (a) Kowalski, K.; Piecuch, P. J. Chem. Phys. 2000, 113, 18. (b) Piecuch, P.; Kowalski, K.; Pimienta, I. S. O.;
McGuire, M. J. Int. Rev. Phys. Chem. 2002, 21, 527. (c) Piecuch, P.; Kowalski, K.; Pimienta, I. S. O.; Fan, P.-D. et al.
Theor. Chem. Acc. 2004, 112, 349.
[2] (a) Piecuch, P.; Włoch, M. J. Chem. Phys. 2005, 123, 224105. (b) Piecuch, P.; Włoch, M.; Gour, J. R.; Kinal, A.
Chem. Phys. Lett. 2006, 418, 467. (c) Włoch, M.; Lodriguito, M.; Piecuch, P.; Gour, J. R. Mol. Phys. 2006, 104, 2149.
[3] (a) Włoch, M.; Gour, J. R.; Piecuch, P. J. Phys. Chem. A 2007, 111, 11359. (b) Piecuch, P.; Gour, J. R.; Włoch, M.
Int. J. Quantum Chem. 2008, 108, 2128.
[4] (a) Li, W.; Piecuch, P.; Gour, J. R.; Li, S., in preparation. (b) Li, W.; Piecuch, P.; Gour, J. R., in preparation.
[5] (a) Li, S.; Ma, J.; Jiang, Y. J. Comp. Chem. 2002, 23, 237. (b) Li, S.; Shen, J.; Li, W.; Jiang, Y. J. Chem. Phys. 2006,
125, 074109.
PL-038
Efficient ab initio Monte Carlo simulations of molecules in solution
Peter Pulay and Michel Dupuis
Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences,
University of Arkansas, Fayetteville, Arkansas, USA
and
Chemical and Material Science Division, Pacific Northwest National Laboratory,
Richland, Washington 99354
An efficient method is introduced for the Monte Carlo simulation of molecules in solution. The response of the dissolved
system to the long-range electrostatic field of the solvent molecules is evaluated using precalculated multipole moments
and polarizabilities, and possibly hyperpolarizabilities of the solute. This obviates the need to perform a new high-level
(ab initio or DFT) calculation for every solvent configuration. Reliable statistics, which usually requires averaging over
millions of solvent configurations, can be collected using only a limited number of high-level calculations. Other (van der
Waals) interactions have short range, and change only if the solvent molecules in the first solvation shell are moved. This
method can be applied to any quantum chemical technique, and is most important for the description of reactions in
solution where simpler methods, like force field techniques, are inadequate. Application to simple prototype reactions in
solution will be presented.
PL-039
48 Book of Programme and Abstract for TACC2008 QM ⁄ QM Electronic Embedding Models for Materials Chemistry
Krishnan Raghavachari, Hrant P. Hratchian and Priya V. Parandekar
Indiana University, Bloomington – USA
The development of accurate and broadly applicable models for large molecules/materials continues to be a significant
challenge in quantum chemistry. Hybrid models, such as the popular ONIOM‐based QM ⁄ QM schemes (where the
central region and the surrounding region are partitioned and treated with two different levels of theory), offer a
promising avenue for modeling large systems. However, most QM ⁄ QM applications typically use only a mechanical
embedding scheme where the wavefunction in the central region is unaffected by the electronic structure of the
surrounding region. We are presently developing a sequence of electronic embedding schemes for more realistic
simulations. The resulting hierarchy, where the treatment ranges from simple point charge embedding to interaction
integrals in the Hamiltonian matrix, will be discussed. We will also describe our current development status and present
results from initial applications to materials studies.
PL-040
Anomalous Dynamics of Water in Bulk Liquid and in Hydration Layer of Proteins and DNA
Biman Bagchi
SSCU, Indian Institute of Science, Bangalore 560012, India.
Water exhibits remarkable anomalies in its thermodynamic properties, with an apparent divergence of response functions
(specific heat at constant pressure (CP), isothermal compressibility (κT) and thermal expansion coefficient (αP)) at low
temperature below its freezing temperature. Here we show that temporally and spatially correlated large amplitude
collective fluctuation in the number of the four (N4C) and five-coordinated ( N5C) water molecules
microscopic explanation of the anomalies.
can provide a
Near the anomalous region, we find an intriguing emergence of
intermittency and accompanied 1/f noise in the fluctuation of N4C and N5C. In addition, these fluctuations are found to
exhibit dynamic heterogeneity accompanied by a growing correlation length. While investigating the dynamics of water
in the hydration layer of a DNA, we find signatures of a dynamical transition in both translational and orientational
dynamics of water molecules in both the major and the minor grooves of a DNA duplex at T = 255 K which is slightly
higher than the temperature (T = 247 K) where the bulk water is conjectured to undergo a dynamical transition [1]. We
find that Adams-Gibbs relation between configurational entropy and translational diffusion holds quite well when the two
quantities are plotted together in a master plot for different region of aqueous DNA duplex (bulk, major and minor
grooves) at different temperatures [1,2]. Water molecules in the hydration layer of a lysozyme are found to exhibit three
distinct (as compared to Lagge-Hynes H-bond breaking in bulk water) H-bond breaking mechanisms [3]. The calculated
time dependent angular van Hove self-correlation function (G(　,t)) which has a pronounced two-peak structure in the
hydration layer can be traced to the constrained translational motion in the layer. The longevity of the surrounding
hydrogen bond network is found to be significantly enhanced near a hydrophilic residue [3].
[1] D. Biswal, B. Jana, S. Pal and B. Bagchi, Dynamical transition of water in the grooves of DNA duplex at low
temperature, (Submitted to J. Phys. Chem. B).
[2] B. Jana, S. Pal and B. Bagchi, Entropy of water in the hydration layer of major and minor grooves of DNA, J. Phys.
Chem. B. 2006, 110, 19611 -19618.
[3] B. Jana, S. Pal and B. Bagchi, Hydrogen bond breaking mechanism and water reorientational dynamics in the
hydration layer of lysozyme, J. Phys. Chem. B. 2008, 112, 9112-9117.
49 Book of Programme and Abstract for TACC2008 PL-041
Chemical Reactions in Room-Temperature Ionic Liquids
Hyung J. Kim*
Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
and
School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea
In this lecture, we present results of our recent molecular dynamics (MD) simulations and theoretical model study of
charge shift and transfer processes in imidazolium-based room-temperature ionic liquids (RTILs). The examples include
unimolecular ionization of haloalkanes, bimolecular ion associations and electron transfer reactions. We discuss reaction
free energetics and dynamics of these systems and their solvation structure in RTILs with special attention paid to the
aspects shared by and the contrasts with normal polar solvents. To be specific, we make a detailed analysis of barrier
crossing dynamics of electron transfer
in RTILs and normal solvents and their influence on reaction kinetics via MD. We compare the MD results with the
predictions of the Kramers theory and Grote-Hynes theory and discuss the implications of our findings for other reactions
in RTILs. In the case of SN1, the unimolecular ionization pathway and its variations with solvents are studied.
*Permanent address: Carnegie Mellon University. Email: [email protected]
PL-042
Water Dynamics; Fluctuations, Phase-Transitions and Reactions
Iwao Ohmine
Chemistry Department, Nagoya University, Furou-cho, Chikusa-ku, Nagoya, Japan 464-8602
Water is the most ambient substance on earth and has many anomalous properties arising from the nature of its hydrogen
bond structure and rearrangement. One of t distinct characters of water is that the system exhibits large intermittent
fluctuations, which affects reactions in aqueous environments.
Developing various theoretical methods, We have
investigated the following four aspects of water dynamics; (1) Intermittent collective motions in water (2) Experimental
methods to detect intermediate-range order structural changes in liquid, (3) Phase Transition of water (freezing and
melting processes of water and ice), and (4) Chemical reaction and bimolecular reaction dynamics in water.
Hydrogen-bond-network rearrangement (HBNR) dynamics in water; Landscape of liquid water potential energy
surface was intensively analyzed with developing various theoretical methods.
Experimental Observation of HBNR dynamics; A new theory of multi-dimensional spectroscopy has been developed
to deal with phase-space dynamics of a system and extract the important motions causing large rearrangement in complex
dynamics.
This highly nonlinear laser photolysis, called off-resonant fifth-order two-dimensional (2D-) Raman
spectroscopy, has the two-dimensional time axes and detects nonlinear couplings among intermolecular motions.
2D-Raman spectroscopy is found to be susceptible to the nonlinear anharmonic dynamics and intermediate-range
structural order.
Mechanisms of water freezing; The first successful simulation for pure water freezing process revealed that intermittent
collective fluctuation associated with HBN rearrangement plays an important role in the initial nucleus formation. New
graphical analysis, defining basic three-dimensional units of the network (called fragments), is introduced in order to
characterize HBN structure in water freezing process.
A detailed mechanism of ice melting will be discussed.
Biomolecular reactions involving water molecules; The study of water was extended to deal with its role in functions
of biological systems such as ion-channel, Photoactive Yellow Protein (PYP) and Bacteriorhodopsin.
Mechanism of proton transfer in water and ice, and the pH curve of water at various temperatures will be also
50 Book of Programme and Abstract for TACC2008 discussed.
PL-043
Simulation Studies of Heterogeneous Atmospheric Chemical Processes
Douglas J. Tobias
Department of Chemistry, University of California, Irvine, California, 92697-2025 USA
Aerosols formed from microscopic droplets of water are the sites of chemical reactions that influence the composition of
the atmosphere and Earth's radiative balance.
The gas-liquid interface at the surface of aqueous aerosol particles is a
unique environment for chemistry that does not take place in bulk solution. A full understanding of the kinetics and
mechanisms of aerosol chemistry, and the optical properties and hygroscopicity of aerosol particles, requires a molecular
picture of structure and dynamics at the air/solution interface that is difficult to obtain experimentally.
In this talk I will
survey our molecular dynamics simulations, based both on empirical force fields and forces computed from electronic
structure via density functional theory, aimed at characterizing the composition and reactivity of aqueous aerosols
containing inorganic ions and organic surfactants, and their interactions with atmospheric trace gases (e.g., pollutants).
I will also present results from experiments carried out by our collaborators that validate our simulations, and show how
a combined theoretical/experimental approach can lead to new insight that has implications for air quality on a regional
scale.
PL-044
Recent progress in theory of intermolecular forces
Krzysztof Szalewicz1
1
Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
Intermolecular forces determine properties of condensed phases and of biological systems. These properties can be
predicted provided the intermolecular interaction potentials are known. So far, such potentials were mostly obtained by
fitting experimental data. With recent progress in electronic structure methods, potentials computed from first principles
are surpassing the empirical ones in terms of quality of predictions. Examples of water [1] and of benzene [2] will be
discussed to illustrate this point. It is also now possible to now obtain pair potentials for fairly large systems, including
monomers containing 20 or more atoms, due to the development of symmetry-adapted perturbation theory (SAPT) based
on density-functional theory (DFT) description of monomers [SAPT(DFT)] [3.5]. This method gives results comparable
to those of the coupled-cluster approach with single, double, and noniterative triple excitations at a much lower
computational cost. Interaction energies for systems as large as the dimer of perylene, containing 64 atoms, have been
computed using SAPT(DFT). These developments will enable important investigations of interactions of biomolecules.
[1] Bukowski, R.; Szalewicz, K.; Groenenboom, G. C.; van der Avoird, A. Science 2007, 315, 1249.1252.
[2] Podeszwa, R.; Bukowski, R.; Szalewicz, K. J. Phys. Chem. A 2006, 110, 10345.10354.
[3] Misquitta, A. J.; Jeziorski, B.; Szalewicz, K. Phys. Rev. Lett. 2003, 91, 033201.
[4] Misquitta, A. J.; Podeszwa, R.; Jeziorski, B.; Szalewicz, K. J. Chem. Phys. 2005, 123, 214103.
[5] Podeszwa, R.; Bukowski, R.; Szalewicz, K. J. Chem. Theory Comput. 2006, 2, 400.412.
PL-045
Importance and Application of “Computational Resources for Drug Discovery” Plateform
G. P. S. Raghava and CRDD Team, Bioinformatics Centre, Institute of
51 Book of Programme and Abstract for TACC2008 Microbial Technology, Chandigarh
An escalating magnitude of drug resistance among pathogens has been installing a worrisome exploration in the present
remedial scenario for neglected diseases. It was a heart dying situation that after investing $800 million and 15 years of
atrocious labor to introduce drug in the market, the companies came to know that pathogens had already attained
resistance against it, a setback that actually made companies to focus on “blockbuster” drugs. Though many steps have
been undertaken till date to fight this deadly threat, nevertheless hop of academia with its research capabilities has
provided a ray of hope to combat global crises. The superlative model to demonstrate the involvement of academia in this
realm is introduction of an open source portal, namely, “Computational Resources in Drug Discovery” (CRDD) being
initiated with a notion to reduce the costly affairs coupled with drug discovery process. CRDD provides a global platform
where the best brains can collaborate and collectively endeavor to solve the complex problems associated with
identification of potential targets to lead discovery for neglected diseases like Malaria, Tuberculosis, Leshmaniasis, etc.
just under one roof. The use of bioinformatics has allowed the identification of some hidden potential targets; hence,
CRDD has implemented the computational resources for experimentalists/researchers working in the field of
computer-aided drug design to discover drugs against them. Moreover, CRDD offers web backed servers for most of the
chemoinformatics and bioinformatics based java libraries which otherwise a complicated task for the biologist to
implement. In addition, the idea of virtual job system through CRDD would help in the utilization of best talent minds
globally. Nonetheless, CRDD is on its way to insert more features still the best is yet to come……..
Web Site: http://crdd.osdd.net/ & http://www.imtech.res.in/raghava/
PL-046
O, Proton(s), Where Art Thou?
Qiang Cui,
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University
Avenue, Madison, WI 53706
In this talk, I’ll discuss several topics inspired by our long-term goal of understanding proton pumping in biomolecular
systems using theoretical techniques. As stringent tests for the theoretical methods and computational protein model for
complex biomolecular systems, pKa calculations are carried out using “brutal-force” QM/MM free energy perturbation
methods for titratible amino acids in different protein environments. These include surface-exposed and buried residues
in soluable proteins and buried residues in membrane proteins. The magnitude of errors introduced by the lack of
electronic polarization in the MM force field, limited accuracy in the QM method, approximations in the solvent
boundary condition as well as the impact of sampling are discussed.
The calibrated QM/MM method is then applied to
study the pKa of hydronium in two proton pumps, bacteriorhodopsin and cytochrome c oxidase; the results are discussed
in the context of pumping mechanisms of these systems. Finally, if time permits, we will discuss how QM/MM
simulations are used to analyze the infrared spectra for the proton release group (PRG) in bacteriorhodopsin, in which the
QM/MM results provide an alternative explanation for the “continuum band” near 2000cm-1 identified experimentally.
PL-047
Simple models for the description of molecular conductors
Matthias Ernzerhof
Department of Chemistry, University of Montreal
C.P. 6128, Succursale A, Montreal, Quebec H3C 3J7, Canada
52 Book of Programme and Abstract for TACC2008 Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on
molecular electronic devices (MEDs). Also meta-stable states, which emit electrons at a characteristic rate, can be
looked upon as a transport problem.
To model these phenomena, we use a non-Hermitian Hamiltonian [1] for the
description of open systems that exchange current density with their environment. In MEDs, for instance, the infinite
contacts are replaced by complex source-sink potentials (SSPs) [2]. Using these SSPs, we derive qualitative,
molecular-orbital-based rules relating molecular structure and conductance [2,3]. Including electron-correlation effects in
our approach [4], we present a simple model for a fundamental process in molecular electronics:
the change in
conductance upon bond breaking. In the limit where the electron repulsion is strong compared to the binding energy (as it
is the case in a stretched bond) interesting phenomena are observed that cannot be accounted for with conventional
(independent electron) approaches.
[1] M. Ernzerhof, M. Zhuang, J. Chem. Phys. 119, 4134 (2003).
[2] F. Goyer, M. Ernzerhof, and M. Zhuang, J. Chem. Phys. 126, 144104 (2007); M. Ernzerhof, J. Chem. Phys. 127,
204709 (2007).
[3] M. Ernzerhof, M. Zhuang, and P. Rocheleau, J. Chem. Phys., 123, 134704 (2005); M. Ernzerhof, H. Bahmann, F.
Goyer, M. Zhuang, and P. Rocheleau, J. Chem. Theory Comput., 2, 1291 (2006).
[4] M. Ernzerhof, J. Chem. Phys. 125, 124104 (2006); A. Goker, F. Goyer, and M. Ernzerhof, submitted.
PL-048
Ultrafast electronic processes at organic semiconductor junctions: a molecular-level, quantum-dynamical
perspective
H. Tamura1, J. G. S. Ramon2, E. R. Bittner2, I. Burghardt1
1
Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, F–75231 Paris cedex 05, France
2
Department of Chemistry and Texas Center for Superconductivity, University of Houston, Houston, Texas 77204, USA
Semiconducting π-conjugated polymers are promising low-cost and flexible materials for electronic devices such as
organic light-emitting diodes (OLEDs) and solar cells. Many of the unique properties of these materials stem from the
combination of the molecular structure of their building blocks and the extended nature of the π-conjugated system. Thus,
excitonic states, i.e., electron-hole quasi-particle states that are delocalized over several or many monomer units, play a
central role for the optoelectronic properties. In the present contribution, we focus on the elementary photophysical
events at polymer heterojunctions, which provide highly efficient exciton dissociation sites at the interface between
different phase-segregated polymers. A molecular-level electronic structure and quantum-dynamical analysis of exciton
decay at a TFB:F8BT heterojunction [1-2] is presented, with a focus on the role of electron-phonon coupling and the
relevance of stacking at the heterojunction interface [2]. Quantum dynamical simulations were carried out using the
multiconfiguration time-dependent Hartree (MCTDH) method [3] in conjunction with a linear vibronic coupling model
parameterized for the three most relevant electronic states and 20-30 vibrational modes [4]. The exciton dissociation and
concomitant generation of a charge-separated interfacial state (“exciplex”) are shown to occur on an ultrafast
(femtosecond to picosecond) time scale. The details of the dynamics sensitively depend on the interplay of
high-frequency C=C stretch modes and low-frequency ring-torsional modes, as evidenced most clearly by a hierarchical
representation of the electron-phonon interaction, using a chain of effective phonon modes [4]. Further, the local
interface structure at the heterojunction and the presence of intermediate (“bridge”) states are found to play a crucial role.
We conjecture that the dynamical robustness of the ultrafast exciton decay indeed results from the presence of such
intermediate states which open multiple decay pathways in a landscape of intersecting surfaces. The coherent, highly
nonequilibrium dynamics is consistent with time-resolved spectroscopic observations [1].
[1] A. C. Morteani, P. Sreearunothai, L. M. Herz, R. H. Friend, C. Silva, Phys. Rev. Lett. 2004, 92, 247402; A. C.
53 Book of Programme and Abstract for TACC2008 Morteani et al.: Organic Light-Emitting Devices, Eds. K.Müllen and U. Scherf (VCH-Wiley, 2006).
[2] J. G. S. Ramon, E. R. Bittner, J. Chem. Phys. 2007, 126, 181101; E. R. Bittner, I. Burghardt, R. H. Friend, Chem.
Phys., 2008, submitted.
[3] M. H. Beck, A. Jäckle, G. A. Worth, H.-D. Meyer, Phys. Rep. 2000, 324, 1.
[4] H. Tamura, E. R. Bittner, I. Burghardt, J. Chem. Phys., 2007, 126, 021103, 2007, 127, 034706; H. Tamura, J. G. S.
Ramon, E. R. Bittner, I. Burghardt, J. Phys. Chem. B 2008, 112, 495, Phys. Rev. Lett. 2008, 100, 107402.
PL-049
Theoretical Studies of Proton Translocation in Membrane Proteins
Régis Pomès
Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, and Department of Biochemistry, University
of Toronto
In membrane proteins, as in water, the long-range transport of protons can be achieved by a Grotthuss mechanism
involving the chemical exchange of hydrogen nuclei along hydrogen bonds forming dynamic networks. In this process of
structural diffusion, small-amplitude fluctuations mediate long-range transport of H+. We use atomistic molecular
simulations to study the balance of fundamental physical properties controlling structural diffusion in narrow,
water-filled biological channels and in channel-like cavities of membrane proteins. In particular, we examine the
molecular basis for the modulation of proton permeation in ion channels and the directional movement of protons in
energy-transducing enzymes.
Abstract ‐ Invited and Oral Presentation 1.
Electronic Structure IN-ES001
New Developments in Computationally Efficient Generalized Van Vleck Perturbation Theory
Mark R. Hoffmann
Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, USA
The second-order Generalized Van Vleck Perturbation Theory (GVVPT2) variant of multi-reference perturbation theory
[J. Chem. Phys. 117, 4133 (2002)] has been modified to incorporate use of the Graphical Unitary Group Approach
(GUGA) to calculate the Hamiltonian matrix elements in the basis of Gelfand-Tsetlin state functions. Using the GUGA
scheme together with the macroconfiguration technique, the modified version of GVVPT2 is significantly more
computationally efficient than previous variants.
Speed-up ratios vary by specifics of the calculation, but are ca.
100-fold for chemically interesting molecules using good quality basis sets. Moreover, the facile computation of one
particle density and transition density matrices in the GUGA formalism can be exploited. The combination of the use of
incomplete model spaces, as facilitated by macroconfigurations, and the GUGA scheme, with internal-external
partitioning of the Hamiltonian matrix elements, allows chemically difficult larger problems to be described with the
GVVPT2 method.
GUGA modifications developed for the second order. GVVPT3 is consistently more accurate than GVVPT2, and
GVVPT3 energies and energy differences are shown to be competitive with established high accuracy methods, such as
MRCISD and CCSDT, at lower computational costs. The combination of computational efficiency and capabilities of
54 Book of Programme and Abstract for TACC2008 describing whole potential energy surfaces of ground and excited electronic states suggests that GVVPT3 be examined as
a potent new tool in computational chemistry.
IN-ES002
Block correlated coupled cluster theory for bond breaking potential energy surfaces
Shuhua Li
School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education,
Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, 210093, P. R. China.
In this talk, I will present the general formulism of block correlated coupled cluster (BCCC) theory with a complete
active-space self-consistent-field (CASSCF) reference function [1,2]. This theory provides an alternative multireference
coupled cluster framework to describe the ground-state potential energy surfaces involving the bond breaking processes.
In this approach, a multireference block is defined to incorporate the nondynamic correlation, and all other blocks
involve just a single spin orbital. The cluster operators are truncated up to the four-block correlation level, leading to the
CAS-BCCC4 scheme. The CAS-BCCC4 method computationally scales as the traditional single-reference CCSD, which
is expected to be applicable for medium-sized molecules. We have applied the present approach to investigate the
potential energy surfaces for single bond breaking processes in F2, HF, and CH4, and for double bond or triple bond
breaking processes in H2O, C2 and N2 [2-4]. A comparison of our results with those from full configuration interaction
calculations shows that the present approach can provide quantitative descriptions for all the studied systems.
[1] S. Li*, J. Chem. Phys. 120, 5017 (2004).
[2] T. Fang, S. Li*, J. Chem. Phys. 127, 204108 (2007).
[3] J. Shen, T. Fang, W. Hua, S. Li* J. Phys. Chem. A 112, 4703 (2008).
[4] T. Fang, J. Shen, S. Li* J. Chem. Phys. 128, 224107 (2008).
IN-ES003
Methodological Advances in State-Specific Multireference Coupled Cluster Theory. Applications to Benzynes,
Antiaromatics, Novel Carbenes, and Benchmark Systems
Wesley D. Allen, Francesco A. Evangelista, Andrew C. Simmonett,
and Henry F. Schaefer III
Center for Computational Chemistry and Department of Chemistry,University of Georgia, Athens, GA 30602, USA
The first production-level code (psimrcc) for state-specific and rigorously size-extensive Mukherjee multireference
coupled cluster singles and doubles (Mk-MRCCSD) computations has been developed. This breakthrough was aided
by our derivation of closed-form expressions for the terms coupling different references in the amplitude equations.
Moreover, a hierarchy of aMk-MRCCSDT-n (n = 1a, 1b, 2, 3) methods for the iterative, approximate inclusion of
connected triple excitations has been formulated and implemented for the first time. The effectiveness of our Mk-MRCC
methods is established by extensive computations on benchmark problems, including the low-lying electronic states of C,
O, NH, OH+, O2, NF, CH2, SiH2, and H2CO, the dissociation of F2, and the ozone graveyard for theory. In chemical
applications of Mk-MRCCSD theory with the cc-pVTZ basis set, outstanding results have been obtained for the optimum
geometric structures, vibrational frequencies, and adiabatic excitation energies of ortho-, meta-, and para-benzyne, as
well the automerization barriers of cyclobutadiene and other antiaromatic systems.
Finally, we report Mk-MRCC
predictions of UV/Vis spectra of novel carbenes that have led to the identification of these species in matrix isolation
experiments.
IN-ES004
55 Book of Programme and Abstract for TACC2008 Theory and applications of perturbative coupled-cluster methods
Mihály Kállay1, Jürgen Gauss2
1
Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest
P.O.Box 91, H-1521 Hungary
2
Institut für Physikalische Chemie, Universit鋞 Mainz, D-55099 Mainz, Germany
We discuss the possibilities for the generalization of the approximate triples
models such as the popular coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] method to quadruple
excitations. The theoryand implementation of approximate coupled-cluster singles, doubles, triples, and quadruples
(CCSDTQ) methods are discussed with special regard togeneral single determinant reference functions. It is
demonstrated that the generalization of perturbative triples approaches is not straightforward. In contrast to the
corresponding triples methods, there are several possibilities to introduce approximations. However, it is difficult to
develop a consistent approach that is applicable to both canonical and non-canonical Hartree–Fock reference
determinants. Several such approximations have been implemented and their performance for total energies and heats of
formation has been assessed. The numerical results show that the performance of the methods does not depend on the
approximations assumed. The applicability of our approaches is illustrated by chemical applications. It is demonstrated
that the proposed approaches enables us to consider the effect of quadruple excitations and thus to achieve kJ/mol
accuracy for molecular systems consisting of up to 10-12 atoms.
IN-ES005
New developments of the Cholesky Decomposition technique in Quantum Chemistry
Lindh, Roland
Lund University, Sweden, [email protected]
The group in Lund has over the last few years implemented the Cholesky Decomposition (CD) technique for
two-electron integrals for virtually all type of wave function models. In this process we have been able to use the close
relationship between density fitting (DF) (or resolution of identity (RI) ) and CD technique to come up with novel
features. Those include analytic CD gradients, the 1-center approximation of the CD approximation, on-the-fly designed
un-biased auxiliary basis sets for DF (or RI), etc. In this lectures I will present these results along with some more recent
developments offered by the CD technique.
IN-ES006
A Linear Scaling Subspace Iteration Algorithm with Optimally Localized Wave Functions
for Kohn-Sham Density-Functional Theory
Carlos J. Garcĺa-Cervera*
Mathematics Department, University of California, Santa Barbara, CA 93106, USA.
Email: [email protected]. URL: http://www.math.ucsb.edu/"cgarcia.
We present a new linear scaling algorithm for Kohn-Sham density functional theory. Our starting point is the
non-orthogonal formulation for the Kohn-Sham functional. The energy is invariant under nonsingular linear
transformation of the space spanned by the wave functions, and as a consequence, the Kohn-Sham functional can be
thought of as a functional acting on subspaces. The goal then is to find the minimizing subspace, that is,
the subspace
generated by the eigenfunctions corresponding to the lower end of the spectrum of the self-consistent Hamiltonian. The
advantage of this viewpoint is that the specific representation of thesubspace is not relevant, and therefore we can choose
a representation that is convenient for our purposes. Linear scaling can be achieved by choosing a representation in terms
56 Book of Programme and Abstract for TACC2008 of optimally localized non-orthogonal wave functions. Non-orthogonal wave functions have better localization properties
than orthogonal orbitals, which constitutes an additional advantage of this approach. This work has been done in
collaboration with Weinan E, Jianfeng Lu, and Yulin Xuan, at Princeton University.
OR-ES007
Elongation cutoff technique: an efficient sparse matrix algebra approach to linear scaling
Jacek Korchowiec
K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060
Krakow, POLAND
Huge progress in computer technology brings about conditions for ab initio computational methods to be of practical
value in chemistry, biochemistry and material science. However, the application of Hartree-Fock (HF), Kohn-Sham (KS),
and post-HF computational methods to huge molecular systems is limited due to undesired scaling behavior. The expense
α
of a given method is usually expressed as N , where
N and α are the number of basis functions applied in the
calculations and scaling exponent, respectively. In this presentation we would like to describe the elongation method [1]
and its scaling behavior. It is demonstrated that the elongation cutoff technique (ECT) [2] substantially speeds up the
quantum-chemical calculation at HF and KS level of theory and is especially well suited for parallel performance. A
comparison of ECT timings for model systems with the reference calculations is given. The analysis includes the overall
CPU (central processing unit) time and its most time consuming steps for ‘direct’ and ‘conventional’ types of
calculations.
IN-ES008
A scheme with combination of methods: Highly efficient quantum calculations of acetylene-vinylidene
isomerization in full-dimensionality
Bin Li, Wensheng Bian*
State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry,
Chinese Academy of Sciences, 100190 Beijing, China
Interest in acetylene–vinylidene isomerization is long-standing. The first experimental evidence for the existence of
vinylidene was found by the Lineberger group in the 1980s [1], in which the lifetime of vinylidene was estimated to be
on the order of subpicoseconds. However, in 1998, a very long vinylidene lifetime of at least 3.5 microseconds was
claimed by Levin et al. [2] in their coulomb explosion imaging experiments. Full-dimensional (~six degrees of freedom)
quantum studies of acetylene–vinylidene have recently been realized by a few groups [3-5] using different methods.
We report our full-dimensional quantum-mechanical calculations on the isomerization of acetylene to vinylidene on an
ab initio potential energy surface. Our theoretical scheme is a combination of several methods. To exploit the full parity
and permutation symmetry, the CC-HH diatom-diatom Jacobi coordinates are chosen for vinylidene configuration; phase
space optimization in combination with physical considerations [7] is used to obtain an efficient radial discrete variable
representation, whereas a basis contraction scheme is applied for angular coordinates; The preconditioned inexact
spectral transform method combined with an efficient preconditioner is employed to compute eigenstates within a desired
spectral window. Complex absorbing potentials are used to deal with the isomerization behaviour of vinylidene. Our
computation is very efficient. For example, a recent calculation with a basis of 192 000 using the coupled two-term
Lanczos method requires 145 000 iterations. In contrast, we are able to compute the same vinylidene states to higher
accuracy with a basis of 340 200 using only 6 336 total iterations (537 Lanczos and 11.8 average QMR iterations).
Vinylidene vibrational states in the high-energy region (above 20400 cm-1 relative to the acetylene minimum) are well
57 Book of Programme and Abstract for TACC2008 converged and reported. Our calculations on the lifetime of vinylidene will also be reported and discussed in terms of
experimental divergences. More definite assignments on vibrational states than previous studies are acquired using the
normal mode projection. The corresponding calculations are also done for C2D2, and several vinylidene states are
reported for the first time.
[1] K. M. Ervin, J. Ho, and W. C. Lineberger, J. Chem. Phys. 1989, 91, 5974.
[2] J. Levin, H. Feldman, A. Baer et al., Phys. Rev. Lett. 1998, 81, 3347.
[3] S. Zou, J. M. Bowman, and A. Brown, J. Chem. Phys. 2003, 118, 10012.
[4] I. N. Kozin, M. M. Law, J. Tennyson, and J. M. Huston, J. Chem. Phys.2005, 122, 064309.
[5] J. C. Tremblay and T. Carrington Jr., J. Chem. Phys. 2006, 125, 094311.
[6] S. Zou and J. M. Bowman, Chem. Phys. Lett. 2003, 368, 421.
[7] W. Bian and B. Poirier, J. Chem. Phys. 2004, 121, 4467.
Supported by National Natural Science Foundation of China
IN-ES009
Quantum dynamics at conical intersections
Stuart C. Althorpe
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW.
A conical intersection is a funnel-shaped object, produced where two electronic potential energy surfaces cross. The
Born-Oppenheimer approximation breaks down near the intersection, with the result that the system can relax from the
upper to the lower state on a timescale of tens of femtoseconds. Much is now understood about the electronic structure
that gives rise to conical intersections, but much less is known about the quantum effects experienced by the atomic
nuclei in the vicinity of an intersection. This talk will present recent findings about the properties of the nuclear wave
function that describes the dynamics of the nuclei in the vicinity of a conical intersection. Specifically, we will build on
recent topological results, which show that a nuclear wave function confined to the ground state surface can be split into
contributions from reaction paths that loop in opposite senses about the intersection [1,2]. We will explain how these
results can be generalised to analyse a nuclear wave function describing coupled dynamics on two potential energy
surfaces.
58 Book of Programme and Abstract for TACC2008 Fig. 1
Schematic diagram (taken from ref. 1), showing how a nuclear wave function confined to one potential surface
can be decomposed into contributions from paths that loop in clockwise and anti-clockwise senses around the conical
intersection.
1.
J.C. Juanes-Marcos, S.C. Althorpe and E. Wrede, Science 309, 1227 (2005).
2.
S.C. Althorpe, J. Chem. Phys. 124, 084105 (2006).
IN-ES010
An Endeavor at Constructing an Accurate Two-Component Relativistic Method for Heavy and Super-Heavy
Elements
Masahiko Hada and Seino Junji
Department of Chemistry, Graduate School of Science and Engineering,
Tokyo Metropolitan University, Minami-Osawa 1-1, Hachi-oji-city, Tokyo,
Japan, 192-0397
Recently some accurate two-component relativistic theories, which are equivalent in energy to the four-component Dirac
theory in any one-electron molecular systems, have been proposed and extremely accurate and low-cost
quantum-chemical methods are expected to be developed. In our paper, we show a series of calculations using the
infinite-order Douglas-Kroll (IODK)
transformation in the two-electron Coulomb terms r-1, and examine its
applicability to heavy and super-heavy elements [1,2]. Figure 1 shows deviations from the Dirac-Coulomb method in
total energy. The IODK/IODK, in which both one- and two-electron terms are transformed by IODK, is almost
equivalent to the Dirac-Coulomb method even in super-heavy elements.
IODK/BP
40
ΔE /a.u.
20
IODK/IODK
0
IODK/FW
-20
NR/C
-40
0
20
DKH2/C
40
60
80
IODK/C
100
120
Z (Nuclear Charge)
Figure 1. Total SCF energy deviations of some relativistic methods, relative to the Dirac-Coulomb method
[1] J. Seino and M. Hada, Chem. Phys. Letters, 2007, 442, 134-139.
[2] J. Seino and M. Hada, Chem. Phys. Letters, in press.
IN-ES011
Chiroptical Response and Local Correlation
T. Daniel Crawford
Department of Chemistry, Virginia Tech, Blacksburg, Virginia, 24061, USA
The most significant obstacle to the application of advanced quantum chemical methods such as coupled cluster theory to
large molecules is their high-degree polynomial scaling with the size of the system. Although methods that diminish this
59 Book of Programme and Abstract for TACC2008 scaling by exploiting the localizability of electron correlation have yielded impressive results for energetics and potential
energy surfaces, their efficacy for many other properties remains unclear. This paper will discuss recent progress in the
development of locally correlated coupled cluster models for chiroptical response, viz. optical rotation and circular
dichroism of large chiral molecules.
IN-ES012
New correlation functionals in DFT: theory and tests
Vincent Tognettia, Carlo Adamoa, and Pietro Cortonab
a
Laboratoire d’Electrochimie et de Chimie Analytique, UMR 7575, Ecole Nationale Supérieure de Chimie de Paris,
11 rue P. et M. Curie, F-75231 Paris Cedex 05, France.
b
Laboratoire Structure, Propriété et Modélisation des Solides, UMR 8580, Ecole Centrale Paris,
Grande Voie des Vignes, F-92295 Chatenay-Malabry, France.
A crucial step of any DFT calculations is the choice of the approximate exchange-correlation functional to be used. In
this communication I will focus on the correlation energy, a functional for which three new approximations have been
recently proposed [1-3]. The first one is a local functional which was derived by applying a Colle-Salvetti-like approach
to the homogeneous electron gas. Quite unusually, an expression for the kinetic part of the correlation energy was at first
obtained. Then, the total correlation energy was deduced by means of the virial theorem. The second and the third
functional belong to the GGA family and were deduced by an approach similar to the one adopted by Perdew, Burke, and
Ernzerhof [4]: an analytical expression depending on the density, the reduced density gradient, and the relative
spin-polarization was chosen and the constants appearing in it were determined without fitting reference data, but
requiring that some physical constraints are satisfied. The procedure by which the three functionals have been
constructed will be outlined and their performances will be analyzed and compared with those of the standard LDA and
GGA functionals. Strong improvements have been found for a variety of atomic and molecular properties.
[1] S. Ragot and P. Cortona, J. Chem. Phys., 2004, 121, 7671.
[2] V. Tognetti, P. Cortona and C. Adamo, J. Chem. Phys., 2008,128, 034101.
[3] V. Tognetti, P. Cortona and C. Adamo, Chem. Phys. Lett., 2008, 460, 536.
[4] J. P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett., 1996, 77, 3865.
IN-ES013
Static Electron Correlation in Molecules: Spin-restricted Density Functional Approach
M. Filatov and A. Kazaryan
University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, the Netherlands
Application of density functional theory to the description of static electron correlation in molecules is reviewed. The
emphasis is made on the use of ensemble approach in density functional theory which leads to the formulation of the
spin-restricted ensemble-referenced Kohn-Sham (REKS) method. A variety of density functional methods (including
REKS) is applied to the study of bonding in low-spin ground states of molecular systems which represent difficult cases
for both single-reference spin-restricted and spin-unrestricted Kohn-Sham formalisms. The test cases include weakly
bound molecular aggregates, such as nitric oxide dimer, and singlet-triplet energy gaps in a series of strongly correlated
bi-nuclear copper complexes. Comparison of the results of the calculations with the available experimental data and the
results of high-level ab initio calculations shows that REKS is capable of providing a good description of static
correlation effects in these systems. A possibility for the calculation of excitation energies within the REKS formalism is
outlined. The REKS method is applied to the calculation of the ground and the lowest singlet excited state potential
60 Book of Programme and Abstract for TACC2008 energy surfaces in unsaturated organic molecules. The results of REKS calculations are compared with the experimental
excitation energies and with the results of high level ab initio calculations (CASSCF/CASPT2). It is demonstrated that
the lowest exited state potential energy surfaces can be described reasonably with the use of REKS. Implications of these
findings for density functional description of strongly correlated molecular systems are discussed and perspectives for
future method development are outlined.
IN-ES014
Conceptual DFT : Redox Reactions Revisited
P. Geerlings, J. Moens, P. Jaque*, G. Roos
Eenheid Algemene Chemie, Faculty of Sciences, Vrije Universiteit Brussel (Free University of Brussels - VUB),
Pleinlaan 2, 1050 Brussels, Belgium
* Laboratorio de Quimica Téorica Computacional – Pontificia Universidad Católica de Chile, Santiago, Chile
Conceptual Density Functional Theory[1-4] has offered the possibility for sharp definitions of widely used but often
vaguely defined concepts such as electronegativity, hardness, softness … thus enabling their numerical evaluation and
their use (both qualitatively and quantitatively) as such or within the context of principles such as Sanderson's
Electronegativity Equalization Principle, Pearson's Hard and Soft Acids and Basis Principle… A closer look at the
reactions studied in the past shows the prevalence of generalized acid base reactions and fundamental types of organic
reactions. Remarkable, redox reactions did not receive much attention [5] despite the fact that they are archetypical
reactions involving a change in the number of electrons which is one of the basic variables, together with the external
potential in a perturbational approach to chemical reactivity [6]. In the first part of the talk we prove the usefulness of
global and local electrophilicity descriptors [7] for the prediction of the redox characteristics of first row transition metal
ions. A scaled electrophilicity turns out to yield a good quantitative estimate of the redox potential. The role of the first
and second solvatation spheres in the electron uptake process is highlighted [8]. In the second part a formula is derived
for the chemical potential of the electrode in terms of the intrinsic properties of oxidized and reduced states of the
electroactive species. In a different approach the redox potential is solely expressed in terms of oxidized and reduced
species respectively. Applications are shown on a large collection of organic and inorganic systems in different solvents
[9].
[1] Parr, R.G.; Yang, W. Density Functional Theory of Atoms and Molecules, Oxford University Press, New York, 1981.
[2] Parr, R.G.; Yang, W., Annu. Rev. Phys. Chem. 1995, 46, 79.
[3] Chermette, H. J. Comput. Chem. 1999, 20, 129.
[4] Geerlings, P.; De Proft, F.; Langenaeker, W. Chem. Rev. 2003, 103,1793.
[5] Moens, J.; Geerlings, P.; Roos, G. Chem. Eur. J. 2007, 13, 8174.
[6] Ayers, P.W.; Anderson, J.S.M.; Bartolotti, L.J. Int. J. Quant. Chem.2005, 101, 520.
[7] Chattaraj, P.K.; Sarkar, U.; Roy, D.R. Chem. Rev. 2006, 106, 2065.
[8] Moens, J.; Roos, G.; Jaque, P.; De Proft, F.; Geerlings, P. Chem. Eur. J.2007, 13, 9331.
[9] Moens, J.; Jaque, P.; De Proft, F.; Geerlings, P. J. Phys. Chem.A 2008, 112, xxx.
IN-ES015
Solving longstanding problems in DFT with orbital-dependent functionals
Andreas Görling
Chair of Theoretical Chemistry,University of Erlangen-Nuremberg, Germany
61 Book of Programme and Abstract for TACC2008 The concept of orbital-dependent functionals in DFT is presented [1]. The optimized effective potential (OEP) method
for constructing local multiplicative exchange-correlation potentials is considered [2, 3] and a numerical stable OEP
approach based on Gaussian basis sets is introduced [4]. Exact-exchange Kohn-Sham calculations based on this OEP
approach yield orbital and eigenvalue spectra that are superior to those obtained by Hartree-Fock or conventional
Kohn-Sham calculations. A multiconfiguration OEP approach for a density-functional treatment of static correlation is
presented [5]. Finally, a time-dependent DFT approach that is capable of correctly treating charge-transfer excitations is
discussed.
[1] A. Görling, J. Chem. Phys., 123, 062203 (2005).
[2] A. Görling, A. Hesselmann, M. Jones, and M. Levy, J. Chem. Phys. 128, 104104 (2008).
[3] A. Hesselmann and A. Görling, Chem. Phys. Lett. 455, 110 (2008).
[4] A. Hesselmann, A. W. Götz, F. Della Sala, and A. Görling, J. Chem. Phys. 127, 054102(2007).
[5] M. Weimer, F. Della Sala, and A. Görling, J. Chem. Phys 128, 144109 (2008).
IN-ES016
Localized electronic excitations in condensed phase from orbital-free embedding calculations
T.A. Wesolowski
Department of Physical Chemistry, University of Geneva
We overview the generalization of the Wesolowski-Warshel embeding formalism [1] to study response properties [2-3].
Applications of this generalized formalism to study electronic excitations in chromophores interacting with
hydrogen-bonded molecules in the environment will be overviewed [4-5]. The case of the environment induced shifts of
electronic excitations in a clusters involving 7-hydroxyquinoline and not-absorbing but hydrogen-bonded small
molecules (water, ammonia, etc) will be covered in detail.
[1] T.A. Wesolowski and A. Warshel J. Phys. Chem. 97 (1993) 8050
[2] M. Casida and T.A. Wesolowski, Int. J. Quantum Chem. 96 (2004) 577
[3] T.A. Wesolowski, J. Am. Chem. Soc. 126 (2004) 11444
[4] J. Neugebauer, M.J. Louwerse, E.J. Baerends, T.A. Wesolowski, J. Chem. Phys. 122 (2005) 094115
[5] J. Neugebauer, C.R. Jacob, T.A. Wesolowski, E.J. Baerends, J. Phys. Chem. A. 109 (2005) 7805
[6] Fradelos, Kaminski, Wesolowski, et al. in preparation
OR-ES017
INTERPRETING MOLECULAR VIBRATIONAL SPECTRA BY PERIODIC ORBITS
Stavros C. Farantos
Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, and Department of
Chemistry, University of Crete, Iraklion 71110, Crete, GREECE
Vibrationally excited molecules are non-linear dynamical systems, and hence the correspondence of
classical
non-linear effects such as chaos, resonances and bifurcations, to quantum mechanical behaviours come into play.
Several research groups have shown the importance of Periodic Orbits (PO) for the assignment of complex molecular
vibrational spectra [1,2], as well as the interpretation of quantum mechanical calculations that produce hundreds of
vibrational levels and eigenfunctions [3]. In this presentation we demonstrate that the methods of locating Periodic
Orbits can be extended to polyatomic molecules [4], as are the active sites of some
proteins. Stable PO reveal stable
62 Book of Programme and Abstract for TACC2008 regions in phase space where wave functions could be localized, and thus observed
spectroscopic features are
elucidated.
[1] M. Joyeux, S. Yu. Grebenshchikov, J. Bredenbeck, R. Schinke, and S. C. Farantos, Adv. Chem. Phys., 2005, 130,
267-303.
[2] S. C. Farantos, Z.W. Qu, H. Zhu, and R. Schinke, Int. J. Bifurcation Chaos Appl. Sci. Eng., 2006, 16, 1913-1928.
[3] Chuanxiu Xu, Bin Jiang, Daiqian Xie, Stavros C. Farantos, Shi Ying Lin, and Hua Guo, J. Phys. Chem. A, 2007,
111, 10353-10361.
[4]
S. C. Farantos, J. Chem. Phys., 2007, 126, 175101
IN-ES018
New developments in the Amsterdam Density Functional (ADF) program suite
Stan van Gisbergen
Scientific Computing & Modelling NV, Theoretical Chemistry, Vrije Universiteit, Amsterdam Area, Netherlands
The presentation will focus on recent improvements in, and practical applications of, the Amsterdam Density Functional
(ADF) program suite for Density Functional Theory (DFT) calculations on molecular and periodic systems as available
in the new release, ADF2008. New functionality [such as new exchange-correlation functionals, magnetic properties,
thermodynamical properties of liquids, multi-level methods], improved user-friendliness and visualization options, and
speed improvements for applications ranging from chemical engineering to surface science to biological systems will be
touched upon.
OR-ES019
Relativistic quantum chemistry of heavy elements, hadronic atoms and heavy ions collisions
Alexander V. Glushkov1,2
1
2
Odessa University, P.O.Box 24a, Odessa-9, South-East, 65009, Ukraine
Institute for Spectrsocopy, Russian Acad. Sci., Troitsk, Moscow reg., 142090, Russia
E-mail:
[email protected]
The gauge-invariant QED perturbation theory approach [1] to relativistic calculation of the spectra for heavy and
superheavy elements (isotopes) and hadronic atomic systems ions with an account of relativistic, correlation, nuclear,
radiative effects is presented. Zeroth approximation is generated by the effective ab initio model functional, constructed
on the basis of the comprehensive gauge invariance QED procedure. The wave functions zeroth basis is found from the
Klein-Gordon (pion atom) or Dirac (kaon, hyperon) equation. The potential includes the core ab initio potential, the
electric and polarization potentials of a nucleus (the Gauss and Fermi models and relativistic Dirac-Kohn-Sham approach
for charge distribution in a nucleus are considered). For superheavy ions the correlation corrections of high orders are
accounted for within the Green function method. The magnetic inter-electron interaction is accounted for in the lowest
order, the Lamb shift polarization part- in the Uhling-Serber approximation and the self-energy part – within the Green
functions method. We carried out calculations :1).energy levels, hfs parameters for superheavy Li-like ions for different
models of the charge distribution in a nucleus and super heavy atoms Z=114-118; 3). Shifts and widths of transitions
(2p-1s,3d-2p, 4f-3d) in the pionic, kaonic atoms (18O,
24
Mg etc.) and also K--4He. Further a new consistent unified
quantum mechanics and QED approach is developed and applied for description of the heavy ions collisions and heavy
quasimolecules. To calculate the collision cross-section and quasi-molecule energy characteristics we use modified
versions of the relativistic energy approach, based on the S-matrix Gell-Mann and Low formalism, and operator
perturbation theory approach [2]. The nuclear subsystem and electron subsystem has been considered as two parts of the
63 Book of Programme and Abstract for TACC2008 complicated system, interacting with each other through the model potential. The nuclear system dynamics has been
treated within the Dirac equation with effective potential. All the spontaneous decay or the new particle (particles)
production processes are excluded in the zeroth order. The calculation is carried out for the
238
U+238U,
232
Th+250Cf and
238
U+248Cm systems and diatomics with X112 , X114 atoms.
1. A.V.Glushkov, JETP Lett. 55 108 (1992), A.V.Glushkov and L.N.Ivanov, Phys.Lett.A. 170, 36 (1992); Preprint
Institute for Spectroscopy of Russian Acd.Sci., N-,AS1-3, Troitsk-Moscow,1992;
A.V.Glushkov, E.P. Ivanova,
J.Quant. Spectr. Rad. Tr. (US) 36,127 (1986); A.Glushkov etal, In: New Projects and New lines of research in Nuclear
Physics, eds.Fazio G., Hanappe F. (World Sci.. Singapore,2003); A.V.Glushkov, In: Low Energy Antiproton Phys., AIP
Serie.796, 206 (2005); Recent Advances in Theory of Phys. and Chem. Systems (Springer), 15, 285-300 (2006);
2. A.V.Glushkov and L.N.Ivanov, J.Phys.B. 26, L379 (1993); A.V.Glushkov et al, Nucl. Phys.A. 734S, 21 (2004); Int.
Journ. Quant.Chem. 99, 879 (2004); 99, 936 (2004); 105, 512 (2005); 105, 562 (2005); J.Phys.CS. 178, 188 (2005); 178,
199 (2005);. Recent Advances in Theory of Phys. and Chem. Systems (Springer) 15, 301-308 (2006).
IN-ES020
New Development of Tri‐atomic State‐to‐state Reaction Scattering Calculation
Using Time‐dependent Wave Packet Method
Zhigang Suna.b, Soo‐Ying Leea, Donghui Zhangb
a
Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological
University, SPMS‐04‐01, 21 Nanyang Link, Singapore, 637371
b
State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry,
Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian,116023, P.R. China
First, we introduce a 3D quantum time‐dependent wave packet method for calculating state‐to‐state reactive cross
sections for the A+BC→AB+C/AC+B reactions. The method avoids the coordinates problem by solving the scattering
dynamics processes in a single reactant Jacobi coordinates. The product state generation probabilities are then determined
by evaluating their wave function at each propagation time step on their discrete variable representation points which is
optimized in the product basis representation. These grid points are very efficient for representing the product state wave
functions and only very limited number of them are necessary for a complete state‐to‐state reaction information
extraction, which make the computational time for evaluating them negligible. The method only use single reactant
Jacobi coordinates thus is complementary to the current approaches for extracting state‐to‐state information using
time‐dependent wavepacket method. It allows state‐to‐state cross sections to be calculated efficiently for reaction systems
with deep potential well, with long range interaction potential, or with scattering resonance states and is enlightening to
develop more efficient quantum method for simulating reactive scattering and photodissociation processes. We apply this
2
method to the H+H (for J=0.42) reactions, and obtain the state‐to‐state differential cross sections. This method is
2
further used to extract state‐to‐state cross sections of H+O reaction scattering. which has deep‐well and long range
interaction potential to demonstrate its advantages. The results from selected initial state as (v0,j0)=(0,0), (0,1) and (1,0)
2
are given to show non‐statistics behaviors of H+O reaction scattering.
Second, we describe the time‐dependent, wave‐packet based methodology for the calculation of state‐to‐state differential
cross sections for the reaction of Cl with H2. We describe a model including two coupled potential energy surfaces,
simplified from the exact 6‐state description. Our model includes the crucial spin‐orbit coupling which is responsible for
the largest non Born‐Oppenheimer effects in the Cl+H2 reaction, but neglects the off‐diagonal electronically diabatic
coupling and Coriolis couplings. Our model allows computationally efficient determination of accurate state‐to‐state
64 Book of Programme and Abstract for TACC2008 information for the reactivity of both the ground and excited Cl atoms. Comparisons with more exact time‐independent
calculations and experimental results demonstrate the accuracy of our method.
IN-ES021
Toward exact numerical solutions of the nonrelativistic Schrödinger equation of polyatomic molecules
So Hirata,a Toru Shiozaki,a,b Muneaki Kamiya,a and Edward F. Valeevc
a
Department of Chemistry, University of Florida, Gainesville, Florida 32611-8435
b
Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8656
c
Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061-0002
An ultimate objective of electronic structure theory may be to solve the Schrödinger equa-tion of general polyatomic
molecules and macromolecules within a controlled absolute ac-curacy, typically, 1 kcal mol–1. To achieve this without
relying on statistical or empirical treatments, one must have rapidly converging series of approximations in both
electron-correlation treatments and basis sets. Our efforts toward this objective are based on the ba-sis-set-free,
grid-based, numerical solutions of the Hartree–Fock equations and on the high-rank, explicitly-correlated coupled-cluster
methods with Gaussian basis sets, which are implemented by computer algebra. We will discuss the details of these
methods.
1.
T. Shiozaki, M. Kamiya, S. Hirata and E. F. Valeev, (submitted, 2008), “Explicitly-correlated coupled-cluster
singles and doubles (CCSD-R12) method based on complete diagrammatic equations.”
2.
T. Shiozaki, M. Kamiya, S. Hirata, and E. F. Valeev, Physical Chemistry Chemical Physics 10, 3358–3370 (2008),
“Equations of explicitly-correlated coupled-cluster methods.”
3.
T.
Shiozaki and S. Hirata, Physical Review A (Rapid Communications) 76, 040503(R) (2007) (4 pages),
“Grid-based numerical Hartree–Fock solutions of polyatomic molecules.”
IN-ES022
Sturmian exponential type orbitals and geminals for structure, properties and electron correlation.
Philip E Hoggan
University Blaise Pascal, 24 Avenue des Landais, Clermont-Ferrand, France
Sturmian functions are complete without continuum states. They also orthogonalise the potential related to their
argument. Sturmians are thus good starting points for the construction of geminal trial functions that explicitly include
inter-particle (electron-electron) distances. These Sturmian geminals are functions of the electron-electron vector. This
paper discusses the use of Sturmians (as a function of the usual electron position vector) and in particular the evaluation
of molecular integrals in a Sturmian basis. Their analytical computation can be pursued by techniques that include
symbolic computation methods. The functions may also be determined directly for two centers and thus the Diatomics In
Molecules strategy may be employed for bound and unbound atom pairs within molecules. These ideas have been used to
construct an improved Slater-Type Orbital Package (STOP) for the evaluation of three- and four-center molecular
integrals that are needed to perform meaningful molecular calculations. Early presentations of this project goes back to
1988 (ICQC Jerusalem) and has regularly been updated since.
Keywords: analytical Coulomb potential, Coulomb Sturmians, Spectral forms, explicit correlation.
1. J. Avery, Hyperspherical Harmonics and Generalized Sturmians, Kluwer, Boston (2000).
2. C. A. Weatherford, E. Red and P. E. Hoggan, Mol. Phys. 103 2169-2172 (2005).
65 Book of Programme and Abstract for TACC2008 3. (i) A. Bouferguene, M. Fares and P. E. Hoggan, International Journal of Quantum Chemistry 57, 801-809 (1996).
(ii) A. Bouferguene and P. E. Hoggan, STOP: Slater Type Orbital Package, Q.C.P.E. 67 (1996).
4. N. Absi and P. E. Hoggan, Int. J. Quantum Chem. 106, 2881-2888 (2006).
IN-ES023
Divide-and-conquer electronic structure method: Extension to post-HF correlation theories
Masato Kobayashi and Hiromi Nakai
Department of Chemistry and Biochemistry, chool of Advanced Science and Engineering, Waseda University,
3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
We have assessed the performance of Yang’s divide-and-conquer (DC) electronic structure method [1,2] when applied to
the Hartree-Fock (HF) procedure [3,4]. After DC-HF calculation, one can obtain the total density matrix, which is
expressed as sum of subsystem density matrices, and the molecular orbitals corresponding to local subsystems. Recently,
we have proposed the linear-scaling post-HF correlation methodology using subsystem orbitals [5,6]. In this scheme, the
correlation energy corresponding to a subsystem is evaluated with the strategy of the energy density analysis (EDA) [7].
In this presentation, we will show the procedure and performance of this DC-based correlation method, especially
applied to the second-order Møller-Plesset perturbation (MP2) [5] and coupled-cluster with singles and doubles
excitations (CCSD) [6] theories. Furthermore, our recent improvement of this method using two different localization
regions for subsystems, which we call dual-level DC-based correlation method, will be presented.
[1] W. Yang, Phys. Rev. Lett. 66 (1991) 1438.
[2] W. Yang, T.-S. Lee, J. Chem. Phys. 103 (1995) 5674.
[3] T. Akama, M. Kobayashi, H. Nakai, J. Comput. Chem. 28 (2007) 2003.
[4] T. Akama, A. Fujii, M. Kobayashi, H. Nakai, Mol. Phys. 105 (2007) 2799.
[5] M. Kobayashi, Y. Imamura, H. Nakai, J. Chem. Phys. 127 (2007) 074103.
[6] M. Kobayashi, H. Nakai, submitted.
[7] H. Nakai, Chem. Phys. Lett. 363 (2002) 73.
IN-ES024
Excitation energies with time-dependent density matrix functional theory
Evert Jan Baerends, K. J. H. Giesbertz, O. V. Gritsenko, K. Pernal
Section Theoretical Chemistry, Faculty of Exact Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam,
The Netherlands
Time-dependent density functional theory in its current adiabatic implementations exhibits three striking failures: a)
totally wrong behavior of the excited state surface along a bond-breaking coordinate; b) lack of doubly excited
configurations, affecting again excited state surfaces; c) much too low charge transfer excitation energies. We address
these problems with time-dependent density matrix theory (TDDMFT).1,2 For two-electron systems the exact
exchange-correlation functional is known in DMFT, hence exact response equations can be formulated. This affords a
study of the performance of TDDMFT in the TDDFT failure cases mentioned (which are all strikingly exhibited by
prototype two-electron systems such as dissociating H2 and HeH+). At the same time, adiabatic approximations, which
will eventually be necessary, can be tested without being obscured by approximations in the functional. We find:3 a) In
the fully non-adiabatic (w-dependent, exact) formulation of linear response TDDMFT, it can be shown that
LR-TDDMFT is able to provide exact excitation energies; in particular the first order (linear response) formulation does
not prohibit the correct representation of doubly excited states; b) Within previously formulated simple adiabatic
66 Book of Programme and Abstract for TACC2008 approximations2 the bonding-to-antibonding excited state surface as well as charge transfer excitations are described
without problems, but not the double excitations; c) An adiabatic approximation is formulated in which also the double
excitations are fully accounted for.
1. K. Pernal, O. Gritsenko and E. J. Baerends, Phys. Rev. A 75, 012506 (2007)
2. K. Pernal, K. J. H. Giesbertz, O. Gritsenko and E. J. Baerends, J. Chem. Phys. 127, 21401 (2007)
3. K. J. H. Giesbertz, E. J. Baerends, K. Pernal, O. Gritsenko, Phys. Rev. Lett. (2008), to be publ.; J. Chem. Phys.
submitted
IN-ES025
ab-initio Density Matrix Renormalization Group and Tensor Network wavefunctions
Garnet Kin-Lic Chan
Department of Chemistry and Chemical Biology
Cornell University, Ithaca, NY14853-1301
In recent years, the Density Matrix Renormalization Group has openedup the ab-initio simulation of complex
multireference quantum chemical problems involving very large numbers of active electrons. I will give examples from
our recent work that demonstrate the power of the method in studies on light-harvesting pigments, conjugated polymers,
graphene nanosheets, and prototype metal-insulator transitions. From a quantum chemical perspective, the density matrix
renormalization group is based on a new class of wavefunctions with an intriguing structure. These wavefunctions form
part of a much widerset of so-called "tensor networks" which provide a new paradigm to model and understand
correlations in strongly interacting problems. I will discuss these new developments and their implications for quantum
chemistry at the end of my talk.
IN-ES026
Relativistic and QED Treatment of Long-Range Resonant Interactions between Like Atoms
Wojciech Skomorowski, Tatiana Korona, Robert Moszynski
Department of Chemistry, University of WarsawPasteura1, 02-093 Warsaw, Poland
Theory of long-range relativistic interactions between identical atoms in their ground and excited states is formulated
with an emphasis on the spin-orbit interactions. It is shown that the relativistic resonant interaction between like atoms,
one in the ground 1S state and the other in an excited 3L state, shows a R-(2L+1) behavior. Other contributions to the
resonant relativistic potential are also considered and a complete treatment of the Casimir-Polder retardation effects
within the long-wavelength quantum electrodynamics formalism is reported. Numerical results illustrating these
theoretical developments are presented on the example of the calcium and strontium diatomic molecules. The accuracy of
the results is proven by comparison of the computed and measured lifetimes for the electronically excited states of
these atoms, and of the computed and measured transition frequencies in the high-resolution photoassociation spectra.
The transition frequencies in the ultracold regime, from the rovibrational continuum of the ground electronic state to the
long-range rovibrational levels of the excited electronic states corresponding to the 1S+3P dissociation, and bound by
spin-orbit interactions, represent a very stringent test for the present theoretical developments.
IN-ES028
Relativistic Methods Based on the Regular Approximation and the Normalized Elimination of the Small
Component Application to Mercury Bonding
67 Book of Programme and Abstract for TACC2008 Dieter Cremer1, Michael Filatov2, and Elfi Kraka3
1
Department of Chemistry and Department of Physics, University of the Pacific, 3601 Pacific Ave, Stockton, CA, 95211;
2
University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, the Netherlands;
3
Department of Chemistry, University of the Pacific, 3601 Pacific Ave, Stockton, CA, 95211; E-mail:
[email protected]
A set of generally applicable relativistic methods is presented, which makes it possible to obtain quantum chemical
descriptions of atoms and molecules with increasing accuracy at the all-electron level. The methods are based on the
Regular Approximation and the Normalized Elimination of the Small Component (NESC) and can be applied in
connection with DFT, HF, CASSCF, many body perturbation theory, or coupled cluster methods. [1-3]
The relativistic methods are applied to assess bonding energies in mercury compounds and to compare bonding with
related molecules containing other group IIB elements. The dissociation energy of HgX molecules varies from just a few
kcal/mol to 50 kcal/mol and more. The importance of relativistic corrections for calculated bonding energies is
demonstrated and a general applicable rationale for mercury bonding is presented. On the basis of this rationale, bonding
in transition metal molecules with electron structures closely related to those of HgX molecules are discussed.
1. M. Filatov and D. Cremer, Chem. Phys. Chem. 5, 1547 (2004).
2. M. Filatov and D. Cremer, J. Chem. Phys. 122, 064104 (2005).
3. K. G. Dyall, J. Chem. Phys. 106, 9618 (1997); M. Filatov and K. G. Dyall, Theor. Chem. Acc. 117, 333 (2007).
IN-ES029
Stable long-time semiclassical description of zero-point energy in high-dimensional molecular systems
Vitaly A. Rassolov and Sophya Garashchuk
Dept of Chemistry and Biochemistry, University of South Carolina, SC 29208
Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys. 120, 1181
(2004)] is further
developed to give stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The
method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the
linearization errors are added into the time evolution equations for the classical and nonclassical components of the
momentum operator. The wavefunction normalization and energy are rigorously conserved. Numerical tests are
performed for model systems of up to 40 degrees of freedom.
OR-ES030
Toward High-Accuracy ab Initio Potentials At Low Cost
António J.C. Varandasa
a
Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal.
This talk consists of two parts. First, we show how a potential energy surface (PES) can be predicted at a high level of ab
initio theory by performing calculations with small basis sets followed by scaling1,2 the electron correlation to the target
basis set. By further extrapolation of the energy to the complete basis set limit3,4, a PES of submillihartree or even better
accuracy can be obtained4,5.
The method can be as cost effective as Kohn-Sham density functional theory for
medium-size systems when raw energies from Møller-Plesset perturbation theory using double and triple-zeta correlation
68 Book of Programme and Abstract for TACC2008 consistent basis sets are utilized6,7. The implications8 of (avoided) crossings on the extrapolation method as well as its
performance on the calculation of tensorial properties9 will also be addressed. The second part of the talk focuses on how
to upgrade a PES to spectroscopic accuracy10, and model a multi-sheeted form via a novel global-diabatization-angle
approach11. Time permitting, illustrative dynamics results will be surveyed.
1
2
3
4
5
6
7
8
9
Varandas, A.J.C; Piecuch, P. Chem. Phys. Lett. 2006, 430, 448.
Varandas, A.J.C. J. Chem. Phys. Lett. 2007, 443, 398.
Varandas, A.J.C. J. Chem. Phys. 2007, 126, 244105.
Varandas, A.J.C. J. Phys. Chem. A 2008, 112, 1841.
Varandas, A.J.C. J. Chem. Phys. 2007, 127, 114316.
Varandas, A.J.C. J. Comp. Chem. (in press).
Varandas, A.J.C. Chem. Phys. Lett. (in press).
Varandas, A.J.C. (submitted).
Junqueira, G.; Varandas, A.J.C. J. Phys. Chem. A (in press).
10
11
Galvão, B.; Rodrigues, S.P.J.; Varandas, A.J.C. J. Chem. Phys. 2008, 127, 044302.
Mota, V.C.; Varandas, A.J.C. J. Phys. Chem. A 2008, 112, 3768.
IN-ES031
VBPT2: A Valence Bond Method that Incorporates Perturbation Theory
Zhenhua Chen, Jinshuai Song, Wei Wu*
Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
E-mail: [email protected], Fax: (86)592-2183047
A post-VBSCF method, called valence bond second-order perturbation theory (VBPT2), is developed. By introducing a
virtual orbital set, which is orthogonal to occupied nonorthogonal orbitals, and a generalized Fock matrix constructed
from the density matrix of VBSCF wave function, the partition of the zero-order Hamilton for multi-reference
perturbation theory is obtained. The first order wave function is constructed from single and double replacement of the
occupied orbitals in VBSCF structures by virtual orbitals. Although the exited structures can not retain the same
electronic pairing pattern and charge distribution as corresponding VBSCF structures, the fundamental weight and energy
correction to VBSCF structures can be obtained approximately.
The VBPT2 method was tested by calculating the bond energies of H2, F2, N2, and O2, the barriers of identity hydrogen
abstraction reactions, X• + X’H Æ XH + X’• (X , X ’ = H, CH3), the bind energy of water, and the single and triple
splitting of CH2. It is shown that the VBPT2 method gives results that are in good agreement with the VBCI method and
molecular orbital based MRPT and MRCI at the same truncation level, and the computational effort is greatly reduced,
compared to that of VBCI method.
[1] Wu, Wei; Song, Lingchun; et al, J. Phys. Chem. A 2002, 106, 2721
IN-ES032
Benchmark calculations of exited states in heavy elements compounds: new strategies and results
Ephraim Eliav
School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel
69 Book of Programme and Abstract for TACC2008 In heavy and super-heavy atomic and molecular systems relativistic, QED and electron correlation effects are often of the
same order of magnitude, nonadditive and strongly intertwined. Calculations of excited states in such systems are
particular challenging due to additional complications caused by high density and quasi-degeneracy of the energy spectra.
The high-level first principles methods appropriate for benchmark calculations of electronic structure and energy spectra
of heavy quasi-degenerate systems should be size-extensive and sizeconsistent,
as well as include correlation effects
(dynamic and nondynamic) and relativity simultaneously to high order. Presented methods include different forms of
fully relativistic
(based on Hamiltonians derived from QED) multi-root multireference coupled cluster (MRCC)
approaches, which satisfy all the benchmark criteria, enumerated above. The traditional forms of the multi-root MRCC
method are based on the Hilbert-space (HS) or Fock-space (FS) formulations and usually use the effective Hamiltonian
formalism [1]. The strong and weak sides of these formulations are reanalyzed. Few reformulations of the MRCC
including efficient solution of intruder states problem as well more balance treatment of dynamic and nondynamic
correlation and relativistic effects are presented. The new approaches use extrapolated intermediate Hamiltonian (XIH)
techniques [2] and have several methodological and computational advantages, based on opportunity to make different
extrapolation procedures proceeding from the approximate intermediate Hamiltonian to the precise effective Hamiltonian
with relatively large dimensions. Among others the mixed sector intermediate Hamiltonian scheme (MSIH) [3] could be
regarded as a particularly perspective approach. This approach is as a generalization of both FS and HS methods. In
contrast to the traditional Fock-space schemes, the starting point in the MSIH approach can be extended to certain non
closed-shell configurations and it’s effective Hamiltonian, like in the Hilbert-space case, includes nondiagonal elements
formally belonging to different Fock-space sectors. On the other hand the MSIH method includes many dynamic
correlation terms missed in the Hilbert-space formulation. Applications presented, include energy levels of some
open-shell heavy and super-heavy atomic and molecular systems. Excellent agreement with experiment (when available)
and significant improvement compared with traditional multireference coupled cluster approaches is obtained.
1. D. Mukherjee and S. Pal, Advan. Quantum Chem. 1989, 20, 292.
2. E. Eliav; M. J. Vilkas, Y. Ishikawa, Uzi Kaldor. J. Chem. Phys., 2005, 122, 224113/1-224113/5.
3. A. Landau, E. Eliav, Y. Ishikawa and U. Kaldor, J. Chem. Phys., 2004, 121, pp. 6634-6639
IN-ES033
Why multireference approaches: biradicals, excited states and nonadiabatic photodynamics
Hans Lischka
Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
In spite of the overwhelming success of single-reference methods such as Møller-Plesset perturbation theory and coupled
cluster methods or standard density functional theory important classes of interesting chemical problems exist, which are
not well covered by these methods. In this talk several examples will be discussed within the framework of
multireference configuration interaction (MRCI) theory and applications will be described, which are primarily based on
the COLUMBUS program system (http://www.univie.ac.at/columbus) under special usage of its capabilities for analytic
MRCI gradients and nonadiabatic coupling vectors. The examples given include bond-stretch isomerization
(benzo[1,2:4,5]dicyclobutadiene, [2.2.2]propellane and the Grob rearrangenment), excited state energy surfaces of DNA
bases and conical intersections and nonadiabatic dynamics simulations of the photostability of DNA bases using the
newly-developed NEWTON-X program system (http://www.univie.ac.at/newtonx).
70 Book of Programme and Abstract for TACC2008 IN-ES034
The Reduced Density Matrix Method: Application Of T20 N-representability Condition and Development of
Highly Accurate Solver.
Maho Nakata*, Bastiaan J. Braams, Katsuki Fujisawa, Mituhiro Fukuda, Jerome K. Percus, Makoto Yamashita, and
Zhengji Zhao
*Advanced Center for Computing and Communication, RIKEN
For ground state calculations of the electronic systems, since one- and two- body interactions are involved, we only need
the second order reduced density matrices (2-RDMs) to calculate the energy and other important physical properties. The
advantages of using 2-RDMs as basic variables instead of using the wavefunction methods are: (i) 2-RDMs have only
four variables regardless of the number of electrons in the system whereas wave function has N variables, (ii) for the
ground state; calculation becomes minimization of a linear functional. So there is a hope that we can construct an
efficient method than traditional wavefunction methods.
For the 2-RDM, the condition which correspond to Pauli principle, called N-representability condition, is the major
obstacle for this scheme. We obtain unphysical 2-RDMs and the energy can be far below the exact one. Unfortunately,
the algorithm “is this 2-RDM N-representable?” is known to be NP-hard, i.e., it is believed that there can be no
polynomial algorithm for its solution. Still, some effective necessary conditions, P, Q and G are known. These conditions
are of the positive semidefiniteness of the 2-RDM, and preliminary study in 1960s show promising results but somehow
diminished. The reasons may be: (i) there was no systematic way to do calculations, and (ii) lack of computer resources.
Recently, M. Nakata et al. found that minimizing over approximate N-representable 2-RDM, P, Q and G conditions can
be formulated as the standard type of semidefinite programming and applied to various realistic molecules and atoms.
Result is quite satisfactory. Then, Z. Zhao et al., implemented another positive semidefinite type condition called T1 and
T2, which is hidden in Erdahl’s paper. Result is almost same accuracy with CCSD(T) for small systems.
In this study [Nakata, M.; Braams, B. J.; Fujisawa, K.; Fukuda, M.; Percus, J. K.; Yamashita, M.; Zhao, Z; J. Chem.
Phys., J. Chem. Phys. 128, 16 164113 (2008).], we applied the T20 condition which is recently re-derived by Mazziotti
and Braams et al. in the same book, and applied to larger atoms and molecules. We gained several sub milli Hartree by
replacing T2 by T20. Besides, we developed a SDP solver which uses multiple precision arithmetic library called
SDPA-GMP, and successfully applied to the one dimensional Hubbard model at high correlation limit.
Keywords: reduced density matrix, N-representability conditions, semidefinite programming
IN-ES035
Resonance Assisted Hydrogen Bonds: myth or reality?
71 Book of Programme and Abstract for TACC2008 Pablo Sanz,a Otilia Mó,a Manuel Yáñez,a and José Elguerobb
a
Departamento de Química, C-9, Universidad Autónoma de Madrid,Cantoblanco,28049 Madrid, Spain.
b
Instituto de Química Médica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
The intramolecular hydrogen bond (IMHB) in malonaldehyde is usually taken as a paradigmatic example of resonance
assisted hydrogen bond (RAHB). However, neither the coupling constants nor the chemical shifts provide any evidence
for the existence of this phenomenon.1,2 The analysis of the IMHB within a series of 40 different enols of β-diketones3
and 32 different enols of derivatives of cyclobutane, cyclobutene and cyclobutadiene and their nitrogen counterparts,4
leads to the conclusions that the strength of the IMHB in unsaturated compounds is not a consequence of a RAHB effect,
but primarily a consequence of the structure of the σ-skeleton of the system that keeps the HB donor and the HB acceptor
coplanar and closer to each other.3 As a matter of fact, when the saturated compounds are constrained to have the
HB-donor and the HB-acceptor lying in the same plane and at the same distance as in the corresponding unsaturated
analogue, the IMHB is of similar or even larger strength. Similarly, the properties of IMHBs in tropolone, aminotropone
and aminotroponimine and in their saturated analogues do not show any evidence either of resonance assisted hydrogen
bond effects.
[1] Alkorta, I.; Elguero, J.; Mó, O.; Yáñez, M.; Del Bene, J. E., Mol. Phys. 2004, 102, 2563.
[2] Alkorta, I.; Elguero, J.; Mó, O.; Yáñez, M.; Del Bene, J. E., Chem. Phys. Lett. 2005, 411, 411.
[3] Sanz, P.; Mó, O.; Yáñez, M.; Elguero, J., J. Phys. Chem. A 2007, 111, 3585.
[4] Sanz, P.; Mó, O.; Yáñez, M.; Elguero, J., ChemPhysChem 2007, 8, 1950.
[5] Sanz, P.; Mó, O.; Yáñez, M.; Elguero, J., Chem. Eur. J. 2008, (In press).
OR-ES036
Proposal of a Communications Theory of Quantum Mechanics.
Theoretical Examination of the 'Gyromagnetic Ratio'.
Does light reflected by an electron rotate through double the angle through which the electron itself rotates?
Is the 'Two-Slit' experiment best explained by aliasing, first solved by Harry Nyquist (1926)?
Coogan, Anthony. (Private library and Internet researcher).
Information about the electron is conveyed to the detector by way of electromagnetic radiation reflected by the electron.
The probability wave of the electron is treated like Schrodinger's except that it is real. The reflected wave is discrete
rather than continuous, consisting of many photons.
The angle through which the reflected light rotates is double that of the electron, according to classical theory, similarly
to the operation of the navigator's sextant. This will be demonstrated using a torch and mirror. Thus, the spin of the
electron appears to be ½ but is really 1.
The famous 'Two-Slit' experiment suggests that electrons can be in two or more places at once. This appears to be
remarkably similar to aliasing, a well-known problem in telecommunications. It is likely to arise in analogue-to-digital
systems where precautions are not taken. A solution for this was simply demonstrated by Nyquist in 1926. Although he
was working with telegraph signals, the basic theory remains the same. Simple diagrams and a Java applet will show the
problem and its solution. The solution is consistent with the model presented.
It is hoped that better visualisation and understanding of quantum mechanics in general will result from this theory. The
removal of confusion will help interpretation of magnetic moment and other experiments
72 Book of Programme and Abstract for TACC2008 IN-ES037
Faster DFT with mrXC
Jing Kong and Nick Russ
Q-Chem Inc., 5001 Baum Blvd., 15668 Pittsburgh, USA
E-mail: [email protected] www.q-chem.com
A new algorithm, which speeds up DFT exchange-correlation numerical integration by 5-7 times with no loss of
accuracy, will be presented. The new method, called multiresolution exchange-correlation (mrXC), takes advantage of
the variation in resolution among the Gaussian basis functions, and shifts the calculation associated with low-resolution
(smooth) basis function pairs to an even-spaced cubic grid. MrXC does not alter the formulism of the current standard
algorithm based on the atom-centered grid (ACG), but instead employs two fast and accurate transformations between
the ACG and the cubic grid. The implementation of mrXC with local density approximation has been published [1]. We
have recently implemented mrXC for GGA functionals and for nuclear gradient calculation. In this conference, we will
present the results of the implementation in Q-Chem program [2], which requires additional algorithmic design.
[1] J. Kong, S.T. Brown and L. Fusti-Molnar, J. Chem. Phys. 2006, 124, 94109.
[2] Q-Chem is an ab initio quantum chemistry program. The latest release of Q-Chem 3.1 represents the state-of-art of
quantum chemistry. Y. Shao, et al, Phys. Chem. Chem. Phys., 2006, 8, 3172.
IN-ES038
Extending the applicability of B3LYP
Xin Xu*, Jianming Wu, Ying Zhang
State Key Laboratory of Physical Chemistry of Solid Surfaces; Center for Theoretical Chemistry, College for Chemistry
and Chemical Engineering, Xiamen University, Xiamen 361005, China
Density functional theory (DFT) has become the method of choice for first principles quantum chemical calculations of
the electronic structure and properties of many chemical systems. Based on the number of occurrences of functional
names in the journal titles and abstracts analyzed from the ISI Web of Science (2007), B3LYP is by far the most popular
density functional in chemistry, representing 80% of the total of occurrences of density functionals in the literature, in the
period 1990-2006.
Is B3LYP good for everything? How can we go beyond B3LYP?
Our strategies fall into two categories. One is to design a systematic correction scheme on top of B3LYP, such that all
B3LYP data, already and continuously built-up in the literature, can be used with higher accuracy and thus higher
reliability at no extra cost as compared to B3LYP. The other is to develop new density functional. The new functional
should maintain the advantage of B3LYP, while surmount its known difficulties, leading to a general functional with
more predictive power.
In this talk, progress along these two lines in our group will be reported.
OR-ES039
73 Book of Programme and Abstract for TACC2008 Local Reactivity Index Deduced from Mocular Orbitals works in Reactivity Prediction
Shuwen Yao
Henan Institute of Science and Technology, 4 Huanlan Road, Xinxiang, Henan, 453003, P.R.China
Quantum molecular properties own nearsigtedness nature, reasonable reactivity indexes consequently should be local
ones. Other reactivity indexes do not take into account contributions from sub frontier orbitals nor their corresponding
orbital energies, which is vital in determining species reactivity [1]. In this report, it is shown that a function of the
reactive site, which is deduced from the contributions of all the molecular orbitals, succeed in correlating with reaction
energy. The function is defined as F=SUM(Co*Co/e(exp(4)), where Co is the coeffient of molecular orbital on the
reactive site, and e is orbital energy. All the numerical values come from G03 calculation. Three case studies verify the
above therorem a). For substituent benzene nucleophilic reaction, reactivity strength correlates to the defined function
with R=0.89, better than Fukui function. b) For OH radical absorbs on various gold surfaces, a perfect curve correlation
is obtained (see fig. below).
Au13+Au5+Au6
250
function4value of gold3selectron
200
150
100
50
-75,7500
-75,7400
-75,7300
-75,7200
-75,7100
-75,7000
-75,6900
0
-75,6800
adsorption energy (plus the constant Oh energy)
c). For H atom reaction with carbon lines, a good
correlation curve is also obtained.
Using the above defined the function, we can identify the most preferable reaction site among multiple possibilities. It is
also useful in determining reacitve site within macromolecues and determining absorption site on complex surfaces
without the need of a large amount of computational trials.
[1] Weitao Yang, Robert G. Parr.Hardness, Softness, and the Fukui Function in the Electronic Theory of Metals and
Catalysis.Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 20 (Oct. 15,
1985), pp. 6723-6726
IN-ES040
Improving the predictions of noncovalent interactions in DFT with atom-centered potentials
Lin, I-Chun
Department of Chemical System Engineering, University of Tokyo, Japan
[email protected]
The Kohn--Sham formulation of density functional theory (DFT) has posed itself as one of the most popular and versatile
methods for condensed phase studies owing to its reasonable accuracy and affordable computational cost. DFT, in
principle, yields exact ground state energy, including dispersion forces that are of primordial importance in chemical and
biological systems. Yet with many exchange- correlation functionals in practical use, DFT either provides sporadic
results or fails completely to account for these forces. In consequence, various methods offering remedy for this
shortcoming have been proposed in this active field of research. In particular, dispersion-corrected atom-centered
74 Book of Programme and Abstract for TACC2008 potentials (DCACPs) serve as a robust and efficient way to include these weak forces in a fully self-consistent manner
within current DFT frameworks.
Here, we present a library of DCACPs calibrated with an improved penalty functional against high-level ab initio
references. In addition, its applications to systems of major chemical and biological interest such as intercalators of DNA
(many targeted as potential anti-cancer drugs) and liquid water will be discussed. The success of DCACPs in these
applications not only justifies the use of DCACPs but more importantly, provides insights to the role weak interactions
play in the systems investigated.
2.
Statistical Mechanics and Multiscale Issues IN-SM001
Integrated Temperature enhanced Sampling (ITS) method Simulation Results on water/air Interfaces
Gao Yiqin
Department of Chemistry, Texas A&M University, College Station, TX 77843-3012, USA
[email protected]
In this talk, I will first discuss an integrated temperature enhanced sampling (ITS) method and compare its efficiency
with other methods. Through an iterative procedure, the method achieves a uniform sampling of a large energy range in a
single continuous trajectory. It can be easily applied to large systems. The method was applied to calculate the
thermodynamics of polypeptide/protein folding. It was also used to study polypeptide aggregation and test the sequence
dependence in the formation of fibrillar and crystalline structures by polypeptides. It was shown that ITS allows very fast
configuration and energy space sampling in both applications. In the second part of my talk, I will report simulation
results on water/air interfaces and provide a simple explanation of the structure of the interfaces. We show that by
introducing two surface specific effects, the optimization in hydrogen bond formation and the minimization of the
exposure of partial charges to the gas phase, the sum frequency experimental results as well as simulation results
obtained using a large number of water models can be easily understood.
IN-SM002
Multiscale modelling of carbon based nanomaterials: fundamentals and applications to nanoelectronics
Elena Bichoutskaia
School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
Recent interest in molecular manufacturing is challenging the scientific community to develop nanometer size devices for
applications in new generations of molecular electronic computers and electromechanics. These new application areas
require novel and sophisticated approaches for design and performance prediction. Thus, theory and modelling are
playing an ever-increasing role in these areas to reduce development costs and manufacturing times.
In this talk, a condensed overview of the recent progress in fundamental understanding of electromechanical behaviour
and properties of carbon-based nanomaterials and their applications in nanodevices is presented. Recent experiments on
encapsulation of nanocrystals within carbon nanotubes and on the controlled and reversible telescopic extension of
carbon nanotubes are reviewed, with particular emphasis on the physics that defines these processes.
75 Book of Programme and Abstract for TACC2008 Behaviour and properties of materials can be explained by the quantum mechanics of their basic ingredients, i.e.
electrons and ions. I use density functional theory, which has proven to be a powerful quantum-mechanical method in
predicting the electronic structure of solids. It is the most rigorous approach, but it is limited by the power of computers
to relatively small systems. To study the properties of systems larger than computational quantum mechanics can handle,
I use large-scale atomistic simulations in which the description of the atomic interactions is approximated and defined by
effective interatomic potentials. To solve the problems for which most existing simulation models are inadequate, I
develop analytical models that incorporate the results from atomistic/ab initio calculations and explain the underlying
chemistry and physics.
IN-SM003
Proton Transport in Polymeric Membranes: Insights from Atomistic Simulations and Electronic Structure
Computations
M. Dupuis*, R. Devanathan, V.A. Glezakou, and A. Venkatnathan
Pacific Northwest National Laboratory, Chemical and Materials Sciences Division
P.O.Box 999, Battelle Blvd., Richland, WA 99352, USA
[email protected]
We will highlight a theoretical characterization of the selective transport of protons through polymeric membranes, a
property central to the operation of polymer electrolyte membrane fuel cells (PEMFCs). A fundamental understanding of
the factors affecting selective ionic and molecular transport under low levels of hydration will enable the rational design
of the next generation of polymer membranes. We have undertaken multi-scale simulations of proton transport and
membrane dynamics that are informed by detailed ab initio quantum chemical calculations. We will also discuss the
general concept of acidity in the context of cluster solvation (relevant to very low hydration conditions in membranes) as
characterized through meta-dynamics calculations.
This work is supported by the DOE’s Office of Basic Energy Sciences, Chemical Sciences Division.
IN-SM004
Investigation of proton transfer events and optical properties of the light driven proton pump Bacteriorhodopsin
using multi-scale QM/MM methods
Marcus Elstner
Theoretical Chemistry, University of Braunschweig, Hans-Sommer Str. 10, 38106 Braunschweig, Germany
Fax: ++49-531-391-5327, [email protected]
In the last years, we have studied the light driven proton pump Bacteriorhodpsin (bR) in some detail using QM/MM MD
techniques. bR is a seven trans-membrane helix protein, which pumps a proton across the membrane upon light
absorption. Ground state geometry optimizations and MD simulations are performed with DFT-B3LYP and SCC-DFTB
[1] in the QM region, while the CHARMM force field is applied for MM and the Generalized Solvent Boundary
Potential is used to describe the solvent continuum.
The retinal chromophore is a considerable challenge for theoretical
chemistry methods, since already the ground state structure is sensitive with respect to a balanced description of electron
correlation effects and the excitation involves considerable charge transfer. Since CIS and CASSCF methods have been
shown to be quantitatively inaccurate and TD-DFT approaches fail completely, [2]
excitation energies and absorption
spectra are calculated for optimized geometries and along MD trajectories using SORCI [3] and OM2/MRCI [4]. The
computational efficiency allows for the computation of vibrational and optical absorption spectra and the consideration of
various mutated structures. Our results allow to explain the spectral shift between bR and SRII, in particular to
76 Book of Programme and Abstract for TACC2008 discriminate between the effects of the Schiff base region and global electrostatic interactions [5]. In order to investigate
the effect of protein polarization on the excited states energies, we have combined the MRCI methods within
QM/QM/MM algorithms and with a polarizable force field model [6]. The various proton transfer steps are investigated
using reaction path methods [7] and umbrella sampling techniques.
[1] Elstner et al., Phys. Rev. B 58 (1998) 7260.
[2] Wanko et al, J. Phys. Chem. B 109 (2005) 3606, J. Chem. Phys. 120 (2004) 1674. J. Computer-Aided Mol. Design,s
20 (2006) 511
[3] F. Neese, J. Chem. Phys., 119 (2003) 9428 .
[4] W. Weber, W. Thiel, Theor. Chem. Acc., 103 (2000) 495 .
[5] Hoffmann et al., JACS 128 (2006) 10808. [6] Wanko et al, JPC B, in print.
[6] Bondar et al, JACS 44 (2004) 14668, STRUCTURE 12 (2004) 1281, J. Struc. Biol. 157 (2007) 454.
IN-SM005
Structural and Dynamical Coarse Graining of Macromolecular Systems
Marina G. Guenza
Department of Chemistry and Institute of Theoretical Science
University of Oregon, Eugene, OR 97403 USA
The dynamics of macromolecular systems is characterized by several lengthscales, and related timescales, where relevant
phenomena occur. [1] This define the complex nature of the liquid and requires the development of new theoretical
approaches that can bridge information between the different lengthscales (timescales) of interest. We present methods to
coarse-grain the structure of soft-matter systems, which provide effective analytical potentials that are input to multiscale
simulations. We alsopresent methods to coarse-grain the dynamics of macromolecules in dilute solution and in the melt
state. Theoretical predictions for the dynamics of polymer liquids [1, 2] and proteins [3] show quantitative agreement
with experimental data and with simulations.
[1] M. G. Guenza, J. Phys.: Condens. Matter 2008, 20, 033101.
[2] E. J. Sambriski, M. G. Guenza, Phys. Rev. E 2007, 76, 051801.
[3] E. Caballero-Manrique, J. K. Bray, W. A. Deutschman, F. W. Dahlquist, M. G.
Guenza, Biophys. J. 2007, 93, 4128.
IN-SM006
The Mixed Quantum Classical Molecular Dynamics Study of Diatomic
Molecule Vibrational Frequency Shifts in Nano-Confined Solvent
Fan Hu, Rongrong Mao, Shenmin Li
Liaoning Key Laboratory of Bio-organic Chemistry, Dalian University, Dalian 116622, PR China
A detailed study of the origins of vibrational frequency shifts of diatomic probe molecule in nano-confined solvent is
presented. Specifically, vibrationally adiabatic mixed quantum classical molecular dynamics simulations are used to
obtain the instantaneous frequency shifts andcorrelate the shifts to solvent configurations, geometry confinement and
surface effect. With this approach, important mechanistic questions are addressed, including the following: How many
solvent atoms determine the frequency shift? What solvent atom configurations lead to blue shifts and which to red shifts?
What is the effect of geometrical confinement? The mechanistic analysis can be generally applied and should be useful in
77 Book of Programme and Abstract for TACC2008 understanding what information is provided by infrared and Raman spectra about the environment of the probed
vibrational mode.
[1] C.M. Morales; W.H. Thompson, J. Phys. Chem. B 2008, 112, 313.
[2] S. Li; W.H. Thompson, Chem. Phys. Lett. 2005, 405, 304.
This work has been supported by the National Natural Science Foundation of China (Grant
No. 20573012, 20633050) and Educational Bureau of Liaoning Province (Grant No. 05L027)
OR-SM007
Quantum Dynamics in terms of Cumulant
Yasuteru shigeta
Institute of Picobiology, Graduate School of Life science, University ofHyogo,
Koto 3-2-1 Kamigori-cho, 678-1297 Hyogo, Japan
Recent experimental advances offer new information across many different time scales of interest, ranging from
submillisecond slow macroscopic structural transitions to subpicosecond electronic rearrangements, and femtosecond
nonadiabatic dynamics. In order to describe these phenomena, one should adopt quantum mechanics, which cost too
much. Quite recently, we have developed a quantal cumulant dynamics (QCD) in order to treat large quantum systems
with low costs [1-6]. The key ideas are that a coordinate shift operator acting on a potential operator is introduced and
that a cumulant expansion technique is applied to evaluate the expectation value of the shift operator. In the presentation,
we derive the coupled equations of motion of coordinates, momenta, cumulants that consist of symmetric-ordered
products of the coordinate and the momentum fluctuation operators. We apply the methodology to describe quantum
nature of structural transitions of Morse clusters. We have evaluated a Lindemann index of small quantum clusters and
observed quantum isotope effects on their melting behavior. The quantum effects shallow the potential and elongate the
equilibrium distance of the Morse potential. These features result in increase of transition temperatures of freezing and
melting toward those of classical ones.
[1] H. Miyachi, Y. Shigeta, K. Hirao, Chem. Phys. Lett. 432, 582 (2006).
[2] Y. Shigeta, H. Miyachi, K. Hirao, J. Chem. Phys. 125, 244102 (2006).
[3] Y. Shigeta, H. Miyachi, K. Hirao, Chem. Phys. Lett. 443, 414 (2007).
[4] Y. Shigeta, J. Chem. Phys. 128, 161103 (2008).
[5] Y. Shigeta, Chem. Phys. Lett. 461, 310 (2008).
[6] Y. Shigeta, H. Miyachi, T. Matsui, K. Hirao, Bull. Chem. Soc. Jpn. In press.
IN-SM008
Accurate QM/MM hierarchies for solvation and enzymes
Seiichiro Ten-no
Graduate School of Information Science, Nagoya University, Chikusa-ku, Nagoya 464-8601 Japan
The generalized hybrid orbital (GHO) QM/MM method [1], which is free from link atoms, has been extended by
introducing charge equalization and orthogonalization schemes about auxiliary orbitals. [2] The method has been applied
to PKA(c-AMP dependent protein kinase) and other enzyme reactions. We are also presenting a parallel implementation
of the QM/MM molecular dynamics method with the analytic energy gradient of GHO-MP2.
78 Book of Programme and Abstract for TACC2008 Another QM/MM hierarchy is the use of RISM integral equation theory. It was revealed that the partial wave (PW)
expression leads to reliable solvation free energies and partition coefficients compared with the HNC free energy
expression. [3] We investigate the performance of the PW energy functional using more systematic force field and
perturbational treatment of solute polarization effects. Moreover, we will present results of solvation and CC2 excitation
energies from the QM/MM/MM hybrid scheme with GHO.
All of the above-mentioned QM/MM methods are available in the GELLAN quantum chemistry program. [4]
[1] J. Pu, J. Gao, and D. G. Truhlar, J. Phys. Chem. A, 2004, 108, 632.
[2] J. Jung, C. H. Choi, Y. Sugita, and S. Ten-no, J. Chem. Phys., 2007, 127,204102.
[3] K. Sato, H. Chuman, and S. Ten-no, J. Phys. Chem. B, 2005, 109, 17290.
[4] GELLAN, A hierarchical quantum chemistry program, Nagoya univ.
(http://www.gellan.cs.is.nagoya-u.ac.jp/english/index.html)
IN-SM009
Using novel methodology, parallel algorithms and computer simulation to probe biophysical, materials and
chemical systems.
Martyna,Glenn J
IBM TJ Watson Lab
The goal of simulation studies is to provide insight into important ystems of scientific and technical interest. Today, these
systems involve reating accurately complex heterogeneous interfaces. The modeling of these anostructures is reviewed
with application to problems in engineering, physics, and biochemistry. In particular,
studies of perpendicular magnetic
recording, buckytube field effect transistors and the properties of biometic systems are discussed. Opportunities to exploit
the power of IBM's BlueGeneLight series supercomputer are described throughout the presention including parallel
scaling results on BG/L for our ab initio molecular dynamics software package.
IN-SM010
Efficient techniques for non-adiabatic molecular dynamics
Jiri Pittner
J. Heyrovsky Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolejskova 318223 Prague
Molecular dynamics (MD) represents an important tool for modeling of the behavior of molecular systems in time. When
applied to problems from photochemistry, a treatment of excited states and crossings between different potential energy
surfaces has to be incorporated in the MD scheme. The exact calculation of non-adiabatic couplings is computationally
rather expensive and limited to a narrow subset of quantum chemistry methods. We will present efficient techniques
which allow to approximately compute the non-adiabatic couplings from overlaps of CASSCF or MRCI wave functions,
or from TDDFT response functions, as well as first illustrative applications.
IN-SM011
Accurate First Principles Intermolecular Potentials in Modeling of Molecular Crystals
Rafał Podeszwa,1, 2 Betsy M. Rice,3 and Krzysztof Szalewicz2
1
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
2
Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
3
The U.S. Army Research Laboratory,
79 Book of Programme and Abstract for TACC2008 Aberdeen Proving Ground, Maryland 21005, USA Symmetry-adapted perturbation theory (SAPT) based on Kohn-Sham
orbitals and frequencydependent density susceptibilities [SAPT(DFT)] [1, 2] has been shown to provide a similar
accuracy of interaction energies as high-level wave-function-based methods [1, 3] with a greatly reduced computational
cost [2, 4]. The SAPT(DFT) method has been successfully applied to -　interactions [5, 6] and the full potential
energy surface for the benzene dimer [5] has been used in interpreting benzene dimer spectra [7, 8] resolving several
problems. We demonstrate [9] that intermolecular potentials obtained with SAPT(DFT) provides sufficient accuracy
and numerical efficiency for predicting properties of two molecular crystals: cyclotrimethylene trinitramine (RDX) and
benzene. The SAPT(DFT) potential of the RDX dimer [10] was used in simulations of several hypothetical RDX crystal
structures. The results of the simulations showed that the structure corresponding to the experimental crystal lattice has
the lowest energy. For the benzene crystal, the SAPT(DFT)-based potential [5], together with threebody SAPT(DFT)
non-additive corrections [11], yielded the lattice energy accurate to within a few percent of the experimental values,
significantly better than previous attempts in evaluating this property [12] and better than a recent approach that
neglected non-additive effects [13]. The decomposition of the energy shows large importance of the dispersion
interaction in the crystal binding of both systems.
[1] Misquitta, A. J.; Podeszwa, R.; Jeziorski, B.; Szalewicz, K. J. Chem. Phys. 2005, 123, 214103.
[2] Podeszwa, R.; Bukowski, R.; Szalewicz, K. J. Chem. Theory Comput. 2006, 2, 400–412.
[3] Podeszwa, R.; Szalewicz, K. Chem. Phys. Lett. 2005, 412, 488–493.
[4] Bukowski, R.; Podeszwa, R.; Szalewicz, K. Chem. Phys. Lett. 2005, 414, 111–116.
[5] Podeszwa, R.; Bukowski, R.; Szalewicz, K. J. Phys. Chem. A 2006, 110, 10345–10354.
[6] Podeszwa, R.; Szalewicz, K. Phys. Chem. Chem. Phys. 2008, 10, 2735–2746.
[7] Wang, W.; Pitoˇnák, M.; Hobza, P. Chem. Phys. Chem. 2007, 8, 2107–2111.
[8] Erlekam, U.; Frankowski, M.; von Helden, G.; Meijer, G. Phys. Chem. Chem. Phys. 2007, 9, 3786–3789.
[9] Podeszwa, R.; Rice, B. M.; Szalewicz, K. submitted to Phys. Rev. Lett.
[10] Podeszwa, R.; Bukowski, R.; Rice, B. M.; Szalewicz, K. Phys. Chem. Chem. Phys. 2007, 9, 5561–5569.
[11] Podeszwa, R.; Szalewicz, K. J. Chem. Phys. 2007, 126, 194101.
[12] Schweizer, W. B.; Dunitz, J. D. J. Chem. Theory Comput. 2006, 2, 288–291.
[13] Ringer, A. L.; Sherrill, C. D. Chem. Eur. J. 2008, 14, 2542–2547.
IN-SM012
Multimillion-To-Billion Atom Molecular Dynamics Simulations Of Shear Deformation, Fracture And
Nanoindentation In Silica Glass
Rajiv K. Kalia, Aiichiro Nakano, and Priya Vashishta
Collaboratory for Advanced Computing and Simulations
University of Southern California, Los Angeles, CA 90089-0242, USA
Cavitation is a ubiquitous form of damage in the ductile fracture of metallic alloys. However, recent Atomic Force
Microscopy studies of stress corrosion cracking and molecular dynamics (MD) simulations of dynamic fracture reveal
that the key damage mechanism during crack xtension in “brittle” glasses also involves cavitation, albeit at the nanometer
scale. In this talk, I will present results of our multimillion-to-billion atom MD simulations on: (1) nucleation, growth and
coalescence of damage nanocavities in dynamic fracture of amorphous silica (a-SiO2); (2) deformation and breakup
mechanisms for nanovoids in shearing silica glass; and (3) defect migration and recombination in nanoindentation of
a-SiO2.
IN-SM013
80 Book of Programme and Abstract for TACC2008 Novel Empirical Potential Functions and Monte Carlo Sampling Techniques
Jianpeng Ma
Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030.
In protein structure modeling, two major issues are effective potential function and powerful sampling technique.
In this talk, recent results in both directions will be discussed. In terms of potential function, we have developed an
orientation-dependent statistical all-atom potential derived from side-chain packing.
Test of the new potential on decoy
set recognition indicates that it outperforms all the known statistical potential functions in the literature. Applications of
this potential in substantially improving side-chain modeling will also be discussed. In terms of sampling technique, I
will discuss some new results of a novel Monte Carlo sampling technique that performs simulation via direct
computation of partition functions.
Finally, results on using low-frequency normal modes for refining X-ray
crystallographic temperature factors will also be discussed.
IN-SM014
Nonlinear Dynamics and Nonequilibrium Thermodynamics in Mesoscopic chemical Systems
Zhonghuai Hou
Department of Chemical Physics, Hefei National Lab for Physical Science at Microscale
University of Science and Technology of China, Hefei, Anhui, 230026
[email protected]
When driven far from equilibrium, chemical reaction systems may show a variety of nonlinear dynamical behaviors,
including multistability, oscillation, pattern formation, and chaos. Understanding the dynamical mechanisms and
nonequilibrium thermodynamics of these ‘dissipative structures’, named by Prigogine, has been an important topic in
chemical kinetics and nonequilibrium statistical physics ever since 1970s.
Recently, the effects of internal noise, resulting from the stochastic nature of the discrete chemical reaction events and
low number of reactants, in mesoscopic reaction systems such as a biological cell have drawn growing attention. Using
kinetic Monte Carlo simulations and chemical Langevin equations, we have studied the effect of internal noise on
chemical oscillation behaviors, in a parameter region subthreshold to the supercritical Hopf bifurcation[1-4]. Noise
induced oscillation can be observed, the effective signal-to-noise ratio of which undergoes a maximum with the variation
of the internal noise level, demonstrating the occurrence of internal noise coherent resonance (INCR), also known as
known as system size resonance. We have developed a stochastic normal form theory which successfully explains such
simulation results[5-6].
In addition, we have studied fluctuation theorem (FT), which is a very important progress in nonequilibrium
thermodynamics very recently, in such mesoscopic oscillation systems[7]. Specifically, the entropy production along a
stochastic limit cycle has been investigated, which is shown to satisfy FT, and is a function of the system size, oscillation
frequency and oscillation amplitude. In the large system size limit, the entropy production approaches a constant value
when the control parameter stays at the deterministic steady state region, while it increases linearly in the deterministic
oscillatory region. Such results can also be well-understood by the stochastic normal form theory.
1.
Hou Z H, Xin H W. J. Chem. Phys., 2003, 119: 11508-11512
2.
Hou Z H and Xin H W. ChemPhysChem, 2004, 5: 407-410
3.
Gong Y B, Hou Z H, Xin H W. J.Phys.Chem.B, 2004, 108: 17796-17799
4.
Hou Z H, Rao T, Xin H W. J. Chem. Phys. 2005, 122, 134708
Hou Z H, Xiao T J, Xin H W. ChemPhysChem 2006, 7, 1520
6.
Xiao TJ, Ma J, Hou ZH, Xin HW. New. J. Phys. 2007, 9, 403
7.
Xiao TJ, Hou ZH, Xin HW. J. Chem. Phys.2008 (submitted)
IN-SM015
Developing a Reliable Semi-Empirical QM/MD Treatment of Carbohydrates for investigating Multidimensional
Reaction Surfaces
Kevin J. Naidoo and Christopher Barnett
Department of Chemistry, University of Cape Town, Rondebosch, South Africa, 7701
Previously we developed a technique based on hybrid quantum mechanical (QM)/molecular mechanical (MM) methods
that produce reaction surfaces.[1] In this procedure the chemical steps involved in enzyme catalysis include the effect of
the enzyme and its environment. To calculate a multidimensional reaction surface adequate sampling of the reaction
coordinate space in reasonable computational time is necessary. Currently this is possible only via semi-empirical QM
methods which are less accurate than their ab initio counterparts. Two popular methods, AM1 and PM3, have been used
in a large number of studies but they are not accurate enough for describing reactions that involve carbohydrates. A likely
solution is to produce a semi-empirical parameter set at the DFT level of accuracy for either PM3 or SCC-DFTB.
However, a reliable semi-empirical parameter set describing carbohydrate energetics in a chemical reaction must produce
accurate conformational surfaces for the rotational frequency of the primary alcohols and ring puckering of furanose and
pyranose.
Here we present:
the free energy surfaces for the rotational frequency of hydroxymethyl groups of pyranose and furanose.
Newman representations of the hydroxymethyl group rotamers for D-glucose
and the free energy surfaces and dynamics of ring puckering and barrier heights of transition between ring forms for
pyranose and furanose.
Tetrahydropyran ring pucker conformations. C stands for chair, B for boat, S for skew and H for half-chair
The carbohydrate ring puckering behaviour is an especially important test because most carbohydrate substrates in
enzyme reactions pucker out of the low energy chair form when in the transition state.
82 Book of Programme and Abstract for TACC2008 [1] Rajamani, R.; Naidoo, K. J.; Gao, J. J. Comput. Chem 2003, 24, 1775.
IN-SM016
Theory of Non-Markovian Rate Processes
Ji-Hyun Kim, Sangyun Lee and Sangyoub Lee
Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
Starting from a multidimensional reaction kinetic equation with a general time evolution operator and a reaction sink
function K, we derive formally exact expressions for the survival probability, reaction time distribution, and mean
reaction time by using the projection operator technique. These rate expressions are given in the rational function form
with the irreducible memory function
as the key ingredient. This approach has an advantage over the direct
perturbation approaches that use the reaction term as the small parameter, in that
perturbatively treated with
has a structure that can be
as the small parameter. The well-known Wilemski-Fixman type rate expressions are
reproduced as the zeroth-order approximation from the present theory. Practical methods for evaluating the formal rate
expressions are presented, and the results calculated for a model of electron transfer in non-Debye solvents are compared
with computer simulations. It is found that the present approach is very promising for the study of non-Markovian
dispersive kinetics.
IN-SM017
Dynamics and self-assembly of peptides and lipid-like molecules. New paradigm for lipid diffusion
Mikko Karttunen
Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
Web: www.softsimu.org
In this contribution, I will discuss self-assembly in micellar systems [1], and the role of molecular level interactions in
those processes. I will also demonstrate how micellar fission can be controlled and show the existence of a new fission
pathway in charged micelles. These results are based on extensive, 200-400 ns, detailed atomistic molecular dynamics
simulations.
In addition, I will discuss the role of fluctuations and interactions in determining lipid dynamics [2,3] and the binding of
petides on solid surfaces in biomineralization [4]. In the former case, it will be shown that collective motions are one of
the determining factors in lipid diffusion, and in the later, MD simulations are directly linked to experiments and we
show the microscopic mechanism behind the inhibition of the growth of calcium oxalate crystals by osteopontin peptides.
Together, the results from all of these problems demonstrate that computer simulations offer an invaluable tool to study
properties of soft systems without disturbing them, are able to access properties not possible by current experimental
techniques, and allow quantitative comparison with experiments.
[1] Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate,
M. Sammalkorpi, M. Karttunen, M. Haataja, J. Phys. Chem. B 111:11722-11733 (2007).
[2] Lateral diffusion in lipid membranes through collective flows, E. Falck, T. Róg, M. Karttunen, I. Vattulainen, J. Am.
Chem. Soc. 130:44-45 (2008).
[3] Transient Ordered Domains in Pure Phospholipid Bilayers, T. Murtola, T. Róg, E. Falck, M. Karttunen, I. Vattulainen,
Phys. Rev. Lett. 97:238102 (2006).
83 Book of Programme and Abstract for TACC2008 [4] Control of calcium oxalate crystal growth by face-specific adsorption of an osteopontin phosphopeptide, B. Grohe, J.
O'Young, A. Ionescu, G. Lajoie, K.A. Rogers, M. Karttunen, H.A. Goldberg and, G.K. Hunter, J. Am. Chem. Soc.
129:14946-14951 (2007)
IN-SM018
Acceleration of SCF convergence in ab initio direct molecular dynamics Simulations
Hiromi Nakai
Department of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
Ab initio direct molecular dynamics (AIMD) simulations have been performed widely for studying dynamical process of
chemical reactions, since ab initio molecular orbital (MO) or density functional theory (DFT) calculations performed
‘on-the-fly’
ensure reliable potential energy and atomic forces, even in the bond breaking region. In constant to this
advantage, MO/DFT calculations require expensive computational costs. As a result, system sizes and/or time scales
treated by AIMD simulations are very limited in comparison with the use of the classical MD. This paper presents a
novel technique to accelerate the self-consistent-field (SCF) convergence in the AIMD simulations, which adopts the
Lagrange interpolation (LI) polynomial technique and predicts initial MO coefficients at the next AIMD step by using
several previous results. Numerical tests confirm that this technique, called LIMO, is both effective and feasible.
[1] T. Atsumi, H. Nakai, J. Chem. Phys., 2008, 128, 094101
OR-SM019
Molecular theory of slip boundary conditions in nanofluidics
Alexander E. Kobryn1 and Andriy Kovalenko1,2
1
National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
2
Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
We propose the first-ever derivation and calculation of the hydrodynamic slip length from the first principles of statistical
mechanics, based on a combination of linear response theory and equilibrium molecular theory of solvation. The slip
length derived is related to the fluid organization near the solid surface, as governed by the solid-liquid interaction, and is
84 Book of Programme and Abstract for TACC2008 expressed in terms of the Green-Kubo-Nakano relations as a function of the anisotropic inhomogeneous time correlation
function of density fluctuations of the liquid in contact with the surface. The time dependence of the correlation function
is factored out by treating it in the hydrodynamic limit. The spatially inhomogeneous two-body correlation function is
represented in the Kirkwood-like approximation as a product of the three-dimensional density distributions of interaction
sites of the liquid near the surface and the site-site pair correlations of the bulk liquid. The presented treatment
generalizes the phenomenological definition of the friction coefficient (as well as the slip length) to a tensor quantity,
which reflects an anisotropic nature of an ordered crystalline or nanopatterned surface. This enables theoretical prediction
of friction forces acting aslant to the liquid flow direction for such surfaces. We derive generic analytical expressions for
the liquid-surface friction coefficient (and slip length) for an arbitrary surface-liquid interaction potential. We further
illustrate it by numerical calculations for a laminar flow of nine different molecular liquids at ambient conditions in
contact with the (100) FCC surface of gold, copper and nickel modeled by using OPLS models for liquids and the Steele
potential for crystalline surfaces. The obtained values for slip length range from few to hundreds of nanometers and
microns and are consistent with experimental measurements.
OR-SM020
Multiple Scale Modeling of Supramolecular Architectures in Solution by 3D molecular theory of salvation
Takeshi Yamazaki†, Hicham Fenniri†,‡, and Andriy Kovalenko†,‡
† National Institute for Nanotechnology and
‡ University of Alberta, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
In this presentation, we will investigate the thermodynamic stability and microscopic solvation structure of organic
nanotubular supramolecules in solution by using the three-dimensional molecular theory of solvation (a.k.a.3D-RISM
theory). The 3D-RISM theory is based on the statistical mechanics of molecular liquids. Starting from the atomistic
solute-solvent molecular interactions, it yields the 3D density distribution of solvent around the solute macromolecule as
well as its solvation thermodynamics, including the free energy of solvation, entropy-enthalpy decomposition, and partial
molar volume, with less computational time compared to molecular simulations. The organic nanotube we study is called
Rosette nanotube (RNT). The RNTs are a new class of organic materials assembled from a single bicyclic block featuring
the complementary hydrogen bonding arrays of both guanine and cytosine, the G^C motif. This building block
self-assembles spontaneously in solvent to form a six-membered supermacrocycle (rosette) maintained by 18 H-bonds,
which then stack up to form a nanotube with a hollow core ~1 nm across and up to several millimeters long. We will
analyze and discuss the role of solvent on self-assembly of RNT. Additionally, we will apply the 3D-RISM theory to the
association of some biomolecules. Our theory shows the solvent effect is a major driving force of these associations.
[1] A. Kovalenko, In Molecular theory of solvation, ed. F. Hirata, Kluwer Academic Publishers, Doerdrecht, 2003, pp.
169-275.
[2] J. G. Moralez, J. Raez, T. Yamazaki, R. K. Motkuri, A. Kovalenko, H. Fenniri, J. Am. Chem. Soc. 2005, 127, 8307.
[3] R. S. Johnson, T. Yamazaki, A. Kovalenko, H. Fenniri, J. Am. Chem. Soc. 2007, 129, 5735.
IN-SM021
COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics
Andreas Klamt
COSMOlogic GbH&CoKG, Burscheider Str. 515, 51381, Leverkusen, Germany, And Inst. of
Phys. and Theor.
Chemistry, University of Regensburg, German
85 Book of Programme and Abstract for TACC2008 Due to the rapid developments of methods and computers, reliable quantum chemical calculations on molecules of up to
50 - 100 atoms can nowadays be done within days on cheap computer hardware. Thus quantum chemistry, and here
especially the density functional theory (DFT), has become an efficient source of molecular information. But the
traditional quantum chemistry is restricted to the calculation of single molecules in vacuum or to small clusters. Hence it
cannot be directly used for the calculation of properties of molecules in liquids or even for fluid phase equilibrium
properties. Therefore, dielectric continuum solvation methods as PCM or COSMO have become quite popular. In this
talk I will specially focus on the extension of COSMO by a combination with statistical thermodynamics, COSMO-RS.
This provides an efficient link between quantum chemistry and fluid phase thermodynamics. COSMO-RS starts from
quantum chemical DFT/COSMO calculations for solutes and solvent molecules, in which each molecule is treated as if
embedded in a conductor. This state of ideal electrostatic screening is used as reference point for the consideration of
molecules in the liquid phase. All interactions are quantified by the screening charge densities on the adjacent surface
pieces. Combined with an extremely efficient and nevertheless exact statistical thermodynamics algorithm of pair-wise
interacting surfaces, this description of molecular interactions in solution enables the calculation of the chemical
potentials of almost arbitrary solutes in almost arbitrary solvents, even in mixtures. Finally this enables the calculation of
phase diagrams of liquid systems, i.e. of activity coefficients, vapor pressures, excess free energies and enthalpies.
COSMO-RS also works for charged species, i.e. to electrolyte systems, pKa-calculation, and even to complex systems
as ionic liquids, micelles and bio-membranes.
IN-SM022
On simple semi-classical tools to improve the capability of
classical mechanics to describe molecular scattering
processes
J.C. Rayez, L. Bonnet and P. Larregaray
Institut des Sciences Moléculaires – UMR 5255/CNRS Université Bordeaux 1 – 33405 TALENCE Cedex (France)
The quantum mechanical description of molecular scattering processes is exact, but mainly limited in practice to
three-atom systems. On the other hand, the quasi-classical trajectory (QCT) method is approximate, but allows the study
of large molecular systems which are more and more studied experimentally today. There is therefore a lot of effort in the
theoretical chemist community to include key quantum mechanical ingredients in the classical treatment of molecular
collisions, or the reverse (1).
The goal of the talk is to present several promising semi-classical tools developed in our group. The first one concerns
the Gaussian Weighting (GW) method (2-4) which might replace with profit the standard binning method to determine
final state distributions. The second is related to an adiabatic correction (5), which improves the efficiency of the GW
method. It consists in removing some vibrationally adiabatic non reactive trajectories in the calculations of final attributes,
according to a given criterion. The third is the parity-restoring approximation (6,7) which is necessary to get correct
sharp forward/backward peaks in differential cross sections from classical calculations on atom-diatom insertion
reactions. The use of these tools is illustrated by the study of some unimolecular dissociations and complex-forming
bimolecular reactions.
1 – W. H. Miller – J. Chem. Phys. 125, (2006) 132305
2 – L. Bonnet and J.-C. Rayez – Chem. Phys. Lett. 397 (2004) 106
3 – M. L. Gonzalez-Martinez, L. Bonnet, P. Larregaray and J.-C. Rayez – J. Chem. Phys. 126 (2007) 041102
4 – L. Banares, F. J. Aoiz, P. Honvault, B. Bussery-Honvault and J.-M. Launay – J. Chem. Phys. 118 (2003) 565
5 – L. Bonnet – J. Chem. Phys. 128 (2008) 044109
86 Book of Programme and Abstract for TACC2008 6 – L. Bonnet, P. Larregaray, J.-C. Rayez and T. Gonzalez-Lezana – Physical Chemistry Chemical Physics 8 (2006)
3951
7 – L. Bonnet, P. Larregaray and J.-C. Rayez – Physical Chemistry Chemical Physics 9 (2007) Advanced article
IN-SM023
Exact reduced density matrix dynamics and the application to electron transfer reactions
Rui-Xue Xu
Hefei National Laboratory for Physical Sciences at Microscale
University of Science and Technology of China
Exact quantum dissipation equations of motion are constructed via the calculus on path integrals with canonical bath.
Hierarchical linear coupled equations are obtained with the bath correlation functions in parametrization expansion forms.
The equations of the corresponding recursive Green’s functions are also constructed, which, for the time-independent
system Hamiltonian, can be resolved in the Laplace domain via the continuedfraction expression. Based on the
continued-fraction formulation, analytic rate expressions are derived for the two-state electron transfer reactions in the
Debye solvent model without any further approximation. Three fundamental issues relating to the electron transfer
processes are studied: the quantum solvation effect and the adiabatic versus nonadiabatic and Markovian versus
non-Markovian characterizations.
[1] Xu RX, Cui P, Li XQ, etc, J. Chem. Phys., 2005, 122, 041103
[2] Han P, Xu RX, etc, J. Phys. Chem. B, 2006, 110, 11438
[3] Xu RX, Yan YJ, Phys. Rev. E, 2007, 75, 031107
[4] Xu RX, Chen Y, etc, J. Phys. Chem. A, 2007, 111, 9618
OR-SM024
The Quantum Field Theory of Molecular Ensembles
Richard N. Porter
Department of Chemistry, State University of New York, Stony Brook, New York, USA 11794-3400
[email protected]
Quantum field theory (QFT) provides a systematic investigative tool for ensembles of molecules. The grand-canonical
ensemble operator (GCEO) for an ideal gas is presented in terms of the Fock creation and annihilation operators. The
ideal GCEO is shown to obey a simple equation which facilitates calculation of quantum-statistical properties of bosonic
and fermionic molecules. Examples are linked-cluster QFT derivations of the grand-canonical partition function and the
Poisson distribution of non-interacting particles. The Boltzmann limit is achieved by omitting exchange diagrams.
Green-function assisted summations ofFeynman diagrams for long-and short-range interactions to infinite order lead to a
useful model of the paircorrelation function for an ensemble of interacting molecules and a new avenue for the study of
dynamics near the critical point for gas-liquid phase transitions.
IN-SM025
Developing ABEEM fluctuating charge force field for proteins
Zhong-Zhi Yang
Department of Chemistry, Liaoning Normal University, Dalian 116029, China
87 Book of Programme and Abstract for TACC2008 E-mail: [email protected]
Based on atom-bond electronegativity equalization method (ABEEM), the ABEEM/MM fluctuating charge force field
for proteins has been proposed. The Lennard-Jones and torsional parameters were optimized to be consistent with the
ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic
fitting function. Molecular dipole moments, dimerization energies and hydrogen bond lengths of complexes are
reasonably achieved by our model, as compared to experimental and/or ab initio results. The ABEEM/MM fluctuating
charge force field reproduces both the peptide conformational energies and structures with satisfactory accuracy.
Transferability of the parameters is tested through applying them to studies of more peptides and a few proteins. The
overall RMS deviations in conformational energies and key dihedral angles are acceptable. The current results agree well
with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results
make us believe that ABEEM fluctuating charge force field can obtain more promising results in protein and
macromolecular modeling with good accuracy but less computer cost.
This research is supported by the grand of NSFC (No. 20633050).
1. Z.Z. Yang, Y. Wu, D..X. Zhao, Atom-bond electronegativity equalization method fused into molecular mechanics. J.
Chem. Phys., 2004, 120: 2541-2557.
2. Y. Wu, Z.Z. Yang, Atom-bond electronegativity equalization method fused into molecular mechanics. II.
J. Phys. Chem. A 2004, 108: 7563-7576.
3. Z.Z. Yang, Q. Zhang, Study of peptide conformation in terms of the ABEEM/MM method. J. Comput. Chem., 2006,
27(1): 1-10.
IN-SM026
Dynamics of single-file water chains inside nanoscale channels: physics, biological significance and applications
Haiping Fang
Shanghai Institute of Applied Physics, Chinese Academic of Sciences, Shanghai, 201800, China
Transportation of water across nanochannels is of great importance for biological activities as well as designing novel
molecular devices/machines/sensors, which has wide applications in nanotechnology. With the development of the
experimental and computational facilities and technologies, it becomes possible to study the water dynamics inside and
across the nanoscale channels by both experiments and numerical simulations. When the radius of a nanochannel is
appropriate, the water molecules inside the channel form single-file structure. In this talk, we present our recent progress
on the understanding of the dynamics of water confined in those nanoscale channels and its applications. It is found that
the water permeation across the channel has an excellent on-off gating behavior. The water conduction across the water
channel keeps almost fixed for a considerable deformation and/or a very small distance of the external charge from the
channel. The channel closes rapidly when the deformation exceeds and/or the distance of the external charge from the
channel is less than a threshold. We also find that the nanopore exhibits unidirectional transportation of the water
molecules when there is a combination of charges positioned adjacent to a nanopore, mimicked from the charge structure
in biological water channels, Aquaporins. The confinement of the water inside the nanopore is very important for the
pumping efficiency.
1.
Rongzheng Wan, Jingyuan Li, Hangjun Lu, Haiping Fang*, Controllable water channel gating of nanometer
dimensions， J. Am. Chem. Soc. 127, 7166 (2005)
2.
Jingyuan Li, Xiaojing Gong, Hangjun Lu, Ding Li, Haiping Fang*, and Ruhong Zhou, Electrostatic Gating of a
Nanometer Water Channel, Proc. Natl. Acad. Sci. USA 104，3687 (2007）
Xiaojing Gong, Jingyuan Li, Hangjun Lu, Rongzheng Wan, Jichen Li, Jun Hu, and Haiping Fang*, A charge driven
molecular water pump, Nature Nanotechnology 2, 709-712 (2007)
4.
Haiping Fang*, Rongzheng Wan, Xiaojing Gong, Hangjun Lu, and Songyan Li, Dynamics of single-file water
chains inside nanoscale channels: physics and biological significance and applications, J. Phys D. (Topical Review), 41,
103002 (2008)
IN-SM027
Simulating self-organization in Biomolecular systems
Alan E. Mark
School of Molecular and Microbial Sciences (SMMS) and Institute for Molecular Biosciences (IMB), University of
Queensland, Brisbane, QLD 4072, Australia.
Computer simulations of proteins, lipids and nucleic acids at equilibrium have become essentially routine.
The
challenge for the future is to use such approaches to understand spontaneous self-organization in biomolecular systems
(folding, aggregation and self-assembly of complexes), processes that cannot be directly observed experimentally.
While it is not yet possible to fold complete proteins using atomic models, dramatic process has been made regarding the
folding and aggregation of peptides,1 the spontaneous self-organization of phospholipids into bilayers and vesicles,2 and
the assembly of peptides and proteins at interfaces in to functional complexes. For example, the ability to model the
spontaneous interaction of peptides with membranes is shedding new light on the mechanism by which antimicrobial
peptides induce the formation of transmebrane pores.3 A range of examples illustrating the extent to which simulations
can be used to understand cooperative phenomena in biomolecular systems will be presented along with examples of
where the methodology must still be developed further.
[1] Periole, X., Vendruscolo, M, and Mark, A. E. Molecular dynamics simulations from putative transition states of
alpha-spectrin SH3 domain.Proteins, Structure, Function, and Bioinformatics, 2007 69, 550.
[2] Marrink, S. J. and Mark, A. E. Molecular dynamics simulation of the formation, structure, and dynamics of small
phospholipid vesicles. J. Am. Chem. Soc. 2003 125, 15242.
[3] Leontiadou, H., Mark, A .E. and Marrink, S.J. Antimicrobial peptides in action. J. Am. Chem. Soc. 2006, 128, 12161.
IN-SM028
Optical Properties of Molecular Aggregates and Conjugated Polymers from First Principles
Vladimir I. Gavrilenko
Norfolk State University, Center for Materials Research, Norfolk VA, USA
Two basic approaches of computational chemistry and physics for first principles studies of optics are compared: the time
dependent Density Functional Theory (DFT), the TDDFT of molecules and clusters, and the abinitio pseudopotentials
theory within a standard DFT (PP-DFT). Effects of intermolecular and inter-chain interaction in optical absorption of dye
organic molecules (Rhodamine 6G, Rh6G), and polymers (poly- (3- methoxythiophene)
(PMT), poly(thienylene
vinylene) (PTV)) are studied. Ground states and equilibrium geometries are determined by the total energy minimization
method. Combination of TDDFT cluster method with PP-DFT approach for infinite chain provides the single-gap
quasiparticle corrections values which are used for realistic prediction of optical absorption by the PP-DFT. For
molecular aggregates our theory predicted substantial red- or blue- shifts of the optical absorption spectra of Rh6G dye
molecules after aggregation in J- or H- dimers, respectively. Predicted dominant optical absorption peak splitting in
Rh6G is interpreted in terms of the inter-molecular interaction. Effects of interchain interaction in optical absorption of
conjugated polymers are calculated theoretically and confirmed by experiment. New geometry phases of conjugated
89 Book of Programme and Abstract for TACC2008 polymers with different interchain distances are predicted. By comparative analysis of experimental and theoretical data,
it is demonstrated that the predicted modifications of the dominant long-wavelength optical absorption peak in
conjugated polymers
(determined by the excitations of delocalized π-electrons) are consistent with the increased
interchain interaction in new phases. This interaction caused additional electronic energy structure transformations and
relevant modifications of optical absorption. The results of this work are discussed in comparison with experimental and
theoretical data available in literature.
IN-SM029
Adaptive Resolution Molecular Dynamics Simulation
Matej Praprotnik , Luigi Delle Site, Kurt Kremer
Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
The Adaptive Resolution Scheme (AdResS)[1] for efficient hybrid atomistic/mesoscale molecular dynamics (MD)
simulations is presented.
The key feature of this particle-based method is that it allows for a dynamical change of
molecular resolution by changing the number of molecular degrees of freedom on-the-fly during the course of an MD
simulation. In this way an all-atom molecular system is maintained at thermodynamical equilibrium with a far simpler
coarse-grained system. Our approach, which concurrently couples the atomic and mesoscopic length scales of the system,
leads to a concept of a geometry induced phase transition and a generalization of the equipartition theorem to fractional
degrees of freedom. So far, we have applied AdResS to molecular liquids. The system is modeled in different domains
at different levels of detail while the liquid molecules move freely between the regions. Examples area simple liquid of
tetrahedral molecules, liquid water, and a generic
solvated macromolecule[2].
[1] M. Praprotnik, L. Delle Site, K. Kremer, J. Chem. Phys. 2005, 123, 224106.
[2] M. Praprotnik, L. Delle Site, K. Kremer, Annu. Rev. Phys. Chem. 2008, 59, 545.
OR-SM030
Simulation of large-scale excited electron dynamics
Julius Su and William A. Goddard III
California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125
To study electron dynamics in large-scale highly excited systems, we have developed eFF, a molecular dynamics model
which includes electrons. In eFF, electrons are represented by Gaussian wave packets whose size and position vary with
time, and the nuclei are represented by point charges. The particles interact via an effective potential which is so simple
that forces acting between thousands of nuclei and electrons can be computed in less than a second on a modern
processor. Using eFF, we explore the thermodynamics of warm dense hydrogen [1], and find excellent agreement with
path integral methods and diamond anvil and shock compression experiments over a temperature range of 0 to 100,000 K
and densities up to 1g/cm3. We also simulate the Auger process (Figure 1) in a diamond nanoparticle (C196H112), and
discover direct and indirect pathways for the desorption of atomic fragments from the surface, in agreement with recent
experiments.
90 Book of Programme and Abstract for TACC2008 Figure 1. Auger process in adamantane. After a core electron is ionized from a tertiary carbon at time zero, a valence
electron fills the core, another valence electron is ejected, and the molecule fragments over tens of femtoseconds.
[1] J. T. Su and W. A. Goddard III, Phys. Rev. Lett. 2007, 99, 185003.
IN-SM031
Study on Non-primitive Mean Spherical Approximation (MSA) to Real Aqueous Electrolyte Solutions
Yi-Gui Li
Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
Based on statistical mechanics, a review of recent theoretical studies on electrolyte models is presented from two
categories: primitive and non-primitive, depending on whether the solvent water molecules are treated as interacting
particles. Among all the electrolyte models, only the Blum-Wei’s non-primitive mean spherical approximation (MSA)
can use the vacuum dielectric costant in its long range electrostatic term. All the other models, the solvent (water)
dielectric constant has to be used whether the water molecules are treated as interacting particles or not. So the
systematical study on non-primitive MSA is summarized. It was shown that the solution from the integral equation
theory (O-Z equation) with ion-ion, ion-dipole and dipole-dipole interactions can reflect the exact microscopic structures
and interactions involved in the ion-dipole mixtures. In the manuscript, the original Blum-Wei’s non-primitive MSA has
been incorporated with the hydrogen bond association term from statistical association fluid theory (SAFT), in which
only the diameters of cation and anion are treated as two adjustable parameters for each electrolyte. The water molecular
parameters can be obtained with an EOS derived also from the combined MSA(dipole) and SAFT(hydrogen bond
association). The mean activity coefficients of 46 single 1:1 electrolytes in aqueous solutions are successfully correlated
and predicted. In addition, the simplified restrictive non-primitive MSA model with equal sizes of cation and anion, with
equal sizes of cation, anion and dipole, and incorporated with the sticky interaction theory have also been tested to real
electrolyte solutions and compared their accuracies with experimental data. We expand Blum-Wei’s MSA as a Taylor
series in the low ionic density region to the third order to obtain an explicit solution by use of Wertheim dielectric
constant theory and compared with the Henderson-Blum-Tani non-primitive electrolyte perturbation theory to show why
the vacuum dielectric constant cannot be used in the long range electrostatic term in some successful EOSs for real
systems, although the dipolar solvent is treated as explicit molecule in these theory. The limitations of the uses for the
non-primitive MSA are also discussed. All the studies show that the non-primitive MSA approach solved from integral
equation theory is of significance both in theoretical research and practical use.
OR-SM032
Molecular Dynamics Simulation on the Structural and Thermodynamic Properties of DNA-Electrolyte Solutions*
Yang-Xin Yu** and Shintaro Fujimoto
Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
91 Book of Programme and Abstract for TACC2008 Deoxyribonucleic acid (DNA) is a well-known substance as a carrier of genetic information. In the living cell, the
phosphate groups on the surface of DNA molecule dissociate and bear negative charges, which make it a typical
polyelectrolyte. The experimental studies of DNA electrolyte solution can be traced back to the classical dialysis
equilibrium method. The membrane equilibrium experiments reveal the thermodynamic properties such as membrane
equilibrium parameter and osmotic pressure, and leave no knowledge of microscopic structure of mobile ions. Molecular
simulations are potential way to investigate the structural and thermodynamic properties of DNA solution.
We studied comprehensive comparative analyses of monovalent counterions condensation around DNA and macroscopic
influence of the counterions. To gain new insight into contribution of monovalent counterion on the whole DNA
molecule, we performed NPT molecular dynamics (MD) simulations on A-DNA and B-DNA in 1:1 electrolyte solutions.
The initial DNA configuration for all simulations was built using a program called “nucgen” in AMBER8. We built an
ideal DNA oligomer model and conducted simulations in explicit water using the AMBER8 and the Amber Parm99 force
field. To address a specific property of the interactions between DNA and monovalent cations, MD simulations with
different salt concentration at each of systems (NaCl, KCl, LiCl, Rb/Cl and Cs/Cl), and at each of additional NaCl
systems with temperature ranging from 283 to 333 K were conducted.
The MD trajectory was analyzed in detail for conformational properties of DNA-counterion systems, such as counterion
distribution around DNA. We started simulation from A-DNA, but the conformation changes to B-DNA after 1ns,
resulting in consistent internal energy, radial distribution functions (RDFs) and density with that started from B-DNA.
This indicates that A-DNA changes to B-DNA in 1:1 electrolyte solutions within 1ns. The simulated results show that the
configuration changes more rapidly in the case of a larger conuterion.
* This work is supported by the National Natural Science Foundation of China (No. 20676065 and No.20736003).
**Corresponding author. E-mail: [email protected]
OR-SM033
Dissipative Particle Dynamics Simulations of Shapes Transformations of Membrane Vesicles from Amphiphilic
Triblock Copolymers
Xuejin Li1, Igor V. Pivkin2, Haojun Liang1,* and George Em Karniadakis2, *
1
Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026,
P. R. China
2
Divison of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
Shapes transformations of vesicles of amphiphilic triblock copolymers are studied by dissipative particle dynamics (DPD)
approach. We observe that even using a relatively simple DPD model for amphiphilic block copolymers, many
characteristics of amphiphiles in dilute solution can be elucidated, like their self assembly into bilayer and spontaneously
form vesicle, and the deformations of such vesicle as well as the distinct vesicle shapes. A variety of complex vesicle
shapes, including some novel ones, such as starfish-shaped, budded and inversed vesicles are observed from the
simulations. The shapes transformations of vesicles obtained from our simulations are in qualitative agreement with
experimental results as well as theoretical predictions. These findings are very interesting and these complex vesicle
shapes confirm that DPD simulation is an effective simulation technique for understanding the properties of amphiphilic
copolymers.
* To whom correspondence should be addressed.
E-mail: [email protected] (H. J. Liang), [email protected] (G. E. Karniadakis).
92 Book of Programme and Abstract for TACC2008 IN-SM034
Probing Dynamics and Impedance of Inhomogeneous Electrolytes
with Alternating-Current Non-Eequilibrium Molecular Dynamics (AC-NEMD) Simulations
Kwong-Yu CHAN and Qingyin ZHANG
Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong.
The alternating current non-equilibrium molecular dynamics (AC-NEMD) simulation technique is applied to several
cases of inhomogeneous electrolytes [1-3]. A sinusoidal external electric field is applied during the molecular dynamics
simulation of an electrolyte, the ionic current response varies in magnitude and phase shift depending on the frequency
and magnitude applied. The frequency dependent current response reveals the relaxation dynamics of the electrolyte. The
electrolytes studied include aqueous electrolyte confined in a cylindrical nanopore with a smooth wall [1,2] and
yttria-stabilized zirconia (YSZ) [3]. The aqueous electrolyte was modeled by both a primitive model and a solvent
primitive model. The YSZ electrolyte was modeled by a Born-Meyer-Buckingham (BMB) model. While the two cases
are very different in geometry and molecular details, both show similar features in the AC-NEMD current response with
a maximum conductivity at an optimum frequency and resistance-capacitance-inductance (RLC) circuit behavior. For
ions confined in a cylindrical channel, the capacitance behavior can be explained by confinement effect and single-file
motion of ions. On the other hand, the barriers along the passage between oxygen vacancy sites in YSZ may provide a
similar effect of “confinement”. In the AC-NEMD, the generated ohmic heat is effectively removed, and a constant
temperature is maintained by either an Anderson thermostat or a Nose-Hoover thermostat.
[1] Y.W. Tang, T. Szalai, and K.-Y. Chan, Molec. Phys., 100 2002, 100, 1497-1505.
[2] Y.W. Tang, K.-Y. Chan, and I. Szalai, Nano Letters, 2003, 3(2), 217-221.
[3] Q. Zhang and K.Y. Chan,
J. Phys. Chem. C
2007, 11, 15832-15838
OR-SM035
Progress towards quantitative molecular modelling: development of new generation force fields.
Jean-Philip Piquemal
Laboratoire de Chimie Théorique, Université Pierre et Marie Curie, UMR 7616 CNRS,
CC 137, 4 Place Jussieu, 75252 Paris Cedex 05, France.
[email protected]
In this talk, we will discuss the methodologies presently available to evaluate many-body interactions in biological
systems. We will present a new energy decomposition scheme based on localized orbitals1 as well as and extension of
the topological analysis of the Electron Localization Function (ELF) to the computation of chemically intuitive
distributed electrostatic moments.2 Implications for the design of accurate next generation polarisable force fields will be
discussed.3
References
1) P. Reinhardt, J-P Piquemal and A. Savin, 2008, submitted.
2) J. Pilmé and J-P Piquemal, J. Comput. Chem., 2008, 29, 1440.
3) a) J-P. Piquemal, G. A. Cisneros, P. Reinhardt, N. Gresh and T. A. Darden, J. Chem. Phys., 2006, 124, 104101; b) N.
Gresh, G. A. Cisneros, T. A. Darden and J-P Piquemal, J. Chem. Theory. Comput., 2007, 3, 1960IN-BIO001
OR-SM036
93 Book of Programme and Abstract for TACC2008 Multiple free energies from a single simulation:
Extending enveloping distribution sampling to non-overlapping phase-space distributions
Clara D. Christ, Wilfred F. van Gunsteren
Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
A recently proposed method to obtain free energy differences for multiple end states from a single simulation of a
reference state which was called enveloping distribution sampling (EDS) is expanded to situations where the end-state
configuration space densities do not show overlap. It uses a reference state Hamiltonian suggested by Han in 1992 in a
molecular dynamics implementation. The method allows to calculate multiple free energy differences “on the fly” from a
single molecular dynamics simulation of the reference state. No computer time has to be spent on the simulation of
intermediate states. Furthermore, the interactions of the unperturbed degrees of freedom i.e. the vast majority of all
interactions have to be calculated only once (per simulation step) for all end states. The reference state Hamiltonian
comprises only few parameters, whose influence on the accuracy and precision of the obtained free energy differences is
investigated. A connection is established between the presented method and the Bennett acceptance ratio method and a
simple algorithm for iterative parameter update is suggested. The method is applied to four two-state test systems (dipole
inversion, van der Waals perturbation, charge inversion and water to methanol conversion) and two multiple-state test
systems (dipole inversion with five charging states, five (dis-)appearing water molecules). Accurate results could be
obtained for all test applications if the parameters of the reference state Hamiltonian were optimized according to a given
algorithm. The deviations from the exact result or from an independent calculation were at most 0.6 kJ/mol. Ongoing
work is focusing on biologically relevant applications such as ligand binding affinity estimation.
[1] K. K. Han, Phys. Lett. A 165, 28 (1992).
[2] C. D. Christ and W. F. van Gunsteren, J. Chem. Phys. 126, 184110 (2007).
[3] C. D. Christ and W. F. van Gunsteren, J. Chem. Phys. 128, 174112 (2008).
IN-SM037
Molecular Simulation of Solubility and Diffusion of Water in Polymer Electrolyte Membranes
Xiaofeng Li, Yue Shi, Qing Chen, Feng, Li, Huai Sun　School of Chemistry and Chemical Technology, Shanghai Jiao Tong University, Shanghai 200240, China
The proton conductivity and the mechanical property of the polymer electrolyte membranes (PEMs) depend heavily on
the equilibrium water content of the polymer systems. Molecular simulation method was used to investigate the
equilibrium solubility and diffusion of water in hydrated Nafion-117 and sulfonated polyarylenethioether sulfone
polymer (SPTES). The simulations were based on the ab initio TEAM force field that was derived based on quantum
mechanics data and optimzied using liquid density and heat of vaporization of model compounds. A combination of the
thermodynamic-integration approach and Widom's particle-insertion method was carried out to determine the excess
chemical potential of water in the PEMs and to estimate of the water-uptake behavior. The dynamics of water molecules
and hydronium ions in PEMs were investigated using molecular dynamics simulations. By comapring the results between
the above mentioned polymers, we hoped to shet lights on the designs of new PEM materials.
Keywords: PEM; Molecular Simulation; Force Field; Solubility; Diffusion
Bioformatics and Biochemistry IN-BIO001
Combined QM/MM studies of enzymatic reactions
Gao, Jiali
IN-BIO002
Stacking interactions in DNA from the combined density functional theory
and symmetry-adapted perturbation theory approach
Georg Jansen
Department of Chemistry, University Duisburg-Essen, Universitatsstr. 5, 45117 Essen, Germany
In the DFT-SAPT method, designed for the accurate calculation of intermolecular interaction energies, density functional
theory is employed to prepare molecular properties such as electron densities and density response functions which then
are used in the framework of symmetry-adapted perturbation theory to determine the interaction energy of two molecules
as a sum of electrostatic, induction and dispersion energies and corresponding exchange corrections [1,2]. Employing a
density-fitting implementation [3] dimers with sixty or more atoms may be studied in extended basis sets. The talk will
first present applications of DFT-SAPT to the study of CH-pi [4] and CH-lone pair [5] interactions, showing that the
results compare very well with those of coupled-cluster calculations including up to non-iterative triple excitations and
with experimental data. Then the talk will concentrate on pi-pi interactions such as the stacking interactions between two
DNA base pairs [6] and discuss the geometry dependence of the total interaction energy and its individual contributions.
[1] G. Jansen, A. HeSelmann, J. Phys. Chem. A 2001, 105, 11156.
[2] A. HeSelmann, G. Jansen, Phys. Chem. Chem. Phys. 2003, 5, 5010.
[3] A. HeSelmann, G. Jansen, M. Schütz, J. Phys. Chem. 2005, 122, 014103.
[4] A. Tekin, G. Jansen, Phys. Chem. Chem. Phys. 2007, 9, 1680.
[5] E. Sanchez-Garcia, A. Mardyukov, A. Tekin, R. Crespo-Otero, L. A. Montero, W. Sander, G. Jansen, Chem. Phys.
2008, 242, 168.
[6] A. Fiethen, G. Jansen, A. HeSelmann, M. Schütz, J. Am. Chem. Soc. 2008, 130, 1802.
IN-BIO003
Bioinorganic Models for Dinuclear Copper Proteins: Aliphatic and Aromatic Hydroxylation from a Quantum
Chemical Point of View
Max C. Holthausen
Institute of Inorganic Chemistry, Goethe-University Frankfurt,
Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
Bioinorganic research has impressively demonstrated that small synthetic complexes containing a [Cu2O2] core can
mediate the selective hydroxyl¬ation of aliphatic and aromatic C-H bonds, mimicking the function of metallo-enzymes
like tyrosinase or DβH [1]. We provide detailed mechanistic views on these oxygenation reactions based on DFT studies:
(a) Aliphatic hydroxylation in Itoh’s system involves C-H bond activation in a nonsynchronous concerted rate-limiting
step [2]. A general mechanistic scenario is developed to explain the reactivity of several related systems.
95 Book of Programme and Abstract for TACC2008 (b) Aromatic hydroxylation in Holland’s system involves a rate-limiting electrophilic attack of the aromatic system and
a prominent two-state reactivity. We propose a dienone species as key intermediate occuring en route to product
formation. Comparison is made to the analogous reaction studied recently in a related copper bis(imine) system [3].
[1] (a) Itoh et al. Angew. Chem. Int. Ed. 2000, 39, 398; (b) Holland et al. Angew. Chem. Int. Ed. 1999, 38, 1139.
[2] Spuhler, Holthausen, Angew. Chem. 2003, 115, 6143.
[3] Sander, Henß, Näther, Würtele, Holthausen, Schindler, Tuczek, Chem. Eur. J., submitted.
IN-BIO004
Hybrid ab initio Valence Bond / Molecular Mechanics (VB/MM), A New Method for Calculating Biochemical
Systems
Avital Sharir-Ivry, Hadar Crown, Avital Shurki*
N
O
N
Cu
N
N
N
N
Cu
O
N
OH
N
N
O
Cu
OH
Cu
O
N
N
N
(a)
(b)
Department of Medicinal Chemistry and Natural Product, School of Pharmacy,
The Lise Meitner-Minerva Center for Computational Quantum Chemistry
The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
The growing demand for realistic methods that would calculate chemical reactions in biological systems resulted with the
development of hybrid quantum mechanical (QM) molecular mechanical (MM) schemes. Recent years have proven
schemes that are based on concepts from valence bond (VB) methodology, to be beneficial for the description of enzyme
catalysis and reactivity. The development of a new hybrid (QM/MM) method where the QM part is treated by ab-initio
Valence Bond (VB) theory will be presented[1]. This VB/MM method utilizes various approximations that will be
explained. Furthermore, examination of these approximations which was based on a recent extension of the method
justifies their use[2].
This VB/MM method has the advantages of Empirical VB (EVB) methodology but should provide better accuracy.
Furthermore, the method does not rely on empirical parameterization for the quantum part. The validity of the method
will be shown to be successful in several examples.
IN-BIO005
Noncovalent Interactions in Extended Systems
C. David Sherrill . Ashley L. Ringer, and Anastasia Senenko
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
Noncovalent interactions have a wide impact on molecular science, including drug binding, biomolecular structure,
supramolecular assembly, and the structures of organic crystals. On the basis of very high accuracy quantum mechanical
computations, the fundamental features of prototype noncovalent interactions have been quantified, yielding new insights.
Now the influence of noncovalent interactions on extended systems is being explored. Potential energy surfaces for the
H2S-benzene prototype have been used to understand geometric distributions of sulfur-pi interactions in the protein data
bank (PDB) [1]. Remarkably, the statistics of these interactions in proteins correlate with the preferred geometries of the
96 Book of Programme and Abstract for TACC2008 simple H2S-benzene model system. If time allows, we will also present high-level quantum computations of the lattice
energy of crystalline benzene [2].
[1] A. L. Ringer, A. Senenko, and C. D. Sherrill, Protein Sci. 2007, 16, 2216.
[2] A. L. Ringer and C. D. Sherrill, Chem. Eur. J. 2008, 14, 2542.
IN-BIO006
Amino acids organisation at inorganic oxides interfaces
Jean-François Lambert, Lorenzo Stievano, Dominique Costa, Frederik Tielens, Irene Lopes
Laboratoire de Réactivité de Surface, Case courrier 178, Université Pierre et Marie Curie 4 pl. Jussieu, 75252 PARIS
CEDEX 05
We have studied the phenomena occuring when amino acids are contacted with divided inorganic materials, collecting
both macroscopic information and spectroscopic data (vibrational spectroscopy, 13C and 15N NMR), and systematically
tried to rationalize our observations on the basis of molecular models obtained by DFT techniques (using both cluster and
periodic models of the silica surface).
The simplest amino acid, glycine, can give rise to molecular adsorption on specific silica surface sites containing several
silanol groups through the formation of well-defined arrays of hydrogen bonds, resulting in a kind of molecular
recognition. The presence of water in the system drastically modifies the adsorbed form, both by competing for
adsorption sites and by taking part in new hydrogen-bonded adducts. Calculations based on the most energetically stable
models of adsorbed glycine compare favorably with spectroscopic properties such as the energies of normal modes of
vibration, while effort is currently directed to the rationalization of NMR parameters.
In addition, in the presence of highly concentrated aqueous solutions, silica can specifically induce the nucleation of the
metastable form of crystalline glycine, instead of the form that normally precipitates from bulk solutions.
On other oxides such as titania and alumina, glycine adsorbs through a different mechanism implying coordinative
binding of the carboxylate to surface cations; those different adsorbed forms have different reactivities on thermal
activation.
Thus, mineral surfaces induce quite specific organisations of amino acids, afinding relevant for prebiotic chemistry
(origins of life) but also for the understanding of proteins adsorption in biomedical devices.
IN-BIO007
Dissociation of Charged Protein Complexes in the Gas Phase
Surajith N. Wanasundara and Mark Thachuk
Department of Chemistry, University of British Columbia, Vancouver, Canada
Several electrospray ionization mass spectrometric (ESI-MS) studies have shown that thedissociation of protein
complexes can produce fragments with asymmetric charge to massratios. Free energy barriers for the dissociation of
charged protein complexes can beused to understand this phenomenon. Relative free energy profiles for the dissociation
ofcharged cytochrome c dimer were estimated by performing constrained molecular dynamicssimulations at selected
fixed center of mass (COM) distances along the dissociation path.Mean number of overcrossings were also plotted with
COM distance in order to understandstructural changes during dissociation. Overall, the experimental observations can
97 Book of Programme and Abstract for TACC2008 berationalized using electrostatic arguments based upon two essential physical quantities:total charge and surface charge
density. A Coulomb repulsion model incorporating these quantities will be discussed.
1. Csiszar, S.; Thachuk, M. Using Ellipsoids to Model Charge Distributions in Gas Phase
Protein Complex Ion Dissociation. Can. J. Chem. 2004, 82, 1736-1744.
2. Wanasundara SN, Thachuk M. J. Am. Soc. Mass Spectrom. 2007; 18: 2242-2253.
IN-BIO008
Modelling interactions between proteins and peptides: applications in the study of pain and toxins.
Brian J Smith
Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research.
1G Royal Parade, Parkville, Victoria 3050, Australia
email: [email protected]
Venoms and toxins are a rich source of potential human therapeutics. For example, Ziconotide is a synthetic polypeptide
derived for the cone shell w-conotoxin M-VII-A, and has been recently approved for use in the treatment of chronic pain.
One common mechanism of action of toxins is via blockage of ion channels. ShK from sea anemone, which binds the
Kv1.3 potassium channel, is one of the most potent inhibitors of potassium channels. Kv1.3 is of particular interest as a
therapeutic target in a variety of diseases associated with dysfunctional immune systems, such as multiple sclerosis,
type-1 diabetes, and rheumatoid arthritis.
Enkephalins are endogenous polypeptides involved in regulating pain. These are pentapeptides that bind to opioid
receptors, members of the G protein-coupled receptors. Met-enkephalin binds preferentially to the d-opioid receptor,
where its effect is likely to be analgesic. Delta agonists also have potential as antidepressants and in ischemic
preconditioning.
We have developed a molecular model of ShK bound to the Kv1.3 potassium channel. Several structures of Kv1.3 were
modelled on the X-ray crystal structure of a related channel, and structures of ShK were obtained from molecular
dynamics simulations starting from the NMR-derived structure. The structures of Kv1.3 and ShK were docked together
using the ZDOCK program, and the interface between ligand and receptor was refined using the RDOCK program. The
final structure obtained was consistent with available mutational data. A D-allo form (mirror image) of ShK was also
docked to Kv1.3, and showed general characteristics of toxin binding.
We have prepared a molecular model of Met-enkephalin bound to the d-opioid receptor. Structures of the receptor were
modelled on the recently determined X-ray structure of human b2-adrenergic G protein-coupled receptor. Structures of
the ligand were obtained from molecular dynamics simulations. Docking of ligand and receptor was performed using the
ZDOCK software, with subsequent refinement with RDOCK. The final model places the ligand in contact with many
residues of the receptor known to be critical for receptor function
OR-BIO009
Insights into the Association and Interaction of Cohesin-dockerin Complex in
Cellulosome Assembly
Xu, Jiancong and Jeremy C. Smith
Center for Molecular Biophysics, Building 6011, MS6309, Oak Ridge National Lab, Oak Ridge, TN, 37830, USA
98 Book of Programme and Abstract for TACC2008 The organization and assembly of cellulosome, an extracellular multi-enzyme complex produced by anaerobic bacteria, is
mediated by the high-affinity interaction of cohesin domains from scaffolding proteins with dockerins of cellulosomal
enzymes. We have performed molecular dynamics simulations on both the wild type (WT) and D39N mutant of the C.
thermocellum cohesin-dockerin complex. The simulations reveal significant differences in their conformations and
protein flexibility. The simulations indicate that D39N mutation likely causes a change of the hydrogen-bonding network
in the recognition strips, the conserved loop regions previously proposed to be involved in binding, presumably through
the electrostatic or salt-bridge interactions between the loops and the helix-3 of the dockerin. Such alteration triggers
significant flexibility of the recognition strips. Results of the root-mean-square fluctuation analysis and principal
component analysis corroborate the above findings. Additional free energy perturbation estimate for the D39N point
mutation yields a 4.8 kcal/mol difference in binding energy, in reasonable agreement with the values determined
experimentally. The free energy profile of cohesin-dockerin association in bulk was also estimated using adaptive biasing
force approach. The preliminary results show an overall 12 kcal/mol barrier and also reveal two critical steps of
cohesin-dockerin association.
OR-BIO010
How nature designed protein mechanical response
Gräter, Frauke
CAS-MPG Partner Institute for Computational Biology(PICB)
Shanghai Institutes for Biological Sciences(SIBS)
Chinese Academy of Sciences(CAS)
Many proteins have evolved in nature to perform intricate mechanical functions. Two intriguing representatives will be
discussed, silk protein fibers and the von Willebrand factor, a blood clotting protein, which have been analyzed by
modeling, molecular dynamics simulations, force distribution and finite element analysis.
Silk has been designed in evolution as one of the most resilient, yet elastic fibers known. As an application of our newly
developed force distribution analysis, we probed the contribution of structural elements to mechanical toughness in silk
crystalline beta-sheet units, the basic force-bearing units in the complex silk fiber structure. On this basis, we developed a
simplified beta-skeleton model for finite element analysis as a first step towards a nano-scale model of full silk fibers.
The von Willebrand factor is activated for blood clotting in response to stresses from shear flow in blood vessels. Our
results on force-induced unfolding and activation of the A-type domains of the von Willebrand factor, a crucial step in
reversing the clot formation, will be presented. We find alternate disulfide bonds and inter-domain interactions as
force-sensitive locking mechanisms.
IN-BIO011
"Fascinating Vesicles"
Siewert-Jan Marrink, H. Jelger Risselada, Martti J. Louhivuori
University of Groningen, The Netherlands
Lipid vesicles, or liposomes, are widely used in biophysical studies as mimics of either complete cells or cell parts such
as endosomes or transport vesicles. In the realm of synthetic biology they furthermore play an important role as artificial
drug carriers, sensors and many more potential applications only limited by imagination. Whereas atomistic simulation
studies traditionally have looked at small planar membrane patches extended to quasi-infinite size by the use of periodic
99 Book of Programme and Abstract for TACC2008 boundary conditions, particle based simulations of vesicles have only appeared on stage since the last five years. Coarse
grained models, in which some of the atomistic detail is averaged out, are particular useful in this respect.
Here I will present the latest results of our group on simulations of vesicles, based on the coarse grained Martini
forcefield [1]. I will discuss equilibration issues of vesicles [2], and show the formation of gel domains in vesicles which
are cooled below the melting temperature of the lipid tails, followed by the formation of raft-like domains in ternary
systems composed of saturated and unsaturated lipids together with cholesterol. The effect of osmotic pressure on the
structure and stability of lipid vesicles and the response of membrane-embedded mechano-sensitive protein channels will
also be discussed [3].
[1] Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H. J. Phys. Chem. B 2007, 111, 7812.
[2] Risselada, H.J., Mark, A.E., Marrink, S.J. J. Phys. Chem. B 2008, 112, 7438.
[3] Yefimov, S., Onck, P.R., van der Giessen, E., Marrink, S.J. Biophys. J. 2008, 94, 2994.
IN-BIO012
Molecular Theory and Simulation for Biochemical Reactions in Crowded Environment
Ramakrishnan Vigneshwar1, Jianwen Jiang1,2* and Raj Rajagopalan1,2
1
Department of Chemical and Biomolecular Engineering, National University of Singapore
2
The Singapore-MIT Alliance, National University of Singapore, Singapore 117576
The internal environment of a biological cell consists of a large number of macromolecules. These macromolecules
collectively occupy about 40 % of the total volume of the cell. This high volume occupancy within the cell has numerous
consequences on the cellular functions, ranging from enzyme activities to self-assembly of biological system. In this
work, a molecular thermodynamic theory is developed to predict biochemical reaction equilibria in crowded environment
and is subsequently compared with results from reactive-canonical Monte Carlo simulations. The reactants, products and
crowders are modeled as coarse-grained spherical or chain-like molecules interacting via a Lennard-Jones potential. The
effects of crowder size, crowder length and product size are examined systematically. We show that the extent of reaction
can be substantially enhanced or reduced by crowders. The theoretical predictions agree well with the simulation results,
and are consistent with experimentally observed crowding effects arising from preferential binding or preferential
exclusion of the crowders.
IN-BIO013
Measuring the impact of genomic sequence variations on gene structure variations and its application to the
association study of genomic sequences and their disease susceptibility
Chaochun Wei
School of Life Science & biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
[email protected]
Single Nucleotide Polymorphism（SNP）is the most important genomic sequence variation within populations. It can
change a gene’s potential of alternative splicing. Different alternative splicing forms of a gene may have different disease
susceptibility. We present here a new measurement to represent the impact of genomic sequence variation on the gene
structure variation, and its application to the association study of genomic sequences and the disease susceptibility of
their genes. A new pair-HMM-based sequence alignment method is introduced to create an “alignment quality value” for
each aligned base pair of the genomic sequence and the EST sequence that contains the SNP. We demonstrate that the
alignment quality value can represent the relative importance of these SNPs on their gene structure variation. By
100 Book of Programme and Abstract for TACC2008 checking the sources of an EST from which a SNP was derived, we can determine if the EST (thus the SNP) is related to
a disease or not. This is a new quantitative way to investigate the relationship of a genomic sequence variation and the
disease susceptibility of its gene.
IN-BIO014
Do point mutations evoke disperse entropic changes throughout a protein domain?
Daniel G. Oblinsky, Bryan M.B. VanSchouwen, Heather L. Gordon, and Stuart M. Rothstein
Department of Chemistry, Brock University, St Catharines, Ontario L2S 3A1 Canada
The 56 amino acid B1 domain of Protein G from Streptococcus exhibits thermal stability over a broad range of
temperatures. It is known experimentally that the thermal stability of the protein changes, sometimes dramatically, when
amino acid substitutions are introduced at position 53. Experimental attempts to attribute this to locally-induced
perturbations, such as steric effects and solvent interactions, have failed. To explore and quantify the remaining
possibility, that point mutations have significant nonlocal effects on protein structure, we performed molecular dynamics
(MD) simulations on the wild type B1 domain and several of its mutants. We then re-sampled, with replacement, the
mutant trajectories one thousand times, each time subjecting the resulting conformations to principal component analysis
of their inter-Cα distances, followed by Procrustes-rotation of the factors to best fit those of the wild type. Our results
suggest that the thermal stability of the mutants decreases as the fit of their Procrustes-rotated factors to the wild type B1
domain deteriorates. We will discuss how figures such as that illustrated below demonstrate that extreme deviations of fit
are attributable to amino acid residues within secondary structure elements far-removed from the site of mutation.
IN-BIO015
Forcing proteins to unfold: simulation, theory and experiment.
Emanuele Paci
University of Leeds, UK
Dynamic force spectroscopy techniques such as atomic forcemicroscopy and optical tweezers have established in the past
few years as an important probe of the chemical and physical properties of biological macromolecules. The mechanical
resistance of proteins or equivalently, the time it takes the protein to switch from the native state to an extended state
101 Book of Programme and Abstract for TACC2008 provides a new perspective on their free-energy landscape. Simulation has proved in the years to be a valuable tool to
interpret experiments by providing an hypothetical atomic-scale picture of the events underlying the forces unfolding. I
will present some recent results which demonstrate how simulation is very valuable in challenging current theories and
allowing their improvement, while simultaneously providing alternative interpretation of some crucial experiments.
IN-BIO016
Insights from implicit solvent models: coiled-coils and protein-membrane interactions
Themis Lazaridis
Department of Chemistry, City College of New York / CUNY
email: [email protected]
Implicit solvation models have generated a lot of interest thanks to their convenience and speed. With minimal effort
these models can be extended to lipid membranes with even greater payoffs. A few years back we extended the EEF1
function for soluble proteins to an implicit membrane model (IMM1) by making the solvation parameters and the
dielectric screening dependent on the vertical coordinate. The membrane surface charge is modeled by use of the
Gouy-Chapman theory. The transmembrane voltage is also straightforward to incorporate. We have developed
approaches for calculating absolute, pH-dependent membrane binding free energies and transmembrane helix association
free energies. We have applied these methods to a number of membrane-active peptides: the influenza hemagglutinin
fusion peptide, alamethicin, the membrane targeting domain of phosphocholine cytidylyltransferase, and alpha-synuclein.
We have also used EEF1 to obtain insights into the determinants of oligomeric state and topology in coiled coils.
OR-BIO017
Inferring transcriptional regulatory network
from ChIP-chip and knock-out data
Liu Qi, Cheng Haoyu
Inferring the interactions of transcription factors with each other and their target genes is one of the key problems of
current bioinformatics research. Since each data source only provides one view of regulation, integrating multiple types
of data is required to get more reliable results. We present a simple method that combines ChIP-chip and TF knock-out
data. We applied our method on yeast data, where it was shown not only to recover the transcription factor-target gene
interactions with higher sensitivity and specificity, but also to identify cooperatives among transcription factors.
OR-BIO018
Theoretical design of new biological catalysts
Ibanez,Vicent Moliner
Departament de Química Física i Analítica, Universitat Jaume I, Castelló (Spain)
The methods and techniques of Computational Chemistry have become a promising complementary tool to design
biological catalysts. An alternative computational protocol is presented in this communication and, although containing
some limitations, it sorts out the difficulties present in previous strategies. This is based on Molecular Dynamic
simulations that, using hybrid quantum mechanics and molecular mechanics (QM/MM) methods, allows obtaining the
TS of the chemical reaction in the presence of a protein environment. All the specific substrate-protein interactions that
are established in the active site of the enzyme can be analyzed, both at the Michaelis complex and at the real TS, which
102 Book of Programme and Abstract for TACC2008 is not necessary equal to the TSA structure obtained by X-ray diffraction. The knowledge of this pattern of interactions
will provide clues to decide which residues of the active site of a CA or an enzyme should be replaced to better stabilize
the TS relative to the Michaelis complex, which would presumably enhance the rate constant of the chemical step of a
full catalytic process. Nevertheless, as all these peaces are part of a complex puzzle, it is not possible to predict that a
single mutation was going to produce a rate enhancement of the chemical reaction without side part effects. In this regard
the free energy profile can be traced from reactants to products, via the corresponding TS, rending theoretical predicted
barriers comparable with experimental data and allowing testing directed mutations. This theoretical strategy can be
considered as a numerical experiment helping experimentalists in active-site redesign by means of a few mutations. Some
efforts in this direction will be presented.
The starting point of our protocol is the X-ray structures of a protein scaffold that presented a threshold value of catalytic
activity for a certain chemical reaction. In particular, we are using Catalytic Antibodies, that are able to catalyze chemical
reaction by their presumably affinity for the TS, or enzymes capable of catalyzing secondary reactions. Since the
catalytic efficiency of both kind of proteins are still far behind primary reactions catalyzed by natural enzymes, the target
will be to obtain novel enzymes with new catalytic functions.
References:
[1] S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán, and M. J. Field, J. Am. Chem. Soc., 2001, 123,
1709-1712.
[2] M. Roca, S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán. Chem. Soc. Rev. 2004, 33, 98-107.
[3] S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón and J. Bertrán, Angew. Chem. Int. Ed. 2007, 46, 286-290.
[4] S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón and J. Bertrán, J. Am. Chem. Soc., 2008, 130, 2894-2895.
[5] S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán. Chem. Soc. Rev. 2008, in press
IN-BIO019
Origin and Evolution of Genetic Novelties
Wen Wang
CAS-Max-Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution,
Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
Rapid accumulation of large scale genomic data has stimulated fast advance of evolutionary genomics, which is mainly
based on comparative study between species by implementing computational approach.
To decipher biological
meanings of genomic sequences an integrated approach combining computational with experimental analyses could be a
promising direction. We have conducted such integrated studies by two inverse ways.
One way to integrate these two
approaches is to obtain general patterns first at the genomic level using computational approach, and then picked a
sample of cases to investigate the concrete biological mechanisms.
One such an example is the study of origin of new
exons. We identified many exons newly evolved in rodents, based on which we discovered that new exons usually
originated from intronic sequences and evolve faster.
We then in-depth investigated some cases by functional
characterization and found that new exons could be an important mechanism of increasing proteome diversity. Another
way of integration can be exemplified by our study on young new genes in Drosophila.
Previously due to lack of
genomic data of close species, we screened young duplicates in 8 species of Drosophila melanogaster subgroup by in situ
hybridizing cDNA probes on polytene chromosomes of the 8 species, and identified many new genes.
Recently, with
the availability of 12 Drosophila genome sequences, we conducted a comprehensive search for young genes and revealed
the general patterns of origin of new genes at the genome level. Our ongoing experimental characterizations on some of
the young genes suggest that young gene can play important roles in development and evolution of the host species.
103 Book of Programme and Abstract for TACC2008 IN-BIO020
A Novel Proton Transfer through Peptide Groups in Proteins
Katsumasa Kamiya1, Yasuteru Shigeta1, Atsushi Oshiyama2
1
Institute of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo,
678-1297, Japan
2
Department of Applied Physics, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-8656, Japan
Proton transfer reactions inside proteins play crucial roles in biological energy transduction. Actually, in mitochondria,
protons are pumped across
mitochondrial inner membranes by cytochrome c oxidase (CcO) to create an
electrochemical proton gradient harnessed to synthesize ATP. Recent experiments performed on the bovine CcO have
suggested a novel proton transfer pathway involving the peptide group connecting Tyr440 and Ser441, where a usual
hydrogen-bond network is interrupted, thus making the proton transfer rather unconventional. In this work, we studied its
mechanism via the metadynamics approach combined with Car-Parrinello molecular dynamics [1,2].
On the basis of the calculations, we have elucidated a multi-step proton transfer pathway that allows for the overcoming
of the peptide group in the bovine CcO. The local rigid -like loop conformation of the peptide backbone, along with
the nearby Na+ ion, brings the two adjacent Tyr440-Ser441 and Ser441-Asp442 peptide groups to face each other,
favoring the multi-step proton transfer path. The present calculations suggest that the bovine CcO crystal structure around
the Tyr440-Ser441 peptide group is particularly suited to promote a proton transfer through peptide groups.
[1] K. Kamiya, M. Boero, M. Tateno, K. Shiraishi, A. Oshiyama, J. Am. Chem. Soc. 129, 9663 (2007).
[2] K. Kamiya, M. Boero, M. Tateno, K. Shiraishi, A. Oshiyama, J. Phys.: Condens. Matter. 19, 365220 (2007).
IN-BIO021
Calculation of Accurate Protein Geometries using PM6 and X-ray structures
Stewart, James
Stewart Computational Chemistry, USA
Using the newly developed semiempirical method PM6, faults in experimentally determined primary structures of
proteins can rapidly be identified. Examples of such faults will be presented. By using a restraining function of the type
proposed by Yu, Yennawar, and Merz, these faults can then be corrected. The resulting general method, which
combines the best features of PM6 and X-ray analyses, allows protein geometries of unprecedented accuracy to be
generated. The issues involved will be discussed and an example of an improved protein structure given.
OR-BIO022
Substrate Specificity in Carboxylesterate Binding
Steven R. Gwaltney
Department of Chemistry, Center for Environmental Health Sciences, and HPC2 Center for Computational Sciences
Mississippi State University, Mississippi State, MS 39762, USA
The human carboxylesterase 1 (hCE1) enzyme catalyzes the hydrolysis of xenobiotic esters. It is one of the body’s
primary defenses against ester-containing toxicants. In addition, hCE1 has been implicated in the hydrolysis of
cholesteryl oleate, and thus in the transport and removal of cholesterol from cells.
104 Book of Programme and Abstract for TACC2008 The p-nitrobenzyl esterase enzyme from Bacillus subtilis (pnb CE) is an analogue to hCE1. To better understand the
source of the variability in carboxylesterase activity, we compared a series of mutant pnb CE enzymes to the wild type.
The mutant enzymes were formed by replacing the leucine residue 362 at the “side door” of the wild type pnb CE with
either a neutral alanine (L362A), a negatively charged glutamate (L362D), or a positively charged arginine (L362R). We
showed the L362R mutant had the largest decrease in activity [1].
This talk will present the results of our molecular dynamics simulations on the binding of the substrate p-Nitrophenyl
valerate with pnb CE. These simulations provide insight into the cause of the differences in activity between the mutant
forms of the enzyme. At the end we will also present simulations of the interactions of oxime reactivators with
cholinesterase enzymes inhibited by nerve agents.
[1] T. M. Streit, A. Borazjani, S. E. Lentz, M. Wierdl, P. M. Potter, S. R. Gwaltney, and M. K. Ross, Biol. Chem. 2008,
389, 149.
IN-BIO023
Yang, Wei
OR-BIO024
A novel rate theory approach to transport in ion channels
P. Fowler, M.S.P. Sansom, E. Abad
Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, South Parks Road, OX1
3QU Oxford, United Kingdom We present a novel rate theory based on the notions of splitting probability and mean first
passage time to describe conduction of single ions in narrow (quasi 1D) channels [1]. In contrast to previous approaches
such as classical transition state theory or Kramers theory, we model ion transport via a hopping model with transition
rates that depend on the full geometry of the potential of mean force (PMF) and the transmembrane potential. Approach
of ions from the bulk solution to the narrow part of the channel is modeled by means of a Smoluchowski equation with a
partially reflecting boundary condition. For the case of a piecewise linear potential, we provide explicit analytic solutions
for the transition rates and the ion flux and show how the model can be used to compute current-voltage curves from
PMFs obtained from molecular dynamics simulations, thereby bridging the gap between the atomistic and the
mesoscopic level of description. Possible extensions of the theory to describe multi-ion conductance are discussed.
[1] E. Abad, P. Fowler, and M. S. P. Sansom, J. Chem. Phys. (accepted).
IN-BIO025
Applications of the Fragment Molecular Orbital Method toBiomolecular Systems
Shigenori Tanaka
Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada, Kobe 657-8501,
Japan
The Fragment Molecular Orbital (FMO) method was proposed by Kitaura et al. through which large biomolecules such
as proteins and nucleic acids can be easily analyzed with chemical accuracy. In the ab initio FMO method, a molecule or
a molecular cluster is divided into fragments, and the MO calculations on the fragments (monomers) and the fragment
pairs (dimers) are performed to obtain the total energy that is expressed as a summation of the fragment energies and
105 Book of Programme and Abstract for TACC2008 inter-fragment interaction energies (IFIEs). In this talk, after giving a brief description of the ab initio FMO method, I
will demonstrate some examples of recent applications in bio-nano fields. The ABINIT-MP and BioStation Viewer
softwares have been developed and used for such calculations. The FMO method was thus applied for problems of
transcriptional regulation, including interactions of nuclear receptor, ligand, transcription factor, and DNA. Detailed
interactions between biomolecules and the roles of each amino acid residue were revealed through analyses of the IFIEs,
charge distribution, and orbital configuration. Electrostatic and vander Waals dispersion interactions were found to be
equally important in molecular recognition. It was thus found that the inclusion of electron correlation effect was
essential to obtain appropriate descriptions. Other applications associated with influenza viral hemagglutinin proteins and
fluorescent proteins are also illustrated.
[1] K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Nakano, and S. Tanaka, J.
Comput. Chem. 2006, 27, 948.
[2] K. Fukuzawa, Y. Mochizuki, S. Tanaka, K. Kitaura, and T. Nakano, J.
Phys. Chem. B 2006, 110, 16102.
[3] M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, J. Phys.
Chem. B 2007, 111, 3525.
IN-BIO026
Human Neutrophil Elastase and Proteinase 3: so similar yet so different
Nathalie Reuter
Computational Biology Unit, Bergen Center for Computational Science,
Univ. of Bergen, Thormohlensgt 55, N-5008 Bergen, Norway,
[email protected], http://www.cbu.uib.no
The human neutrophil elastase (hNE) and proteinase 3 (hPR3) share a high sequence identity and have been thought for a
long time to have close similar localization, ligand specificity and function. However recent studies indicate that they
might have very different physiologic roles. Specifically, hPR3 has intracellular specific protein substrates resulting in
the involvement of PR3 in regulation of intracellular functions1. It also behaves as a peripheral membrane protein2 and
its membrane expression is a risk factor in chronic inflammatory diseases. These activities were not observed for HNE.
Using Molecular Dynamics (MD) simulations we could map the substrate binding sites of both enzymes and propose a
sequence motif specific for hPR3. This led us to design a peptide, which was indeed shown, by enzymatic assays, to be
specific for hPR3 vs. HNE 3. The same computational approach was used to show that peptidic substrates efficiently and
specifically cleaved by hPR3 have a poor interaction pattern with mouse and rat PR3s 4. This is highly relevant in the
development of a murine animal model for studying PR3-related inflammatory pathologies; the design or identification
of substrates specific of the murine PR3 or NE cannot rely on the studies performed on the human enzymes.
Lately we have used MD simulations with the IMM1/GC membrane model to
investigate the structural elements of the
binding of hPR3 to membranes 5. Both the energies and structures resulting from the MD suggest that hPR3 associates
strongly with anionic membranes. We observe a unique interface binding site (IBS) consisting of 5 basic and 6
hydrophobic amino acids. Similar calculations with HNE suggest a different membrane binding mechanism. Our
predictions were recently confirmed by mutagenesis experiments.
1. Witko-Sarsat, V.; Canteloup, S.; Durant, S.; Desdouets, C.; Chabernaud, R.; Lemarchand, P.Descamps-Latscha, B. J
Biol Chem 2002, 277, 47338-47.
106 Book of Programme and Abstract for TACC2008 2. Witko-Sarsat, V.; Cramer, E. M.; Hieblot, C.; Guichard, J.; Nusbaum, P.; Lopez, S.; Lesavre, P.; Halbwachs-Mecarelli,
L. Blood 1999, 94, 2487-96.
3. Hajjar, E.; Korkmaz, B.; Gauthier, F.; Brandsdal, B. O.; Witko-Sarsat, V.; Reuter, N. J Med Chem 2006, 49, 1248-60.
4. Hajjar, E.; Korkmaz, B.; Reuter, N. FEBS Lett 2007, 581, 5685-90.
5. Hajjar, E.; Mihajlovic, M.; Witko-Sarsat, V.; Lazaridis, T.; Reuter, N. Proteins 2007, 71, 1655-1669
OR-BIO027
Interrupting the MDM2-p53 interface with high affinity:Computational studies
Shubhra Ghosh Dastidar1, David P. Lane2, Chandra S. Verma1
1
Bioinformatics Institute, #07-01 Matrix, 30 Biopolis Street, Singapore 138671,
email: [email protected], Tel: +65-6478-8273
2
Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673
The p53 protein is central to maintaining the genomic integrity of a cell and protects cells against tumorigenic
transformations. In normal cells, p53 is controlled by a ubiquitin ligase, MDM2, which targets p53 for proteolysis [1,2].
In tumors which are characterized by over expression of MDM2, an effective strategy could be to disrupt the p53-MDM2
interaction thus stabilizing p53 which would then ensure apoptosis. A small molecule ‘nutlin’ and several peptides and
their derivatives mimicking the interactions of p53 with MDM2 and displacing p53 from MDM2 have demonstrated this
principle [3,4]. One such peptide has been characterized recently that has shown the highest affinity for MDM2 [5]. We
have carried out molecular dynamics simulations to characterize the detailed behavior of the association of this peptide
and its variants with MDM2. Having reproduced the qualitative trend in affinities, we distil the role of specific
interactions that give rise to the enhanced affinity. The role of conformation in modulating the affinity of such peptides is
characterized. The implications for design principles of other peptides and small molecules with improved binding
affinities are discussed.
[1] Vogelstein, B., Lane, D., Levine, A. J., Nature 2000, 408, 307-310.
[2] Wu, X., Bayle, J. H., Olson, D., Levine, A. J., Genes Dev. 1993, 7, 1126
[3] Bottger, A., Bottger, V., Sparks, A., Liu, W. L., Howard, S. F., and Lane, D. P., Curr. Biol. 1997, 7, 860
[4] Vassilev, L. T., Vu, B. T., Graves, B., Carvajal, D., Podlaski, F., Filipovic, Z., Kong, N., Kammlott, U., Lukacs, C.,
Klein, C., Fotouhi, N., Liu, E. A., Science 2004, 303, 844
[5] Zondlo, S. C., Lee, A. E., and Zondlo, N. J., Biochemistry 2006, 45, 11945
OR-BIO028
Hesam T. Dashti1,2, Adel Ardalan1,3, Navid Farajzadeh3
1
Advanced Biomedical Computation Research, University of Arak, Iran.
2
Center of Excellence in Biomathematics, University of Tehran, Iran.
3
Database Research Group (DBRG), University of Tehran, Iran.
Biological Aspects: For long time motif discovery problem was renowned problem in the field of bioinformatics.
Whereas conserved subsequences inside different biological sequences play similar roles, the problem of motif discovery
had been introduced to help researchers in process of identifying sequences’ functionality. Indeed, by experimentally
discovering specific subsequences functionality and using common motif discovery approaches to search the target
subsequence, corresponding sequences can be stratified upon their functionality. There are two obstacles in front of the
motif discovery solutions; the first one comes from residues substitution probability and other one is the length of some
107 Book of Programme and Abstract for TACC2008 biological sequences (around 108) that strongly affects the solutions’ time complexity. On the other hand, there is another
restriction on some motif discovery problems that changes the problem to a different problem of discovering a set of
motifs (commonly a family of motifs) inside biological sequences. Hence, the problem of motif discovery remained as an
open problem in bioinformatics research area where most of current algorithms vacillate in tradeoff of time and accuracy
or can not satisfy whole of restrictions.
Computational Aspects: Many approaches from dynamic programming approaches to exhaustive search methods have
been introduced to solve motif discovery problem [1], but Recurrent Artificial Neural Networks (RANN) have not been
examined yet, where these networks can consider wide ranges of sequences’ entities by using memory stacks. The
RANN topology includes a memory stack inside of its recurrence structure that can store and use some extra information
–except that of input nodes. An unproved claim that can be satisfied via RANN is relation of residues in biological
sequences, where the stack can store some previous residues that may have affect motifs' determining.
Methodology: For a given set C of motifs {Mi=1…n| ∀ i=1…n |Mi|=const.} and given sequence S, this methodology finds
similar subsequences Nj=1…p to Mi on S respecting to k insertions and l substitutions of residues, so length of Nj will be
between |Mi| and |Mi|+k. The network topology used here is composed of |Mi|+k input and also recurrence nodes,
3/2*(|Mi|+k) nodes in hidden layer and one output node to show the net's decision. During the training process, the
network is fed by a couple of motifs from C with k residues inserted into the motif sequence in random positions and l
residues selected in normal distribution to be mutated. During the training iterations the recurrence nodes act on hidden
layer’s output and feed these values back to hidden layer on next iteration. Hence, in each flip flop, in addition of
considering current window’s residues, previous window’s residues are also considered where combining these windows
information hoists network accuracy.
Experiments: We evaluate our methodology on random generated sequences and motifs with and without using
recurrence nodes (i.e. a simple backpropagation network). Moreover we assess recurrent nodes criticality by feeding c.
elegence sequence where some subsequences are extracted from the sequence as motifs. In both random generated and
real sequence examinations, using recurrent nodes improves the methodology accuracy. Histogram of the network output
values shows normal distribution graph around motif subsequence with 0.95 for the graph’s apex.
[1] Rigoutsos, I., et al., Dictionary building via unsupervised hierarchical motif discovery in the sequence space of
natural proteins. Proteins, 1999. 37: p. 264-267
[2] Recurrent Neural Networks: Design and Applications, Larry Medsker and Lakhmi C. Jain, The Crc Press, 1999.
OR-BIO029
Force propagation from molecular dynamics simulations reveals sparse mechanical network in proteins
Wolfram Stacklies, Frauke Gräter
CAS-MPG Partner Institute for Computational Biology (PICB), 320 Yue Yang Road, 200031 Shanghai, P.R. China
Mechanical force is routinely applied to proteins in force probing experiments and simulations to observe a protein's
response to external stress. A yet unanswered question is how force propagates through proteins. How do perturbations
like an external force flow through protein scaffolds and how is this related to protein stability and function? We
elucidate force distribution in the titin I27 domain by monitoring alterations in forces between pairs of atoms in the
folded state upon pulling the protein with a constant force. We find forces to be a more direct measure for internal strain
than the only minor changes in atomic coordinates. We observe that the externally applied force is anisotropically
distributed throughout the protein scaffold highlighting three prominent regions that contribute most of the protein's
mechanical resistance. The functional relevance of the force distribution network is highlighted by additional mutant
108 Book of Programme and Abstract for TACC2008 simulations. The method can easily be extended to other types of perturbation including allosteric signals, such as ligand
binding, phosphorylation, or a change in protonation state.
IN-BIO030
OR-BIO031
Computational Exploration of Conformational Transition Pathway in the Allosteric Process of Calcium-induced
Recoverin
Ji-Lai Li1,2, Cai-Yun Geng1, Xu-Ri Huang*1, Chia-Chung Sun1
1
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University,
Changchun 130023, People’s Republic of China
2
Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, P.R.
China
Fax: (+86) 431-8894-5942
Recoverin is an important neuronal calcium sensor (NCS) protein, which have been implicated in a wide range of Ca2+
signalling events in neurons and photoreceptors. To characterize the conformational transition of recoverin from the
myristoyl sequestered state to the extrusion state, a series of conventional molecular dynamics (CMD) and targeted
molecular dynamics (TMD) simulations were performed. The >30 ns long CMD and TMD simulations on recoverin
revealed a reliably conformational transition pathway, which can be viewed as a sequential two-stage process. A very
important mechanistic conclusion from the present TMD simulations is that the hydrophobic and hydrophilic interactions
modulate the allostery cooperatively in the conformational transition pathway. In the first stage, three salt-bridges broken
between Lys-84 and Gly-124, between Lys-5 and Glu-103 and between Gly-16 and Lys-97 are major components to
destabilize the structure of state T and trigger the swivel of the N- and C-terminal domains. In the second stage, the
rupture of H-bond Phe-56-O…H(O)-Thr-21 leads to the two helices of EF-1 apart from each other, destabilizing the
hydrophobic interactions of the myristoyl group with its environment, whereas the making of H-bond
Leu-108-O…H(O)-Ser-72 helps the interfacial domain to maintain structural integrity in the course of the myristoyl
extrusion. These observations are beneficial to understanding the mechanism of how and why NCS proteins make
progress in the photo-signal transduction processes. Further experimental and theoretical studies are very desirable.
TOC graphic:
Reference
1.
Ames, J. B., R. Ishima, T. Tanaka, J. I. Gordon, L. Stryer, and M. Ikura. 1997. Molecular mechanics of
calcium-myristoyl switches. Nature 389:198-202.
2.
Tanaka, T., J. B. Ames, T. S. Harvey, L. Stryer, and M. Ikura. 1995. Sequestration of the membrane-targeting
109 Bo
8 myristoyl grooup of recoverrin in the calciium-free state.. Nature 376:4
444-447.
3.
Ames, J.
J B., N. Hamaasaki, and T. Molchanova. 2002. Structu
ure and calciuum-binding stuudies of a reccoverin mutannt
(E85Q) in an allosteric inteermediate statee. Biochemisttry 41:5776-57
787.
4.
a A. Wollm
mer. 1993. Tarrgeted molecuular dynamicss simulation of
o
Schlitterr, J., M. Engeels, P. Kruger,, E. Jacoby, and
conformationnal changes: appplication to the
t t↔r transittion in insulin
n. Mol. Sim. 10:291-308.
5.
Rodriguuez-Barrios, F.,
F J. Balzarinni, and F. Gaago. 2005. Th
he molecular basis of resiilience to thee effect of thee
Lys103Asn mutation
m
in noon-nucleosidee HIV-1 reverrse transcriptaase inhibitors studied by taargeted molecular dynamics
simulations. Journal
J
of the American Chhemical Societty 127:7570-7
7578.
OR-BIO032
A QM/MM Investigation
I
of the Catalyytic Mechanissm of the Ferrrochelatase
Yaxue Wanga, Xiaotian Wuua, Taoju Cheena, Yong Shenn*a, Ulf Rydeeb
a School of Chemistry
C
and Chemical Engineering, Sunn Yat-sen Uniiversity, 510275, Guangzhoou;
b Departmentt of Theoreticaal Chemistry,L
Lund Universsity.
o ferrous ironn into protopo
orphyrin IX too form protohheme IX, whiich is the finaal
Ferrochelatase catalyzes thhe insertion of
way. Mutationns in the ferro
ochelatase genne can leads too the disease erythropoieticc
reaction in thhe heme biosyynthetic pathw
porphyria. Hoowever, the loocation of thee metal bindinng site and thee insertion proocess of the m
metal ion into the porphyrinn
are still dispuuted. In this work,
w
the crysstal structure of Bacilllus subtilis
s
ferrocchelatase was used to build
d the QM/MM
M
model to studdy the insertionn process of ferrous
f
ion. Thhe QM/MM optimizations
o
w carried oout by Comqu
were
um which usedd
Turbomole 5.7 at the BP86/6-31G*-RI level (Fe wass described by
y the DZpdf basis set) for the QM partt and Amber 7
M part. The innitial model was
w built as Fig.1a.
F
While the bond of Fe2+ and thee
(with the 19999 force fieldd) for the MM
oxygen atom
m of the resiidue Glu264 dissociated, the first Fe--N bond form
med (Fig.1b)). The energy
y barrier was
14.74KJ·mol--1. However, forming the second
s
Fe-N bond
b
need to overcome a very
v
high enerrgy barrier (70
0.83KJ·mol-1)
if the two prootons remain on
o the porphyrrin. After rem
moving the firsst proton, the second Fe-N bbond formed spontaneouslyy
(Fig.1c). Theen, the bond of Fe2+ andd the nitrogenn of the resiidues His183 was broken (Fig.1d, eneergy barrier is
12.67KJ·mol--1). After rem
moving the seccond proton, one
o water wass released from
m Fe2+ and F
Fe2+ fall into the porphyrinn
ring spontaneeously (Fig.1e)).
Figure 1: Thee insertion proocess of Fe2+ into protoporpphyrin IX
f
Fe-N bonnd formation is the rate-determining stepp of the metaalation reaction. The overalll
The results shhow that the first
metalation prrocess can be described as the followingg steps: the bond
b
of Fe2+ and oxygen aatom of resid
dues Glu264 is
broken, the first
fi Fe-N bonnd forms, rem
move the first proton from the porphyrinn ring, the seccond Fe-N bo
ond forms, thee
bond of Fe2+
+ and the nitroogen of the ressidues His1833 is broken, reemove the second proton, F
Fe2+ falls into
o the porphyrinn
ring spontaneeously.
2) .
Acknowledgeement：Natioonal Natural Sccience Foundaation of the Peeople’s Repubblic of China ((No.90608012
References
110
0 Book of Programme and Abstract for TACC2008 [1] Mattias D. Hansson.; Tobias Karlberg, etc. J. Biochem. 2007, 46, 87.
[2] Yong Shen; Ulf Ryde. Chem. Eur. J. 2005,11,1549.
[3] S. Al-Karadaghi.; M. Hansson.; S. Nikonov,, etc. Structure. 1997, 5, 1501.
OR-BIO034
Insight into the Misfolding Mechanism of Amyloid Fibril
Yong-Jie He，Hai-Feng Chen*
College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
Amyloid-β fibrils are related to some fatal diseases, such as Alzheimer’s disease, Type II diabetes, mellitus transmissible
spongiform encephalopathies and prion diseases. Researches have discovered that these fibril-forming and insoluble
fibril contain short fibril-forming segments, which can form cross-β spine. These sequences have not obvious homology.
Some structural data have been discovered by physical methods such as X-ray diffraction, NMR. In general, they form
steric-zippers by cross-β model. According to the structure, researchers divided these cross-β structures into 8 classes. Up
to date, 5 classes have been discovered. Because the aggregation mechanism of amyloid fibril is unknown, the
mechanism researches have become the hotspot. Here, we use molecular dynamics (MD) simulation to study the stability
of 8 new cross-β short fibril-forming peptides. All of them are 6-residue peptides. At first, we build the hexamer of these
peptides. Then we analysis the hydrophobic and hydrogen bond interactions among the peptides of these hexamers. The
results suggest there are some common properties in all those cross-β structures, providing new evidences to reveal the
misfolding mechanism of amyloid fibrils.
Key words ： Amyloid-β fibrils, molecular dynamics simulation, cross-β spine, structure stability, misfolding
mechanism
*To whom correspondence should be addressed. Tel:0086-21-34204348. Fax:0086-21-34204348.
OR-BIO035
Study on protein-protein interaction and recognition by molecular Docking
Cun-Xin Wang, Chun-Hua Li, Shan Chang, Xin-Qi Gong, Wei-Zu Chen
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124，China
Protein-protein docking is usually exploited with a two-step strategy, i.e., conformational sampling and decoy scoring. In
our work, we proposed a new filter enhanced sampling scheme and added it into the RosettaDock algorithm to improve
the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in
the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water
molecules. A combinatorial scoring function, ComScore, specially designed for the other-type protein–protein complexes
was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der
Waals, and electrostatic interaction energies. Based on above methods, some targets of the CAPRI blind test were
analysed and good results were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the
hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9–12 with good success in rounds
9 and 11. Besides, we proposed a network-based scoring method. In the view of complex network theory, a protein can
be treated as a network and protein-protein docking can be viewed as a particular network rewiring. Two scoring terms
based on the network parameters are proposed, in which the geometric complementarity, hydrophobic-hydrophobic and
polar-polar interactions are taken into account. Compared with a two-term energy function, a new simple scoring
111 Book of Programme and Abstract for TACC2008 function HPNet which includes the two network-based scoring terms shows better discrimination. Furthermore, combing
the network-based scoring terms with some other energy terms, a new multi-term scoring function HPNet-combine can
also make some improvements to the scoring function of RosettaDock.
[1] X. Q. Gong, S. Chang, et al. Proteins, 2007, 69, 859
[2] S. Chang, X. Jiao, et al. Biophys. Chem. 2008, (to be printed)
IN-BIO036
Statistical analysis of protein structures: electron density, conformational analysis, and protein-protein interfaces
Roland L. Dunbrack, Jr.,
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia PA 19111.
[email protected].
The Protein Data Bank (PDB) provides a rich source of information when viewed as a whole. Statistical analysis of
structural features from atom-atom contacts to biological and crystallographic interfaces have become a branch of
modern bioinformatics and computational biology. We will presents results of several studies that seek to improve our
understanding of protein structure and our ability to predict structure from sequence, when an experimental structure is
not yet available. First, electron densities have been used to verify coordinate positions and to understand the nature of
side-chain rotamers and multi-conformational side chains. Second, we have used modern non-parametric statistical
methods including kernel density estimates and the hierarchical Dirichlet process to produce smooth and differentiable
probability density estimates for backbone-dependent rotamer libraries and neighbor-residue-dependent Ramachandran
maps. Finally, we have examined structures of homologous proteins in different crystal forms to identify likely
biologically relevant interfaces.
OR-BIO037
A QM/MM Study of the First Proton Transfer in the Catalytic Cycle of Cytochrome P450cam and Its Mutant
D251N
Dongqi Wang1, Wilfred F. van Gunsteren1, Walter Thiel2
1
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH-8093 Zürich, Switzerland
2
Max-Planck-Institut fuer Kohlenforschung, Muelheim an der Ruhr, Germany
We present a QM/MM study of the first proton transfer in the catalytic cycle of cytochrome P450cam that leads to the
formation of hydroperoxo ferric complex, the so-called "Cpd 0". Experimentally this process is drastically slowed down
when Asp251 is mutated to Asn (D251N) which stresses the importance of Asp251. Thus, our study concentrates on the
Asp251 channel both for the wild-type enzyme and the D251N mutant, using four different active-site models. For the
wildtype, we find a facile concerted mechanism for proton transfer from protonated Asp251 with a barrier of about 1
kcal/mol and a high exothermicity of more than 20 kcal/mol. In the D251N mutant with a neutral Asn251 residue, a
conformer with a flipped Asn251 was obtained (as indicated by classical molecular dynamics simulations). This flip
disrupts the hydrogen-bond network and hence the proton-transfer pathway, which causes a longer lifetime of ferric
peroxo complex (S5) in the D251N mutant (consistent with experimental observations). The entry of an additional water
molecule into the active site of D251N with flipped Asn251 regenerates the hydrogen-bond network and provides a
viable mechanism for proton delivery in the mutant, with a moderate barrier of about 7 kcal/mol.
[1] Wang, D.; Zheng, J.; Shaik, S.; Thiel, W.
J. Phys. Chem. B 2008, 112, 5126-5138.
112 Book of Programme and Abstract for TACC2008 OR-BIO038
Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and
photosynthetic bacteria
Wang,Zhuo
Background
Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event.
Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene
transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome
encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the
chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic
network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic
maps derived from genome data to identify features of chloroplast network properties that are different from
cyanobacteria and to analyze possible functional significance of those features.
Results
The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the
Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in
chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and
reactions in chloroplasts is less than that in cyanobacteria, the chloroplast’s metabolic network has longer average path
length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific
and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular
organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same
module in chloroplasts.
In addition, three pieces of evidences support preferential attachment as primary mechanism of chloroplast metabolism
evolution. Firstly, we found enzymes related to more ancient pathways are more connected, and synthetases have the
highest connectivity. Most of the enzymes shared by the two densest cores between chloroplast and syw are synthetases.
Secondly, the highly conserved functional modules mainly consist of highly connected enzymes. Finally, isozymes and
enzymes from endosymbiotic gene transfer (EGT) distributed mainly in conserved modules and showed higher
connectivity than non-isozymes or non-EGT enzymes.
Conclusions
In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis
that led to the improvement of the photosynthesis efficiency in higher plants. Our findings are consistent with the notion
that since the light energy absorption, transfer and conversion is highly efficient even in photosynthetic bacteria, the
further improvements in photosynthetic efficiency in higher plants may rely on changes in metabolic network properties.
Moreover, though with severe evolutionary constraints imposed by endosymbiosis, preferential attachment is still a
plausible mechanism responsible for evolution of chloroplast metabolic network.
IN-BIO041
Structural and Dynamic Properties of a New Highly Amyloidogenic Chicken Cystatin Mutant I108T
Youtao Song, Yuanyuan Yu, Yuan Liu, Huili Zhang
Liaoning Key-laboratory of Animal Resources and Epidemic Prevention, Liaoning University, Shenyang, China 110036
113 Book of Programme and Abstract for TACC2008 A leucine 68 to glutamine variant (L68Q) of Human cystatin C (HCC) is believed to be the causative agent of an
amyloidotic disease, hereditary cystatin c amyloid angiopathy (HCCAA), which is a dominantly inherited disorder
characterized by tissue deposition of amyloid fibrils in blood vessels. The L68Q variant can form highly
domain-swapped dimers at physiological protein concentrations, thus forming part of the amyloidgenic deposits in the
brain arteries. Chicken cystatin (CC) has a number of similar characteristics to HCC, which makes it ideally suited for
further studying the mechanism of cystatin c-type amyloidogenesis at the molecular level. In our previous biochemical
experiments, chicken cystatin mutant I108T was shown many amyloid characters compared with amyloidogenic mutant
I66Q and wild type chicken cystatin.
In this study, 10-ns molecular dynamics simulations of the I108T, I66Q mutants and wild-type chicken cystatins were
performed to further investigate the amyloidogenic capacity of I108T mutant. Experimental evidence shows that I108T
mutant has an “expand” tendency to destabilize the whole protein and facilitates the aggregation process through four
ways: (1) alter the hydrophobicity and expose large hydrophobic surface area to the solvent; (2) decrease the α-helix
content and convert it into unordered structure; (3) weaken hydrogen between β2- and β3-strand; (4) weaken salt bridge
interactions. Our results strongly suggest that the I108T mutant, which exhibits large structural fluctuations compared
with wild-type chicken cystatin, is a highly amyloidogenic form of chicken cystatin and shares many similar structural
and dynamic features with amyloidogenic I66Q mutant.
Keywords: Chicken cystatin; Molecular dynamics simulations; Amyloidosis; Point mutation
[1] He, J.W., Song, Y.T., Ueyama, N., Saito, A., Azakami, H., Kato, A. Protein Sci. , 2006, 15, 213-222.
[2] Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Grubb, A., Abrahamson, M., Jaskolski, M. Nat. Struct. Biol.
2001, 8, 316-320.
[3] Rodziewicz-Motowidio, S., Wahlbom, M., Wang, X., Gagiewka, J., Janowski, R., Jaskólski, M., Grubb, A., Grzonka,
Z. J. Struct. Biol. 2006, 154, 68–78.
[4] He, J.W., Song, Y.T., Ueyama, N., Harada, A., Azakami, H., Kato, A. J. Biochem. 2005, 137, 477-485.
[5] Phillips, J.C., Braun, R., Wang. W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten,
K. J Comput Chem. 2005, 26, 1781-1802.
[6] Sanders, A., Craven, C.J., Higgins, L.D., Giannini, S., Conroy, M.J., Hounslow, A.M., Waltho, J.P., Staniforth, R.A. J.
Mol. Biol. 2004, 336, 165-178.
[7] Staniforth, R.A., Giannini, S., Higgins, L.D., Conroy, M.J., Hounslow, A.M., Jerala, R., Craven, C.J., Waltho, J.P.
EMBO J. 2001, 20, 4774–4781.
4.
Materials and Nano IN-MN001
Properties of p-electrons in nanographenes
De-en Jiang and Sheng Dai
Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS-6201, Oak Ridge, Tennessee 37831,
USA
Nanographenes are fascinating building blocks for carbon materials. We examine their chemical reactivity and magnetic
properties with first principles density functional calculations. We show that unique electronic states due to zigzag edges
dictate chemical and magnetic properties of these nanographene building blocks.1-6 We introduce the “partial radical”
concept for the carbon atoms at a nanographene ribbon’s zigzag edge to characterize their chemical reactivity.2.This
114 Book of Programme and Abstract for TACC2008 concept stems from the existence of a localized state near the Fermi level for the zigzag edge sites of graphene.1The
existence of this edge state has implications for organic synthesis of intriguing molecules such as rectangular polycyclic
aromatic hydrocarbons, cyclacenes, and short nanotubes.3,5 Moreover, these localized edge states can form spin orders.
We show that an antiferromagnetic ground state appears when zigzag-edged nanographenes, which have two edges,
reach certain critical sizes.3-5 On the other hand, zigzag-edged Möbius nanographenes, having only one edge, are found to
have a ground state with nonzero total magnetization.6 Our findings demonstrate the unique properties of p-electrons in
nanographenes caused by the zigzag edges.
[1] Jiang, D. E.; Sumpter, B. G.; Dai, S. J. Phys. Chem. B 2006, 110, 23628.
[2] Jiang, D. E.; Sumpter, B. G.; Dai, S. J. Chem. Phys. 2007, 126, 134701.
[3] Jiang, D. E.; Sumpter, B. G.; Dai, S. J. Chem. Phys. 2007, 127, 124703.
[4] Jiang, D. E.; Dai, S. J. Phys. Chem. A, ASAP.
[5] Chen, Z.; Jiang, D. E.; Lu, X.; Bettinger, H. F.; Dai, S.; Schleyer, P. v. R.; Houk, K. N. Org. Lett. 2007, 9, 5449.
[6] Jiang, D. E.; Dai, S. J. Phys. Chem. C, submitted.
IN-MN002
The State of Transition Metals in Transition Metal Oxides.
A. Stoyanova1, C. de Graaf2 and R. Broer1
1
Theoretical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG
Groningen, The Netherlands
2
ICREA Researcher at the Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili, Marcel.l
Domingo s/n, 43007 Tarragona, Spain
Many transition metal oxides show intriguing and technological useful properties like colossal magnetic resistance,
ferroelectricity or superconductivity. These properties are believed to be critically dependent on details of the electron
distributions around the transition metal ions and very sensitive to the local distortions that are often present, such as
charge disproportionation, orbital ordering and Jahn-Teller distortion.
We have analysed the mechanisms that drive such distortions in the perovskite type oxides CaFeO3, LaMnO3 and
YNiO3, using CASSCF/CASPT2 results for embedded clusters. A novel scheme was developed to express the
N-electron wave functions in terms of "optimized atomic orbitals" and these orbitals are then used to analyse the wave
functions in Valence Bond terms1 This turns out to be a practical tool to predict, for example, the type of distortions
mentioned above.
Using the above methods we are also able to explain the variations in Mössbauer isomer shifts in CaFeO3 and a series of
other iron containing compounds2. We observe that the isomer shift cannot be directly related to the formal oxidation
state of the Fe ion. Instead, large positive shifts are expected for highly ionic complexes, while small and negative shifts
indicate strong deviations from the ionic model.
1. A. Sadoc, R. Broer and C. de Graaf, J. Chem. Phys. 126, 134709 (2007).
2. A. Sadoc, R. Broer and C. de Graaf, Chem. Phys. Lett. 454, 196 (2007).
IN-MN003
Structure-reactivity relationship for nanostructured bimetallic surfaces
Axel Groß
115 Book of Programme and Abstract for TACC2008 Institute of Theoretical Chemistry, Ulm University, 89069 Ulm/Germany
We have addressed the reactivity of nanostructured bimetallic surface alloys by performingperiodic density functional
theory calculations. The catalytic activity of alloysis determined by electronic, geometric and structural factors which are
often summarized employing the terms ligand and ensemble effects. Using the
Scheme 1 systems PdCu [1] and PtAu [2] among others as examples, we show that
bimetallic systems can exhibit properties that do not correspond to an
intermediate behavior in between those of the pure components but that are
rather beyond those of both components [3]. Furthermore, whereas single
N
atoms of the surface alloys can show a decreasing interaction strength with
adsorbates (ligand effect), the binding at the most favorable adsorption sites can
still become stronger when the concentration of the more reactive metal is
increased (ensemble effect). The electronic and geometric factors underlying
C
Cr
N
Cr
N
C
these phenomena will be discussed.
[1] S. Sakong, C. Mosch, and A. Groß, PCCP 9, 2216 (2007).
[2] Y. Gohda and A. Groß, Surf. Sci. 601, 3702 (2007).
[3] A. Groß, Topics Catal. 37, 29 (2006).
IN-MN004
Bonding Nature and Reaction Behavior of Transition Metal Complexes:
Theoretical Study with Post-Hartree-Fock method
Shigeyoshi Sakaki
Kyoto University, Nishikyo-ku, 615-8510 Kyoto, Japan
Because of various interesting bonding nature and reaction behavior, a lot of theoretical studies have been reported on
transition metal complexes. In most of them, DFT method has been used. Though the DFT method is very powerful,
we need to apply post-Hartree-Fock method to transition metal complexes in many cases.1,2
One of such cases is
1
metal-metal multiple bond and another is reaction of dioxygen molecule with metal complexes.3 Here, we wish to
report our recent two topics; the first is theoretical study of chromium dinuclear complex and the second is theoretical
study of the reaction between iron(III) complex and dioxygen molecule.
In the chromium dinuclear complex (Scheme 1), the DFT method presents too short Cr-Cr distance, while the CASSCF
method presents no minimum in the usual range of Cr-Cr distance.
The MRMP2 method presents the minimum, though
it is still moderately longer than the experimental value. These results clearly indicate that well incorporation of static
and dynamic correlation effects is indispensable for the chromium dinuclear complex. In the similar molybdenum
dinuclear complex, on the other hand, the DFT, CASSCF, and MRMP2 methods present reasonable Mo-Mo distance,
interestingly.
In the reaction of dioxygen molecule with iron(III) complex, the CASPT2 method is indispensable to present reasonable
reaction behavior.
Important points are that the Fe(III) center keeps high spin d5 character and it induces
singlet-coupling with dioxygen molecule with triplet spin state.3
References
1) Saito, K.; Nakao, Y.; Sato, H.; Sakaki, S. J. Phys. Chem. A, 2006, 110, 9710.
2) Ohnishi, Y.; Nakano, Y.; Sato, H.; Sakaki, S. J. Phys. Chem. A, 2007, 111, 7915.
3) Nakatani, N.; Nakao, Y.; Sato, H.; Sakaki, S. J. Phys. Chem. B, submitted.
116 Book of Programme and Abstract for TACC2008 IN-MN005
Rare gas clusters under illumination of short and intense pulses with VUV and X-ray frequencies
Rost, Jan Michael
Max Planck Institute for the Physics of Complex Systems
Nöthnitzer Straße 38, 01187 Dresden, Germany
Novel light sources, the X-ray free electron lasers being built at SLAC in Stanford and at DESY in Hamburg, will
provide light pulses with properties of lasers and synchrotrons at the same time: short in duration and wavelength,
coherent and extremely bright.
Understanding the coupling of light and matter in this new parameter regime is only at its infancy. Starting from a
perspective of strong laser pulses at infrared frequencies, the talk will discuss pulses of successively shorter wavelength
and introduce the mechanisms how they interact with rare gas clusters. Thereby, first experiments from the free
electron laser in Hamburg (FLASH) will be interpreted.
IN-MN006
First-principles design of low-dimensional nanomaterials for spintronics
Jinlong Yang
Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei,
Anhui 230026, People's Republic of China
[email protected]
It is expected that the new generation of devices will exploit spin dependent effects, what has been called spintronics.
Half-metallic (HM) materials are ideal for spintronic applications, such as tunnelling magnetoresistance and giant
magnetoresistance elements, since there would be only one electronic spin channel at the Fermi energy. In this talk, I will
present our works on first-principles design of low-dimensional nanomaterials for spintronics: (1) One-dimensional
transition metal-benzene sandwich polymers: possible ideal conductors for spin transport, and (2) Half-metallic
ferromagnetism in graphene nanoribbons.
IN-MN007
Gold shells shaped by carbon cores: From an Au18 cage to a C10Au18 aurocarbon
Fedor Y. Naumkin
Faculty of Science, UOIT, Oshawa, ON L1H 7K4, Canada
Gold clusters are efficient catalysts whose properties vary with the cluster size and shape. Composition of a metal-based
cluster, variable by doping with other (non)metal atoms, is another factor affecting relevant electronic characteristics
such as ionization energy IE and electron affinity EA.
In the present DFT-based study [1], a new aurocarbon core-shell cluster, C10Au18, is designed as a structural analogue
of a hydrocarbon, with the bonds of carbon skeleton saturated by gold atoms. The resulting gold shell is composed of two
6-atom rings with two triangular caps. The total binding energy with respect to C10 + 18Au is on average ≈1.5 eV per
gold atom. Charge distributions in the neutral cluster and its ions are also investigated and exhibit interesting, sometimes
counterintuitive features.
117 Book of Programme and Abstract for TACC2008 Evolution of the cluster properties is followed from the equivalent empty gold cage to that filled with the carbon core, the
effect of geometry-change only (“inflation” of the cage by the core) being isolated. The Au18 empty-cage isomer of the
same C3 symmetry is considerably shorter along its axis and wider on one side. Upon insertion of the carbon core which
stretches the cage into the near-ellipsoidal gold shell in C10Au18, the singlet-triplet excitation energy drops by more than
an order of magnitude, the EA value reduces only slightly (by 10%), while the IE value decreases significantly (by ≈1.5
eV). These changes are attributed [1] specifically to the shape change of the gold shell, or to its interaction with the core,
or both.
The observed variations could allow selective modification of catalytic properties of gold clusters by doping with
molecular cores. The considerable geometry difference between the empty and carbon-filled gold cage indicates
possibility of stabilizing new shapes of gold shells (collapsing without the core inside). However, the low vertical
excitation energy may correspond to a considerable reactivity of the core-shell cluster in question.
[1] F. Y. Naumkin, Submitted, 2008
IN-MN008
Nanopolaritonics and friction
Daniel Neuhauser and Kenneth Lopata
Chemistry and Biochemistry Department, UCLA 607 Charles E. Young Drive, Los Angeles, CA 90095-1569 USA
Polaritons are combined excitation of metallic plasmons and particle-hole excitations with unique properties in the solid
state, such as Bose-Einstein Condensates at high temperature. We discuss the extension of the polariton to molecular and
nano-system. A combined exciton-plasmon object (the "nanopolariton") will propagate with negative refraction on a
nano scale, leading to potential nanolenses. Further, we show how molecular excitation can be used to guide the plasmon
movement, and modify the amount and polarization of (near-field) light directed to given regions . Several layers of
theory will be discussed, ranging from the simplest few-dipole descriptions to a combined Discrete-Dipole
Approximation for the metals coupled to molecular excitation of the combined system. Strategies for external control of
the response of combined metallic and organic materials will be discussed. Finally, the simulations will culminate in
approximate DFT and in Kohn-Sham DFT simulations of excited molecular-plasmonic systems.
A technically important outcome of the studies came from the need to simulate transfer and scattering, requiring, in the
fully quantum limit, a cheap approach to friction in TDDFT. A physically motivated approach was therefore developed to
inducing a quantum friction while keeping a non-stochastic single wavefunction (or Kohn orbitals) description; the
method is the quantum analogue of Drude friction.
IN-MN009
Computational Explorations of Low-Dimensional Nanomaterials
Zhongfang Chen, Yafei Li, Zhen Zhou
Department of Chemistry, University of Puerto Rico, Rio Piedras Campus, San Juan, PR, USA; Institute of New Energy
Material Chemistry, Nankai University, Tianjin 300071, P. R. China
Low-dimensional nanomaterials exhibit unusual mechanical, optical, electrical and magnetic properties, and promise to
be an exciting field for basic and applied research. Here I present some of our recent progresses on the computational
exploration on such nanomaterials.
118 Book of Programme and Abstract for TACC2008 (1) Boron nitride nanotubes (BNNTs) have rather robust band structures. The electronic structures can only be modified
slightly with the presence of Stone-Wales defects and hydrogen terminated vacancies. The sturdy electronic properties
make BNNTs promising for many applications, especially in nanoelectronics.
(2) The electronic ground states of [n]cyclacenes, as well as short-zigzag nanotubes are open-shell singlets. Similarly,
carbon nanographenes (CNGs) with long zigzag edges have also open-shell singlet ground states. Chemical
modifications that change the long zigzag edge into armchair type can efficiently stabilize the kinetically unstable CNGs.
(3) Similar to CNGs, silicon carbide nanoribbons can be half-metallic.
[1] Li, Y.; Zhou, Z.; Golberg, D.; Bando, Y.; Schleyer, P. v. R.; Chen, Z. J. Phys. Chem. C. 2008, 112, 1365.
[2] Chen, Z.; Jiang, D.; Lu, X.; Bettinger, H. F.; Dai, S.; Schleyer, P. v. R.; Houk, K. N. Org. Lett. 2007, 9, 5449.
[3] Gao, X.; Zhou, Z.; Zhao, Y.; Nagase, S.; Zhang, S. B.; Chen, Z. J. Phys. Chem. C. 2008 (in press)
[4] Li, Y.; Zhou, Z.; Chen, Z. (unpublished results)
IN-MN011
Electrochemistry Coupled Transport Phenomena in Polymer Electrolyte Fuel Cell
Electrodes
Partha P. Mukherjee
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
In the present scenario of a global initiative toward a sustainable energy future, the polymer electrolyte fuel cell (PEFC)
has emerged as one of the most promising alternative energy conversion devices for different applications. Despite
tremendous progress in recent years, a pivotal performance limitation in the PEFC comes from the cathode catalyst layer
(CL) or the electrode [1]. The catalyst layer (CL) plays a crucial role in the overall cell performance due to the sluggish
oxygen reduction reaction, as well as transport limitation originating from widely disparate competing transport
mechanisms encompassing electrochemistry coupled species, charge and liquid water transport. Liquid water covers the
reaction sites rendering reduced catalytic activity as well as blocks the porous pathways thus causing hindered oxygen
transport to the active reaction sites, which lead to CL flooding and severe performance degradation. The macroscopic
fuel cell models available in the literature fail to address the effects of the underlying complex pore morphology of the
electrode. In this work, the development of a comprehensive pore-scale modeling framework [2,3] comprising of a
stochastic microstructure reconstruction model, an electrochemistry coupled direct numerical
simulation (DNS) model and a mesoscopic, two-phase lattice Boltzmann model is presented with the objective to gain
fundamental insight into the intricate structuretransport- performance interplay in the PEFC electrode.
[1] C. Y. Wang, Chem. Rev., 104, 4727 (2004).
[2] P. P. Mukherjee and C. Y. Wang, J. Electrochem. Soc., 153, A840 (2006).
[3] P. P. Mukherjee, P. K. Sinha, and C. Y. Wang, J. Mater. Chem., 17, 3089 (2007).
IN-MN012
119 Bo
8 The General Properties Of
O Nanoparticcles Distributtions
Nikolay V. Sookolov
Saint Tikhon Orthodox Unniversity, Novookuznezkaya ul,
u 23b, Mosccow, 115184, Russia,
R
E-mail: [email protected], tel. +749924435812
There are maany possible variants
v
of nannoparticles disstributions. But, the generaal properties oof nanoparticles distributionn
may be foundd with the aidd of generalizzation of Pafnnutii L. Tcheb
bysheff’s (Chebyshev’s) innequality and corrections too
Andrei N. Koolmogoroff’s (Kolmogorovv’s) estimatioon [1]. Autho
or has found for all posssible variants the universaal
expressions for
fo nanoparticlles distributions with the aiid of his generalizations annd corrections.. These new in
nequalities foor
nanoparticles are followingg
P{M ≥ nm} ≥
M α − [(n − 1)m]α
(k max m)α − [(n − 1)m]α
and
P{M ≥ nm
m} ≤
M α − (k min m)α
,
(nm)α − (k min m)α
s
of nanopparticles with mass more or
o equal nm, n=k
n min+1, kminn+2, …, kmax, kmax and kmiin
where P{M
M ≥ nm} is share
are integers, α is any positive or negattive exponentt,
M α - is the average mean
m
of raiseed mass nano
oparticles withh
mize value of nnanoparticle mass,
m
kmaxm is
exponent α, m is minimizee difference inn mass of nannoparticles, kmin
m m is minim
maximize vallue of nanoparrticle mass.
M α can be determined byy the experim
ment of by the theoretical caalculation. Thee
new algorithm
m for computaational chemisstry to point estimation
e
of nanoparticle
n
d
distribution
haas been createed with the aidd
of stated ineqqualities. It waas made an appplication of thhe new algoriithm to Au naanoparticle disstribution. It is presented onn
the picture.
s are the exxperimental pooints,
▲s are the pooints estimatioons with the aiid of stated geeneral propertiies of nanoparrticle distributtion.
All experimenntal data are fully
fu corresponndent the theooretical stated estimation off nanoparticle distribution.
[1] Nikolay V. Sokolov, Doklady
D
Akaddemii nauk (Ruussian). 2002, 384, 308.
120
Materials Properties from DFT in the Projector Augmented Wave Formalism
Josef W. Zwanziger
Department of Chemistry and Institute for Research in Materials, Dalhousie
University, Halifax, Nova Scotia, B3H 4J3 Canada
Density functional theory using pseudopotentials and planewaves comprises an efficient formalism for studying the
properties of solids using periodic boundary conditions. More recently, the Projector Augmented Wave formalism has
been developed by Blőchl [1] and implemented in several codes (see for example [2]). The advantage of this approach is
that it recovers all-electron accuracy while retaining the computational efficiency of an ultrasoft pseudopotential scheme.
Some observables, such as those associated with magnetic resonance, require this level of accuracy. I will discuss our
recent implementation of several magnetic resonance [3] and optical properties in a PAW framework, and show
examples of their use in the study of strongly correlated electron materials and insulating materials under different stress
loads.
[1] P. Blőchl, Phys. Rev. B 1994, 50, 17953.
[2] M. Torrent, F. Jollet, F. Bottin, G. Zérah, X. Gonze, Comp. Mater. Sci. 2008, 42, 337.
[3] J. Zwanziger, M. Torrent, Appl. Magn. Reson. 2008, 33, 447.
OR-MN014
Adsorption electropositive atoms with an odd number of electrons (H, K, Au) on a perfect TiO2(110) surface
Alexis Markovits1, Monica Calatayud1, Sébastien Fernandez1, and Christian Minot1,2
1 Laboratoire de Chimie Théorique Université Pierre & Marie Curie - Paris 6, CNRS-UMR7616, case 137, 4 place
Jussieu, Paris, F-75252 Cedex France.
2 Dept. Of Physics, CityU, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
E-mail : [email protected] Tel.: +33(0)144272682 Fax: +33(0)144274117
The adsorption of electropositive atoms with an odd number of electrons (H, K, Au) on a perfect TiO2(110) rutile surface
is investigated using periodic DFT calculations (VASP code). The rutile surface, a closed shell system when uncovered,
becomes an open-shell system when covered by one of these adsorbates. One possibility for adsorption is to transfer
electrons from the adsorbate to the rutile-surface, (the rutile is reduced): A• → A+ + e-. The cationic A+ moiety will then
adsorb on basic O2- surface sites forming OH groups. This is the best adsorption mode for H, K and Au. Another solution
is to couple two adsorbates. A to give A+ and A- : 2A• → A+ and A- and subsequent adsorption on basic and acidic
surface sites respectively regenerate the closed-shell system. This is the best adsorption mode for the coadsorption of Au
with H or K. Then, Au-I adsorbs on the surface acidic site, Ti+IV, while H+ (or K+) does on the surface basic sites, O-II. Our
results confirm that K coadsorption should have a significant effect on the binding of Au particles on TiO2 surfaces and
hence on the growth.
Adsorption of atomic hydrogen at room temperature leads to the formation of ordered H, however upon annealing the
sample to above 600 K, surprisingly, no H2 (or H2O) molecules were found to desorb from the surface. An explanation
for this unexpected behavior is provided by ab-initio calculations: the activation energy for H-atoms migrating into the
bulk, 1.11 eV, is significantly smaller than that for recombinative desorption of H2 (or H2O).
OR-MN015
A Universal Model for Nanoporous Carbon Supercapacitors
121 Book of Programme and Abstract for TACC2008 Jingsong Huang, Bobby G. Sumpter, and Vincent Meunier
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6367, USA
Supercapacitors based on nanoporous carbon materials, commonly called electric double-layer capacitors (EDLCs), are
emerging as a novel type of energy-storage device with the potential to substitute batteries in applications that require
high power densities. Nanoporous carbon supercapacitors are generally viewed as a parallel-plate capacitor since
supercapacitors store energy by charge separation in an electric double layer formed at the electrode/electrolyte interface.
The EDLC model has been used to characterize the energy storage of supercapacitors for decades. We comment on the
shortcomings of the EDLC model when applied to nanoporous carbon supercapacitors. In response to the latest
experimental breakthrough in nanoporous carbon supercapacitors, we propose a heuristic model that takes pore curvature
into account as a replacement for the EDLC model. When the pore size is in the mesopore regime (2-50 nm), electrolyte
counterions enter mesoporous carbons and approach the pore wall to form an electric double-cylinder capacitor (EDCC);
in the micropore regime (< 2 nm), solvated/desolvated counterions line up along the pore axis to form an electric
wire-in-cylinder capacitor (EWCC). In the macropore regime (> 50 nm) where pores are large enough so that pore
curvature is no longer significant, the EDCC model can be reduced to the EDLC model. With the backing of
experimental data and density functional theory calculations, we show that the EDCC/EWCC model is universal for
carbon supercapacitors with diverse carbon materials and electrolytes. The strengths and limitations of this new model
are discussed. The new model allows the supercapacitor properties to be correlated with pore size, specific surface area,
Debye length, electrolyte concentration and dielectric constant, and solute ion size, and may lend a support for the
systematic optimization of the properties of carbon supercapacitors through experiments.
[1] Chmiola, J.; Yushin, G.; Gogotsi, Y.; Portet, C.; Simon, P.; Taberna, P. L. Science 2006, 313, 1760.
[2] a) Huang, J.; Sumpter, B. G.; Meunier, V. Angew. Chem., Int. Ed. 2008, 47, 520; Angew. Chem. 2008, 120, 530.
b) Huang, J.; Sumpter, B. G.; Meunier, V. Chem.-Eur. J. 2008, 14, 6614.
This research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National
Laboratory (ORNL) and by the Division of Materials Sciences and Engineering, U.S. Department of Energy under
Contract No. DEAC05-00OR22725 with UT-Battelle, LLC at ORNL.
OR-MN016
A Theoretical Study on the Nonlinear Optical Properties of π-Conjugated Porphyrin Arrays
Li Kai Yan, Feng Long Gu, Yuriko Aoki*
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu
University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
Fused porphyrin arrays have attracted considerable interest in light of their application as molecular wires as well as
nonlinear optical (NLO). Elongation finite-field (elongation-FF) method is applied to determine the NLO properties of
linear porphyrin arrays. It was confirmed that the fused prophyrin exhibits particaly large values in both β and γ. The β
and γ of
large-size fused porphyrin oligomer, which is composed of 20 units of porphyrin, is found to be about 370 and
176 times as large as that of trimer, respectively. The results exhibit remarkable evolution of β/n and γ/n along with an
increasing number of porphyrin units n. This indicates that by tuning the size of porphyrin arrays it is possible to achieve
the large β and γ values.
122 Book of Programme and Abstract for TACC2008 [1] A. Tsuda, H. Furuta, A. Osuka, Angew. Chem. Int. Ed. 2000, 39, 2549.
[2] N. Aratani, A. Osuka, Y. H. Kim, D. H. Jeong, D. Kim, Chem. Int. Ed.2000, 39, 1458.
[3] T. E. O. Screen, J. R. G. Thorme, R. G. Denning, D. G. Bucknall, H. L.Anderson, J. Am. Chem. Soc. 2002, 124,
9712.
[4] A. Imamura, Y. Aoki, and K. Maekawa, J. Chem. Phys. 1991, 95, 5419.
[5] F. L. Gu, Y. Aoki, J. Korchowiec, A. Imamura, B. Kirtman, J. Chem. Phys.2004, 121, 10385.
[6] J. Korchowiec, F. L. Gu, A. Imamura, B. Kirtman, Y. Aoki, Int. J. Quantum Chem. 2005, 102, 785.
IN-MN017
First-Principle Study of Carbon Monoxide Oxidation in Excess of Hydrogen
Wei-Xue Li
State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian, 116023, China
[email protected]
The identification of active phase/center and reaction mechanism, as well as their dependence on the structures and
components, temperatures and partial pressures, are the keys of the heterogeneous catalysis, but remained a challenged
task. Solution relies on the integration of in-situ catalytic reaction of supported nano-catalysts, surface sciences and
theoretical calculations. [1-2] Proton exchange membrane fuel cell (PEMFC), which converts hydrogen to electricity
with water as product only, attracts great attention due to its environmental friendly and high efficiency. However, the
precious transition metal catalyst (Pt) as electrode and the poison of carbon monoxide (CO) prevent its
commercialization, and require stable, cost-effective, highly active and selective catalysts to remove CO without
consuming hydrogen. Extensive efforts concerning the catalysts (bimetallic alloys, core-shell catalysts, metal/metal oxide
etc), supports as well as microscopic reaction mechanisms (active phases/centers, reaction path) have been explored.
Various mechanisms, such as bi-functional, core-shell and interfacial mechanism, have been proposed and remain in
controversial.
Inspired and cooperated with local experimental investigations (group led by Prof. Xinhe Bao), we performed a first
principle density functional theoretical (DFT) study of CO preferential oxidation on PtFe catalyst in excess of hydrogen,
as well as its dependence on the components, partial pressures and temperatures, have been studied in details. It was
found that though Fe is energetically favorable to stay below the Pt surfaces under the ultra high vacuum, the presence of
oxygen would however induce Fe segregation on the Pt surfaces, and partially oxidizes and forms FeO. Under hydrogen
rich conditions, the formation of the hydroxyl groups on FeO enhances significantly the interfacial coupling between Fe
and Pt underneath, which prevents complete oxidation of iron. Molecular oxygen dissociates spontaneously at the FeO/Pt
boundary, and dissociated oxygen atoms was found to be highly active for oxidation of CO adsorbed on Pt. Hydrogen
dissociation and adsorption on Pt is kinetically hindered due to the limited free sites available by CO poison, which
eventually leads to high selectivity in terms of CO oxidation. Our study shows that the core-shell (Fe-Pt) and/or Pt/Fe2O3
is unstable under realistic conditions, and cannot be the active phases. Moreover, both of them are not efficient for O2
activation, and not potential candidates for their lower activity and selectivity, correspondingly. Our study indicates that
123 Book of Programme and Abstract for TACC2008 active phases and active centers can only be formed and works under the realistic conditions, which highlights the
importance of the systematic cooperation between in-situ catalytic characterizations, surface sciences and DFT
calculations. Dual active sites functionalized for different species and reaction paths are essential for optimizing the
catalysts with high activity and selectivity. (We thank great discussion and collaboration with our colleagues Prof. Xinhe
Bao, Dr. Qiang Fu and Dr. Ding Ma.)
[1] J. A. Rodriguez, S. Ma, P. Liu, J. Hrbek, J. Evans, M. Pérez, Science 318 (2007) 1757
[2] S. Alayoglu, A. U. Nilekar, M.Mavrikakis & B. Eichhorn, Nature Materials, 7(2008) 333
OR-MN018
Linking Stability Studies to the Preferential Growth of ZnO
Ozlem Ozcan1, Guido Grundmeier2, Alexander T. Blumenau1
1: Interface Chemistry and Surface Engineering, Max Planck Institut für Eisenforschung, Max-Planck-Str. 2, 40237,
Düsseldorf, Germany
2: Chemical Engineering and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, 33098,
Paderborn, Germany
ZnO is one of the most widely studied oxide materials in the literature due to its great technological importance. The
stabilization mechanism of its polar surfaces is controversially discussed in literature both experimentally and
theoretically [1-2]. Recently, the synthesis of various geometries of nanostructures was realized by a number of groups
[3,4]. Among them, the nanorods growing in c-axis are gaining more and more attention with the intention to be used in
solar cells or laser diodes.
In this study we aim at linking the preferential growth of nanorods to stability studies of ZnO-surfaces. Low index
surfaces of ZnO were analysed with various configurations of adsorbates and step and vacancy configurations for
possible stabilization mechanisms. The DFT calculations were performed with SIESTA Molecular Dynamics Package
[5]. A selection of computational results will be presented with related experimental data and possible technological
highlights especially in the field of corrosion science will be discussed in the presentation.
[1] Dulub, O.; Diebold, U.; Kresse, G. Phys. Rev. Lett., 2003, 90, 245409-1–245409-15.
[2] Valtiner, M.; Borodin, S.; Grundmeier, G. Phys. Chem. Chem. Phys., 2007, 9, 2406–2412.
[3] Vayssieres, L.; Keis, K.; Lindquist, S. E.; Hagfeldt, A. J. Phys. Chem. B, 2001, 105, 3350-3352.
[4] Greene, L. E.; Law, M.; Goldberger, J.; Kim, F.; Johnson, J. C.; Zhang, Y.; Saykally, R. J.; Yang, P. Angew. Chem.
Int. Ed. 2003, 42, 3031-3034.
[5] Soler, J. M.; Artacho, E.; Gale, J. D.; Garcia, A.; Junquera, J.; Ordejon, P.; Portal, D. S. J. Phys.: Condens. Matter,
2002, 14, 2745-2779.
OR-MN019
Periodic Density Functional Theory Study of The oxidative Dehydrogenation of n-butane on the (001) Surface of
V2O5
Nguyễn Ngọc Hà(1), Trần Thành Huế(1), Nguyễn Minh Thọ(2)
(1) Department of Chemistry, Hanoi National University of Education, Vietnam.
(2) Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001Leuven, Belgium.
124 Book of Programme and Abstract for TACC2008 The oxidative dehydrogenation (ODH) of light alkanes is an attractive alternative for the production of more valuable
alkenes. Considerable research efforts have been made towards the development of catalysts active at low temperature
and selective in the formation of alkenes. Most catalysts described in the literature are based on Vanadium oxide as the
main component and many studies concerning the reaction mechanism during the ODH of short alkanes have been
performed but debates still today exist [1]. The objective of this work is to study in detail theoretically the kinetics of
n-butan ODH on the (001) surface of V2O5. The DFT using the plane-waves basis set and pseudopotential has been used
for this purpose. The parameters for calculating: Cell size: 11.5219 x 7.1334 x 15.0489 A0, exchange correlation
functional: GGA – PBE, ultrasoft pseudo potential, the kinetic energy cut-offs of the plane wave basis set were 25 Ryd
and gamma point for k-point sampling. All of the calculations have been done by using PWscf (Plane-Wave self
consistent field) software [2].
The theories of HOMO (Highest Occupied Molecular Orbital), LDOS (Local Density States) at Fermi level and PDOS
(Projected Density of States) are also employed successfully to predict active sites, kinetic calculations are carried out
using Quantum methods and molecular dynamics. NEB (Nudged Elastic Band) is used to elucidate transition state (TS).
The analysis based on analytical methods:local sofness s(r) or LDOS, PDOS as well as HOMO show that the highest
active species belong to the methylene groups CH2 and the terminal apical oxygen in V=O (1-fold O) due to the most
favorable orientations.
Figure 1 show the largest s(r) values for methylene group. That means the density state at Fermi level of this group is the
highest. PDOS's results at surrounding Fermi (Fig. 2) also indicate that density state of p orbitals on the C atom in a
methylene groups is higher than that in a methyl groups.
Ψ(HOMO)_C4H10 = 0.179*2pz_C2+ 0.180*2 pz _C3 + 0.103*1s_H8 +0.103*1s_H9 +
0.103*1s_H10 + 0.104*1s_H11 + 0.046*2 pz _C1 + 0.046*2 pz _C4 + 0.032*1s_H6 + 0.032*1s_H7 +0.032*1s_H13 +
0.032*1s_H14.
Figure 3 illustrates the HOMO of C4H10 molecule. Since the 2p (C) orbitals and 1s(H) orbitals in an methylene group
contribute mostly into wave-function Ψ(HOMO) therefore the electrons of these groups at the highest energy level will
have highest density of probability and consequently methylene groups are the most active in the rection.
125 Book of Programme and Abstract for TACC2008 Potential energy surface (PES) has been studied by optimizing the structure based on DFT using plane-waves basis set
and pseudopotentials. The transition state (TS) is estimated from NEB. The calculated results are in good agreement with
the predicted reaction's sites shown above. The chemisorbed step have an activation energy of Ea = 121.5232 kJ/mol, and
an adsorption energy of Eads = 3.6171 kJ/mol for the methylene group orientation. Meanwhile, the computed activation
energy and adsorption energy are 146.3982 kJ/mol and 19.9973 kJ/mol respectively for the methyl group orientation. The
calculated resutls demonstrate that the abstraction of an H atom from a secondary C atom leading to
[(V=O)CH3CHCH2CH3] species is favorable.
TS of the [(V=O)CH3CHCH2CH3] system leading to 2C4= was sample in detail. The obtained resutls indicated that
n-butane OHD proceeds through two main steps (Reaction coordinate RP_B-2_3 in figure 4):
1. C4H10 chemisorption with Ea = 121.5232 kJ/mol and Eads = 3.6171 kJ/mol.
2. C4H8 (2C4=) desorption with Ea = 105.2380kJ/mol; Eads = 65.7919kJ/mol.
and the adsorption step is the rate determination step.
The principal results of the present study are in agreement with experiemntal result: Ea (experimental) = 112.6297 kJ/mol
[3]
References
[1] F. Gilardoni, A.T. Bell, A. Chakraborty and P. Boulet, " Density functional theory
calculations of the oxidative dehydrogenation of propane on the (010) surface of V2O5", J. Phys.Chem B 104 (2000),
12250 – 12255.
[2] http://www.pwscf.org/
[3] O.Rubio, J.Herguido, M.Menendez, "Oxidative dehydrogenation of n-butane on V/MgO catalysts-kinetic study in
anaerobic conditions", Chemical engineering science 58(2003) 4619-4627.
IN-MN020
Regional DFT - Electronic Stress Tensor Study of Aluminium Nanostructures for Hydrogen Storage
P. Szarek1, K. Ichikawa1, D. Henry2, I. Yarovsky2 and A. Tachibana1*
1Department of Micro Engineering, Kyoto University, Kyoto 606-8501, Japan
2Department of Applied Physics, RMIT University, Melbourne Victoria 3001, Australia
*E-MAIL [email protected]
Nowadays, when technology has already been moved to area of nano-devices, the description of properties at very
microscopic level, within molecules, concerning interatomic interactions, had gained remarkable importance. Since these
properties become affecting functionality and reliability of manufactured devices it is crucial to understand how to
transfer practicality of macro-devices to nano (or subnano) level and what interferes with desirable features. The new
materials for hydrogen storage devices might possibly be based on Al-nanostructures. We have modeled the structures
126 Book of Programme and Abstract for TACC2008 and properties of Al-clusters and characterized atomic and molecular hydrogen adsorbed on its surface. The internal
framework of clusters was studied using Regional DFT method [1] and the insights into bond strengths and surface
reactivity originating from electronic stress tensor [2,3] has been given. The stress tensors are widely used to describe
internal forces of matter. In molecules electronic stress tensor describes distortion of charge density which has primary
significance for physical and chemical properties being displayed.
[1] “Chemical Potential Inequality Principle,” Akitomo Tachibana, Theoretical Chemistry Accounts, 102, 188-195
(1999).
[2] “The field theoretical study of chemical interaction in terms of the Rigged QED: new reactivity indices,” Pawel
Szarek and Akitomo Tachibana, J. Mol. Model. 13, 651-663 (2007).
[3] “ Electronic Stress Tensor Description of Chemical Bonds Using Non-classical Bond Order Concept," Pawel Szarek,
Yutaka Sueda, and Akitomo Tachibana, J. Chem. Phys., in press (2008).
IN-MN021
Electronic properties and aromaticity of medium-sized boron cage clusters
Lu Wang and Jijun Zhao
State Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams, School of Physics and
Optoelectronic Technology, Dalian University of Technology, Dalian 116024, China
Boron is a strongly covalent material and attracts great interests in its chemical behaviors. Geometries, electronic
properties and bonding characteristics of medium-sized boron clusters (from B26 to B56) were studied by ab initio
calculations with density functional theory (DFT) and generalized gradient approximation at level of PBE/6-31+G(d,p).
Global search of the ground-state geometries using simulated annealing incorporated with DFT-based molecular
dynamics shows that medium-sized boron clusters tend to adopt irregular cage configurations with large holes on it.
Other cage-related structural motifs, including fullerene-based cages (generated from carbon fullerenes by adding atoms
in the center of each hexagon or pentagon), superstructures build by B12 icosahedrons, and planar structures have been
considered for comparison. Electronic properties including HOMO, LUMO, dipole moments, and binding energies have
been computed for the lowest-energy cage configurations. Aromaticity of these boron cages was evaluated in terms of the
nucleus-independent chemical shift (NICS). The high negative NICS values (around −40ppm) obtained for these boron
cages show substantial aromaticity.
IN-MN022
Molecular dynamics simulations of mechanical deformation in metallic thin films
A.V. Bolesta, V.M. Fomin
Khristianovich Institute of Theoretical and Applied Mechanics, Institutskaya Str. 4/1, 630090 Novosibirsk, Russia
A rapid development of thin film growth and surface modification techniques demands further study of composition
materials behavior at mechanical loading. The given methods of the surface treatment are used to increase materials
strength and durability. The effects of surface and interface which can be ignored on a macroscale become important for
nano-scale thin films. Free surface and interface of materials with the different mechanical characteristics appears to be a
stress concentrator and is an additional source of dislocations. And, due to a nonuniform character of plastic deformation
development, surface treatment can lead to unexpected mechanical properties modification. The problem on the stress
and strain distribution at the interface is of a great interest too. Evident that all the processes connected with a presence of
interfaces are formed on spatial scales of several lattice constants order – microlevel. The method of numerical
simulation which takes into consideration microlevel is molecular dynamics.
127 Book of Programme and Abstract for TACC2008 We report the results of molecular dynamics study of metallic nanostructure deformation. To simulate interatomic
interaction embedded atom method potentials for Al, Ni and Cu were used. Stress and internal energy distributions were
analyzed for uniaxial quasi-static tension and indentation of nanostructures with various crystallographic orientations and
surface roughness. Comparison of the loading curve characteristic features with the processes on the atomic scale reveals
an influence of the surfaces and interfaces state on the deformation behavior of heterostructure.
IN-MN023
Study of Hydrogen Adsorption on Ti Dopped BC3 Nanotubes using DFT methods
Seifollah Jalili and Mojdeh Akhavan
Department of Chemistry, K. N. Toosi University of Technology, P.O. Box 15875-4416, Tehran, Iran
One of the problems in the practical implementation of hydrogen as a fuel is the lack of an efficient media for hydrogen
storage in ambient conditions. A single Ti atom adsorbed on nanotube surface has shown to bind up to four H2 molecules.
By completely coating the nanotube surface, a storage capacity reaches to 8 wt. % [1]. However, a serious problem that
largely reduces the storage capacity is the clustering of metal atoms on nanotube surface [2].
(a)
(b)
Fig. 1 A (4,0) BC3 nanotube (a) and its different binding sites (b).
In this work, we have studied hydrogen adsorption on a titanium-dopped (4,0) BC3 nanotube (Fig. 1). It is
believed that B atoms enhance the metal binding and inhibit clustering [3]. Geometry optimizations show that only the H
and H′ sites are favorable for Ti adsorption. Other arrangements are relaxed to these structures. The spin-unpolarized
binding energies for H and H′ sites are 5.25 and 4.86 eV, respectively. These energies are larger than 2.2 eV, which is
obtained for carbon nanotubes, because the electron deficient B atoms have higher affinity for Ti atom.
A series of single energy calculations were performed as a hydrogen molecule approaches the Ti atom, and
when the forces acting on H2 were large enough, the system were fully relaxed using DFT calculations. The hydrogen
molecule were approached the Ti in both parallel and perpendicular directions (relative to nanotube axis). The optimized
geometries are shown in Fig. 2. For H site, the hydrogen molecule in both orientations shows molecular adsorption. The
H–H bond length is increased from 0.74 to 0.81 Å. However, for H′ site, the hydrogen molecule is dissociated upon
adsorption. The Ti–H distances are 1.74 and 2.01 Å and the H–H distance increases to 2.67 Å.
128 Book of Programme and Abstract for TACC2008 (a)
(b)
Fig. 2 Optimized structures for H2 molecule adsorbed on a Ti atom in H (a) and H′ (b) sites.
[1] T. Yildirim and S. Ciraci, Phys. Rev. Lett. 2005, 94, 175501
[2] Q. Sun, et al., J. Am. Chem. Soc. 2005, 127, 14582
[3] Y. Zhao, et al., Phys. Rev. Lett. 2005, 94, 155504
IN-MN024
Theoretical studies on the structure design and property evaluation of imidazole and pyrazole compounds
Shu Yuan-jie　,Yin Ming, Xiong Ying , Du Junliang
Institute of Chemical Materials, CAEP, Mianyang 621900, China
Abstract: Theoretical studies on the structure design and property evaluation of imidazole and pyrazole compounds as
new energetic materials have been carried out in this paper. Ten nitroimidazole and nine nitropyrazole compounds have
been designed and investigated by density functional theory. Their optimized geometry structures, electronic structures,
heats of formation and densities were calculated at the B3LYP/6-311G(d,p) level. Results show that the imidazole and
pyrazole rings have some aromaticity. Reactivity of all the compounds was analyzed by electrostatic potential
distribution. VLW equation was used to evaluate detonation velocities and Chapman-Jouguet pressures of the ten
compounds. Detonation performance shows that these compounds are very good candidates for energetic materials.
IN-MN025
The metallophilic attraction: The current situation
Pekka Pyykkö
Department of Chemistry, University of Helsinki, POB 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki, Finland
The ‘metallophilic attraction’ is a label for the experimentally and theoretically observed cohesion between systems
containing closed-shell metal ions, such as Au(I),
in molecules, solids or liquids. The strongest contribution to this
interaction is classical dispersion. It can be theoretically studied using wave-function-based theories, starting from MP2
[1].
Our latest study of this phenomenon is a study of the basis-set limit of this phenomenon for tetrahedral and pyramidal
[E(AuPH3)4]+
systems, E=P [2]. A pyramidal structure is preferred, like for E=As but unlike for E=N. The dimeric,
perpendicular [ClAuPH3]2 model was also studied.
[1] P. Pyykkö, Chem. Rev. 1997, 97, 597.
[2] P. Pyykkö and P. Zaleski-Ejgierd, J. Chem. Phys. 2008, 128, 124309.
First-principles rovibrational spectroscopy
Attila G. Császár
Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1532 Budapest,
Hungary; E-mail: [email protected]
For the accurate first-principles computation of complete (ro)vibrational spectra of many-electron molecules one needs to
solve both the quantum mechanical electronic structure and the nuclear motion problems. In order to obtain results useful
to experimentalists, both tasks should be tackled with approaches allowing high accuracy. Augmentation of the
computations with an empirical determination of energy levels also proves highly useful [1]. State-of-the-art ab initio
electronic structure computations can result in highly accurate potential energy (PES) and dipole moment (DMS)
surfaces, with relativistic, adiabatic and nonadiabatic corrections proving to be increasingly important (see, e.g., Refs. 2
to 4). The quantum mechanical nuclear motion problem must be solved variationally if accuracy and completeness of the
spectrum are of concern. Related strategies, e.g., Ref. 5, based on the discrete variable representation (DVR) of the
Hamiltonian are discussed. Emphasis is placed on the simplicity and generality of the approaches. Representative
numerical results and chemical applications are presented for selected systems, including water, ammonia, and methane.
[1] A. G. Császár, G. Czakó, T. Furtenbacher, and E. Mátyus, An Active Database Approach to Complete Spectra of
Small Molecules, Ann. Rep. Comp. Chem.. 2007, 3, 155-176.
[2] O. L. Polyansky, A. G. Császár, S. V. Shirin, N. F. Zobov, P. Barletta, J. Tennyson, D. W. Schwenke, and P. J.
Knowles, High-Accuracy Ab Initio Rotation-Vibration Transitions of Water, Science 2003, 299, 539-542.
[3] P. Barletta, S. V. Shirin, N. F. Zobov, O. L. Polyansky, J. Tennyson, and A. G. Császár, The CVRQD Ab Initio
Ground-State Potential Energy Surfaces for the Water Molecule, J. Chem. Phys. 2006, 125, 204307.
[4] L. Lodi, R. N. , J. Tennyson, A. E. Lynas-Gray, S. V. Shirin, N. F. Zobov, O. L. Polyansky, A. G. Császár, J. N. P.
van Stralen, and L. Visscher, A New Ab Initio Ground State Dipole Moment Surface for the Water Molecule, J. Chem.
Phys. 2008, 128, 044304.
[5] E. Mátyus, G. Czakó, B. T. Sutcliffe, and A. G. Császár, Variational Vibrational Calculations with Arbitrary
Potentials using the Eckart-Watson Hamiltonians and the Discrete Variable Representation, J. Chem. Phys. 2007, 127,
084102.
OR-MN027
Comparison simulation/experiment in the Low Energy-Loss region: application to lithium battery materials.
Dr. Philippe Moreau
Institut des Matériaux Jean Rouxel, Université de Nantes –CNRS, Nantes, France
Material properties often stem from their electronic structures and in particular from their density of states below and
above their Fermi level. A spectroscopy, such as Electron Energy-Loss Spectroscopy, allows us to probe these densities
of states and is thus well suited to study a wide range of materials. Our group has been involved for some time now in the
development of new materials for the electrochemical storage of energy. Above all, promising positive and negative
electrodes are tested in view of their use in lithium batteries for electrical vehicles. It will be shown how EELS has
become essential to characterize these materials. Owing to the decrease in particle size of the compounds used in the
electrodes (in order to favor the power response), EELS is well suited with its 1 nm spatial resolution. The constantly
improving energy resolution is also an asset.
130 Book of Programme and Abstract for TACC2008 Theoretical calculations are often necessary in order to help the interpretation of the experimental spectra. Some changes
cannot be understood by the sole support of the “finger print” method. Examples will be taken from recent results
obtained using first principles codes (WIEN2k, VASP, ABINIT, DP) all based on the Density Functional Theory. A
special attention will be paid to the lithium K edge. It will be shown that the electrochemical process can be studied in
detail thanks to this edge, rarely exploited in EELS. Our recent work focused on the precise determination of polarization
and local field effects on this edge.
OR-MN028
Theoretical studies of weak Si···H interactions
Sergei F. Vyboishchikov,‡ Georgii I. Nikonov,† and Samat Tussupbayev‡
‡ Institut de Química Computacional, Universitat de Girona, Spain.
† Chemistry Department, Brock University, Canada
The silylium ion [C6(SiMe2)(SiHMe2)5]+ offers an amazing example of multiple Si···H interactions in organic chemistry.
Namely, it shows a symmetric Sia–H–Sia motif supported by two additional Siβ–H···Siα agostic interactions. This cation
is highly fluctional in NMR spectra at room temperature. This fluxionality is attributed to scrambling of the hydride
bridge around the benzene ring. The DFT calculations show that the hydride shift is related to internal rotation of silyl
groups. We found two possible mechanisms of this process, associated with internal rotation of either β- or γ-silyls. We
performed NMR, static DFT, and dynamics studies of this process. The metadynamics calculations revealed intriguing
features of the hydride transfer mechanism. The energy barrier of the process is caused by internal rotation of silyl, while
the hydride transfer itself is intrinsically a very easy process. Vibrational dynamics of the cation is also discussed. The
related cation [1,4-C6(SiMe2)(Me)(SiHMe2)4]+ has a fully different structure with two equivalent Si–H bonds
coordinated to a single sulylium center, affording a pentacoordinate silicon atom featuring a Si–H···Si···H–Si agostic
bond.
The role of Si···H interactions in organometallic chemistry is illustrated by a series of isostructural rhodium silyl hydride
complexes. Some degree of interligand Si···H interaction is found in all cases, which manifest itself in significant Mayer
bond indices and negative J(H–Si). The calculated J(H–Si) are in good accord with experimental data. In
CpRh(SiR3)2H2 and [Cp(Me3P)Rh(SiMe3)2H]+ the hydride interacts with two silyl ligands. The potential energy surface
of hydride displacement is extremely flat. A very low barrier for the hydride shift in CpRh(SiMe3)3H accounts for its
fluxionality. The geometries are influenced both by electronic and steric effects.
[1] Khalimon A.Y., Lin Z., Simionescu R., Vyboishchikov S. F., Nikonov G. I., Angew. Chem. 2007, 46, 4530–4533
[2] Vyboishchikov S. F., Nikonov G. I., Organometallics, 2007, 26, 4160
IN-MN029
Ultra-thin oxide films: new materials with unprecedented properties
Gianfranco Pacchioni
Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi, 53 - 20125 Milano, Italy
Ultra-thin films of oxide materials supported on a metal single crystal can exhibit unusual and unprecedented properties
which have no counterparts in the corresponding bulk surfaces. In this talk we review recent theoretical and experimental
results obtained in this field. The particular structural and electronic properties of the films can be used to induce
self-organization of deposited metal particles; ultra-thin oxide films can also provide an example of two-dimensional
molecular sieves. In fact, Au and Pd atoms exhibit completely different adsorption properties on mono-layer crystalline
131 Book of Programme and Abstract for TACC2008 SiO2/Mo(112) films: while Pd atoms are small enough to penetrate into the film pores and strongly bind at the interface,
Au atoms are too large to penetrate into the structure and interact weakly with the film surface forming Au aggregates
even at temperatures as low as 10K.
Oxide thin films induce significant changes in the work function Φ of the metal support. This can be related to the charge
transfer at the interface between the oxide and the metal. For instance, SiO2 films which are bound to the Mo(112)
substrate by an oxygen atom, lead to the formation of a surface dipole which raises Φ. In other cases, where no charge
transfer occurs, like for TiO2/Pt(111) films, the change in the work function of the system is negligible. Films of ionic
materials like MgO or NaCl, on the contrary, induce a substantial reduction of work function change which is explained
with a “compression” effect, a mechanism of electrostatic nature.
The induced change in work function is intimately connected to another example of unique properties of oxide ultra-thin
films, i.e. the electronic communication between the metal substrate below the oxide layer and a metal atom or a cluster
deposited on the oxide film. Au atoms and clusters deposited on 2-3 layers thick MgO/Ag(100) or MgO/Mo(100) films
become negatively charged, at variance with their counterparts on MgO(100) with dramatic consequences on the
structure and shape of the supported clusters which grow two-dimensional on the thin films and three-dimensional on the
thicker films. This effect can also alter the charge state of point defects created in the oxide layer, thus altering the
chemisorption properties.
IN-MN030
Quantum Chemical Modeling of a Light-Driven Three Strokes Molecular Engine and Its Application in biological
Nanocavities
Xuebo Chen and Massimo Olivucci*
Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403, USA
In this work, we report on the studies of intramolecular proton transfer PES of indanyliden-2-carboxyyl-3,
4-dihydro-2H-pyrroline (see scheme) in gas phase and solvent environment using combined strategy of
CASSCF/CASPT2 and QM/MM(CASPT2//CASSCF/Amber) protocol. Upon the excitation of light, the switch molecule
undergoes the processes of fast excited state intramolecular proton transfer (ESIPT) with 6~7 kcal/mol barrier, cis-trans
isomerization, and the barrierless reverse proton transfer, respectively, and decays to trans-isomer in the ground state.
Similarly, the second beam of light drives trans switch molecule to go through above mentioned three processes leading
to starting point (R(E)) in the ground state. The molecular switch can function as “real engine” in this cycle, where the
process of photoinduced proton transfer is considered to be intake stroke (absorbs the energy of light) and the motion of
rotation looks like power stroke (drives rotary isomerization) and finally reverse proton transfer should be treated as
exhaust stroke (gets ready for another excitation cycle). We also attach this molecular engine with a cyclic peptide to
examine its efficiency. Ab initio molecular dynamic simulations at CPMD (CPMD/Gromacs) level demonstrates that
cis-trans isomerization followed by reverse proton transfer can achieve in 1~2 ps.
132 Book of Programme and Abstract for TACC2008 [1]Douhal, A. Science 1997, 276, 221.
[2] AndruniTw, T.; Ferre, N.; Olivucci, M. Proc. Natl. Acad. Sci. USA 2004, 101, 17908-17913.
OR-MN031
Electric field effects on electronic structures of BN nanotubes with defects or molecule intercalations
Wei He, Shuanglin Hu, Zhenyu Li, and Jinlong Yang
Hefei National Lab for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui
230026, China ([email protected])
It is well known that a transverse electric field leads to a decrease of the band gap of boron nitride nanotubes (BNNTs).
However, the field effects on defective BNNTs and on organic molecule encapsulated BNNT systems are unclear. In this
study, we use density functional theory (DFT) to calculate the electronic structures of these two kinds of systems under
zero and finite electric fields.
BNNTs with antisite, carbon substitution, single vacancy, or Stone-Wales 5775 defects are studied. The energy level of
the defect state shifts with the transverse electric field direction, due to the different electrostatic potential at the defect
site induced by the electric field.
An electrophilic molecule introduces acceptor states in the wide gap of BNNT close to the valence band edge, which
makes the doped system a p-type semiconductor. However, with typical nucleophilic organic molecules, deep occupied
molecular states instead of shallow donor states are observed. An external field reduces the energy gap of BNNT, thus
makes the molecular bands closer to the BNNT band edges and enhances the charge transfers between BNNT and the
molecules. The effect of the electric field direction on the band structure is negligible. The electrostatic shielding of
BNNT to the inside organic molecules is discussed. An interesting negative shielding is predicted, which is a quantum
effect of cooperating polarization. Organic molecule doping strongly modifies the optical property of BNNT, and the
absorption edge is red-shifted under static transverse electric field.
、
IN-0MN032
The investigation of nano-dimensional alloys thermodynamic properties
Golovnev Igor F., Golovneva Elena I., Fomin Vasily M.
133 Book of Programme and Abstract for TACC2008 Khristianovich Institute of Theoretical and Applied Mechanics Siberian Branch of Russian Academy of Sciences,
Institutskaya str. 4/1, 630090, Russia
To present day the problem of creation of nanotermodynamics didn’t arise, the researches by comparison of
thermodynamic, mechanical properties of nanostrustures obtained with the help of atomistic modeling and in the
framework of continual approach wasn’t realized. All of this stipulated the necessity of detailed investigation of
thermomechanical processes in metal alloy by nanoscale length by means of molecular dynamics method, the research of
external parameters influence and the direct comparison with results obtained as in the experiment as in the framework
classical thermodynamics and continual mechanics.
In the work the copper nanocluster by spherical form by radius 20 Ǻ was chosen. The simulation of copper alloy with
silver was performed by Monte-Carlo method; at this the percentage content of silver atoms was taken into account. The
EAM potential Voter [1] was used to describe the interaction between atoms copper, silver and each with other.
So, in the present work it is offered the calculation method of thermodynamical nanostructures properties by molecular
dynamics method. The offered method is based on first principles, and it was approved for the case spherical copper
nanoclusters and nanoalloys CuxAg1-x [2]. Moreover it was created the set of programs allowed to calculate the
thermo-mechanical properties of any alloys for which the interatomic potentials are known.
[1] Voter A.F. Los Alamos Unclassified Technical Report LA-UR-93-3901. 1993.
[2] Golovnev I.F., Golovneva E.I., Fomin V.M. Physical mesomechanics. 2007, 10, 5, 71–76.
OR-MN033
Theoretical Studies on Bis(triphenylsilyl)chromate—as a Homogeneous Model ofPhillips Cr/Silica Catalysts for
Ethylene Polymerization
Boping Liu, Zhen Liu, Qi Dong, Ruihua Cheng
State Key Lab of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237,
Shanghai, China
Although Phillips catalyst is still widely used in the industrial polyethylene processes, the mechanism of ethylene
polymerization over Phillips catalysts has not been made clear yet.1,2 The first alkylation step of the supported chromium
oxide by ethylene is particularly obscure and interesting. In this study, we apply quantum chemical modeling to study the
mechanism of reductive activation and ethylene coordination on Bis(triphenylsilyl)chromate(BCVI), which is a realistic
model of the real industrial Phillips catalyst. Also, Paired interacting orbital (PIO) method was used to investigate the
front orbital interaction between the Cr sites and the coordinated monomer ethylene.3 For reduced BCII molecule, two
stable coordination states were found and the binding energy was calculated separately. Next, both states are used to
investigate if and how polymerization may be initiated and propagated at the chromium centers. Both chromium sites
studied here show promising activity for ethylene polymerization, especially the site of BCII with one benzene ring
intra-coordinated to the Cr site. By combining theoretical investigations and well-defined experiments, one may get
closer to defining the chemical species that make the Phillips catalyst highly active for ethylene polymerization in the
near future.
This work is financially supported by the National Natural Science Foundation of China (No. 20744004 and
No.20774025).
[1] McDaniel, M. P. Adv. Catal. 1985, 33, 47-98.
[2] Groppo, E.; Lamberti, C.; Bordiga, S.; Spoto, G.; Zecchina, A. Chem. Rev. 2005, 105, 115-183.
134 Book of Programme and Abstract for TACC2008 [3]Liu, B. P.; Fang, Y. W.; Terano, M. Mol. Simul. 2004, 30, 963-971.
IN-MN034
Structure and Magnetic Properties of TM-Ligand Clusters and wires
Jinlan wang
Department of Physics, Southeast University, Nanjing, 211189, P. R. China.
Structural and magnetic properties of free-standing multi-decker sandwich clusters transition metal and ligand (organic or
inorganic molecules) sandwich clusters and their corresponding one-dimensional (1D) nanowires (n = ∞) are also studied
by means of all-electron gradient-corrected density functional theory.
The FeCp2 unit retains its molecular form in the TMn(FeCp2)n+1 (TM=V, Ti, Sc) clusters, but it is markedly deformed in
the Mnn(FeCp2)n+1 complexes. The magnetic moment of TMn(FeCp2)n+1 (TM =V, Ti, Mn) increases linearly with size n.
More strikingly, Tin(FeCp2)n+1 and Vn(FeCp2)n+1 exhibit giant magnetic moments 4, 8, 12μB and 1, 6, 11μB (n=1–3),
respectively. The Scn(FeCp2)n+1 clusters however are paramagnetic. Their 1D nanowires are all magnetic semiconductors
with the band gap of 1.395, 1.370, 0.667, 0.366eV for [TM(ferrocene)]∞, TM = V, Mn, Sc, Ti, respectively. The
[V(FeCp2)]∞ nanowire has the highest magnetic moment (5μB) per V- FeCp2 unit among the four nanowires.
We have designed a new inorganic metallocene sandwich [η6-V-(P6)2] and multidecker sandwich clusters up to V4(P6)5.
The binding energies of the Vn(P6)n+1 complexes increase rapidly from half sandwich to the smallest full sandwich and
become gradually afterwards. The HOMO-LUMO gap and the vertical ionization energy decrease with increasing cluster
size. The Vn(P6)n+1 clusters are non-ferromagnetic, and prefer the lowest available spin states. The smallest sandwich
cluster, V(P6)2, has the high stability and might serve as a building block for one-dimensional inorganic polymers with
high stabilities.
[1] Wang, J.; Acioli, P.A.; Jellinek, J. Am. Chem. Soc,2005, 127, 2812.
[2] Wang, J.; Acioli, P.A.; Jellinek, J. Phys. Chem. A 2005, 109, 10180.
[3] Wang,J.; et al., J.Chem. Phys. 2008,128, 104706.
[4] Zhang,X.; Wang, J., J. Phys. Chem. A 2008, 112, 296.
[5] Wang, J. et al. J. Phys. Chem. A, accepted.
[6] Zhang,X.; Wang, J., to be published.
OR-MN035
First-principles study of water clusters confined in nonpolar cavities modeled by carbon fullerenes
Lu Wang 1, Jijun Zhao 1, Haiping Fang2
1
State Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams, School of Physics and
Optoelectronic Technology, Dalian University of Technology, Dalian 116024, China
2
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
Encapsulation of (H2O)n clusters (n=1-22) in fullerene cages of different sizes (60-240 atoms or 0.73-1.41 nm in diameter)
have been investigated using density function theory. A linear relationship between cavity volume and maximum number
of the encapsulated water molecules has been obtained. The interaction between water molecules and fullerene wall was
identified as physisorption with adsorption energy of about 1.1kcal/mol per molecule. The equilibrium configurations of
small confined water clusters (n<12) roughly resemble those of gas-phase clusters, while larger water clusters tend to
adopt cage-like configurations when they are encapsulated in sufficiently large fullerene cages (i.e., diameter larger than
135 Book of Programme and Abstract for TACC2008 1.4nm). The dipole moments of the confined water clusters are smaller than those in the gas phase due to the screening
effect of the outer fullerene cage. The present simulation might shed some light on the behavior of water clusters
confined in the nonpolar cavities of biological interest.
5.
Cheminformatics and Drug Design IN-CD001
G-QSAR: A Novel Group Based QSAR Method
Subhash Ajmani, Kamalakar Jadhav and Sudhir A. Kulkawi
VLife Sciences Technoloies Pvt. Ltd.
Pride Purple Coronet, Ist floor, S No. 287, Barer Road, Pune 411 045, INDlA
In the past four decades the QSAR methodology has evolved from Hansch method, Free-Wilson analysis to conventional
2D/3D QSAR methods. These methods utilize independent substituent based descriptors
descriptors
based on
2D/3D
structure.
Although
these
or whole
molecule
various descriptors leave played important role in
identifying relationship with the activity, there always have been a challenge in terms of interpretation of these models.
Further, these models do not provide site specific clues for the improvement in molecular design. Therefore it is clear that
there is a requirement of QSAR method, which will allow flexibility to study molecular sites of interest. In addition,
unlike 3D-QSAR, this method should not depend upon conformational analysis and alignment of the molecules to
provide clues about sites and nature of interactions responsible for activity variation. Here we propose a new QSAR
methodology (G-QSAR) which utilize descriptors evaluated for the fragments of the molecules. These are generated
using specific fragmentation rules defined for a given dataset. Hence it allows to establish a correlation of chemical group
variation at different molecular sites of interest with the activity. This method also includes interaction of various
molecular sites (as cross terms) to analyze its effects in determining the activity. As a result, G-QSAR method provides
models with predictive ability similar or better to conventional methods. In addition it provide directions for sites of
improvement in the molecules thereby facilitating design of new molecules
IN-CD002
A Quantum of Common Sense in Crystallography
Kenneth M. Merz Jr
Department of Chemistry,Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida,
Gainesville, Florida 32611-8435
The traditional potential function used to model biological systems involves the use of simplified classical force field
methodologies for no better reason than the inherent size of most biological systems and the associated computational
expense. However, molecular systems are widely understood to have quantum mechanical features associated with their
interactions. Indeed, quantum chemical (QM) methods have had tremendous impact on our understanding of “small”
molecular systems, which raises the question can QM methods impact biology in the same way? In this presentation we
will focus on the application of QM methods to solve relevant problems in structural biology and structure-based drug
design (SBDD) that begin to address this question. In particular, we will focus on our developments aimed at using
quantum mechanical methods in X-ray refinement. Finally, we will briefly summarize our vision of the future application
of quantum chemistry to the solution of problems in structural biology and SBDD.
IN-CD003
136 Book of Programme and Abstract for TACC2008 Thermochemical Aspects of Radical Reactions
Johnny Hioe, Hendrik Zipse
Department of Chemistry and Biochemistry, LMU München, Butenandtstrasse 5-15,D-82131 München, Germany
The thermochemical stability of radicals can be defined as the "radical stabilization energy" (RSE) through isodesmic eq.
(1). This stability plays an outstanding role in a variety of reactions of synthetic and biological importance.
•CH3 + H-R
RSE
CH4 + •R
(1)
Using a selection of different theoretical methods suitable for the treatment of open-shell molecules, the stability of
radicals involved in enzymatic transformations will be quantified. Particular attention will be given to the comparison of
substrate radicals with open shell species located on the enzymatic protein structure.
[1] H. Zipse, Topics Curr. Chem. 2006, 263, 163.
IN-CD004
Md and Qmmm Modeling Successfully Predict Binding and Effectiveness Of Novel Colchicine Derivatives Against
Multiple Cancer Cell Lines.
Jack Tuszynski
Department of Experimental Oncology, Cross Cancer Institute and Department of Physics, University of Alberta,
Edmonton, Alberta, Canada
Colchicine is a highly toxic plant-derived alkaloid which inhibits microtubule polymerization by binding to tubulin
dimers. Currently, the chemotherapeutic value of colchicine is limited by its toxicity against normal cells. Theoretically,
this could be remedied by derivatizing colchicine to preferentially bind tubulin isotypes which are more common in
cancer cells than in normal body tissues, and particularly in those cancer types which are resistant to conventional
therapies. In recent studies, it has been demonstrated that class III ß-Tubulin over-expression is associated with
taxane-resistant subsets of non small cell lung cancer, advanced ovarian cancer, breast cancer and cancer of unknown
primary origin. Our study investigates the uses of Quantum Mechanics Molecular Mechanics (QMMM) and Molecular
Dynamics (MD) modeling to construct derivatives of colchicine which will bind class III ß-Tubulin with increased
affinity. Using QMMM and MD modeling techniques, 21 colchicine derivatives were designed to increase affinity for
class III ß-Tubulin by offering a better steric fit into the binding pocket . Derivatives were designed and tested in silico
before being synthesized by organic chemists at Oncovista Inc. of San Antonio, TX. The colchicine derivatives were then
tested in MTS cytotoxicity assays against up to seven different cancer cell lines with differing characteristics and
morphologies. Results were obtained by graphing the MTS absorbance readings, and calculating an EC50 Value (drug
concentration at which 50% of the drug’s effects are seen) using sigmoidal dose-response analysis. Colchicine has an
EC50 Value in the range of 10-7 M, and several of our novel derivatives (ie. CH-32, CH-34 and CH-35) were found to
have EC50 Values in the range of 10-9 M, while other derivatives (ie. CH-6, CH-7 and CH-21) were found to have EC50
values in the range of 10-5 M to 10-6 M. These results indicate that our derivatives have up to 100X greater and lesser
effectiveness than colchicine. Interestingly, comparative derivative cytotoxicity was found to correlate with theoretical
QMMM and MD modeling predictions. Successful derivatives warrant continued investigation, screening and
development. We propose that our modeling system may be used to design any variety of drugs for specific targets such
as vinca alkaloids, taxanes and peloruside.
Acknowledgements: Funding for this project has been provided by the Allard Foundation, Alberta Cancer Board,
Alberta Advanced Education and Technology, NSERC, and US Department of Defense.
137 Book of Programme and Abstract for TACC2008 IN-CD005
A new docking and screening method using a new operator based upon bio-informatics
Hideaki Umeyama, Daisuke Takaya,
MayukoTakeda-Shitaka, Genki Terashi, and Kazuhiko Kanou
School of Pharmacy, Kitasato University 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
Introduction Many disease-protein targets have been found form biochemical experiments. Druggable compounds
which inhibit or activate those significant protein targets must be researched rapidly. Many researches are using in-sillico
screening program such as DOCK, AutoDock and GOLD using classical mechanical potentials. We report the new
method which uses simulated annealing based on bio-informatics on the protein-ligand flexible docking.
Methods We use docking engine based upon bioinformatics such as protein structure prediction and effective usage for
many X-ray or NMR structures of protein-ligand complex. An amino acid sequence of the target protein which is query
sequence are aligned in the filter of CE Z-Score 3.7 for biological similarity significant with the PDB database with some
BLAST alignment methods. In the stage of ligand-docking, fingerprint (FP) is used as the basis set in the bio-informatics
based simulated annealing. FP is composed of two, three or four atoms. Moreover this FP includes the information of
atom-type such as used in Sybyl atom-type [[REF=]] and bond-type. Next FP alignment score is defined to determine the
docking pose of the ligand to be the most stable one.
Results we could make the docking and screening method based upon bio-informatics newly. The accuracy is almost
similar to the GOLD and GLIDE docking methods most famous, and higher than the DOCK, and AutoDock methods
famous.
Conclusions A new docking and screening method based upon bio-informatics were made, and this method covers new
docking poses different from classical mechanical potential methods.
IN-CD006
Topomer CoMFA – a new method in Lead Optimization
Stahl, Gunther
Tripos Inc., USA
The original CoMFA methodology was invented as the first 3D-QSAR technique about 20 years ago. Over many
successful examples in the literature it proved its usefulness in the drug discovery arena. The most challenging task in
CoMFA was always the creation of structural alignments of the molecules of interest. A variety of methods was applied
to solve the alignment problem. However, most attempts to automate the alignment task were unsuccessful. This has cast
a damning light on the usefulness of CoMFA. It also prevented CoMFA to become a screening tool in virtual screening
applications.
The development of the Topomer technology – first used to find shape similar molecules in databases – creates automatic
alignments as part of its methodology. Using these alignments as starting point for CoMFA resulted in very reliable and
extremely quick 3D-QSAR models.
The introduction of a new methodology like this always needs validation and comparison with existing methods to prove
that it is advantageous. We will present the validation studies done for this technology, its application in current research
projects as an outlook on possibilities of its further development.
Novel Interaction Between Influenza Neuraminidase And Oseltamivir And Its Implication On Virtual Screening
And Drug Discovery
Chen, Xiaowu
IN-CD008
Theoretical design of organic molecules with small internal reorganization energies
Yu-Chang Chang, Hsing-Yin Chen, Ming-Yu Kuo, Ito Chao
Institute of Chemistry, Academia Sinica Taipei, 11529, Taiwan
In recent years, organic molecules have been extensively explored for their use as semiconductors in optoelectronic or
electronic devices. In these applications, charge mobility in the device is of great concern. The electronic coupling
between adjacent organic molecules and the reorganization energy during a charge-transport process are two factors that
influence the rate of charge transport and hence the charge mobility. Presently, experimentalists address the former factor
much more than the latter. Therefore, there are two incentives that prompt us to ponder on the principles for designing
molecules with small internal reorganization energies (λ). First, to search for high-performance organic semiconductors
that outperform current materials, it is desirable to take both the electronic coupling and the reorganization energy into
account. However, it is not quite clear how small λ values can be achieved. Second, as λ is a basic property of molecules,
it is fundamentally intriguing and important to understand why certain organic molecules have small λ values while
others do not. By studying known organic semiconductors and testing of new compounds,1-3 we have concluded several
strategies that can reduce λ values.2,3 With such knowledge, theoretical design of molecules with λ values significantly
smaller than that of pentacene have been achieved.3,4
[1] Chen, H.-Y.; Chao, I. Chem. Phys. Lett. 2005, 401, 539.
[2] Chen, H.-Y.; Chao, I. ChemPhysChem 2006, 7, 2003.
[3] Kuo, M.-Y.; Chen, H.-Y.; Chao, I. Chem. Eur. J. 2007, 13, 4750.
[4] Chang, Y.-C; Chao, I. manuscript in preparation.
IN-CD009
Origin of Reaction Barriers and Rational Design in Chemistry
F. Matthias Bickelhaupt
Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der
Vrije Universiteit, De Boelelaan 1083,NL-1081 HV Amsterdam, The Netherlands
Reactivity is one of the central issues (if not the core business) of chemistry. Yet, our understanding of chemical
reactivity, in particular, the height of reaction barriers, still lags behind the minute understanding that we have today of
molecular structure and stability. What is missing is a general model that provides physical insight into why a particular
reaction has a higher or lower barrier than another (competing) reaction.
Here, we present the Activation Strain model which aims at providing such insight into chemical reactivity, in terms the
reactants. In the Activation Strain model, the potential energy surface ∆E(　) along the reaction coordinate is
decomposed into the strain energy ∆Estrain(　)
plus the interaction energy ∆Eint(　)
associated with the geometrical deformation that the reactants undergo,
between the deformed reactants: ∆E(　) = ∆Estrain(　)
+ ∆Ein(　)
139 Book of Programme and Abstract for TACC2008 We provide examples of applications of the Activation Strain model to elementary organic and organometallic reactions,
in order to illustrate how our approach may serve to achieve a more rational design of catalysts and chemical reactions in
general.
[1] G. Th. de Jong, F. M. Bickelhaupt, ChemPhysChem 2007, 8, 1170.
[2] A. P. Bento, F. M. Bickelhaupt, J. Org. Chem. 2007, 72, 2201.
[3] M. A. van Bochove, M. Swart, F. M. Bickelhaupt, J. Am. Chem. Soc. 2006, 128, 10738.
IN-CD010
Study of the ligand – biological receptor interactions for Co(II), Cu(II) and Zn(II) complexes with oxicam
derivatives using “Molecular Docking” and QSAR procedures
Adrian Beteringhe,1 Daniela C. Culita,1 Gabriela Marinescu,1 Sultana Nita,2 Costinel Lepadatu1 and Luminita Patron1
1
Institute of Physical Chemistry ”Ilie Murgulescu” of the Romanian Academy, Laboratory of Coordination and
Supramolecular Chemistry, Splaiul Independentei 202, 060021, Bucharest, Romania
2
National Institute for Chemical Pharmaceutical Research and Development ICCF, Calea Vitan 112, 031299, Bucharest,
Romania
The design and prediction of intra-molecular complexes play a decisive role in the effort to synthesize new therapeutic
agents for the treating or of the curing of disease or disorders.[1]
One of the most useful procedures used in such investigations is the Molecular docking which can in principle provide
information regarding the interaction between the complex compounds and biological receptor.
It has been in this way studied the molecular docking energies of the Co(II), Cu(II) and Zn(II ) complexes obtained with
myeloperoxidase oxicam derivatives. The lowest energy has been obtained for Cu(II) – ampiroxicam myeloperoxidase
complexes (E = -1.854 kcal/mol).
The molecular docking interaction energy values have been used as a response function in QSAR procedures using
finger-print descriptors, and namely the electronegativity of the atoms in molecule for OMO/UMO states (Occupied
Molecular Orbitals / Unoccupied Molecular Orbitals).[2] Such descriptors have provided us information concerning the
mechanism and the participation of the atoms to the ligand – biological receptor interaction.
[1] J. Apostolakis, A. Pluckthun, A. Caflisch, J. Comp. Chem. 1998, 19, 21.
[2] G. Marinescu, L. Patron, D. C. Culita, C. Neagoe, C. I. Lepadatu, I. Balint, L. Bessais and C. B. Cizmas, J. Nanopart.
Res. 2006, 8, 1045.
OR-CD011
A Structural and Free Energy Analysis of Ag+ Complexes to Five Small Peptides
Tamer Shoeib1,2 and Barry L. Sharp1
1Department of Chemistry, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK.
2Department of Chemistry, British University in Egypt, El Sherouk, Egypt.
The complexes of Ag+ with the peptides MetGly, ProGly, GlyPro, GlyHis and GlyProAla were investigated using hybrid
density functional theory at the B3LYP/DZVP level.
Structural information and relative free energies are presented for
140 Book of Programme and Abstract for TACC2008 several isomers for each of the five complexes.
Each of the global minima found for the five complexes is a
charge-solvated ion. An important finding is that the Ag+-ProGly is the only complex where a salt bridge structure is
energetically favored occurring at 4.0 kcal mol-1 higher in free energy than the global minimum. The Ag+ ion in this salt
bridge structure is attached to the carboxylate anion of zwitterionic ProGly in which the terminal amino nitrogen is
protonated. For all the other complexes studied, the salt bridge structure occurs at much higher energies. All the
dipeptide complexes with Ag+, but one, exhibit a di- or tri-coordinate metal where the sites of attachment are amino and
carbonyl groups. However, the highest coordination numbers are not always the global minima due to steric costs. The
global minimum of the Ag+-GlyProAla complex is the only structure found in this study where the metal is
tetra-coordinated, binding to the terminal amino nitrogen and all three carbonyl oxygen atoms. Silver binding to sulfur
and imidazole nitrogen atoms of MetGly and GlyHis respectively are present in the three most energetically favored
species in each of these cases
OR-CD013
Enhancing Ligand Binding Affinity Predictions by Retraining Docking Scores with QSAR Models
Meihua Tu *, Allison Dickey #, Gayle Schulte *
* Pfizer Global Research & Development, Groton, Connecticut
# Department of Chemical Engineering, UC Davis, Davis California
One reason that a Structure Based Drug Design (SBDD) scoring function cannot accurately predict drug-receptor binding
affinity is that it was trained with a diverse set of targets and ligands. Hence, it might miss the target specific
information. Another shortcoming of such general scoring function is that almost all of them do not consider protein
flexibility.
To overcome these limitations, we use existing SAR data of a target to retrain a general scoring function to
be a target specific scoring function.
In our approach, different docking/scoring programs are evaluated for a specific target. The docking score that can best
rank ordering binding affinity will be used for further model building.
Besides docking scores, descriptors used in our
model building include ligand physical chemical properties related to charge, size, hydrophobicity, pKa, etc.
Our final
model is a Cubist regression tree model from the most predictive docking score and the ligand properties.
In this presentation, we will show how this technique helped to improve binding affinity predictions for CETP and other
target.
IN-CD014
Computation of EPR Parameters for Transition Metal Complexes and Metalloenzyme Sites
Martin Kaupp
Universität Würzburg
The computation of EPR parameters for transition metal complexes by DFT methods is still a significantly larger
challenge than it is for organic radicals [1]. The reasons are a) The strong dependence on the quality of the
exchange-correlation functional [2] – so far no “best” functional is available. Progress is hopefully possible with novel
local hybrid functionals [3]. b) Relativistic effects are more pronounced and require, e.g., inclusion of spin-orbit
contributions to metal hyperfine couplings [4], inclusion of scalar relativistic effects, and consideration of spin-orbit
effects beyond leading order for g-tensors [5]. When taking these points into account, even the current methodology
possesses appreciable predictive power. Application examples from the following areas will be provided:
Reinterpretation of EPR parameters for blue copper protein sites [6], application to mono- and multinuclear manganese
141 Book of Programme and Abstract for TACC2008 complexes relevant for photosystem II [7], understanding hyperfine tensors in vanadoarenophanes [8], prediction of EPR
spectra for molybdenum [9] and tungsten enzyme sites and model complexes, evaluation of the nature of Allred’s
[Hg(cyclam)]3+ [10].
[1] Calculation of NMR and EPR Parameters. Theory and Applications (Eds. M. Kaupp, M. Bühl, V. G. Malkin)
Wiley-VCH, Weinheim 2004.
[2] M. Munzarová, M. Kaupp J. Phys. Chem. A 1999, 103, 9966.
[3] See, e.g.: M. Kaupp, H. Bahmann, A. V. Arbuznikov J. Chem. Phys. 2007, 127, 194102, and references therein.
[4] C. Remenyi, A. V. Arbuznikov,. R. Reviakine, J. Vaara, M. Kaupp J. Phys. Chem. A 2004, 108, 5026.
[5] S. Komorovský, M. Repiský, O. L. Malkina, V. G. Malkin, I. Malkin, M. Kaupp J. Chem. Phys. 2006, 124, 084108; I.
Malkin, O. L. Malkina, V. G. Malkin, M. Kaupp J. Chem. Phys. 2005, 123, 244103.
[6] C. Remenyi, R. Reviakine, M. Kaupp J. Phys. Chem. B 2007, 111, 8290.
[7] S. Schinzel, R. Müller, M. Kaupp Theor. Chem. Acc. 2008, 120, 437.
[8] H. Braunschweig, M. Kaupp, C. J. Adams, T. Kupfer, K. Radacki, S. Schinzel J. Am. Chem. Soc. 2008, 130, 11376.
[9] J. Fritscher, P. Hrobárik, M. Kaupp Inorg. Chem. 2007, 46, 8146; J. Phys. Chem. B 2007, 111, 4616.
[10] P. Hrobárik, M. Kaupp, S. Riedel Angew. Chem., in press.
OR-CD015
An optimized method for structure-based ligand optimization
Jian Shen and Roy Vaz
Sanofi Aventis, Inc. 1041 Route 202-206, PO Box 6800, Bridgewater, NJ,
08807, USA ; email: [email protected]
The molecular-mechanics-based interaction energy has long been used in drug designs owing to its speed and simple
interpretation [1-3]. Coupled with ligand docking and implicit salvation calculation, the method can account for many
variations in receptor-ligand binding, and thereby provides a practical way for selecting synthetic targets in lead
optimization. Challenges in using the method include parameter optimization, result managing and user friendly interface.
More recently, a few software venders begin to supply similar tools to ease some difficulties in these calculations. We
will discuss these approaches as well as our own experience along the line.
IN-CD016
Using EADock, a new docking program based on the CHARMM force field, to design inhibitors of important
cancer protein targets
Michielin, Olivier
In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches
suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high
accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed
when the binding mode of lead compounds is not determined experimentally but is required for structure-based lead
optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid
evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity.
EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was
carried out on more than 260 crystallized protein-ligand complexes. Using local dockings or blind dockings, high success
rates of 75 and 65% respectively were obtained.
142 Book of Programme and Abstract for TACC2008 The use of EADock in real drug design applications will be illustrated by the development of micro and nano-molar
range ligands for a variety of important targets in oncology.
OR-CD017
A method for building virtual combinatorial chemical library
Junhui Gao
Software Development Department,Technic Director
Shanghai Center for Bioinformation Technology
F1.12,No.100 QinZhou Road,Shanghai,China 200235
This work is a method for building virtual combinatorial chemical library. By improving SMILES format, adding the
position description for replacing site, we can describe the backbone and fragment of molecules,then by using the full
permutation method and energy optimized program, we can build virtual combinatorial chemical library.
The author developed the software in windows style.Before building,by entering ADME filters,user can discard
molecules which may be not good in theory.Then the molecules generated in chemical library can be observed in graphic
environment. In additon,adding,deleting and updating fragement of molecule in database are supported.
OR-CD018
Towards accurate protein-ligand docking: Implementation of a combined quantum mechanical (QM) and
polarizable molecular mechanical (MMpol) model
Qiantao Wang and Richard A. Bryce,
School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
Virtual screening of compounds, especially using protein-ligand docking, has been widely used in drug design; it
provides a convenient way to identify potential lead molecules against a target receptor. The quality of protein-ligand
docking relies on the accuracy of the protein-ligand scoring function. In this work, we seek to employ a combined
QM/MM approach to score the ligand, treating the ligand quantum mechanically and the protein using a molecular
mechanics force field. Furthermore, we refine our classical model of the protein by incorporating explicit electronic
polarizability using atom-centred point dipoles (an adaptation of the QM/MMpol model). We discuss here the theoretical
basis of our implementation of the QM/MMpol model in the widely-used simulation package, AMBER, for NDDO-based
QM methods. Using this model, we find an improvement in accuracy for describing cation-pi interactions compared to
non-polarizable QM/MM approaches. Further model refinement also yields improved performance in describing
interactions representative of biological contacts. The implications for improved scoring of protein-ligand docking poses
are discussed.
OR-CD019
Force-Field Based Scoring Function and Molecular Dynamics Refinement for Virtual Drug Screening
Yin, Shuangye
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA
Virtual screening is becoming an important tool for drug discovery. However, the application of virtual screening
has been limited by the lack of accurate scoring functions for protein-ligand binding [1, 2]. Here, we present a novel
143 Book of Programme and Abstract for TACC2008 scoring function, MedusaScore, for evaluating protein-ligand binding. MedusaScore is based on extension of our Medusa
force field [3, 4] and describes the physical protein-ligand interactions including van der Waals, solvation and hydrogen
bonding energies. To ensure the best transferability of the scoring function, we do not use any protein-ligand
experimental data for parameter training. We benchmark the MedusaScore for docking decoy recognition and binding
affinity prediction and find superior performance compared to other widely used scoring functions. Statistical analysis
indicates that major source of inaccuracy of MedusaScore may arise from the unaccounted entropic loss upon ligand
binding, which suggests avenues of approach for further MedusaScore improvement. We also demonstrate that Discrete
Molecular Dynamics (DMD) [5] simulations with MedusaScore can recover native-like structures from incorrect poses
generated by docking programs.
[1] Warren, G. L. et al. J. Med. Chem. 2006, 49, 5912
[2] Wang, R. X. et al. J. Chem. Inf. Comput. Sci 2004, 44, 2114
[3] Ding, F. and Dokholyan, N. V. PLoS. Comput. Biol. 2006, 2, e85
[4] Yin, S. Y, Ding, F. and Dokholyan, N. V. Nat. Methods 2007, 4, 466
[5] Ding, F. et al. Structure 2008, in press.
IN-CD020
PubChem: NIH's public repository for biological test results
Yanli Wang, Steve Bryant
National Center for Biotechnology Information, National Library of Medicine,National Institutes of Health, Bethesda,
MD 20894, USA.
PubChem(http://pubchem.ncbi.nlm.nih.gov) is a public archive for chemical structures and the results of biological
activity tests hosted by the U.S. National Institutes of Health(NIH). PubChem currently contains about 40 million
chemical substance records, representing 19 million unique chemical structures, and the results of over 1000 biological
screens, with a total of about 28 million substance test results. PubChem’s contents are derived from the voluntary
contributions of over 70 commercial, academic and government organizations, with the majority of biological test results
derived from NIH’s Molecular Libraries project. The goal of PubChem is to make comprehensive information about
chemical structures and biological test results freely accessible to biomedical researchers.
To this end, PubChem
suoports several ways to retrieve chemical and biological information from bioassay results as well as a number of means
to conduct in-depth analysis and comparison of the biological test results.
PubChem continues to host and distribute
the biological test results from the NIH Molecular Libraries project as this project enters into the probe production phase.
PubChem also welcomes further voluntary contributions of chemical structure and biological test information via a web
based deposition interface .
(http://pubchem.ncbi.nlm.nih.gov/deposit/deposit.cgi).
OR-CD021
HyperProtein -a New Bioinformatics Program
Neil S. Ostlund
Hypercube, Inc., 1115 NW 4th St., Gainesville, Florida, USA
With the help of an NIH SSTR grant held jointly by Hypercube, Inc. and the Foundation for Applied Molecular
Evolution, a new commercial program called HyperProtein has been created. This program combines the protein
molecular modeling capabilities of HyperChem with new bioinformatics and phylogenetics capabilities. For example,
144 Book of Programme and Abstract for TACC2008 one can click on the branch of an evolutionary tree and display, in 3D, the amino acid residues that differ in the two
genetic species separated by the branch of the tree.
HyperProtein has a new multi-window Graphical User Interface (GUI) resembling that of Visual Studio with a variable
number of sizeable windows in a grid pattern containing molecular structures, sequence alignments, phylogenetic trees,
text, etc.
The GUI is organized around Projects consisting of components of various data objects that update
synchronously.
Numerous options are available for displaying
and manipulating the fundamental bioinformatics
entities, sequence alignments and their corresponding representations as phylogenetic trees.
The unique capability of HyperProtein is probably its combination of molecular modeling and bioinformatics within the
same product and GUI. While its functionality consists of multiple algorithms for alignment, tree generation, prediction
of structure from sequence, and other operations on protein sequences and structures,
most of these have been
available before in other (possible text-oriented) products. HyperProtein takes these existing capabilities and puts them
together into an easy to use, graphically-oriented product.
The product is scriptable, using either TCl or Perl scripts and as such its capabilities can be extended to include,
specifically, new algorithms for manipulating sequences.
In its present form, HyperProtein is solely focused on protein families and their sequences rather than the corresponding
nucleic acid sequences. As such, some evolutionary information is missing that the use of codons would improve upon.
A future version will expand the product to become intelligent about both amino acid sequences and nucleic acid
sequences.
IN-CD022
In silico platform for mechanistic study of Traditional Chinese Medicine
Lin Tao1, Jing Zhao1, Kailin Tang1, Hao Ye1, Zhiwei Cao1,2
1, Shanghai Center for Bioinformatics Technology, 100 Qinzhou Road, Shanghai 200235, China
2,School of Life Sciences and Technology, 1239 Siping Road, Tongji University, Shanghai 200092, China
To understand the molecular mechanism and pharmacology of bioactive compounds derived from Chinese medicinal
plants is helpful to facilitate effects evaluation for Chinese herbal medicine. It is also important to accelerate new drug
development by understanding the mechanism of Traditional Chinese Medicine (TCM). By integrating a series of
high-quality curated TCM, pharma-informatics databases and a drug-target auto-search algorithm (INVDOCK), we build
an in silico platform for the mechanistic analysis of Chinese herbal medicine. With this platform, we can indentify
bioactive compounds in Chinese medicinal plants, predict potential drug target proteins, and analyze molecular
mechanism from the view of system biology, such as metabolic pathway analysis, protein-protein interaction network
analysis, protein-disease relationship analysis, drug target comparison between western drug and Eastern drug, and so on.
Some of technologies and databases have been either published in top international journals or been patented. In the
projects of ganoderic acid D and multi-ingredients of ginkgo leaf, several important targets predicted with our platform
have been further confirmed by experiments. All these show that the platform may potentially be used as a fast-speed and
low-cost tool to facilitate the study of molecular mechanism of TCM.
IN-CD023
Wang, Yifei
Computational Investigations of Enzyme Mechanisms: An Application to the B12-Independent Glycerol
Dehydratase
David M. Smith
Centre for Computational Solutions in the Life Sciences, Rudjer Boskovic Institute, Zagreb 10002, Croatia.
The biological dehydration of 1,2-diols has been traditionally thought to be exclusively dependent on Coenzyme B12, in
a non-REDOX process. Recently, however, a B12-independent enzyme system has been discovered in which glycerol is
dehydrated with the assistance of an Fe-S cluster that effects the reductive cleavage of S-adenosylmethionine (SAM)
[1,2]. In this contribution, results from a computational investigation of the mechanistic aspects of this reaction will be
presented. Particular focus will be placed on the substrate transformation and its comparison to the B12-dependent
system. The significance of the similarities and differences between the two biological dehydration strategies will be
discussed.
[1] C. Raynaud, P. Sarcabal, I. Meynial-Salles, C. Croux, P. Soucaille, Proc. Natl. Acad. Sci. USA, 2003, 100, 5010.
[2] J. R. O’Brien, C. Raynaud, C. Croux, L. Girbal, P. Soucaille, W.N. Lanzilotta, Biochemistry, 2004, 43, 4635.
IN-CD025
Controlling the Formation of Low Barrier Hydrogen Bonds
Chin-Hui Yu
Department of Chemistry, National Tsing Hua University101 Kuang Fu Road, Section 230013 HsinChu , Taiwan
The hydrogen bond (HB) between histidine and aspartic acid as part of the active site in many enzymes brings low barrier
hydrogen bonds (LBHBs) to the attention of scientists [1]. The focuses are the possibility of the formation of LBHBs,
factors that tune the strength of the HBs, and the solvation and microsolvation effects on LBHBs as well as HBs.
The formation of LBHB can be studied with satisfactory precision by investigating the α-hydrogen bond (α-HB) in a
cluster ion made from trichloroacetic acid (TcaH), 5-methyl-1H- imidazole (MimH) and acetate ion (Ac−).
[Tca−HMim−HAc]− The proton affinity (PA) of the [Tca−HMim]− ion [2] correlates nearly linearly with the position of H　and this property of
the [Tca−HMim]− ion has been successfully used for the analysis of LBHBs [3,4]. Calculations with other clusters with
similar geometries showed the results obtained with the [Tca−HMim]− ion can be generalized.
Both minimum energy positions of Hα within the α-LBHB can be described as individual hydrogen bonds and the LBHB
is formed from the mutual interactions of the components [2]. This model can be used to describe the proton movement
in the α-HB [3] as well as the existence of LBHBs [2]. However, the formation of LBHBs is further complicated by a
strong geometric factor [4]. The dissociation behaviour of the α-double hydrogen bonds showed that the commonly
assumed prerequisite for LBHB formation, ΔPA = 0, is strictly true only for infinitely long LBHBs and hence needs to be
reconsidered.
Calculations on the LBHB between 4,5-dihydroimidazole and various amines revealed the existence of a minimum bond
length for LBHB, which restricts the bond length of LBHBs in the range of 2.66 Å to 2.77Å in this system.
146 Book of Programme and Abstract for TACC2008 The general influence of the chemical environment on a LBHB is studied with model systems involve several oriented
water molecules as well as with PCM calculations on [TcaH−MimH]. The results show that neutral LBHBs can be
stabilized effectively either by correctly positioned water molecules or by a solvent cage.
1. J. A. Gerlt, M. M. Kreevoy, W.W. Cleland, P. A. Frey Chem. & Biol. 4 (1997) 259-267
2. Lankau, T.; Yu, C.H. Phys. Chem. Chem. Phys. 2007, 9, 299.
3. Lankau, T.; Yu, C.H. Chem. Phys. Lett. 2006, 424, 264.
4. Lankau, T.; Yu, C.H. Chem. Phys. Lett. 2007, 433, 275.
IN-CD026
Quantum Mechanical and Experimental Study of Anomerization Pathways of Pyranosides
Hiroko Satoh,1,2 Jürg Hutter,3 Hans Peter Lüthi,1Shino Manabe,4 Kazuyuki Ishii,4 Yukishige Ito4
1
Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland,2National Institute of Informatics, 101-8430
Tokyo, Japan,3Institute of Physical Chemistry, University of Zürich, 8057 Zürich,Switzerland,4RIKEN (The Institute of
Physical and Chemical Research), 351-0198Saitama, Japan
Stereocontrol of glycosides is an important issue in carbohydratechemistry. Crinch and Manabe independently found that
pyranosides with N-benzyl-2,3-trans-oxazolidinone groups can easily anomerize from the β to α direction1,2. Based on
further experimental studies, we assumed that the reaction was induced by endo-cleavage. It has been known that the
endo-cleavage can occur under strong acid or protic conditions, but the anomerization took place under weak Lewis acid,
where general glycosides are never endo-cleaved.
We investigated this phenomenon for model structures with B3LIP/6-31G(d,p) using Gaussian03. The computations
showed that the structures with N-benzyl-2,3-trans-oxazolidinone groups have clearly lower transition state energies. It is
also found that the length of the C1-O bond in the pyran ring became longer with a Lewis acid approaching, and the bond
in the structures with N-benzyl-2,3-trans-oxazolidinone groups was easier to break. These series of computations suggest
that a Lewis acid induces the bond between the pyran-oxygen and anomeric carbon to break, followed by rotation of the
C1-C2 bond to give the α form via lower transition states. All results are consistent with the experiments. Further
experiments performed on related compounds are in good agreement with the computations.
[1] Crinch, D.; Vinod, A. U. J. Org. Chem. 2005, 70, 1291-1296.
[2] Manabe, S.; Ishii, K.; Ito, Y. J. Am. Chem. Soc. 2006, 128, 10666-10667
OR-CD027
Molecular Dynamics Study of Interaction between DNA and POU Cooperating with HMG Implies the
Mechanism of Synergistic Transcription Performed by Oct and Sox
Peng Lian†,ᇞ , Yongxiang Shi*,† , Yuxiang Bu*,‡ , Dongqing Weiᇞ
†School of Life Science, ‡Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China；
ᇞDepartment of Bioinformics, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China；
Transcription factors Oct and Sox play pivotal roles in regulating early embryonic stem cells’ development and
determining cell fate. Generally, their binding sites are adjacent and they regulate genes’ expression together. Many
biologists and chemists are attracted by this co-operational transcription, but details of the reaction course are known
little. In this study, we focus on the synergistic transcription’s actual executors POUS and HMG domain to explore their
mechanism. Molecular dynamics (MD) and steered molecular dynamics simulations (SMD) are used to get a clear view.
147 Bo
8 Two importannt kinds of intteractions, PO
OUS-DNA and POUS-HMG
G, are investigated. It is foound that they play differennt
roles both in polymerizatioon and depolyymerization of the POU/HM
MG/DNA ternnary transcripption complex
x. POUS-DNA
A
mploys high innteraction eneergy to mainttain the stabiliity of ternary complex. Hoowever, interaaction betweenn
interaction em
POUS and HM
MG has the abbility to regulaate the speed of both reactions. These finndings suggest that artificiaal mutations onn
POUS-DNA interface are more effectivve to interdict the forming of
o the ternaryy complex andd they will pro
ovide valuablee
B
theoretic referrences for Devvelopmental Biology.
OR-CD028
New Antivirral Compoun
nd Discovery and Design through Co
omputational Screening aand Scaffold Replacemen
nt
against Denggue Virus E Protein
P
Zhigang Zhouu, Mansoora Khaliq, Jae-E
Eun Suk, Ze Li,
L Chinmay Patkar,
P
Richaard J. Kuhn, M
Mark Cushmaan, Carol Bethh
Post
o Medicinal Chemistry and
a Molecularr Pharmacolo
ogy and Depaartment of B
Biological Sciences, Purduee
Department of
University, West
W Lafayettee, IN 47907, USA
U
world. There is no effectivee
Mosquito-borrne flavivirusees are human pathogens off a major burden in many reegions of the w
medicine avaailable to treatt the infectionns caused by dengue,
d
Westt Nile, etc flavviviruses. To find and develop drugs foor
these diseasess is important to public health. In the worrk, potential compounds
c
haave been screeened from chemical libraries
through a serries of compuutational highh through-put screening app
proaches. Sevveral compounnds have beeen found to bee
active to inhiibit virus reprroduction at μM concentraations. One of
o these comppounds was fo
found by saturration transfeer
difference NMR
N
spectrooscopy to bind
b
virus and to com
mpete for binding
b
E protein with
h the ligandd
N-octyl--　-D
D-glucoside, known
k
to bindd the pocket. Two of these active compoounds have beeen selected as
a templates too
design new compound. Neew compounds were designned by an approach combinning traditionaal design and computationaal
structure-baseed design andd were syntheesized. Severaal newly-desiigned compouunds have demonstrated very promisingg
activity closee to nM conccentration in biology
b
test. Optimization of these leadd compounds to improve their drugablee
properties is undergoing.
u
monstrates a successful
s
druug discovery and
a design app
proach based on
o computatioonal structure--based design.
This work dem
Figure 1. Thee target: Denguue E protein with
w binding (B
BOG) site at middle.
m
OR-CD029
V
Bond (MS-EVB) Model
M
for Pro
oton Transferr in Imidazolle
A Multistate Empirical Valence
Tianying Yann,1 Hanning Chhen,2 Gregoryy A. Voth*,2
1Institute of New
N
Energy Material Cheemistry, Department of Maaterial Chemisstry, Nankai U
University, Tiianjin 3000711,
China
B
M
Modeling
and Simulation and
a Department of Chemisstry, Universitty of Utah, Salt Lake Cityy,
2Center for Biophysical
Utah 84112-00850, USA
148
8 Book of Programme and Abstract for TACC2008 A multistate empirical valence bond (MS-EVB) model, with multiple reaction centers on the proton donor molecule
(MS-EVB), has been developed for the proton solvation and transportation in the imidazole system. The model was
constructed by fitting the ab initio potential energy surface for the proton shuttling between two imidazole molecules, and
also calibrated against ab initio optimized imidazolium clusters. Molecular dynamics simulation was performed for an
excess proton in imidazole liquid at 393 K, and the Grotthuss mechanism (structure diffusion) and the vehicular
mechanism are compared for the proton diffusion process. The reorientational motion of the imidazole molecules within
the first solvation shell of the proton, as correlated to the proton diffusion, was also investigated.
IN-CD030
Ab initio NMR chemical shift calculations using fragment molecular orbitals
Satoshi Yokojima1, Qi Gao1,2, Jun-Wei Shen1, Toshiyuki Kohno3, Toyokazu Ishida4, Dmitri G. Fedorov4, Kazuo Kitaura4,
Minoru Sakurai2, Masamichi Fujihira2, Shinichiro Nakamura1
1Mitsubishi Chemical Group Science and Technology Research Center, Inc.,1000 Kamoshida-cho, Aoba-ku, Yokohama
227-8502, Japan;
2Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama
226-8501, Japan;
3Mitsubishi Kagaku Institute of Life Sciences (MITILS), 11 Minamiooya, Machida, Tokyo 194-8511, Japan;
4National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568,
Japan
To understand functions of a biomolecule and the role of the structure in drug design, it is important to determine the
structure and its dynamics accurately in vivo and in vitro. NMR is appropriate for such experiments, but it requires
difficult assignments. Thus, it is desirable to develop a fast and accurate computational method to aid in determining the
structure by NMR.
We proposed an efficient computational method to calculate NMR chemical shifts of large biomolecular systems. It is
based on the fragment molecular orbital (FMO) method[1] combined with the gauge-including atomic orbital (GIAO)
and continuous set of gauge transformations (CSGT) methods. The method accurately reproduced the conventional ab
initio NMR values for a 10-residues peptide [2]. It was also applied to ubiquitin (76 amino-acid residues), and the
calculated chemical shifts agree well with experimentally measured shifts [2].
In this talk, these results will be explained briefly. In addition, our current effort to achieve higher accuracy will be given.
[1] K. Kitaura, E. Ikeo, T. Asada, T. Nakano, and M. Uebayasi, Chem. Phys. Lett. 1999, 313, 701; D.G. Fedorov, K.
Kitaura, J. Chem. Phys. 2004, 120, 6832.
[2] Q. Gao, S. Yokojima, T. Kohno, T. Ishida, D. G. Fedorov, K. Kitaura, M. Fujihira, S. Nakamura, Chem. Phys. Lett.
2007, 445, 331.
OR-CD031
Improved Protein Long Loop Structure Prediction
Zhiyong Zhou1, Kai Zhu1, Yixiang Cao1, Richard A. Friesner2, Ramy Farid1
1. Schrodinger, Inc, 120 West 45th Street, New York, NY 10036, USA
2. Dept. of Chemistry, Columbia University, New York, NY 10027, USA
149 Book of Programme and Abstract for TACC2008 The prediction of protein long loop geometries (up to ~11-13 residues) has historically presented significant difficulties
for protein structure prediction methods. To improve long loop prediction, a general purpose, energy-based scoring
function has been developed that incorporates a modified hydrophobic term and a variable internal dielectric constant as
a function of interacting residues. This scoring function has been implemented within the Prime 2.0 application along
with an improved multi-stage sampling methodology. Validation was performed using a diverse set of 197 loops ranging
from 4-12 residues in length. We find 97% of loops with 7-9 residues and 86% of loops with 10-12 residues are predicted
with an RMSD of less than 2.5 A. These long loop predictions, to our knowledge, represent the best results presented in
the literature to date. Physical rational for the variable internal dielectric approach and the utility to structure-based
design of improved long loop prediction will be illustrated.
IN-CD036
Activity in the Thioredoxin Family: Structure, Dynamics and Electrostatics
Lennart Nilsson,
Department of Biosciences and Nutrition, Karolinska Institutet
The variety of functions performed by proteins of the thioredoxin superfamily, including glutaredoxins, involves the wide
range of redox potential associated with the -Cys-X-X-Cys- motif found in their active sites. The determinants of these
differences in redox potential are still obscure. A better understanding requires a detailed characterization of the reduced
state of these enzymes, especially because the lowered pKa of the reduced N-terminal active-site cysteine is a key feature
of these enzymes' chemistry, including their redox potential. Analysis of the factors controlling this pKa is complicated
by the apparent structural heterogeneity of the reduced active sites across glutaredoxins. We used long molecular
dynamics simulations and electrostatic calculations to analyze the structure, dynamics and electrostatics in several
members of this family, also including mutants. Comparison with experimental data is drawn whenever possible. It is
shown that a dynamic model is essential to capture the structural properties of the cationic sidechains around the
-C-X-X-C-sequence in the active site.
6.
Chemical Modelling for a Sustainable Environment IN-EV001
Role of Extracellular Domains in Modulating Ion Permeation through the Nicotinic Receptor Channel
Chen, Xiaolin
Oak Ridge National Laboratory, USA
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels responsible for neurotransmitter-mediated
signal transduction at synapses throughout the central and peripheral nervous systems. Binding of neurotransmitter
molecules to subunit interfaces in the N-terminal extracellular domain induces structural rearrangements of the
membrane-spanning domain permitting the influx of cations. Understanding the mechanisms of gating and ion
permeation in nAChRs has been a long-standing challenge in biophysics. In this talk, I will present a microscopic view of
how cationic ions transport through the entire length of the nAChR channel. Our calculation indicates the existence of a
hydrophobic constriction in the middle of the pore, substantiating the hydrophobic gating hypothesis for the nAChR.
Moreover, our simulations, in conjunction with some preliminary experimental data on the nAChR and the acetylcholine
binding protein, have pointed to another possible location of the charge selectivity region - a ring of arginine residues
located at the extracellular domain. This region has not been implicated in contributing to cation selectivity and represent
150 Book of Programme and Abstract for TACC2008 new candidate determinants of selectivity.
IN-EV002
Lead Toxicity: Quantum-Mechanical Exploration of Lead Poisoned Zinc Fingers
Andrzej A. Jarzęcki
Department of Chemistry, Graduate Center and Brooklyn College, the City University of New York, 2900 Bedford Ave.
Brooklyn, NY 11210
Structure and spectroscopy of simple models of mononuclear lead domains, which are probably formed in lead poisoned
proteins are investigated by quantum-mechanical calculations. We demonstrated – in agreement with experimental data –
that lead binds tightly, especially to cysteine-rich sites, and introduces new coordination preferences and structures that
do not stabilize the proper forms of structural zinc-binding domains (zinc fingers). Lead coordination modes in protein
environment and the role of lead’s sterochemically active lone-pair orbital are discussed. Computed electronic excitation
spectra confirm that characteristic UV signals observed around 260 nm for lead-sulfur complexes are the
ligand-to-metal-charge-transfer (LMCT) bands. These UV bands could serve as identification of lead in environment but
elevated structural diversity of lead in poisoned proteins, its recognition, and classification demands more accurate
structural and dynamic probes for formation of lead domains.
We have shown that resonance Raman (RR)
spectroscopy guided by model calculations could serve as such a probe. We present a novel, more reliable approach to
model resonance Raman intensity patterns and applied the methodology to predict the patterns resulting from resonant
excitations in the region of sulfur-to-lead-charge-transfer bands. We have explored the theoretical possibility for
spectroscopic detection of specific coordination of lead in hope to provide better understanding of lead poisoning
mechanisms.
OR-EV003
Rotational Barriers, Energy differences and Thermodynamics Parameters of Furfural, 2-Furoylfluoride and their
Sulfur and Selenium Analogues: DFT Study in the Gas and Solution Phases
Ramasami, Ponnadurai
Department of Chemistry, University of Mauritius, Réduit, Mauritius.
The anti and syn conformers of furfural, 2-furoylfluoride and their sulfur and selenium analogues [1] have been studied
in the gas and solution phases. Transition states have also been modelled. All computations have been done using density
functional theory method with B3LYP as the functional and 6-311++G(d,p) as the basis sets. The optimised molecular
structures and related parameters of these conformers have been computed. The infrared wavenumbers and Raman
activities of these conformers have also been computed and they have been assigned appropriately. The energy
differences between the anti and syn conformers, associated barriers and thermodynamic parameters have been derived
from the computations. It is found that the structural parameters of the conformers are not much different in the gas and
solution phases. However in the gas phase, for furfural and its sulfur and selenium analogues, the anti conformer is
always more stable but increasing the polarity of the solvents leads to the syn conformer becoming more stable. The syn
conformer is more stable that the anti conformer for 2-furoylfluoride and its sulfur and selenium analogues in both the
gas and solution phases. The rotational barrier is always larger than the energy difference and both of these parameters
increase when the solvent becomes more polar. These results from this work illustrate the peculiar characteristic of
fluorine affecting conformations of molecules and can serve to be useful as these compounds are commonly used as
ligands.
151 Book of Programme and Abstract for TACC2008 [1] H. Ashish; P. Ramasami, Mol. Phys. 2008, 106, 175.
IN-EV004
Molecular dynamics study of cation permations through nicotinic acetylcholine receptor channel.
Hai-Long Wang1, Xiaolin Cheng2, Palmer Taylor3, J. Andrew McCammon4, Steven M. Sine1
1Receptor Biology Laboratory, Departments of Physiology and Biomedical Engineering and Neurology, Mayo Clinic
College of Medicine, Rochester, Minnesota 55905, USA
2Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
3Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San
Diego, La Jolla, California 92093, USA
4Howard Hughes Medical Institute, Department of Chemistry-Biochemistry and Pharmacology, University of California
San Diego, La Jolla, California 92093,USA
We used molecular dynamics (MD) simulations to explore the transport of single cations through the channel of the
muscle nicotinic acetylcholine receptor (nAChR). Four MD simulations of 16 ns were performed at physiological and
hyperpolarized membrane potentials, with and without restraints of the structure, but all without bound agonist. With the
structure unrestrained and a potential of –100 mV, one cation traversed the channel during a transient period of channel
hydration; at –200 mV, the channel was continuously hydrated and two cations traversed the channel. With the structure
restrained, however, cations did not traverse the channel at either membrane potential, even though the channel was
continuously hydrated. The overall results show that cation selective transport through the nAChR channel is governed
by electrostatic interactions to achieve charge selectivity, but ion translocation relies on channel hydration, facilitated by
a transmembrane field, coupled with dynamic fluctuations of the channel structure.
OR-EV005
Modeling In Environmental Chemistry With The Aid Of Generalization To Pafnutii L. Tchebycheff’S
(Chebyshev’S) Inequality
Nikolay V. Sokolov
Saint Tikhon Orthodox University, Novokuznezkaya ul, 23b, Moscow, 115184, Russia,
E-mail: [email protected], tel. +74992435812
There is a problem of estimation of probabilities to chemical substances in computational environmental chemistry.
There are many possible variants of distributions to chemical substances in nature. The general properties of any
distribution may be found with the aid of generalization of Pafnutii L. Tchebysheff’s (Chebyshev’s) inequality and
corrections to Andrei N. Kolmogoroff’s (Kolmogorov’s) estimation [1]. Author has found for all possible variants the
universal expressions to distributions of chemical substances in nature with the aid of his generalizations and corrections
as following:
This expression has been used for point estimation to concentration of concentration of ammonia in Australian Cabooture
River and dispersed particles in Yellow Sea near Incheon and under condition of unknown distribution function. The
experimental data are shown by blue on pictures. The results of point estimations are shown by red. All experimental data
are fully corresponded to the stated inequality. Thus, it may be used for ecological analysis under unknown distribution
function.
[1] Nikolay V. Sokolov, Doklady Akademii nauk (Russian). 2002, 384, 308.
152 Book of Programme and Abstract for TACC2008 IN-EV006
Evaluation of Phase Transition Temperatures of Phosphatidylcholine Lipids based on DFT Born-Oppenheimer
Dynamics of Monomers.
S. Krishnamurty, T. Mineva, A. Goursot
Institut Gerhardt, UMR 5253 CNRS, Ecole de Chimie de Montpellier, 34296 Montpellier Cédex 5, France.
D.R. Salahub
Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive
NW, Calgary, Alberta, Canada T2N 1N4
The longstanding interest in studying phospholipid assemblies is mostly due to the fact that they are the building blocks
of biomembranes. Experimental studies have recognized that the knowledge of the properties of a phospholipid monomer
within an assembly is essential for understanding the bilayer functional role. Along with experimental work, a large
number of classical molecular dynamic simulations have been performed in order to model phase changes, hydration
effects, order parameters, effects of ions. Due to the large size of the systems, their study with quantum chemical
methods has been so far very limited.
In this work, we investigate the evolution of the DMPC, DPPC, DSPC and DOPC molecules as a function of time using
Born-Oppenheimer molecular dynamics (BOMD), based on a DFT method, augmented with a damped empirical
dispersion energy. These molecules have the same polar head group (phosphatidylcholine), whereas they differ by the
length and/or nature of their alkyl chains. DMPC, DPPC and DSPC have saturated alkyl chains with 14, 16 and 18
carbons, respectively, whereas DOPC has 17 carbon chains with one unsaturation at the 8th-9th carbons. The
corresponding experimental bilayer phase transition temperatures (Tc) are 24 (DMPC), 41 (DPPC), 58 (DSPC) and
-22°C (DOPC). BOMD simulations have been performed for every lipid monomer at five different temperatures. Density
of states, using the multiple histogram method [1] and root mean square displacements of atoms plotted as a function of
temperature, have provided calculated Tc values. This analysis of the dynamics shows that the experimental Tc values
are well reproduced using single molecules, which leads to the conclusion that the gel to liquid crystalline phase
transition is mainly an intrinsic molecular property, related to the flexibility of the alkyl chains and modulated by the
internal head – glycerol interaction.
[1] (a) Ferrenberg, A.M.; Swendesen, R.H. Phys. Rev. Lett. 1988, 61, 2635; (b) Labastic, P.; Whetten, R. L. Phys. Rev.
Lett., 1990, 65, 1567.IN-EV007
IN-EV007
Hydrogen bond fluctuations and vibrational spectral diffusion in normal and supercritical water
Amalendu Chandra
Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in deuterated water and
aqueous solutions is presented without using any empirical model potential. The time dependent changes of vibrational
frequencies of OD stretch modes due to hydrogen bond fluctuations are calculated for pure water and aqueous ionic
solutions under normal and supercritical conditions. The frequency fluctuations are subsequently used to calculate
spectral diffusion and frequency correlation functions to connect the dynamics of hydrogen bonds and dangling OD
groups [1,2] to ultrafast vibrational spectroscopy [3,4]. For normal water and aqueous solutions with a single ion, the
present study confirms the results of earlier theoretical studies using a different methodology [5] while new theoretical
results are provided for concentrated solutions under normal conditions and also for supercritical aqueous systems.
153 Book of Programme and Abstract for TACC2008 [1] B. S. Mallik, A. Semparithi and A. Chandra, J. Phys. Chem. A 2008, 112, 5104; J. Chem. Phys. (submitted).
[2] B. S. Mallik and A. Chandra, J. Mol. Liq. 2008, in press; J. Phys. Chem. A (submitted).
[3] C. J. Fecko, J. J. Loparo, S. T. Roberts and A. Tokmakoff, J. Chem. Phys. 2005, 122, 054506; J. B. Asbury et al. J.
Phys. Chem. A 2004, 108, 1107; S. Park and M. D. Fayer, Proc. Natl. Acad. Sci. 2007, 104, 16731; M. F. Kropman and
H. J.Bakker, Science, 2001, 291, 2118.
[4] D. Schwarzer, J. Lindner and P. Vöhringer, J. Chem. Phys. 2005, 123,
161105; J. Phys. Chem. A 2006, 110,
2858.
[5] R. Rey, K. B. Möller and J. T. Hynes, J. Phys. Chem. A 2002, 106, 11993; B. Nigro, S. Re, D. Laage, R. Rey and J. T.
Hynes, J. Phys. Chem. A 2006, 110, 11237; C. P. Lawrence and J. L. Skinner, J. Chem. Phys. 2003, 118, 264.
OR-EV008
A Molecular Dynamics Study of the anomalous pKW in near-critical and supercritical Water
A. J. Masters *, S. J. Halstead**
* School of Chemical Engineering & Analytical Science, the University of Manchester, Oxford Road, M13 9PL,
Manchester, UK
** Department of Applied Chemistry, Harbin Institute of Technology, 150001, Harbin, Heilong Jiang, China
The ionic product of water, Kw, is believed to play a vital role in many biological and industrial chemical processes. It
varies dramatically and in a curious fashion as one goes from water under ambient conditions though the near-critical
region into the supercritical state (647.3 K, 21 MPa 1).
As one goes from ambient to near-critical conditions, Kw
changes from 10-14 to 10-11 2 – a considerable increase that allows near-critical water to catalyse acid-base reactions
without the need for added catalyst. This facilitates all manner of organic reactions which do not take place in water
under normal conditions 3-7. As one goes into the super-critical state, Kw drops rapidly to ca. 10-17. In order to
understand this peculiar variation, we performed molecular dynamics simulations of hydroxide and hydronium ions in
water over a wide range of temperatures and pressures. Using thermodynamic integration techniques, we were able to
predict the variation of Kw with state point and thus reproduce the trend found experimentally.
Furthermore we gained
insight into the mechanisms that cause this behaviour and we discuss the relative contributions of temperature, entropic
effects and electrostatic stabilization to this process. Finally we present a simple model which, we believe, captures the
essential science behind this seemingly anomalous behaviour.
[1] Shaw, R. W.; Thomas, B. B.; Antony, A. C.; Charles, A. E.; Franck, E. U., Chem. Eng. News 1991, 69(51), 26
[2] Takahashi, H; Satou, W; Hori, T; Nitta, T. J. Chem. Phys. 2005, 122, 044504
[3] Savage, P, Chem. Rev. 1999, 99(2), 603
[4] Broll, D; Kaul, C; Kramer, A; Krammer, P; Richter, T; Jung, M; Vogel, H; Zehner, P, Angew. Chem. Int. Ed. 1999,
38, 2998
[5] Ikushima, Y; Hatakeda, K; Sato, O; Yokoyama, T; Arai, M, Angew. Chem. Int. Ed. 1999, 38, 2910
[6] Arita, T; Nakahara, K; Nagamib, K; Kajimotoa, O, Tet. Lett. 2003, 44, 1083
[7] Anikeew, V; Menion, D; Ermakova, A., Russian J. Phys. Chem. 2001, 75(8), 1259
IN-EV009
Vertical Electron Binding Energy And Oxidation Free Energy of The Aqueous Hydroxide Anion.
Christopher Adriaanse, Marialore Sulpizi, Joost VandeVondele*, Michiel Sprik
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
Email contact: [email protected]
154 Book of Programme and Abstract for TACC2008 Recent progress in photo electron spectroscopy (PES) of liquids has made it possible to determine vertical detachment
energies of aqueous solutes. The results for small anions, such as halides and the hydroxide ion are of particular interest[1]
for understanding of theelectronic structure of aqueous systems. First ionization energies of these anionic speciesall fall
in a band of 9.0 to 10.0 eV, just below the liquid water PES threshold of 10 eV.
The value for OH− given by Winter et
al[1] is 9.2 eV. This should be compared to the absolute oxidation free energy of 6.6 eV (the OH•/OH− redox potential +
absolute SHE reference). The 2.6 eV difference is attributed to reorganization of solvent. It is still a
considerable
challenge for computational chemistry to reproduce and explain this 2.6 eV gap between the vertical and adiabatic
ionization energy of the aqueous hydroxide ion. In this talk we discuss our attempts to do this using density functional
theory based ab initio molecular dynamics methods. Part of the problem is a serious flaw in the standard gradient
corrected density functionals used in these simulations. The proximity in energy to the valence band of water means that
the hole created by oxidizing the hydroxide anion to the OH radical has the tendency to delocalize over neighbouring
water molecules, which even leads to spurious hemibonds[2]. We have countered the overstabilization of delocalized
unpaired electrons by an empirical self interaction correction scheme which has enabled us to stabilize the OH radical as
a hydrogen bonded species. The scheme was validated by computing the free energy for oxidation of SH− and O−2 by
the OH radical in solution which we found in fair agreement with experimental redox potentials (errors are in the order of
0.2 eV). Using this approach we observed a marked asymmetry in the reorganization of the solvent, with the
reorganization energy in response to the OH•/OH−reduction 1 eV larger than the reorganization energy for the reverse
half reaction. Due to the limited size of the MD model systems we recover only part of 2.6 eV reorganization energy
deduced from experiments. Still we believe we are on the right way as we will argue when discussing the implications of
our result for the electronic structure of waterat the end of the talk.
1. B. Winter et al. J. Am. Chem. Soc. 128, 3864 (2006).
2. J. VandeVondele and M. Sprik, Phys. Chem. Chem. Phys. 7, 1363 (2005).
* Institute of Physical Chemistry, University of Zurich, Switzerland
IN-EV010
Design of New Materials by Computer Simulations: Light Metal Nanostructures for Hydrogen Storage
David Henry1, Alexander Goldberg2, Adrian Varano1 and Irene Yarovsky1
1School of Applied Sciences, RMIT University, Melbourne, 3001, Australia
2Accelrys Inc., San Diego, USA
Aluminium clusters are of interest due to their potential to form alanides which may lead to inexpensive light weight
materials for hydrogen storage. Key features for successful hydrogen storage materials include high hydrogen content
and thermodynamically and kinetically favourable processes for adsorption and desorption of hydrogen. We use
theoretical Density Functional Theory (DFT) techniques [1] to investigate the interactions of hydrogen with light metal
nanostructures to identify materials suitable for high capacity hydrogen storage. We assessed various theoretical
techniques for modelling Al clusters, including the comparison with experimental data and other theoretical calculations
[2]. We performed DFT calculations on bare and hydrogenated Al13 [3] and Al12 [4] clusters. Our newly identified
Al12H20 cluster is of particular interest for hydrogen storage application as it has a relatively high hydrogen storage
capacity. We investigated the structure and properties of Al12XHn (X = Mg, Al, Si and n = 0,1,2) clusters with the
dopant X as the core and surface atom and also identified transition states and calculated reaction energetics of hydrogen
dissociation on the surface of the clean and doped clusters. Our recent results for Al24Mg2 dimers reveal that hydrogen
molecule can spontaneously dissociate and adsorb on the surface of those dimers if certain geometric conditions are met.
These results suggest that doped Al clusters can be used as building blocks of a novel solid state material for hydrogen
storage.
155 Book of Programme and Abstract for TACC2008 [1] B.J. Delley, Chem. Phys. 2000, 113, pp. 7756-7764.
[2] D.Henry, A. Varano, I. Yarovsky, J. Phys. Chem. A, accepted, 2008
[3] Yarovsky, A. Goldberg, Molecular Simulation, 2005, 31, 475
[4] Goldberg, I. Yarovsky, Phys. Rev. B, 2007, 75, 195403
OR-EV011
Supercritical carbon dioxide extraction of nimbin from neem seeds- an optimization study
G.Zahedi a , A. Elkamel b , S. Monjezia
aSimulation and AI Research Center, Department of Chemical Engineering, Razi University, Kermanshah, Iran
bDepartment of Chemical Engineering, University of Waterloo, Waterloo, Ont., Canada, N2L 3G1
In this paper supercritical extraction of nimbin from neem seeds have been studied. In order to investigate effect of
parameters on nimbin extraction yield, a partial differential model based on mass conservation was developed. The
obtained model was solved numerically using MATLAB software.
The results were successfully validated with
laboratory experimental data. In another step of research optimum amount of operating parameters were found based on
Gradient Search (GS) optimization profit was set as objective function during optimization programming. Optimum
amount of temperature, pressure, CO2 flow rate and particle diameter were found to be 305 K , 177.339 bar, 0.9660
cm3/min and 0.0575 cm
respectively. Finally ability of Genetic Algorithm (GA) in optimization was investigated.
Comparison between GS and GA optimization implies that GA optimization routine is 4.6 times faster than GS method
but GS optimization routine is more accurate than GA routine.
Key words: neem extraction, supercritical extraction, modeling, genetic algorithm, optimizationIN-EV012
IN-EV012
Dispersion Coe¢ cients and van der Waals Potential of Mercury
K.T. Tang
Department of Physics, Paci.c Lutheran University, Tacoma, Washington, 98447, U.S.A.
Abstract Wolfsohn.s parameters for the frequency dependent polarizability α(ω) of mercury are modi.ed to .t the recent
interferometric laser measurements. The resulting α(ω) are extended to imaginary frequencies α(iω) and used to calculate
the upper and lower bounds of the dipole dispersion coe¢ cent in the long range dimer potential. The new value of C6 =
392±4 au is much greater than the generally accepted TDMP2 value. With the corresponding changes in the
dipole-quadrupole and dipole-octopole interactions, new dispersion coe¢ cients C8 and C10 are obtained. Together with
the experimentally determined De (well-depth) and Re (equilibrium distance), the Tang-Toennies model is used to
predict the shape of the entire dimer potential energy curve. The new potential is found to be in excellent agreement with
the ab initio CCSD(T) calculations and the parameters ωe and χeωe agree with the spectroscopic measurements within the
small experimental errors.
OR-EV013
Development Of Molecular Mechanics (MM) Force Fields For Modelling Of Copper(II)
Amino Acid Complexes In Different Environments
Sabolovic, Jasmina
Institute for Medical Research and Occupational Health, Ksaverska cesta 2, P.O. Box 291, HR-10001 Zagreb, Croatia
156 Book of Programme and Abstract for TACC2008 To reliably predict the properties in solution using molecular dynamics (MD) method, it is necessary to apply a reliable
MM force field. We develop MM models and force fields for copper(II) amino acid complexes with the aim to predict
the properties of that class of compounds in different environments (vacuum, crystal, solution) by using the same set of
potential energy functions and empirical parameters [1]. The effects of surrounding environment of a molecule are
calculated explicitly by including the environment in the calculations. The force field parametrisation is based on
experimental crystal and molecular structures and quantum chemical studies. Very good match between the MM
equilibrium structures calculated in simulated crystalline surroundings and in vacuo with experimental crystal data and ab
initio derived geometries, respectively, proved the reliability of the force field FFW [1] to reproduce the geometries and
intermolecular interactions of anhydrous and aqua copper(II) complexes with aliphatic amino acids in vacuo and in
crystal [1-3]. However, FFW failed to reproduce water properties (e.g. diffusion coefficient, density) in MD simulations.
Thus, the force field was reparametrised by using the empirical parameters of the SPC/E water model. The new force
field can reproduce well the structural properties in crystal, in vacuo, and in aqueous solution. Its efficacy and predictive
ability will be addressed.
[1] J. Sabolović, C. S. Tautermann, T. Loerting, K. R. Liedl, Inorg. Chem., 2003, 42, 2268.
[2] J. Sabolović, B. Kaitner, Polyhedron, 2007, 26, 1987.
[3] J. Sabolović, B. Kaitner, Inorg. Chim. Acta, 2008, 361, 2418.
OR-EV014
Molecular dynamics study of molecular characteristics influence on detonation Phenomena
A.V. Utkin, I.F. Golovnev, and V.M. Fomin
Khristianovich Institute of Theoretical and Applied Mechanics SB RAS, Institutskaja Str. 4/1, 630090, Novosibirsk,
Russia
In the present study, the molecular-dynamics method has been used to examine the influence of the thermal effect of the
chemical reaction on processes in a detonating molecular crystal. Molecular dynamics data are compared with predictions
of the continuum theory of detonation.
Investigation into the influence of the thermal effect of the chemical reaction Q on the physical parameters of the
detonation wave and determining the general features associated with wide-range variation of Q are of considerable
interest. This issue is hard to examine experimentally because different values of Q refer to different explosives (with
different densities, chemical compositions, etc.). For this reason, the dependence of detonation-wave characteristics on
the thermal effect of the chemical reaction cannot be measured directly in an actual experiment. At the same time, the
molecular dynamics method allows easy modification of reaction exothermicity by varying the shape of the potential
surface. As certain properties of the system, such as density, velocity of sound, and Young’s modulus are unchanged
thereby, it is possible to uniquely determine the relation between the thermal effect of the chemical reaction and the
structure of the detonation wave. The main conclusions from the study performed can be formulated as follows. A
comparison of molecular dynamics data with the values predicted by the continuum theory of detonation yields good
agreement in terms of both detonation velocity and thermodynamic parameters at the Chapman-Jouguet point. The
Chapman-Jouguet condition is shown to result from the dynamics law for atomic motion. An increase in the thermal
effect of the chemical reaction yields a practically linear increase in squared detonation-wave velocity, pressure, and
squared mass velocity at the Chapman-Jouguet point.
OR-ENV021
157 Book of Programme and Abstract for TACC2008 Exploring the structure characters of the protic ionic liquids in different solvents: a theoretical investigation
Li, Haoran
Zhejiang University, China
Investigation of the structure of protic ionic liquids is showing a very rapid expansion during the last five years,
especially when Earle et al. demonstrated that some ionic liquids are volatile, and so it can be distilled at low pressure
without decomposition. Although many recent publications reported their gas phase state, the nature of the species that
are presented in gas phase still remained controversial. In order to circumvent this impediment, the presented study used
quantum chemistry calculations to investigate the structure characters of the protic ionic liquids.
The calculation results indicate both molecular and ionic aggregates can co-exist in some of the protic ionic liquids, and
the dielectric constant of the solvents had great effects on this balance. In the gas phase, most of the protic ionic liquids
trend to exist as molecular cluster. However, the protic ionic liquids trend to exist as ion cluster in the liquids states, and
this tendency was increased with the increasing of the dielectric constant of the solvents. All of the relative energies, the
relative enthalpy, and the relative Gibbs free energies increased with the increasing of the dielectric constant. The present
work can help us to deepen our understanding of the structures of the protic ionic liquids
OR-ENV022
H6 (hexahydrogen) cation revisited
Andreas Mauracher, Michael Probst, Diethard Boehme, Paul Scheier, Tilmann Märk
Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
Recent experimental studies on molecular hydrogen inserted into droplets of liquid Helium and subsequently ionized [1]
have exhibited an interesting stability of some even-numbered Hn + clusters. H6 + is found to be especially abundant. Hn
+ clusters have been the subject of many quantum-chemical studies but since previous experiments have found
odd-numbered clusters to be dominant, even-numbered ones clusters have received less attention. Previous theoretical
works [2] indicate that there exist two low-lying isomers of this prototypical cluster cation - the most stable one with
three H2 units perpendicular to each other and the other one a with H3 at the center. We searched the potential energy
surface and checked the stability of a series of other geometries. We did not discover isomers that were more stable than
the ones already known but found some other ones that indicate an interesting degree of complexity in such a small
system. The experiments show also a unexpected stability of the cluster H30+. It is discussed if in this cluster H6 + is
solvated by twelve hydrogen molecules and how this might be the case and which other possibilities exist. Our
calculations were performed mostly on the QCI/aug-cc-pVTZ level of theory without providing for the quantum nature
of hydrogen atoms. For the energy surface this is meaningful nevertheless but the cluster geometries are not quantitative
anymore; this point is discussed as well.
[1] Diethard Boehme, Paul Scheier, Andreas Mauracher, Michael Probst, Tilmann Märk, Phys.Rev.Lett., submitted 2008
[2] Yuzuru Kurosaki, Toshiyuki Takayanagi, J.Chem.Phy. 1998, 109, 4327
IN-ENV023
Solvent Dynamics Effect in Condensed-Phase Electron-Transfer Reactions
Tianjin Zhu
Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11796
Dongqing Wei
158 Book of Programme and Abstract for TACC2008 Department of Bioinformics, Shanghai Jiao Tong UniVersity, Shanghai, People’s Republic of China
Channel-based reaction-diffusion equations are solved analytically for two electron transfer (ET) models, where the fast
inner-sphere coordinate leads to an ET reaction treated by Fermi’s golden rule, and the slow solvent coordinate moves
via diffusion. The analytic solution has let us derive an ET rate constant that modifies the Marcus-Jortner formula by
adding a constant R which we call a dynamic correction factor. The dynamic correction factor measures the effect of
solvent friction. When the relaxation of solvent dynamics is fast, the dynamic correction can be neglected and the ET rate
constant reduces to the traditional Marcus-Jortner formula. If the solvent dynamic relaxation is slow, the dynamic
correction can be very large and the ET rate can be reduced by orders of magnitude. Using a generalized
Zusman-Sumi-Marcus model as a starting point, we introduce two variants, GZSM-A and GZSM-B, where in model A,
only one quantum mode is considered for inner-sphere motion and in model B, a classical mode for inner-sphere motion
is added. By comparing the two models with experimental data, it is shown that model B is better than model A. For the
solvents that have a relaxation time ranging between 0 and 5 ps, our result agrees fairly well with experimental data; for
the solvents that have a relaxation time ranging between 5 and 40 ps, our result deviates from the experimental values.
After introducing an adjustable scaling index in the effective time correlation function of the reaction coordinate, good
agreement is achieved between the experiment and the theory for model B for all of the solvents studied in this paper.
IN-ENV024
From s-block to Transition Metal Species:
Quantitative Modeling via the correlation consistent Composite Approach (ccCA)
Nathan J. DeYonker, T. Gavin Williams, Benjamin Mintz, Brian P. Prascher, Thomas R. Cundari, and Angela K. Wilson
University of North Texas, Department of Chemistry and the Center for Advanced Scientific Computing and Modeling
(CASCaM), Box 305070, Denton, Texas, 76203-5070, U.S.A.
Modern computational chemistry has become a viable approach to address a wide range of chemistry that is difficult or
cost-prohibitive to evaluate by other means –from the description of short-lived excited states, to the understanding of
complex interactions. Ab initio computational chemistry approaches have reached the level where they are an invaluable
aid in quantitative predictions of kinetic and thermodynamics properties. For the majority of small molecules (~2-10
main-group atoms), the accuracy obtainable by ab initio computational chemistry rivals, and sometimes even surpasses
experiment. Computational cost, however, quickly becomes problematic for quantitative predictions, as molecule size
increases, and, as the level of sophistication of methodology required increases. Composite methods have emerged as a
way to reduce computational cost requirements, while still achieving quantitative accuracy in energetic predictions.
Unfortunately, overall,
many composite methods are still plagued with problems such as high computational cost,
required modifications for different portions of the periodic table (e.g., s-block elements), inability to address transition
metal species, and/or significant parameterization. We have developed a composite method, the correlation consistent
Composite Approach [1,2], which can be used throughout the periodic table, does not require parameterization, and does
address the thermochemistry of metal complexes.
[1] N.J. DeYonker, T.R. Cundari, and A.K. Wilson, J. Chem. Phys., 124, 114104, (2006).
[2] N.J. DeYonker, Be.J. Mintz, T.R. Cundari, and A.K. Wilson, J. Chem. Theor. Comp. 4, 328 (2008).
OR-ENV025
Theoretical study of OH formation from ozonolysis of Limonene
Xu, Yisheng
159 Book of Programme and Abstract for TACC2008 Chinese Research Academy of Environmental Sciences, Beijing, China
Tropospheric ozone is formed by photochemical reactions involving volatile organic compounds (VOCs) and the oxides
of nitrogen NO and NO2. A substantial portion of the VOCs, particularly alkenes, may also be degraded by reaction with
Ozone to form OH radical, which further react with VOCs to produce organic peroxy radicals facilitating the cycle of NO
to NO2. Controls on anthropogenic NOx in addition to anthropogenic VOCs are now thought to be needed to reduce
Ozone in regions characterized by strong biogenic VOC sources.
The formation and unimolecular reaction of primary ozonides and carbonyl oxides arising from the O3-initiated reactions
of limonene have been investigated using density functional theory and ab initio molecular orbital calculations. The
activation energies of O3 cycloaddition to the two double bonds of limonene are found to be comparable, implying that
the initial two O3 addition pathways are nearly equally accessible. The reaction energies of O3 addition to limonene are
between -47 and -51 kcal/mol. Cleavage of primary ozonides to form carbonyl oxides occurs with a barrier of 14-19
kcal/mol above the ground state of the primary ozonide, and the decomposition energies range from -13 to -20 kcal/mol.
The computational results indicate that the CI13 have much higher barriers for H-migration to form Hydroperoxide than
for cyclization to form dioxirane about 12.0 kcal/mol. The experiments of secondary organic aerosol particles generating
by reaction d-limonene vapor and ozone in Telflon reaction chamber are going in our lab by means of in situ detection
with ATOFMS and PTRMS spectra.
IN-ENV026
Mechanisms of Hydrocarbon Oxidation, Pyrolysis, and Soot Formation
Wesley D. Allen
Center for Computational Chemistry and Department of Chemistry,
University of Georgia, Athens, GA 30602 USA
Myriad environmental, toxicological, technical, and inherent scientific concerns continue to stimulate both experimental
and theoretical research on the ubiquitous processes of hydrocarbon oxidation, pyrolysis, and soot formation. We have
employed high-level focal point methods to converge on the ab initio limits of several key systems representative of such
chemistry.
Explicit computations were executed with basis sets as large as cc-pV6Z and correlation treatments as
extensive as coupled cluster through full triples with perturbative inclusion of quadruple excitations [CCSDT(Q)]. The
celebrated C2H5 + O2 reaction is an archetype for hydrocarbon combustion. Our computations of unprecedented rigor
have established that the critical step in this reaction is the concerted elimination of HO2 from the ethylperoxy
intermediate (C2H5O2), whose barrier lies 3.0 kcal mol–1 below the reactants.
The cracking of aromatic compounds
contained in common hydrocarbon fuels generates significant ortho-benzyne (C6H4). Our research demonstrates that
above 1400 K ortho-benzyne undergoes a fascinating retro-Diels-Alder fragmentation to diacetylene + acetylene,
providing a mechanism for the decomposition and subsequent oxidation of aromatic fuels in combustion environments.
Vital to understanding the formation of soot, or more specifically polycyclic aromatic hydrocarbons (PAHs), is the
mechanism for creating the first aromatic ring in the combustion of aliphatic fuels.
The participation of
even-carbon-atom pathways in benzene formation depends on the energy differences of the n- and i- isomers of
four-carbon chains, a topic of much past debate. Our converged computations prove that the resonance-stabilized
i-C4H3 and i-C4H5 isomers, which do not form strongly-bound complexes with acetylene, lie 11.8 and 10.7 kcal mol–1
below E-n-C4H3 and E-n-C4H5, respectively.
These thermochemical determinations indicate that under typical flame
conditions even-carbon routes to benzene are not operative; instead, the predominant mechanism is an odd-carbon
pathway involving the recombination of propargyl radicals (C3H3).
OR-EV027
160 Book of Programme and Abstract for TACC2008 Structure, Stability and Distribution of Neutral Water Clusters in high-Temperature low-Density Fluids
Kono H. Lemke1 & and Terry M. Seward2
1Department of Earth Sciences, University of Hong Kong, Pokfulam Road, Hong Kong, [email protected];
2Department of Earth Sciences, University of Bristol, Bristol, UK
Low-density aqueous fluids occur ubiquitously close to and on the Earth’s surface over a wide range of temperatures
ranging from atmospheric water vapor up to high-pressure supercritical steam. These volatile molecular components,
however, do not exist as “anhydrous” molecular moieties but as hydrated clusters. Our current understanding of the
interaction of water with such clusters in steam and/or low-density supercritical water and in magmatic gases is
rudimentary.
The work here presents new results for the equilibrium constant Kp for water clustering reactions in the temperature
range 298-1000K at 1bar and at vapor saturation pressure with up to five water molecules, using the highlevel ab initio
complete basis set theory (CBS-QCI/APNO) procedure [1]. Our newly calculated values for Kp are in good agreement
with those obtained from thermal conductivity measurements [2] as well as those obtained from high temperature IR
studies [3-5]. For example, water dimerization enthalpies and entropies obtained in this study are -14.5 kJ/mol and -77.0
J/Kmol, respectively, and are in excellent agreement with those obtained from TC measurements [2] (i.e. ΔH=-15.02.1
kJ/mol and ΔS=-77.8J/Kmol). Calculations for larger clusters with up to five water molecules indicate that clustering
equilibrium constants decrease with increasing temperature, however, it appears that while water cluster abundances at
1bar depend chiefly on the temperature-dependent changes of the equilibrium constant only, at vapor-liquid equilibrium
abundances of higher clusters are governed by the shifting balance between the competing contributions of the
equilibrium constant and the exponential water monomer term.
[1] Montgomery et al., J. Chem. Phys. 1994, 101, 5900.
[2] Curtiss et al., J. Chem. Phys. 1979, 71, 2703.
[3] Jin and Ikawa, J. Chem. Phys. 2003, 119, 12432.
[4] Vigasin et al., J. Mol. Struc. 2005, 742, 173.
[5] Ptashnik, J. Quant. Spec. Rad. Trans. 2008, 109, 831.
OR-ENV028
Sporadic Metal Layers: Ion- Molecule chemistry of Metal cations and its implications for the upper atmosphere
Richard J. Plowrighta, Timothy G. Wrighta, John M. C. Planeb
aSchool of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
bSchool of Chemistry, University of Leeds, Leeds LS2 9JT, UK
The mesosphere-lower thermosphere (MLT) region of the atmosphere is the only region of the Earth’s atmosphere in
which metals exist in a free atomic state. It is known that their presence in this region occurs via the ablation of meteors
entering the upper atmosphere, but certain aspects of their chemistry are still unclear. One interesting phenomenon in this
region of the atmosphere is sporadic neutral metal layers, which have been observed for many metals such as Fe, Mg, Na,
K and Ca. To date, the most promising explanation for the formation of these layers is neutralization of cationic
metal-containing complexes concentrated in so-called sporadic E layers. Neutralization of bare metal cations in sporadic
E layers can occur though radiative recombination with electrons, but this process has been shown to be very inefficient.
Instead, metal cations can complex to ligands, such as N2, which undergo subsequent ligand switching reactions with
other atmospheric components, resulting in dissociative electron recombination. Using high level ab initio theory, the
structure of metal cation complexes that can be formed in this region and the thermodynamic and RRKM kinetic
161 Book of Programme and Abstract for TACC2008 parameters for a number of recombination and ligand switching reactions can be determined. These parameters are
incorporated into atmospheric models, allowing reactions that govern metal ion-molecule chemistry in the upper
atmosphere - and therefore the neutralization processes in the formation of sporadic neutral metal layers - to be explored.
[1] Plane, J. M. C.; Plowright, R. J.; Wright, T. G.; J. Phys. Chem. A. 2006, 110, 3093.
[2] Plowright, R. J.; Wright T. G.; Plane J. M. C.; - Submitted to J. Phys. Chem. A.
(http://dx.doi.org/10.1021/jp8022343)
OR-ENV029
Displacement Matrix Elements of Deng-Fan Potential for Modelling Molecular Vibrations
Zimei Rong
Queen Mary University of London
The diatomic potential is a fundamental starting point in quantum chemistry for calculating molecular spectra, molecular
scattering and molecular structure. The Morse potential [1] is the most popular anharmonic potential model used in this
context. Another potential, the Deng-Fan potential, [2] has a similar shape but has the correct asymptotic behaviour as the
bond length approaches zero. The Morse and Deng-Fan potentials were used in a complementary way to calculate the
frequency and intensities of X-H (X = C, N, O and Cl) stretching vibrations [3] and DNA phase transitions [4] using
displacement matrix elements. Exact analytic expressions for the displacement matrix elements of the Morse potential
have been previously derived [5]. This report presents exact analytic displacement matrix elements for the Deng-Fan
oscillator, where v, u and n are positive integers. The wave function |v> and |u> are arbitrary and the order of
displacement n is not greater than 6. Intermediate variables were employed to keep the expressions compact and the
computation fast. These analytic displacement matrix elements were verified by comparison with the results of traditional
numerical integration of the analytic wave functions. Compared with the numerical integration method, however, the
current analytic expressions provide greater simplicity with lower computational expense. We believe that these
expressions for displacement matrix elements are generally applicable for computation in quantum chemistry.
[1] Morse P M, 1929, Phys. Rev. 34, 57
[2] Deng Z H and Fan Y P, 1957, Shandong University Journal 7, 162
[3] Rong Z, Kjaergaard H G and Sage M L, 2003, Mol. Phys. 101, 2285
[4] Nyeo S L and Yang I C, 2001, Phys. Rev. E 63, 046109
[5] Rong Z, Cavagnat D and Lespade L, 2003, LNCS 2658, 350
162 Book of Programme and Abstract for TACC2008 Poster PO-001
Phenalenyl-Based Three-Component Systems for Remote Control of Hydrogen Bonds
Wei-Tou Peng, Ito Chao*
Institute of Chemistry, Academia Sinica
Taipei 11529, Taiwan
We have studied remote control of hydrogen bonds with conjugated three-component systems consisting of a reaction
center, a conjugated bridge, and a binding site.1-3 In this study, we use the phenalenyl radical as the reaction center (see
Figure 1). The HOMO and LUMO of phenalenyl only distribute on the sixα-carbons ,but not the three β-carbons, so
different charge transfer properties can be obtained by attaching a bridge unit at the two different sites. The neutral,
oxidation, and reduction states of compounds 1 and 2 are studied and their ability for hydrogen bonding are calculated. In
our calculation, 1 shows a larger binding change at both the oxidation and reduction states, i.e. when oxidated, the
hydrogen bond interaction enhanced more than that of 2, and the strength of hydrogen bond also decreased more at the
reduction state. As a result, it is envisioned that one can utilize redox reactions to provide competitive control of
hydrogen bonds in a more sophisticated phenalenyl-based system.
(a)
(b)
1
2
Figure 1. Three-component systems with a conjugate bridge attached on (a) the α-position and (b) the β-position.
[1] Chao, I.; Hwang, T.-S. Angew. Chem. Int. Ed. 2001, 40, 2703.
[2] Hwang, T.-S.; Juan, N.; Chen, H.-Y.; Chen, C.-C.; Lo, S.-J.; Chao, I. Chem. Eur. J. 2004, 10, 1616.
[3] Lo, S.-J.; Li, W.-S.; Chen, H.-Y.; Chao, I. Chem. Eur. J. 2005, 11, 6533.
PO-002
Computatinal Design of Multifunctional Peptides
For Detection of Chemical Agents
Zhifeng Kuang, Sang N. Kim, Wendy J. Crookes-Goodson, Rajesh R. Naik and Barry L. Farmer
Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson AFB, OH 45433
The extreme sensitivity of single-wall carbon nanotubes (SWNTs) to their chemical environment has made themselves
promising platforms for flexible, lightweight, sensitive sensors for the detection of chemical agents and explosives. By
use of computational modeling and simulations, multifunctional peptides are designed to detect chemical agents and
explosives. First, the different binding sites to different agents are explored by use of the AutoDock simulations. Then the
binding free energy is estimated by use of the MD-PB/SA method. Computational analysis show that those peptides
consist of two active sites: one for SWNTS and the other for chemical agents or explosives. The revealed binding motifs
indicate that the aromatic interactions are dominant force for the binding. These designs are tested by SWNT-FET
electronic devices.
163 Book of Programme and Abstract for TACC2008 PO-003
Prediction of protein-protein interaction sites using Granularity computing of quotient space theory
Xiuquan Du, Jiaxing Cheng
The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education,
Anhui University, Hefei, 230039, China
In this paper, combining the protein features with the theory of granular computing of quotient space based on
protein-protein interaction sites classification algorithm is proposed, (i.e. PPI−GS Model). Such algorithm uses the
support vector machine (SVM) with better generalization ability to get different classification results, and construct
different quotient space by using these results. The final result is got by granularity synthesis method to organize these
quotient spaces. The experiment suggests that this new method is in effect. Also, the potency of the granular computing
of quotient space in the application of protein-protein interaction sites prediction and processing is demonstrated.
PO-004
Theoretical Investigation of the Reaction Mechanism of the Dinuclear Zinc Enzyme Dihydroorotase
Rong-Zhen Liaoa,b, Jian-Guo Yua, Frank M. Raushelc, Fahmi Himob, Ruo-Zhuang Liua
a
School of Chemistry, Beijing Normal University, Beijing 100875, P.R.China.
b
Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm,
Sweden.
c
Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA.
The reaction mechanism of the dinuclear zinc enzyme dihydroorotase was investigated by using hybrid density functional
theory. This enzyme catalyzes the reversible interconversion of dihydroorotate and carbamoyl aspartate as illustrated in
Scheme 11,2. Two reaction mechanisms in which the important active site residue Asp250 was either protonated or
unprotonated were considered. The calculations establish that Asp250 must be unprotonated for the reaction to take place.
The bridging hydroxide is shown to be capable of performing nucleophilic attack on the substrate from its bridging
position and the role of Znβ is argued to be the stabilization of the tetrahedral intermediate and the transition state leading
to it, thereby lowering the barrier for the nucleophilic attack. It is furthermore concluded that the rate-limiting step is the
protonation of the amide nitrogen by Asp250 coupled with C-N bond cleavage, which is consistent with previous
experimental findings from isotope labeling studies.
1. J. B. Thoden, G. N. Jr. Phillips, T. M. Neal, F. M. Raushel, H. M. Holden, Biochemistry 2001, 40, 6989-6997.
2. T. N. Porter, Y. Li, F. M. Raushel, Biochemistry 2004, 43, 16285-16292.
PO-005
A new proposed mechanism of ATP hydrolysis in nature
Huan-Xiang Liua, Jun-Min Quana, Yun-Dong Wua,b
a
Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China
164 Book of Programme and Abstract for TACC2008 b
Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong
Kong, China
Among the different nucleotides and their derivatives, adenosine 5’-triphosphate (ATP) has a prominent role as a basic
building block of energy metabolism, where it is a principal form of energy available to cells. Similar to ATP, other
nucleoside 5’-triphosphates (such GTP, CTP, UTP) also can perform dephosphorylation and release energy. However,
why does nature select ATP as the main energy source? In this study, based on some remarkable experimental facts, we
try to explore several possbile ways of ATP hydrolysis from reaction mechanism by using DFT calculations. Here, two
possible ways that adenine help to ATP hydrolysis were explored. One is to use N1 to attack gamma phosphorus atom
and then increase the hydrolysis rate since N is much better nucleophile than oxygen. In the second way, adenine do not
act as nucleophile but catalyze the hydrolysis process as a general base. In addition, for comparison, the ATP hydrolysis
that adenine doesn’t involve was also studied. In every way, both associative and dissociative mechanisms were
investigated. The preliminary results indicate ATP can hydrolyze faster when considering the influence of adenine.
PO-006
Theoretical Study on the Structure of 4,4'-Azobenzene Sulphonate and Layered Double Hydroxide
Yue Zhu, Min Pu, Rui-Fang Liu, Ying-Hui Zhou, Yi-Ying Yang
State Key Laboratory of Chemical Resource Engineering,
Beijing University of Chemical Technology, Beijing 100029, PR China
Azobenzene derivatives can exist in two forms, the cis and trans isomers, which can isomerize both photochemically and
thermally, and they have been widely used as photo-storage, optical switching, optical sensors, etc., [1,2] but pure
azobenzenes are oxidized easily. The chemical stability of azobenzenes can be improved by intercalating them into the
interlayer of LDH [3], because there exist supramolecular interactions between anion and lamellae. On the basis of the
optimized geometry of 4,4'-ABS and Mg/Al lamella, 4,4'-ABS-lamellae model is built. These geometries are fully
optimized by density functional theory (DFT) method at the B3LYP/6-311++G(d,p) level, and the zero-point energy is
obtained through vibrational analysis. Time dependent density functional theory (TD-DFT) is used for the excited-state
calculations of 4,4'-ABS. The results show that the energy of trans is 61.86 kJ/mol lower than the cis in the ground-state.
The energy barrier of the isomerization pathway (from cis to trans) is 85.10 kJ/mol. For the singlet vertical excitations,
the S1? S0 transition energy of both trans and cis-4,4'-ABS are nearly same, with a very weak in trans and the slighter
intensity in cis. The S2? S0 transition of the cis is much less intense and slightly higher in energy than that of the trans.
For 4,4'-ABS-lamellae, the calculated results reveal that the interlayer trans-4,4'-ABS anions are perpendicular to LDH
layers, with a gallery height of 2.067 nm and the calculated binding energy of 332.65 kJ/mol. Because of the strong
electrostatic interaction between host and guest, the isomerization of 4,4'-ABS anion is restricted in the interlayer space.
The work is financially supported by the National Natural Science Foundation.
[1] T. Hugel, N. B. Holland, Cattani A, et al. Science. 2002, 296, 1103.
[2] C. R. Crecca, A. E. Roitberg. J. Phys. Chem. A. 2006, 110, 8188.
[3] L. Y. Liu, M. Pu, L. Yang, et al. Mater. Chem. Phys. 2007, 106, 422.
PO-007
Theoretical Study on the Mechanism of Catalytic Synthesis of Ethyl Tertiary Butyl Ether over Zeolite
Min Pu, Zhi-Hai Ren, Yue Zhu, Biao-Hua Chen
State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology
Beijing, 100029, China
165 Book of Programme and Abstract for TACC2008 Ethyl tertiary butyl ether (ETBE) has been used as one gasoline additive in order to promote the complete combustion of
fuel oil and reduce the air contamination [1]. ETBE may be slowly biodegraded under natural aerobic and anaerobic
conditions [2]. Therefore, the synthesis of ETBE has attracted much attention because of its great demand in the field of
energy sources [3]. The synthesis and decomposition reaction path of ETBE over the surface of zeolite was studied with
density functional theory (DFT) method. The structures of reactant, product and transition state on the reaction path were
optimized by B3LYP method at the 6-31G(d,p) and 6-311++G(d,p) levels, respectively. The zero point energy was
calculated through vibrational analysis. The equilibrium states and transition state were verified according to the numbers
of imaginary frequency of the geometric structure. The calculation results showed that the reactants were firstly adsorbed
on the surface of zeolite, and then the catalytic reaction took place over the acidic site H atom and the neighboring O
atom of acidic site in the form of proton transformation. The intrinsic reaction coordinates traced from the transition state
determined that the reactants and the product was ethanol – isobutene and ETBE, respectively. The activation energy of
synthesis and decomposition of ETBE catalyzed on the surface of zeolite was about 93.11 and 117.67 kJ·mol-1 at the
6-311++G(d,p) level, respectively. This meant that the reaction of ETBE was easier to perform than that of MTBE
relatively.
The work is financially supported by the State Key Basic Research Program (2004CB217804).
[1] Gonzalez-Olmos R, Iglesias M, J. Chem. Thermodyn, 2007, 39, 1557.
[2] Vlasenko NV, Kochkin YN, Puziy AM, J. Mol. Catal. A, 2006, 253, 192.
[3] Hammond G.P., Kallu S.,. McManus MC, Appl. Energy, 2008, 85, 506.
PO-008
Protein folding core revealed by Elastic Network Model
Ji guo Su, Chun Hua Li, Wei Zu Chen, Cun Xin Wang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
Folding core formation is considered to be a key event of protein folding. However, both experiments and simulations
have found that it is a challenging task to identify which residues form the folding core. The protein folding core is the
subset of the protein’s structure which is formed early during protein folding and broken later during protein unfolding.
In this work, an iterative use of Gaussian Network Model (GNM) was adopted to simulate the protein unfolding process
and the persistent contacts during unfolding were identified. The Gaussian network model has been successful in
predicting atomic fluctuations around an energy minimum. However, in the Gaussian network model, the normal mode
description is linear and cannot be accurate in studying protein folding/unfolding, which has many local minima in the
energy landscape. In order to describe the nonlinearity of the conformational changes during protein unfolding, a method
based on the iterative use of normal mode calculation was proposed. The protein unfolding process was mimicked
through breaking the native contacts between the residues one by one according to the fluctuations of the distance
between them. This process is similar to the way that these native contacts break in response to slowly increasing
temperature. The larger the fluctuation is, the easier the breaking of the contact between them. The unfolding processes
of 25 proteins were simulated with this method and the persistent contacts during unfolding were identified. The
secondary structures that formed the persistent contacts were considered to be the folding cores. It is found that the
folding cores revealed by this method are consistent with those obtained by Hydrogen exchange experiments. The results
imply that our method is efficient to identify protein folding core from its native structures.
[1] T. Haliloglu, I. Bahar, and B. Erman. Phys. Rev. Lett. 1997, 79, 3090
[2] J. G. Su, C. H. Li, R. Hao, W. Z. Chen, and C. X. Wang, Biophys. J. 2008, ( to be printed)
Modeling and analysis the tertiary structures of the SOX4 mutants encoded proteins of lung cancer tissues based
on Pdb-Viewer and MATLAB
Qilong Chen
Bioelectronic Center of Shanghai University, Shanghai,China
SOX genes have been associated with a variety of human tumors. In particular, SOX4 plays a role in tumorigenesis and is
highly associated with many tumors. In earlier studies, we have reported that 2 point mutations were identified in the
SOX4 HMG-box in lung cancer cases, namely, G→A and G→C. Moreover, in order to insights into the molecular basis
of protein function, the tertiary structures of SOX4 proteins were modeled using computer programs Swiss-Pdb-Viewer
and MATLAB, homology modeling method, and the known tertiary structure of SOX2 as templates. The
three-dimensional structures of predicted SOX4 proteins are visualized using Visualization Tool of MATLAB. The results
showed that the tertiary structures of the mutant and normal SOX4 are similar, appears to three α-helices and two loop
regions, especially, the loop regions of SOX protein HMG-box are relatively unstable thermodynamically. However, the
side-chain conformations of the codon 107 region were relatively unstable. It suggested that the instability of codon 107
might affect the flexibility of the side chains of mutant SOX4 and could affect the functions of the corresponding protein.
Analysis of the Electrostatic Surfaces showed the C-terminal half of SOX4 form an N/C cavity where interactions with
organic molecules or proteins could be possible. These results indicated that the spatial structure of SOX4 more likely to
regulate the activity and function of this protein, and mutations in the SOX4 gene were likely to be associated with lung
carcinogenesis and tumor metastasis.
PO-010
Effect of micropore volume on the hydrogen adsorption into the aluminophosphate molecular sieves: GCMC
simulation
Mee Kyung Songa, KwangYon Kima, Kyoung Tai Noa, Oh Young Kwonb
a
Bioniformatics & Molecular Design Research Center, Seoul 120749, Korea
b
Chirolite Inc., Sungnam, Gyeonggido 462120 Korea
Since hydrogen has been regarded as a renewable energy carrier, microporous metal organic frameworks have initiated
intensive research on those materials. However, zeolites have no attention as to the hydrogen storage materials although
they have many structural advantages as gas storage adsorbents. By controlling the pore size, surface area and basicity of
zeolites, the adsorption capacity can be improved. Recently, systematic investigations of hydrogen adsorption on zeolites
have been carried out by experimentally [1] and theoretically [2]. It revealed that the hydrogen uptake in zeolites is
strongly dependent on the temperature, type of framework and cation, surface area and micropore volume.
Aluminophosphates (AlPOs) have onedimensional straight channel with chemical compositions of AlPO4 that do not
have any strong acidity nor basicity. Therefore, it is good candidate to study the sorption properties depending upon the
pore size or micropore volume. In this study, we applied Grand canonical Monte Carlo (GCMC) simulations of hydrogen
adsorption on several AlPOs that have the similar surface area, pore volume and the framework structure. The effect of
pore size and micropore volume on the hydrogen uptake was investigated. The adsorption capacities per unit micropore
volume increase as the pore size decreases. For all model AlPOs, the hydrogen exists homogeneously near the oxygen
atoms in the framework.
Acknowledgement: This research was performed for the Hydrogen Energy R&D Center, one of the 21st Century
167 Book of Programme and Abstract for TACC2008 Frontier R&D Program, funded by the Ministry of Science and Technology of Korea.
[1] S.H. Jhung, HK. Kim, J.W. Yoon, JS. Chang, J. Phys. Chem. B, 2006, 110, 9371.
[2] M.K. Song, K.T. No, Cat. Today, 2007, 120, 374.
PO-011
Delayed coupling adjusted calcium signaling in a noise perturbed system
Lin Jia, Xiufeng, Langb
a. Department of Chemistry, Capital Normal University, Beijing 100037, China
b. School of Science, Beijing University of Aeronautics and Astronautics, Beijing 100083,China
Since the diffusion time of Ca2+ through gap junctions is much smaller than the period of the Ca2+ oscillations, the effect
of delay is seldom discussed. However, related experimental research show that there are always delays in the onset of
Ca2+ signals
[1]
, and the delay may be comparatively very long (several seconds) because of some random slow events
before the signal transduction process (eg. cross-linking of some other critical substance for the signaling). Our
simulation investigation shows that such delay effect in the coupling not only can significantly change the signal
characters like the frequency and strength, but also capable of suppressing the stochastic resonance (SR) phenomenon.
Under weak noise, the adjustment of coupling strength can also optimally enhance the signal to noise ratio (SNR) at
intermediate value, which means the delayed coupling is also helpful to optimize the calcium signaling.
Since the calcium signal plays a significant role in triggering and controlling many cellular functions and processes, and
different genes can be activated by varying its frequency or strength
[2]
. This research is of significance in the
2+
investigations of Ca signals in complex living systems.
[1] E. J. Pettit, M.B. Hallett, Biochem. J., 1995, 310, 445; G. M. Roberts, E. V. Davies, E. J. Pettit, and M. B. Hallett,
Exptl. Cell Res. 1997, 230, 303.
[2] R.E. Dolmetsch, K. Xu, and R.S. Lewis, Nature, 1998, 392,933;
PO-012
QSAR Studies of Hallucinogenic Phenylalkylamines by Using Neural Network and Support Vector Machine
Approaches
Zhuoyong Zhang, Liying An, and Yuhong Xiang
Department of Chemistry, Capital Normal University, 105 Xisanhuan North, 100037, Beijing, China
Quantitative structure-activity relationship (QSAR)study on hallucinogenic phenykylamines will be given in this
presentation. A data set of 88 phenylalkylamines [1] has been used to establish prediction models for their hallucinogenic
activities. These chemicals are among the most widely abused hallucinogens especially for young people. Owing to the
difficulty of assaying hallucinogenic activities, it is important to develop predictive methods. Based on our previous work
[2], quantitative structure-activity relationships of phenylalkylamines were determined using three methods, multiple
liner regression (MLR), generalized regression neural network (GRNN), and support vector machine (SVM). Seven
descriptors, accounting for distributions of atomic charges, molecular orbital energy, molecular size and hydrophobic
property were selected by stepwise regression method to build QSAR models. Comparison of the results obtained from
the three models showed that the SVM and GRNN methods exhibited better performance than MLR method. Although
better results were obtained for the training set by GRNN method, the test set prediction did not show superiority. SVM
revealed better performance for the QSAR model of phenylalkylamines investigated. All the three methods should be
168 Book of Programme and Abstract for TACC2008 useful to rapidly identify potential hallucinogenic phenylalkylamines.
[1] Clare BW, J. Med. Chem. 1990, 33, 678.
[2] Zhang Z, An, L, Hu, W, and Xiang, Y, J. Comput. Mol. Des. 2007, 21,145
PO-013
Design and Computational Investigations of Molecular Quasicrystals
Zhongfu Zhou & Kenneth D.M. Harris
School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
A revolutionary discovery in solid state science was made in 1984 when Schechtman and coworkers [1] showed that
certain materials such as metal alloys AlxMny can exhibit diffraction patterns with 10-fold symmetry. Following the
pioneering work in this field, several other materials have been discovered that exhibit diffraction patterns with 10-fold
and other “forbidden” symmetries, and their properties have been investigated experimentally and theoretically [2]. The
term "quasicrystal" is now widely adopted for such materials. Despite the huge interest in quasicrystals during the
intervening period, all examples reported to date have been metal alloy materials, and there has been no example of a
quasicrystal composed of molecular entities. We have demonstrated for the first time [3] that it is feasible to construct
quasicrystals using organic molecules as discrete building units, based on exploiting similar principles to those used for
the structural design of crystalline molecular materials. Our designed molecular quasicrystals (an example is shown in
Figure 1), which are based on a standard Penrose tiling, are shown to be energetically stable and to give rise to a 10-fold
symmetric diffraction patterns. The strategy may be readily extended to the design of other molecular quasicrystals based
on generalized Penrose tilings and other quasiperiodic tilings. We are carrying out further investigations to the designed
molecular quasicrystals, such ab initio calculations of electron structures, the issues relating to the experimental
realization, and also exploring the special features of such materials and their potential applications.
Figure 1. The molecular quasicrystal constructed from a Penrose tiling and its diffraction pattern.
[1] Shechtman, D., Blech, I.,Gratias, D. & Cahn, J.W. Phys. Rev. Lett. 53, 1951 (1984).
[2] Steurer, W. Z. Kristallogr. 219, 391 (2004).
[3] Zhou, Z. & Harris K.D.M. ChemPhysChem. 7, 1649 (2006).
PO-014
First princple calculation on the binding modes and critical stabilty constants of Aluminum chelators
Xi Chena,Chang-Guo Zhanb
a
Contribution from College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
169 Book of Programme and Abstract for TACC2008 b
Divition of Pharmaceutical Science, College of Pharmacy, University of Kentucky, 907 Rose Street, Lexington,
Kentucky 40536, USA
We first report the electronic structure study on the critical stability constants of the complexing reactions of aluminum
ions with a series of chelators. Two types of ligands and their complexes with Al3+were examined: two of them were
hexadentate ligands and the others were tetradentate ligands. By using a set of electronic structure methods, we
calculated the Gibbs free energy changes, i. e. ΔGbind, for these reactions. Compared with the Gibbs free energy
changes derived from experimental critical stability constants value log K, the calculated value systematically
overestimated the binding free energies of these reactions. However, we found the calculated ΔGbind correlated linearly
with the experimental log K value. Based on this finding, we built a linear equation logK = -0.2565×ΔGbind - 2.07 (n = 5,
r = 0.9975, RMSD = 0.272). The predicted stability constants are in good agreement with available experimental data.
Our work provides a new way to predict the chelating ability of aluminum chelators.
[1] J. L. Domingo, Journal of Alzheimers Disease 2006, 10, 331.
[2] S. Sulkova, A. Valek, Nieren-Und Hochdruckkrankheiten 1991, 20, 339.
[3] M. E. Debroe, P. C. Dhaese, F. L. Vandevyver, L. V. Lamberts, Nieren-Und Hochdruckkrankheiten 1991, 20, 311.
[4] R. A. Yokel, Coordination Chemistry Reviews 2002, 228, 97.
[5] R. A. Yokel, Journal of Toxicology and Environmental Health 1994, 41, 131.
[6] J. L. Domingo, Adverse Drug Reactions and Toxicological Reviews 1996, 15, 145.
[7] M. A. Santos, S. Gama, L. Gano, E. Farkas, Journal of Inorganic Biochemistry 2005, 99, 1845.
[8] R. W. Shin, T. P. A. Kruck, H. Murayama, T. Kitamoto, Brain Research 2003, 961, 139.
[9] T. P. A. Kruck, T. E. Burrow, Journal of Inorganic Biochemistry 2002, 88, 19.
[10] Q.-Y. Z. Yu-Hua Qi, Lu Xu, J. Chem. Inf. Comput. Sci 2002, 42, 1471.
[11] V. P. Solov’ev, J. Chem. Inf. Comput. Sci. 2000, 40, 847.
[12] A. D. Becke, Journal of Chemical Physics 1993, 98, 5648.
[13] C. T. Lee, W. T. Yang, R. G. Parr, Physical Review B 1988, 37, 785.
[14] M. Headgordon, J. A. Pople, M. J. Frisch, Chemical Physics Letters 1988, 153, 503.
[15] E. Cances, B. Mennucci, J. Tomasi, Journal of Chemical Physics 1997, 107, 3032.
PO-015
Theoretical Study of the Electronic Excited-State Hydrogen Bonding Dynamics and Its Important Roles on
Photochemistry and Photobiophysics
Guang-Jiu Zhao (赵广久) and Ke-Li Han（韩克利）
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, Dalian 116023, P. R. China
Intermolecular hydrogen bonding, as a site-specific interaction between hydrogen donor and acceptor molecules, is a
very important type of solute-solvent interactions. It plays an important role on the photochemistry of the
hydrogen-bonded systems in their electronically excited states. Herein, we have shown our recent investigations about
the dynamic effects of hydrogen bonding on photochemistry of chromophores in solution. The electronically excited
states of chromophores were theoretically studied using the time-dependent density functional theory (TDDFT) method.
At the same time, the electronic and infrared spectra in both the ground state and electronically excited states were also
simulated. By monitoring the spectral shifts of some characterized vibrational modes involved in the formation of
hydrogen bonds in different electronic states, it has been demonstrated for the first time that the intermolecular hydrogen
bonds between chromophores and hydrogen bonding solvents are significantly strengthened or weakened in the
electronically excited state. The intermolecular hydrogen bond strengthening and weakening behaviors in different
170 Book of Programme and Abstract for TACC2008 electronically excited states are concerted to dynamically tune energy gaps of these electronic states and hence account
for the photochemistry of chromophores in solution. We also clarify the relationship between electronic spectral shifts
and the excited-state hydrogen bonding dynamics for the first time. Moreover, the electronic excited-state hydrogen
bonding dynamics is tightly related with some photochemical processes, such as internal conversion (IC), photoinduced
electron transfer (PET), twisted intramolecular charge transfer (TICT), site-specific solvation, fluorescence quenching or
enhancement, etc. Our investigations about the hydrogen bonding dynamics in electronically excited states may play
important role in photobiophysics.
1. Guang-Jiu Zhao and Ke-Li Han, J. Phys. Chem. A 111, 2469–2474 (2007).
(Top 20 of the most-cited JPC A
articles published in 2007)
2. Guang-Jiu Zhao and Ke-Li Han, J. Phys. Chem. A 111, 9218–9223 (2007).
3. Guang-Jiu Zhao, Jian-Yong Liu, Li-Chuan Zhou, and Ke-Li Han J. Phys. Chem. B 111, 8940–8945 (2007).
4. Guang-Jiu Zhao and Ke-Li Han, J. Chem. Phys. 127, 024306 (2007).
5. Guang-Jiu Zhao, Ke-Li Han, Yi-Bo Lei, and Yu-Sheng Dou J. Chem. Phys. 127, 094307 (2007).
6. Guang-Jiu Zhao and Ke-Li Han, Biophys. J. 94, 38–46 (2008).
7. Guang-Jiu Zhao, Yu-Hui Liu, Ke-Li Han, and Yusheng Dou Chem. Phys. Lett. 453, 29–34 (2008).
8. Guang-Jiu Zhao and Ke-Li Han, J. Comput. Chem. DOI: 10.1002/jcc.20957.
9. Guang-Jiu Zhao, Rui-Kui Chen, Meng-Tao Sun, Guang-Yue Li, Jian-Yong Liu, Yun-Ling Gao, Ke-Li Han, Xi-Chuan
Yang, and Li-Cheng Sun
Chem. Eur. J. (2008) In press.
PO-016
Application Perspectives in the KOA Predicting Models: Validation, Application Domain and Algorithm
Jingwen Chen, Haiying Yu, Xuehua Li, Xianliang Qiao
Key Laboratory of Industrial Ecology and Environmental Engineering (MOE),
Department of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
Several models have been developed to estimate the logarithm of octanol-air partition coefficient (logKOA), including (a)
the fast estimation method that employ the octanol-water partition coefficient (KOW) and Henry’s law constant (H), (b)
the QSPR method that employ theoretical (quantum chemical) molecular structural descriptors, and (c) the method based
on fragment constants and structural correction factors. We further tried a direct method by computing the solvation free
energy of organic chemical molecules in octanol (ΔG) using quantum chemical solvent models. The prediction accuracy
and precision, application domains and algorithms for the 4 methods were compared. Generally the QSPR and fragment
constant methods gave more accurate predictions for the compounds within the application domains and could predict
KOA values at different environmental temperatures. The KOW-H method and ΔG method have broader applicability
domains. The KOW-H method is limited by the lack of sufficient data of KOW, H and their temperature dependence, and
errors in KOW and H values can be propagated or magnified due to the division. Theoretically the application domain of
the ΔG method can extend to every compound; nevertheless the method relies on the accurate calculation of ΔG, which
rests with the development of solvent models in theoretical chemistry.
PO-017
Unique Reactivity of Confined Metal Overlayers on Si(111)
Guo Huimina, Liu Xina,b, Li Wei-Xueb
a
Department of Chemistry and College of Advanced Science and Technology, Dalian University of Technology, 116024,
Dalian, China
b
State Key Laboratory of Catalysis and Center for Theoretical andComputational Chemistry, Dalian Institute of Chemical
171 Book of Programme and Abstract for TACC2008 Physics, CAS, 116023, Dalian, China
Extensive efforts have been made to understand the unusual reactivity of the supported metal clusters/overlayer, where
the center of metal d bands has been thought to be crucial [1]. When the metal clusters/overlayers are deposited on
semi-conducting substrates, the localization of sp electrons may be enhanced and even quantized [2, 3]. The change in
electronic structures may have significant effects on their surface reactivity, which are illustrated here by a comparative
study on CCl4 dissociation reactivity of Ag(111) surface and √3×√3-Ag-Si surface. A distinct reactivity between these
two surfaces has been found, where CCl4 dissociation takes places on Ag(111), while desorption is dominated process
for later one. It is found that on Ag(111) surface, delocalized Ag 5sp electrons can transfer easily to the approaching
molecules, which facilities C-Cl bond breaking and Ag-Cl bond making. However, for the √3×√3-Ag-Si surface, the Ag
5sp electrons are confined at the Ag-Si interface, and not available any more. Consequently, the charge transfer between
molecules and the √3×√3-Ag-Si surface is limited, and the processes of bond breaking and making become demanding.
Current work shows that even for transition metals, its sp electrons can be modified and/or confined by careful
fabrication of the metal overlayers on semiconducting substrates with dramatically different surface reactivity.
1. F.Abild-Pedersen, et. al., Phys. Rev. Lett. 2007, 99, 016105.
2. G. Pacchioni, et. al. Phys. Rev. Lett. 2005, 94, 226104.
3. X. C. Ma, et. al., Proc. Natl. Acad. Sci. USA 2007,104, 9204.
4. Y. Y. Yao, X. Liu, et. al., ChemPhysChem, 2008, 9,975
PO-018
Decomposition Mechanism Studies of Energetic Molecules
Using HOMO and LUMO Orbital Energy Driven Molecular Dynamics
Yanhua Donga, and Yanfeng Songb, Hakima Abou-Rachid*c
a
The College of Computer Science and Technology, Jilin Normal University, Siping, Jilin, China, 136000
b
c
Q-Science Company, 8331 Ouimet, Brossard, Quebec, Canada, J4Y 3B4
Defence R&D-Canada, Valcartier 2459 Blv. Pie-XI North, Quebec, QC, Canada, G3J 1X5
Here we present decomposition mechanism studies of energetic molecules using HOMO and LUMO orbital energy
driven molecular dynamics method [1-2]. This method is based on molecular HOMO and LUMO orbital energy gap as a
biasing potential to accelerate rare chemical reactions in molecular dynamic simulations. Under the frozen orbital
approximation, electronic hardness η of a system may be expressed as this gap. The principle of maximum hardness
states that the hardness is maximum for chemical systems in their ground states. As a reaction progresses towards a
transition state, electronic density is transferred from the HOMO to the LUMO and the system becomes softer due to the
mixing of virtual orbital. The hardness, the HOMO-LUMO gap, attains a minimum at the transition state and the system
then proceeds towards another ground state with increasing this gap once again. Thus, in HOMO-LUMO driven reactions,
the gap behaves in a predictable manner, being a minimum at the transition state and maximum at the products and
reactants. On the other hand, electronic chemical potential, measuring the escaping tendency of an electronic cloud, has a
maximum at transition states while minimum at products and reactants. Therefore, a biased total energy may be defined
as:
Ebiased = Eg ± α m (ε L m ε H )
where Eg is ground state total energy of the system, ε L is LUMO orbital energy and
ε H HOMO orbital energy. The α
is
a tuned parameter.
172 Book of Programme and Abstract for TACC2008 In decomposition chemical reactions of some energetic molecules, proton transfer, bond breaking and forming have a big
impact on the change of HOMO-LUMO gap together with HOMO and LUMO orbital spatial distribution. For instance,
bond forming spatial area usually corresponds to HOMO orbital with electron density accumulation while bond breaking
spatial area corresponds to LUMO orbital with less electron density. Thus, decomposition chemical reactions of energetic
molecules with proton transfer, bond breaking and forming can be characterized by this method. Here, we show
decomposition mechanism of energetic molecules, such as HMX and RDX.
1. Mosey, N.J.; Hu, A.; Woo, T. K. Chemical Physics Letters 2003, 373, 498-505.
2. Anguang Hu, Brian Larade, Hakima Abou-Rachid, Louis-Simon Lussier, Hong Guo, Propellants, Explosives,
Pyrotechnics, 2006, 31, 355-360.
PO-019
COMPARITIVE STUDIES ON GELATION BEHAVIOUR OF SPIDER, SILKWORM AND HUSK PROTEINS
Aby Abrahama, Nambratha NRa, Pavithra HSa, Pramila VBa, Amith RKa, Anil Kumarb, Savithri Bhatc
a
Dept. of Biotechnology, BMS College of Engineering, Basavangudi, Bangalore-560019, India
b
c
Dept. of Biotechnology, Devi Ahilya Vishwavidyalaya, Indore- 452001, India
Asst. Prof., Dept. of Biotechnology, BMSCE, Bangalore, India, Author for correspondence;
The gels have an important role in biomedical engineering primarily as a medium to inject cells into the living body;
significant studies have also been carried out to understand the behaviors of spider-silk gels, an analogue to silkworms’
silk. There has been a constant effort made to explore their applications in tissue engineering and related biomedical
fields. In this study, we have introduced the rice protein as an alternative to silk protein gels which via Insilco studies
found to have domains similar to silk proteins. The sources studied for the protein were husk and root and protein was
extracted using 6NHCl and 6M CaCl2. There was no significant difference between husk or root source material for HCl
extraction in terms of protein yield. The gellation of proteins extracted from spider, silkworm and husk were compared in
the presence of plasticizers and solvents which revealed that the husk protein gelled with water and glycerol at pH and
temperature similar to silkworm and spider silk, but in 14 days and 7 days respectively. Thus, the present study opens a
new source and alternative to silk gels and a new biomaterial for tissue engineering and allied applications.
E-mail : [email protected]
PO-020
Strcture and Energy of The Aminolysis of Alkylsulfinyl Halides
Dae Dong Sunga and Ikchoon Leeb
a
Department of Chemistry, Dong-A University, Saha-Gu, Busan, 604-714, Korea
b
Department of Chemistry, Inha University, Inchon, 402-75,1 Korea
[email protected]
Abstract.
The reaction mechanism of the aminolysis of alkanesulfinyl chloride (and fluoride) have been investigated
theoretically for their structure and energies of the zwitterionic intermediates in forming during the reaction
**
**
at the level
**
of RHF/6-31G , B3LYP/6-31G , and B3LYP/6-311+G . In all cases, the zwitterions show a kind of pseudo-trigonal
bipyramidal (ψ-TBP) structure indicating an addition-elimination pathway is involved in the gas phase as well as in the
aqueous solution. The reorganization to a TBP structure in the gas phase, and that to a solution phase structure explicitly
solvated by 5 water molecules, required substantially lower energy approximately 5 kcal/mol
2
3
energy from sp to sp carbon center in the aminolysis of carbonyl compounds
than the reorganization
about 35 kcal/mol. A discrete change
in the reorganization energy (ΔEre) has been observed at 5 water molecules (n = 5) as the zwitterion is microsolvated
173 Book of Programme and Abstract for TACC2008 successively from n = 0 to 5. The solvation energy (ΔEs) and solvent assistance (ΔEsa) increased linearly with the number
(n) of microsolvating water molecules. Accounts of electron correlation effects in the DFT calculation have led to a much
larger (ca. 40% increase) solvation stabilization and to a considerably shorter S-N bond length (by ca. 0.3Å for Z5w)
compared with the uncorrelated RHF results with 6-31G** basis sets.
Keywords: : Sulfinyl derivatives, DFT, Microsolvation, Addition-elimination, Zwitterion.
PO-021
4-Hydroxyphenylacetic acid: inhibition of monophenolase and activation of diphenolase of mushroom (Agaricus
bisporus) tyrosinase
Shu-Bai Li, Yong Xue, Hai-Tao Zhang, Hua-Li Nie*, Li-Min Zhu*
College of Chemistry, Chemical Engineering and Biotechnology, Donghua University,
2999 Renmin North Road, Shanghai 201620, China
Tyrosinase is a key enzyme of melanin biosynthesis and plays a vital role involving in food storage and skin
pigmentation [1]. Tyrosinase inhibitors and activators have become increasing important in food, pharmaceutical,
cosmetic, and pesticide industries. In this study, we found that 4-hydroxyphenylacetic acid (HPA) can not only inhibit
monophenolase activity but also activate diphenolase activity of mushroom tyrosinase, interestedly. As shown in Fig. 1
(L-tyrosine as substrate), IC50 was estimated to be 0.77 mM and the marked lag period was from 64 sec in absence of
HPA and 184 sec in its presence of 0.8 mM. As shown in Fig. 2 (L-DOPA as substrate), the enzyme activity increased
with the increasing HPA concentrations. When HPA concentration reached to 0.7 mM, the activation ratio was 108%.
The kinetic studies of the enzyme (L-DOPA as substrate) by Lineweaver-Burk plot were investigated in Fig. 3. The plots
were a family of straight lines intersecting at the 2nd quadrant. The results showed that Km decreased while Vm increased
with an increase in HPA concentration, and HPA was a competitive and uncompetitive mixed-type activator [2].
Acknowledgements: This work was sponsored by Esquel Group (Guangdong), Natural Science Foundation of China
(50773009), and program for Changjiang Scholars and Innovative Research Team in university (IRT0526).
*Corresponding author. E-mail: [email protected] (H.-L. Nie)[email protected] (L.-M. Zhu)
[1] J.C. Espín, H.J. Whichers, J. Arg. Food Chem. 1999, 47, 2638.
[2] L. Qiu, Q.-X. Chen, Q. Wang, H. Huang, K.-K. Song, Bioorg. Med. Chem. 2005,13, 6206.
PO-022
DFT Calculations on CrO+ as a Model System for Ethylene Polymerization over Phillips Catalyst
Lei zhong, Zhen Liu, Qi Dong, Ruihua Cheng, Boping Liu
State Key Lab of Chemical Engineering, East China University of Science and Technology
Meilong Road No. 130, 200237, Shanghai, China
174 Book of Programme and Abstract for TACC2008 Although extensive research has been performed on the Phillips catalyst, the oxidation state, structure and composition of
the active sites remain unkown, which is a great barrier to the understanding and improvement in industrial application.1
Therefore, some simple models such as CrO+ have been employed in the mechanism research.2 In this work, the
mechanism for ethylene polymerization, catalyzed by a CrO+ model, is proposed and investigated with density functional
theory (DFT) method. A detailed spin state analysis for active species in the mechanism shows that the quartet spin state
represents the ground spin state for all stationary points. The most possible reaction pathway is figured out for the
ethylene dimerization on CrO+ to give a butane, and, the metallacycle mechanism is energetically favorable.
No.20774025).
[1] Groppo, E.; Lamberti, C.; Bordiga, S.; Spoto, G.; Zecchina, A. Chem. Rev. 2005, 105, 115.
[2] Hanmura, T.; Ichihashi, M.; Monoi, T.; Matsuura, K.; Kondow, T. J. Phys. Chem. A 2004, 108, 10434.
PO-023
Different Reactivities of TiO2 polymorphs: Comparative DFT calculations of water and formic acid adsorption at
anatase and brookite TiO2 surfaces
Wei-Kun Li, Xue-Qing Gong,* and Guanzhong Lu
Research Institute of Industrial Catalysis, East China University of Science and Technology, 130 Meilong Road,
Shanghai 200237, P. R. China
Density functional theory calculations have been performed to determine the relationship between structures and
reactivity of anatase and brookite TiO2 surfaces. Brookite TiO2(210) has the same structural building block of anatase
TiO2(101), but interatomic distances are slightly shorter and the blocks are arranged in a different way. Our calculations
show that these differences significantly change the reactivity toward adsorption of various molecules and metal clusters,
and most importantly, generate highly active sites at the junction between different structural units on brookite TiO2(210).
These results suggest that brookite TiO2(210) would exhibit distinct activity, which may be useful in catalytic and
photocatalytic applications.[1,2]
Figure 1. Calculated structures (top view) of (a) anatase TiO2(101) and (b) brookite TiO2(210). Dashed rectangles in
blue specify building blocks of the surfaces and the atomic components are shown in the inset (side view). The shaded
area in b indicates the gap between two rows of building blocks, and the dashed arrows point to the nearest two Ti5c
separated by the gap.
[1] Wei-Kun Li, Xue-Qing Gong, Guanzhong Lu, and Annabella Selloni, J. Phys. Chem. C. 2008, In press.
175 Book of Programme and Abstract for TACC2008 [2] X. Q. Gong and A. Selloni, Phys. Rev. B. 2007, 76, 235307.
PO-024
First-Principles Calculations of the Surface Properties of TiO2/CeO2 Mixed Oxide
Shu-Lei Zhao, Xue-Qing Gong,* and Guanzhong Lu,*
Research Institute of Industrial Catalysis, East China University of Science and Technology, 130 Meilong Road,
Shanghai 200237, P. R. China
Theoretical calculations have been performed to study the surface properties of the mixed oxide (anatase and ceria) using
density functional theory (DFT). Using the model with CeO2 units adsorbed at the vicinal anatase TiO2(134)[1], we have
investigated their interactions and the surface reactivities before and after ceria adsorption. The calculation results show
that: (i) adsorbed ceria can affect the surface properties greatly and make the oxygen vacancy formation much easier (the
vacancy formation energy reduces from 4.35eV to 2.43eV); (ii) the defective surface can adsorb the molecular oxygen
strongly (adsorption energy =2.41eV) and is not favorable for adsorption of the carbon monoxide (adsorption energy =
0.35eV). The results are in good line with some recent experimental findings.
A
B
Figure 1. Calculated structures (side view) of (A) vicinal anatase TiO2(134) and (B) vicinal anatase TiO2(134) mixed
with CeO2 at step.
[1] Xue-Qing Gong, Annabella Selloni, Matthias Batzill, and Ulrike Diebold Nature Materials 2006, 5, 665.
PO-025
Molecular Modelling Study on Selective Flotation Mechanism of Sodium Chloride Particle with
Dodecylmorpholine
WANG Lijuan, LIU Gousheng, YU Jianguo
Institute of Process Engineering for Natural Resources, East China University of Science and Technology,
Shanghai200237, China
Dodecylmorpholine (DMP) is the collector of Sodium Chloride of high efficiency and selectivity in the process of
reverse flotation-cold crystallization to produce Potassium Chloride. Study on the flotation mechanism is of profound
theoretical significance to improve the present technic, as well as to provide rational basis for the design of flotation
reagents. However, there are arguments against the selective flotation mechanism of NaCl with DMP. In this paper,
molecular modelling approach is used in the theoretical computation on the mineral-reagentinter actionsin a
alite-sylvite-carnallite- Dodecylmorpholine system.
176 Book of Programme and Abstract for TACC2008 Software programs such as Hyperchem6.0, Material Studio4.0 are used to model minerals, DMP, and mineral-reagent
systems, as well as to do some primary geometry optimization. Gaussian03 is mainly used to do quantum chemical
computation.
The atomistic structure of DMP is optimized by HF and DFT method respectively using different basis sets such as
6-31G, 6-31G(d, p). The optimized structural parameters compare well with those reported in literatures. Charges on the
constituent atoms show that O is the active adsorption atom of DMP.
The unit cell and the cleavage surfaces of minerals are modelled and then optimized by plane-wave pseudopotential
method. The lattice parameters of the optimized crystal structures also compare well with experimental measurements.
The surface energy is then calculated for this optimized mineral surface. Plane that has the lowest surface energy is
selected as the adsorption plane for flotation reagents. eg, Halite (100) surface is decided to be the adsorption plane for
DMP.
The optimized reagent molecule is docked on the mineral surface to create the initial geometry of surface-reagent
complex. Several initial conformations are assessed so as to locate the minimum energy conformation of the
mineral-reagent complex. The interaction energy is calculated for the most favorable conformation.
The results show that the theoretically computed interaction energy of halite-DMP is stronger as compared to carnallite
and sylvite, which indicate that DMP is more easily to adsorb on NaCl(100) surface, Thus demonstrate that DMP is more
selective for halite floatation. Charges transfers and bonds formations are also discussed to give a further explanation of
selective flotation mechanism of NaCl with DMP.
Keywords: molecular modeling; quantum chemical computation; HF; DFT; plane-wave pseudopotential method;
interaction energy.
PO-026
Mechanism of Ethylene Dimerization on CrOH+ Studied by Density Functional Theory (DFT) Method
Zhen Liu, Yun Yang, Qi Dong, Ruihua Cheng, Boping Liu
State Key Lab of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237,
Shanghai, China
In spite of the great importance of Phillips Cr-based catalyst in the industrial processes, its formation of active sites and
polymerization mechanisms of this catalyst still remain unclear.1,2 It was reported that two ethylene molecules can
adsorb on CrOH+ stably and dimerized to form 1-butene molecule.3 In this contribution, we apply quantum chemical
molecular modeling to study the interaction between ethylene molecules and CrOH+ ion. Multiple stable coordination
states were found in this study. Starting from the most stable state of the two ethylene molecules coordination on CrOH+,
four possible reaction paths were proposed to form 1-butene molecule through ethylene dimerization on CrOH+. The one
with the lowest energy barrier was considered to be the most facile path to form 1-butene. Much deeper understanding on
the initiation mechanism over Cr-based polymerization catalyst had been achieved.
No.20774025).
[1] McDaniel, M. P. Adv. Catal. 1985, 33, 47.
177 Book of Programme and Abstract for TACC2008 [2] Groppo, E.; Lamberti, C.; Bordiga, S.; Spoto, G.; Zecchina, A. Chem. Rev. 2005, 105, 115.
[3] Hanmura, T.; Ichihashi, M.; Monoi, T.; Matsuura, K.; Kondow, T. J. Phys. Chem. A 2005, 109, 6465.
PO-028
Evaluation On The Structural As Selective Electrodes For Removing Trace Metal Ions By Some Compounds As
Selective Sensors With Using Semi-Empirical Calculations
Shahnaz Sheykh Shoaie
Education & Training of Kerman, Kerman, Iran
Recently have been reported some ionophores in construction of PVC- based membrane selective sensors for Fe+3, Ni+2,
Co+2, Hg+2 and Cd+2 ions by some imine compounds. Imines are one of the most important classes of ligand in
coordination chemistry. In this work we will report the optimized structures of four imines compounds. Using AM1, PM3
and MNDO semi-empirical methods for optimization of these compounds, then we have been compared all of theoretical
data with experimental data in the literatures.
[1]. Fujimoto, H.; Kato, S.; Yamabe, S.; Fukui, K, J. Chem. Phys., 1974, 60(2), 572.
[2]. Fujimoto, H.; Kato, S.; Yamabe, S.; Fukui, K, J. Chem. Phys., 1974, 60(2), 572.
PO-029
Hydrophobic Matching in mixed DMPC/DDPC lipid bilayers
Fuchang Yin and James Kindt
Department of Chemistry and the Cherry L. Emerson Center for Scientific Computation, Emory University, GA 30322,
USA
1
Hydrophobic matching plays an essential role in protein-lipid interactions . Molecular Dynamics (MD) method has been
used in studying the physical properties of the protein-lipid system in both coarse-grained and atomistic models, and
distortions of lipid membranes were observed. MD simulations are seriously limited by the slow rate of diffusive mixing
in their ability to predict lateral distributions of different lipid types within mixed-lipid bilayers using atomistic models.
A method to overcome this limitation, using configuration-bias Monte Carlo (MC) “mutation” moves to transform lipids
from one type to another in dynamic equilibrium, is demonstrated in binary fluid-phase mixtures of lipids whose tails
differ in length by four carbons. The hybrid MC-MD method operates within a semigrand canonical ensemble, so that an
equilibrium composition of the mixture is determined by a constant difference in chemical potential (Δμ) chosen for the
components. In the present work the interaction of mixed lipid bilayer and a transmembrane peptide was studied,
containing the hydrophobic transmembrane region of tyrosine kinase receptor neu, NeuTM35, 128 DMPC/DDPC mixed
lipid bilayer and 3676 TIP3P water. The peptide was aligned in the center of the lipid bilayer along the norm of the
bilayer surface and positional restrains were applied during the simulation. Three lipid compositions were performed and
results show that the longer tail lipid DMPC is more likely to present around the peptide than DDPC, indicating strong
hydrophobic matching effect between DMPC and the NeuTM35 peptide.
[1] de Planque, M. R. R.; Killian, J. A., Mol. Membr. Biol. 2003, 20, (4), 271-284.
[2] Jason de Joannis, Yong Jiang, Fuchang Yin, James Kindt. J. Phys. Chem. B 2006, 110, (51), 25875-25882.
PO-030
Prediction of Gas Chromatographic Retention Time of Iodobenzenes using MLR
178 Book of Programme and Abstract for TACC2008 Pouneh Ebrahimi1, Fariba Safa2 and Faramarz Rostami Ch.1
1
High Education Center, Gorgan University of Agricultural Sciences & Natural Resources, P. O. Box 163, Gonbad, Iran
2
Department of Chemistry, Islamic Azad University, Rasht branch, P. O. Box 41335-3516, Rasht, Iran
The construction of structure-gas chromatographic retention models of organic compounds is an important topic in
quantitative structure-property relationship studies. Correlations between gas chromatographic retention data and
molecular structures can provide more profound insights into interactions between the solutes and the stationary phase.
Numerous investigators have reported very good correlations between retention parameters and molecular descriptors
such as geometric, electronic, polar, steric and topological ones [1-4]. In this study, a QSRR study based on multiple
linear regression (MLR) techniques was carried out for the prediction of GC retention times of a set of 44 iodobenzenes
on DB-5 stationary phase. The descriptors that appear in the selected MLR model are molecular weight, zero-order
molecular connectivity index, polarizability and net charge on most positive atom in the molecule. The statistical
parameters derived from the model show that the linear regression between the retention times and the descriptors is
satisfactory (r= 0.96, SE= 4.5 and F= 256). The average percentage deviation between the experimental values of
retention times and the values predicting using MLR model for the prediction set is 6.3%.
1-W. Guo, Y. Lu, X. M. Zheng, Talanta 2000, 51, 479.
2- T. Kortvelyesi, M. Gorgenyi, K. Heberger, Anal. Chim. Acta 2001, 428, 73.
3- M. H. Fatemi, J. Chromatogr. A 2002, 955, 273.
4- Y. Gao, Y. Wang, X. Yao, X. Zhang, M. Liu, Z. Hu, B. Fan, Talanta 2003, 59, 229.
PO-031
Modeling of Retention time for some Iodobenzenes on DB-5 Stationary Phase using ANN-MLR
Pouneh Ebrahimi1
1
High Education Center, Gorgan University of Agricultural Sciences & Natural Resources, P. O. Box 163, Gonbad, Iran
A QSRR study was performed to develop a predictive model correlating the observed retention times of some
Iodobenzenes with their molecular structures in gas chromatography. The iodobenzene series included the aromatic
amine compounds, which derivatized with iodine and had been previously studied, on DB-5 stationary phase [1]. At first,
a model was generated using only calculated descriptors and MLR technique. At the same time, we also paid much
attention to investigate whether the use of neural network back propagation algorithm could give more accurate
predictions than classic multiple regression method. For this purpose, in order to obtain a parsimonious model, the
network architecture was modified and tested. The number of hidden layer nodes, learning rates and momentum were
parameters optimized. The results showed that ANN model closely relate the retention time values of 44 Iodobenzene
compounds on DB-5 stationary phase to some of their calculated descriptors and the neural network model could exceed
the level of the multiple regression method. The stability and validity of
models were tested by leave-one-out
cross-validation technique. The results of the study indicated that a four parameter equation can be utilized for prediction
of retention time of compounds on DB stationary phase using ANN technique. In this manner, one can get a deeper
insight into the mechanism of chromatographic separation.
[1] T. C. Schmidt et. al., J. Chromatogr. A 1998, 810, 161-172.
PO-032
DFT Study of Electric Field Effect on Carbon Monoxide Adsorption on Pt(111) Surface
Li Yanwei* and Yao Jinhuan
179 Book of Programme and Abstract for TACC2008 Department of Material and Chemical Engineering, Guilin University of Technology, Guilin 541004, P.R. China
The adsorption of CO on Pt(111) surface is of great importance in material science due to the high economical and
environmental implications[1]. To reveal the site which is occupied by the CO molecule, much effort has been devoted
both experimentally and theoretically during the last few decades[1]. The purpose of this work is to study CO adsorption
on Pt(111) surface under the influence of electric field by DFT calculations. The Pt(111) surface is epresented by cluster
model as shown in Figure 1. The applied electric field from zero to 2.57×109 Vm-1) is uniform electric field and
perpendicular to t(111) surface. All calculations are carried out at the B3LYP level with anl2dz basis set to Au atoms and
6-31G* basis set for C and O atoms. The esults show that the hollow site is favored when electric field is zero. After he
electric field is introduced, the binding energy changes as shown in figure 2. The findings of this work is instructive to
study the process and mechanism of CO poisoning of Pt anode for fuel cell.
[1] K. Doll. Surf. Sci. 2004, 573: 464.
* Corresponding author. Tel.: +86-773-5896446; E-mail: [email protected] (Li Yanwei)
PO-033
Design a RPR-based Negotiation Mechanism for E-Marketplaces
Zhitao Hea, Wei Shangb, Yuboc
a
School of Management, Harbin Institute of Technology, [email protected]
b
c
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, [email protected]
School of Management, Harbin Institute of Technology, [email protected]
The evolution of e-marketplaces calls for negotiation support for electronic transactions. A negotiation mechanism based
on reservation price reporting (RPR) mechanism is proposed to facilitate effective negotiation support mechanisms in
e-marketplaces. The decision support extension and multi-issue and multi-party extension of the RPR mechanism are
developed to enhance the applicability of RPR mechanisms. A Finite State Machine model is employed in the design of
negotiation agents to implement the RPR-based mechanisms. Preliminary experiment proved that the proposed
mechanisms and corresponding implementations are effective and feasible for negotiation in e-marketplaces.
PO-034
Studies on the Chemical Constituents of “JinKuiShenQi Pills” Metabolized in Vivo
Li Wen-lana,b, DU Juan, Cheng Bin, Ji Yu-bin Yu Ying-ying, Wang Xiao-dong
a.Center of Research and Development on Life Sciences and Environmental Sciences, Harbin University of Commerce,
b. Engineering research center of natural anticancer drugs, ministry of educatuion, NO.138, Tongda Street, Harbin, China
180 Book of Programme and Abstract for TACC2008 To identify the chemical constituents in Jinkuishenqi pills metabolized in vivo. Analysis and comparison were carried out
by LC- ESI-MS among rats’ serum samples obtained after oral administration of different ingredient preparations such as
Jinkuishenqi pills , Jinkuishenqi Pills without one of ingredients and single ingredient crude drug and control serum. The
compounds absorbed into blood , their original crude drugs and their metabolites were identified. Seventeen compounds
were detected after oral administration of Jinkuishenqi Pills, six of that are metabolites and others are the original form of
the compounds contained in Jinkuishenqi pills. Identified and presumed 12 constituents absorbed into blood by LCESI-MS technique. Among the total, the prime contents are galic acid, 5-HMFA, morroniside, loganin, Oxypaeoniflorin,
paeoniflorinhandhpaeonolh
The
metabolized
contents
Gare,
4-dihydroxyacetophenone,4-methoxylacetophenone-2-O-glycuronate,h2,4-dihydroxyacetophenone-S-O-sulphate,2-dihyd
roxy-4-methoxylacetophenone-S-O-sulphate. The compounds absorbed into blood and its metabolites are capable of
being the effective constituents , the results provide a basic data for the further studies on effective constituents and the
effecting mechanism of Jinkuishenqi pills.
Key words: Jinkuishenqi pills; LC-ESI-MS; metabolized in vivo
[1].HUANG Hou-cai, PENG Yun-ru, SHEN Ming-qin. Chinese Journal of comparative medicine. 2004,14(3): 155.
[2].PENG Yun-ru, SHEN Ming-qin, LUO Yu-hui, et,al.. Chinese Traditional Patent Medicine,2004,26(5): 395.
[3].ZENG Xiao-wei, BAO Su-zhen, LIU Ming-zhe, et,al. Chinese Journal of Integrated Traditional and Western
Medicine,2004,21(3) :238.
[4].ZHENG Xiao-wei, SONG Hong, LI Rong-qun. China Journal of Traditional Chinese Medicine and Pharmacy, 2003,
18(7) :413.
[5].MA Hong, SHEN Ji-yi, ZHANG Ming-wei, et,al. Pharmacology and Clinics of Chinese Materia
Medica,2000,16(6) :5.
[6]. LI Wen-lan, SUN Zhi, CHENG Bin, et,al. Spectroscopy and Spectral Analysis, 2008,28(8):1.
[7].LI Wen-lan, CHENG Bin, JI Yu-bin. Journal of Natural Science of Heilongjiang University.2007,24(6):791
[8].GUO Ji-fen, CHEN Xiao-yan, ZHONG Da-fang. Pharmaceutical Analysis.2001,21(3):167.
[9].CHEN Huai-xia, DU Peng, HAN Feng-mei, et,al. Acta Pharmaceutica Sinica, 2006,41(6): 518.
[10].HAN Feng-mei, ZHU Ming-ming, CHEN Huai-xia, et,al. Acta Pharmaceutica Sinica, 2006,41(9): 846.
[11].WEI Ying-jie, LI Ping, SHU Bin, et,al. Chinese Journal of Analytical Chemistry,2007,35(1):13
[12].CHEN Xiao-yan, ZHONG Da-fang, JIANG Hao, et,al. Acta Pharmaceutica Sinica,1998, 33 (11):849.
[13].CHEN Huai-xia, SHEN Shao-lin, HAN Feng-mei, et,al. Acta Pharmaceutica Sinica, 2006,41(5): 467.
PO-035
Biotransformation of Paeonol and Study on Relationship Between it and Cytochrome P450
Li Wenlana,b, Wang Jia, Ji Yu-bin, Hu Zheng-ting, Wang Xiao-dong, Yu Ying-ying
a
Center of Research and Development on Life Sciences and Environmental Sciences, Harbin University of Commerce,
b
Engineering research center of natural anticancer drugs, ministry of educatuion, NO.138, Tongda Street, Harbin, China
Objective: Metabolic enzyme and biotransformation of paeonol were studied by extraorgan incubation in homogenized
liver. And then rational clinical administration of paeonol was provided with scientific evidences. Methods: The content
of surplus paeonol in homogenized liver was measured by HPLC. The effects of inductors and inhibitors on metabolism
of paeonol were analyzed. Metabolites and metabolic pathways of paeonol were investigated by HPLC/MS/MS. Results:
The metabolic rate of paeonol in the main CYP3A inductor, Dexamethasone (DEX) group, was higher than control group
significantly. But, Phenobarbital (PB) group, the main CYP2B inductor, had no significant difference between these and
control groups. Further more, the specific CYP3A inhibitor Meletin, could inhibit metabolism of paeonol significantly;
The metabolites of paeonol in rat homogenized liver were 4-methoxyacetophenone-2-O-glucuronide and
2,4-dihydroxyacetophenone-5-O-sulphate. Conclusion: CYP3A is the main enzyme taking part in the biotransformation
181 Book of Programme and Abstract for TACC2008 of paeonol in rats. The medicine, which has induce and inhibit effects on CYP3A, may have interactions with paeonol.
Key words: paeonol; liver homogenate; metabolism in vitro; CYP450
[1].L i H K, Dai M , Wang D L , et al1 Ch in J Tradit Med Sci Tech , 2005, 12 (3) : 129.
[2].Sun W F, Gao S J , Gao J X, et al. Chin J Clin Rehabil , 2004, 8 (16) : 3088.
[3].Emerich D F, Dean R L , Exp Neurol, 2002, 173(1) : 168.
[4].Sun W F, Wang Z H, Gap J X, et al. Chin J Clin Rehabil , 2004, 8 (19) : 3792.
[5].W u G X, L i C Y, Xia J , et al. Chin J Clin Rehabil , 2003, 7 (10) : 1502.
[6].Sun G P, Shen Y X, Zhang L L , et al. Acta Univ Med Anhui , 2002, 37 (3) : 183.
[7].Ji C Y, Tan S Y, Liu C Q. Chin J Clin Rehabil , 2005, 9 (6) : 122.
[8].Sun G P, Shen Y X, Zhang L L , et al. Chin Pharmacol Bull , 2003,19 (2) : 160.
[9].Ji C Y, Tan S Y, Liu C Q. Chin J Clin Oncol , 2005, 32 (9) : 513.
[10]. Sun G P, Wang H, Shen Y M , et al. Chin Pharma col Bull , 2004, 20(5) : 550.
[11].Liu C Q , Tan S Y, Ji C Y, et al. Chin Pharm acol Bull , 2005, 21 (10) : 1251.
[12].Chou T C. Brit J Pharmacol, 2003, 139 (6) : 1146.
[13].Qi J S, Li E, Wang F. Chin J Integr Tradit West Med , 2003, 23 (2) : 132.
[14].Yang L Y, Cao Y, Wei Y J , et al. Chin J Dermatol , 2003, 36(4) : 207.
PO-036
Monolayer and Multilayer Compact Film Formations on Different Substrates by Physical Deposition
Xiao-Lin Wang, Zhong-Yuan Lu, Ze-Sheng Li
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University,
Changchun 130023, P.R. China
Dissipative particle dynamics simulations are applied to investigate the monolayer and multilayer film formations on
different solid substrates by physical deposition. The influences of the polymer concentration, the polymer chain length,
the solvent quality, and the interactions between the polymer solution and the solid substrate surface on the film
formation dynamics and the mechanism are studied in detail. The results are analyzed in terms of the thickness and the
shape of the deposited film, the kinetics of phase separation in the polymer solution, and the contact angle formed
between the polymer aggregations and the substrate surface. Moreover, we suggest two strategies, designing a deposition
process analogous to “chemical titration” and physically blocking interlayer diffusion by a simple crosslinked network
barrier, to deposit the compact monolayer and multilayer films with better quality, respectively.
Xiao-Lin Wang’s E-mail: [email protected]
PO-037
Comprehensive Evaluation System Uncertainty on Durability of Concrete Structure
Wang Chang-longa, QI Yan-mingb, Gao Hong-juna, Li Yaoa
a
School of Civil Engineering, Hebei University of Engineering, Handan, Hebei, 056038, China
b
School of Arts, Hebei University of Engineering, Handan, Hebei, 056038, China
[email protected], [email protected]
Considered in assessing durability of concrete structures on the basis of factors was finished. Concrete structures for
specific components, to assess the durability nodes do not contain many intellectual, select the most impact on the
durability of concrete structures to assess factors as indicators, used uncertainty comprehensive evaluation model, the
182 Book of Programme and Abstract for TACC2008 establishment of concrete structures to assess the durability of the indicator system proposed index's categorization
weight of the new method. Applications used by the model shows that the accuracy and applicability.
[1] Shi Changying, Jiao Fenghua, Wang Lijuan. Calculating model for index weights in the fuzzy synthetical evaluation
system of concrete structure durability[J].Journal of Xi’an University of Science-technology and Architecture (Science),
2006,38(1):105-108.
[2] Wang Guangyuan. Unascertained information and its mathematical treatment [J]. Journal of Harbin University of C.
E. & Architecture, 1990(4) :1-10.
[3] Liu Kaidi, Cao Qingkui, Pang Yanjun. A method of fault diagnosis based on unaseertained set [J]. Acta Automatica
Sinica, 2004,30(5): 747-756.
[4] Xia Ning. Research on the durability of reinforced concrete structures [D] Yangzhou: Yangzhou University, 2002.
[5] Guo Fengzhe. Detection and evaluation of durability for existing reinforced concrete bridges [D]. Southwest
Jiaotong University, 2005
[6] Li Yan-cang, Shi Hua-wang. A coalmine safety assessment model based on unascertained measures[J], Coal
Engineering,2004,(11):52-54.
PO-038
The Analysis of the Eutrophic Status in the Largest Lake in Changshu City
a,b
a,b
Qin Yi , Li Ruijie ，Cao Jingjingb
a Key Laboratory of Coastal Disaster and Defence, Ministry of Education(Hohai University) , Nanjing, China
b Laboratory of Marine Environment, Hohai University 1 Xikang Rd. Nanjing, China
(Qin Yi, Ph.D Candidate of Hohai University, [email protected])
Changshu city is in the Changjiang River Basin. Based on the observed and the calculating results of the largest lake in
Changshu City, simulate the flow field and the diffusion of the nitrogen (N) and phosphorus (P) in the lake. And utilize
the observed data and the calculating results of the water concentration field of the lake to analyze the water quality in the
dry season. From the results, it is shown that the velocity of the lake is small and the direction is from the northwest to
the southeast as the topographic form is the northwest higher than the southeast. Both the observed and the computed
results of the N and P concentration show that the lake is subjected to eutrophication. The results will provide the advice
to improve the water environmental quality of the lake in Changshu City, the ecological regime and scientific
management of the lake.
1. Gu Jun-ming. Study on Water Resource of Changshu. Journal of Changshu College. Vol.17, No.2, ( Mar.2003) 81-83
2. Li Rui-jie, Yan Yi-xin, Song Zhi-yao. Calculation of Suspended Sediment Transport in Taiping Waterway. Journal of
Sediment Research. No.4, (2003) 46-51
3. Wang Wei-lun, Chen Long-xing. Soil-Water Protection and Environmental Construction of Changshu City. Resource
Development and Market. Vol.11, No.4, (1995) 176-178
4. Zhang Fa-bing, Hu Wei-ping, Qin Bo-qiang. Numerical Analysis on Influence of Topography on Wind-driven Current
in Lake. Journal of Hydraulic Engineering. Vol.12, (2004) 34-38
5. Peng Qin-wen. Research on Stochastic Diffusion Water Quality Model. Advances in Water Science. Vol.17, No.1,
(2006) 113-115
6. Chong Jia-rong, LING Qu-fei, YANG Cai-gen. Investigation and Fishery Utilization of the Plankton in Kuncheng
Lake. Journal of Xinyang Normal University (Natural Science Edition). Vol.16, No.4, (Oct.2003) 444-446
PO-039
183 Book of Programme and Abstract for TACC2008 Development of Algorithms for the Direct Complete Active Space Self-Consistent Field (CASSCF) Method and
the Direct Restricted Active Space Self-Consistent Field (RASSCF) Method
Shaopeng Li, Michael J Bearpark, Michael A Robb
Department of Chemistry, Imperial College London, South Kensington, Campus, London SW7 2AZ, United Kingdom
In order to study the excited-state reactivity, minima, and transition structures etc. of molecules, the complete active
space self-consistent-field (CASSCF) [1] method, which is a computational electronic method, is widely used. However,
the current CASSCF implementation in Gaussian has a problem that this method accesses computer memory in an
inefficient way, because data is fetched from and stored in widely-separated main memory addresses. The first aim of
this project is to test whether a reorganized version of implementation that accesses memory sequentially makes efficient
use of the processor’s fast cache memory, and speeds up the current CASSCF calculations by an order of magnitude or
more. The next aim is to reorganize the implementation for the current variant of CASSCF (restricted active space (RAS)
SCF [2]) in the same way, which should allow even larger molecules to be studied. And these larger molecules studies
are the third aim of the project. So far, the theory essential for reorganizing the current CASSCF code has been worked
out, and a first implementation tested.
[1] Roos BO, Taylor PR, Siegbahn PEM, Chem. Phys., 1980, 48, 157.
[2] Olsen J, Ross BO, Jørgensen P, Jensen HJA, J. Chem. Phys., 1988, 89, 2185; Malmqvist PA, Rendell A, Roos BO, J.
Phys. Chem., 1990, 94, 5477; Klene M, Robb MA, Blancafort L, Frisch MJ, J. Chem. Phys., 2003, 119, 713.
PO-040
An Explicitly Spin-free Compact Open-shell Coupled Cluster Theory Using a Multi-reference Combinatoric
Exponential Ansatz: Formal Development and Applications
Dipayan Dattaa and Debashis Mukherjeea,b
a
Department of Physical Chemistry,
b
Raman Center for Atomic, Molecular and Optical Sciences Indian Association for the Cultivation of Science, Kolkata
700 032, INDIA
e-mail: [email protected]
Development of an explicitly spin-free coupled-cluster (CC) formalism for open-shell systems continues to remain a
subject of major interest. Description of the general open-shell systems often require multi-reference formalisms.
Although the State-Universal Multi-reference Coupled Cluster (SU-MRCC) theory using the Jeziorski-Monkhorst Ansatz
for the wave-operator with the cluster operators defined in the spin-orbital basis retains the simplicity and compactness of
the formulation, it generally leads to spin-broken solutions. Use of spin-free cluster operators is needed to generate
spin-eigenfunctions. These cluster operators have quasiparticle annihilation operators labeled by the open-shell orbitals
and in addition to the excitation operators, one must include operators with “spectator scattering”. These operators are
generally non-commuting and can be contracted among them. This results in a non-terminating series for the amplitude
equations. We present a new multi-reference combinatoric exponential Ansatz for the wave-operator with the spin-free
non-commuting cluster operators that essentially has the same physical content as the Jeziorski-Monkhorst Ansatz with
the commuting cluster operators. An important innovation of this Ansatz is the choice of an appropriate automorphic
factor accompanying each contracted composite of cluster operators in order to ensure that each such composite appears
only once in the wave-operator. The resulting CC equations consist of two types of terms: a direct term and a folded term
containing the effective Hamiltonian operator. It is emphasized that although the direct term terminates exactly at the
quartic power of the cluster amplitudes, termination of the folded term depends on the valence-rank of the effective
Hamiltonian operator and the excitation rank of the cluster operators at which the theory is truncated. On the omission of
contractions among the cluster operators, our theory reduces to the spin-free CC theory with a multi-reference normal
184 Book of Programme and Abstract for TACC2008 ordered exponential Ansatz. Illustrative applications are presented by computing the state energies, ionization and
excitation energies of neutral doublet radicals and doublet molecular cations and comparing our results with the other
open-shell CC theories, benchmark full CI results and experimental results. Highly encouraging results show the efficacy
of the method.
PO-041
Vibrational spectral diffusion in aqueous solutions
Bhabani S. Mallik and Amalendu Chandra
Department of Chemistry, Indian Institute of Technology Kanpur U.P. - 208016, INDIA
A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in deuterated water and
aqueous ionic solution is presented without using any empirical model potential. Using the method of ab initio molecular
dynamics [1] for trajectory generation and a time series analysis for fluctuating frequency calculations, it is shown that,
for pure heavy water, the dynamics of spectral diffusion of OD bonds has a fast component (~ 100 fs) corresponding to
dynamics of intact hydrogen bonds and a slower long-time component (~ 2 ps) corresponding to lifetimes of hydrogen
bonds. The relaxation is found to occur at a slower rate for hydration shell water molecules around a chloride ion and also
with increase of ion concentration[2]. Such assignments are confirmed by independent calculations of power spectra of
intermolecular motion and hydrogen bond kinetics using population correlation function formalism [2]. Our theoretical
results are compared with those of recent time dependent infrared spectroscopic experiments on water and aqueous ionic
solutions [3].
[1] Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471;
[2] Mallik, B.S.; Semparithi, A.; Chandra, A.
Hutter, J. et al., CPMD, see www.cpmd.org.
J. Phys. Chem. A (in press); J. Chem. Phys. (Submitted)
[3] Park, S.; Fayer, M.D. Proc. Natl. Acas. Sci. 2007, 104, 16731; Fecko, C.J.;
A. J. Chem. Phys. 2005, 122, 054506;
Asbury, J.B.
Loparo, J.J.; Roberts, S.T.; Tokmakoff,
et al., J. Phys. Chem. A 2004, 108, 1107.
PO-042
Migration of protonic defects in confined aqueous systems
Arindam Bankura and Amalendu Chandra
Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
The hydration structure and dynamics of protonic defects in hydrogen bonded chains have been a topic of considerable
current interest [1]. In this study, we carry out ab initio molecular dynamics and QM/MM simulations [2] to investigate
the solvation structure and dynamics of protonic defects with an excess proton and also with a proton less in water-filled
nanotubes of varying length. The rate constants of proton transfers and their relations to hydrogen bond dynamics are
determined by using the so-called population correlation function approach [3,4]. We find that the proton mobility along
one-dimensional water chains is significantly high compared that in bulk water. Also the rate is found to increase with
increase of chainlength as this minimizes the defects created by periodic boundary condition employed in simulations.
Results are also discussed for proton transfer in a water planer monolayer confined between two graphite sheets.
[1] Jessica M. J. Swanson, C. Mark Maupin, Hanning Chen, Matt K. Petersen, Jiancong Xu, Yujie Wu, and Gregory A.
Voth J. Phys. Chem. B. 2000, 111, 4300; C.Dellago, M. M. Naor, G. Hummer,
Phys. Rev. Lett. 2003, 90, 105902.
[2] R. Car and M. Parrinello, Phys. Rev. Lett. 1985, 55, 2471; A. Laio, J. VandeVondele and U. Roethlisberger, J. Chem.
Phys. 2002, 116, 6941.
[3] A. Bankura and A. Chandra, Pramana - J. Phys. 2005, 65, 763; A. Bankura and A. Chandra (to be published).
185 Book of Programme and Abstract for TACC2008 [4] A. Chandra, Phys. Rev. lett. 2000, 85, 768; A. Chandra, M. Tuckerman and D. Marx, Phys. Rev. Lett. 2007, 99,
145901.
PO-043
Software Development and Application to Estimate Melting Points
Jun Li, Junxian Chen, Hai Whang Lee, Chan Kyung Kim
Department of Chemistry, Inha University, 253 Yonghyun-dong, Nam-ku, 402-751, Incheon, Korea
As fundamental physical property of organic compounds, melting points have found wide use in the domains of process
simulation and product design. However, it is not always possible to find reliable experimental values of melting points
for the compounds of interest, nor it is practical to measure the properties as the need arises. So, estimation of the melting
points is required and important work. In this work, three published methods[1-3] were made into programs using C#
from the Microsoft. In these methods, melting points were estimated from the enthalpies and entropies of melting or
group vector space methods. These programs allow us to estimate the melting points faster, and some molecules are
calculated and analyzed here. We also estimated the melting points of some high energetic materials[4,5] using these
methods. Improvement of prediction of melting point will be discussed in detail.
[1] L. Zhao, S. H. Yalkowsky, Ind. Eng. Chem. Res. 1999, 38, 3581
[2] A. Jain, G. Yang, S. H. Yalkowsky, Ind. Eng. Chem. Res. 2004, 43, 7618.
[3] X. Wen, Y. Qiang, Ind. Eng. Chem. Res. 2002, 41, 5534.
[4] M. H. Keshavarz, J. Hazard. Mat. A, 2006, 138, 448.
[5] M. H. Keshavarz, H. R. Pouretedal, J. Hazard. Mat. 2007, 148, 592.
This work is supported by Defense Acquisition Program Administration and Agency for Defence Development and
BK21 program.
PO-044
Theoretical Study on the Proton Transfers of Non-fluorinated Polymers for Fuel Cells
Junxian Chen, Jun Li, Hai Whang Lee, Chan Kyung Kim
Department of Chemistry, Inha University, 253 Yonghyun-dong, Nam-ku, 402-751, Incheon, Korea
The intramolecular proton transfers of non-fluorinated polymers for fuel cells have been examined theoretically by using
the B3LYP method with 6-31+G* basis set.[1] The non-fluorinated polymers with acidic functional groups such as
–SO3H, -CO2H –SO2H –PO3H and -PO4H have been selected as model compounds. This work shows that alkyl chains
get bent severely as the chain lengths became longer. This indicates that the entropy effects could become unfavorable
when the number of alkyl chains is increased. On the other hand, the comparison of the mechanisms of proton transfer
reaction among these model compounds provides a theoretical basis for designing new polymer electrolytes as useful
materials for fuel cells.[2]
[1]Frisch M. J. etc. Gaussian 03, revision B. 03.Gaussian Inc: Pittsburgh, PA, 2004.
[2] Hickner M. J.; Ghassmi H.; Kim Y. S.; Einsla B. R.; McGrath J. E.. Chem. Rev. 2004, 104, 4587.
PO-045
Open-Shell Local Coupled Cluster Theory
186 Book of Programme and Abstract for TACC2008 Y. Liu and H.-J.Werner
Institut für Theoretische Chemie, Universität Stuttgart, Stuttgart, Germany
The local correlation methods as originally proposed by Pulay[1, 2] and implemented previously for closed-shell
methods in our group[3, 4, 5] have been generalized and implemented for spinrestricted high-spin open-shell MP2
(RMP2) and unrestricted coupled cluster (UCCSD) methods, using ROMP2 orbitals. Localization is performed
separately in the closed-shell and open-shell orbital spaces. The excitations are restricted to domains, and only strong
pairs are treated at the highest level. Provided that the open-shell orbital(s) are well localized, this leads to linear scaling
of the computational effort with molecular size. Local density fitting approximations[6] are used to compute all integrals.
The methods are tested for computing ionization potentials and electron affinities, as well as by studying open-shell
copper-oxygen complexes with ammonia ligands. The accuracy is comparable to the corresponding canonical methods.
The implementation of perturbative corrections for triple excitations is in progress.
[1] P. Pulay, Chem. Phys. Lett. 100, 151 (1983).
[2] S. Saebø and P. Pulay, J. Chem. Phys. 88, 1884 (1988).
[3] C. Hampel and H.-J. Werner, J. Chem. Phys. 104, 6286 (1996).
[4] M. Schütz and H.-J. Werner, Chem. Phys. Lett. 318, 370 (2000).
[5] M. Schütz and H.-J. Werner, J. Chem. Phys. 114, 661 (2001).
[6] H.-J. Werner, F. R. Manby, and P.J. Knowles, J. Chem. Phys. 118, 8149 (2003).
PO-046
Quantum Mechanical and Molecular Mechanical Method Combined with Reference Interaction Site Model
Theory to investigate the electronic structure and solvation structure of proteins.
Norio Yoshida and Fumio Hirata
Institute for Molecular Science, 38, Myodaiji, Okazaki, Aichi, Japan
Quantum mechanical and molecular mechanical (QM/MM) method has been widely applied to investigate the property
of the large molecular systems.[1] In order to perform the QM/MM simulation of the protein, usually, an important
region for foucused phenomena is only treated as a QM region, thus, the remaining part is treated as an MM region. For
example, the reaction center of enzymatic reaction is treated as a QM region, and the remaining part of the enzyme and
solvent molecules are treated as an MM region. In our approach, the solvent molecules are treated by reference
interaction site model (RISM) theory which is a statistical mechanics theory.[2,3] RISM theory has been applied to large
molecular systems, such as molecular recognition of proteins, successfully. The advantage of our approach is that the
solvent distribution which independent on initial state of the system can be evaluated. In the present study, we employ
QM/MM/RISM method to investigate the redox reaction of Flavin adenine dinucleotide (FAD) in water. The structure
and stability of reactant (FAD), product (FADH2) and radical (FADH•) are considered by means of QM/MM/RISM
method.
[1] (a) Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 6, 700.
(b) Gao, J. Acc. Chem. Res. 1996, 29, 298. (c) Monard, G.; Merz, K. M., Jr.Acc. Chem. Res. 1999, 32, 904 and
references therein.
[2] Singer, J.; Chandler, D. Mol. Phys. 1985, 55, 621.
[3] Hirata, F., Ed. Molecular Theory of Solvation; Kluwer Academic Publishers: Boston, MA, 2003.
PO-047
187 Book of Programme and Abstract for TACC2008 Combination of Molecular Dynamics Method and 3D-RISM Theory for
Conformational Sampling of Flexible Molecules in Solution
Tatsuhiko Miyata, Fumio Hirata
Department of Theoretical and Computational Molecular Science, Institute
for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585,JAPAN
We have developed an algorithm for sampling the conformational space of flexible molecules in solution, which
combines the molecular dynamics (MD) simulation and the 3D-RISM theory [1]. We report the method and an
application to acetylacetone as a simple model solute. The solvent-induced force acting on solute atoms is evaluated as
the gradient of solvation free energy with respect to the solute-atom coordinates. In order to enhance the speed of
computation, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator
Algorithm) to the combined MD/3d-RISM method. Thanks to the multiple timestep algorithm, one can choose a longer
timestep for renewing the gradient of solvation free energy compared with that of the conformational update. The
multiple timestep algorithm succeeded in enhancing the speed of computation significantly without losing numerical
accuracies: it was enhanced by 3.4 times for acetylacetone. Acetylacetone possesses an intramolecular hydrogen-bonding
capability between the hydroxyl group and the carbonyl oxygen atom. The molecule is significantly stabilized due to this
hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of
the MD simulation in gas phase, whereas in the aqueous solutions the bond was disrupted in a significant number of
conformations. This result reflects the fact that in aqueous solutions the energetic disadvantage due to the disruption of an
intramolecular hydrogen bond can be compensated by the strengthened solute-solvent hydrogen bonds.
[1] T. Miyata and F. Hirata, J. Comput. Chem., 2008, 29, 871.
PO-048
Theoretical investigation on the thermal decomposition mechanisms of some high nitrogen s-tetrazines
Xiong Yinga, Shu Yuan-jiea, Wang Xin-fenga, Zhou Geb
a
Institute of Chemical Materials, CAEP, Mianyang 621900, China
b
Department of Chemistry, Sichuan University, Chengdu 610064, China
By combining the power of ab initio molecular dynamics (AIMD) method and density functional theory (DFT), the
thermal decomposition mechanisms of s-tetrazine molecule and its five derivatives were studied. The present study
suggests that s-tetrazine molecule undergoes concerted triple dissociation, just as its photolysis mechanism. The tetrazine
ring in the tetrazine derivatives may be broken by three modes: concerted triple dissociation, concerted double
dissociation or single dissociation, but the triple dissociation is generally dominant. The stability of the tetrazine ring can
evidently be strengthened by these substituents with nitrogen. If the stability of the substituent is better than that of the
tetrazine ring, decomposition occurs first through the ring breaking. Otherwise, the substituent first reacts. Moreover,
some new conclusions about intermolecular reaction effect on the thermal decomposition mechanisms of tetrazines were
achieved.
PO-049
A Theoretical Study on the Air-Stability of n-Channel Organic Field-Effect Transistors
Ming-Yu Kuo, Yu-Chang Chang, Hsiu-Feng Lu, Chih-Ping Chen, and Ito Chao* Institute of Chemistry, Academia
Sinica Taipei, 11529, Taiwan
For n-channel OFET organic materials, one of the conventional thoughts of achieving air-stable device operation is via
188 Book of Programme and Abstract for TACC2008 functionalizing the semiconducting cores with fluoro side chains that provides a “kinetic barrier” to inhibit the
permeation of moisture against oxidation.[1] However, Weitz et al. have experimentally proved that the “kinetic barrier”
is literally not accountable for the air-stable OFET performance. With density functional calculations (DFT), systematic
studies of adiabatic electron affinities (EAs) of 42 known air-stable/air-unstable n-channel organic semiconductors were
conducted. In this contribution, we suggest that EA of n-channel materials is closely associated with the air-stability of
OFET devices, rather than the fluoro side chains. Consequently, DFT calculations can be employed for screening
compounds or core structures in molecular design.
[1] Jones, B. A.; Facchetti, A.; Wasielewski, M. R.; Marks, T. J. J. Am.Chem. Soc. 2007, 129, 15259.
[2] Weitz, R. T.; Amsharov, K.; Zschieschang, U.; Villas, E. B.; Goswami,D. K.; Burghard, M.; Dosch, H.; Jansen, M.;
Kern, K.; Klauk, H. J. Am.Chem. Soc. 2008, 130, 4637.
PO-050
Electronic coupling in ground and excited state molecules
Chao-Ping Hsu
Institute of Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2 Nankang, Taipei, 115 Taiwan
The rate of charge transfer (CT) and excitation energy transfer (EET) between two molecules in a material directly affect
the charge mobility and spectroscopic characteristics. The rates of these processes can be well described by the Fermi
golden rule and its extensions, where nuclear dynamics are treated. The electronic coupling is kept as a parameter to be
determined either by fitting to experimental data or from a separate calculation. However, it is not intuitively clear how
one might obtain an off-diagonal matrix element (so-called “coupling”) out of diagonalized solutions that typical
quantum calculations yield. There are a number of schemes in the literature that allow us to define and calculate the
electronic couplings. We have improved or extended some of the methods to characterize electronic coupling factors,
under an ab initio Hamiltonian. We have developed and characterize the Spin-Flip schemes to account for the CT
coupling.1,2 The generalized Mullikan-Hush (GMH) scheme has been used widely to account for the CT coupling with
either a semi-empirical Hamiltonian or a multi-reference theory. We found that the failure of GMH with the
configuration interaction singles (CIS) can be corrected by employing a image charge solvation model.3 We have also
extend the methodologies for CT coupling to characterize the EET coupling in both spin-conserve and spin-exchange
cases.4-6 In one recent work,5 we have obtained the EET couplings in the states where excitations are localized. Our new
scheme has allowed us to rigorously characterize the magnitude of Dexter’s exchange coupling.5 Applications and
insights derived from our new computational schemes will be included in the presentation.
(1) You, Z. Q.; Shao, Y. H.; Hsu, C. P. Chem. Phys. Lett. 2004, 390, 116.
(2) Yang, C.-H.; Hsu, C.-P. J. Chem. Phys. 2006, 124, 244507.
(3) Chen, H. C.; Hsu, C. P. J. Phys. Chem. A 2005, 109, 11989.
(4) You, Z.-Q.; Hsu, C.-P.; Fleming, G. R. J. Chem. Phys. 2006, 124, 44506.
(5) Hsu, C. P.; You, Z. Q.; Chen, H. C. J. Phys. Chem. C 2008, 112, 1204.
189 Book of Programme and Abstract for TACC2008 (6) You, Z. Q.; Hsu, C. P. manuscript in preparation 2008.
PO-051
Theoretical Study on the Interaction of Pentacene and p-Sexiphenyl with Rubbed Polymethylene and SAM
Surfaces
Hsiu-Feng Lu, Yu-Tai Tao and Ito Chao*
Institute of Chemistry, Academia Sinica, Taiwan, ROC
Organic materials have great potential in the application of modern electronic devices. Pentacene is a notable material
due to its high field-effect mobility in competition with amorphous silicon. p-Sexiphenyl is a p-type semiconductor with
good optical and electronic properties, such as photoluminescene in the blue visible region and good hole mobility.
However, their charge mobilities are sensitive to their orientation and morphology on the surface. Experiments have
shown that p-sexiphenyl molecules lay flat on the rubbed polymethylene surface, but stand perpendicular on the SAM
(self-assembled monolayer) surface.1 However, pentacene molecules favor to stand on both the rubbed polymethylene
and SAM surfaces.2 To sort out the major factor controlling the orientations of pentacene and p-sexiphenyl on modified
surfaces, in this study we calculate the CH/π interactions3 between pentacene (or p-hexaphenyl) and CH groups of the
surface.
[1] Hu, W.-S.; Lin, Y.-F.; Tao, Y.-T.; Hsu, Y.-J.; Wei, D.-H.; Macromolecules 2005, 38, 9617.
[2] Hu, W.-S.; Weng, S.-Z.; Tao, Y.-T.; Liu, H.-J.; Lee, H.-Y.; Fan, L.-J.; Yang, Y.-W. Langmuir 2007, 23, 12901.
[3] Nishio, M. CrystEngComm. 2004, 6, 130.
PO-052
Molecular Dynamics Simulations of the Adsorption and Crystallization of Long Alkanes on PE(110) and
Amorphous Carbon Surfaces
Rongliang Wu, Xiaozhen Yang
Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Polymer Physics and Chemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
Molecular dynamics simulations have been performed with explicit atom models for alkanes with 10 to 100 backbone
carbons on realistic surfaces of PE(110) and amorphous carbon. The force field used adopt that of Smith et al1 for
alkanes and the surfaces are obtained from Materials Studio 3.1 with thicknesses around 1.6 nm, which is larger than the
non-bonded cutoff length. The simulation times span from 10- 40 ns depending on the length of the alkanes investigated.
The density distributions normal to the surfaces demonstrate that the orderings of alkanes adjacent to the surfaces already
exist in melts for at least three layers and clear distinctions of layered structures can be observed after quenching the
systems. The alkanes on the PE(110) surface get more ordered than those on the amorphous carbon surfaces. The running
orientation parameters of each layer give clear evidence that the orientations of alkanes are induced layer by layer on
PE(110) surfaces while no such phenomenon are observed for those on amorphous carbon surfaces. The current
investigations have offered molecular scale hint for the mechanism of polymer crystallization, which is still under
debate.2,3
(1) Smith, G. D.; Yoon, D. Y. J. Chem. Phys. 1994, 100, 649.
(2) Waheed, N.; Ko, M. J.; Rutledge, G. C. Polymer 2005, 46, 8689.
(3) Welch, P.; Muthukumar, M. Phys. Rev. Lett. 2001, 87, 218302.
Real-time Investigation and Determination of Diffusion Coefficient for Drug in Hydrogels using Electronic
Speckle Pattern Interferometry
Shuaixia Tan, Hongjun Dai, Ning Zhao, Jian Xu
State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, P. R.
China, North 1 Street, Zhongguancun, Haidian district, Beijing, 100190,China
Investigation of solute transport and release in hydrogels is a valid method to understand the diffusion and release of
drugs in living tissues and to design feasible drug delivery device. In this study, real-time electronic speckle pattern
interferometry is developed to study such diffusion processes. The fringe images, which are the phase difference due to
the change in refractive index by drug diffusion at different time instance, can be displayed on computer in vivo. To
avoid the fringe is too dense to distinguish difficultly, different minus image is chosen. The living movies show that,
there is a heartland and fringes grow out incessantly during the drug diffusion. Fick’s law for diffusion is solved
numerically and fit the experimental data to obtain the diffusion coefficients in gel by MATLAB software. At the
considered range of agarose concentration, the diffusion coefficients range from 4.35 to 5.1×10-4 mm2/s for levofloxacin.
The diffusion coefficient decreases with the concentration of agarose hydrogels and levofloxain as well. In addition, the
theoretical hydrodynamic radius from the Stoke-Einstein equation is evaluated.
[1] X. Zhang, N. Hirota, T. Narita, J. P. Gong, Y. Osada, K. Chen, J. Phys. Chem. B 1999, 103, 6069.
[2] S. Liang, J. Xu, L. Weng, H. Dai, X. Zhang, L. Zhang, J. Control Release 2006, 115, 189.
Acknowledgements: The anthors thank the NSFC 50425312, 20574076 and 50521302 for financial support.
PO-054
Dynamics of Hydrogen bonds in Ionic Liquids
Baofu Qiao
State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences
Zhongguancun North First Street 2, Beijing, 100190, China
Hydrogen bond interaction is believed to play an important role in lots of systems, for example biology. in spite of its
191 Book of Programme and Abstract for TACC2008 importance, hydrogen bond is seldom studied, especially its dynamics [1].
Based on the method proposed by Luzar and co-workers [2, 3], we studied the dynamics of hydrogen bonds of several
room-temperature ionic liquids (RTIL). RTIL is a class of salts whose melting temperatures are below 100 ±C. RTIL is
advertised as “green solvent” and ”designer solvent”. We investigated three different anions, Cl-, BF4-, and Tf2N-, in the
presence of the same cation, 1-ethyl-3-methylimidazolium (EMIM+), that is [EMIM][Cl], [EMIM][BF4] and
[EMIM][Tf2N]. Based on the calculated lifetime of hydrogen bonds, we found that the strength of the hydrogen bonds
follow the order: [EMIM][Cl]> [EMIM][Tf2N]>[EMIM][BF4]. It can be explained by the distribution of partial charges
and the formation of hydrogen bond networks in multi-atomic anion RTILs. We also find that the strength of hydrogen
bonds is consistent with that of experimental diffusion coefficient of cations and the viscosities. Some static structures
were also obtained.
[1] van der Spoel, D.; van Maaren, P. J.; Larsson, P.; Timneanu, N. J. Phys. Chem. B 2006, 110, 4393.
[2] Luzar, A.; Chandler, D. Nature 1996, 379, 55.
[3] Luzar, A. J. Chem. Phys. 2000, 113, 10663.
PO-055
Reacting media models building optimization
Chernykh I.G.a, Stoyanovskaya O.P.b, Zasypkina O.A.c
aInstitute of Computational Mathematics and Mathematical Geophysics SB RAS, Lavrentjeva ave., 6, Novosibirsk,
630090, Russia.
bBoreskov Institute of Catalysis SB RAS, Lavrentjeva ave., 5, Novosibirsk,630090, Russia.
cNovosibirsk State University, Novosibirsk, Pirogova str. 2, Novosibirsk,630090, Russia.
The optimization of kinetic scheme of chemical process is the important stage of reacting media models building. This
iterative method consists from the next steps: proposition of scheme from theory, translation scheme to the system of
ordinary differential equation (ODE), finding solution of this system, comparison results with experimental data,
modification of kinetics scheme. ChemPAK software package was created for automation of this process. ChemPAK
consists of network database, computational modules and visual interface. User can create and edit systems of chemical
equations with unlimited number of equations with easy-to-use interface, translate systems of chemical equations to
systems of ODE, add some new equations to the translated system and solve this system by using one of ChemPAK
computational modules. The problem of modeling kinetics of Butlerov reaction in circumstellar disk was solved with
using of ChemPAK [1]. Butlerov reaction consists of 44 reversible chemical equations. Also the problem of homogenous
pyrolysis of C2-C3 hydrocarbons under CO2-laser-induced heating was solved. Reaction scheme for this task consists of
more than 100 chemical equations.
[1] Chernykh I.G., Zasypkina O.A. Computer simulation of the sugar synthesis of Butlerov reaction in a circumstellar
disk // II International Conference "Biosphere Origin and Evolution", Abstracts, Greece. - 2007. - P.187
[2] Chernykh I.G., Stoyanovskaya O.P. Homogenous pyrolysis of C2-C3 hydrocarbons under CO2-laser-induced heating
// 4th EFCATS School on Catalysis ‘Catalyst Design - from Molecular to Industrial Level’, September 20-24, 2006,
Tsars Village (St. Petersburg), Russia, p. 165
PO-056
Quantum Chemical Quantitative Structure Activity Studies of Anticancer Activity of Aldohexose
chloroethylnitrosourea Analogs
192 Book of Programme and Abstract for TACC2008 1
Ibrahim Ali Noorbatchaa, Maimonah Eissaa, and Syed Zahir Ididb
aBiomolecular Engineering Research Unit, Department of Biotechnology Engineering, Faculty of Engineering,
International Islamic University Malaysia, Jalan Gombak, 53100 Kuala Lumpur, Malaysia and
bDepartment of Biomedical Science, Faculty of Science, International Islamic University Malaysia, Bandar Indera
Mahota, 25200 Kuantan, Pahang, Malaysia
Quantitative structure activity relationship (QSAR) involving 18 aldohexose chloroethylnitrosourea compounds having
anticancer activity against Ip-Implanted Murine L1210 Lymphoid Leukemia, is investigated using semi-empirical
quantum chemical AM1 methods.
O
OH
O
R
N
N
N
O
OH
O
R
N
N
N
Cl
Cl
O
O
HO
OH
OH
HO
OH
OH
Quantum chemical methods are used to calculate several electronic and molecular properties of these compounds and
these properties are used to obtain the best QSAR using statistical procedures.
A best QSAR with correlation
2
coefficient, R = 0.7270 is established with four theoretical molecular descriptors. The QSAR obtained in our study can
be used to predict the anticancer activity of new aldohexose chloroethylnitrosourea (CENU) analogs, without resorting to
any experimental studies.
PO-057
The role of diffusion in catalyst design for dehydrogenation of diethylbenzene to divinylbenzene
M. E. Zeynalia*, and A. R. Abbasnejadb
a,bPetrochemical Synthesis Group, Petrochemical Faculty, Iran Polymer and Petrochemical Institute (IPPI), P. O. Box:
14965/115, Tehran, Iran,
Divinylbenzene can be produced by catalytic dehydrogenation of diethylbenzene at 600-650 °C and atmospheric pressure.
The catalyst was prepared by coprecipitation of iron and chromium hydroxide from nitrates solution followed by doping
with potassium carbonate, drying and calcination at different temperatures. For availability the internal surface area of the
catalyst for reactant the pores must be in proper sizes to allow the reactant to diffuse and penetrate inside the catalyst
pellets.
In this study different mechanisms of diffusion such as Knudsen and bulk were investigated for diethylbenzene diffusion
into catalyst and it was concluded that the pore sizes should be in the range that permit transitional diffusion (both
Knudsen and bulk diffusion). The catalyst grain size can be controlled and varied by different parameters such as speed
of mixing, temperature and pH. The effects of grain size formed during coprecipitation and calcination temperature on
pore size distribution and porosity of the catalyst pellet which affect the effective diffusivity were studied. Pore size
distribution of the catalyst was obtained and the effective diffusivities were calculated by numerical integration of
Johanson-Stewart equation [1] for different grain sizes and calcination temperatures. Dependency of Thiele modulus and
effectiveness factor of catalyst on effective diffusivity was determined. Finally the effect of diffusion coefficient on the
performance of a typical fixed bed reactor for preparation of divinylbenzene from dehydrogenation of diethylbenzene
was investigated.
[1]-Z. Bensetiti, D. Schweich and C.A.M. Abreu, Braz. J. Chem. Eng. vol. 14, no. 3, (1997)
193 Book of Programme and Abstract for TACC2008 E-mail: [email protected]
PO-058
DFT study of O2 Adsorption on (100) Chromium surface
A. V. Moradia*, M. T. Baeib
aDepartments of Chemistry, Gorgan Branch, Islamic Azad University, Gorgan,Iran
bDepartments of Chemistry, Azadshahr Branch, Islamic Azad University, Azadshahr, Iran
In this manuscript, we have studied the adsorption processes of O2 on the Cr (100) surface of Vanadium using LANL2DZ,
6-31G* and 6-31G** basis sets by GGA approximation of theory. The most stable adsorption configuration has been
found on transition metal surface with chemisorption’s energies. Although similar in type and energy, the adsorption on
the Cr (100) surface shows a markedly different optimized geometry. There are Three possible adsorption sites, top,
bridge and center site, were considered in the calculations.The calculations have performed for small cluster representing
three adjacent metal sites,Upon the adsorption, the molecule forms strong covalent bonds with the surface, whereupon
the structure of nearby single O=O and O-Cr bonds change at various positions of top, bridge and center sites(vertical
and horizontal) in this model. We have predicted the existence of a new ordered structure comparable in stability to one
proposed previously. We confirm every three different symmetrical sites (except the vertical bridge site approach) are
important for the chemisorption’s processes, because the O2 molecule dissociate. The geometry of Cr (100) surface has
also been optimized theoretically in O2 various distances.
Keywords: Chemisorption, O2, Cr (100), GGA
[1] D. E. Jiang, E. A. Carter, Surf. Sci. 570 (2004) 167.
[2] P. Legare, Surf. Sci. 580 (2005) 137.
[3] D. E. Jiang, E. A. Carter, J. Phys. Rev. 71 (2005) 45402.
PO-059
Chemisorption of Oxygen Molecule on Vanadium-Surface Nanocluster by Quantum Mechanics Studies
M. T. Baei1,*, A. V. Moradi2
1
Departments of Chemistry, Azadshahr Branch, Islamic Azad University, Azadshahr, Iran
2
Departments of Chemistry, Gorgan Branch, Islamic Azad University, Gorgan,Iran
In present investigation, we have employed the adsorption of O=O at bcc site of V (100) with use of LANL2DZ, 6-31G*
and 6-31G** basis sets by GGA approximation of theory. The most stable adsorption configuration has been found on
transition metal surface with chemisorption’s energies. Although similar in type and energy, the adsorption on the V (100)
surface shows a markedly different optimized geometry.
The calculations have performed for small cluster representing three adjacent metal sites,Upon the adsorption, the
molecule forms strong covalent bonds with the surface, whereupon the structure of nearby single O=O and O-V bonds
change at various positions of top, bridge and center sites (vertical and horizontal) in this model. We have predicted the
existence of a new ordered structure comparable in stability to one proposed previously. We confirm every three different
symmetrical sites (except the vertical bridge site approach) are important for the chemisorption’s processes, because the
O2 molecule dissociate. The geometry of V (100) surface has also been optimized theoretically in O2 various distance.
Keywords: Chemisorption, O2, V (100), GGA
E-mail:[email protected]
194 Book of Programme and Abstract for TACC2008 [1] D. E. Jiang, E. A. Carter, Surf. Sci. 570 (2004) 167.
[2] P. Legare, Surf. Sci. 580 (2005) 137.
[3] D. E. Jiang, E. A. Carter, J. Phys. Rev. 71 (2005) 45402.
PO-060
Mono-heteroatom effects on singlet-triplet energy gaps of divalent five-membered ring XC3H3C (X=CH, N, P and
As)
E. Vessally　Department of Science, Payame Noor University, Zanjan Branch, Zanjan, Iran
Divalent carbenes and their analogues are strongly reactive [1]. The carbenes could play from fleeting intermediates to
powerful reagents [2]. Heteroatom effects was investigated on singlet-triplet energy gaps of divalent five-membered ring
XC3H3C, 1X and 2X (X=CH, N, P and As) at B3LYP/6-311++G** level. All triplet states of 1X and 2X are more stable
than the related singlet state. ΔGs-t between singlet and triplet states of 1X and 2X were changed in the order (in
kcal/mol): 1As (14.43) > 1P (10.07) > 1CH (9.60) > 1N (8.50) and 2N (11.56) > 2CH (9.60) > 2P (3.07) > 2As (2.13).
..
..
X
X
1X
2X
X = N, P and As
[1] P. P. Gaspar and R. West In: Z. Rappoport and Y. Apeloig, Editors, Chemistry of organic silicon compounds vol. 2,
Wiley, Chichester (1997), p. 2436.
[2] FontisMedia S. A.: Lausanne and Marcel Dekker, Carbene Chemistry: From Fleeting Intermediates to Powerful
Reagents, Inc.: New York, Basel. (2002).
PO-061
Electronic effects in norbornadiene-quadricyclane system for maximizing the solar energy storage: DFT
calculations
M. Motallebzadeh, E. Vessally
Young Researchers club, Miyaneh Branch, Miyaneh, Iran
Islamic Azad University, Miyaneh Branch, Miyaneh, Iran
The norbornadiene, 1, to quadricyclane, 2, system is used
for solar energy storage, in molecular switching, in
optoelectronic devices, as a data storage compound, as photodynamic chemosensor for metal cations, as a potential
photoresponsive organic magnet and as an energetic binder for solid rocket propellants [1]. Extend of the solar energy
stored in this system is measured simply by calculating the energy difference between the ground states of 1 and 2. Free
energy gaps between 1G and 2G, ΔG(1G)-(2G), as well as solar energy storage are increased when the electron donating
substituents is occurred in position 2 in 1G and 2G. The detailed results are discussed.
G1
1
G1
hν
G2
2
G2
Heat
2
1
G1 -NH2, -OH, -CH3, -H, -F, -CF3, -NO2
G2 -NH2, -OH, -CH3, -H, -F, -CF3, -NO2
[1] M.Z. Kassaee, E. Vessally, Journal of Molecular Structure (THEOCHEM), 2005, 716, 159.
Corresponding author: Tel. 09122257098 E-mail: [email protected]
PO-063
Aromaticity in BN-containing Heterocycles
Hossein Fallah-Bagher-Shaidaei,* Fedyeh Dabiri and Leila Ghalandari
Department of Chemistry, Islamic Azad University-Rasht Branch, P. O. Box 41335-3516,
Rasht, Iran.
Although the aromaticity concept was originally restricted to cyclic aromatic molecules, attempts have been made in
analyzing the behavior of the corresponding analogues like borazine (inorganic benzene)[1]. There have been theoretical
calculations on the aromaticity of BN-containing heterocyles but most of them focus on borazine[2].Compared to
benzene the cyclic delocalization of π electrons is often considered as being reduced due to the large electronegativity
difference between boron and nitrogen. In this study we report structural and magnetic properties of a large set of planar
five and six-membered BN-containing heterocycles using NICS-based magnetic criteria [3]. The BN heterocycles can be
obtained conceptually by replacing each CC group of corresponding homocyclic five or six-membered rings by an
isoelectronic BN group (Figure 1).All of the geometries were calculated by Density Functional Theory (DFT) at B3LYP
level with 6-311+G** basis set. Magnetic properties have been calculated after full geometry optimization using the
gauge-including atomic orbitals (GIAO) method.
H
N
H
N
BH
N
H
HB
HC
HN
BH
N
H
HN
BH
BH
N
N
H
CH
NH HC
NH HC
N
N
H
B
H
N
NH HB
HC
NH
BH HC
N
H
BH
N
H
Figure 1. Some representative BN-containing Five and Six-membered Heterocyles studied.
[1] Haiduc, I.; Sowerby, D. B. The Chemistry of Inorganic Homo- and Heterocycles, Vol 1 and 2; Academic, London,
1987.
[2] (a) Fowler, P. W.; Steiner, E. J. Phys. Chem. A., 1997, 101, 1409.
[3] (a) Fallah-Bagher-Shaidaei, H.; Wannere, C. S.; Corminboeuf, C.; Puchta, R.;
Schleyer, P. v. R. Org. Lett. 2006, 8, 863-866.(b) Fallah-Bagher-Shaidaei, H.; Oral Presentation at 18th Conference on
196 Book of Programme and Abstract for TACC2008 Physical Organic Chemistry, 2006. Warsaw, Poland. (http://science24.com/event/icpoc18/journal/Symposium1) (c)
Fallah-Bagher-Shaidaei, H.; Schleyer, P. v. R. Abstract book of 12th International Conference on the Applications of DFT
in Chemistry and Physics. 2007, 128, Amsterdam, the Netherlands. (d) Fallah-Bagher-Shaidaei, H. et. al, Aromaticity
of Heteroatomic Ring Systems, accepted as Oral presentation at 19th Conference on Physical Organic Chemistry,13-18
July 2008, Santiago de Compostela, Spain.
PO-064
Prediction of Gas Chromatographic Retention Indices of Some Saturated Alcohols on Different Stationary Phases
Using Novel Atom-Type-Based Topological Descriptor
Fariba Safa
Department of Chemistry, Islamic Azad University-Rasht Branch, P.O.Box 41335-3516, Rasht, Iran
The novel atom-type-based index, AT, was used as structural descriptor in quantitative structure-retention relationship
study of a set of saturated alcohols on six different stationary phases (SE-30, OV-3, OV-7, OV-11, OV-17 and OV-25).
At first, multiple linear regression models for the gas chromatographic Kovats retention indices of 25 saturated alcohols
on each stationary phase were developed using AT and Randic’s first-order molecular connectivity indices, showing high
values of multiple correlation coefficient and Fisher-ratio statistics. The stability and statistical validity of the models
were verified by leave-one-out cross validation technique (R2cv ≥ 0.993). Then a single combined model, added
McReynolds polarity term as a descriptor, was developed for all the 139 data points on the stationary phases and the
results were extremely satisfactory (R2=0.997, SE=7.48 and F=7583). External validation was performed by division of
the entire data set into six subsets and prediction of each subset from the other five and showed good predictive ability of
the model developed. Based on the results of the study, the role of different structural features of the model compounds
in the retention behavior can be illustrated by calculation of fraction contribution of the individual indices. The results
indicate successful application of the novel topological index for simultaneous prediction of gas chromatographic
retention indices of saturated alcohols on different stationary phases.
[1] R. Kaliszan, Structure and Retention in Chromatography: A Chemometric approach, Harwood, Amsterdam, 1997.
[2] B. Ren, Chemom. Intell. Lab. Sys. 2003, 66, 29.
PO-065
Fourier Transform Infrared Study on Types of Commercial and Special Acrylic Fibers in the Fabrication of
Carbon Fibers
R. Eslami Farsania, A. Shokuhfarb and A. Sedghic
aIslamic Azad University-South Tehran Branch, 14638-13313, Tehran, Iran, [email protected]
bK.N.Toosi University of Technology, Tehran, Iran
cFaculty of Engineering, I.K.I. University, Qazvin, Iran
Acrylic fibers are used in weaving (blanket, carpet and clothes) and in engineering- housing (instead of asbestos) and
most importantly for producing carbon fibers. In recent decade acrylic fibers are considered as main material for
production of carbon fibers. The manufacture of carbon fibers from acrylic precursors is mainly composed of two steps
including thermal stabilization and carbonization. The first step (stabilization) involves heating the acrylic fibers to
approximately 180 to 300 ºC in an oxygen-containing atmosphere to further orient and then crosslink the molecules, so
that they can survive higher temperature pyrolysis without decomposing. The chemistry of the stabilization process is
complex, but consists of cyclization of the nitrile groups (C≡N) and cross-linking of the chain molecules followed by
dehydrogenation and oxidative reactions. This process transforms the linear polymer (or laterally ordered polymer) into a
197 Book of Programme and Abstract for TACC2008 ladder structure which renders the polymer thermally stable and prevents melting during the subsequent carbonization
process. The second step involves a carbonizing heat treatment of the stabilized acrylic fibers to remove the non-carbon
elements in the form of different gases. Carbonization is carried out at temperatures ranging from 700 to 1500 ºC in an
inert atmosphere. During this process, the fibers shrink in diameter and lose approximately 50% of it's weight.
In this paper, chemical structure of three acrylic fibers types contain itaconic acid (IA), sodium methallyl sulfonate (SMS)
and sodium 2-methyl-2-acrylamidopropane sulfonate (SAMPS) comonomers were studied by fourier transform infrared
(FT-IR) spectroscopy in order to find the effects of acrylic fiber precursor type on the chemical interaction during
stabilization and properties of fabricated carbon fibers. The results of FT-IR show the FT-IR peaks related to C≡N bonds
in acrylic fibers contain IA comonomer have been completely removed during stabilization, while for SAMPS and SMS
this peak just reduced. Also the FT-IR peak related to CH2 bond for acrylic fibers contain IA comonomer has been
reduced sharply in comparison with other acrylic fibers. These changes show that cyclization reaction of nitrile groups
and stabilization reactions in acrylic fibers having IA comonomer were completed. These reactions increase tensile
strength of carbon fibers produced from this material in comparison with other carbon fibers which are produced from
acrylic fibers contain SAMPS and SMS.
PO-066
Structural Flexibility and Rigidity Analysis of HIV-1 gp120
Hepan Tan, AJ Rader
Department of Physics, IUPUI
402 N. Blackford St., LD156U, Indianapolis, IN 46202, U.S.A.
The acquired-immunodeficiency syndrome (AIDS) has evolved into a major worldwide epidemic. Significant effort has
been made in the development of antiviral therapies. A new strategy for vaccine and drug design that complements the
existing cocktail therapy is to target entry of the human immunodeficiency virus (HIV). Such an approach provides the
advantage of interfering with multiple intermediates in this multi-step process. The extraordinary conformational
flexibility, glycosylation and strain variations of viral glycoprotein gp120 cause general viral evasion of humoral immune
response and thus complicate the development of an effective vaccine. Especially difficult to define are the conformation
of gp120 prior to CD4 engagement as well as the relative orientations of the V1/V2 and V3 loops with respect to the
inner and outer domains. In this study we used FIRST (Floppy Inclusion and Rigid Substructure Topography), a program
based on graph theory, to analyze the flexibility and rigidity of all known HIV-1 gp120 structures. A flexibility index is
used to describe and compare the spatial distribution of protein flexibility and rigidity of these structures in isolation and
in complex with CD4, CD4-mimics and neutralizing antibodies. Using this flexibility analysis we identify a putative,
consensus rigid core region (_2) as well as the LRC (Largest Rigid Cluster) with implications for vaccine design and
drug discovery. Detailed comparison for the flexibility index based on strain variations, stabilization mutations as well as
CD4 mimics/b12 binding were carried out. Keywords: H1V-1 gp120; flexibility index; graph theory, FIRST (Floppy
Inclusion and Rigid Substructure Topography); putative binding, rigid core
Keywords: H1V-1 gp120; flexibility index; graph theory, FIRST (Floppy Inclusion and Rigid Substructure Topography);
putative binding, rigid core
PO-067
Interaction of Sugar-Based Amphiphilic 14-Member Macrocycles with Metal Ions
Jacek Korchowiec,† Beata Korchowiec,† and Ewa Rogalska‡
†
Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
198 Book of Programme and Abstract for TACC2008 Groupe d’Etude des Vecteurs Supramoléculaires du Médicament, UMR 7565 CNRS/Nancy Université, Faculté des
Sciences, BP 239, 54506 Vandoeuvre-lès-Nancy cedex,
France
Designing macrocyclic ligands for selective ion complexation is of great fundamental and applied importance. The class
of macrocycles, called crown ethers, has the ability to bind metal cations. By changing the size of the ring, the donor
atoms and the substituents, the properties of the system can be easily modified. In consequence, the molecular and, in
particular, chiral recognition can be tuned-in. The latter effect can be used in developing different catalysts, including
enzyme models. In this presentation, the interactions of two 14-member amphiphilic dioxadithia crown ethers with Li+,
Na+, K+, Mg++, Ca++ and Zn++ cations [1] are demonstrated at B3LYP/6-31G(d) level of theory. Two types of complexes,
one with the cation bonded to the ether oxygen atoms, and the second with the cation bonded to the alkoxy and suger
oxygen atoms were located. The system interaction energy was decomposed into electrostatic (ES), polarization (P),
charge-transfer (CT), exchange (EX) and geometry deformation (DEF) contributions using a self-consistent charge and
configuration method for subsystems (SCCCMS) [2]. The complexes with dications are more stable compared to
monocations. The stability within a given group of periodic table elements decreases with the period number. The highest
stability is observed for the complex formed with zinc. It was shown that P and ES contributions are responsible for
stabilization in the dicationic systems; in the monocationic systems, the CT stabilization is comparable to the P and ES
energy terms. The latter shows in the electron density reorganization plots as well. The individual stabilizing energy
components, ES, P, and CT, show the same trend as the total interaction energy. The destabilizing contributions, EX and
DEF, show the opposite trend. The obtained picture of interactions is consistent with the bond-order data.
[1] Y. Corvis, B. Korchowiec, J. Korchowiec, M. Badis, E. Mironiuk-Puchalska, I. Fokt,
W. Priebe, and Ewa
Rogalska, J. Phys. Chem. B submitted.
[2] J. Korchowiec and T. Uchimaru, J. Chem. Phys. 112 (2000) 1623; J. Korchowiec, Int. J. Quantum Chem. 101 (2005)
714.
PO-068
Elongation-MP2 formalism – implementation and efficiency
Marcin Makowski
Department of Theoretical Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
The elongation method was proposed by Imamura[1] as a theoretical tool that mimics experimental synthesis in the aim
of calculating electronic structure of quasi-linear polymers. Originally, it was applied at semi-empirical level, but since
then the huge progress has been made in both its scope and efficiency. Nowadays, the method is a fully applicable for
electronic structure calculations at Hartree-Fock (HF) and DFT levels of theory[2]. Due to near-linear-scaling of
computational cost it constitutes viable alternative to traditional quantum-chemical computational schemes.
Elongation-MP2 (ELG-MP2) formalism is a first try to extend the elongation method capabilities to describe electron
correlation effects on the ground of ab initio methods. It combines an elongation HF approach providing regionally
localized molecular orbitals with local MP2 (LMP2) ideas as proposed by Pulay[3]. Implementation of ELG-MP2 has
been made in the framework of GAMESS package[4]. The tests for the model systems like water chains, polyacethylene
or polyglycine showed that the method can provide both chemical-level accuracy and efficiency far superior than the
conventional MP2 and at least competitive to LMP2 approaches.
The further work currently being in progress in our group includes implementing calculations of ELG-MP2
wave-function properties like dipole moments, (hyper-)polarizibilities and nuclear gradients. We also try to incorporate
density-fitting techniques to improve efficiency of ELG-MP2 and extend the formalism towards coupled clusters
methodologies.
199 Book of Programme and Abstract for TACC2008 [1] A. Imamura, Y. Aoki, K. Maekawa, J Chem Phys. 1991, 94, 5419.
[2] M. Makowski, J. Korchowiec, F. L. Gu, Y. Aoki, J Comput Chem. 2006, 27, 1603.
[3] S. Saebo, P. Pulay, Annu Rev Phys Chem. 1993, 44, 213.
[4] M. W. Schmidt et al., J Comput Chem. 1993, 14, 1347.
PO-069
Asymmetric bio-sulfoxidation to synthesize (R)-pantoprazole by mushroom tyrosinase
Xin-Yu Lua, Ying-Jie Liub, Tao Qiua, Chao-Hua Zhua, Ying-Li Liub*
a Institute of Design and Research, Jiangsu Polytechnic University, 1 Gehu Road, Changzhou 213164, China
b Great (Changzhou) New Material Technology Inc., 8 Ganxi, XinChang Industrial Park, Liyang 213372, China
Biotransformation has become recognized as an important method for chemical transformation due to environmentally
friendly conditions. Pantoprazole is a novel proton pump inhibitor, the inhibition was found to be greater and longer
lasting than that obtained with omeprazole and lansoprazole [1]. On the other hand, pantoprazole has a pair of enantiomer,
which may exhibit differential stereochemically dependent metabolism and enzyme inhibition. According to the FDA
policy, both enantiomers of pharmaceutically interesting chiral sulfoxides need to be synthesized and their biological
activity determined. Tyrosinase was found to be active in the sulfoxidation of thioanisol, producing the (R)-sulfoxide
with high enantiomeric excess [2]. In this paper, pantoprazole intermediate (A, Fig. 1) was oxidized to (R)-Pantoprazole
(B, Fig.1) by mushroom tyrosinase. The reaction process (Fig. 1) was in a mixed aqueous buffer pH
6.8-methanol–glycerol solvent with diphenolic substrate and it was also studied over a range of temperatures. This
research may offer some ideas for the synthesis of (R)-sulfoxides.
Fig. 1 The synthesis of (R)-Pantoprazole under the catalysis of mushroom tyrosinase.
Acknowledgements: This work was sponsored by Great (Changzhou) New Material Technology Inc.
[1] H.-J. Lin, W.-C. Lo, Y.-C. Cheng, C.-L. Perng, Clinical Therapeutics. 2006, 28,1303.
[2] L. Casella, A. Granata, E. Monzani, R. Pievo, L. Pattarello, L. Bubacco, Micron.2004, 35, 141.
*Corresponding author. E-mail: [email protected]
PO-070
A density functional theory study on blue-emitting iridium complexes
with different ancillary ligands
Houyu Zhang, Xin Gu, and Yuguang Ma
State Key Laboratory of Supramolecular Structure and Materials, Jilin university, Changchun 130012, P. R. China
Phosphorescent iridium complexes have drawn more and more attention due to their practical applications in light
emitting diodes[1]. The fundamental research on excited state behaviors and related quantum efficiency are key issues in
the field[2]. In this work, the structural and electronic properties of two heteroleptic complexes Ir(dfppy)2(pic) and
Ir(dfppy)2(acac) have been investigated theoretically, where dfppy = 2-(2,4-difluorophenyl) pyridine, pic = picolinic acid
and acac = acetoylacetonate. The geometries of ground and excited states are optimized at PBE0/LANL2DZ and
200 Book of Programme and Abstract for TACC2008 CIS/LANL2DZ levels, respectively. Time-dependent density functional theory (TDDFT) method is employed to explore
the absorption and emission properties. The luminescence of each complex originates from the lowest triplet excited state，
which is assigned to the mixing of 3MLCT and 3ILCT characters. The effects of ancillary ligands pic and acac on
absorption and emission spectra are observed by analysis of TDDFT results. The connection between the nature of
excited states and the behavior of the complexes with different ancillary ligands is elucidated. Calculated results will
provide some hints in designing highly efficient blue phosphorescent materials.
[1] Baldo, M. A.; Thompson, M. E.; Forrest, S. R. Nature 2000, 403, 750
[2] Hay, P. J. J. Phys. Chem. A 2002, 106, 1634.
PO-071
Electronic structures and spectroscopic properties of phosphorescent iridium(III) complexes with phenylpyrazole
ligands by a density functional theory study
Xin Gu, Houyu Zhang, Yuguang Ma
State key laboratory of supramolecular structure and materials, Jilin University, Changchun 130012, People’s Republic
of China
Phosphorescent Ir(III) complexes Ir(ppz) , Ir(ppz) (pic), Ir(ppz) (acac) and Ir(ppz) (dbm) (here ppz = phenylpyrazole, pic
3
2
2
2
= picolinate, acac = acetylacetonate and dbm = dibenzoylmethanate), have been investigated theoretically. Density
functional theory (DFT) and time dependent DFT calculations are performed on the ground and excited states of the
investigated complexes to provide insight into the structural, electronic, and optical properties of these systems.
Calculated results testify that ancillary ligands have little influence on the highest occupied molecular orbital (HOMO)
and great effect on lowest unoccupied molecular orbital (LUMO) by lowering the LUMO energy levels dramatically. The
transition of Ir(ppz) is attributed to [d(Ir)+ π (C^N)-- π*(C^N)]; whereas that of Ir(ppz) (pic) is related to [d(Ir)+ π
3
2
(C^N)-- π* (LX)]; and Ir(ppz) (acac), Ir(ppz) (dbm) are categorized as [d(Ir)+ π (LX)-- π* (LX)] charge transfer. In these
2
2
complexes emission color and quantum yield can be turned with different ancillary ligands.
[1] T. Sajoto, P.I. Djurovich, A. Tamayo, M. Yousufuddin, R. Bau, M.E. Thompson, Inorg. Chem. 2005, 44, 7992.
PO-072
Research on the various factors influencing the Moisture Absorption of Sodium Polyacrylate
Chunxiao Zhanga, Wanxi Zhanga,b, Fuchen Baic, Xiyao Zhanga, Jian Liua
a School of Material Science and Engineering, Jilin University, Changchun 130025, P.R.China
b Dalian University of Technology，Dalian, 116000, P.R.China
c Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun 130022, P.R.China
In this paper, sodium polyacrylate was synthesized with acrylic acid as monomer, sodium bisulfate and ammonium
persulfate as the initiator by means of aqueous solution polymerization. The factors such as monomer concentration,
dosage of initiator, reaction temperature and so on influencing on the properties of moisture absorption were
systematically investigated. The experimental results indicated that the property of this polymer was obviously better
than the traditional materials, such as silica gel, molecular sieve and so on. The best reaction condition and formula were
based on the orthogonal experiment design. The optimum moisture absorption amount of sodium polyacrylate reached to
0.97g/g. The mathematical correlation on various factors and moisture absorption rate was obtained based on the multiple
201 Book of Programme and Abstract for TACC2008 regression analysis. The Moisture Content Intuitive Analysis Table indicated the sequence of the factors influencing on
hygroscopicity was shown as follows: monomer concentration>reaction temperature>reaction time>initiator
amount >crosslinker amount.
Keywords: moisture absorption; sodium polyacrylate; aqueous solution polymerization; orthogonal experiment.
PO-073
Simulation and modeling of interior water-endurance property of
polyacrylate latex films
Haitao Zhang, Yuan Zhou, Shijin Dong, Weiqun Jin, Hongyan Wang*
College of Chemistry, Jilin University, Changchun, 130012, P.R.China
Modeling of water-endurance property of interior polyacrylate films was built by experiments and molecular dynamics
simulations. Two primary parameters, aqueous functionality of complex system (φ ) and diffusion coefficient of water
( D), were used in the formula. 9 group emulsions were repared and their water absorption ratios were forecasted.
Comparing the esults forecasted with determined, the mean relation error was less than 5%.
[1] Accelrys Inc. San Diego, CA: Accelrys Inc. 2003
[2] Zhengxia Chen, Qiang Gu, Haifeng Zou, Tianqi Zhao, Hongyan Wang. J.POLYM. SCI. POL. PHYS.
2007,45,884-891.
[3] Xuejun Cui, Shuangling Zhong, Hongyan Wang. J. POWER. SOURCES. 2007,173,28-35.
PO-074
Statistical Mechanics of Semiflexible Polymer
Chun-Cheng Zuo, Yong-Wu Zhao* Feng Ji, Qian-Qian Cao, Jing-Song Yang
Jilin University, College of Mechanical Science and Engineering 130025, China,
Statistical mechanics of semiflexible polymer in a solution is presented in this paper. A semiflexible polymer chain is
modeled as a bead-rod wormlike chain. Using Brownian dynamics, the salt-induced change in mean-square end-to-end
distance of polymer is calculated. The concept of electrostatic persistence length is introduced to account for the elastic
properties of semiflexible polymers. The computational results show us that the bare persistence is dominated above the
salt concentrations of 3 mmol/L, while the electrostatic persistence length is more powerful below the salt concentration
of 0.6 mmol/L. Moreover, the decreasing in the ionic strength can result in the increase in the mean-square end-to-end
202 Book of Programme and Abstract for TACC2008 distance, which indicates the more effective interactions between charges of polymers in lower concentration. The
numerical results are in agreement with theoretical predictions.
Key words: mean-square end-to-end distance, persistence length, wormlike chain, Brownian dynamics, statistical
mechanics
PO-076
Computational Method of Analyzing Secondary Structure of Protein, Based on IR Spectroscopy
Junho Lyoo, June-Young Park, Jingun Kim, Jung Whan Oh
Korea Science Academy, 111 Baek-yang-gwan-mun-ro, 614-822 Busan, South Korea
We calculated vibrational spectroscopic properties, such as, local and normal mode frequencies, coupling constant,
dipole and rotational strengths. We calculated a part of polypeptides, named alanine dipeptide analog (ADA), instead of
an usual protein polymer, composed of more than about 3000 atoms, since we already know ADA can represent a kind of
secondary structures of protein by assigning two specific dihedral angles in the ADA. By using this technique, we
confirmed that an approximation method, fragment analysis can be used for predicting the vibrational circular dichroism
spectra by comparing with the properties calculated by using the density functional theory.
PO-077
Molecular Dynamics Simulation on the Spectrum and Dynamics of H2O in Ionic Liquids
Tian Guocai*, Hua Yixin
Faculty of Materials and Metallurgical Engineering, Kunming University of Science and Technology, Kunming, Yunnan
Province 650093, P.R. China,
[email protected]
Ionic liquids which are liquids at ambient temperature, are completely omposed of anions and cations. They have many
attractive properties and ave been widely and successfully applied many fileds such as organic ynthesis, catalysts,
materials preparation, chemical engineering, extraction nd electro-deposition of metals. However, one of the barriers in
the pplication of RILs is the general lack of physical property data for these ompounds toward fundamental
understanding of the system. The IR pectrum and the reorientation dynamics of water in ionic liquids [Emim+]R R:
[PF6]-, [BF4]-, [CF3SO3]-, [NO3]-） were studied by molecular dynamics imulation. It was found that the water
molecules in those ionic liquids are ostly in the free (not self-associated) state, bounded via H-bonding with BF4]-,
[NO3]-, [CF3SO3]-, and the strength of H-bonding in the ordering PF6]-< [BF4]-< [CF3SO3]-< [NO3]-, which agrees
well with the experimental bserves.
Fig.1 The power spectrum of velocity of H atoms of water in Emim-R（R: [PF6]-,[BF4]-,
[NO3]-, [CF3SO3]-, [NO3]-）obtained by molecular dynamics simulation
203 Book of Programme and Abstract for TACC2008 [1] T Welton. Chem. Rev., 1999, 99(8): 2071
[2] L. Cammsrata, S. G. Kazarian T. welton,Phys.Chem.Chem.Phys.,2001,3: 192-5200
[3] A. Dominguez-Vidal, N Kaun, B. Lwndl, J. Phys.Chem.B 2007,111:4446
PO-078
Theoretical study of the Grignard reagents in solution
Toshifumi MORI, Shigeki KATO
Department of Chemistry, Graduate School of Science, Kyoto University,
Kitashirakawa-Oiwake Cho, 606-8502, Kyoto, Japan
In spite of its variety of applications, the chemistry of organometallic ompounds in solution is still quite mysterious. This
is because the strong solute-solvent interactions as well as complicated electronic structures make the problem very
difficult. Therefore, efficient solvent models as well as accurate quantum chemical methods are necessary in theoretical
approaches. Here, we developed the RISM-MP2 free energy gradient method [1], which allows us to obtain equilibrium
solvated structures of molecules in solution efficiently with microscopic solvent. This method was applied to study a
Grignard reagent CH3MgCl in diethyl ether (Et2O) solution. The equilibrium structures of CH3MgCl and the reaction
with acetone were studied. Usually CH3MgCl is thought to take the equilibria [2],
However, taking into account the effect of solvent molecules properly, we found an alternative dimer conformation (Fig.
1), which was as stable as the monomer. Moreover, this new dimer seems to be important for the reaction with acetone,
since its barrier for the reaction is quite lower than the mechanism from the monomer or the classical dimer
conformations. The importance of the accurate level quantum chemical calculation as well as the role of solvent was
confirmed through our work.
[1] Toshifumi Mori, Shigeki Kato, Chem. Phys. Lett. 2007, 437, 159
[2] J. Axten, J. Troy, C. W. Bock et al., Struct. Chem. 1994, 99, 5
PO-079
Change of flexibility upon binding with the substrate in psychrophilic and mesophilic enzymes
Takahiro Kosugi and Shigehiko Hayashi
Department of Chemistry, Graduate School of Science, Kyoto University,
Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
It is known that some enzymes exhibit peculiar temperature dependence. In particular, psychrophilic enzymes are
significantly more active at low temperatures compared to homologous mesophlic ones in spite of close similarity of the
204 Book of Programme and Abstract for TACC2008 amino acids constituting the active sites. Although it is often considered that the catalytic activity at low temperature is
related to structural flexibility of the enzyme, it is still not clear how the flexibility affects the activity. Moreover, it is not
known which enzymatic step is relevant to the temperature dependence. It may be binding of the substrate, making or
breaking of the chemical bonds or unbinding of the product. At the first stage of our research, we compared the change of
flexibility upon binding with the substrate in psychrophilic and mesophilic α-amylases.
We calculated the difference of root mean square fluctuations and entropies between free and complex states of the
enzymes with molecular dynamics simulation. Quasiharmonic approximation1 was used to calculate entropies. By
dividing the entropies into contributions of each residue, we found the remarkable difference of entropies in the active
site between psychrophilic and mesophilic α-amylases. It is suggested that the structural flexibility that alters the entropy
in the active site is responsible for the temperature dependence of enzyme.
[1] Karplus, M.; Kushick, J. Macromolecules 1981, 14, 325.
PO-081
Structures and energetics of Gly–(H2O)5: Thermodynamic and kinetic stabilities
Ju-Young Kim a, Suk Im a, Sungyul Lee*a, C. Desfrançois*b
aCollege of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701,
Republic of Korea
b Laboratoire de Physique des Lasers, UMR 7538 CNRS – Universite Paris-Nord, 93430 Villetaneuse, France
Calculations are presented for glycine–(H2O)5 clusters, with glycine in canonical or zwitterionic form. The energies of
zwitterionic conformers are calculated to be higher than the canonical ones by 2–4 kcal/mol. The dynamic pathways of
canonical zwitterions isomerization are presented, along with the magnitude of the activation barriers. We find that some
of the zwitterionic glycine–(H2O)5 clusters are kinetically stable for experimental observation due to considerable
barriers (~9 kcal/mol).
[1] M.N. Blom et al., J. Phys. Chem. A. 2007, 111, 7309.
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205 Book of Programme and Abstract for TACC2008 [20] R.R. Julian, M.F. Jarrold, J. Phys. Chem. A 2004, 108, 10861.
[21] J.H. Jensen, M.S. Gordon, J. Am. Chem. Soc. 1995, 117, 8159.
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[31] M.J. Frisch et al., GAUSSIAN 03, Gaussian Inc., Wallingford, CT,2004.
PO-082
Structures and electronic spectra of CdSe – Cys complexes: DFT Study of a Simple Peptide-coated Nanocluster
Sang-Yoon Chung, Ho-Sung Kim, Christopher Liu, Daniel Neuhauser, and Sungyul Lee
College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
We present DFT structures and TD-DFT electronic excitation energies of several small CdSe nanoclusters with the
composition CdnSen (n = 3, 6, 10, 13). We examine the effects on the geometries and excitation spectra of the
nanoclusters induced by two chemical changes: peptide-binding and ligand passivation. We use cysteine (Cys) as a model
peptide and hydrogen atoms as surface-bound solvent ligands. By comparing the results calculated for bare,
hydrogen-passivated (CdnSenH2n), as well as the corresponding Cys-bound clusters (CdnSen – Cys and CdnSenH2n –
Cys), we find that Cys-binding blue-shifts the electronic excitations of bare nanoclusters, but red-shifts those of
hydrogen-passivated nanoclusters. Bond formation between a cadmium atom of the nanocluster and a sulfur atom of Cys
is energetically favored. Further, this is distinguishable by a significant red-shift of the excitation energies.
[1]Sarikaya, M.; Tamerler, C.; Jen, A.; Schulten, K.; Baneyx, F. Nature-Materials 2004, 2, 577.
[2] Deglmann, P.; Ahlrichs, R.; Tsereteli, K. J. Chem. Phys. 2002, 116, 1585.
[3] L.-s.; Hu, J.; Yang, W.; Alivisatos, A. P. Nano Letters, 2001, 1, 349
[4] Aryal, B. P.; Benson, D. E. J. Am. Chem. Soc. 2006, 128, 15986.
[5]Rempel, J.; Trout, B.; Bawendi, M.; Jensen, K. J. Phys. Chem. B, 2006, 110, 18007
[6] Li, L.-s.; Hu, J.; Yang, W.; Alivisatos, A. P. Nano Letters, 2001, 1, 34
PO-083
Solvent - mediated tautomerization of protonated nicotine
Suk Ima, Ju-Young Kima, Sungyul Leea*, and C. Desfrançois2*
aCollege of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
bLaboratoire de Physique des Lasers, UMR 7538 CNRS - Universite Paris-Nord, 93430 Villetaneuse, France
We present calculations for the mechanism and the barrier heights of tautomerization of protonated nicotine. We
calculate the structures of nicotine - H+(H2O)n (n = 0 ~ 4) clusters, and find the dynamic pathways for proton transfer
from the pyridine (sp2) to the pyrrolidine (sp3) site. Tautomerization of the bare protonated nicotine is calculated to
proceed via a considerable overall barrier (~70 kcal/mol), indicating that the proton transfer will not occur in the gas
206 Book of Programme and Abstract for TACC2008 phase. We predict that water molecules may drastically (to ~10 kcal/mol) lower the barriers of the sp2 _ sp3
tautomerization. Our calculated results are discussed in relation to the experimental observations that nicotine is
protonated on the pyridine site in the gas phase, whereas on the pyrrolidine site in aqueous solution.
[1] Domino, E. F, Neuropsychopharmacology 1998, 18, 456.
[2] Hammond, P. S, J.Comput.-Aided. Mol. Des. 2005, 19, 1.
[3] Henchman, R. H, Biophys. J. 2005, 88, 2564.
[4] Yuan, H., Bioorg. Med. Chem. 2006, 14, 7936.
[5] Kawashima, K.; Misawa, Life Sci. 2007, 80, 2206.
[6] Graton, J J. Am. Chem. Soc. 2002, 124, 10552.
[7] Cashin, A. L.J. Am.Chem. Soc. 2005, 127, 350.
[8] Woods, A. S. J. Proteome Res. 2004, 3, 478.
[9] Lee, W. Y.; Sine, S. M. Nature 2005, 438, 243.
[10] Karlin, A., Pharmacogenomics J. 2001, 1, 221.
[11] Arnaud, V., Chem.s Eur. J. 2007, 13, 1499.
[12] Zhong, W. G., Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 12088.
[13] Schmitt, J. D., Med. Chem. 1999, 42,3066.
[14] Beene, D. L.,. Biochemistry 2002, 41, 10262.
[15] Biot, C.,Biol. Chem. 2002, 277, 40816.
[16] Elmore, D. E., J. Org. Chem. 2000, 65, 742.
[17] Graton, J., J. Am. Chem. Soc. 2003, 125, 5988.
[18] Munoz-Caro, C.,. THEOCHEM 2005, 726, 115.
[19] Segall, M. D., Mol. Phys. 1998, 93, 365.
[20] Vistoli, G., Arch. Biochem. Biophys. 2007, 464, 112.
[21] Vistoli, G., J. Am. Chem. Soc. 2002, 124,7472.
[22] Vistoli, G., J. Med. Chem. 2005, 48, 6926.
[23] Marino, T., Theor. Chem. Acc. 2001,107, 8.
[24] Chothia, C., Proc. Natl. Acad. Sci. U.S.A. 1970, 65, 477.
[25] Elmore, D. E., J. Org. Chem. 2000, 65, 742.
PO-085
The Coordination Number of Cu(I) within CopperChaperones
Tamar Ansbacher, Hemant Kumar Srivastava, Jan M. L. Martin and Avital Shurki*
Department of Medicinal Chemistry and Natural Product, School of Pharmacy,
The Lise Meitner-Minerva Center for Computational Quantum Chemistry
The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
Copper ions are essential elements in living organisms, as they are involved in redox catalysis. In spite of their crucial
function, Cu(I) ions are toxic, and their homeostasis is therefore, tightly regulated. Metallochaperones are recently found
to be key proteins in the regulation mechanism of copper ions. These special proteins, responsible for copper transport in
the cell, bind Cu(I) ions with high affinity and release the ions to the target protein very efficiently. It is believed, that
Cu(I) is bound to the copperchaperone through two cystein residues, resulting with a special coordination of two,
although suggestions of different coordination numbers have also been mentioned. The mechanism and the exact
coordination during copper transport to the target protein are still unknown.
Our work tries to address this question. Predicting coordination number of a metal ion is a challenging problem. Hence,
207 Book of Programme and Abstract for TACC2008 our first step towards understanding involved finding a reliable computational method that would correctly predict the
coordination number of various known Cu(I) complexes. We then address the question of Cu(I) coordination within the
copperchaperone.
PO-086
The eSOC System and Drug Discovery
Liangying Luo, Ruisheng Zhang*, Huarong Sun, Kai Pan
Engineering Research Center of Open Source Software and Real–time Systems, Ministry of Education
Department of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu, P.R.China, 730000
*. Corresponding Author:[email protected]
Nowadays the drug discovery process is being more and more complex and costly .With using new technologies for more
efficient and effective development of new drugs, this presents a new problem because these technologies generate huge
amounts of data and information that must be organized, integrated, interpreted and analyzed. Otherwise, drug discovery
process almost comprises a number of sub processes and large scale of complex computing, which are extremely time
and energy consuming. Those problems will solve in our eSOC System. In our system we offer a database visualization
tools used to search heterogeneous database and store chemical document. Use grid technology to improve the efficiency
of computing. We have developed a visual scientific workflow designer for drug discovery researchers, a graphical tool
for assembling and configuring the drug discovery processes, which facilitates researchers to compose a scientific
workflow by just dragging and dropping the graph elements on to a canvas. In this paper we will introduce how to use
our eSOC system for faster time-to-market, greater throughput, and improved quality and innovation.
PO-087
An implementation of Substructure Search in Chemical DataBase Management System
Kai Pan*, Ruisheng Zhang, Huarong Sun, Liangying Luo, Lian Li.
Engineering Research Center of Open Source Software and Real–time Systems, Ministry of Education Department of
Information Science and Engineering, Lanzhou University, Lanzhou, Gansu, P.R.China, 730000
One of the critical problems in chemical database is how to find a given structure from massive, complex structural data
efficiently and correctly in a database. Substructure search has been studied to solve this problem. Substructure search is
also vital to Data mining and Knowledge discovering. Many scientists have done a lot of study in this topic, and most of
these studies are based on subgraph search. In this paper, we will introduce an implement of 2D (2 dimension)
substructure search in MyChemDB (Chemical DataBase Management System), simultaneously, we will indicate the
approach of improving the search performance. This implement utilize the substring matching based on the linear code.
PO-088
A personalized DB tool for Bio- and Chemoinformatics
Huarong Sun, Ruisheng Zhang, Liangying Luo, Kai Pan, Ting Ning
School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu, P.R.China, 730000
In order to improve the environment for researchers on bio- and chemoinformatics, a personalized DB tool named
Biosware was developed. Biosware provides the facilities for data management, including storing chemical files,
208 Book of Programme and Abstract for TACC2008 displaying and editing chemical structure. It made use of Apache Derby, which served as database engine.
Entity-Relationship model was designed to solve the storing problem of various data. A TableViewer was designed for
the visualization of chemical data. Finally, Biosware system was demonstrated through a drug design application, where
the steps of data preparation were expatiated. The results show that Biosware is an effective tool to support research for
scientists, and it facilitates the management of data.
[1] S. Nair Achuthsankar, “Computational Biology & Bioinformatics - A gentle Overview,” [Online].
Availiable:http://print.achuth. googlepages.com/BINFTutorialV5.0CSI07.pdf
[2] A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7
[3] Gilbert, D. Bioinformatics software resources. Briefings in Bioinformatics, Briefings in Bioinformatics, 2004
5(3):300-304.
PO-089
The analysis of chemical features in the core promoter of E. coli
Xiao Hui Wang, Hong Lin Zhai
College of Chemistry & Chemical Engineering, Lanzhou University South Tianshui road 222, Lanzhou, Gansu, 730000,
P.R. China
The characteristics of DNA sequence, such as intrinsic curvature, bendability, staking energy, propeller etc., are highly
correlated with their chemical properties of molecular structure. In this work, the core promoter sequence of Escherichia
coli (E. coli) was translated into digital signals with chemical properties for the first time, and wavelet analysis was
employed to find out the chemical features of the core promoter sequence. Results of this investigation confirmed the
vital role of characteristic modules -10 region and -35 region in regulation, and their possible reaction pathways and
positions were discussed. Furthermore, a novel feature was discovered firstly at -53 region, and it could be initial site
where the DNA sequence was combined with the RNA polymerase.
PO-091
DFT Study on the Hydration Structure of Monomeric Aluminum (III)-Water Complexes and the Deprotonation
Effect
Wenjing Yang, Qiang Miao, Zhaosheng Qian, Cheng Yang, Lina He,
Xiaojie Lu, Ming Ji, Shuping Bi*
School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry of China & Key
Laboratory of MOE for Life Science, Nanjing University, Nanjing 210093, People’s Republic of China
The hydration effect plays an important role in the reactivity of Al(III) in aqueous solution, which becomes one of the
focus of research in properties and hydrolysis-polymerization reaction of aqueous Al(III) ion. In this paper, density
functional theory (DFT) method is performed on the investigation of the structures and characteristics of hydration shell
in the mononuclear Al(III)-water complexes with different charges to understand the hydration effect. Computational
results show that the structure of the outer hydration sphere deforms greatly with the deprotonation, while the inner
hydration sphere changes slightly. When the deprotonation partly or totally proceeds in the outer hydration sphere, the
Al(III)-water complexes undergo spontaneous proton transfer during the optimization. The protons in the inner hydration
sphere transfer to the outer hydration sphere in the complexes with +2 and +1 charge. In the neutral complexes, the
protons transfer between two hydration spheres and only in the outer hydration sphere in the different deprotoned
structures. The motivation of the proton transfer is the dispersedly distribution of negative charges and the formation of
H-bond. Acknowledgements.
209 Book of Programme and Abstract for TACC2008 This project is supported by the National Natural Science Foundation of China (no. 20777030 & NFFTBS-J063042), and
the State Education Administration of China for PhD Program (20050284030).
[1] Kubicki, J. D., J. Phys. Chem. A 2001, 105, 8756.
[2] Bock, C. W.; Markham, G. D.; Katz, A. K.; Glusker, J. P., Inorg. Chem. 2003, 42, 1538.
[3] Undsemaa, M.; Tamm, T., Chem. Phys. Lett. 2004, 400, 54
[4] Miao, Q.; Cao, Q.; Bi, S., J. Chem. Phys. 2004, 121, 4650.
[5] Rudolph, W. W.; Mason, R.; Pye, C. C., Phys. Chem. Chem. Phys. 2000, 2, 5030.
[6] Bylaska, E.; Valiev, M.; Rustad, R. J.; Weare, J. H., J. Chem. Phys. 2007, 126, 104505.
[7] Amira, S.; Spangberg, D.; Hermansson, K., J. Chem. Phys. 2006, 124, 104501.
[8] Martínez, J. M.; Pappalardo, R. R.; Marcos, E. S., J. Am. Chem. Soc. 1999, 121, 3175.
[9] Lubin, M. I.; Bylaska, E. J.; Weare, J. H., Chem. Phys. Lett. 2000, 322, 447.
[10] Ikeda, T.; Hirata, M.; Kimura, T., J. Chem. Phys. 2006, 124, 074503
PO-092
Density Functional Theory Study on the Interaction between Chloride and Al (III)-Water Complexes
Wenjing Yang, Qiang Miao, Zhaosheng Qian, Cheng Yang, Lina He, Shuping Bi*
School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry of China & Key
Laboratory of MOE for Life Science, Nanjing University, Nanjing 210093, People’s Republic of China
The hydrolysis-polymerization reaction of Al(III) can be influenced by many factors; one of them is the effect from the
coanions. Since AlCl3 is extensively used in the research of hydrolysis-polymerization reaction of Al(III), we applied the
-
density functional theory to investigate the interaction between Cl and Al(III)-water complexes, including gas-phase
-
cluster model and supermolecule model. We found that the interaction between Cl and Al(III)-water complexes depends
on the synergetic effect of the electrostatic force and the H-bond effect. The results from the gas-phase cluster model
-
3+
show that for the Al(III)-water complexes with positive charge, Cl has a tendency to coordinate with Al
since the
electrostatic attraction plays a main role; for the neutral Al(III)-water complexes, the interaction depends on the structure
of the complexes due to the compensation of electrostatic force and H-bond effect; for the Al(III)-water complex with
-
negative charge, Cl has little influence on the complex because the electrostatic repulsion become the main effect in the
interaction. The results from supermolecule model indicate that the addition of the second hydration sphere, consisting of
12 explicit water molecules, greatly improves the H-bond effect and effectively counteract the electrostatic force between
-
-
Cl and Al(III)-water complexes. Only in the Al(III)-water complex with high charge(+3), Cl is prone to coordinate with
3+
-
Al , while in the other lower charged Al(III)-water complexes, the complexes with Cl in the second hydration sphere
are more stable because of the strong H-bond effect caused by the second hydration sphere.
[1] Pophristic, V.; Klein, M. L.; Holerca, M. N., J. Phys. Chem. A 2004, 108, 113.
[2] Lauenstein, A.; Hermansson, K.; Lindgren, J.; Probst, M.; Bopp, P. A., Int. J. Quantum Chem. 2000, 80, 892.
[3] Niedner-Schatteburg, G.; Bondybey, V. E., Chem. Rev. 2000, 100, 4059. [4] Bock, C. W.; Markham, G. D.; Katz, A.
K.; Glusker, J. P., Inorg. Chem. 2003, 42, 1538.
[5] Siu, C.; Petru Balaj, O.; Bondybey, V. E.; Beyer, M. K.; J. Am. Chem. Soc.2007, 129, 3238.
[6] Yamanaka, K.; Kameda, Y.; Amo, Y.; Usuki, T.; J. Phys. Chem. B 2007, 111, 11337.
[7] Martínez, J. M.; Pappalardo, R. R.; Marcos, E. S., J. Am. Chem. Soc. 1999, 121, 3175.
[8] Ikeda, T.; Hirata, M.; Kimura, T., J. Chem. Phys. 2006, 124, 074503
Charge-transport Properties of Metal and Nonmetallic Phthalocyanine Iodides. Effects of Packing, Dopant,
Central Metal, and Core Modification
Shuang Chen and Jing Ma*
School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory
of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, 210093, P. R. China
The charge-transport properties of the one-dimensional stacking metal and nonmetallic phthalocyanine iodides (M(Pc)I,
M=Fe, Co, Ni, Cu and H2(Pc)I) have been theoretically investigated. On the basis of the tight-binding approximation1
and the two-state theory2, both the site energy correction3 and the Fock matrix4 methods are employed to calculate the
transfer integral. The intermolecular motions, including interplanar translation, twist, slip, and tilt, have important
impacts on the transfer integral. The content of the dopant is a crucial factor for modulation of charge-transport properties.
Central metals of Pc ligand affect the transfer integrals a little, but significantly affect the reorganization energies. High
hole-transfer rates (up to 1015 or 1016) in metal and nonmetallic phthalocanines are predicted through our calculations.
The extension of the π-conjugation in macrocyclic ligand brings about considerable influence on the transfer integrals.
[1] Coropceanu, V.; Cornil, J.; Filho, D. A. d. S.; Olivier, Y.; Silbey, R.; Brédas, J.-L, Chem. Rev. 2007, 107, 926.
[2] Newton, M. D., Chem. Rev. 1991, 91, 767.
[3] Valeev, E. F.; Coropceanu, V.; Filho, D. A. d. S.; Salman, S.; Brédas, J.-L., J. Am. Chem. Soc. 2006, 128, 9882.
[4] Wang, L. J.; Peng, Q.; Li, Q. K.; Shuai, Z., J. Chem. Phys. 2007, 127, 044506.
PO-094
Solvent and Stacking Effects on the Electronic Structures of Alkynylgold Triphenylphosphine Oligomers
Yi Liaoa,b, Jing Maa*
a School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Nanjing
University, Nanjing, 210093, P.R. China
b Institute of Functional Material Chemistry, Department of Chemistry Northeast Normal University, Changchun,
130024, P.R. China
In recent years, oligomeric conjugated gold acetylides have attracted growing attention owing to the aurophilic nature of
gold and the associated rich photoluminescence properties. [1-3] The effects of intermolecular Au···Au and π-π
interactions on the electronic structures of gold(I) triphenylphosphine acetylides are investigated by using the density
functional theory (DFT) and the time-dependent density functional theory (TDDFT). The lowest dipole-allowed vertical
excitation energy is red shifted from monomer to Au···Au linked dimer, and then keeps invariant as the packing extended
from dimer to tetramer and hexamer. A polarized continuum model (PCM) study on the monomer and dimer in several
solutions indicates that the lowest vertical excitation energies exhibit blue shift as the solvent polarity increases.
[1] McArdle, C. P.; Irwin, M. J.; Jennings, M. C.; Puddephatt, R. J. Angew.Chem. Int. Ed. 1999, 38, 3376.
[2] Liau, R. Y.; Schier, A.; Schmidbaur, H. Organometallics 2003, 22, 3199.
[3] Vicente, J.; Chicote, M. T.; Alvarez-Falcón, M. M.; Jones, P. G. Organometallics 2005, 24, 4666.
PO-095
Fragmentation-based QM/MM Simulations of Solution Conformations
of Macromolecules
211 Book of Programme and Abstract for TACC2008 Hui Li, Wei Li, Shuhua Li, Jing Ma*
School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE,
Nanjing University, Nanjing, 210093, P. R. China
We have combined the molecular fragmentation quantum mechanics (QM) calculations with the molecular mechanics
(MM) to construct the ragmentation QM/MM method, and applied it in simulations of dilute olutions of macromolecules.
[1] We adopt the electrostatics embedding M/MM model, where the low-cost generalized energy-based fragmentation
GEBF) [2] calculations are employed for QM part. Conformation energy alculations, geometry optimizations and
Born-Oppenheimer molecular ynamics (BOMD) simulations of poly (ethylene oxide), PEOn, and olyethylene, PEn in
aqueous solution have been performed to test the erformance of fragmentation QM/MM method. The characteristics of
PEOn nd PEn solutions (such as intermolecular hydrogen bonding and chain onfigurations) obtained from the
fragmentation QM/MM simulations are onsistent with the conventional QM/MM method. The length dependence of hain
conformations and dynamics of PEO and PE oligomers in aqueous olutions is also investigated through the fragmentation
QM/MM molecular ynamics simulations.
[1] Li, H.; Li, W.; Li, S.; Ma, J. J. Phys .Chem. B 2008, accepted.
[2] Li, W.; Li, S.; Jiang, Y. J. Phys. Chem. A 2007, 111, 2193-2199.
PO-096
Swelling behaviors and interlayer structure of K- and Cs-smectites: a molecular dynamic simulation study
Liu Xiandong, Lu Xiancai, Wang Rucheng
School of Earth Sciences and engineering, Nanjing University, 210093, Nanjing, P. R. China
Smectites present widely in soils and sediments and they play important roles in many geological processes, industrial
and engineering applications. Water can enter the interlayer space of smectite and thereby put clay platelets apart, which
causes clay swelling. Although some studies have been done, the underlying thermodynamic constraints and molecular
mechanism of swelling and hydration are still poorly understood. We employ molecular simulations to study the
clay-swelling inhibiting function of potassium and cesium, and the transport properties of interlayer water and ions of
smectites. NPT molecular dynamic simulations were performed using the LAMMPS code [1] to mimic experimental
environments (298 K, 1 atm). Clayff was used as the force field which incorporated the SPC water model.[2] The results
show that Cs- and K-smectites swell in a similar way, showing characteristic swelling plateaus and similar trends of
swelling energetic profiles. The global minima of the calculated immersion energy indicate that the most stable swelling
state corresponds to the full-monolayer hydrates. A novel microstructure of 1-layer Cs and K-hydrate is responsible for
the surprising stability: ions are all fixed in coordination cages composed of surface hexagon oxygen and water
molecules. Furthermore, both K- and Cs-smectites with different water contents, the interlayer water and ions diffuse
much slower than bulk water, and their mobility is remarkably higher along the horizontal plane than other directions,
which may be caused by the confining effects of nanosized interlayer space.
[1] S. J. Plimpton, J. Comp. Phys. 1995, 117, 1-19. The URL is www.cs.sandia.gov/~sjplimp/lammps.html.
[2] R. T. Cygan, J. J. Liang, A. G. Kalinichev, J. Phys. Chem. B. 2004, 108, 1255-1266.
PO-097
Characterizing potential infection virus for its host: Nucleotide sequence pattern analysis
Qiang Miao1, Xingjun Tian2, Zhilin Wang1, Junjie Zhu1
1School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR of China
212 Book of Programme and Abstract for TACC2008 2Department of Biology, Nanjing University, Nanjing 210093, PR of China
H5N1 avian influenza is regularly breaking out in birds across Asia, the Middle East, Africa and Europe, and has crossed
the species barrier to infect humans with great risk of human-to-human transmission. Moreover, AIDS, Dengue, and
Ebola haemorrhagic fever (EHF) have become major international public health concern in recent years. How many
potential viral viruses we will be against to? Can we find a collection of virus information for alerting all infection
viruses for human beings? The complete human genome makes this possible to systematically survey and obtaining a
gene or a sub-molecule level description in the species correlation within a safety and harmonic ecosystem. We have
performed population analysis of short nucleotide sequence patterns (NSP) for the genomes of human and over twenty
selected organisms. The NSP incompatibility of human with viruses may match the levels order of immune reaction in
human cell against to these viruses invasion. It suggests that human being be free infection from or greater harmful by
these viruses. The viruses with small NSP exceptions are of the potential capability of cell infection but gentle immune
reactions. It is hoped that the population analysis of short nucleotide sequence patterns for selected organism genomes
and the NSP incompatibility analysis among genomes could provide helps in finding an alternate point of view in
understanding of the DNA or RNA structure and organization, in virus detection and diagnosis, in antisense technology,
and in anti-virus drug and vaccine design as well as in helping virus chip design.
[1] J. C. Venter et al., Science, 2001, 291, 1304.
[2] C Burge, AM Campbell and S Karlin, PNAS, 1992, 89, 1358.
PO-098
Zipf’s Power Law and k-word distribution in Human genome cDNA
Qiang Miao, Zhilin Wang
School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR of China
The Zipf’s power law is obeyed universally by random processes and stochastic symbolic systems. We report application
of the power law and the k-word distribution in human genome cDNA (build 35).
[1] Chikara Furusawa and Kunihiko Kaneko, Phys. Rev. Lett. 2003, 90, 088102.
[2] K. E. Kechedzhi, O. V. Usatenko, and V. A. Yampol’skii, Phys. Rev. E, 2005, 72, 046138.
[3] David B. Searls, Nature, 2002, 420, 211.
A New Target for Synthesis: Theoretical Prediction for the Reaction between oron Nitride Nanotube and
Dichlorocarbene
Ruifang Li,* Zhenfeng Shang, Guichang Wang and Xiufang Xu
Chemisty Department of Nankai University, Tianjin, 300071, China
A comparative study of Reaction A, ASWCNT (5,5) and CCl2, and Reaction B, ASWBNNT (5,5) and CCl2 were
performed by ONIOM (B3LYP/6-31G*: AM1) method in Gaussian03 program package. The obtained results are the
following. (1) The two reactions are both exothermic reactions, closed and open cycloaddition product is optimized for
Reaction A and Reaction B, respectively. (2) The mechanism of Reaction B is a two-step mechanism as illustrated in the
right Figure.(3) Values of the energy barrier suggest that CCl2 reacts with BNNT (energy barrier is 1.1 kcal/mol) easier
than with CNT (energy barrier is13.8 kcal/mol). During the addition process, CCl2 prefers to attack the boron atom of
BNNT first to form an intermediate, then the final open product is formed. So we may say that the reaction between
ASWBNNT and CCl2 maybe a new target for synthesis for experimentalists.
(1) Zhao, W.; Song, C.; Pehrsson, P. E. J. Am. Chem. Soc. 2002, 124, 12418.
(2) Tasis, D.; Tagmatarchis, N.; Bianco, A.; Prato, M. Chem. Rev. 2006, 106, 1105
(3) Lu X.; Tian F. and Zhang Q. J. Phys. Chem. B 2003, 107, 8388
(4) Cho. E.; Kim, H.; Chem. Phys. Lett. 2006, 419, 134
(5) Holger F. Bettinger Chem. Eur. J. 2006, 12, 4372
(6) George E. Froudakis Nano. Lett. 2001, 1, 531
(7) Charles W. Bauschlicher, Jr. Nano. Lett. 2001, 1, 223
(8) Vladimir A. Basiuk Nano. Lett. 2002, 2, 835
(9) Lu X.; Tian F.; Xu, X.; Wang N., Zhang Q. J. Am. Chem. Soc. 2003, 125, 1045
(10) Z. Chen, S. Nagase, A. Hirsch, R. C. Haddon, W. Thiel and P. R. Schleyer,
Angew. Chem. Int. Ed., 2004, 43, 1552-1554
(11) Zhou Z.; Zhao J.; Chen Z. and Schleyer P. R. J. Phys. Chem. B 2006, 110, 25678
(12) Su M. J. Phys. Chem. B 2005, 109, 21647-21657
(13) Q. Huang, Y. Bando, C. Zhi, D. Golberg, K. Kurashima, F. Xu, L. Gao, Angew.
Chem. Int. Ed., 2006, 45, 2044-2047
* Corresponding author: Tel: 022-23502684, E-mail: [email protected]
PO-100
214 Book of Programme and Abstract for TACC2008 Structure of the Liquid-Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics Study
Shu Wang,a,‡ Shu Li,a Lei Liu,a Tianying Yan,a,b,* Xueping Gao,a and G. A. Voth c.*
a
College of Chemistry, Nankai University, Tianjin 300071, China
b
c
Institute of Scientific Computing, Nankai University, Tianjin 300071, China
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah Salt Lake City, UT
84112-0850
*
Molecular dynamics simulations for the liquid-vacuum interface of the ionic liquid 1-ethyl-3-methylimidazolium nitrate
(EMIM+/NO3-) were performed for both electronically polarizable and nonpolarizable potential energy surfaces. The
interfacial structural properties, such as the oscillation in the number density profile, the orientational ordering, and the
local clustering in the interfacial region, were calculated. The simulations with both the polarizable and nonpolarizable
model demonstrate the existence of an inhomogeneous interfacial structure normal to the surface layer. It was found for
both models that the ethyl tail group on EMIM+ is likely to protrude outward from the surface. In the outmost surface
layer, the cation is likely to lie on the surface with the imidazolium ring parallel to the interface, while there is a second
region with enhanced density from that in the bulk where the cation preferably slants with the imidazolium ring tending
to be perpendicular to the surface. The results also reveal that the electronic polarization effect is important for the ionic
liquid interface. It is found that the cation is likely to be segregated at the ionic liquid surface for the polarizable model,
while for the nonpolarizable model, the anion is found to be more likely to exhibit such behavior. The surface tension of
the polarizable model (58.5 ± 0.5mN/m) is much smaller than that of the nonpolarizable model (82.7 ± 0.6mN/m), in
better agreement with extrapolated experimental measurements on similar ionic liquid systems.
PO-101
Molecular Dynamics Simulation of LiTFSI – Acetamide Electrolytes: Structural Properties
Shu Li, Xue-Ping Gao, Tianying Yan*
Institute of New Energy Material Chemistry, Department of Material Chemistry, Nankai University, Tianjin 300071,
China
New room-temperature molten salt (RTMS) electrolytes have attracted much attention in recent years. In the paper we
performed MD simulation to study the liquid structure of the non-aqueous electrolytes composed of acetamide and
lithium bis(trifluoromethylsulfonyl)imide (LiTFSI), with the LiTFSI:acetamide molar ratios 1:2, 1:4, and 1:6. We studied
the dependence of the coordination and local environment of Li+, the conformation of TFSI- in the first coordination of
Li+, and the size and charge distribution of clusters on concentration. Also the effect of these structural properties on Li+
transportation has been studied.
215 Book of Programme and Abstract for TACC2008 Fig. 1 Two dimensional partial radial distribution function,
gij (r,Φ), in which r denotes the center-of-mass distance
between the Li+ cation and the TFSI- anion, and Φ denotes
the torsional angle between the two S-C bonds of the TFSIanion. The RDFs are shown in both the surface plot (left
column) and the contour plot (right column); (a)
LiTFSI1-ACE2,
(b)
LiTFSI1-ACE4,
and
(c)
LiTFSI1-ACE6. The value of gij (r,Φ) is denoted by the
color bar shown in the contour plot.
PO-102
The Solvation Structure of Ethanol around Fullerene C60
Zhen Caoa, Yuxing Penga, Shu Lia,Lei Liua, Bin Liu,a Tianying Yana,b*
aInstitute of New Energy Material Chemistry, Department of Material Chemistry, Nankai University, Tianjin 300071,
China
bInstitute of Scientific Computing, Nankai University, Tianjin 300071, China
*Email: [email protected]
The ethanol solution containing one or two fullerene C60 molecules were studied via molecular dynamic simulation. We
find the ethanol molecules form several solvation shells around the centre fullerene molecule. The ethanol molecules in
the first solvation shell tend to have their non-polar alkyl groups exposed to the C60 surface, while the polar hydroxyl
groups are pointing outward to form a hydrogen bond network with the molecules in the first and second solvation shells.
The potential of mean force (PMF) curve shows it is easier for C60 molecules to flee out of the free energy well and form
the metastable structure, though C60 tend to aggregate in the ethanol solution. Analysis of the orientation of ethanol near
the intersolute area shows the ethanol molecules tend to have their methyl groups penetrate into the intersolute region,
although the hydroxyl groups have smaller volume. Such tendency is weakened with the elongation of distance between
two fullerene molecules. We find the relaxation of the dynamic properties of the ethanol solvation shells is much slower
than the solvation shells in water solution. In addition, the relaxation of the ethanol molecules in the first solvation shell
is slower than that of the ethanol molecules in other solvation shells.
PO-103
Accurate Quartic Force Fields for CCH- and NH2Xinchuan Huang, David W. Schwenke, Timothy J. Lee
NASA Ames Research Center, Moffett Field, CA 94035, USA
A series of high-quality purely ab initio quartic force fields (QFF) are reported for NH2- and CCH-, based on CCSD (T)
energies computed with Dunning’s correlation-consistent T, Q, 5Z-level basis. Energy extrapolation to the complete basis
set limit, core-correlation effect, scalar relativistic effect, and higher-order correlation effects beyond the CCSD (T)
method are systematically investigated. Higher-order electron correlation is approximated by the ACPF method. All
effects are included in a single QFF computed from a single grid of points expanded about a “best guess” reference
geometry. Analytical transformation to the exact minimum allows for use of second-order perturbation theory as well as
216 Book of Programme and Abstract for TACC2008 exact variational methods for solution of the nuclear Schrödinger equation. Equilibrium structures, vibrational
frequencies, rotational constants, and other spectroscopic constants are reported and compared to experimental values and
previous theoretical studies. Excellent agreement is found between this work and the available experimental data.
Isotopic effects on spectroscopic constants and vibrational fundamentals are discussed. We believe this study will
facilitate the identification of NH2- and CCH-, and their isotopologues, in astronomical observations.
PO-104
Spin Distribution in Low-Spin Iron (III) Porphyrin Complexes with Different Electronic Structures
Ru-Jen Cheng, Ping-Yu Chen, Ya-Ping Han, Chia-Wei Chao
Department of Chemistry, National Chung-Hsing University, 250 Kuo-Kuang Road, Taichung, Taiwan 402, Republic of
China
NMR spectra of paramagnetic transition metal complexes is a direct projection of the spin distribution on the molecule
that provides unique probe for the electronic nature of the complexes. Modern implementation of density functional
theory makes the theoretical calculation of metalloporphyrins with versatile electronic structures feasible and provides
rather accurate spin-density distributions in paramagnetic systems.
The complementary nature of theoretical
calculations and NMR spectroscopy of paramagnetic molecules has been proved to be very successful disclosing the
major contribution from different electronic states.1,2
Two different electronic structures (dxy)2(dxzdyz)3 and (dxzdyz)4(dxy)1 have been recognized for six-coordinate low-spin
iron(III) porphyrin complexes. Ruffled deformation of the porphyrin macrocycle changes the electronic structure from
the classical (dxy)2(dxzdyz)3 to the unusual (dxzdyz)4(dxy)1.
+
Combined analysis of the 1H and
13
C NMR isotropic shifts,
+
spin densities of the planar [Fe(TPP)(Im)2] and the ruffled [Fe(TiPP)(4-CNPy)2] complexes have been established with
the application of Karplus-Frankel equation. Spin densities from our ADF-based calculations show reasonably good
correlation with the data for planar [Fe(TPP)(Im)2]+ complex, but are quite distinct from the data reported for ruffled
[Fe(TiPP)(4-CNPy)2]+ complex. It is evident that mixing of the and spin densities in nonplanar porphyrin system
inhibits the proper application of Karplus-Frankel equation.
[1] Cheng, R.-J.; Chen, P.-Y.; Lovell, T.; Liu, T.; Noodleman, L.; Case, D. A. J. Am. Chem. Soc. 2003, 125, 6774-6783.
[2] Cheng, R.-J.; Wang, Y.-K.; Chen, P.-Y.; Han, Y.-P.; Chang, C.-C. Chem. Commun. 2005, 1312-1314.
PO-105
Tying Protein Druggability Prediction with Fragment-based Virtual Screening
Niu Huang1 and Matthew P Jacobson2
1.
National Institute of Biological Sciences, Beijing No. 7 Science Park Road, Zhongguancun Life Science Park,
Changping District, Beijing 102206, P. R. China.
2.
Department of Pharmaceutical Chemistry University of California
San Francisco 600 16th Street, Genentech Hall San Francisco, CA 94158-2517, U.S.A
The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules) would greatly
benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess
the protein druggability by computationally screening a fragment-like compound library. This approach estimates the
binding affinity of small molecule hits using an all-atom molecular mechanics force field combined with an implicit
solvent model, which neither is resorting to any physicochemical parameters of the binding site nor requiring any
knowledge about a potential ligand molecule. Theoretically speaking, it is equivalent to a NMR-based fragment
217 Book of Programme and Abstract for TACC2008 screening method, and encouragingly, the hit rate calculated from screening a diverse fragment library using our
approach was shown to correlate with the hit rate measured experimentally from NMR-based screening method. We
performed a large-scale validation of the approach on four datasets, namely, Hajduk’s training dataset and external
dataset, a known drug target dataset and a protein-protein interaction dataset. It was shown to accurately distinguish
between experimentally validated druggable and non-druggable sites, especially in treating the highly charged or polar
binding sites. We demonstrated that it can be used to characterize the critical binding interactions and importantly, many
top scored fragment hits are structurally similar to the corresponding chemical group of the crystal ligands. This further
ties the protein druggability prediction with the fragment-based drug design.
PO-106
A Docking Study of PDK1 Inhibitor Ligands
Topp Lin and Ying-chieh Sun*
Chemistry Department, National Taiwan Normal Univ., 88, TingChow Rd. Sec. 4, Taipei 116, Taiwan
Inhibition of PDK1 kinase activity is one of the targets in developing cancer drug. In the present study, a docking
calculation for ligand-PDK1 kinase complexes was carried out using the Autodock program. Experimental binding
modes of 9 available lignad-PDK1 structures were reproduced. The binding energies of these complexes were correlated
well with experimental IC50 values except 2 ligands. Toward designing better inhibitors, we have carried out docking
calculation for a number of derivatives of an inhibitor of low IC50 value (in nM range), UCN. The calculations for
several derivatives gave lower binding energy, suggesting that they are better inhibitors. The rationals of the calculated
binding energies are discussed. In addition, calculations for a series of celebrex-based compounds were also carried out.
Their correlations with experimental available IC50 values will be discussed as well.
PO-107
Theoretical Studies of Nucleophilic Substitution Reactions of Iodonium Salts
M. A. Carroll,a,* P. K. D. Dawson,a M. Gray.b
a
School of Natural Sciences - Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K.; b Institute of
Pharmacy, Chemistry and Biomedical Sciences, University of Sunderland, Sunderland, SR1 3SD, UK.
Compounds containing organic trivalent iodine groups were first prepared over a century ago.1 Some of the more
interesting chemical aspects of these compounds are due to the ability of the trivalent iodine moiety to act as a good
nucleofuge: a leaving group ability 106 times greater than triflate.2 Iodine (III) reagents give rise to several key reactions,
including: (1) ‘mild’ oxidation of several types of functional groups such as alcohols, amines and sulfides; (2) they are
susceptible to nucleophilic attack from external species, with loss of the iodine (III);3 (3) loss of iodine (III) can also
generate reactive species such as cations, carbenes and nitrenes.4
One particular aspect of our research is concerned with an internal nucleophilic substitution reaction that occurs within
trivalent iodine compounds: that of an equatorial carbon based iodine (III) ligand with an apical heteroatom based ligand
– similar to the reductive elimination reaction from a metal centre.5 Unlike diaryliodonium salts and alkynyliodonium
salts, reports describing the preparation and reactivity of alkenyliodonium salts are relatively uncommon. We have
carried out in silico calculations of the nucleophilic substitution reaction involving a range of alkenylaryliodonium
chlorides, shown in Scheme 1. The nucleophilic substitution reaction results in the formation of a mixture of
vinylchloride/aryliodide and vinyliodide/arylchloride products.
218 Book of Programme and Abstract for TACC2008 We have found that:
•
Ground state calculations show that there is a preference for the most electronegative/sterically unhindered carbon
ligand occupying the apical positions around the iodine (III).
•
Calculations on the ground state geometries of 1 and 2 shows the reaction to be transition state controlled, with the
relative energies of the respective transition states determining the products ratios of 3 and 4.
•
Formation of the reaction product can be controlled electronically and/or sterically – in agreement with results from
other varieties of iodonium salts.6
[1] Reviews: (a) Stang P, J. Org.Chem., 2003, 68, 2997; (b) Wirth T, Hirt UH, Chem. Rev., 1996, 96, 1123;
[2] Okuyama T, Takino T, Sueda T, Ochiai M, J. Am. Chem. Soc., 1995, 117, 3360;
[3] Okuyama T, Takino T, Sato K, Ochiai M, J. Am. Chem. Soc., 1998, 120, 2275;
[4] Gronheid R, Lodder G, Ochiai M, Okuyama T, J. Am. Chem. Soc., 2001, 123, 8760;
[5] Yoshida M, Komata A, Hara S, Tetrahedron, 2006, 62, 8636;
[6] Carroll MA, Martin- Santamaria S, Pike VW, Rzepa HS, Widdowson DA, J. Chem. Soc., Perkin Trans. 2, 1999,
PO-108
Classification of DNA Sequences Basing on the Dinucleotide Compositions
Wei You
Department of Mechanical and Electrical Engineering, North China Institute of Science and Technology, Mailbox 206#,
Yanjiao, East Beijing, 101601, China
Back-propagation artificial neural network model was developed to classify the DNA sequences of several bacteria. The
“dinucleotides compositions” method was used to characterize the DNA sequences which transform every DNA
sequence to a 16-dimension vector. All DNA sequences may be characterized by 16 eigenvalues by using the method,
thus, the method is helpful to solve the problem that it is difficult to compare the DNA sequences with different length.
Neural network model was trained using “leave-one-out” method and was applied in the classification of the DNA
sequences of several bacteria. Results showed that the accuracy of classification was 84.3%, which proved that the model
was satisfactory in summary. The method has considerable theoretical meaning and application value in the field of
bioinformatics, however, the author stated that the applicability of the characterization strategy still needs to be
improved.
PO-109
Similarity Analysis of DNA Sequences Using “Molecular Connectivity Indices” Method
Wei You
Department of Mechanical and Electrical Engineering, North China Institute of Science and Technology, Mailbox 206#,
Yanjiao, East Beijing, 101601, China
219 Book of Programme and Abstract for TACC2008 Email: [email protected]
According to “molecular connectivity indices” method, four parameters basing on the locations and occurrence
frequencies of four bases (A, C, G, T) in DNA sequences were extracted to characterize the DNA sequences of different
species. According to the method, any one DNA sequence may be characterized by four eigenvalues, thereby, the method
solved the problem that it is difficult to compare the DNA sequences with different length. Similarity analysis among
several species was performed basing on Euclidean distance and phylogenetic tree. The results showed that the
computation results are in agreement with the phylogenetic tree and conform to the evolutionary rules of biological
species. The method is valuable in the homology study of species and it also may be applied in other fields of
bioinformatics.
PO-110
Theoretical Characterization photophysical and charge-transport properties of hole-blocking material-TAZ
Hongze Gao,a Houyu Zhang,a Yue Wang*,a and Zhong-Min Su*,a,b
a
State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, Jilin, P.R. China,
and b Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024,
Jilin, P.R. China
Abstract
The
ground,
ionic
and
singly
excited
structure
of
the
hole-blocking
material,
3-(4-biphenylyl)-4-phenyl-5-(4-tert-butylphenyl)-1,2,4-triazole (TAZ), has been optimized respectively by density
functional theory (DFT) and single-excitation configuration interaction (CIS) methods. Calculated emission energy of
TAZ is shown to be consistent with the experimental data. By analyzing the partial density states (PDOS) of these
ligands contributing to the total density of states (TDOS), it is concluded that TAZ still favor electron carrier, but cannot
do so under positive charged state.
[1] J. Kido, C. Ohtaki, K. Hongawa, K. Okuyama, and K. Nagai, Jpn. J. Appl. Phys. 1993, 32, L917.
[2] J. Kido, K. Hongawa, K. Okuyama, and K. Nagai, Appl. Phys. Lett. 1993, 63, 2627.
[3] J. Kido, K. Hongawa, K. Okuyama, and K. Nagai, Appl. Phys. Lett. 1994, 64, 815.
[4] P. E. Burrows, S. R. Forrest, and M. E. Thompson, Curr. Opin. Solid State & Mater. Sci. 1997, 2, 236.
[5] C. L. Lee, K. B. Lee, and J. J. Kim, Appl. Phys. Lett. 2000, 77, 2280.
* To whom correspondence should be addressed. E-mail:
[email protected]; [email protected].
PO-111
220 Book of Programme and Abstract for TACC2008 Theoretical
study
of
two-dimensional
nonlinear
optical
responses
in
donor-acceptor
substituted
difunctionalization hexamolybdates
Zhongmin Su, Chunguang Liu, Wei Guan, Likai Yan, and Guochun Yang
Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R.
China
The two-dimensional (2-D) NLO responses of a series of dipolar donor-acceptor difunctionalization hexamolybdates was
investigated by using TDDFT. All of these complexes possess large off-diagonal hyperpolarizability tensors, and thus
display good 2-D NLO properties. The in-plane 2-D NLO properties of these complexes can be associated with the
various low-energy charge-transfer states and are achieved by a 2-D Λ-like structure. Furthermore, these CT transitions
that are polarized perpendicular to the molecular dipolar axis contribute to the off-diagonal hyperpolarizability tensors,
and the parallel transitions account for the diagonal hyperpolarizability tensor. Introduction of heterocycles and ethyne π
conjugated bridge significantly enhances the second-order NLO response. Complex Ib (tetrazine ring derivative) displays
a large 2-D second-order NLO responses because of the strong, lowest energy, perpendicular CT transition.
[1] Pope, M. T., Heteropoly and Isopoly Oxometalates, Springer Verlag: New York, 1983.
[2] Hill, C. L., Ed. Chem. Rev., 1998, 98, 1.
[3] Poblet, J. M., López, X., Bo, C., Chem. Soc. Rev., 2003, 32, 297.
[4] Guan, W., Yang, G. C., Yan, L. K., Su, Z. M., Inorg. Chem. 2006, 45, 7864.
[5] Guan, W., Yang, G. C., Yan, L. K., Su, Z. M., Eur. J. Inorg. Chem. 2006, 4179.
[6] Yang, G. C., Guan, W., Yan, L. K., Su, Z. M., Xu, L., Wang, E. B., J. Phys. Chem. B, 2006, 110, 23092.
[7] Guan, W., Yang, G. C., Liu, C. G., Song, P., Fang, L., Yan, L. K., Su, Z. M., Inorg. Chem. 2008, 47, 5245-5252.
PO-112
The research of radar absorbing structures made of glass/carbon fibers/epoxy composites filled with carbon
nanotubes
Zhengquan Zhang*, Tiehu Li, Deqi Jing, Qiang Zhuang
Department of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072 China
Radar absorbing structures (RAS) is a functional composite, which can't only load bearing, but also absorb
electromagnetic wave energy by inducing dielectric loss and minimizing reflected electromagnetic waves. Therefore, the
development of the RAS haves become essential for reducing RCS of the object. The composites possess excellent
specific stiffness and strength. The electromagnetic wave properties of the RAS can be tailored by controlling the content
of the lossy materials.
In the paper, RAS composed of glass fibers, carbon fibers and epoxy resin filled with carbon nanotubes (CNT), was
designed and prepared in the frequency range of 8.2-12.4GHz. The permittivity of the composite was measured by using
a network analyzer, HP8510B. The contents of the composites were observed to be different from each composite. As a
result of the experiment, it was found that the composites can be suitable to be used as RAS. By the calculation of the
reflection of electromagnetic waves energy based on the genetic algorithm (GA) in the RAS, it was discovered that the
composites can be applied to design an optional RAS composites filled with CNT.
*Corresponding author Tel.: + 86 29 88460337; fax: +86 29 88492870 Email address: [email protected]
PO-113
221 Book of Programme and Abstract for TACC2008 Crystal Packing of TCNQ Anion π-radicals Governed by Intermolecular Covalent π−π Bonding
Jingsong Huang,a Stephanie Kingsbury,b and Miklos Kerteszc
a
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6367, USA; b Chemistry Department, Carthage College,
2001 Alford Park Drive, Kenosha, WI 53140-1994, USA;
c
Chemistry Department, Georgetown University, 37th & O
Street, Washington, D.C. 20057-1227, USA
On the basis of a thorough Cambridge Structural Database survey, we present a statistical analysis of the packing of
TCNQ anion π-radical in TCNQ charge transfer salts, which reveals three packing motifs between neighboring TCNQs:
one with a zero longitudinal offset and an approximate 1 Å transversal offset, another with an approximate 2 Å
longitudinal offset and zero transversal offset, and the third with a relatively long σ-bond in the length of r = 1.6−1.7 Å
connecting two TCNQ fragments. We also present density functional theory (DFT) calculations of the total energy,
covalent π−π bonding interaction energy, and Coulombic repulsion energy for the [TCNQ] 2 2− π-dimers with various
packing geometries, from which we find that the interactions between TCNQ π-radicals include contributions from
intermolecular covalent π−π bonding interaction and local dipole repulsions, in addition to Coulombic repulsion, van der
Waals, and the attractive forces between counter-cations and TCNQ anions pointed out recently by other groups for
TCNE anion radicals. We also arrive at an approximate formula for intermolecular interaction energy, Eint = Ecoul + Ebond
+ EvdW, for systems in vacuum, while in the solid state Ecoul is counterbalanced by the attractive electrostatic forces
between counter-cations and TCNQ anions. We conclude that crystal packing of TCNQ charge transfer salts is
predominantly determined by the intermolecular covalent π−π bonding term, Ebond.
[1] Review (TCNE): Miller, J.S.; Novoa, J.J. Acc. Chem. Res., 2007, 40,189.
[2] Huang, J. S.; Kingsbury, S.; Kertesz, M. Phys. Chem. Chem. Phys. 2008, invited contribution for the Special Issue on
stacking interactions.
PO-114
Monte-Carlo Quantum Chemistry of Biomolecules: Energy and Structural Properties of Biogene Amines and
Account for Laser and Neutron Capture Effects
Alexander V. Glushkov1,2
1
Odessa University, P.O.Box 24a, Odessa-9, South-East, 65009, Ukraine
2
Institute for Spectrsocopy, Russian Acad. Sci., Troitsk, Moscow reg., 142090, Russia
E-mail:
[email protected]
Paper is devoted to the Monte-Carlo computational studying the structural, and spectroscopic properties for the
biomolecules, in particular, biogene amines: serotonine (ST), histamine (HM), γ-amino oil acid (AC) and the laser and
neutron capture action on the indicated properties of studied molecules. The ST (or 5-hydroxitriptamine, 5-HT) is
produced by means of the hydroxciliration of essencial amine acid of the triptophane [1]. ST influences mainly in a place
of its appearance and calls for blood vessel narrowing in places of the trombocites decay. Probably, serotonine ST is the
mediator for transition of the nervous pulses in some branch of the brain. HM is produced in cells (mastocides) from the
histidine amino acid. The γ-amino oil acid AC is produced in the brain substance and probably plays a role of the
mediator or inhibitor of pulses. Many biomolecules (BM) are composed not only by hydrophilic, but also by hydrophobic
groups, in the vicinity of which the water-water (or blood plasma) interaction is expected to be present even in the zeroth
approximation. We present results of the Monte-Carlo calculating the cluster consisting of the serotonine ST (histamine
HM) molecules and 100 molecules of water. All relevant interaction potentials are obtained by means of quantum
calculation [1]. The water-water interaction potential was found by Matsouka etal by CI method. The BM-water
222 Book of Programme and Abstract for TACC2008 interaction potential was obtained in the SCF approximation Calculation is carried out at T=300K; All molecules are
treated as rigid. The results for interaction energies are given below in table:
Potential,
kJmol-1
Neutral molecule
zwitterion
Water-water
-27.7 ± 0.8
-27.2
± 0.7
ST-water
-59.5 ±2.0
-348.5
± 15.0
HM-water
-37,8 ±2.0
-178,4
± 15.0
The zwitterion appears as expected to be strongly favoured with respect to
neutral molecule. The HM in the
“zwitterion” more intensively (on the order) catalyses the gastric juice secretion and secretion from other endocrine
glands. The similar situation is with action of the HM in the inflammatory and allergic reactions with further increasing
vessel walls permeability and action of the ST with further blood-vessel narrowing in places of the trombocites decay.
We at first consider the possibilities of laser and neutron capture action on different of molecules, including an analysis
of Szilard-Chalmers (n,γ), (n,n), Mössbauer and GM [2] effects. Some new bio-nano-technologies are analysed.
[1] E. Clementi et al, Gazz. Chim. Ital. 108 (1978) 157-174; J. Am.Chem. Soc. 99 (1977) 5531-42 ; A.Glushkov,
Journ.Struct. Chem. 34 (1993) 3-10; 31 (1990) 9-15; 32 (1992) 11-16; Rus. J. Phys. Chem. 66 (1992) 1259-76; 66
(1992) 589-596; A. Glushkov, S.Malinovskaya, Rus. J. Phys. Chem. 62 (1988) 100-106; 65 (1991) 2970-78;
[2] A. Glushkov, S.Malinovskaya, In: New projects and new lines of research in nuclear physics. Eds. G.Fazio and
F.Hanappe, Singapore : World Scientific.-2003.-P.242-250 ; Int.J.Quant.Chem 99 (2004) 889-896 ; 104 (2005) 496-500;
Europ.Phys.Journ. , in print (2008) ; Mol.Phys., in print (2008).
PO-115
Theoretical investigation on the chemical origin of the interaction between the special pair in the photosynthetic
reaction center
Hideki Yamasaki, Yu Takano, and Haruki Nakamura
Institute for Protein Research, Osaka University, Yamadaoka 3-2, 565-0871, Suita, Osaka, Japan
The special pair (SP) is a dimer of chlorophyll molecules (Chl) and is essential for the charge separation in the reaction
center (RC). The proper spatial arrangements of Chls in RC are important for this process.
In this study, the dimeric interaction of SP has been investigated using quantum chemical calculations at the
MP2/6-31G(d)(0.25) level of theory. We estimated the interaction energies (Eints) of a variety of substituted models of SP
from the SPns model, in which all side groups were replaced with hydrogen atoms, to the SPall model, in which only the
tail of the phytyl group from F5 was substituted with a hydrogen atom.
The models containing only the non-polar ethyl group of ring B or the acetyl group were more stable than SPns by 4.3 or
7.6 kcal/mol, respectively. It indicates that these groups contribute to the stabilization of SP. The orientations of the ethyl
groups were controlled by the surrounding conserved amino acids. By combining our previous studies1 of the effect on
the methyl ester and phytyl groups on the electronic asymmetry of SP, we conclude that each side group of Chl has
specific roles in the function of RC.
[1] Hideki Yamasaki et al., Chem. Phys. Lett. 2007, 447, 324.
PO-119
Four-component relativistic theory for NMR parameters
Lan Cheng, Yunlong Xiao, and Wenjian Liu
223 Book of Programme and Abstract for TACC2008 Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking
University, Beijing 100871, P. R. China
Theoretical calculations, nonrelativistic[1] or relativistic[2], on NMR spectroscopic parameters such as shielding tensors
have a long history. Embarrassingly enough, however, the most relativistic method, namely four-component relativistic
theory, for magnetic properties has not been developed to the same level of sophistication as for electric properties. The
underlying reason is that, compared to an electric perturbation, a magnetic perturbation has a much stronger influence on
the coupling of the large and small components of the Dirac spinor, causing contributions of negative energy states to
magnetic properties to be of O(c0) instead of O(c-4) as for electric properties. That is, if the contributions of negative
energy states are neglected, the entire diamagnetic term will be missed, even at the nonrelativistic limit. The key issue is
therefore how to account effectively for such contributions in a four-component relativistic treatment. Standard linear
response theory is just too painful to be of practical use: It requires unaffordable large basis sets of high angular momenta
to compensate for the lack of the magnetic balance condition.[3] Here we propose several novel schemes to take explicitly
into account the magnetic balance condition, in addition to the kinetic balance condition. These include the orbital
decomposition approach,[4] external-field dependent unitary transformation at operator level, and the full-field dependent
unitary transformation but at matrix level.[5] The corresponding approximate variants are obtained by consistent neglect
of negative energy states. Our recent developments[6] include the GIAO for distributed gauges and a noncollinear
exchange-correlation kernel for the response functions. It should be noted that the formalism is completely general and
can be extended to wave function based theory as well. It can therefore be claimed that relativistic theory for magnetic
properties has been solved!
[1] N. F. Ramsey, Phys. Rev. 1950, 78, 699; 1951, 83, 540; 1956, 86, 243.
[2] P. Pyykkö, Chem. Phys. 1977, 22, 289.
[3] G. A. Aucar, T. Saue, L. Visscher, and H. J. Aa. Jensen, J. Chem. Phys. 1999, 110, 6208; W. Kutzelnigg, Phys. Rev.
A. 2003, 67, 032109.
[4] Y. Xiao, D. Peng, and W. Liu, J. Chem. Phys. 2007, 126, R081101.
[5] Y. Xiao, W. Liu, L. Cheng, and D. Peng, J. Chem. Phys. 2007, 126, 214101.
[6] L. Cheng, Y. Xiao, and W. Liu (to be published).
PO-120
Waiting Cycle Times and Generalized Haldane Equality in the Steady-State Cycle Kinetics
Hao Ge, Hao Ge
School of Mathematical Sciences, Peking University, Beijing 100871, People’s Republic of China
Enzyme kinetics are cyclic. A reversible three-step mechanism of the Michaelis-Menten kinetics is investigated in detail,
and three kinds of waiting cycle times T, T+, T- are defined. It is shown that the mean waiting cycle times < T >, < T+ >,
and < T- > are the reciprocal of the steady-state cycle fluxes Jss, J+ss and J-ss respectively. Also the distribution of T+
conditioned on T+ < T- is identical to the distribution of T- conditioned on T- < T+, which is referred to as the generalized
Haldane equality [2] and was first observed in the experiment of kinesin
[3]
. Consequently, the mean dwell times of the
forward and backward cycles are both the same as <T>, which leads to the definition of time-averaged cycle entropy
production rate [1].
It is also shown that the moment generating function of the stochastic number of substrate cycle follows the fluctuation
theorem with Lebowitz-Spohn type symmetry, and moreover, we obtain the Jarzynski-Hatano-Sasa-type equality for the
fluctuating chemical work done for sustaining the NESS. Similar results have been derived in the semi-Markov model [2].
224 Book of Programme and Abstract for TACC2008 Furthermore,.analogous results including the interesting generalize Haldane equality could also be derived in the
multi-substrate case, and the relationship between specificity constants and cycle fluxes has just been investigated
recently
[4]
. The generalization is not very straightforward, and the derivation here is much more difficult than the
previous single substrate case.
[1] Ge, H.: J. Phys. Chem. B 2008, 112, 61-70.
[2] Qian, H. and Xie, X.S.: Phys. Rev. E 2005, 74, 010902(R)
[3] Carter, N. J.; Cross, R. A: Nature 2005, 435, 308-312.
[4] Ge, H. and Qian, M.: J. Theor. Comput. Chem. 2008 (accepted)
PO-121
Quantum modeling of hydrogen interaction with beryllium (0001)
A. Allouche
Physique des Interactions Ioniques et Moléculaires, CNRS and Université de Provence, Campus Scientifique de Saint
Jérôme, service 242, 13397 Marseille Cedex 20 – France
Beryllium, tungsten and carbon are planned as wall materials for the future international tokamak (ITER). Although
beryllium is not situated in a region submitted to the most dramatic plasma interaction, its reactivity towards hydrogen
atom impinging is of fundamental importance. Therefore a new field of investigation is open for the computational
quantum communities, going from solid-state physics to surface physics and catalysis. The latter domain and chemical
reactivity are more particularly involved because of hydrogen retention: the chemistry of the beryllium based materials
towards hydrogen isotopes is largely unknown. This article is devoted to theoretical study of hydrogen beryllium
interaction based on the first principles DFT method, with periodic boundary conditions and utltrasoft pseudopotential.
The two processes of hydrogen adsorption on the beryllium (0001) surface and of hydrogen retention into the bulk are
investigated. Activation energy to desorption from the surface has been calculated by the Nudged Elastic Band (NEB)
method. Comparison is proposed to former theoretical works and to Temperature Programmed Desorption Spectroscopy
(TPD). Maximum rates of hydrogen retention on the surface and in the bulk have been calculated and proved to be in
good agreement with experimental results.
PO-122
Photo-excitation and photo-ionization dynamics of water photolysis and excited state dynamics of pyrrole-water
complexes
Anupriya Kumar, Maciej Kołaski, Han Myoung Lee and Kwang S. Kim
Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784,
Korea
Despite the importance of the water photolysis in atmospheric chemistry, its mechanism is not well understood. Two
different mechanisms of the water photolysis have been proposed. The first mechanism is driven by water
photoexcitation, followed by the reaction of the active hydrogen radical with water clusters. The second mechanism is
governed by the ionization process. Both photo-excited and photo-ionized mechanisms are complementary, which is
elucidated by using Excited State (ES) Ab Initio Molecular Dynamics (AIMD) simulations based on
Complete-Active-Space Self-Consistent-Field (CASSCF) approach and unrestricted Møller-Plesset second-order
perturbation theory (UMP2) based Born-Oppenheimer Molecular Dynamics (BOMD) simulations. In the case of
pyrrole-(H2O)n clusters, ground state structures are investigated using ab initio calculations. The charge-transfer driven
225 Book of Programme and Abstract for TACC2008 femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the
complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the
charge density is located over the farthest water molecule which is repelled by the depleted π-electron cloud of pyrrole
ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34 a.u.)
around ~100 fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the
pyrrole and the π H-bonded water molecule and then the charge transfer takes place from this water molecule to the σ
H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53 a.u.)
around ~100 fs.
[1] Anupriya Kumar, Maciej Kołaski, and Kwang S. Kim, J. Chem. Phys.
2008, 128, 034304.
[2] Anupriya Kumar, Maciej Kołaski, Han Myoung Lee, and Kwang S. Kim
J. Phys. Chem. A 2008 (in press).
PO-123
Woo Youn Kim and Kwang S. Kim*
Center for Superfunctional Materials, Dept. of Chemistry, Pohang University of Science and Technology, San 31,
Hyojadong, Namgu, Pohang 790-784, Korea
Based on first principles theory, we have investigated metallic nanowires. We discuss the thinning process of silver
nanowires (NW) [1] and the design of linear single atomic chains which is stabilized by the charge-transfer-driven
alloying process [2]. The pathway of thinning process for transient silver NWs is discussed. The unambiguous
identification of the structure of a NW is made with the study of conductance (G) vis-a-vis transient NW structure. The
puzzling experimental observation of fractionally quantized G values is explained.
We also discuss the negative differential resistance (NDR) of molecular electronic devices with carbon nanotube (CNT)
electrodes [3-5]. We find that in the presence of an applied field, metallic CNTs can form asymmetric couplings even if
symmetric structures are employed.
We also discuss a novel spin-valve device based on carbon-based systems [6]. In particular, we predict that graphen
nanpribbon devices can be used as key components of a magnetoresistive random access memory [7]. The magnetic
resistance of the proposed spin-valve device shows millions %, as compared to the present highest value (a few
hundreds %). The origin of the extraordinary behavior is explained. The device is able to play a role as a spin filter which
selectively transmits near 100% spin-polarized current. The domain wall formation energies for both collinear and
non-collinear types of spin waves were investigated. The non-collinear spin states were fully taken into account in a
self-consistent manner with the non-equilibrium Green’s function approach by using the Postrans program package [4].
The study of the cases for the non-collinear type domain wall is the first fully self-consistent ab initio results for
transmission calculations.
[1] D. Cheng, et al., Phys. Rev. Lett. 96, 096104 (2006).
226 Book of Programme and Abstract for TACC2008 [2] Y. C. Choi, et al., Phys. Rev. Lett. 98, 076101 (2007).
[3] W. Y. Kim, S. K. Kwon, and K. S. Kim, Phys. Rev. B 76, 033425 (2007).
[4] W. Y. Kim and K. S. Kim, J. Comput. Chem. 29, 1073 (2008).
[5] W. Y. Kim, Y. C. Choi, and K. S. Kim, J. Materials Chem. (in press).
[6] M. Diefenbach and K. S. Kim, Angew. Chem. Int. Ed. 46, 7640 (2007).
[7] W. Y. Kim and K. S. Kim, Nature Nanotech. (in press).
PO-125
Chiral induction: The transfer of chirality from chiral solutes and surfaces to achiral solvents
Shihao Wang, Natalie M. Cann
Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
In this presentation, results of molecular dynamics simulations will be presented on the transfer of chirality from chiral
molecules and surfaces to achiral solvents. 3D decompositions of the induced chirality in achiral solvents around chiral
solutes and surfaces will be shown, which provide detailed information on the regions and patterns of the chirality
transfer.Three chiral solutes (styrene oxide, n-(1-(4-bromophenyl)ethyl)pivalamide, and acenaphthenol) and two solvents
(ethanol and benzyl alcohol) have been selected to study the detailed aspects of chirality transfer about chiral solutes.
These aspects include the importance of solvent polarizability, the relationship between chirality transfer and
hydrogen-bonding, the impact of solute conformational averaging, and the details of solvent-solute interactions. Chiral
induction has also been studied for surfaces used in chiral chromatography, such as the Whelk-O1, leucine- and
phenylglycine-based chiral stationary phases. Here, emphasis is placed on the location of the chirality transfer zones on
each surface and the solvent characteristics in these zones.
PO-126
Docking studies of few substituted 5-benzyl-2, 4-thiazolidinedione with PPAR-γ for antidiabetic activity
L. V. Sonawane*, V. M. Balaramnavar, S. B. Bari, S. J. Surana
R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist- Dhule, Maharashtra (INDIA).
Email- [email protected]
Mob. No. +919881409073
Docking studies of few substituted 5-benzyl-2, 4-thiazolidinedione moiety, which acts as peroxisome
proliferator-activated receptor γ agonist was performed by using Glide v4.5. The substituted 5-benzyl-2,
4-thiazolidinedione head group for each ligand was treated as anchor and the conformation of the remaining molecule
was searched for the most energetically stable interaction with PPAR-γ. According to the crystal structure, the agonists
were found to possess configuration similar to rosiglitazone, when bound to PPAR- γ. The docking studies reveal
hydrogen bond formation to THR241 with Gscore
-2.22 and energy -30.0. In the present study we found hydrogen
bond formation of most of compounds with good Gscore and low energy as compared to the most active rosiglitazone.
227 Book of Programme and Abstract for TACC2008 Reference and Notes:
1. Reviews on PPAR and insulin resistance: (a) Olefsky, J.M.; Saltiel, A. R. Trends Endocrinol. Metab., 2000, 11, 362;(b)
Berger, J.; Wagner, J. A. Diabetes Technol. Therap., 2002, 4, 163; (c) Berger, J.; Moller, D. E. Annu. Rev. Med., 2002,
53, 409; (d) Knouff, C.; Auwerx, J. Endocrine Rev., 2004, 25, 899–918.
2. Liu, Kun.; Black, Regina.; Acton John.; Mosley Ralph. Bioorg. Med. Chem. Lett., 2005, 15, 2437–2440.
3. Lehmann, J. M.; Moore, L. B.; Smith-Oliver, T. A.; Wilkison, W. O.; Willson, T. M.; Kliewer, S. A. J. Biol. Chem.,
1995, 270, 12953-12956.
4. Willson, T. M.; Brown, P. J.; Sternbach, D. D.; Henke, B. R. J. Med. Chem., 2000, 43, 527-550.
5. Day, C. Diabet. Med., 1999, 16, 179–192.
6. Spiegelman, B.M. Diabetes, 1998, 47, 507–514.
7. Willson, T.M.; Cobb, J.E.; Cowan, D.J.; Wiethe, R.W.; Correa, I. D.; Prakash, S. R. Beck, K.D.; Moore, L.B.; Kliewer,
S.A.; Lehmann, J. M. J. Med. Chem., 1996, 39, 665–668.
8. Lowell, B.B. Cell, 1999, 99, 239–242.
9. Rocchi, S.; Auwerx, J. Ann. Med., 1999, 31, 342–351.
10. Okuno, A.; Tamemoto, H.; Tobe, K.; Ueki, K.; Mori, Y.; Iwamoto, K.; Umesono, K.; Akanuma, Y.; Fujiwara, T.;
Horikoshi, H.; Yazaki, Y.; Kadowaki, T. J. Clin. Invest., 1998, 101, 1354–1361.
11. Nolte, R.T.; Wisely, G. B.; Westin, S.; Cobb, J.E.; Lambert, M.H.; Kurokawa, R.; Rosenfeld, M.G.; Willson, T.M.;
Glass, C.K.; Milburn, M.V. Nature, 1998, 395, 137–143.
12. Uppenberg, J.; Svensson, C.; Jaki, M.; Bertilsson, G.; Jendeberg, L.; Berkenstam, A. J. Biol. Chem., 1998, 273,
31108–31112.
PO-127
Dynamic modeling and simulation of heavy paraffin dehydrogenation reactor for selective olefin production in
Linear Alkyl Benzene (LAB) production plant
G. Zahedi, H. Yaqubi
Simulation and Artificial Intelligence Research Center, Department of Chemical Engineering, Razi University,
Kermanshah, Iran, 67149
Modeling of a heterogeneous industrial fixed bed reactor for selective dehydrogenation of heavy paraffin with
Pt-Sn-Al2O3 catalyst has been the subject of current study. By applying mass balance, momentum balance for appropriate
element of reactor and using pressure drop, rate and deactivation equations, a detailed model of the reactor has been
obtained.
Mass balance equations have been written for five different components. In order to estimate reactor
production by the passage of time, the reactor model which is a set of partial differential equations, ordinary differential
equations and algebraic equations has been solved numerically.
Paraffins, olefins, dienes, aromatics and hydrogen mole percent as a function of time and reactor radius have been found
by numerical solution of the model. Results of model have been compared with industrial reactor data at different
operation times. The comparison successfully confirms validity of proposed model.
Key words: paraffins, dehydrogenation, fixed bed reactor, modeling, linear alkyl benzen
228 Book of Programme and Abstract for TACC2008 Figure . Paraffin molar percent as a function of time and reactor radius.
1
Corresponding Author, [email protected], fax: +98-831-4274542
PO-128
Molecular thermodynamics of trifluoroethanol-induced helix formation: Analyses of the solvation structure and
free energy by the 3D-RISM theory
Takashi Imai1, Andriy Kovalenko2, Fumio Hirata3, Akinori Kidera1,4
1
Research Program for Computational Science, RIKEN, Wako, Saitama 351-0112, Japan, 2National Institute for
Nanotechnology, National Research Council of Canada, Edmonton, Alberta T6G 2M9, Canada, 3Department of
Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan, 4International Graduate School of
Arts and Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
It has been shown that 2,2,2-trifluoroethanol (TFE) induces the helical structure of peptides and proteins. Extensive
experiments and simulations have been devoted to understanding the effect and severalpossible mechanisms have been
proposed. However, the molecular mechanism is still not completely elucidated. Lower permittivity of TFE than water
can partly explain the effect because it can stabilize the intramolecular hydrogen bond. However, it cannot explain the
strong propensity of TFE compared to other ordinary alcohols. It has been lately considered that the characteristic
solvation structure of TFE is a significant key to resolve the problem. Not only the energetic contribution but also the
entropic factor of solvation may be involved.
In this study, we employ a statistical-mechanical theory of molecular liquids, known as the 3D-RISM theory, which
yields the solvent distribution and the thermodynamic quantities from the intermolecular interactions. In order to clarify
the molecular mechanism of helix induction by TFE, we analyze the differences in the free energies, including the
solvation energy and entropy, and the solvation structure associated with the helix-coil equilibrium of melittin, a natural
peptide of 26 residues, in water, TFE, and the mixture, using the 3D-RISM theory. We will also investigate with an
alanine-homopeptide to simplify the mechanism by excluding the complicated side-chain contribution.
PO-129
Evaluation of Electrostatic Interaction by Charge-Neutralizing principle in Molecular Dynamics Method
Ikuo Fukuda1, Yasushige Yonezawa2, and Haruki Nakamura2
1
RIKEN (The Institute of Physical and Chemical Research) 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 2 Institute for
Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
We present results from a recently developed new method for molecular dynamics to calculate electrostatic interaction of
physical systems. Investigations are done regarding the charge-neutralized summation method proposed by Wolf et al.
[1,2] for evaluating in a simple pairwise manner the coulombic energy of point particle system. Although it provides
successful results [3,4] and leads a very effective computational scheme [5], in a straightforward application of this
229 Book of Programme and Abstract for TACC2008 method to molecular dynamics calculation one encounters problematic aspects including the smoothness of the potential
function and the consistent estimation of the total energy. On the basis of the charge-neutralizing principle via a
consideration of a certain theoretical framework, a novel molecular dynamics formulation for this method is proposed to
solve the problems. This provides consistent force and potential functions and a simple effective formula for the total
energy of the system. To clarify the new concept, we demonstrate the relationship between the charge neutrality and the
mirror-image charge expression and discuss the choice of the force function. Theoretical and numerical results for the
current scheme are given and individual aspects are discussed in comparative studies.
[1] D. Wolf, Phys. Rev. Lett. 1992, 68, 3315.
[2] D. Wolf, P. Keblinski, S. R. Phillpot, and J. Eggebrecht, J. Chem. Phys. 1999, 110, 8254.
[3] C. Avendaño and A. Gil-Villegas, Mol. Phys. 2006, 104, 1475.
[4] M. Sepliarsky, M. G. Stachiotti, and R. L. Migoni, Phys. Rev. Lett. 2006, 96, 137603.
[5] G. Kikugawa et al., J. Comput. Chem. 2008, in press.
PO-130
THE STRUCTURAL PROPERTY INVESTIGATION FOR SOME TWO AND THREE DENTATE SCHIFF
BASE LIGANDS BY SEMI-EMPIRICAL CALCULATIONS
Iran Sheikhshoaie
Chemistry Department, Shahid Bahonar University of Kerman, Iran
e-mail: [email protected]
The effect of some organic compounds (two and three dentate Schiff base ligands) 1-4 (Fig. 1) with C=N and OH groups
on the inhibition efficiency for corrosion of metal has been investigated by some theoretical methods. The molecular
orbital calculations explain the adsorption of the inhibitors to the surface through the C=N and OH centers with may be
due to the lengthening of the C=N and OH bond lengths and the increasing of election density on the nitrogen and
oxygen atoms. The calculations explain that the presence of electrophilic group shows the highest charge density on the
nitrogen and oxygen atoms and the highest protection efficiency due to its polar interaction with a metal surface.
[1]. Bilgic, S.; Sahin, M. Materials Chemistry and Physics, 2001, 70, 290.
[2]. Poling, G.W. J. Electrochem. Soc. 1967, 114, 1209.
[3]. Vosta, J.; Eliasek, J. Corros. Sci. 1971, 11, 223.
[4]. Sayos, R.; Gonzalez, M. Corros. Sci. 1986, 26, 927
PO-131
A Theoretical Investigation On The Nonlinear Optical (Nlo) Property Of Four π- Conjugated Salen Based
Compounds
Iran Sheikhshoaei
Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
In this work we were studied some electronic property for a set of azo salen based Schiff base compounds by AM1
semi-empirical method. We were calculated the first hyperplarizability (β) for these compounds with π- conjugated
system. All calculations were performed using AM1 at high precision with MOPAC 7.0 program. Calculations regarding
second-order optical nonlinearly of this Schiff-base were performed based on a field finite method. Some of these
compounds (Schem1) have a good NLO property and R group play a major role in designing of the NLO property for
230 Book of Programme and Abstract for TACC2008 these compounds. Using the AM1 SCF-MO method as implemented in MOPAC program performed all of the molecular
orbital calculations. All calculations were performed using AM1 at high precision [1-4].
H
C
N
N
R
N
N
OH
R= H, NO2, CH3, C(CH3)3, Cl
[1] M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, J. J. P. Stewart, J. Am. Chem. Soc. 1985, 107, 3902.
[2]. J. J. P. Stewart, MOPAC, A Semiempirical Molecular Orbital Program QCPE, 1983, 455, Version 7.0(1995).
[3] S. D. Bella, I. Fragala, T. J. Marks, M. A. Ratner, J. Am. Chem. Soc. 1996, 118, 12747.
[4]. A. Elmali, A. Karakas, H. Unver, Chemical Physics, 2005, 309, 251.
PO-132
Optimal dynamics discrimination of similar quantum systems
Li, Baiqing
School of Chemistry and Chemical Engineering, Shandong University, Jinan, China
A paradigm for discriminating similar quantum systems in the laboratory is presented based on optimal control principles
with the aid of closed loop learning algorithms.
Both static signals and time series signals can be used for
discrimination purposes. The quantum dynamic process is simulated for a mixture of three similar species in the
presence of detrimental factors including environmental decoherence, laser noise, signal detection error and limited
signal detection resolution. It is also shown that the ODD process operates by drawing on constructive and destructive
interference effects.
PO-133
Effect of Surfactant Molecule Structure on the Foam Stability Characterized by Molecular Dynamic Simulations
Xiujuan He, Ying Li*，Jing Tan, Xiaoying Hu
School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, China
Foam is a colloidal system consisting of a dispersed gas phase and a continuous liquid phase, which is widely used in
industrial region and our daily life, such as mineral floatation, enhanced oil recovery and detergent. When choosing
between the many foam agents available, both natural and artificially prepared, or designing new ones, one would often
like these which meet the specific demands of each application favorable. So it is valuable to know how the foam
apparent properties depend on its molecular structure.
In this paper, molecule dynamic (MD) simulations, resolving the full chemical details, combined experimental method
have been carried out to develop a direct relationship between the configuration of the adsorbed layer and the resulting
foam properties of the system. With a full-atom model, the structure of the film is examined in detail with particular
emphasis on the conformations of the alkyl chains of the surfactants in the film. Experimentally, Static stability of foams
has been measured by foam decay measurements, and foam viscosity was investigated by Rotation disturbing method.
By this judicious combination of simulations and experiments, how the surfactant structure and the monolayer
231 Book of Programme and Abstract for TACC2008 configuration in foam film are related to its apparent foam properties can be analyzed and thus the molecular or colloidal
options for achieving the property specifications in industrial applications can be identified.
(a)
(b)
Fig.1. Snapshots of equilibrium configuration of foam film: (a) SDS systems; (b) SDBS systems. For visual clarity, the
sodium ions are drawn as van der Waals spheres, and water molecules are line style, and the other atoms are drawn by
stick style.
[1] Seung Soon Jang, J. Phys. Chem. B. 2006, 110, 7992
[2] Fernando Bresme; Jordi Faraudo, Langmuir 2004, 20, 5127
PO-134\
Evidence of high-pressure Rh sesquioxide in the Rh/γ-alumina catalytic system
Shuping Zhuo1, Karl Sohlberg2
1
2
School of Chem. Eng., Shandong University of Technology, Zibo 255049, P. R. China
Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104
Abstract: We report an investigation of Rh-containing nanostructures dispersed on γ-alumina. This system is
representative of many common heterogeneous catalysts that consist of transition metals dispersed on a high surface area
support. Previous atomic-resolution Z-contrast STEM observations have shown the Rh particles to exist as thin “rafts” on
the (100) surface of γ-alumina. This finding is intriguing given that the preferred surface exposure of γ-alumina is (110).
Here we present first-principles density functional studies suggesting that these Rh-containing structures consist of the
high-pressure rhodium sesquioxide (II) phase growing on the surface.
PO-135
Analysis of Blend Spectra of Nitrophenol Isomers with Doolittle Multivariate Calibration
GAO Yibo, YU Meili , LIU Xin, Ding Yaping
Department of Chemistry, Shanghai University, Shanghai 200444, P R. China
In this paper, Doolittle algorithm was introduced into the field of chemometrics. It is a numerical analysis method that
can avoid matrix invertion and improve sensitivity by reducing the orders of matrixes, speeding up the operation of
[ ]
matrixes and raising the efficiency of computation 1,2 . The process of the Doolittle algorithm is implemented by LU
decomposition which can decompose matrix A (a nonsingular matrix with rank n) into the product of a lower triangular
matrix and an upper triangular matrix. The decomposition process is as follows.
The matrix A∈Rn×n (∣A∣≠0) can be expressed as the formula: A = LU.
232 Book of Programme and Abstract for TACC2008 ⎛1
⎜
l21
L=⎜
⎜ ...
⎜⎜
⎝ ln1
0
...
1
...
...
...
... ln,n−1
0⎞
⎟
0⎟
...⎟
⎟
1 ⎟⎠
⎛ U11
⎜
0
U=⎜
⎜ ...
⎜
⎝ 0
U12 ... U1n ⎞
⎟
U 22 ... U 2n ⎟
... ... ... ⎟
⎟
... 0 U nn ⎠
The solution of equation (A·x = b) can be obtained by solving L·y = b and
U·x = y.
In this paper, Doolittle multivariate calibration was applied to solve the problem of overlapped spectra of
multi-components such as nitrophenol isomers.
Fig.1 shows the spectra of three pure components of nitrophenol isomers. It can be seen that the spectra of the mixed
system of the isomers from 200nm to 250nm overlapped seriously, so it is hard to analyze the system without separation.
While according to the Lambert-Beer law and the absorbency information obtained of calibration system, the
concentration of artificial synthesized samples can be worked out with Doolittle multivariate calibration.The result shows
that Doolittle multivariate calibration is superior to K-matrix.The relative standard deviation of Doolittle multivariate
calibration is from -8.44% to 8.38%, while relative standard deviation of K-matrix is from -14.51% to 12.65%. It is
demonstrated that Doolittle algorithm is effective in analytical chemistry and it must have broader prospects in analytical
chemistry and chemometrics.
o - n itr o p h e n o l
p - n itr o p h e n o l
m - n itr o p h e n o l
2 .2
2 .0
1 .8
1 .6
absorbency
1 .4
1 .2
1 .0
0 .8
0 .6
0 .4
0 .2
0 .0
-0 .2
2 0 0
3 0 0
4 0 0
5 0 0
w a v e le n g th
Fig.1 Spectra of three pure samples
[1] Q.Y. Li, N.C. Wang, D.Y. Yi, Modern Numerical Analysis, Science Publication in Beijing, 1995.
[2]K.E.Agensin, Numerical Analysis Introduction, Shanghai, Science and Technology Publication in Shanghai, 1986.
PO-136
Subcellular Location Predicting by Using AdaBoost
Wen-Cong Lu1*，Bing Niu2, Yu-huan Jin1
1 Department of Chemistry, College of Sciences, Shanghai University, 99 Shang-Da Road, Shanghai, China，200444
2 School of Materials Science and Engineering, Shanghai University, 149 Yan-Chang Road, Shanghai， China，
200072
Protein subcellular localization, which tells where a protein resides in a cell, is an important characteristic of a protein,
and relates closely to the function of proteins. The prediction of their subcellular localization plays an important role in
the prediction of protein function, genome annotation and drug design. Therefore, it is an important and challenging role
to predict subcellular localization using bio-informatics approach. In this paper, a robust predictor, AdaBoost Learner
based on its amino acid composition is introduced to predict protein subcellular localization – a dataset derived from
SWISSPROT 33.0. Jackknife test and independent set test were used to demonstrate that Adaboost is a robust and
efficient model in predicting protein subcellular localization. As a result, the correct prediction rates were 74.98% and
80.12% for the Jackknife test and independent dataset test respectively, which are higher than using other existing
233 Book of Programme and Abstract for TACC2008 predictors(See Table 1). An online server for predicting subcellular localization of proteins based on AdaBoost classifier
was available on http://chemdata.shu.edu.cn/sl12H.
Table 1 Overall rate of correct prediction using different method
ANN
SVM
AdaBoost
Jackknife test
65.67%
73.00%
74.98%
Independent set test
73.76%
73.00%
80.12%
[1]. Eisenhaber F, Bork P. Wanted: subcellular localization of proteins based on sequence [J ].T rans. Cell B iol. ,1998, 8:
169～ 170.
[2] Nakai K (2000) Advances in Protein Chemistry 54:277-344.
[3] Nakai K., Kanehisa M (1991) Proteins: Structure, Function, and Genetics 1: 95-110.
[4] Nakai K, Kanehisa M (1992) Genomics 14: 897-911.
[5] Von Heijne G, Nielsen H, Engelbrecht J, Brunak S (1997) Protein Engineering 10: 1–6.
[6] Nakashima H., Nishikawa K (1994) Journal Molecular Biology 238: 54-61.
[7] Freund Y, Schapire RE (1997) HJournal of Computer and System SciencesH
PO-137
Predicting toxic action mechanisms of phenols using AdaBoost Learner
Bing Niu1, Yuhuan Jin 2, WenCong Lu1,2*, GuoZheng LiP3,
1) School of Materials Science and Engineering, Shanghai University, 149 Yan-Chang Road, Shanghai 200072, People’s
Republic of China
2) Department of Chemistry, College of Sciences, Shanghai University, 99 Shang-Da Road, Shanghai 200444, People’s
Republic of China
3) School of Computer Science & Engineering, Shanghai University, Shanghai, 200072, China
AdaBoost Learner is employed to investigate Structure-Activity Relationships (SARs) of phenols based on molecular
descriptors. In this paper, the performance of AdaBoost Learner is compared with linear discriminant functions (LDFs)
and artificial neural networks (ANNs), which are the most common algorithms used for SARs analysis. AdaBoost
Learner performed better then LDFs and ANNs in predicting the mechanism of toxicity of phenols based on molecular
descriptors (See Table 1). It can be concluded that AdaBoost has a potential to improve the performance of SARs
analysis. We believe that AdaBoost Learner will play an important and complementary role to the existing algorithms for
the prediction of the mechanisms of toxicity based on SARs. We have developed an online web server for the prediction
of ecotoxicity mechanisms of phenols, accessible at http://chemdata.shu.edu.cn/ecotoxity/.
Table 1 Overall rate of correct prediction using different method
LDF
ANN
AdaBoost
Jackknife test
88.3%
76.7%
91.4%
Independent set test
81.4%
79.1%
88.4%
[1]Schultz, T. W.; Applehans, F. M.; Riggin, G. W. 1987, 13, (1), 76-83
[2]Freund, Y.; Schapire, R. E.. Journal of Computer and System Sciences 1997, 55, (1), 119-139.
[3]Ren, S. Chemosphere 2003, 53, (9), 1053-1065. [4]Quinlan, R. C4. 5: Programs for Machine Learning Morgan
Kaufmann Publishers: San Mateo, CA, 1993
E-mail address: [email protected]
Emulation and Simulation of Dynamic Weighting Signal
Che xinsheng a, Zhang yanjun b, Zhang xiaoyu c
Shenyang University of Technology, 110178，Shenyang，China
This paper discusses the researching process of simulating dynamic weighting signal in the aspect of signal on MATLAB,
based on the conception and researching method of virtual instrument. The signal simulation includes parts of the
production line、the mechanism of balance (a Second-Order Underdamped System)、response of object、response of
the mechanism and power frequency noise. This paper analyzes the structure of dynamic weighting device and
mathematical model of the signal simulation structure in the background of dynamic monitoring of dynamic weighting
on packing production line. Virtual instrument function is designed on MATLAB, the simulating signal is generated by
MCU, D/A converters and RS232 serial interfaces. Users can get signal from the output channel of virtual instrument
signal source according to the signal’s feature, and send the signal to electronic measuring unit, and perform debugging
and studying. Comparation is made between the simulate signal and the filed signal.
*Email:
a. [email protected]
b. [email protected]
c. [email protected]
PO-139
Molecular dynamic studies on the gated loop domain of the imidazolonepropionase Da LinTaia, Jun-Min Quan*a,
Yun-Dong Wu*a,c
a
Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China, bDepartment of
Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
([email protected], [email protected] )
Induced fit movement of an enzyme molecule upon the binding of substrate has been characterized for many enzymes
and is essential for catalysis. Imdazolonepropionase [1], one of the aminohydrolases[2], has similar conformational change
in the catalytic cycle, but the mechanism through which the gated loop domain of imdazolonepropionase shield or open
the active site remains elusive. Here we presented molecular dynamics simulations with explicit solvent model on the
empty imdazolonepropionase and imdazolonepropionase in complex with different ligands. Our results demonstrate that
the polarity of the active site is the major determinants of gating the loop domain of imdazolonepropionase. In the empty
enzyme, solvation of the active site is significant due to the interactions of the water molecules with the positively
charged Zn cation and the polar residues around the active site, which induces the opening of the loop domain as shown
in the figure. As the substrate binds with imdazolonepropionase, which excludes the solvent molecules by blocking the
polar residues around the active site through hydrogen bonds and salt bridge, making the active site more hydrophobic, in
turn inducing the hydrophobic loop domain closing up. As formation of the highly polar product, the loop domain is
opened again due to the instability of highly charged ligand in the hydrophobic interior of enzyme.
235 Book of Programme and Abstract for TACC2008 [1]: Yamei Yu, et al. JBC, 2006, 281, 36929–36936.
[2]: Clara M. Seibert and Frank M. Raushel. Biochemistry. 2005, 44, 6383-6391,.
PO-140
Investigations on the cleavage of the von Willebrand factor by ADAMTS13
Carsten Baldauf and Frauke Gräter
Protein Mechanics and Evolution Group, CAS/MPG-PICB, 320 Yue Yang Lu, 200031 Shanghai, China.
[[email protected]]
The von Willebrand factor (VWF) is a multi-functional and multimeric protein involved in hemostasis. VWF deficiency
results in von Willebrand disease. The VWF is also involved in other diseases, e.g. thrombotic thrombocytopenic purpura.
Shear-activated VWF of a critical size is cleaved by the protease ADAMTS13 in order to regulate the size and therewith
the blood clotting activity. A homology model of the A2 domain (cf. Figure 1) shows a covered cleavage site
Y1605-M1606 on a central ƒÀ-strand of a Rossman fold motif.
A hypothesis for the mechanism is a shear-dependent partial unfolding of the A2 domain leading to the presentation of
the cleavage site to the blood and therewith to ADAMTS13.
In order to prove this hypothesis we re-modeled domain A2 and the arrangement of the central A domains. Performing
steered MD (SMD) simulations provides insight in the mechanism of VWF size regulation in atomic detail.
Figure 1: Domain structure of the mature VWF monomer.
PO-141
236 Book of Programme and Abstract for TACC2008 How sequence determines elasticity of disordered proteins
Shanmei Cheng, Frauke Graeter
CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences & Chinese Academy
of Science. 320 Yue Yang Road, Shanghai, China, 200031
Elastomeric proteins play a crucial role in a wide range of living organisms and tissues, many of which are natively
unfolded. These disordered proteins feature an elasticity specifically tailored for their distinct force-bearing and sensing
function. Their amino acid sequences typically show low sequence complexity and amino acid compositional bias, but
how protein sequence and elasticity are interrelated and how nature has composed sequences to yield proteins of required
mechanical response are currently unknown. We investigate three different natural disordered proteins with elastomeric
function, namely FG repeats in the nuclear core complex, resilin in wing tendons from adult dragonfly, and PPAK of the
muscle protein titin. We obtained force-extension curves for these proteins and poly-glycine and poly-alanine as
references, using molecular dynamics simulations and umbrella sampling. In agreement with CD experiments [1], we
find high populations of poly-proline II type structure in all cases. For comparison, we estimated the force-extension due
to purely entropic coiling by modeling the respective protein as entropic chain. Separation of entropic coiling,
electrostatic repulsion, and solvent-induced hydrophobic effects allowed relating the obtained elasticity for FG repeats,
resilin and PPAK to their primary sequence. Our results, which are directly testable by force spectroscopy experiments,
shed the first light on how evolution designed unfolded elastomeric proteins for different functional contexts.
[1] Bochicchio B, Pepe A, Tamburro AM, Chirality. 2008.
PO-142
Hydrolysis of Peptide Bonds under Stress:
A QM/MM Study
Fei Xia and Gräter Frauke
CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences,
320 Yue Yang Road, 200031 Shanghai, China
Chemical and enzymatic reactions can be guided by mechanical stress. While single molecule force spectroscopy
experiments are an emerging technique to study the chemistry of bond cleavage under external forces [1], the theoretical
basis for the force dependency of reaction rates is limited to simple models. We here will focus on the force dependency
of peptide bond hydrolysis in water. Hydrolysis of the peptide bonds in the aqueous solution usually follows the
mechanisms of the hydroxide attacking the carbonyl carbon atoms directly. With an activation barrier of 20 kcal/mol,
the peptide hydrolysis is rather slow at room temperature. In general, bond scission can be expected to be accelerated by
external mechanical forces acting on it, following an exponential dependency. We test this by examining the effect of
force on the electronic and molecular structures and energies including quantum and dynamical effects.
Peptide
hydrolysis under a range of constant force has been investigated with combined quantum mechanics and molecular
mechanics method. Transition path sampling has been used to sample rare events and to collect reactive trajectories in the
small time scales. Our investigations can explain how mechanical forces alter both the reactivity and mechanism of
peptide hydrolysis in water, which also can give first insight into how enzymatic activity contributes to the coupling of
mechanical stress with proteolysis in the cell.
[1] Wiita, A. P.; Ainavarapu, S. R. K.; Huang, H. H.; Fernandez, J. M. PNAS 2006, 103, 7222.
Wiita, A. P.;
Perez-Jimenez, R.; Walther, K. A.; Gräter, F.; Berne, B. J.; Holmgren, A.; Sanchez-Ruiz, J. M.; Fernandez, J. M. Nature
2007, 92, 225.
Force distribution explains toughness of silk-like crystalline units
Senbo Xiao, Wolfram Stacklies, Frauke Graeter*
CAS-MPG partner Institute for Computatinal Biology, Yueyang Road 320,
Shanghai, China, 200031
Silk is one of the most resilient, yet elastic fibers known. Silk proteins feature alanine and glycine rich repeats forming
crystalline units, which cross-link the otherwise amorphous protein phase. These beta-sheet rich periodic stacks have
been suggested to give silk its toughness by acting as crosslinks of protein chains. The molecular determinants of the
crystalline beta-sheet units, and of silk elasticity and toughness in general, are however currently largely unknown. We
use molecular dynamics simulations and examine the elasticity of four different silk protein crystals, antiparallel and
parallel (Ala)n and (GlyAla)n units, as they occur in spider and silk moth silk, respectively. Structural parameters and
elastic moduli are in agreement with X-ray diffraction data. We find parallel units to outperform anti-parallel analogues,
and (Ala)n to outperform (GlyAla). By means of force distribution analysis we find that the overall toughness to both,
hydrogen bonding along the sheet, and sidechain packing between sheets, and ascribe the different mechanical response
to their distinct hydrogen bond pattern.
* [email protected]
PO-144
Solvent Effects on Isolated Formamide and its Monohydrated Complex:
Observations from PCM Study
Anqun Chen, Xuemei Pu*, Menglong Li, Zhining Wen, Anmin Tian
Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
Solvent effects (viz. water, dimethysulfoxide, acetonitrile, ethanol, tetrahydrofuran,
carbontetrachloride) on isolated
formamide (FMA) and its monohydrated complex, where water is simultaneously acting as a proton donor to the
carbonyl group oxygen atom and as a proton acceptor from the amino, bridging the peptide functional group in a close
cyclic structure, are studied using polarizable continuum model (PCM)
method at the B3LYP/6-311++G (d, p) level of
theory. Effects of non-specific solvation and the specific H-bonding between formamide and the water molecule on
geometries, vibrational frequencies, energies, 1H chemical shifts and n→π* transition energies are discussed by
comparisons of results from different-polarity solvents with one from gas phase and by comparisons of results from the
monomer with that from the complex. Natural bond orbital (NBO) and atoms in molecules (AIM) theories are used to
analyze the nature of H-bond interactions and the origin of solvent effects. The results reveal that the solvent enhances
the H-bonding of O-H┅O type while weakens the other H-bonding of N-H┅O type. Ultimately, the binding energy of
complex is lowered with increasing solvent polarity but the solvent stabilization effect increases. The chemical shift of
formyl proton is almost insensitive to the non-specific solvations and the specific solute-water H-bonding but the 1H
chemical shifts of amino protons are increased by the two effects. Especially, the specific H-bonding play more important
role than the non-specific solvation in influencing the chemical shift of one amino proton involved in the H-bond in
complex. Thereby, the solvent polarity increase the chemical shift of one amino proton without the H-bonding in
complex but the chemical shift of the other amino proton involved in the H-bond displays an opposite dependence on the
solvent polarity, resulting from the solvent-weakened H-bonding of the N-H┅O type. TDDFT calculation indicates that
both the non-specific solvations and the specific H-bonding cause a blue shift of n→π* transition energy. The blue shift
induced by the non-specific solvation is weakened by the specific H-bonding while the blue shift caused by the
H-bonding is also lowered by the polar solvent because the polar solvents decrease the H-bonding strength. On the whole,
238 Book of Programme and Abstract for TACC2008 the polar solvent leads to larger variations than the nonpolar one but the variation change little as the solvent polarity
further increases, attaining one large value with ε > 24.55.
1. Hudson, E. P.; Eppler, R. K.; Clark, D. S. Curr. Opin. Biotech. 2005, 16, 637.
2. Mennucci, B. J. Am. Chem. Soc. 2002, 124, 1506.
3. Improta, R.; Barone, V. J. Am. Chem. Soc. 2004, 126, 14320.
4. Meng, S.C.; Ma, J.; Jiang, Y. S. J. Phys. Chem. B 2007, 111, 4128
PO-145
Molecular Dynamics Simulations to Determine the Effect of Temperatures and Salt in Aqueous Solution on the
Structures of Polyacrylamide
Ge Zhoua, Jianhui Luob, Qiang Yina, Pingmei Wangb, Bo Jianga
a College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, PR China
b Research Institute of Petroleum Exploration & Development of PetroChina, 10083, Beijing, PR China
Polyacrylamide (PAM) belongs to a unique class of water-soluble polymer.
It plays an important role in many
industrial fields. Usually, the temperature and the NaCl concentration in the solution are the main factors influencing the
viscosity of aqueous PAM solution in industrial systems. The effects of the temperature and the NaCl concentration on
the viscosity of PAM solution are likely to be represented to the changes of the structures of the polymer molecules.
Molecular dynamics (MD) simulation has provided a powerful tool to understand the dynamics of a polymer at atomic
detail, which can lead to significant insights into the atomic motions [1, 2]. MD simulations were conducted to investigate
the effect of the temperatures and NaCl concentrations on the structures of PAM. The analyses of radius of gyration of
backbone Cα of PAM and accessible surface area (ASA) of entire PAM were performed. The results showed that radius
of gyration of PAM firstly decrease and then increase with the increase of NaCl concentrations at constant temperature.
Overall, the radius of gyration of the backbone Cα of PAM showed a slightly decreasing tendency with the temperature
rising. ASA of PAM exhibited the same tendency as the radius of gyration of PAM. In relatively low concentrations of
NaCl solutions, change of temperature has slight influence on ASA of PAM. In relatively high concentrations of NaCl
solutions, change of temperature has relatively obvious influence on ASA of PAM. From our work, it became clear to
understand the changes of the structures of PAM in aqueous solutions at atomic level.
[1] M.P. Allen, D.J. Tildesley, Computer Simulation of Liquid, Clarendon Press: Oxford, UK, 1987.
[2] D.C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press: Cambridge, UK, 1995.
PO-146
Exploring the Molecular Interaction in Ab aggregation by MD Simulation
Chewook Lee Sihyun Ham
Department of Chemistry, Sookmyung Women’s University 52 Hyochangwon-gil Yongsan-gu, Seoul, 140-742, KOREA
Amyloid ß(Aß)-protein is widely interested in pathological folding and oligomer formation as the key protein of amyloid
deposits causing Alzheimer disease (AD). To find the initial conditions of aggregation and its structural characteristics,
10 molecular dynamics (MD) simulations were performed on Aß42 monomer in explicit water condition for a total of
500 ns. Its hydrated structures were mainly coiled-coil or helix-coil structures, but ß-sheet structures were hardly
observed. In a certain stage of MD simulations, characteristic structures having the maximum values of main chain (MC)
– MC contact were founded. From these structures, we knew about correlation between MC-MC contact values of
hydrophobic side-chains in Aß(17-26) and Aß(33-42) and solvent accessible surface area (SASA) of them. However,
239 Book of Programme and Abstract for TACC2008 these structures were not directly related to the most populated structures in these MD simulations. The features revealed
by these MD simulation studies were useful to understanding properties that are need to be aggregated and its mechanism
of Aß42.
PO-147
Theoretical approaches on the role of secondary structure propensity in oligomerization process of amyloid beta
peptide
Jooyeon Hong and Sihyun Ham*
Department of Chemistry, Sookmyung Women’s University, Seoul 140-742, Korea
According to the amyloid hypothesis, Alzheimer’s disease (AD), a neurodegenerative disorder, is a result of deposition in
brain tissues of Aβ peptides, a normal product in the amyloid precursor protein metabolism. It is known that polypeptide
aggregation proceeds through the formation of transient intermediates which assemble into more stable oligomers which
is characterized by a common cross β-sheet structure. But the aggregation mechanisms in the amyloid structures with a
characteristic cross-β-pattern are still elusive part. One of the major components of the plaques, Aβ1-42 is interesting
because it is associated with their ability to form amyloid oligomers and fibrils, which have long been considered to be
the primary pathogenic agents of the Alzheimer’s disease. Among the Aβ1-42 sequences, 16-22 residues (KLVFFAE)
are widely known as the central hydrophobic core to form oligomers or fibrils. Density Functional Theory calculations
were used to investigate the conformational preferences and thermodynamic properties of Aβ16-22 observed in the
oligomerization process according to increasing the oligomers up to the trimers. The results of these theoretical
approaches would give the structural preferences and thermodynamic stabilities of the secondary structures formations in
the process of Aβ16-22 oligomerization.
PO-148
Judging Isomeric Compound Based on Elementary Operations on a Matrix
LI Qingyu, CAI Meilin, HUANG Gangyong
Computer Science and Engineering department of South China University of Technology, GuangZhou, 510006,
P.R.China
[email protected], 15913142533
Judging isomeric compound is one of the research hotspots in modern organic chemistry and biotic science. But at
present there isn’t an effective method to judge isomeric compounds. Finding the longest carbon chain to make the
carbon atoms in order is the normal way, but this method is an NP problem. This paper present a simple and effective
method to determine the isomeric compound. Adopting the random number to abstract a molecule’s structure to be a
simple graph made up with points, lines and then judging the simple graphs isomorphism instead of judging the structure
of molecule planar are of the same is the way to be expatiated. First, transform structure of molecule to corresponding
matrix. Second, a row code XOR distance matrix and a row code AOR distance matrix are computed in terms of the
graph adjacency matrix. Third, an identical row-row set between matrices is sought. If such a row-row set exists, then the
two graphs are isomorphic and they are isomeric compounds. Otherwise they are not isomeric compound. At last, an
isomorphic function is obtained from the identical row-row set with the property of one-to-one correspondence between
vertices of the two graphs that preserves the adjacency relationship, that is the relationship of chemistry element.
PO-149
Prediction of key residues and interactions in the dimmer structure of small heat shock protein HtpX-3 in
240 Book of Programme and Abstract for TACC2008 thermophilic archaeon Sulfolobus solfataricus
Wencheng Lia, Zhenzhen Wena, Bo Yanga, Yonghua Wangb*, Xiaoning Wanga*
a
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China;
b
Key Lab of Fermentation and Enzymatic Engineering, College of Light Industry and Food Engineering, South China
University of Technology, Guangzhou, China,510641;
Email [email protected]
HtpX-3 is a small heat shock protein of hsp20 family, which has a potentially important role in the thermo-adaptation of
thermophilic archaeon Sulfolobus solfataricus. The dimmer structure HtpX-3 was constructed using homology modelling
method in MODELLER. The roles of conserved residues and key non-bonded interactions were predicted from the
structure of the dimmer. The information may be valuable in designing experiments of gene mutagenesis and are
valuable to the study of the function of HtpX-3.
Fig. 1. (a) Some very conserved residues shown as ball-stick model in HtpX-3 dimmer structure.
(b) Potential hydrogen bonds and ionic interaction between the loop region and the beta-sheet of its dimmer partner.
(c) Potential ionic interactions on the dimmer interface.
PO-150
Atomistic modelling of soot particles and of their interaction with surrounding molecules
J. C. Rayez, M. T. Rayez (a), B. Collignon, S. Picaud and P. N. M. Hoang (b)
a)
ISM – UMR 5255 CNRS / Université Bordeaux 1, F – 33405 Talence Cedex, France([email protected])
b)
Institut UTINAM – UMR 6213 CNRS / Université de Franche-Comté, F- 25030 Besançon Cedex, France
([email protected])
241 Book of Programme and Abstract for TACC2008 Nowadays, understanding the aviation’s impact on radiative forcing, climate change, air quality and human health is a
challenging task of great importance. In spite of the efforts undertaken to date by the scientific community, there is a lack
of knowledge about the structure, the morphology, the composition, and the physico-chemical properties of aircraft
engine soot that are released in the atmosphere.
We present here a modelling study of the soot particles and of their interaction with water and Polycyclic Aromatic
Hydrocarbons (PAHs). This work may lead to a better understanding, at the molecular level, of the role of the soot
structural and chemical characteristics on water condensation and on the ability of these particles to act as condensation
clouds nuclei. It may also lead to a better understanding of the chemical reactivity at the surface of these soot particles
and thus on how soot may influence the atmospheric chemistry.
Molecular dynamic simulations are used to study the adsorption of water molecules on partially oxidized graphite
containing COOH and OH sites. More specifically, the competition between the OH and COOH sites with respect to
water adsorption is characterized at three different temperatures (200, 250 and 300K). The simulations show a strong
preferential clustering of water molecules around the COOH sites irrespective of the temperature. In fact water molecules
can be trapped by the OH sites only when the temperature is sufficiently low, or when the local density of OH sites is
sufficiently high.
These results give insights into the water adsorption mechanisms on oxidized graphite surfaces
constituting black carbons or soot particles by aircraft.
Soot particles are also suspected to modify the atmospheric chemistry by providing surfaces for heterogeneous reactions.
However, because ab initio calculations on such large systems are not realistic, we have developed mixed
classical/semi-empirical calculations (hereafter called the SE-D method) to characterize the oxidation by OH of PAHs on
small graphite cluster modelling soot surfaces.
PO-151
Density Functional Theory Study of forming diradicals on the Gilch polymerization
Yong-Quan Ha, Qi Qi,Yue-Ming Sun
School of Chemistry and Chemical Engineering, Southeast University, 211189, Nanjing
On Gilch polymerization ,the real monomer ,α-halo-p-quinodimethane(m), Could be dimeriaed into diradicals. The
geometries, vibrational frequencies, and energies of all stationary points involved in the title reaction are calculated at the
b3lyp/6-31G level. Relationships of reactants, intermediates,
transition states and products are confirmed by the
intrinsic reaction coordinate (IRC) calculations. The results show that the reaction pathway leading to the major product
is as follows: 2m->TS(t-t)->S(t-t)->T(t-t). The step ,2m->TS(t-t), was the controlled by activation energy and reaction
rate. However, it need more energy to overcome corresponding activation energy to creat TS(h-h)or TS(h-t). Hence, We
favored that the Gilch polmerization is radical chian growth; and the diradical appeared mainly as T(t-t) .
242 Book of Programme and Abstract for TACC2008 [1] Thorsten Schwalm, Jens Wiesecke, Stefan Immel, and Matthias Rehahn, Macromolecules, 2007, 40, 8842-8854
[2] Jens Wiesecke, Matthias Rehahn，Macromol. Rapid Commun. 2007, 28, 188–193
PO-152
Molecular Structure, electronic, and optical properties study of new naphthalimides
Qi Qi, Yongquan Ha, Yueming Sun*, Wei Jiang.
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P.R. China
Two naphthalimides, Diphenylamino-7H-benzimidazo(2,1-a)benz(d.e)isoquinolin-7-ones (BBD-2-a, BBd-2-b) was
prepared in our lab. The molecular structure of them were calculated at the B3LYP/6-31G* levels and compared with its
analogue. The lowest three single-single state have been obtained by Zerner’s intermediate neglect of differential
overlap/S (ZINDO/S) calculation performed on the B3LYP/6-31G* optimized structure. The substitution of
N-benezene-naphthalene and benzimido part resulted in red-shift of absorption spectra respectively. The strong
absorption spectra from ZINDO/S located at 401.6 nm，426.4 nm separately. The absorption have some contribution
fromπ-π* and n-π*state due to a partial conjugation between isoquinoline and N-benezene-naphthalene. As a result, two
compounds’ red shift effect was well reproduced from their conjugated geometry, dipole moment, electron negative,
electronic structure.
[1] W. Jiang, et al, submitted.
[2] J. Gan, Q. L. Song, X. Y. Hou, K. C. Chen, H. Tian, J. Photochem. Photobiol. A 2004,162,399
[3] Y. Q. Gao, R. A. Marous, J. Phys. Chem. A. 2002, 106, 1956-1960.
PO-153
A Dual Functional Inhibitor Mediating Transcriptional Activation against AP-1 and NF-kB: 3D-QSAR and
Molecular Docking Analyses
Li Qian, Yong Shen*, Tifang Miao, Siyan Liao, Kangcheng Zheng*
School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of
China. E-mail: [email protected] (Shen); [email protected] (Zheng)
Currently, inhibition of transcriptional activation in T cells against protein-1 (AP-1) and nuclear factor kappa B (NF-κB)
has become an attractive target in the development of novel anti-inflammatory drugs, and it has been proposed that
[1-3]
quinazoline analogues are very prospective inhibitors against the activation of AP-1 and NF-κB.
However, the
theoretical studies on the quantitative structure-activity relationships (QSARs) and inhibition mechanism of this kind of
compound remain infrequent yet. So it is a very interesting work to perform a theoretical study on the QSARs and
inhibition mechanism of these compounds.
243 Book of Programme and Abstract for TACC2008 Here
a
series
of
novel
quinazoline
analogues,
i.e.,
recently
ethyl-4-[(3-methyl-2,5-dioxo(3-pyrrolinyl))amino]-2-(trifluoromethyl)pyrimidine-
reported
analogues
of
5-carboxylate were selected to
perform 3D-QSAR studies with comparative molecular field analysis (CoMFA) and comparative molecular similarity
index analysis (CoMSIA) as well as docking analyses. 3D-QSAR results show the established models having a
2
considerable predictive ability, in which the cross-validation coefficients q are 0.644 and 0.636 for the CoMFA and
CoMSIA models, respectively. Docking results show that there are considerable lower average values of the flexible and
rigid energy scores on related binding sites. In particular, it is very interesting to find that the binding sites just fall on the
joint region between NF-κB (and AP-1) and DNA. Based on this finding, the compound on these sites must greatly
weaken the interaction between AP-1 (or NF-κB) and DNA, and thus induce the strong inhibition of the gene expression
against inflammatory diseases. It may be the reason that the quinazoline analogues have inhibition function. These results
can offer valuable theoretical references in the pharmaceutical molecular design and the action mechanism analysis for
this kind of dual functional inhibitor against AP-1 and NF-kB.
Acknowledgments: We are pleased to thank the financial supports of National Natural Science Foundation of the
People’s Republic of China. We heartily thank the Molecular Discovery Ltd. for giving us the Dock 6.0 program as a
freeware. We are also pleased to thank the College of Life Sciences, Sun Yat-Sen University for the SYBYL 6.9
computation environment support.
[1] M. S. S. Palanki, P. E. Erdman and A. M. Manning, et al, Bioorg. Med. Chem. Lett. 2000, 10, 1645.
[2] M. S. S Palanki, Curr. Med. Chem. 2002, 9, 219.
[3] M. S. S. Palanki,
PO-155
Tracking the Folding/Unfolding Equilibrium of Mixed α/β- Peptides in Solution by MD Simulations
Dongqi Wang, Wilfred F. van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology,
ETH, CH-8093 Zürich, Switzerland
We present a molecular dynamics simulation study of two peptides containing α-amino acid residues and β- ones. Two
peptides differ in dominant fold: one shows a helical fold, the other a β-hairpin, according to experiment.
The
simulations at 300 K and 340 K were done starting from an NMR model structure and from an extended (denatured)
structure. The typical structural features of the two peptides are reproduced and a folding/unfolding equilibrium is
observed on the nano-second time scale at 300 K. The analysis of NOE distance bounds and 3J-values gives results
consistent with the experimental data. We conclude that our simulations are complementary to the experiments by
providing detailed information on the conformational distributions.
PO-157
Exploring Protein Energy Landscapes with Molecular Dynamics Simulation
Sishi Tang and David A. Case
The Scripps Research Institute, La Jolla, CA, USA, 92037.
Molecular dynamics (MD) simulation has been widely used to elucidate the role of protein motions in biological
functions, including enzymatic catalysis,
signal transduction, ligand binding and macromolecular assembly1-4 .
244 Book of Programme and Abstract for TACC2008 Nevertheless, the effectiveness of atomic-level MD simulation in exploring the potential energy landscape remains to be
evaluated systematically. In this exploratory study, we will assess the energy landscape probed by MD simulation of
ribonuclease A and GB3 protein, both of which are wellcharacterized by extensive biochemical and biophysical studies.5,
6
MD simulation will be performed on these model systems, generating trajectories in microcanonical (NVE) ensemble.
The resulting snapshots will be analyzed in terms of structural evolution and energy fluctuations. The inherent structures
and local energy minima will be acquired via direct quenching of MD configurations, where the solvent effects will be
incorporated by the generalized Born implicit solvent model.7, 8 The conformational substates will be identified via
cluster analysis and principal component projections.
Subsequently, the relationship between potential energy
landscapes and conformational substates will be derived, and the effect of protein size on their relaxation behavior and
sampling convergence will be delineated.
[1] A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425.
[2] Q. Z. Cui, R. K. Z. Tan, S. C. Harvey, D. A. Case, Multiscale Modeling &
Simulation. 2006, 5, 1248.
[3] M. Karplus, J. A. McCammon, Nat. Struct. Biol. 2002, 9, 646.
[4] J. Ma, M. Karplus, J. Mol. Biol. 1997, 274, 114.
[5] R. T. Raines, Chem Rev. 1998, 98, 1045.
[6] T. S. Ulmer, B. E. Ramirez, F. Delaglio, A. Bax, J. Am. Chem. Soc. 2003,
125, 9179.
[7] F. H. Stillinger, T. A. Weber, Science. 1984, 225, 983.
[8] D. Bashford, D. A. Case, Annu Rev Phys Chem. 2000, 51, 129.
PO-159
A novel scoring schema for protein identification by using tandem mass spectrometry data
Chen Shu, Tonghua Li*
Tongji University, No.1239 of Siping Road, 200092 Shanghai, P.R.China
With the Development of mass spectrometry technique, large scale of data is generated in a very short time. Tandem
mass spectrometry (MS/MS) is a powerful tool for protein identification, and the scoring function is the core of this
process. Nowadays, abundant scoring functions have been developed for protein identification with tandem mass
spectrometry data. MOWSE and MASCOT adopt p-value as an alternative way to evaluate the probability of recognizing
a set of fragments in a protein database. SEQUEST is based on cross correlation analysis. ProbID adopts a Bayesian
approach to interpret mass spectra data.
In this paper, a novel scoring schema was developed with the principle of relative entropy. We pretreated data with
half-decimal place rules [1], LC local retention time and precursor ions’ charge. We plotted the half-decimal chart with
experimental tandem mass spectrometry data by using integer part as abscissa and decimal part as ordinate. Having fitted
the bound line of the points, we filtered the data by taking out the part outside the bound line. For precursor ions with the
same mass may be detected for several times in MS/MS, we selected the peptides whose local retention time was within a
certain range. Then we dealt with the selected peptides with different charge separately and considered the results
synthetically. In the scoring process, hypothetic spectrum was generated as same as the literature. We adopted relative
entropy as a criterion to measure the similarity between the hypothetic and the observed spectra [2]. Relative entropy is a
statistical tool to measure distance between two distributions. The smaller the relative entropy was, the more likely that
the spectrum was generated by that particular peptide. We successfully identified several new proteins of the 18-protein
dataset which hadn’t yet been identified in our previous work.
*Supported by the National Natural Science Funds(No.20675057,20705024).
245 Book of Programme and Abstract for TACC2008 [1] Mann M. Proceeding of the 43rd ASMS Conference. 1995, 639~640
[2] Zhuo Zhang, Shiwei Sun et al. BMC Bioinformatics. 2006, 7, 222
PO-160
Metabonomics Analysis of Human Plasma on Gastric Cancer Using Pattern Recognition
Yuan Tu, Tonghua Li*,Kai Chen
Tongji University, Siping Road NO.1239, 200092 Shanghai, P.R.China
The global analysis of 1H-NMR spectra may be the best approach for developing a rapid measurement of cancer
diagnosis
[1]
, while multivariate data analysis to search for patterns within groups of spectra with similar metabolic
characteristics is the core of NMR metabonomics. The plasma samples of 50 people, of whom 25 are gastric cancer
patients and the rest are normal, were investigated by metabonomic analysis based on 1H-NMR. Following the standard
spectral processing and specific data preprocessing containing the water resonance removal (δ 4.5-5.0)
[2]
, unsupervised
PCA and supervised PCR, PLS and KPLS were conducted on the data as well as compared with each other to obtain the
best algorithm. Also complemented was the conventional plasma chemistry and histopathological diagnosis. The PCA
method correctly separated cancer patients from that of normal ones, as shown using the scores plot, while the relatively
better method KPLS showed the very consistent result with that of the histopathological diagnosis, with the predicting
accuracy of 96%. According to the NMR spectra and the data analysis results, some amino acids, glucose and lipids
[3]
can be identified as well as some characterized metabolites. Results of this study suggest that 1H-NMR spectra of human
plasma analyzed using PCA and KPLS statistical methods indicates good separation of cancer-bearing patients from
normal ones and justifies the excellent predicting ability for early cancer diagnosis.
*Supported by the National Natural Science Funds (No.20675057,20705024)
[1] Tracy L. Whiteheada, Behjatolah Monzavi-Karbassib, Thomas Kieber-Emmonsb, Metabolomics. 2005, 1, 269-278.
[2] Ivan K. S. Yap, T. Andrew Clayton, Jeremy K. Nicholson, et al., J. Proteome Res. 2006, 5, 2675-2684.
[3] Eleni Skordi, Ivan K. S. Yap, Jeremy K. Nicholson, et al., J. Proteome Res. 2007,6,4572-4581.
PO-161
The new development about peptide elution time prediction
Xiaomin Xu, Tonghua Li *
Tongji University, Siping Road No.1239, 200092 Shanghai, P.R. China
With the liquid chromatography (LC)-tandem mass spectrometry (MS/MS) is growing, several methods and software
tools are available for identifying peptides/proteins. But the final results include large numbers of false positive
identifications. In the study, we have been working to apply the LC retention time to improve the confidence in peptide
identifications. Many methods are available for building the models, like multiple linear regressions (MLR), Principal
Component Analysis (PCA), Partial Least Squares (PLS), and Artificial Neural Network (ANN). Although these methods
for selecting variables are effective mostly, they have some limitations. In this paper, the Kernel Partial Least Squares
(KPLS), the Support Vector Regresses (SVR) and the Projection Pursuit (PP) are used to build the predictive model.
KPLS is a kernel function which was used in the method PLS to improve the ability of the predictive model.[1] SVR is a
method which control the accuracy of nonlinear function, with the global optimize, good generalization ability. PP is a
term describing a type of statistical technique that can deal with high dimensional non-normal data sets.[2] The data set of
346 peptides in the 560 to 4000 Da mass rages from the protein which was cut by the trypsin. The retention time is from
10.7 to 36 min. The hydrophobicity, the van der Waals volume, the sum of retention times of the amino acids composing
246 Book of Programme and Abstract for TACC2008 the peptide are as the variables at first.[3] Increasing the new descriptors to 50 and using the 20 amino acids’ descriptors
as the variables singly are attempted. After the variables selection, the peptide length and hydrophobicity are selected as
important variables. The R square about model is 0.94.
* Supported by the National Natural Science Funds(No.20675057,20705024)
[1]Baudat G., Anouar F., Feature vector selection and projection using kernels. Neurocomputing, 2003, 55: 21-38
[2]J.H. Friedman, J.W. Turkey, IEEE Trans. Comput. 23 (9) (1974)881-890
[3]Tomasz Baczek, Roman Kaliszan. J. Proteome Res. 2005, 4, 555-563
PO-162
A holistic carbon-atom cybernetics in the emergence of genetic information and heredity
Chi Ming Yang (杨池明)
(System Biology and Neurochemistry, College of Science, Tongji University, Shanghai, China Email:
[email protected]; [email protected])
Carbon is supposed to be a major player in the evolutionary scheme of the universe because of its abundance and its
ability to form complex species. Amongst the four most abundant elements in naturally available biomolecules, i.e.,
carbon, oxygen, hydrogen and nitrogen, carbon is also believed to be a key element in the evolution of prebiotic
molecules. In modern biological world, the numbers of carbon atoms within biomolecules or within particular functional
and/or structural moieties of the biomolecules can often provide a pivotal clue to their biochemical origins and
evolutionary connections.
In stark contrast with the four nucleobases in the genetic codons, the 20 amino acid (AA) molecules, as an integral part of
the genetic regime, display a complex structural and functional diversity. Modern interests in the occurrence of this
intricate subset of 20 different AA’s began with the landmark Miller Experiment. For the past few decades, considerable
effort has been expended in striving for a general principle that can explain the form of the genetic coding contents.
Despite this, a mechanistic understanding of the selection of AA’s by genetic codons throughout biological evolution
remains elusive.
Although modern biology is dominated by the effort to relate molecular structure to function, it appears that a
fundamental principle, that pertain to the arithmetic of natural numbers and underlie the genetic coding process, may
reside deep inside the atomic level.
Analysis of the carbon atom numbers in the gene-coded AA side chains shall provide information on the evolutionary
state of the current genetic codons. To this end, a synthon principle in synthetic organic chemistry approach is introduced
aiming at elucidating the molecular versus atomic information logic underlying the genetic coding contents, and their
intrinsic relations to the origin and evolution of the genetic codons and life.
We have previously explored the organizational features of the genetic codon network, which allows us a clearer view of
the current genetic apparatus. We found that the internal relation within the 64 genetic codons and the degeneracy of
codons can be explicitly described within the unprecedented framework of a quasi-28-gon, its symmetry is similar to
simple spherical viruses. Moreover, the 28-gon model allows investigation of the atomic and molecular contents and
properties in unprecedented details.
This new conceptual model based on the structural regularity of the codons displays two evolutionary axes in the genetic
codon network on the basis of the chemical properties of the coding contents. Three discrete evolutionary stages and two
247 Book of Programme and Abstract for TACC2008 evolutionary axes within the 20 standard AA’s were identified. The evolutionary axis hypothesis is supported by several
observations.
Using the synthon approach to analyzing the carbon atoms, we observed that the side chain of AA’s equals their
backbone components in terms of carbon atoms. Such atomic constraints on the evolutionary selection of the AA’s are
insightful. A conclusion can be reached that elevated levels of amino-acid side chain function complexity together with
increasing numbers of side-chain carbon atoms along the evolutionary axes may be is a representative indicator of
evolution.
Furthermore, on the basis of above, the sum of the total number of side chain skeleton-atom number (SCSAN) within the
AA’s encoded by 16 groups of the genetic code doublets equals 100; and the sum of the backbone skeleton-atom
numbers in (NH2CH(…)COOH) from the 20 AA’s also equals 100. This unexpected observation allowed us to suggest
that the genesis of the general backbone of alpha- AA’s may be intrinsically associated with, even determined by, the AA
side chains throughout the origin and evolution process of the 20 AA’s, and the total number of the side chain groups
together with the overall side-chain skeleton atom numbers may be inherently constrained by the general AA backbone.
That is, there shall be a direct, pivotal link between the AA backbone and the origin of each side chain.
Biomolecular transformations are accomplished primarily through covalent bond formation and breaking, such as C-C
bond formation and breaking, oxygenation and de-oxygenation, amidation and de-amidation, hydrogenation,
de-hydogenation, and so on. This same logic shall also apply to the prebiotic synthesis. Although the biosynthesis of
standard AA have now been well established, our understanding of the origin mechanism for abiotic formation of AA’s
has long lagged behind their modern biosynthesis, and mechanistic elucidation for the abiotic generation of these AA’s
remains little explored except the Miller and Urey’s Experiment using ammonia, methane, hydrogen and water with
electrical sparks. Yet most related fundamental questions remain open. Consider the same synthon shared by the four
nucleic bases and the AA backbone, some alternative, though hypothetical, nevertheless chemically feasible pathways to
the abiotic formation of simple AA’s are postulated.
[1]
Crick, F. H. C., J. Mol. Biol. 1968, 38, 367–379.
[2]
Bada, J. L., Lazcano A., Nature, 2002, 416(6880), 475.
[3]
Szathmáry, E., Nature Reviews Genetics 2003, 4, 995 -1001.
[4]
Gilbert, W., de Souza, S. J., Long, M., Proc Natl Acad Sci U S A. 1997, 94, 7698-703.
[5]
Weber, A. L., Miller, S. L., J. Mol. Evol. 1981, 17, 273–284.
[6]
Eigen, M., Gardiner, W., Schuster, P., Winkler-Oswatitsch, R., Sci. Am. 1981, 244, 88–92, 96.
[7]
Henning, et al., Science, 1998, 282, 2204.
[8]
Yang Chi Ming, Bulletin of Mathematical Biology, 2004, 66, 1241-1257.
PO-163
Ab initio calculation of electronic structure of protein in solution
Haoping Zheng
Pohl Institute of Solid State Physics, Tongji University, 1239 Siping Road,
Shanghai 200092, China
The calculation of electronic structure of a protein is almost impossible if we use traditional free-cluster method based on
density functional theory, because of its incredible huge computational effort. There has been a great deal of interest in
developing so-called O(M) methods, for which the computational effort scales linearly with number M of atoms [1]. The
self-consistent cluster-embedding (SCCE) method
[2]
uses a set of localized one-electron wave functions to describe
248 Book of Programme and Abstract for TACC2008 system. Its computational effort can scale quasi-linearly with the number of atoms, while the calculation precision is kept.
Using the SCCE method, the electronic structures of four isolated proteins have been obtained by first-principles,
all-electron, ab initio calculation [3]. There is no pseudopotential, no adjustable parameter in the calculation, and the
Gaussian bases used can be considered as adequate. The calculation can currently give following information of a protein:
(a) Eigenstates, total energy and charge density. (b) Active sites and reactive sites, and the energy change for an active
site getting or losing an electron. (c) Changeable parts of the protein without electron transfer. (d) Total force acting on
each atomic nucleus, which offers an independent theoretical estimate for the precision of structural determination by the
NMR.
We are constructing the equivalent potentials of water for the electronic structures of 20 amino acids [4]. When this is
finished, the reliable electronic structure calculation of a protein in solution will be a reality. It will be possible to
understand biology functions in viewpoint of electronic structure.
[1] T.A. Wesolowski, In: Computational Chemistry: Reviews of Current Trends, J. Leszczynski, Ed. (World Scientific,
Singapore 2006) X, 1-82.
[2] Haoping Zheng, Phys. Lett. A 1997, 226, 223.
[3] Haoping Zheng, Phys. Rev. E 2003, 68, 051908.
[4] T. Zhang, H. Zheng, S. Yan, J. Comput. Chem. 2007, 28, 1848.
PO-164
High-pressure thermodynamic study of Ir by first principle calculation
Hong Fanga, Bo Liua, Mu Gua*, Xiaolin Liua, Shiming Huanga, Chen Nia，Rongbo Wangb
a
Laboratory of Waves and Microstructure Materials, Pohl Institute of Solid State Physics, Tongji University, Shanghai
200092, China
b
Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, Sichuan, China
Based on previous experimental and theoretical work, lattice dynamic and thermodynamic properties of Ir under high
pressure are studied by using density-functional theory (DFT) within quasiharmonic approximation. Several possible
phases (fcc, bcc, bct and hcp) under pressure have been investigated by comparing their corresponding total energies at
different volumes. It turns out that, for Ir, fcc structure is the most stable structure among these testing structures and no
transition to hcp occurs at pressures beyond 60 GPa. Then, we calculate the volume per atom under different pressures
with a semi-core potential in LDA approximation. A third order Birch-Murnaghan equation fitting to the results reveal
both the equilibrium ambient volume and the bulk modulus of Ir. These values show a better agreement with
experimental ones compared to the previous calculations. Also, phonon dispersion relations under different pressures are
computed. Giving the electronic band structure, anomalies on phonon spectrum are analyzed. The thermal equation of
state (P-V-T) is obtained. For the first time, as far as we know, the dependence of Debye temperature of Ir on both
pressure and temperature is calculated. Moreover, the contribution of electronic heat capacity at very low and high
temperature is studied to reveal its significance. The calculation results are compared to the experimental data whenever
they exist to guarantee the validity.
PO-165
Prediction of MHC-binding peptides, using different data representations
Pu Zhao, Tonghua Li *
Tongji University, Siping Road No. 1239, 200092 Shanghai, P. R. China
249 Book of Programme and Abstract for TACC2008 Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational
methods
[1]
have been developed for predicting MHC-binding peptides. A large variety of machine-learning techniques
are commonly used in this field, such as position-specific scoring matrices (PSSMs), artificial neural networks (ANNs),
hidden Markov models (HMMs), support vector machines (SVMs), and so on
[2]
. This work explored SVM as such a
method for developing prediction systems of HLA-A*0201 by using 1024 binders and 1825 non-binders [3]. Data
representations play a key role in SVM models, so we examined different types of inputs variables for predicting
MHC-binding peptides. We first used indicators for the 20 amino acids at each position of the 9-mer peptide. The second
set of variables we evaluated was based on global composition of several properties, and three descriptors composition
(C), transition (T), and distribution (D), are introduced. Another way we used to express data is that each amino acid is
encoded by ten factors, and these orthogonal factors were obtained from 188 physicochemical properties of 20 amino
acids via multivariate statistical analyses [4]. The accuracies of these SVM models were 82-86%. As a matter of fact,
some positions within the peptides are extremely important to bind to a specific MHC molecule, and some amino acids
are high-frequency in these positions. This work create a new representation focused on these statistical information, and
achieved an impressive accuracy of 88.6%.
*Supported by the National Natural Science Funds (No.20675057,20705024)
[1] Hagmann,M., Science. 2000, 290, 80.
[2] Lundegaard,C., Lund,O., Kesmir,C., et al. Bioinformatics.2007,23, 3265.
[3] Zhang. G. L., Khan. A. M., Srinivasan. K. N., et al. Nucl. Acids. Res. 2005, 33, W172.
[4] Kidera,A., Konishi,Y., Oka,M., et al. J Protein Chem. 1985, 4, 23.
PO-166
Theoretical study of the molecular properties and chemical reactivity of flavonoids related to their antioxidant
activity
Ihsan Shehadi *, Deema Al-Jayousi, Ahmed Almehdi
Department of Chemistry, United Arab Emirates University P.O. Box 17551, AlAin, United Arab Emirates
A series of density functional theory calculations for 28 flavonoids belonging to the major flavonoids' families were
carried out to establish the structural requirements of flavonoids for appreciable radical-scavenging activity. Energy of
the same number and type of nuclei were compared. On the other hand, the dipole moments were compared for
flavonoids of similar structures but different substituents i.e OCH3 and/or OH. Methoxy groups introduced unfavorable
steric effects and therefore decreased the dipole moments of the studied flavonoids. Calculations of HOMO-LUMO gaps
were performed to give insights of flavonoids' reactivity. Flavonols exhibited the lowest HOMO-LUMO gap among all
other classes in this study. Chemical potential properties of flavonoids to measure their tendency to give or capture
electrons and therefore their antioxidant potential were computed. Flavonols showed the lowest values among all classes
which is another proof of their antioxidant ability. Structure-activity relationships are well established from density
functional calculations. Multiple hydroxyl groups confer upon the molecule substantial antioxidant activity. Methoxy
groups introduce unfavorable steric effects. A double bond and carbonyl function in the heterocycle of the nuclear
structure increases activity by affording a more stable flavonoid radical through electron delocalization.
[1] Monica Leopoldini, I. P. P., Nino Russo, and Marirosa Toscano, J.Phys. Chem. A , 2004, 108, 92.
[2] Ana Maria Mendoza-Wilson, D. G.-M., J. Mol. Struct.: THEOCHEM, 2006, 761, 97.
PO-167
250 Book of Programme and Abstract for TACC2008 Theoretical Investigations of the Structure, Bonding and Electrochemistry of _2S2 _itrosyl Complexes of Iron and
Cobalt
John P. Graham
United Arab Emirates University, Department of Chemistry, Al Ain, UAE
Density functional calculations were used to study the structure, bonding and properties of the N2S2 nitrosyl complexes
M(NO)(bme-pda), M(NO)(bme-dach), and M(NO)(bme-daco), M=Fe, Co. These complexes are of interest as model
systems for N2S2M centers in metalloproteins such as acetyl-CoA synthase and nitrile hydratase. The complexes studied
in this work have been shown to exhibit unusual structural and electrochemical properties [1]. Calculated optimal
geometries and vibrational frequencies are compared to experimental data and found to be in excellent agreement in most
cases. A very small energy barrier for rotation of the NO ligand relative to the S-donor atoms of the N2S2 ligand is
calculated. Unusual electrochemical properties of the complexes are investigated using molecular orbital analysis and
calculation of absolute reduction potentials. It is concluded that reduction of the Fe complexes may produce unexpected
triplet-state products. The reduced triplet-state Fe complexes are determined to be of lower energy than the expected
singlet products.
[1] Chiang, C-Y; Lee, J.; Darlymple, C.; Sarahan, M.; Reibenspies, J;Darensburg, M. Inorg. Chem. 2005, 44, 9007.
PO-168
A density Function Theory Study of the α-Olefin Selectivity in Fischer-Tropsch Synthesis
Jun Cheng
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
Selectivity is a fundamental issue in catalysis. While other issues, such as reactivity, have been extensively investigated
and a great progress has been mad, the theoretical understanding of selectivity in heterogeneous catalysis is much short of
chemists’ expectation. Here we present one of the first attempts to understand the selectivity in heterogeneous catalysis
using density functional theory (DFT) calculations. In this work, we investigate the α-Olefin selectivity, one of the
fundamental issues in Fisher-Tropsch (FT) synthesis. It is usually measured by the paraffin/olefin (P/O) ratio in FT
products, and experimental work interestingly found that the P/O ratio depends on the chain length exponentially.
Combining extensive DFT calculations and kinetic analyses we satisfactorily solve this puzzle in the literature, and
moreover our results provide insight into improving the α-Olefin selectivity. This combination may be a good approach
to study the selectivity issues in heterogeneous catalysis in general.
PO-169
DFT study of C–H bond activation and C–C coupling in a binuclear ruthenium complex
Samat Tussupbayev* and Sergei F. Vyboishchikov
Institut de Química Computacional, Universitat de Girona,
17071 Girona, Catalonia, Spain
Polynuclear transition metal polyhydride complexes exhibit unique reactivity toward a variety of substrates. A
fascinating example is given by the reaction of diruthenium complex CpRu(μ-H)4RuCp with ethylene to yield bis(vinyl)
complex A1.
251 Book of Programme and Abstract for TACC2008 Subsequent
C–C
coupling
between
the
coordinated
ethylene
and
two
vinyl
ligands
in
A
gives
2,5-dimethylruthenacyclopentadiene complex B.
We performed a computational study of the mechanism of these reactions using both traditional DFT approach and
molecular dynamics2,3. We found that the reaction proceeds through a large number of intermediates and transition states.
Agostic interactions are of importance in the multistep transformations. Interconversion between bridging and terminal
hydrides occurs frequently in the course of the reaction. It plays a significant role in the cooperativity of the Ru centers.
The rate-determining step of the C–H bond activation reaction is the initial coordination of ethylene to the reactant with a
≠
⊿ G298 barrier of 27 kcal·mol–1. The metadynamics simulations reveal intriguing details of the ethylene coordination
step.
[1] Takao, T.; Suzuki, H.; Tanaka, M. Organometallics, 1994, 13, 2554.
[2] Tussupbayev, S.; Vyboishchikov, S. F. Organometallics 2007, 26, 56.
[3] Tussupbayev, S.; Vyboishchikov, S. F. Organometallics 2008, in press.
*E-Mail: [email protected]
PO-170
Small-world network approach to identify nucleus residues of small proteins
a,b
a
a
a
a,b
Haiyan Li , Jihua Wang ,*, Liling Zhao , Xianghua Dou , Xiuping Luo
a. Key Lab of Biophysics in Universities of Shandong , Dezhou 253023, Shandong, China
b.College of Physics & Electronic, Shandong normal university, Jinan 250014, Shandong, China
Identifying nucleus residues is crucial for studying the folding mechanisms of proteins. Folding nuclei can be defined as
the minimal stable element of structure whose existence results in subsequent rapid assembly of the native state.
Hydrophobic core composition is another determinant of protein folding rate. Lattice model studies showed that passing
through the transition state with subsequent rapid assembly of the native conformation requires the formation of some
(small) number of specific obligatory contacts (protein-folding nucleus) . Further studies suggested that the folding
nucleus location may depend more on the topology of the native structure than on a particular sequence that folds into
that structure. This view also received support from experimental analysis.
In this work, the protein structure is modeled as a network with the amino acid residues the vertices and contacts between
them the edges. The amino acid networks for native states of 81 proteins are constructed. We find that the amino acid
networks are characterized by low values of clustering coefficient and the average shortest path length. The shape of the
degree distribution is Poisson distribution, which are the typical property of small-world networks. We performed two
independent MD simulations of 12 ns for GB1 and CI2 at 498K, respectively. The amino acid networks of protein
GB1and CI2 are constructed at three different states, the native, the transition, and denatured states on the unfolding
pathway. The Changes of the network parameters on the unfolding pathway of GB1and CI2 are analyzed. The nucleus
residues of GB1 and CI2 are identified by the analysis of the network parameter: betweenness of transition states. The
results are consistent with the previous experimental and theoretical studies.
252 Book of Programme and Abstract for TACC2008 [1] Xiong Jiao, Shan Chang, Chun-hua Li, Wei-zu Chen, and Cun-xin Wang, PHYSICAL REVIEW E, 2007, 75 , 051903
[2] M. Vendruscolo,N. V. Dokholyan, E. Paci and M. Karplus, PHYSICAL REVIEW E, 2002, 75, 061910
[3] Nikolay V. Dokholyan, Lewyn Li, Feng Ding, and EugeneI.Shakhnovich, PNAS, 2002, 99, 8637–8641
PO-171
An Analysis of the Avian Influenza Virus Using Z-Curve Method
YANG Yan-ling a,b, WANG Ji-hua a,b *
a. Key Lab of Biophysics in Universities of Shandong,
b. Physics Department of De Zhou University, 253023, P. R. China
It has been more than 120 years since the Avian Influenza broke out in Italy in 1878, which made many countries suffer a
lot. What’s more, it also influenced people’s daily life, even their lives. The Avian Influenza is a syndrome caused by
Influenza Virus A, which can be divided into three types: non-pathogenic, low pathogenic and high pathogenic strain
according to their pathogenicity[1]. The High Pathogenic Avian Influenza can easily make the poultry died. Furthermore,
this kind of virus is aberrant and may infect human beings. The WHO reported that 371 persons had been infected by the
H5N1 Avian Influenza Virus up to March 5, 2008, and 235 among them had died.
This paper picks up 100 DNA sequences of the H5N1 (HA) Avian Influenza Virus from the NCBI database, which root
in the same kind of host--chicken in China, Egypt, Thailand, Nigeria, Indonesia, etc, in 2008. Based on the Z Curve
Theory[2,3], the corresponding curves are drawn and analyzed, then the content of 4 bases is calculated, respectively. The
conclusion is that each kind of Z-curve is almost similar, especially 3D curve, xn − n curve and zn′ −n curve, see Figure1.
Furthermore, the content of A, C, G and T base in these sequences is almost equal, respectively. And GC content in all
these sequences is 0.41.
Fig 1 The 3D curves for three DNA sequences coming from China,
Papua, Egypt, respectively. These Z curves are very similar in global and local.
253 Book of Programme and Abstract for TACC2008 [1] Stevens J, Blixt O, Tumpey Tm et al. Science, 2006, 312: 404-410
[2] Zhang, R. and Zhang, C. T. Archaeal, 2005, 1: 335-346
[3] Wang, J. H, Wang, B. Q. and Zhang, L.S. J. Biomol., 2004, 19:129-135
PO-172
Unfolding Study of small Protein in the Physical Property Space
Jihua Wang* and Li-Ling Zhao
Key Lab of Biophysics in universities of Shandong (Dezhou University), Dezhou 253023, China
Protein folding problem is critical in molecular biology, not only because it is one of the fundamental problems
remaining in protein science, but also because many fatal diseases are directly related to protein misfolding, such as
Alzheimer’s disease. In this work, multiple molecular dynamics simulations of protein G and protein L unfolding
trajectories provide a direct demonstration of the diversity of unfolding pathway and give a statistically utmost unfolding
pathway under the physical property space.
We chose twelve physical properties of the protein to construct a 12-dimensional property space. Then the
12-dimentional property space was reduced to a 3-dimentional principle component property space. Under the property
space, the multiple unfolding trajectories look like “trees”, which have some common characters. The “root of the tree”
corresponds to the native state, the “bole” homologizes the partially unfolded conformations, and the “crown” is in
correspondence to the unfolded state. The unfolding trajectories of protein G (GB1) can be divided into three types of
unfolding pathways, the quickly two-state unfolding pathway, the three-state unfolding pathway and the slowly two-state
unfolding pathway. The quickly two-state unfolding pathway may be a statistically utmost unfolding pathway or a
preferred pathway of GB1. The simulation results show that sometime GB1 may unfold along two-state unfolding
pathway, sometime it may unfold according to three-state unfolding pathway, which can explain the two appeared
ambivalent experiment results. In the property space all the unfolding trajectories construct a thermal unfolding pathway
ensemble of GB1. The unfolding pathway ensemble resembles a funnel that is gradually emanative from the native state
ensemble to the unfolded state ensemble. The unfolded states of the independent unfolding simulation trajectories of GB1
have substantial overlaps, indicating that the thermal unfolded states are confined by the physical property values, and the
number of protein unfolded state are much less than that was believed before.
We found that proteins with similar native state topologies had the similar unfolding property trajectories and similar
unfolded state ensemble under the property space, which agreed with the previous study under Cartesian space. By
studying the protein G and protein L under the property space, we demonstrate that the two proteins have the similar
unfolding pathways that can be divided into three types and they have the similar preferred pathway. Moreover, the
unfolding simulation time of the two proteins is different and protein L unfolds faster than protein G. Additionally, the
distributing area of unfolded state ensemble of protein L is larger than that of protein G.
This work was supported by a grant from Chinese National Key Fundamental Research Project (No. 90403120) and
Shandong Fundamental Research Project (NO.Y2005D12).
PO-173
Construction of empirical topologies from Infomax Gene Networks based on mRNA microarray data
254 Book of Programme and Abstract for TACC2008 Hesam T. Dashti1,2, Mary Kloc3 , Tong Lee4, Gregory Michelotti5, Tingting Zhang6, Amir Assadi2,3
1
Department of Computer Science, Tehran University, Tehran, Iran
2
Advanced Biomedical Computation Research Center, University of Arak, Iran
3
Department of Mathematics, University of Wisconsin-Madison, Madison, USA
4
Department of Psychiatry, Duke University & Medical Center, Durham, NC 27710, USA
5
Department of Anesthesiology, Duke University & Medical Center, Durham, USA
6
Department of Research Partnering, Roche Palo Alto LLC, CA 94304, USA
Biological Motivation: This research introduces novel mathematical methods for exploring genome-scale mRNA
expression data and extracting significant biological features and patterns those are not typically discernible by
commonly used statistical analyses. We employ the appropriate objective functions to extract maximum information
contents from a set of signals (such as functions on a set with no particular topology) to impose another genre of
constraints on the topology of the set. The basic topological invariants of this structure (called an Empirical Topology on
the Genome Space) are connected components that are maximal subsets allowing the empirical functions remain
continuous in this topology. The connected components form the nodes of a network whose graph-theoretic connectivity
could be extracted via additional constraints that require the empirical topology maintain the maximum information
content even in the presence of noise and other stochastic variability. This point of view leads to construction of the new
network structure in systems biology, called an InfoMax Gene Network, which is suitable for exploring genome-scale
inter-relationships among families of genes, for example, in order to specify pathways activated during the experiments
that perturb a control experimental system. These ideas are applied to a collection of data from mRNA microarray chips
from animal models of the Parkinson’s Disease (PD).
Mathematical Methodology on Biological Aspects: The long-term utility of levodopa treatment against PD is known to
be limited by its subsequent induction of dyskinesia. In our previous research [1] we have determined the striate mRNA
expression profiles associated with dyskenesia and its reversal by the pergolide-ketanserin regimen, where the research’s
result (microarray chip experiments called G) on Parkinsonian rats is employed in current research. The chip shows
27342 examined genes’ expressions levels on two drugs injection. These occasions are arranged in three columns A, B,
and C; the column A values represent gene’s expression value when it received pergolide followed by ketanserin; group B
received pergolide followed by saline; and finally group C, the control group, received saline on both occasions. The
normalized values provide triplets of positive numbers D = { (A(n) , B(n) , C(n)) : n = 1,2,… 27342}. In this way support
vector machines’ objective function (kernel function) is employed to project G into high-dimensional space P (f : G→P)
such that G’s entries (the genes) correlation to construct the network’s nodes can be distinguished clearly. During the
mapping process, that maps the entries by mapping their features (ABC set), consists in concept of continues topology
which was the research’s aim. In this space, a metric on distance of entries by considering the projected features are
determined that induces determining of inter-relationships of the network’s nodes. Therefore via projection process and
also using empirical topology we can construct couple of gene’s pathway. Our experiment’s result is validated and
evaluated by the KEGG pathways. The comparison of notable results validates precision of our proposed method.
[1] G.A. Michelotti, T.H. Lee et al, Gene expression patterns in levodopa-induced abnormal involuntary movement and
its pharmacological reversal in hemiparkinsonian rats (Duke University & Medical Center).
[2] Cristianini, J.S.-T., Support Vector Machines and other kernel-based learning methods. 2000: Cambridge University
Press
PO-174
First principle study of the oxygen vacancy in fluorite CeO2
Y. Q. Song1*, H. W. Zhang1, Q. Y. Wen1, Y. X. Li1, L. Peng1, Q. H. Yang1, and John Q. Xiao2
255 Book of Programme and Abstract for TACC2008 1. State Key Laboratory of Electronic Films and Integrated Devices, University of Electronic Science and Technology of
China, Chengdu 610054, People’s Republic of China
2. Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
Diluted Co doped CeO2 has been experimentally reported a promising diluted magnetic oxide with the Curie temperature
well above room temperature. However, the mechanism responding for the magnetic origination is controversy yet. Until
now the oxygen vacancy (VO) mediated ferromagnetism (FM) is a widely accepted point. But it should be worth of
special notice for oxygen vacancies. As VOs not only modulate the charge of neighboring doped transitional elements but
also lead to a change of the band structure of the host oxides, both factors may make significant contribution to the
observed FM. Therefore, it is essential to understand the role of VO contribution to the FM first.
In this paper we have calculate the band structure and density of state (DOS) of CeO2 with and without introducing VO
density, in order to investigate the influence of VO and to check that whether the additional VO can bring FM into CeO2.
Our calculations are performed by means of the full potential linearized augmented plane wave (FP-LAPW) method and
generalized gradient approximation (GGA) within the density functional theory (DFT) framework, using the WIEN2k
package. The spin and nonspin-polarized SCF calculation has been done. The calculated DOS and band structure indicate
that defectless CeO2 is non-magnetic, wide gaped insulator. Including certain VO in CeO2 unit can obviously pull the d &
f orbits of Ce closer to Fermi level, but it is not enough for VO alone to spin polarized the neighboring unpaired electrons
spin and thus not bring magnetic moments either. The calculated results are consistent with previous experimental
investigations. The recent finding of FM in CeO2 nanoparticles should be pay special attentions on its FM origination
mechanism. For example, the FM in CeO2 nanoparticles may due to period breakage of the crystal and (or) asymmetry of
the surface electron density caused by small size effect, rather than simply attribute to VO alone.
PO-175
The Influences of Vanadium on TiV Alloy Performances
Yuanxun Li, Sisun Liao, Huaiwu Zhang, Yingli Liu
State Key Laboratory of Electronic Thin Film and Integrated Devices,
University of Electronic Science and Technology of China, Chengdu 610054, P. R. China
In order to improve the abilities of hydrogen storage, Helium (He) storage and resistance to hydrogen embrittlement for
the application of the target material of neutron tube, the vanadium element (V) was always introduced to Ti to form the
alloy of TiV. This paper mainly focused on the influences of V on TiV alloy performances. The crystal cell parameters
by the analysis of XRD were firstly calculated and it was found that the addition of vanadium atom would lead the
transformation of a and c of crystal parameters and thus change the performances of TiV. Based on the above results, the
bonding energies of TiV and TiVD with different content of V were calculated by the first-principles method. The
calculating results showed that with atom V goes into the crystal, the intensity between atoms and the stability of system
will increase in the HCP structure of alloy TiV. And in the FCC structure of alloy TiVD, the bonding energy of Ti V D
3
1
increases with the increase of content V while bonding energy of Ti D decreases when the content V is over 7.5%. The
4
bonding energy of Ti He, Ti V He and Ti He were also enhanced with the content V increasing, while the properties of
6
5
1
6
store He in alloy will decrease quickly when the content V is enough high, which indicates that the proper content of
atom V will benefit for the store of atom He.
The Thermal Stability and Degradation Kinetics of
Rod-shaped Polyaniline-Barium Ferrite Nanocomposites
Yuanxun Li, Huaiwu Zhang, Yingli Liu, Likun Han
State Key Laboratory of Electronic Thin Film and Integrated Devices, University of Electronic Science and Technology
of China, Chengdu 610054, P. R. China
In order to provide a new functional hybrid between organic and inorganic materials, the composites of conducting
polymer and ferrites were often designed and fabricated for their potential applications in the fields of electronics,
photonics, mechanics, and sensing. However, a critical issue for utilization of the composite is the thermal stability which
limits not only the high temperature performances but also the processing routes available for consolidating the
composites. This paper mainly focused on the thermal stability ad degradation kinetics of a novel rod-shaped
polyaniline-barium ferrite nanocomposite with special magnetic and electronic performances. The IPDT value (integral
procedural decomposition temperature) was firstly calculated to scale the thermal stability of the polyaniline-barium
ferrite composite and the results showed that the thermal stability of PANI/BaFe12O19 composite is higher than that of
the pure PANI, which indicates that some interaction exists between BaFe12O19 nanoparticles and PANI backbone. The
kinetic parameters of the composites were calculated like the activation energy for decomposition and the Arrhenius
pre-exponential factors in their pyrolysis region using Acher and Coats-Redfern methods. And the thermal degradation
kinetics equations can be expressed as:
d α / dT =
[
]
−1
2 A
−1 / 3
exp (− E / RT ) ⋅ (1 − α )
−1
3 β
which indicates that the degradation mechanism is three-dimensional diffusion.
PO-177
The interfacial structure of self-assembled switchable peptide surfactants
Ying Xue1,2, Lizhong He3, Anton P. J. Middelberg3, and A. E. Mark1,2
1. Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry,
University of Groningen, 9747AG, Groningen the Netherlands.
2. School of Molecular and Microbial Science (SMMS), and the Institute for Molecular Biosciences (IMB), University of
Queensland, QLD 4072, Brisbane, Australia.
3. Center for Biomolecular Engineering, University of Queensland, QLD 4072, Brisbane, Australia.
Recently a range of surface active peptides have been designed which form interfacial networks that can be switched
between a high- and low elasticity state, giving the possibility to stabilize or destabilize emulsions and foams in a
controlled manner. In this work, we report molecular dynamics (MD) simulations and neutron reflection (NR) studies of
the interfacial structure of two stimuli-responsive peptides, AM1 and Lac21E. The simulations were used to investigate
the structural and dynamic properties of peptides both in solution and at an air/water interface. The interfacial
self-assembled density predicted by the simulations was in close agreement with experiment. The volume fraction of
peptides normal to the interface calculated from the simulations also reproduced in detail the experimental neutron
reflectivity measurements at different contrast variation, confirming that the peptides form a well defined structure at the
interface. The elastic properties of the film were estimated at different pH values from the fluctuations in the lateral
pressure and compared to experimental measurements of the Young’s modulus. It was found that although the peptides
were unstructed in solution they folded on contact with the air/water interface forms highly ordered domains which could
explain the mechanical properties of the systems observed experimentally.
257 Book of Programme and Abstract for TACC2008 [1] Annette F. Dexter, Andrew s. Malcolm and Anton P. J. Middelberg, Nature Materials. 2006, 5, 502 – 506.
[2] Ying Xue, Lizhong He, et al, J. Physical Chemistry, B. in preparation
PO-178
The effect of Polyethylene Glycol (PEG) Spacers on the Conformational Properties of Small Peptides: A
Molecular Dynamics Study
Ying Xue1,2, Peter Surawski3, Matt.Trau3, and A. E. Mark1,2
1. Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry,
University of Groningen, 9747AG, Groningen the Netherlands.
2. School of Molecular and Microbial Science (SMMS), and the Institute for Molecular Biosciences (IMB), University of
Queensland, QLD 4072, Brisbane, Australia.
3. Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, QLD 4072, Brisbane,
Australia.
Polyethylene Glycol (PEG) is used as an inert spacer in a growing number of biotechnological applications such as for
the display of peptide epitopes in micro array techniques. Using molecular dynamics (MD) simulation techniques, we
have investigated the influence of the PEG spacer on the conformation properties of the peptides to which it’s attached. A
series of five peptides with differing physical-chemical properties were examined. Based on an analysis of backbone φ/ψ
angles and the relative populations of alternative conformations, it was shown that when isolated in solution the PEG
spacer had little effect on the conformation of the peptide to which it was attached. However, when constrained to a two
dimensional lattice mimicking a peptide displayed on a surface, the PEG-peptide units tended to form collapsed states
dramatically reducing the accessibility of the peptides to solvent.
[1] J. Milton Harris and Robert B. Chess, Nature review. Drug discovery. 2003, 2, 214-221.
[2] Miller, C. R., Vogen, R., Surawski, P. P. T., et al, Langmuir. 2005, 21, 9733-9740.
[3] Ying Xue, Peter Surawski, et al. Langmuir. In preparation.
PO-179
Intrinsic Reaction Coordinate Analysis of Activation of CH4 by Molybdenum atoms: Density Functional Study of
Crossing Seams of Potential Energy Surfaces
Zhen Guo and David Lee Phillips
Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hongkong
Density functional theory calculations were performed to investigate the quintet, triplet and singlet potential energy
surfaces associated with the C-H activation of methane by laser-ablated molybdenum (Mo) atoms recently observed
experimentally by Andrews and coworkers.1 The present computational study aims to better understand the nature of the
reaction mechanisms for C-H activation by Mo atoms. The processes for activation of methane by the excited Mo atoms
appear to produce CH3-MoH, CH2=MoH2, and CH≡MoH3 complexes.
[1] Andrews, L.; Cho, H.-G.; Wang, X. Angew. Chem., Int. Ed. 2005, 44, 113 (Zr + CH4),
[2] Cho, H.-G.; Wang, X.; Andrews, L. J. Am. Chem. Soc. 2005, 127,465 (Zr + CH4).
PO-181
258 Book of Programme and Abstract for TACC2008 In silico prediction of escape mutants of the HIV-1 protease
Alina Agramonte Delgado1,*, Rolando Pajón Feyt 2,
Ramón Carrasco Velar3, Juan A.Padrón 4
1. University of Informatics Sciences, Havana, Cuba.
2. Centre for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba.
3. Centre for Pharmaceutical Chemistry (CQF), Havana, Cuba.
4. Laboratory for Theoretical and Computational Chemistry, Chemistry Faculty, Havana University, Havana, Cuba.
The “reverse vaccinology” is a new approach that allows the in silico study of a vaccine candidate. This method reduces
the time needed for the identification of these vaccines candidates and increases the success rate in those that
conventional ways seems impossible. Its principal weakness consists of the experimental appearance of escape mutants at
short-medium time. In this work, a first approach to predict the emergence of drug-resistant mutants under positive
selection in the HIV-1 protease, correlating structural variables with the occurrence of viable mutants at population level,
is proposed. Single-point mutants in a protein evolving under positive selection pressure don't randomly occur. They
depends on the structural capability of the protein to accept changes without compromising function; that’s why it is
necessary to predict those sites where it is more likely to appear viable mutations which can be selected as escape
mutants after drug treatments. To carry out the analysis, several bioinformatics tools were used. These tools are
integrated on a distributed calculation platform implemented in our University. All drug-resistant mutants of human
immunodeficiency virus type 1 (HIV-1) protease, were retrieved from Los Alamos HIV drug resistance database
(http://hiv-web.lanl.gov). Structural models were generated and the energy contribution in the stability of the protein for
each single point mutant was evaluated. Maximum likelihood analysis provides strong evidence of positive selection
acting on 19 residues of the HIV-1 protease. This number represents 48% of the total drug-resistant mutants reported in
the database, until February 2007. Most of the analyzed drug-resistant mutants favorably contribute to the stability of the
protein structure. They show a good correlation between the susceptibility to the occurrence of positive selection on a
single point mutation and a favorable contribution of them to the stability of the protein structure. With these results, the
computational Grid technology is put in hands of the researchers as an efficient tool to detect viable positive selective
mutants. In this sense, it is possible to say that this strategy can be the first step to design a rational automated approach
for the search of vaccine candidates to this specific therapeutic target and some others.
PO-182
The role of hydrogen bonds and cation-bridges on the thermodynamic stability of humic acids: modeling study
A. J. A. Aquino1,2, D. Tunega1,2, H. Pašalić2, G. Haberhauer3, M. H. Gerzabek1, H. Lischka2
1University of Natural Resources and Applied Life Sciences Vienna, Vienna, Austria,
2University of Vienna, Vienna, Austria,
3Austrian Research Centres Seibersdorf, Seibersdorf, Austria
Humic substances (HSs) constitute a major fraction of the dissolved and particulate organic matter in natural ecosystems
and provide numerous sites for adsorption and chemical reactions. They are generally recognized as large
macromolecular, amorphous species of variable size, structure and chemical composition making its modeling a
complicated task. The most active sites in humic acids (HAs) are carboxyl groups therefore, oligomers of polyacrylic
acid with different length have been chosen as model compounds for HAs in the present work. The capability of them to
form hydrogen-bonded complexes is demonstrated through the interaction with acetic acid, the herbicide
(4-chloro-2-methylphenoxy) acetic acid (MCPA). Moreover, deprotoned carboxyl groups are able to form very stable
cation-bridged complexes. This is investigated as well. All calculations were done by means of density functional theory.
Solvation effects, as an important phenomenon, were computed by means of a combination of microsolvation (explicit
259 Book of Programme and Abstract for TACC2008 insertion of water molecules) and global solvation (polarizable continuum approach). The stability of hydrogen bonded
complexes in solution is characterized by a strong competition between solute and solvent molecules. The cation-bridged
complexes of the negatively charged (deprotonated) ligands were found to be strongly favored explaining the capability
of humic acids to fixate anionic species from soil solutions and the ability to form cross-linking structures within the
humic acid macromolecules.
PO-183
Targeting type II fatty acid synthetic pathway ---design of new antibiotics
Yao Shen and Olaf Wiest
Department of Chemistry & Biochemistry, University of Notre Dame 253 Nieuwland Science Hall, 46556, Notre Dame,
IN, USA
Jiangxia Liu and Zoltan Oltvai
Department of Pathology, University of Pittsburgh Scaife Hall 741, 3550 Terrace St. Pittsburgh, PA 15261
The type II fatty acid synthetic pathway has proven to be indispensable for most bacteria by both experimental data and
systems biology analysis. The structure and function of the individual enzymes are very distinct from their human
counterparts, making the type II pathway an attractive target to develop new and specific antibacterial drugs. Based on
the X-ray structures of fatty acid enzymes, computational techniques like docking and molecular dynamics can be
employed for drug discovery, with the goal to find inhibitors for the whole type II fatty acid synthetic pathway.
Malonyl-CoA:ACP Transacylase (FabD) is a member of the type II pathway. Very few inhibitors have been reported for
this essential enzyme in the public domain. Computational screening using a docking program-Glide on multiple crystal
structures of FabD is used as an initial screen to find potential inhibitors. Compounds identified as potential inhibitors
from virtual screen are further tested by in-vitro enzyme assay. 6 out of 15 tested compounds showed potent inhibition in
the FabD assay. Structure-activity analysis of both inhibitory and non-inhibitory compounds reveals the trends of
structural features for inhibition of FabD. Modification of these compounds can generate stronger inhibitors. Molecular
dynamics as well as other computer techniques provided further structural insights into the active site interactions.
Other enzymes such as FabH, FabB, in the type II fatty acid synthetic pathway have also been subjected to virtual
screening. A few compounds showing potential inhibition are picked out for further assay.
PO-184
Sporadic metal layers: Ion-molecule chemistry of metal cations and its implication for the upper atmosphere
Richard J. Plowrighta, Timothy G. Wrighta, John M. C. Planeb
a. School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
b. School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
The mesosphere-lower thermosphere (MLT) region of the atmosphere is the only region of the Earth’s atmosphere in
which metals exist in a free atomic state. It is known that their presence in this region occurs via the ablation of meteors
entering the upper atmosphere, but certain aspects of their chemistry are still unclear. One interesting phenomenon in this
region of the atmosphere is sporadic neutral metal layers, which have been observed for many metals such as Fe, Mg, Na,
K and Ca. To date, the most promising explanation for the formation of these layers is neutralization of cationic
metal-containing complexes concentrated in so-called sporadic E layers.
Neutralization of bare metal cations in sporadic E layers can occur though radiative recombination with electrons, but
260 Book of Programme and Abstract for TACC2008 this process has been shown to be very inefficient. Instead, metal cations can complex to ligands, such as N2, which
undergo subsequent ligand switching reactions with other atmospheric components, resulting in dissociative electron
recombination.
Using high level ab initio theory, the structure of metal cation complexes that can be formed in this region and the
thermodynamic and RRKM kinetic parameters for a number of recombination and ligand switching reactions can be
determined. These parameters are incorporated into atmospheric models, allowing reactions that govern metal
ion-molecule chemistry in the upper atmosphere - and therefore the neutralization processes in the formation of sporadic
neutral metal layers - to be explored.
[1] Plane, J. M. C.; Plowright, R. J.; Wright, T. G.; J. Phys. Chem. A. 2006, 110, 3093.
[2] Plowright, R. J.; Wright T. G.; Plane J. M. C.; - Submitted to J. Phys. Chem. A. (http://dx.doi.org/10.1021/jp8022343)
PO-186
Theoretical study on the structures and absorption spectra of protonated phthalocyanine
Tong-tong Lu, Mei Xiang, Hai-long Wang, Tian-jing He, Dong-ming Chen
Department of Chemical Physics, University of Science and Technology of China, No. 96 Jinzhai Road, 230026 Hefei,
Anhui, China
The protonation of phthalocyanine (Pc) is of fundamental importance in Pc researches since many synthetic works of Pc
derivatives are carried out in acidic media [1]. Numerous experimental efforts, mainly using spectroscopic and/or
conductometric techniques, have been made to reveal the nature of Pc protonation. However, several fundamental
problems, such as the sites and the degrees of protonation, remain unclear at this stage. In the present work, we have
systematically studied the ground-state structures of various protonation products of the free base phthalocyanine (H2Pc)
using the density functional theory computations. It was found that the N-protonation tends to increase the nearby N-C
bonds and the C-N-C angles. In addition, the protonation at the isoindole-nitrogen atoms results in evident out-of-plane
deformation of the Pc ring due to the steric hindrance of the central cavity. The calculations demonstrated that the
protonation at the meso-nitrogen sites is energetically more facile than that at the isoindole-nitrogen sites. H6Pc4+(IS1),
for which all the four meso-nitrogens are protonated, was calculated to be most stable among all the protonated products
of H2Pc. TDDFT calculations were carried out for H2Pc and two typical N-protonated species of H2Pc, i.e., H6Pc4+(IS1)
and the inner diprotonated H4Pc2+(IS4). H6Pc4+(IS1) was predicted to have two electronic transitions (11B3U and 11B2U
states) in the Q band region, which is consistent with the experimental observation for the H2SO4 solution of H2Pc. On
the basis of the calculated weights of major configurations for each excited state, the 11B3u and 11B2U states of H6Pc4+(IS1)
are considered to associate with the HOMO→LUMO and HOMO→LUMO+1 excitations, respectively.
[1] Leznoff C.C., Lever A.B.P., Phthalocyanines: Properties and Applications, Vol.1, VCH, New York, 1989.
PO-187
Interaction Between 1,3,5–Trithiane And Iodine Monobromide In Halomethane Sotutions
Abolfazl Semnani1,∗, Hamid Reza Pouretedal2, Mohammad Hossein Keshavarz2,
Ali Reza Firooz3 and Mohsen Oftadeh4
1
Faculty of Sciences,University of Shahrekord, Shahrekord,
2
Malek-e-ashtar University of Technology, Shahin–Shahr,
3
University of Isfahan, Isfahan, 4Payam-Nor of Isfahan, Isfahan, I. R. IRAN
261 Book of Programme and Abstract for TACC2008 A spectrophotometric study concerning the interaction between 1,3,5-trithiane (TT) as n-donor and iodine monobromide
as σ-cteptor has been performed in dichloromethane, trichloromethane and tetrachloromethane solutions at 10 oC. The
results are indicative of the formation of 1:1 charge transfer complexes through equilibrium reactions in all solvents.
Followed by conversion of charge transfer complex to ionic adduct in di- and trichloromethance solutions. The stability
constants and ε values of complexes are obtained from the fitting of absorbance-mole ratio data in MATLAB software
and in different solvents found vary in the order: CCl4>CHCl3>CH2Cl2 for stabilities and reverse for ε values. The rate
constants of conversion of charge transfer to ionic complexes are obtained from the slops of Ln(At/Ao) vs. t plots and
found vary in the order CH2Cl2>CHCl3. The possible reasons for the observed trends in stability constants, ε values and
rate constants discussed. The contribution of dipole-dipole interactions are obtained by the semi-empirical calculations in
Gaussian 98 and it was found that contribution of these forces is considerable.
PO-188
Detection of carbofuran based on carbon nanotubes modified biosensors
Shu Ping Zhang a *, Yi Zheng a, Da Wang Yub
a College of Science, University of Shanghai for Science and Technology,
Shanghai 200093, China
b College of Science, Shanghai University, Shanghai 200072, China
A sensitive and stable enzyme biosensor based on efficient immobilization of acetylcholinesterase (AChE) to
MWNTs-modified glassy carbon electrode (GCE) with chitosan (CS) by layer-by-layer (LBL) technique for rapid
determination of carbofuran has been devised. Because of the excellent biocompatibility and good stability of CS, it
prevented leakage of the AChE from electrode. Multiwall carbon nanotubes (MWNTs) promoted electronic transmission
at a lower potential and catalyzed the electro-oxidation of thiocholine, thus amplifying the sensitivity and amperometric
response of the biosensor. Based on the inhibition of carbamate pesticide on the enzymatic activity of AChE, we use
carbofuran as a model pesticide. The inhibition of carbofuran to the biosensor was proportional to concentration of
carbofuran in the range from 10-10 g/L to 10-3g/L, with a detection limit of 10-12 g/L. The operational stability of the
sensor was good and the storage stability was acceptable. This biosensor is a promising new method for pesticide
analysis.
PO-189
Excitation Energy Calculations with R12 Corrections
Urszula Gora1, 2, Monika Musiał1, Jozef Noga3, and Stanisław Kucharski1
1. Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowce, Poland
2. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
3. Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, Slovakia
Since Hylleras demonstrated that the inclusion of a correlation factor depending on the interelectronic distance r12 into
the wave function leads to an excellent description of short-range electron correlation, much progress has been achieved
in this field. The one of the most popular formulation is the linear r12 Ansatz of Kutzelnigg. Much improvement has been
achieved for this model in terms of different Ansätze, different approximations, and more efficient implementations.
Noga et al. combined the R12 approach with Coupled Cluster (CC) theory to derive the explicitly correlated CCSD-R12
model, which allows to obtain highly accurate results for ground-state energies and basics molecular properties. However
methods giving accurate ground-state energies do not automatically provide the same accuracy for excitation energies.
262 Book of Programme and Abstract for TACC2008 The presented poster shows one of the way of implementation the explicitly correlated CCSD-R12 model to the
excitation energy calculations. The main idea is to combine the so called standard R12 approximation with Equation of
Motion (EOM) approach. The program is based on the Feynman diagram formalism and ACES II and DIRCCR12-OS
packages.
PO-190
Hesam T. Dashti1,2, Adel Ardalan1,3, Navid Farajzadeh3
1
Advanced Biomedical Computation Research, University of Arak, Iran.
2
Center of Excellence in Biomathematics, University of Tehran, Iran.
3
Database Research Group (DBRG), University of Tehran, Iran.
Biological Aspects: For long time motif discovery problem was renowned problem in the field of bioinformatics.
Whereas conserved subsequences inside different biological sequences play similar roles, the problem of motif discovery
had been introduced to help researchers in process of identifying sequences’ functionality. Indeed, by experimentally
discovering specific subsequences functionality and using common motif discovery approaches to search the target
subsequence, corresponding sequences can be stratified upon their functionality. There are two obstacles in front of the
motif discovery solutions; the first one comes from residues substitution probability and other one is the length of some
biological sequences (around 108) that strongly affects the solutions’ time complexity. On the other hand, there is another
restriction on some motif discovery problems that changes the problem to a different problem of discovering a set of
motifs (commonly a family of motifs) inside biological sequences. Hence, the problem of motif discovery remained as an
open problem in bioinformatics research area where most of current algorithms vacillate in tradeoff of time and accuracy
or can not satisfy whole of restrictions.
Computational Aspects: Many approaches from dynamic programming approaches to exhaustive search methods have
been introduced to solve motif discovery problem [1], but Recurrent Artificial Neural Networks (RANN) have not been
examined yet, where these networks can consider wide ranges of sequences’ entities by using memory stacks. The
RANN topology includes a memory stack inside of its recurrence structure that can store and use some extra information
–except that of input nodes. An unproved claim that can be satisfied via RANN is relation of residues in biological
sequences, where the stack can store some previous residues that may have affect motifs' determining.
Methodology: For a given set C of motifs {Mi=1…n| ∀ i=1…n |Mi|=const.} and given sequence S, this methodology finds
similar subsequences Nj=1…p to Mi on S respecting to k insertions and l substitutions of residues, so length of Nj will be
between |Mi| and |Mi|+k. The network topology used here is composed of |Mi|+k input and also recurrence nodes,
3/2*(|Mi|+k) nodes in hidden layer and one output node to show the net's decision. During the training process, the
network is fed by a couple of motifs from C with k residues inserted into the motif sequence in random positions and l
residues selected in normal distribution to be mutated. During the training iterations the recurrence nodes act on hidden
layer’s output and feed these values back to hidden layer on next iteration. Hence, in each flip flop, in addition of
considering current window’s residues, previous window’s residues are also considered where combining these windows
information hoists network accuracy.
Experiments: We evaluate our methodology on random generated sequences and motifs with and without using
recurrence nodes (i.e. a simple backpropagation network). Moreover we assess recurrent nodes criticality by feeding c.
elegence sequence where some subsequences are extracted from the sequence as motifs. In both random generated and
real sequence examinations, using recurrent nodes improves the methodology accuracy. Histogram of the network output
values shows normal distribution graph around motif subsequence with 0.95 for the graph’s apex.
263 Book of Programme and Abstract for TACC2008 [1] Rigoutsos, I., et al., Dictionary building via unsupervised hierarchical motif discovery in the sequence space of
natural proteins. Proteins, 1999. 37: p. 264-267
[2] Recurrent Neural Networks: Design and Applications, Larry Medsker and Lakhmi C. Jain, The Crc Press, 1999.
PO-191
Designing Three layer Architecture Software for prediction of fluctuations pathways Using Computational
methods to formulate the signaling pathway models base on ODE and biological Networks
Shervin Mohammadi Tari
School of Computer Science, University Of Tehran, Iran
Modeling complex processes such as signal transduction pathways, is one of the most significant issues in the systems
biology in which many approaches from different fields of science and technology are proposed to introduce efficient,
understandable and extendable solutions to model complex biochemical structures with input data from various sources.
For example, modeling of the biochemical reaction networks such as PIN (Protein Interaction Network) typically
proceeds by solving ordinary differential equations (ODEs) or stochastic simulation via the Gillespie algorithm and also
some computational methods such as process algebra techniques, which have been successfully applied to the analysis of
signaling pathways. Moreover, the excitement in today’s biology is driven by the huge amounts of information generated
by high-throughput data acquisition technologies.
In this study, I introduced the 3-tier architecture software (1.User Interface, 2. Business Logic, 3.Database) which is able
to connect to the pathway databases by using modeling methods to predict the pathway’s fluctuations based on the
combination of data derived from database and the experimental data which user adds. This software derives the user
experimental data at the “User Interface layer” (It should be a Concentration’s pathway species). In the “Business Logic
Layer” I combined that information with the specific data about the concentration of the indicator species of the pathway
from “Pathway Databases” (such as ‘NCICB Pathway Interaction Database’, ‘KEGG Pathway Database’ and ‘SPAD:
Signaling PAthway Database’) then using ODEs or stochastic simulation (such as markov chain) over the kinetic
formulas of the pathway’s inner interactions to predict and figure out the pathway’s fluctuations. I have also used
biological Networks to find out other pathways influenced that specific pathway by some known interactions which
change the concentration’s of specific species depends on the biochemical conditions which consequently change the
behavior of the pathway.
PO-192
A Structure Knowledge-based Method for Protein Thermostability Prediction and Design
He Zhang and George N. Phillips, Jr.
Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
The thermostability of proteins has been a subject of a large number of both fundamental and applied studies, the former
exploring physical mechanisms of thermostability and linking them to protein folding and even to protein evolution in
structure space and sequence space, while the latter aiming at design of thermostable proteins via rational design, directed
evolution and the combination of two approaches. We developed a new computational framework for protein
thermostability prediction and design, based on the knowledge of secondary structure database (DSSP). A library for
protein fragments of length 4 is built and studied for the mapping between structure space and sequence space. The
designed protein sequence is calculated by consensus analysis of the templates and fragment library. This framework can
provide formulism of Local Structural Entropy (LSE) algorithm[1] for protein thermostability prediction and improve the
264 Book of Programme and Abstract for TACC2008 design protocol based on LSE[2]. We applied the new method for thermostability design of both kinases and cellulases.
The results indicate that fragment-based method, which made significant progresses in the fields of ab initio structure
prediction and de novo sequence design, can also be used for protein thermostability studies.
[1] Chen-Hsiung Chan, Han-Kuen Liang, Nai-Wan Hsiao, Ming-Tat Ko, Ping-Chiang Lyu and Jenn-Kang Hwang,
PROTEINS. 2004, 57, 684.
[2] Euiyoung Bae, Ryan M. Bannen and George N. Phillips, Jr., PNAS. 2008. (In Press).
PO-193
Unusual structural and electronic features of small CnAlm clusters
Fedor Y. Naumkin
Faculty of Science, UOIT, Oshawa, ON L1H 7K4, Canada
Adding non-metal atoms to metal clusters affects their properties and can allow modifying them in the desired directions.
Doping by molecular species opens a further ample multi-dimensionality for such property tuning. Both host and dopant
components of such clusters can acquire unusual geometries and the system may then exhibit unique properties.
Small alumino-carbon clusters based on C2 and C3 with 2-8 Al atoms attached have been studied [1] at an MP2 level.
Using even number of aluminum atoms allowed electronic shell-closure, and the singlet states are found to be the
lowest-energy ones for all clusters studied.
The structures of CnAlm favour planar CAl3 units (preserving geometry of isolated such tetra-atom). C2Al4 and C3Al6 are
predicted to be all-flat, with carbon molecules symmetrically framed by Al atoms and C atoms exhibiting unusual planar
tetra-coordination. Other clusters have the di- and tri-carbon attached to the aluminum sub-cluster surfaces or sunk into
their “bulk”. Adding the molecular carbon dopant can thus either generally preserve or considerably alter the (isolated)
aluminum cluster structure.
Electronic (singlet-triplet) de/excitation or dis/charging the systems leads to reversible switching between the different
types of carbon-aluminum junctions. This would suggest possibility of shape variations controlled by electric current at
nanoscale, with potential applications in molecular electronics and spintronics, molecular machinery, etc.
Hyper-coordination of C atoms is a common feature of the CnAlm clusters (with up to hepta-coordinated carbons),
supported by high negative charges (up to ≈ –2e) on those atoms. Critical examination of such cases with the AIM
techniques, however, undermines the potential hyper-valence of C atoms in most (but not all) cases. The nature of the
C-Al bonding is largely ionic, with a weak covalent character for the bonds mainly along the C-C axis, in accord with the
electron density distributions.
[1]. F. Y. Naumkin, J. Phys. Chem. A, 2008, 112, 4660.
PO-194
Molecular Dynamics Study of Antibiotic Binding to the Ribosome
Xiaoxia Gea, Benoit Rouxb
a. Department of Biophysics and Physiology, Weill Medical School of Cornell University, 1300 York Ave., New York,
NY 10021
a, b Department of Biochemistry & Molecular Biology, The University of Chicago, 929 E 57th St, W323A, Chicago, IL
Molecular Dynamics (MD) simulations have been carried out to study the ribosome-antibiotics interactions. Free Energy
Perturbation (FEP) method was used to calculate the binding free energy of antibiotics to the ribosomal large subunit.
Generalized Solvent Boundary Potential (GSBP) method, which includes both the solvent-shielded static field from the
distant atom of macromolecule and the reaction field from the dielectric solvent acting on the atoms of the simulation
region, was used. Because binding specificity is often dominated by local interactions in the vicinity of the ligand while
the remote regions of the receptor contribute only in an average manner, GSBP has all atoms in the inner region
belonging to ligand, macromolecule or solvent undergo explicit dynamics, whereas the influence of the macromolecule
and solvent atom outside this inner region are included implicitly. Potential of Mean Force (PMF) calculations from the
umbrella sampling have been performed to accurately sample the conformation of the antibiotics in the ribosomal
binding site and in the bulk.
The results of binding free energy calculation and analysis of conformational dynamics of representative antibiotics
binding to the ribosome have provided the insight into the mechanism of protein synthesis and ribosomal inhibition by
antibiotics, which in turn will shed light on the future development of ribosomal drugs for treating diseases like cancer,
etc.
[1] W. Im, S. Berneche and B. Roux. J. Chem. Phys. 2001, 114(7), 2924.
[2] Y. Deng and B. Roux, J. Chem. Theory Comput. 2006, 2, 1255.
[3] J. Wang, Y. Deng and B. Roux, Biophys. J., 2006, 91, 2798.
[4] J. L. Hansen, P. B. Moore and T. A. Steitz, J. Mol. Biol., 2003, 330, 1061.
PO-196
The First Principle Calculation on Composites of TiB2/Cu and Doped Series
MIN Xin-min1,2, LAN Dongxai2
1
Chemistry Department, School of Science, Wuhan University of Technology, Wuhan 430070, P.R.China
2
State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology,
Wuhan 430070, P.R.China
TiB2 is with layered structure and the good properties of high melting point, intensity, rigidity, anti-corruption. Cu-base
material is of merit of high intensity, electronic conductivity et al，and can be widely used in electric power, electron,
machine industries and so on. The composites of ceramic and metal may consist the excellencies of both phases, so it is
important to improve the property of the TiB2 or Cu composite to fit the development of industry and technology.
Otherwise, the preparation of dense TiB2/Cu composite is quite difficult because of the bad wettability of TiB2-Cu. It was
studied that the additives of Mo and Fe can improve the wettability, and made the products more uniform. In this paper
the composites of TiB2/Cu and doping Fe, Mo，comparing with their single phases series, were calculated by the density
function and discrete variational method (DFT-DVM), one of the first principle calculation methords, to study the
relation among electronic structure, chemical bond and properties.
The results shown that some of electrons of Cu phase translate to the TiB2 phase in the composite of TiB2/Cu. The
covalent bond of TiB2 phase of TiB2/Cu is stronger than that of the TiB2 single phase. There is weak ionic and covalent
interaction in the interface between Cu and TiB2 phase. Fe and Mo can replace Cu or Ti in TiB2/Cu composite. The
calculated total energy of TiB2/Cu-doped with Fe or Mo replacing Ti is lower than that replacing Cu. When Fe or Mo
doping into composite, the ionic and covalent bond, and the interaction between Cu and TiB2 phase all become stronger.
The influence of doping Mo is more obvious than that of doping Fe. The results are consistent with the experiment that
additives of Mo and Fe can improve preparation of TiB2/Cu composite, and effect of additive of Mo is more obvious than
266 Book of Programme and Abstract for TACC2008 that of Fe.
PO-197
Quantum Chemical Calculation of Maleic Anhydride Ring-opening Reaction
Zhang ming, Qin yan, Huang zhixiong
Wuhan University of Technology, Wuhan, 430070, China
The stable structures of Maleic anhydride and transient formations (Ts1,Ts2) of maleic anhydride (MAH) and ethanol
ring-opening reaction were investigated mainly using Density Functional Theory (DFT) with B3LYP/6-31G level. All
transient formations were studied by the Intrinsic Reaction Coordinate Method (IRC) calculation. The Computation
results show that the reaction was exothermic and matched up well with experiment.
PO-198
A computational exploration of substitute effects on the trans-diastereoselective triethylsilane reduction of
maliminium
Jian-Liang Ye, Pan-Yuan Zhang, Pei-Qiang Huang*, Xin Lu*
Department of Chemistry, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Key
Laboratory for Chemical Biology of Fujian Province and State Key Laboratory for Physical Chemistry of Solid
Surfaces, Xiamen University, 361005, Xiamen, China
Pyrrolidines with a N-α-chiral carbon are common skeletal component of many important bioactive alkaloids[1]. The
chiral center can be effectively formed through Lewis acid-mediated triethylsilane reduction of maliminium which was
shown to proceed with high trans-diastereoslectivity, whereas the 4-hydroxyl protecting group employed has distinct
effect on the diastereoslectivity[2]. We have recently performed density-functional calculations (at B3LYP/6-31+G(2d,
p)//B3LYP/6-31G** level) to explore the origin of such substituent-diastereoselectivity dependence. The computations
revealed that the preferential formation of hydrogen cis-transfer product can be ascribed to electrostatic interaction
between the H-SiEt3 and 4-oxygen atom. In case a silanic R group is used, the through-bond n(O)
d(SiR)
backdonation decreases the electrostatic interaction between the 4-oxygen atom and the incoming Et3SiH, leading to
lower diastereoselectivity. However, when more bulky TIPS group is used, the steric repulsion between TIPS and Et3Si
dominates and the diastereoselectivity inverses accordingly.
[1] Huang P.-Q. Synlett 2006, 1133.
[2]He,
B.
Y.;
Wu,
T.
J.;
Yu,
X.
Y.;
Huang,
P.-Q.
Tetrahedron:
Asymmetry
2003,
14,
2101.
PO-199
Exploring the Reaction Mechanism of Carbon Monoxide Dehydrogenase: Insights from QM Calculations
267 Book of Programme and Abstract for TACC2008 Hujun Xie, Ruibo Wu, Zexing Cao*
Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
The catalytic oxidation of CO to CO2 by carbon monoxide dehydrogenases has been explored theoretically, and a large
C-cluster model including the metal core [Ni-4Fe-4S] and surrounding residues and crystal water molecules was used in
density functional calculations. The key species involved in the oxidation of CO at cluster C, Cred1, Cred2, and Cint, have
been elucidated. On the basis of computational results, the plausible enzymatic mechanism for the CO oxidation was
proposed, and stepwise proton transfers were involved in the catalytic reaction. The first proton abstraction from the
Fe1-bound water leads to a precursor to accommodate CO binding and the subsequently consecutive proton transfer from
the metal-bound carboxylate to the amino acid residues facilitates the release of CO2. The hydrogen-bond network
around the C-cluster, formed by conserved residues His93, His96, Glu299, Lys563, and four water molecules in the
active domain plays an important role in the proton transfer and the intermediate stabilization. Predicted geometries of
key species show good agreement with their reported crystal structures.
*Email: [email protected],
Fax: (86)592-2183047
PO-200
Theoretical Studies on Butene Isomerization Catalyzed by 4-H proton of 1-Ethyl-3-Methyl-Imidazolium
Tetrafluoroborate Ionic Liquid
Hai-Xia Wang, Xiao Feng, Min Pua
School of Science, Xi'an Jiaotong University, Xi'an China a. State Key Laboratory of Chemical Resource Engineering,
Beijing University of Chemical Technology, Beijing China
Room temperature ionic liquids fully consisted of cation and anion have been widely used in the fields of catalysis and
separation [1]. 1-Ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) is a typical alkylimidazole-based ionic liquid
and represented many excellent physical and chemical properties [2]. In this work the initial structural models of all the
species in the butane isomerization catalyzed by EMImBF4 was firstly established by molecular mechanical method, then
the geometries of reactant, transition state and product are fully optimized by DFT method at the level of
B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p), respectively. The zero-point energy correction at the same computing
level was obtained through vibrational analysis. The computing results showed that 1-butene can directly transform to
2-butene catalyzed by the 4-H atom on the imidazole ring of EMImBF4. The apparent energy barriers of the butene
catalytic isomerization forward and reverse are 211.1 and 227.6 kJ.mol-1, respectively. The reaction mechanism can be
described as that EmimBF4 supplies a proton on the imidazole ring to the carbon atom of double bond of butene and
abstracts a proton from the single bond carbon atom, which makes the double bond of butene shifting. The computed
intrinsic reaction coordinate path finally confirmed the double bond migration of butene catalyzed by EmimBF4 was an
elementary process and the shift of double bond and the exchange of hydrogen was a synergetic process. It may be the
reason why ionic liquid has high catalytic activity.
[1] Welton T. Chem. Rev. 1999, 99, 2071.
[2] Lopez-Pastor M., Ayora-Canada M. J., Valcarcel M., et al. J. Phys. Chem. B. 2006, 110, 10896.
*This work was financially supported by the National Natural Science Foundation.
PO-201
Genome-wide analysis of microsatellite sequence in seven filamentous fungi
268 Book of Programme and Abstract for TACC2008 Cheng-yun Li, Lin Liu, Jing Yang，Jin-bin Li, Yuan Su,
Yue Zhang, Yun-yue Wang, You-yong Zhu
Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural
University, Heilongtan, Kunming, Yunnan Province, 650201, China
Abundance of microsatellites with repeated unit lengths of 1-6 base pairs in seven fungi: Aspergillus nidulans, Coprinus
cinereus, Cryptococcus neoformans (serotype A), Fusarium graminearum, Magnaporthe grisea, Neurospora crassa and
Ustilago maydis were investigated on genomic scale. The results showed that each species has its specific profile for
different types and different motifs of SSR loci. Ascomycetes fungi M. grisea, N. crassa and basidiomycete fungus U.
maydis adopt much more microsatellites than other fungi we examined. Total amount of 15,751, 14,788 and 6,854 SSR
loci were observed respectively, average density is 406, 389 and 347 per Mbp sequence; overall length of SSR sequence
was 0.82%, 0.95% and 0.79% of genomic sequence respectively. While ascomycetes fungus F. graminearum and A.
nidulans contains the least SSRs in the genomic DNA, only 4,679 and 4,837 tracts were observed in 36 Mb and 30 Mb
genomic sequence respectively, about occupied 0.27% and 0.31% of genomic DNA, and average density is 130 and 161
SSR loci per Mbp sequence. The intermediate frequency of SSR was observed in genome of basidiomycete fungi C.
neoformans, and C. cinereus, SSR density is 249, and 226 SSR loci per Mbp sequence respectively. Microsatellite repeats
in protein coding regions are investigated in Aspergillus nidulans, Magnaporthe grisea, and Neurospora crassa also, the
results show that the difference of different types and motifs among three fungi is very little than that in whole genomic
sequence. For dinucleotide repeats, AG and AC repeats was relative higher occurred in protein coding region of A.
nidulans than other two fungi. For trinucleotide repeats, overrepresent (comparing to the total base pair of protein coding
region) of AGC, GGC, AGG, ACG and ACC was observed in coding region, frequencies of AAC and AAG were not
difference between coding and non-coding region, AAT, AGT and ATG were underrepresent in coding region excepted
for A. nidulans, in which ATG was overrepresentative.
PO-202
Explore the structure-reactivity relation of ionic liquid supported acetylacetone catalysts
Xingbang Hu, Haoran Li* and Congmin Wang
Dept. Chemistry of Zhejiang University, Hangzhou, 310027
The excellent characters of ionic liquid (IL) have attracted more and more research interests.1 In this research field, to
support catalyst on IL is a new branch, for the purpose of recycling the catalysts. 2 Based on many previous experiments,
it can be concluded that the influence of ionic liquid support on the reactivity of the catalyst was quite complicated. 3-4 To
establish the structure-reactivity relation will be greatly helpful for understanding the essence of the reactivity of the IL
supported catalysts.
Here, we investigate the influence of IL support on the structure characters and reactivity of the catalyst by quantum
chemistry calculations. Total eleven different catalysts including five non IL supported (NIL-catalyst) and six IL
supported catalysts (IL-catalyst) were selected carefully for the oxidation reaction of methane. 5-8 The obtained results
revealed that IL support can change the molecular orbital of the acetylacetone-Fe catalyst greatly and make the catalyst
more active. Though the intrinsic catalyzing mechanism of the IL-catalyst is similar to that of the NIL-catalyst for the
methane oxidation, it was found that IL support can reduce the barrier of the reaction obviously. However, not all IL
supported methods have obvious influence on the reactivity of the catalyst. The ability of IL support to enhance the
reactivity is even stronger than that of other normal factors, such as forming hydrogen bond or cooperating with axial
ligand. Further researches suggest that the spin densities of Fe/O and the charges carried by O are strongly related to the
reactivity of the catalysts. As the spin density carried by O increases or the spin density carried by Fe decreases, the
reactivity of the catalyst is enhanced.
269 Book of Programme and Abstract for TACC2008 [1] Dupont, J.; de Souza, R. F.; Suarez, P. A. Z. Chem. Rev. 2002, 102, 3667-3692.
[2] Miao, W. S.; Chan, T. H. Adv. Synth. Catal. 2006, 348, 1711-1718.
[3] Geldbach, T. J.; Dyson, P. J. J. Am. Chem. Soc. 2004, 126, 8114-8115.
[4] Baleizao, C.; Gigante, B.; Garcia, H.; Corma, A. Tetrahedron 2004, 60, 10461-10468.
[5] Hu, X. B.; Li, H. R.; Wang, C. M. J. Phys. Chem. B 2006, 110, 14046-14049
[6] Hu, X. B.; Li, H. R. J. Phys. Chem. A 2007, 111, 8352-8356.
[7] Hu, X. B.; Li, H. R.; Zhang, L.; Han, S. J. J. Phys. Chem. B 2007, 111, 9347-9354.
[8] Hu, X. B.; Li, H. R.; Wang, C. M.Chem. Phys. Lett. 2006, 426, 39-42
PO-203
Research on ammonia nitrogen pollution forecast Based on RBP neural network model
Feng Xiujuan1,2,*; Zhu Yichun2;Tao tao1; Du Li2
1. School of Environmental Science and Engineering, HuaZhong University of Science and Technology,WuHan HuBei
430074;
2.School of Architectural and Mapping Engineering, Jiangxi University of Science and Technology, Ganzhou Jiangxi
341000
The ion rare earth in-situ soaking ore craft is from natural buries under the condition in the non-isotropic ore body to
leach the rare-earth salts with the leaching agent one mining method. Soaked the ore fluid to select is the sulfuric acid
ammonium salt, the ammonium salt causes the ammonia nitrogen pollution to the mining area surface water, this article
has utilized in the artificial neural networks theory and method radial direction primary function law (RBF) has
established the surface water quality appraisal RBP neural network model, has carried on the forecast to the Jiangxi rare
earth mining area surface water ammonia nitrogen pollution condition. The result indicated that, with the RBP neural
network model appraisal rare earth mining area surface water ammonia nitrogen pollution forecast result and the actual
mining pollution condition match case, in-situ soaks the ore technology for the improvement, reduces the environmental
pollution, has the practical application value.
PO-204
Modulatory ion binding sites in the ligand binding domain of glutamate receptors of the kainate subtype:
dynamics and thermodynamics
Ranjit Vijayan and Philip C. Biggin
Ionotropic glutamate receptors (iGluR), activated by the amino acid L-glutamate, form a large family of ligand gated ion
channels that mediate the majority of excitatory neurotransmission in the brain. Pharmacologically, the iGluR family is
broadly categorized as α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), N-methyl-D-aspartate (NMDA)
and kainate, based on selectivity. Ions play a modulatory role in many receptors. Recent studies have shown that kainate
receptors, but not AMPA or NMDA receptors, require both Na+ and Cl- in the extracellular region to function. Whilst only
the anion binding site was identified, it was suggested that both anions and cations bind in the ligand binding domain [1].
Using computational approaches
[3]
, we identified two cation binding sites located symmetrically opposite the anion
binding site and within the same dimer interface cavity. Multiple molecular dynamics simulations and relative binding
free energy calculations using thermodynamic integration were performed to study the anion and cation binding sites in
270 Book of Programme and Abstract for TACC2008 detail. Simulations confirm that the identified locations are indeed cation binding sites. The rank order of binding for
alkali-metal ions was determined which is indicative of their binding affinities. Electrostatic calculations and free energy
profiles suggest that cations bind first followed by the anion. The computational results have now been confirmed using
electrophysiological and crystallographic data [2].
[1] A. J. R. Plested and M. L. Mayer. Structure and mechanism of kainate receptor modulation by anions. Neuron,
53(6):829–841, Mar 2007.
[2] A. J. R. Plested, R. Vijayan, Philip C. Biggin and M. L. Mayer. Molecular basis of kainate receptor modulation by
sodium. Neuron, 2008 (In Press).
[3] R. Vijayan, A. J. R. Plested, M. L. Mayer and Philip C. Biggin. Modulatory ion binding sites in the ligand-binding
domain of kainate receptors: dynamics and thermodynamics. (Manuscript in preparation).
PO-205
Hybrid Hamiltonian Replica Exchange molecular dynamics simulation method employing the Poisson–Boltzmann
model
Yuguang Mu
A hybrid Hamiltonian replica exchange molecular dynamics simulation scheme based on explicit water model hybrided
with Poisson–Boltzmann model is brought out. In this method the motions of atoms are governed by potential energy
obtained from explicit water model. However, the exchanges between different replicas under different temperatures are
controlled by the solvation energies of the solute calculated using the Poisson–Boltzmann model. In order to get the
correct canonical ensembles, the van der Waals radii, which are used to define the dielectric boundary, have to be
optimized. The conformational spaces of three distinct pentapeptides, Met-enkephalin, alanine 5, and glycine 5, are
explored. We find that with the optimized radii the structural ensembles are nearly identical to those obtained by standard
replica exchange simulations while the number of replica needed is reduced greatly. Moreover reversible folding of a
beta-hairpin peptide, chignolin, is demonstrated. Initiated from extended structures the peptide folded
and unfolded
several times in 7 out of 8 replica trajectories. Compared with 130ns standard replica exchange simulation using 24
replicas on the same system the hybrid Hamiltonian replica exchange molecular dynamics simulation presents consistent
results.
[1] Yuguang Mu, Ye Yang and Weixin Xu, Hybrid Hamiltonian Replica Exchange Molecular Dynamics Simulation
Method Employing Poisson-Boltzmann Model, J. Chem. Phys. 127 (2007) 084119-7.
[2] G. Biukovic, M. Rossle, S. Gayen,Yuguang. Mu, and G. Grueber,
Small-Angle X-ray Scattering Reveals the Solution Structure of the Peripheral Stalk Subunit H of the A1AO ATP
Synthase from Methanocaldococcus jannaschii and Its Binding to the Catalytic A Subunit, Biochemistry 46 (2007)
2070-2078.
[3] Yuguang. Mu, L. Nordenskiold and JP Tam,
Folding, misfolding and amyloid protofibril formation of WW domain
FBP28 Biophysical Journal 90 (2006) 3983-3992.
[4] Yuguang. Mu, PH. Nguyen and G. Stock, Energy landscape of a small peptide revealed by dihedral principal
coordinate analysis Proteins: structure, function, and bioinformatics. 58 (2005) 45-52.
PO-206
Evolutionary changes of chloroplast metabolic structure enable stable photosynthetic rates under environments
which can cause high rates of mutation
Zhuo Wang1,2, Qi Chen1, Xin-guang Zhu3, Dongqing Wei1, Yixue Li2, Lei Liu2
271 Bo
8 1
College of life science andd technology, Shanghai Jiaoo Tong Univerrsity.
2
Shanghai Ceenter for Bioinnformation Tecchnology.
3
Department of Plant Bioloogy, Universitty of Illinois at
a Urbana-Chaampaign
e
from cyanobacteria
c
a as a result off endosymbio
osis. Our previious study has suggested th
hat chloroplasst
Chloroplast evolved
metabolic nettwork, compaared to its anccestor cyanobacteria, becam
me denser aroound the Calvvin cycle thou
ugh the overalll
metabolic nettwork becamee looser. We hyypothesize thaat such changees in chloroplaast metabolic structure enab
ble chloroplasst
capacity of keeeping relativee stable photoosynthetic ratee under mutational pressure. We use Fluxx Balance Anaalysis (FBA) too
test this hypotthesis by com
mparing metabolic networks of chloroplasst and one reprresentative cyyanobacteria Synechococcu
S
s
sp. WH8102 (syw).
(
o chloroplast and syw werre reconstructted based on Database of Chloroplast/P
Photosynthesis
The metaboliic networks of
Related Genees and KEGG database resppectively. We use FBA to simulate
s
the flux
fl distributioon in the two networks, andd
evaluate the flux
f
variation under differeent in silico sinngle-enzyme knockouts. Thhe target funcction is maxim
mization of thee
rate of phospphoglycerate (PGA)
(
formaation, which is
i the key steep of CO2 fixxation. Constrraints of fluxees in differennt
reactions werre extracted byy literature surrvey.
n Calvin cycle including tthe rate of PG
GA formationn,
Our FBA anaalysis suggestted a) Chlorooplast has higgher fluxes in
compared to syw; b) Fluxees in Calvin cyycle of chlorooplast show hiigher resistancces to null muutation compaared to syw; c)
c
o null mutationn than those ooutside Calvin
n cycle in bothh
Fluxes througgh reactions inn Calvin cyclee show higherr resistance to
chloroplast annd syw.
c
a suggested thhat the changes of metabolicc
In conclusionn, the FBA on metabolic neetworks of chlloroplast and cyanobacteria
structure enabble chloroplasst keep more robust and stabble photosynth
hesis under ennvironment whhere higher raate of mutationn
is possible, e.g. when UV light
l
is abundaant.
PO-207
S
of Optiical Stability of Pyoluteorin(Plt)
Theoretical Study
Congying Daai1,2, Xue-hongg Zhang*1, Xijjun Wang1, JJJ Zhu2 and DQ
Q Wei*1
1
College of Life
L Science annd Biotechnology, Shanghaai Jiao Tong University,
U
Shaanghai, China;;
2
Henan Norm
mal University,, Xinxiang, Chhina and Statee University of
o New York at
a Stony Brookk, USA
Plt) is a new biological
b
pessticide which is easily decomposed in light.
l
In this ppaper, we rep
port theoreticaal
Pyoluteorin(P
studies of optical stability of Plt and itts potential suubstitute comp
pounds using DFT methodd at B3LYP/6-31G(d) levell.
w calculatedd which is fou
und to be acceessible withinn the energy rang
r
of visiblee
Firstly, the firrst excited ennergy of Plt was
light wave. Then,
T
some similar compoounds(See bellow, Fig.1-8) were proposed and their first excited energies weree
calculated. Thhe pyrrole grroup was kept in designingg new compo
ounds becausee it was thouught to be imp
mportant for itts
biological acttivity. Results show that twoo of designed compounds should
s
be stable in visible liight by compaaring their firsst
excited energgies with the visible light wave energy range. But their
t
biologicaal activity reqquires furtherr experimentaal
studies.
Energy off the first excitted state(*10-19J)
plt
4.86
#5
5
4.95
#1
4.27
#6
6
4.95
#2
5.57
#7
7
4.80
272
2 Bo
8 Fig.1 Plt
OH
NC
#3
7.17
#8
8
4.53
#4
4.86
VLE*
V
2.84~4.97
Cl
Cl
OH
Cl
Cl
N
H
OH
N
O
OH
#1
#
#2
#3
Cl
Cl
Cl
Cl
CH3
#5
C
O
O
#
#6
OH
Cl
N
OH
O
Cl
CN
OH
N
OH
#44
OH
OH
Cl
O
CN
N
H
O
OH
C(CH3)3
N
H
O
#7
OH
O
#88
[1] Vladimir Kocourek, Jana Hajslovaa, Katerina Hooladova, Jan Poustka. Jouurnal of Chroomatography A,
A 1998, 8000,
297–304
[2] He,Yanjinng ,Hu,Hongboo, Xu,Yuquann,Zhang,Xue-hhong. Agrocheemicals, 2006, 45, 155-157
PO-208
Multiscale Simulations
S
o Shock and
of
d Thermal Decomposition
n of Energettic Materialss
1
2
1*
Xi-Jun Wangg , Lai-Yu Luu , Dong-Qingg Wei
1
College of Life
L Science and Biotechnnology, Shangghai Jiaotong
g University, Shanghai ,Chhina;
2
Sichuan Uniiversity, Chenngdu, China
wang.xijun@
@hotmail.com
m
In this paperr, atomic simuulation study of shock andd detonation of solid enerrgetic materiaals were revieewed and new
w
progresses weere reported.
t proceduree of detonatioon of condennsed energeticc materials , C-J
C model annd Z-N-D mo
odel had beenn
To describe the
employed succcessively, bassed on the appproximation of
o “stable deto
onation in onee dimension”,, in which threee stages weree
defined: the shock and coompress zone,, detonation reaction
r
zone, and Taylor expansion zoone. Howeverr, the detail of
o
l
We havve studied the changes of properties
p
of nnitrosamine compounds(fo
c
or
detonation prrocess is still known very little.
example, nitrromethane, TA
ATB and HMX) under extrreme high preessure using classical
c
MD and the first principle MD
D
with DFT undder periodicall boundary coondition, respeectively. We found
f
that som
me specific boonds, i.e. N-N
N in HMX, aree
significantly changed withh increasing of
o pressure. Recently,
R
a neew multiscalee simulation method nameed MSST was
onation of coondensed nitroomethane witth the densityy
formulated by Reed etc. to study the detail of shoock and deto
metallic layer was
w found in tthe process off compressionn.
functional-based tight-bindding method (DFTB). A traansient semim
However, moore studies are needed to expploring the shocked materiaals.
c
waas also used to
t explore thee mechanism of decompossition and sen
nsitivity of thee
The electroniic structural calculation
energetic com
mpounds. ”Thee Principle off the Smallest Bond Order (PSBO)” has been widely uused to find trigger
t
bond inn
molecules off energetic coompounds annd characterizze their sensitivities. Accordingly, N-N
NO2 and C-N
NO2 bond inn
nitrosamine compounds
c
orr nitro compouunds were thoought to break
k firstly in theermal decompposition. How
wever, quantum
m
273
3 Book of Programme and Abstract for TACC2008 chemistry computations also show that several other path of decomposition are possible. Then “the least activation
energy” was proposed to characterize the sensitivity of energetic Compounds. However, further study combined of
theoretical and experimental is needed to get more insight in the thermal decomposition.
[1] Hong Liu, Dongqing Wei, Jijun Zhao and Zhizheng Gong, “Ab Initio MD Studies of Nitromethane Under
Compression”, Chinese Journal of High Pressure Physics, 18，319(2004); - Hong Liu, Jijun Zhao, Guangfu Ji, Dongqing
Wei, Zizheng Gong, “Vibrational properties of molecule and crystal of TATB: A comparative density functional study”,
Phys. Lett. A, 358, 63–69(2006); Hong Liu, Jijun Zhao, Dongqing Wei, Zizheng Gong, “Structural and Vibrational
Properties of Solid Nitromethane under High Pressure by Density Functional Theory”, J. Chem. Phys., 124,
124501(2006); Lian Dan, Lu Lai-Yu, Wei Dong-Qing. High-Pressure Behaviour of β-HMX Crystal Studied by DFT-LDA,
Chinese Phys. Lett. (2008)25, 899-902
[2] Evan J. Reed, M. Riad Manaa, Laurence E. Fried. Nature Physics, (2008) 4, 72-76
[3] XIAO Ji-jun, LI Ji-shan, Theoretical Identification for Impact Sensitivity--from Thermodynamic Judge to Kinetic
Judge, Chinese Energetic Materials, (2002) 10, 178
PO-209
Learn on the fly technique combined with QM/MM approach: Defects in semiconductors at finite temperature
Martina Miskufova
Chemistry Department, University College London
Learn on the fly (LOTF) is a novel hybrid scheme for performing molecular dynamics (MD) calculations on large
systems which contain regions that require quantum mechanical (QM) treatment. For system sizes which are too large to
be treated purely at the QM level, a class of hybrid techniques known as QM/MM is commonly employed. QM/MM
methods describe the active region at the QM level and the remainder of the system at the molecular mechanics (MM)
level, with some additional terms in the Hamiltonian describing the interaction between the two. The QM region usually
includes any part of the system that cannot be described with sufficient accuracy at the MM level. Examples of such
situations include ligand binding to an active site in protein modeling, or bond breaking associated with defect diffusion
in solids. The QM/MM approach allows one to achieve QM accuracy with relatively modest computational effort.
While QM/MM methods have proven successful, they suffer a number of shortcomings stemming from the treatment of
the QM-MM boundary. LOTF aims to reduce these boundary effects by performing at each step two QM/MM
calculations with different sizes of the QM region, and carefully considering in the case of each atom which of the two
calculations yields a force that is both accurate and free of boundary effects. Another feature of the LOTF scheme is the
extrapolation of the force calculation for a number of MD time steps, using an adjustable potential, and thus speeding up
the calculation. Examples of previous applications include silicon vacancy diffusivity and crack propagation in silicon.
LOTF has been interfaced with Chemshell, a popular and versatile QM/MM program, in the current work, greatly
increasing the range of calculations that can be performed with LOTF. The details of the implementation will be
presented here, as well as the initial results of the LOTF studies of defects in semiconductors.
PO-210
Molecular Modelling of Alginate Oligosaccharides in the EPS Matrix
Hoda Abdel-Aal Bettley and Richard A. Bryce
School of Pharmacy and Pharmaceutical Sciences, University of Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom
274 Book of Programme and Abstract for TACC2008 Alginic acids are helical heteropolysaccharides comprising alternating blocks of α-(1→4)-linked L-guluronic acid (G)
and β-(1→4)-linked D-mannuronic acid (M). These biopolymers occur in high abundance in nature, from seaweeds to
bacteria. Alginate copolymers form a major constituent of the extracellular polymeric substances (EPS) matrix of
microorganisms such as Pseudomonas aeruginosa. A molecular level understanding of the properties of alginate
polymers would lead to insights into their physical behaviour, which is dominated by their ability to coordinate divalent
cations, notably calcium, and thus form gels. However, experimental techniques have struggled to characterize these
polysaccharide gel systems. Therefore, molecular modeling methods, and in particular molecular dynamics, are well
suited to studying these flexible systems in aqueous solution and their interaction with ions.
We perform parametrization of a molecular mechanical (MM) force field against high level quantum mechanical
calculations. The model is subsequently validated using available experimental data. Subsequently, we use this MM force
field to develop molecular models of alginate-like systems, with progressively increasing complexity. The four possible
uronic acid disaccharides were modelled using adiabatic mapping and molecular dynamics (MD) simulations. The
behaviour of alginic polysaccharides in aqueous solution and their ion interactions were studied, considering three
separate representative 18-mer chain, through 30 ns MD simulation; G18, (GM)9 and (G3M3)3. For comparison, replica
exchange MD simulations were performed for 6 ns on G18, and (GM)9.
Finally, we construct double-stranded alginate models composed of two hexasaccharides in an effort to explore the
existence and nature of the egg-box model. Proposed by Grant et al., this egg-box arrangement involves the packing of a
calcium ion between adjacent guluronate residues, two from each alginate chain. Nevertheless, there still remains debate
over the exact measurement of calcium in this system, whether it can be described as an egg-box, and the number and
identity of corresponding oxygens involved. Our simulations clearly predict the existence of an egg-box formation in the
[G6]2 model and describe in detail its molecular features and dynamics. There is also growing evidence of Ca2+
interaction with mannuronic-rich alginates.
Consequently, we study via MD the double stranded [(GM)3]2 and [G3M3]2 systems. Analysis reveals a complex
dependence of chelation site on residue type and relative sequence. We obtain structure-property relationships for the
alginate components, considering implications for protein-carbohydrate interactions and enzyme activity in the EPS.
PO-211
Phase Equilibria Of Mixtures Of Non-Polar Molecules: CO2, CH4, C2H6, and CO2 + CH4
Hainam Do
School of Chemistry, University of Nottingham
Phase equilibria properties of carbon dioxide, methane, ethane, and binary mixture of carbon dioxide-methane were
obtained by using NVT-Gibbs ensemble Monte Carlo simulations. Literature data for the effective pair potentials were
used to describe the interactions of pure substances. For carbon dioxide, the EPM potential model was employed. TraPPE
potential was used to model the interaction of methane and ethane. The phase equilibrium properties of carbon dioxide,
methane and ethane were calculated. Their critical temperature and critical density were also predicted. For carbon
dioxide, the simulated results agree very well with the results reported by the author of the EPM model within the
statistical uncertainties. It was found that the EPM model slightly underestimates the vapour pressure of carbon dioxide,
and could be use to reproduce the heat of vaporization within the statistical uncertainties. It was also found that the EPM
model slightly overestimates the critical temperature, and slight underestimates the critical density of carbon dioxide. The
TraPPE potential can be used to reproduce the phase coexistence and critical properties of methane with very small error
(less than 2%). For ethane, the TraPPE potential successfully reproduced the liquid densities, but gas densities showed a
large deviation from experimental data. The vapour-liquid equilibrium of the binary mixture, carbon dioxide-methane,
275 Book of Programme and Abstract for TACC2008 was predicted using EPM potential for carbon dioxide and TraPPE potential for methane. The interaction between carbon
dioxide and methane was estimated from the pair potentials of the pure components using common mixing rules without
any adjustable binary parameters. Although there was not any literature data to compare with the simulated results for the
binary mixtures, their critical point coexistence curve shows a good trend in comparison to the critical point coexistence
curve of the pure components.
PO-212
Mechanistic Investigation of Methyltrioxorhenium-Catalyzed Olefin Cyclization
Yi Luo, Satoshi Maeda, and Koichi Ohno
Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
The methyltrioxorhenium (MTO)-catalyzed epoxidation of olefin (oxygen transfer) with H2O2 has been a fascinating
research topic for a long time because of its not only scientific interest but also industrial importance. It is arguable
whether such oxygen-transfer reaction follows concerted or stepwise mechanism. The related mechanistic studies usually
imply the rhenium peroxides, such as I in Chart 1, as an active species in the oxygen-transfer process. This led the
scientists to use MTO as a catalyst in certain organic reactions that do not involve peroxide. Motivated by the
isoelectronic principle, efforts have been made for II and III (Chart 1), analogous to I, with the aim of exploring their
reactivities. Like the I, the II and III may also transfer NR or CHR group to electron-rich acceptor, such as olefin. It was
computationally suggested that the I- and II-catalyzed group-transfer events followed different mechanism, which caused
us to wonder the situation of the III (R = H) involved reactions. In this study, the reactions shown in Scheme 1 are
computationally investigated. The scaled hypersphere search (SHS) method[1,2] has been used to explore the reaction
potential energy surface (PES). Both concerted and stepwise reaction pathways are discovered. Such PES will be
presented in detail.
[1] For the SHS method, see: (a) Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277. (b) Maeda, S.; Ohno, K. J. Phys.
Chem. A 2005, 109, 5742. (c) Ohno, K.; Maeda, S. J. Phys. Chem. A 2006, 110, 8933.
[2] For applications of the SHS to transition-metal complex system, see: (a) Maeda, S.; Ohno, K. J. Phys. Chem. A 2007,
111, 13168. (b) Luo, Y.; Ohno, K. Organometallics 2007, 26, 3597. (c) Luo, Y.; Ohno, K.; Maeda, S. J. Phys. Chem. A
2008, 112, (in press).
PO-213
Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Lipase catalysis reactions
Xinchi Hou2,Jingfang Wang1,Dong-Qing Wei1*
1College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai ,China;
2Liaoning University, China
The QM/MM method, which takes advantage of the accuracy of QM method and high efficiency of MM method, has
been proven to be a mighty tool for molecule simulations and widely used in research of chemical reactions and biologic
macromolecules especially the mechanisms of enzyme catalysis reactions.
Lipase was one of the important enzymes for various industries. It has merits of highly active,good specificity,high
276 Book of Programme and Abstract for TACC2008 enantioselectivity and can find wide applications in chemical engineering and food industry,etc.Our study is investigate
the lipase catalysis reactions in different conditions by QM/MM method.The role of the active-site interactions in
different states is discussed . Compared with the previous correlative experiments, the result would demonstrate the
transformation rules of pivotal properties in the reactions .It would provide significant insights into the origins of lipase
catalysis and play an important role in the further research on the relationship between the enzyme and engineering.
PO-214
A simplified tether model for bio-molecular motor transporting cargo
Li Fang-Zhen, Jiang Li-Chun
School of Computer Science & Engineering, Shandong Economic University 7366 Er Huan Dong Rd, Jinan 250014,
China
Bio-molecular motors are proteins or protein complexes that function as transporting engines in biological cells. In this
article we model the tether between motor and its cargo as a symmetric linear potential. Different from Elston and
Peskin’s work for which performance of the system was discussed only in some limiting cases, our study produces
analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which
makes it possible to discuss dynamics of the motor-cargo system in detail. It turns out that the tether strength between
motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed
by former researchers yet. Value of the threshold depends on diffusion coefficients of cargo and motor and also on the
strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when strength of the
ratchet tends to infinity.
PO-215
Preliminary study of the function of phosphorothioation of DNA in bacteria
Hui Gu, Xijun Wang, Congying Dai, Dongqing Wei
College of Life Science and Biotechnology, Shanghai Jiao Tong University Shanghai 200240, China
Biochemists and gene therapy researchers have been making DNA
bearing phosphorothioates in laboratories for decades. Because this
functional group confers stability against nucleases, it has many
applications in antisense studies. However, lately microbiologist
Zixin Deng and Wang et al.[1] have discovered that some bacterial
DNA contains phosphorothioate linkages (see Fig.1), the first known
physiological modification of DNA’s backbone rather than
synthesized modification.
What is the purpose of the newfound
backbone motif? Maybe phosphorothioates defends DNA against
nucleases, similar to the host defense mechanism “restriction and
modification system” of DNA methylation.
In order to uncover these puzzles, quantum chemical method at
DFT/STO-3G level was used to investigate the structural differences
Fig.1 SULFUR SURPRISE
between unmodified DNA and DNA with phosphorothioate linkages
from those related bacteria. And then the interactions between such two types of DNA and the nucleases will be studied
respectively by means of molecular dynamics (MD) simulation. Our preliminary calculation results show us that the
non-bridging oxygen atom (unmodified oligodeoxyribonucleotide) bears a higher negative charge than the non-bridging
277 Book of Programme and Abstract for TACC2008 sulfur (modified type) and that the former structure contains a higher energy than the latter one.
This dinucleotide, which occurs naturally in bacterial genomic DNA, possesses a sulfur atom in place of one of the
non-bridging oxygen atoms on its phosphate group.
[1] Lianrong Wang. et al. Phosphorothioation of DNA in bacteria by dnd genes. Nat. Chem. Biol. 3, 709~710 (2007).
[2] Fritz Eckstein. Phosphorothioation of DNA in bacteria. Nat Chem Biol. 2007 Nov; 3(11):689~690
PO-216
Molecular Dynamics of the Rab5a A30P Polymorphism and its Affect on Active Site
Ke Gong, Bei Tang and Dongqing Wei*
College of Life Sciences and Biotechnology Shanghai Jiaotong University, Shanghai 200240, P. R. China
The Ras-like human GTPase Rab5a is related to early endosome fusion in endocytosis and budding process. Early
biochemical data show that the A30P mutant can seriously reduce its hydrolysis activity while stimulates its binding
rate.[1] Here we performed molecular dynamics simulations for the wildtype and the A30P with and without ligand at
298K to see how this polymorphism affects its structure and biochemical changes. [2] The result shows that replacing
Ala with Pro residue changes its structure fluctuation in the ligand-binding domain. The simulation also shows a greater
pocket distance in A30P mutants that may lead to more chances for GTP bind to the protein. Moreover, the analysis of
hydrolysis residues and the waters around reflect a difficulty on GTPase process in A30P mutants.
[1] Liang, Z., Mather, T., and Li, G. (2000) Biochem. J. 346, 501–508
[2] Zhu, G., Liu, J., Terzyan, S., Zhai, P., Li, G. & Zhang,X. C. (2003). J. Biol. Chem. 278, 2452–2460.
PO-217
The role of charge seperation of dipole in the ferroelectric liquid crystal phases
Jin-He Hu1,2, Li-Wei Yan1,2，Dong-Qing Wei1*, Zi-Zheng Gong3, Yong-Xin Guo2
1. College of Life Science and Biotechnology, Shanghai Jiaotong University, China 200240.
2. Physics Department, Liaoning University, Shenyang, China.
3. China Academy of Space Technology, Beijing, China
A recent work[1] by our group show that the charge seperation of dipole particle plays a significant role on the phase
transition of ferroelectric liquid crystal phases. Molecular dynamics (MD) simulations were performed and the real
dipoles were used with a reduced distance between the two charges compared to the previous work[1]，so that it is closer
to the point dipole model. The potential energy consists of the site-site Lennard-Jones potential and electrostatic
contribution of partial charges. Results show that chain-like structures in low density regime, nematic, columinar and
ferroelectric solid phase are formed, just as previous work[1]. We also find a smectic phase. Details analysis were made
regarding fluctuation of the order parameters
P1
and
P2
as functions of densitty.
[1] D. Q. Wei, Y. J. Wang, L.Wang ,Z. Z.Gong ,and Y. X. Guo, Phys. Rev. E. 75,061702(2007)
PO-218
The mechanism of formation of the α-hydrophosphonate: a theoretical study
278 Book of Programme and Abstract for TACC2008 Zeng zhiping, Zhao YuFen
Department of Chemistry, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China. Correspondence e-mail:
[email protected]
Since its discovery in 19481, the Pudovik reaction has become one of the most versatile opproaches to form the
phophorus-carbon bond. However, the mechanism is a debatable subject.
O
O
P
O
O
C
O
O
O
P
C
O
O
O
O
P
C
Scheme 1
O
scheme 2
A total of four distinct mechanisms (scheme 1) have been proposed to date, including two stepwise paths (A and B ), a
concerted five-member ring transition-state path C and four-member ring transition-state path D.
'H NMR and IR spectroscopic studies of the alkali metal salts of dialkyl phosphites suggest that predominant form for the
anion is trivalent (P-O-M not M-P=O).our calculation based upon DFT2 study also confirms the experiment results.
[1] A.N.PUDOVIK., Izv.Akad.Nauk SSSR, Otd.Khim.Nauk USSR 1948, 151.
[2] Gaussian, Inc.etc.
PO-219
The Role of Molecular Conformation in the Eleetronic Transport Properties of BPE Molecular Junction
Wu, Yu
Institute of Anpplied physics, Guizhou Education college, Guiyang, 550003. China
[email protected]
Based on the hybrid density functional theory and Green's function theory, we systemic studied the electronic transport
properties of bis-(4-mereaptqphenyl)-ether (BPE) molecular junction, and discussed the role of angle between two
phenyls. The difference of the influence on the conductance from contact and BPE confqrmation also were presented.
Beside the cqntact between the molecules and electrodes, we found that the conformation of the molecular inside the
electrodes played a role in the electronic transport of molecular junction. Perhaps it is very useful in the future design of
molecular devices.
PO-220
Preliminary Studies OF Cytochrame P450 and Metobolizing Mechanism of CYP2E1
Jue Li, and Jing-Fang Wang, Dong-Qing Wei
Shanghai Jiaotong University, Department of Bioinformatics and Biostatistics, College of Life Sciences and
279 Book of Programme and Abstract for TACC2008 Biotechnology, No.800 Dongchuan Road, Minhang District, Shanghai, China
The metabolism of drugs in humanbeings involves a series of enzymes. The cytochrome P450s (CYPs) are considered to
have closest relationships with drug metabolism. Among CYPs, CYP2E1 is responsible for metabolizing four percent
drugs, for example, narcotic, ethanol, acetaminophen, and nitrosamine which is carcinogenic. In our investigations,
CYP2C5 whose crystal strucutre is know was used as a template to build a homology modeling of CYP2E1.
Subsequently, molecular docking was employed to place 12 substrates to the binding site of CYP2E1 using our in-house
software Shanghai Molecular Modeling (SAMM), and the binding pockets were fully explored. By hydrophilic or
hydrophobic surface analysis, six molecules (methoxyflurane, acetaminophen, aniline, benzene, chlorzoxazone, ethanol,
N,N-dimethyl formamide and theophylline) were selected to perform 4ns molecular dynamics simulations. Compaired
with previous photoaffinity labeling studies，it was find that Leu368 plays a central role in both offering the hydrophobic
surface and interacting with substrates. And some residues (Ile115, Phe298, and Val364) can stablize substrates by
forming corresponding hydrogen bonds. In addition, Ile115, Phe116, Asp295, Phe298, and Leu368 were also found to
have close relationships with the interacitons of CYP2E1 with substrates. All these findings are of some help, eventually,
for conducting mutagenesis studies, providing insights into personalziation of drug treatments and stimulating novel
strategies for finding desired personalized drugs.
[1] Jin-Young Park and Dan Harris, Construction and Assessment of Models of CYP2E1: Predictions of Metabolism
from Docking, Molecular Dynamics, and Density Functional Theoretical Calculations, J. Med. Chem.
2003(46):1645-1660.
[2] Samuel L. Collom, Arvind P. Jamakhandi, Alan J. Tackett, Anna Radominska-Pandya, and Grover P. Miller,
CYP2E1 Active Site Residues in Substrate Recognition Sequence 5 Identified by Photoaffinity Labeling and Homology
Modeling, Arch Biochem Biophys. 2007 March 1; 459(1): 59–69.
PO-221
THE APPLICATION OF ANN TO QSAR AND ADME/T
Shuhao Yu, Dong-Qing Wei*
Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University ,400 Dongchuan Road., 200240 Shanghai,
China
We are making efforts to implent some non-linear regression methods in the SAMM software(Shanghai Molecular
Modeling), developed by our group. It has been shown that the artificial neural network (ANN) is very useful in
selecting sutaible QSAR descriptors[1]. Usually, the partial least-squares (PLS) has been used to find the relationship
between the biological activity and strcutural information of molecules[2-5]. We show ANN could be a practical
alternative. This BP artificial neural network is programmed and integrated into SAMM with a user interface. A series
of tests show that ANN perform quite decently.
Currently, we are developing software to make ADME/T prediction.
[1] Suzanne Sirois, S., Tsoukas, G.M., Chou, K.C., Wei, D.Q., Boucher, C. and Hatzakis, G.E. “Selection of
molecular descriptors with artificial intelligence for the understanding of HIV-1 protease peptidomimetic
inhibitors-activity”, Medicinal Chemistry, 2005, 1, 173.
[2] Jacobs, M. N., G. T. Nolan, et al.. "Lignads, bacteriocides and organochlorine compounds activate the human
pregnane X receptor (PXR).". Toxicol Appl Pharmacol.2005,209,123.
[2] Colman, P. M .Influenza virus neuraminidase: Structure, antibodies and inhibitors . Protein Sci. 1994,3,1687.
[4] Von I M, Wu W Y, Kok G B.A novel class of herbicides, Specific inhibitors . Nature, 1993,363,418
[5] Lewis, D. F., C. Ioannides, et al. "Quantitative structure-activity relationships in a series of endogenous and synthetic
steroids exhibiting induction of CYP3A activity and hepatomegaly associated with increased DNA synthesis." . Steroid
280 Book of Programme and Abstract for TACC2008 Biochem Mol Biol.2000, 74,179.
PO-222
Molecular Dynamics Simulations of Protein Tyrosine Phosphatase 1B: From the Active Site to the Second
Phosphatyrosine Binding Site
Jing-Fang Wang1,2 and Dong-Qing Wei1,2
1.
2.
Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Science Chinese Academy
of Science, Shanghai 200031, China
Protein tyrosine phosphatase 1B is a significant drug target for type II diabetes and obesity. It is a major negative
regulator of both insulin and leptin simulated signal transduction. The objective of the current study was to investigate
the structural factors responsible for the high inhibitory potency and selectivity of the inhibitors INTA and INTB, the
most potent and selective PTP1B inhibitors so far, using series molecular dynamics (MD) simulations. Long time scale
MD simulations had been simultaneously performed on PTP1B complexed with inhibitor INTA and INTB, as well as
uncomplexed PTP1B, with the purpose of analyzing the interactions between target protein and inhibitors, and revealing
the possible mechanism of their inhibition and recognition. Additionaly, to investigate the most significant collective
modes of motions of all the systems, the covariance matrix corresponding to the Ca-atom coordinates was calculated and
the essential dynamics analysis was utilized. By diagonalizing the covariance matrix, the anharmonic and large-scale
motions of the target protein are isolated from the harmonic and small-scale motions. It is found that the flexibility of the
WPD-Loop decreases upon ligand binding. However, the fluctuations in R-Loop and S-Loop increase sharply, which
indicates that the aforementioned loops have special conformation motions for the substrate binding. In addition, strong
fluctuations in W-Loop, a long loop far away from the inhibitor binding site, has been detected in all the three models.
All these findings are in good agreement with the previous experimental results, and may provide a novel strategy for
developing inhibitors by targeting not only both of the two aryl phosphate binding sites but also the adjacent peripheral
sites.
Keywords: Protein tyrosine phosphatase 1B; Molecular dynamics Simulations; Essential dynamics analysis; Mechanism
of the substrate inhibition and recognition; Flexibility of WPD-Loop; Novel strategy for developing PTP1B inhibitors
PO-223
Database of the Cytochrome P450 SNPs and Their Catalytic Activity
Tao Zhang, Dongqing Wei，Yuan Shang，Yuqing Zhong，Yukun Wang，Xiangyu Wang
Cytochrome P450 is an important monooxygenase that metabolizes variety of substrates including endogenous and
exogenous compounds. In human the Cytochrome P450 play a significant role in the biological process especially in the
xenobiotic detoxification and steroid hormones synthesis. Single nucleotide polymorphisms (SNPs) represent a high
natural genetic variability in human genome, which result in the dramatically change of protein function. The specialized
database, which is different from other cytochroeme P450 databases, is exclusively dedicate to the change of catalytic
activity caused by SNPs of all the human cytochrome P450 subfamily. The database will cover over 6000 entries and
contain information about not only the pharmacokinetic properties of substrates or drugs, such as Michaelis-Menten
Constant (Km) and
Maximum Velocity（Vmax）but also the related allele and structure of substrates or drugs. Also the
available data in database can be retrieved together with corresponding literature reference. In addition, the database will
provide the direct links to the SNP Database in NCBI, DrugBank Database and other protein databases. The database is
designed to serve as the useful tool for studying the relationship between the SNPs and the catalytic activity of
281 Book of Programme and Abstract for TACC2008 Cytochrome P450. Meanwhile the database is helpful to develop the new drugs and select Cytochrome P450-selective
substrates or drugs for in vivo or in vitro studies. Thus the database can provide the valuable data source for studying
properties of natural and artificial Cytochrome P450 mutants using selective metabolic reactions and deventually
developing the personalized drug.
PO-224
Interaction Dynamics at different levels: protein, ligands and ion-channels
Chen, Su-Shing
PO-225
Site-Directed Drug DiscoveryÒ. A knowledge-based efficient approach for hit and lead generation to 7TM
receptors.
Thomas M. Frimurer
Computational Chemistry, 7TM Pharma, 3 Fremtidsvej, DK-2970 Hoersholm, Denmark
The identification of small focused libraries for a given target facilitates the screening and hit validation. A
knowledge-based process (Site-Directed Drug Discovery(R)) for structure-guided design of small molecule ligands for
7TM receptors has been devised to produce small diverse libraries. The process involves analysis of physicogenetic
relationships of binding sites of 7TM receptors and design of pharmacophores by incorporation of target and ligand
information. The pharmacophore queries are used for in silico screening and construction of customized small libraries
that will be illustrated for CRTH2. Initial hits obtained have been optimized into selective orally active functional
antagonists.
PO-226
Making use of full molecular symmetry in relativistic electronic structure calculations
Daoling Peng, Jianyi Ma, Wenjian Liu*
Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking
University, Beijing, 100871, People's Republic of China.
[email protected]
Under the Born-Oppenheimer approximation, the non-relativistic and relativistic molecular Hamiltonians have the same
generic second quantized form, differing only in the orbitals/spinors. Therefore it is highly desirable to have the same
algorithm incorporating the full molecular symmetry for both boson and fermion types of irreducible representations. The
key point is how to make the double point group adapted symmetry functions also form Kramers pairs such that the
resulting operator matrices have the desired structure (i.e., quaternion, complex, or real). It turns out that this can be
achieved simply by adding in an appropriate phase factor into or making a suitable unitary transformation of the
symmetry functions. As for a direct product basis (e.g., in two-electron repulsion integrals or spin-orbit coupling
integrals), a simple modification of the Clebsh-Gordan coefficients does the whole job. The scheme has been
implemented into the Beijing Density Functional program package (BDF) [1] to handle arbitrary single and double
point groups.
Illustrations are made for both spin-dependent (four- and two-component) and spin-free (scalar
relativistic and non-relativistic) ground state and time-dependent Kohn-Sham calculations.
[1] W. Liu, G. Hong, D. Dai, L. Li, M. Dolg. Theor. Chem. Acc., 96, 75 (1997).
Fingerprint and its application in similarity search
YuYao, Jing He and Dong-Qing Wei*
Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong
University, Shanghai 200240, China
A chemical fingerprint is a list of binary values which characterize a molecule. MACCS fingerprint is one of 2D
fingerprints. The MACCS keys are a set of questions about a chemical structure. The result of this, a list of binary values,
is MACCS KEY fingerprint.
Substructures matching Algorithms are mainly used in 2D substructures search which has been applied to data mining
and knowledge discovering in database. VF algorithm（Void-Filling Algorithm） is a backtracking Algorithm for the
graph isomorphism and graph-subgraph matching problems with good performance and transplantable character.
We try to use VF algorithm to MACCS fingerprint , on which we want to carry out similarity search . On the other
hand , based on known compound activities, we optimize MACCS KEY, and optimized keys which have activity
message , can forecast unknown compound activity。
The innovation of our work is that we put VF algorithm to our MACCS fingerprint processes, unlike character string
matching, VF Algorithm doesn’t need ask or search structure , and it is also improved by adding atom and bond
messages to fit chemical structure matching.
The purport is that we give a method to analyze the activities of compounds found out by structure similarity search.
Activity forecast through optimized keys can decrease the quantity of activity test and avoid its heavy workload and
long experiment period.
PO-228
Research on the IAI of substituted aromatic compounds with Topological Indices and artificial neural network*
FENG, Chang-jun
CAI, Ke-ying
School of Chemistry & Chemical Engineering, Xuzhou Institute of Technology, 221008, Xuzhou China
On the basis of the revision of Kier’s[1] atomic price, molecular connectivity index and conjugated matrix , a novel
molecular connectivity index (mG) is defined and calculated for 46 substituted aromatic molecules in this paper. The
QSBR model of biodegradation index(IAI[2])under anaerobic conditions for 46 organic pollutants is constructed from
2G, 4G, E2, E9(electrotopological state index(Ej)[3,4]) and M29(electronegativity distance vector (Mk)[5-7]) the
traditional correlation coefficient (R2) and the standard errors are 0.803 and 0.263, respectively:IAI = 0.292 - 0.089 E2 0.095 E9 -0.140 M29 + 0.030 2G - 0.003 4G, n=46, R = 0.896, F = 32.644. The result demonstrates that the model is
highly reliable and has good predictive ability from the point of view of statistics. Form the five parameters of the model,
it is known that the dominant influence factors of IAI are the molecular structure fragments: -C-, ≡C-, >C-, -N- and the
space factors of 2G, 4G for organic pollutant. The five structural parameters are used as the input neurons of artificial
neural network, and a 5: 6:1 network architecture is employed. A satisfied model can be constructed with the
back-propagation algorithm[8], the correlation coefficient R2 and the standard errors are 0.997 and 0.031, respectively.
This shows that the relationship between IAI and five structural parameters is good nonlinear correlation relationship.
The results showed that the new parameter 2G, 4G, E2, E9 and M29 have good rationality and efficiency for the IAI of
substituted aromatic compounds.
283 Book of Programme and Abstract for TACC2008 Keywords: substituted aromatic compound; biodegradation index(IAI); novel molecular connectivity index;
electrotopological state index; electronegativity distance vector
* The Stade Key Laboratory of Environmental Simulation and Pollution Control of China Project Proposal(.KJ2007001) ,
the State Key Laboratory of Pollution Control and Reuse of China Project Proposal (PCRRF07009) and Natural Science
Incubation Foundation of Xuzhou Normal University (05PLY04).
[1] Kier, L. B.; Hall, L. H. Molecular Connectivity in Structure-Activity Analysis, John Wiley, New York, 1986, pp.
69～75.
[2] Yang Hongwei,_ Jiang Zhanpeng, Shi Shaoqi, Li Ruihua. Science of the Total Environment 2006, 358, 265– 276
[3] Hall, L. H., Kier, L. B. .J.Chem.Inf.Comput.Sci.,1995, 35, 1039
[4] Hall, L. H., Kier, L. B. Brown B B. J.Chem.Inf.Comput.Sci.,1995, 35, 1074
[5] Liu,S.-S.; Yin, C.-S.; Li, Z.-L.; Cai , S.-X. J. Chem. Inf. Comput. Sci. 2001, 41, 321
[6] Liu,S.-S.;
Yin, C.-S.; Wang , L.-S. J. Chem. Inf. Comput. Sci. 2002, 42, 749
[7] Liu, S.- S.; Liu, H.- L.; Shi, Y.-Y.; Wang, L.- S. Int. Elec. J. Mol. Des. 2002, 1, 310
[8] Ruan Xiao-Gang. Neurocomputing science[M]. Beijing: National Defense Industry Press, 2006, 343～415
Notice: Prof. Feng Chang-Jun was born in Mar. 1954, and he is a professor and doctor. The mail research directions are
the design, characterization and quantitative structure-activity relationship(QSAR) of inorganic and organic
compounds.E-mail: [email protected]
PO-229
Tangled of Extended Goldberg polyhedral
Hu, Guang
Department of chemistry, Lanzhou university, China
[email protected]
Goldberg polyhedra are a kind of ‘multi-symmetric’ polyhedra, which can be used to model bio-chemical molecules,
such as virus and fullerenes. Inspired by novel experimental results, we constructed two new types of icosahedral solids
named as Extended Goldberg polyhedra. Here, we utilize even or odd tangles in knot theory as building blocks to
assembly polyhedral links on the basis of Extended Goldberg polyhedra. As results, some knotted structures including
small rings and more complicated interwoven networks are obtained by even and odd tangles, respectively. Furthermore,
the chirality determinant and the component algorithm of these links are given. This study provides insight into the
molecular design and theoretical characterization of the viral cross linking and DNA cage.
PO-230
TheoreticTheoretical Modeling of the two new mono-epoxylignans derived from the fruits of Forsythia suspensa
Vahl
Jia n Cui, Yan Zha ng, Fengjua n Zhao, Yu Xu*, Xiangla n Piao*
Institute of Chinese Minority Traditiona l Center, Central University for Nationalities , Zhongguancun South Street
No.27, 100081 Beijing, People's Republic of China
Forsythia suspensa Vahl (Oleaceae) is a climbing pla nt, which is widely distributed in China, Korea and Japan. The
extract of the dried fruits has long been used in the Chinese, Korean and Japanese folk med icines to treat gonorrhea,
284 Book of Programme and Abstract for TACC2008 erysipedas, infla mma tion, pharryngits, pyrexia, tonsillitis, and ulcer.2,3 Moreover, it has also been shown that the crude
drug exhibit potentia l antibacteria l, antiviral, choleretic and antipyretic effects. Phytochemica l studies on the plant have
shown that phenolic compounds including lignans and flavonols, one class of the major components, are responsible for
the variousbiological activities of the herb1.
The 3D structures of two new mono-epoxylignans 2, forsythialan A and B which were previously isolated by our group,
are theoretica lly investigated in the present paper by mea ns of density functiona l theory. Severa l local minima of A
and B are located on their potentia l energy surfaces. Both the calculated NMR data and IR absorptions of the global
minima of A and B are comparable with their correspond ing experimental values, which suggests the global minima
should be the most probable alternative structures for A and B.
[1] Li, Q.; Fen, W. S. J. Henan Uni. Chin. Med. 2005, 20, 78.
[2] Piao , X. L.; Moon, H. J.; Cui, J.; Piao. X. S., Bioorg. Med. Chem. Lett.2008, 18, 1980.
285 Book of Programme and Abstract for TACC2008 List of participants (Alphabetic order) Abad, Enrique
University of Oxford, UK
Abou-Rachid, Hakima
Defence R&D-Canada, Canada
Allen, Wesley
University of Georgia, USA
Allouche, Alain
Althorpe, Stuart C
Aquino, Adelia
Physique des Interactions Ioniques et Moléculaires,
France
University of Cambridge,UK
University of Natural Resources and Applied Life
Sciences,Austria
[email protected]
[email protected]
a
[email protected]
[email protected]
[email protected]
[email protected]
Ardalan, Adel
University of Tehran, Iran
[email protected]
Assadi, Amir
University of Arak, Iran
[email protected]
Islamic Azad University, Iran
[email protected]
Baerends, Evert Jan
VU University, The Netherlands
[email protected]
Bagchi, Biman
Indian Institute of Technology, India
[email protected]
Baldauf, Carsten
CAS/MPG- PICB, China
[email protected]
Bankura, Arindam
Indian Institute of Technology, India
[email protected]
Beteringhe, Adrian
Institute of Physical Chemistry, Romania
[email protected]
The University of Manchester, UK
[email protected]
Bhat, Savithri
Devi Ahilya Vishwavidyalaya, India
[email protected]
Bi, Shuping
Nanjing University, China
Bian, Wensheng
Institute of Chemistry, Chinese Academy of Sciences
[email protected]
Bichoutskaia, Elena
University of Nottingham, UK
[email protected]
Bickelhaupt, Matthias
VU University, The Netherlands
[email protected]
Blum, Lesser
University of Puerto Rico, USA
[email protected]
Baei, Mohammad
Taghi
Bettley, Hoda
Abdel-Aal
Bolesta, Alexey
Khristianovich Institute of Theoretical and Applied
Mechanics, Russia
[email protected]
Broer, Ria
University of Groningen, Netherlands
[email protected]
Brooks III, Charles L.
The Scripps Research Institute,USA
[email protected]
Brooks, Bemard
NIH, USA
[email protected]
Bryant, Stephen
NIH, USA
[email protected]
Burghardt, Irene
Ecole Normale Supérieure, France
[email protected]
Cao, Zhiwei
Tongji Univerversity, China
[email protected]
Carloni, Paolo
SISSA, Italy
[email protected]
Chan, Garnet
Cornell University, USA
[email protected]
286 Book of Programme and Abstract for TACC2008 CHAN, Kwong-Yu
The University of Hong Kong, China
[email protected]
Chandra, Amalendu
Institute of Technology, Kanpur, India
[email protected]
Chang, Yu-Chang
Institute of Chemistry, Academia Sinica,Taiwan,
[email protected]
Chao, Ito
Institute of Chemistry, Academia Sinica, Taiwan,
[email protected]
Che, Xinsheng
Shenyang University of Technology, China
[email protected]
Shu,Chen
Tongji University, China
[email protected]
Chen, Dong-ming
University of Science and Technology of China,
China
[email protected]
Chen, Feiwu
University of Science and Technology Beijing, China
[email protected]
Chen, Haifeng
Shanghai Jiao Tong University, China
[email protected]
Chen, Junxian
Inha University,Korea
[email protected]
Chen, Lan
Peking University, China
[email protected]
Chen, Qi
Shanghai Jiao Tong Univeristy, China
[email protected]
Chen, Qilong
Bio-electronic Centre of Shanghai University,China
[email protected]
Chen, Shuang
[email protected]
Chen, Su-Shing
Univeristy of Florida, USA
[email protected]
Chen, Xi
Central China Normal University,China
[email protected]
Chen, Xiangrong
Sichuan University, China
[email protected]
Chen, Xiaowu
Gilead Sciences, USA
[email protected]
Chen, Xuebo
Bowling Green State University, USA
[email protected]
Chen, Jingwen
Dalian University of Technology, China
[email protected]
Chen, Zhongfang
Rensselaer Polytechnic Institute, USA
[email protected]
Cheng, Jun
Univeristy of Cambridge, UK
[email protected]
Cheng, Ru Jen
National Chung-Hsing University, Taiwan,ROC
[email protected]
Cheng, Xiaolin
[email protected]
Cheng, Lan
[email protected]
Cheng, Shanmei
Chinese Academy of Science, China
[email protected]
Chernykh, I.G.
SBRAS, Russia
[email protected]
Christ, Clara D.
Swiss Federal Institute of Technology, Switzerland
[email protected]
Clementi, Enrico
Université de Montréal, Canada
[email protected]
Coogan, Anthony
Private library and Internet researcher
[email protected]
Cortona, Pietro
Ecole Centrale Paris, France
[email protected]
Crawford, Daniel
Virginia Technology, USA
[email protected]
Cremer, Dieter
University of the Pacific, USA
[email protected]
Csaszar, Attila
Eotvos University, Hungary
[email protected]
Cui, Qiang
University of Wisconsin, USA
[email protected]
287 Book of Programme and Abstract for TACC2008 Dabiri, Fedyeh
Islamic Azad University-Rasht Branch, Iran
[email protected]
Dai, Cong-Ying
[email protected]
Dashti, Hesam T.
University of Arak, Iran
[email protected]
Bioinformatics Institute, Singapore
[email protected]
Dastidar, Shubhra
Ghosh
Datta, Dipayan
Dawson,P. K. D.
Delgado, Alina
Indian Association for the Cultivation of Science,
INDIA
School of Natural Sciences - Chemistry, Newcastle
University, U.K.
[email protected]
[email protected]
University of Informatics Sciences,Cuba
[email protected]
Ding, Yaping
Shanghai University,China
[email protected]
Dinur, Uri
The Hebrew University of Jerusalem
[email protected]
Do, Hainam
[email protected]
Du, Xiuquan
Anhui University, China
[email protected]
Duan, Yong
UC Davis Genome Center, USA
[email protected]
Agramonte
Dunbrack, Roland
Dupuis, Michel
Ebrahimi, Pouneh
Institute for Cancer Research, Fox Chase Cancer
Center, USA
Pacific Northwest National Laboratory, USA
Gorgan University of Agricultural Sciences &
Natural Resources, Iran
[email protected]
[email protected]
[email protected]
Eliav, Ephraim
Tel Aviv University,Israel
[email protected]
Elstner, Marcus
Technical University Carolo-Wilhelmina, Germany
[email protected]
Ernzerhof, Matthias
Universite de Montreal, Canada
[email protected]
Fang, Haiping
Shanghai Institute of Applied Physics, CAS, China
[email protected]
Fang, Hong
Tongji University,China
[email protected]
Farantos, Stavros C.
University of Crete, Greece
[email protected]
Farsani, R.Eslami
Fei,Xia
Feng, Changjun
Feng, Xiujuan
Islamic Azad University-South Tehran Branch,
Iran,
CAS-MPG partner Institute for Computatinal
Biology, China
Xuzhou Institute of Technology, China
Jiangxi University of Science and Technology，
China
[email protected]
[email protected]
[email protected]
[email protected]
Filatov, Michael
[email protected]
Frenking, Gernot
Fachbereich Chemie der Philipps-Universität
[email protected]
Friesner, Richard A.
Columbia University, USA
[email protected]
Frimurer, Thomas
7TM Pharma
[email protected]
Fukuda,Ikuo
RIKEN , Japan
[email protected]
288 Book of Programme and Abstract for TACC2008 Gagliardi, Laura
University of Geneva, Switzerland
[email protected]
Gao, Hongze
Northeast Normal University, China
[email protected]
Gao, Jiali
University of Minnesota, USA
[email protected]
Gao, Junhui
Gao, Yiqin
Garcia-Cervera,Carlos
J
Gavrilenko, Vladimir
Shanghai Center for Bioinformation
[email protected]
Technology,China
Texas A&M University, USA
[email protected]
University of California, Santa Barbara, USA
[email protected]
Norfolk State University, Center for Materials
Research, USA
[email protected]
Ge, Hao
[email protected]
Ge, Xiaoxia
Weill Medical School of Cornell University,USA
[email protected]
Geerlings, Paul
Free University of Brussels, Belgium
[email protected]
Gerber, Benny
University of California, USA
[email protected]
Gerber, R.B.
The Hebrew University of Jerusalem,
Glushkov, Alexander
Odessa University, Ukraine
Goerling,Andreas
University of Erlangen-Nuremberg, Germany
Golovneva,Elena I
Branch of Russian Academy of Sciences, Russia
[email protected]
Gora,Urszula
University of Silesia, Poland
[email protected]
Gori-Giorgi, Paola
Universite Pierre et Marie Curie, France
[email protected]
Görling, Andreas
University of Erlangen, Germany
[email protected]
Goursot, Annick
Institut fédératif Charles Gerhardt, France
[email protected]
Graham,John P.
United Arab Emirates University, Al Ain, UAE
[email protected]
Gräter, Frauke
Israel
Shanghai Institutes for Biological Sciences(SIBS),
China
[email protected]
[email protected]
[email protected]
n.de
[email protected]
Groß, Axel
University of Ulm, Germany
[email protected]
Gu, Hui
[email protected]
Gu,Xin
Jilin University, China
[email protected]
Guenza,Marina
University of Oregon, USA
[email protected]
Guo, Hong
University of Tennessee, USA
[email protected]
Guo,Zhen
The University of Hong Kong, Hong Kong
[email protected]
Gwaltney, Steven
Mississippi State University, USA
[email protected]
Ha, Yong-Quan
Southeast University,China
HADA, Masahiko
Tokyo Metropolitan University, Japan
[email protected]
Halstead, S. J.
Harbin Institute of Technology,China
[email protected]
Han, Keli
Dalian Institute of Chemical Physics, China
[email protected]
289 Book of Programme and Abstract for TACC2008 Hannongbua, Supa
Kasetsart University, Thailand
[email protected]
Hase, William L.
Texas Tech University, USA
[email protected]
He, Zhitao
Harbin Institute of Technology, China
[email protected]
Helgaker, Trygve
University of Oslo, Norway
[email protected]
Hirao, Kimihiko
University of Tokyo, Japan
[email protected]
Hirata, Fumio
Institute for Moleculear Science, Japan
[email protected]
Hirata, So
University of Florida, USA
[email protected]
Hirst, Jonathan D.
[email protected]
Hobza, Pavel
Czech Academy, Czech Republic
[email protected]
Hoffmann, Mark
University of North Dakota, USA
[email protected]
Hoggan, Philip
University Blaise Pascal, France
[email protected]
Holthausen, Max C.
Frankfurt University, Germany
Hong, Jooyeon
Sookmyung Women’s University, Korea
[email protected]
Hou, Xin-Chi
[email protected]
Hou, Zhonghuai
University of Science and Technology of
China,China
[email protected]
.de
[email protected]
Hsu, Chao-Ping
Institute of Chemistry, Academia Sinica, Taiwan
[email protected]
Hu, Guang
Lanshou Univeriwty, China
[email protected]
Hu, Xingbang
[email protected]
Huang, Jingsong
[email protected]
Huang, Niu
National Institute of Biological Sciences,China
[email protected]
Huang, Xinchuan
NASA Ames Research Center, USA
[email protected]
Huang, Pei-Qiang
Xiamen University, China
[email protected]
Huang, Xur
[email protected]
Im, Suk
Kyunghee University, Korea
[email protected]
Imai, Takashi
Research Program for Computational Science, Japan
[email protected]
Jalili, Seifollah
K. N. Toosi University of Technology, Iran
[email protected]
Jansen, Georg
University Duisburg-Essen, Germany
[email protected]
Jarzecki, Andrzej
The City University of New York, USA
[email protected]
Ji, Lin
Capital Normal University, China
[email protected]
Jiang, De-en
Oak Ridge National Laboratory
[email protected]
Jiang, Jianwen
National University of Singapore
[email protected]
Kalia, Rajiv K.
University of Southern California, USA
[email protected]
Kallay, Mihaly
Budapest University of Technology and Economics,
Hungary
[email protected]
290 Book of Programme and Abstract for TACC2008 Kamiya, Katsumasa
University of Hyogo, Japan
[email protected]
Karplus, Martin
Harvard University, USA
[email protected]
Karttunen, Mikko
University of Western Ontario, Canada
[email protected]
Kato, Shigeki
Kyoto University, Japan
[email protected]
Kaupp, Martin
Universität Würzburg
[email protected]
Kim, Chan Kyung
Inha Univeristy, Korea
[email protected]
Kim, Hyung
Carnegie Mellon University, USA
[email protected]
Kim, Kwang S.
Pohang University of Science and Technology, Korea
[email protected]
Kim, Woo Youn
Pohang University of Science and Technology,Korea
[email protected]
Kim,Ho-Sung
[email protected]
Kim,Ju-Young
[email protected]
Klamt, Andreas
COSMOlogic, Germany
[email protected]
Kobayashi,Masato
Waseda University, Japan
[email protected]
Kobryn, Alexander E.
National Institute for Nanotechnology,Canada
[email protected]
Kong, Jing
Q-Chem Incorporation, USA
[email protected]
Korchowiec,Jacek
Jagiellonian University, Poland
[email protected]
Kosugi, Takahiro
Kyoto University,Japan
[email protected]
Krzysztof,Szalewicz
University of Delaware, USA
[email protected]
Kuang, Zhifeng
Air Force Research Laboratory,
[email protected]
Kumar,Anupriya
Pohang University of Science and Technology,
Korea
[email protected]
Kurnikova, Maria
Carnegie Mellon University ， USA
[email protected]
Lambert,Jean-François
Université Pierre et Marie Curie, France
[email protected]
Lazaridis,Themis
The City University of New York, USA
[email protected]
Lee, Sangyoub
Seoul National University,South Korea
[email protected]
Lee,Chewook
Sookmyung Women’s University, KOREA
[email protected]
Lee,Ikchoon
Inha University, Korea
[email protected]
Lei, zhong
East China University of Science and Technology,
China
[email protected]
Lemke, Kono H.
University of Hong Kong, China
[email protected]
Li, Baiqing
Shandong University, China
[email protected]
Li, Haiyan
Universities of Shandong,China
[email protected]
Li, Haoran
[email protected]
Li, Hui
Nanjing University,China
[email protected]
Li, Jun
Inha University, Korea
[email protected]
Li, Ruifang
Nankai University, China
[email protected]
291 Book of Programme and Abstract for TACC2008 Li, Shuhua
Li, Weikun
[email protected]
China
Li, Weixue
State Key Laboratory of Catalysis, CAS, China
[email protected]
Li, Wencheng
South China University of Technology,China
[email protected]
Li, Wenlan
Harbin University of Commerce, China
[email protected]
Li, Xuejin
[email protected]
Li, Yigui
Tsinghua University, China
[email protected]
Li, Ying
Li, Yixue
[email protected]
Li, Zhenyu
[email protected]
Li,Chengyun
Yunnan Agricultural University, China
[email protected]
Li,Fang-Zhen
Shandong Economic University, China
[email protected]
Li,Qingyu
South China University of Technology, China
[email protected]
Li,Shaopeng
Imperial College London, United Kingdom
[email protected]
Li,Shenmin
Dalian University,China
[email protected]
Li,Shu-Bai
Donghua University, China
[email protected]
Li,Wencheng
South China University of Technology, China
[email protected]
Li,Yuanxun
University of Electronic Science and Technology of
China
[email protected]
Lian, Peng
[email protected]
Liao, Rong-Zhen
Beijing Normal University,China
[email protected]
Liao,Yi
[email protected]
Lilienfeld, Anatole
Sandia National Laboratories, USA
[email protected]
Lim, Carmay
Institute of Biomedical Sciences, Academia Sinica,
Taiwan, ROC
[email protected]
Lin, I-Chun
University of Tokyo，Japan
[email protected]
Lindh, Roland
Lund University, Sweden
[email protected]
Lischka, Hans
University of Vienna,Austria
[email protected]
Liu, Boping
China
[email protected]
Liu, Huanxiang
Beijing University,China
[email protected]
Liu, Qi
[email protected]
Liu, Wenjian
Beijing University, China
[email protected]
Liu, Xin
Dalian University of Technology,China
Liu,Yu
Liu,Zhen
Universität Stuttgart, Germany
East China University of Science and
[email protected]
[email protected]
292 Book of Programme and Abstract for TACC2008 Technology,China
Lu, Tongtong
[email protected]
Lu, Wen-Cong
College of Sciences,China
[email protected]
Lu, Xiancai
[email protected]
Lu, Hsiu-Feng
Institute of Chemistry, Academia Sinica, Taiwan,
ROC
[email protected]
Luo, Liangying
Lanzhou University, China
[email protected]
Luo, Yi
Tohoku University, Japan
[email protected]
Luzar, Alenka
Virginia Commonwealth University, USA
[email protected]
Lyoo,Junho
Korea Science Academy, Korea
[email protected]
Ma, Jianpeng
Baylor College of Medicine, USA
[email protected]
Ma, Jianyi
[email protected]
Makowski, Marcin
Jagiellonian University, Poland
[email protected]
Mallik,Bhabani S.
Indian Institute of Technology Kanpur U.P. , INDIA
[email protected]
Marcus, Rudolph A.
California Institute of Technology, USA
[email protected]
Mark, Alan E.
University of Queensland, Australia
[email protected]
Marrink, Siewert-Jan
[email protected]
Martin, Gershom
Weizmann Institute of Science, Israel
[email protected]
Martyna,Glenn J
IBM TJ Watson Lab
[email protected]
Merz, Ken
University Florida, USA
[email protected]
Miao, Qiang
[email protected]
MIN Xin-min
Wuhan University of Technology, China
[email protected]
Minot,Christian
Université Pierre & Marie Curie, France
[email protected]
Miskufova, Martina
University College London, UK
[email protected]
Miyata, Tatsuhiko
Institute for Molecular Science,Japan
[email protected]
Moliner,Vicent
Universitat Jaume I, Spain
[email protected]
Moreau, Philippe
Université de Nantes –CNRS, France
[email protected]
Mori,Toshifumi
[email protected]
Moszynski, Robert
University of Warsaw, Poland
[email protected]
Mu, Yuguang
Nangyang Technology University, Singapore
[email protected]
Mukamel, Shaul
University of California, USA
[email protected]
Mukherjee, Debashis
Indian Association for the cultivation of Science,
India
[email protected]
Mukherjee,Partha P
Los Alamos National Laboratory, USA
[email protected]
Naidoo, Kevin J.
University of Cape Town, South Africa
[email protected]
Nakai, Hiromi
Weseda University, Japan
[email protected]
293 Book of Programme and Abstract for TACC2008 Nakata, Maho
Revanuri.S, Narendra
Advanced Center for Computing and
Communication, RIKEN
[email protected]
Goa University,Goa, India
[email protected]
Naumkin, Fedor Y.
UOIT, Canada
[email protected]
Neuhauser,Daniel
UCLA, USA
[email protected]
Nguyen, Ngoc Ha
Hanoi National University of Education, Vietnam
[email protected]
Nilsson, Lennart
Karolinska Institutet, Sweden
[email protected]
Niu, Bing
Shanghai University,China
[email protected]
International Islamic University , Malaysia
[email protected]
Oh, Young-Ho
Kyunghee UniVersity,Korea
[email protected]
Oh,Young-Ho
Kyunghee UniVersity, S.Korea
[email protected]
Ohmine, Iwao
Nagoya University, Japan
[email protected]
Ostlund, Neil S.
Hypercube, Inc., USA
[email protected]
Ou, Hong-Yu
Shanghai Jiao Tong University， China
[email protected]
Ozcan1, Ozlem
Max Planck Institut für Eisenforschung, Germany
[email protected]
Pacchioni, Gianfranco
University of Milano Bicocca, Italy
[email protected]
Paci, Emanuele
University of Leeds, UK
[email protected]
Pan, Kai
[email protected]
Parrinello, Michelle
ETH, Switzerland
[email protected]
Patel, Sandeep
University of Delaware, USA
[email protected]
Patey, Gren
University of British Columbia, Canada
[email protected]
Babu
Noorbatcha, Ibrahim
Ali
Peng,Wei-Tou
Institute of Chemistry, Academia Sinica,
Taiwan,ROC
[email protected]
Piecuch, Piotr
Michigan State University, USA
[email protected]
Piquemal, Jean-Philip
Université Pierre et Marie Curie, France
[email protected]
Pirzadeh, Payman
University of Calgary, Canada
[email protected]
Pittner, Jiri
Czech Academy, Czech Republic
[email protected]
Plowright, Richard
[email protected]
Podeszwa, Rafal_
University of Warsaw, Poland
[email protected]
Pomes, Regis
University of Toronto, Canada
[email protected]
Porter, Richard N.
State University of New York, USA
[email protected]
Praprotnik, Matej
Max Planck Institute for Polymer Research, German
[email protected]
Probst, Michael
University of Innsbruck, Austria
[email protected]
Pu, Min
Beijing University of Chemical Technology,China
[email protected]
Pu, Xuemei
[email protected]
294 Book of Programme and Abstract for TACC2008 Pulay, Peter
University of Arkansas, USA
[email protected]
Pyykkö, Pekka
University of Helsinki, Finland
[email protected]
Qi, Qi
Southeast University,China
[email protected]
Qiao, Baofu
Chinese Academy of Sciences,China
[email protected]
Qin , Yi
Hohai University,China
[email protected]
Institute of Microbial Technology, India
[email protected]
Indiana University, USA
[email protected]
Ramasami, Ponnadurai
University of Mauritius, Mauritius.
[email protected]
Rassolov,Vitaly
University of South Carolina, USA
[email protected]
Rayez, Jean-Claude
Institute of Molecular Sciences, France
[email protected]
Reuter, Nathalie
Univ. of Bergen, Norway
[email protected]
Rong, Zimei
Queen Mary University of London，UK
[email protected]
Roos, Björn
University of Lund, Sweden
[email protected]
Raghava, Gajendra P.
S.
Raghavachari,
Krisahnan
Rost, Jan Michael
Max Planck Institute for the Physics of Complex
Systems, German
[email protected]
Rothstein, Stuart M
Brock University, Canada
[email protected]
Rupnik, Kresimir
Louisiana State University, USA
[email protected]
Russo, Nino
University of Calabria, Italy
[email protected]
Sabolovic, Jasmina
Institute for Medical Research and Occupational
Health, Croatia
[email protected]
Safa,Fariba
Islamic Azad University-Rasht Branch, Iran
Sakaki, Shigeyoshi.
Salahub, Dennis
University of Calgary, Canada
[email protected]
Satoh, Hiroko
ETH Zürich, Switzerland
[email protected]
Semnani,Abolfazl
University of Shahrekord,IRAN
[email protected]
Senbo,Xiao
CAS-MPG partner Institute for Computatinal
Biology, China
[email protected]
[email protected]
p
[email protected]
Shehadi,Ihsan
United Arab Emirates University , Al-Ain
Sheikhshoaei, Iran
Shahid Bahonar University of Kerman,Iran
Shen, Jian
Sanofi-aventis, Inc.
[email protected]
Shen,Yong
Sun Yat-Sen University,China
[email protected]
Sherrill, David
Georgia Institute of Technology, USA
[email protected]
Shigeta, Yasuteru
Hyogo Univ., Japan
[email protected]
Education & Training of Kerman,Iran
[email protected]
Shoaie, Shahnaz
Sheykh
[email protected]
295 Book of Programme and Abstract for TACC2008 Shoeib, Tamer
Loughborough University, UK.
[email protected]
Shu, Yuan-jie
Institute of Chemical Materials, CAEP, China
[email protected]
Shurki, Avital
The Hebrew University of Jerusalem, Israel
[email protected]
Skala, Lubomir
Charles University, Czech Republic
[email protected]
Smith, Brian
WEHI Melbourne, Australia
[email protected]
Smith, David
Rudjer Boskovic Institute, Croatia
[email protected]
Smith, Jeremy
University Heidelberg, Germany
[email protected]
Sokolov, Nikolay V.
Saint Tikhon Orthodox University, Moscow, Russia
[email protected]
Sonawane, Lalit V.
Song. Youtao
Song, Yuanqiang
Song, Mee Kyung
R. C. Patel Institute of Pharmaceutical Education and
Research, India
Liaoning University, China
University of Electronic Science and Technology of
China
[email protected]
[email protected]
[email protected]
Bioniformatics & Molecular Design Research Center,
Korea
Sprik, Michiel
University of Cambridge, UK
[email protected]
Stacklies, Wolfram
Partner Institute for Computational Biology,China
[email protected]
Stahl, Gunther
Tripos Inc., USA
[email protected]
Stewart, James
Stewart Computational Chemistry, USA
[email protected]
Su, Zhongmin
Northeast Normal University, China
[email protected]
Su, Ji-guo
Beijing University of Technology,China
[email protected]
Su, Julius
California Institute of Technology, USA
[email protected]
Sun, Huai
[email protected]
Sun, Huarong
[email protected]
Sun, Zhigang
Nanyang Technological University, Singapore
[email protected]
Sun,Ying-chieh
National Taiwan Normal Univ.,Taiwan
[email protected]
Sung, Dae Dong
Dong-A University,Korea
[email protected]
Tachibana, Akitomo
Kyoto University, JAPAN
[email protected]
Tai, Da Lin
Quan, Jun-Min
Shenzhen Graduate School of Peking
University,China
Shenzhen Graduate School of Peking
University,China
[email protected]
[email protected]
Tan, Hepan
IUPUI,USA
[email protected]
Tanaka, Shigenori
Kobe University, Japan
[email protected]
Tang, Bei
[email protected]
Tang, Kwong-Tin
Paci…c Lutheran University, USA
[email protected]
Tang, Shuai-Xia
Chinese Academy of Sciences,China
[email protected]
296 Book of Programme and Abstract for TACC2008 Tang,Sishi
Tari, Shervin
The Scripps Research Institute, La Jolla, CA, USA,
92037.
[email protected]
University Of Tehran, Iran
[email protected]
Ten-no, Seiichiro
Nagoya University, Japan
[email protected]
Thachuk, Mark
University of British Columbia,, Canada
[email protected]
Thiel, Walter
Max-Planck-Institut Fur Kohlenforschung, Germany
[email protected]
Mohammadi
Tian, Guocai
Kunming University of Science and
Technology,China
[email protected]
Tobias, Doug
University of California, Irvine, USA
[email protected]
Tu, Yuan
[email protected]
Tu,Meihua
Pfizer Global Research & Development, Groton,
Connecticut, USA
[email protected]
Tuñón,Iñaki
University of Valencia, Spain
[email protected]
Tussupbayev, Samat
Universitat de Girona,Spain
[email protected]
Tuszynski,Jack
University Avenue, Canada
[email protected]
Umeyama,Hideaki
Kitasato University, USA
[email protected]
Utkin,Andrey V.
Van der Avoird, Ad
Van Gisbergen, Stan
Van Gunsteren,
Khristianovich Institute of Theoretical and Applied
Mechanics, Russia
Radboud University, The Netherlands
Scientific Computing & Modelling NV, The
Netherlands
[email protected]
[email protected]
[email protected]
ETH Zürich, Switzerland
[email protected]
Varandas, Antonio
Universidade de Coimbra, Portugal.
[email protected]
Vessally, E.
Islamic Azad University, Iran
[email protected]
Vijayan, Ranjit
Oxford OX1 3QU, UK
[email protected]
Voth Gregory A.
University of Utah, USA
[email protected]
Brock University,Canada
[email protected]
Wan, Jian
Central China Normal University, China
[email protected],
Wang, Alex
University of British Columbia, Canada
[email protected]
Wang, Chang-long
Hebei University of Engineering,China
[email protected]
Wang, Cunxin
Beijing University of Technology, China
[email protected]
Wilfred F.
Vyboishchikov, Sergei
F.
Wang, Dongqi
Swiss Federal Institute of Technology, ETH,
Switzerland
[email protected]
Wang, Hailong
Mayo Clinic College of Medicine, USA
[email protected]
Wang, Hongyan
Jilin University,China
[email protected]
Wang, Jihua
Universities of Shandong,China
[email protected]
297 Book of Programme and Abstract for TACC2008 Wang, Jinlan
Southeast University, China
[email protected]
Wang, Jingfang
Shanghai Jiao Tong University
[email protected]
Wang, Lu
[email protected]
Wang, Renxiao
Shanghai Institute of Organic Chemistry, CAS, China
[email protected]
Wang, Shihao
Queen’s University,Canada
[email protected]
Wang, Wen
Kunming Institute of Zoology, CAS, China
[email protected]
Wang, Xiaohui
Wang, Xiaolin
Harebin Industry University, China
[email protected]
Wang, XiJun
[email protected]
Wang, Yanli
NCBI/NLM/NIH/GOV
[email protected]
Wang, Yaxue
Sun Yat-sen University, China
[email protected]
Wang, Yifei
Shanghai University, China
Wang, Zhuo
Wang, Zhuo
University of Illinois at Urbana-Champaign, USA
Wang, Haixia
Xi'an Jiaotong University,China
Wang, Lijuan
China
[email protected]
[email protected]
[email protected].
Wang, Qiaotao
University of Manchester, UK
Wang, Shihao
Queen’s University,Canada
[email protected]
Wang, Shu
[email protected]
Wei, Chaochun
[email protected]
Wei, Dongqing
[email protected]
Werner, Hans-Joachim
University of Stuttgart, Germany
[email protected]
Wesolowski, Tomasz
University of Geneva, Switzerland.
[email protected]
Whangbo, Mike.H
North Carolina State University, USA
[email protected]
Wilson, Angela
University of North Texas, USA
[email protected]
Wu, Rongliang
Institute of Chemistry,China
[email protected]
Wu, Wei
[email protected]
Xie, Hujun
[email protected]
Xie, Lu
uk
Shanghai Center for Bioinformation Technology,
China
Xiong, Ying
Institute of Chemical Materials, CAEP, China
[email protected]
Xu, Jiancong
Oak Ridge National Lab,USA
[email protected]
Xu, Ruixue
[email protected]
Xu, Xiaomin
[email protected]
298 Book of Programme and Abstract for TACC2008 Xu, Xin
Xu,Yisheng
Chinese Research Academy of Environmental
Sciences,China
[email protected]
[email protected]
Xu, Yu
Central University for Nationalities, China
[email protected]
Xue,Ying
University of Groningen, Netherlands
[email protected]
Yamasaki, Hideki
Osaka University,Japan
[email protected]
Yamazaki, Takeshi
University of Alberta,Canada
[email protected]
Yan, Likai
Kyushu University, Japan
[email protected]
Yan, Tianying
[email protected]
Yañez, Manuel
Autonoma University of Madrid, Spain
[email protected]
Yang, Chiming
[email protected]
Yang, Jinlong
University of Science and Technology, China
[email protected]
Yang, Wei
Florida State University, USA
[email protected]
Yang, Weitao
Duke University, USA
[email protected]
Yang, Zhongzhi
Liaoning Normal University, China
[email protected]
Li Yanwei
Guilin University of Technology, China
[email protected]
Yao,Shen
University of Notre Dame,USA
[email protected]
Yao,Shuwen
Henan Institute of Science and Technology, China
[email protected]
Yarovsky, Irene
RMIT University, Australia
[email protected]
Yin, Fuchang
Emory University,USA
[email protected]
Yin, Shuangye
University of North Carolina at Chapel Hill, USA
[email protected]
Yokojima,Satoshi
Yoshida, Norio
You, Wei
Mitsubishi Chemical Group Science and Technology
Research Center, Japan
Institute for Molecular Science, Japan
North China Institute of Science and Technology,
China
[email protected]
[email protected]
[email protected]
Yu, Chin-hui
National Tsing Hua University, Taiwan
[email protected]
Yu, Shuhao
[email protected]
Yu, Yangxin
[email protected]
Yu, Yang-Xin
[email protected]
Yu, Yao
Yu, Zhongheng
Institute of Chemistry, CAS, China
[email protected]
Yuan, Bo
[email protected]
Zahedi, Gholamreza
Razi University, Iran
[email protected]
Zeng, Zhiping
[email protected]
Zeynali, M. E.
IPPI,Iran,
[email protected]
299 Book of Programme and Abstract for TACC2008 Zhang, Chunxiao
[email protected]
Zhang, He
University of Wisconsin-Madison, USA
[email protected]
Zhang, Min
Wuhan University of Technology, China
Zhang, ShuPing
University of Shanghai for Science and
Technology,China
[email protected]
Zhang, Tao
[email protected]
Zhang, Zhuoyong
Capital Normal University, China
[email protected]
Zhang, Houyu
Jilin university,China
[email protected]
Zhang,Zhengquan
Northwestern Polytechnical University, China
[email protected]
Zhao, Guang-Jiu
Dalian Institute of Chemical Physics,China
[email protected]
Zhao, Jijun
[email protected]
Zhao, Pu
Tongji University,China
[email protected]
Zhao,Shu-Lei
Technology,China
[email protected]
Zhao,Yong-Wu
Jilin University,China
[email protected]
Zhen Cao
[email protected]
Zheng, Haoping
[email protected]
Zhong, Lei
Technology,China
[email protected]
Zhou, Ge
[email protected]
Zhou, Zhiyong
Schrodinger, Inc, USA
[email protected]
Zhou, Zhongfu
Cardiff University,UK
[email protected]
Zhou,zhigang
Purdue University, USA
[email protected]
Zhu, Chao-Hua
Jiangsu Polytechnic University,China
[email protected]
Zhu,Jianjun
State University of New York, USA
[email protected]
Zhuo, Shuping
[email protected]
Zipse, Hendrik
University Munich, Germany
[email protected]
Zwanziger, Josef W.
Dalhousie University, Canada
[email protected]
300 Book of Programme and Abstract for TACC2008 Additional Informations International Association of Scientists in the Interdisciplinary Areas(IASIA) Interdisciplinary sciences enjoy rapid development lately because these areas represent the forefront of the
scientific research and technology. We find it necessary to establish an international association to bring
together scientists whose research is in the interdisciplinary areas of biological sciences, information sciences,
physics, mathematics, chemistry, mechanics, also advanced technology.
IASIA is a voluntary, non- profit-making organization of individuals who are actively interested in the
interdisciplinary sciences.
The objectives of the Association are to promote international cooperation, and to encourage advancement
and understanding in the field of interdisciplinary sciences. The association seeks to achieve these goals by
sponsoring international conferences, by encouraging regional activities and by providing relevant information
to its members.
IASIA is registered in Canada. The contact information is:
International Association of Scientists in the Interdisciplinary Areas(IASIA)
165 Saguenay, Bromont,
Quebec, Canada J2L 3J8
Tel. 1-450-578-3368
Fax. 1-450-534-1933165 Sagaunay
E-Mail:[email protected]
web:http://interdisciplinarysciences.org.
A new journal named "Interdisciplinary Sciences" was created and operated by IASIA:
Interdisciplinary Sciences -- Computational Life Sciences
Editor-in-Chief, Dongqing Wei, Ph.D., Professor
Department of Bioinformatics, College of Life Sciences and Biotechnology
Room 4-211, Life Science Building, Shanghai Jiaotong University
800 Dongchuan Road, Minhang District Shanghai, 200240, China
e-mail: [email protected], phone: 13918500529
In 2008, IASIA sponsors two conferences:
1. 2nd International Conference of IEEE Bioinformatics and Biomedical Engineering:
http://www.icbbe.org/icbbe2008submission/website/icbbe/index.aspx held on May 17-19, 2008 in
Shanghai, China(more than 500 attendance).
2. Theory and Application of Theoretical Chemistry(TACC 2008): http://tacc2008.sjtu.edu.cn/index.php
held on Sept. 23-27, 2008 in Shanghai, China.
301 Book of Programme and Abstract for TACC2008 165 Saguenay, Bromont, Quebec, Canada J2L 3J8, Tel. 1-450-578-3368, Fax. 1-450-534-1933
IASIA Membership Application Form
* The membership fee is waived until further noticed.
This form constitutes a legally binding agreement. Payment must be received within 1 month after the
invoice date (registration will not be effective until payment has been received). The annual fee for
members follows the calendar year. Only one person should apply per form. The membership
automatically continues for the next calendar year, unless written notice is given to the Secretary of
the Board ([email protected]), at least one month proceeding to the next calendar year.
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302 Bo
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生物学与化学
学
组合化学的研
研究工具，实
实现了计算机
机
信息学以及组
辅助药物设计
计的各种方法
法。
多年的研究成
成果与合作经
经
结合 Trripos 科学家多
验，新版本从
从应用的角度
度对 SYBYL 的各功能模
模块进行了分类整理或组合
合，使研究者
者的工作效率
率得到大幅提
提
高。SYBYL
L8.0 特别推出
出了全新的药
药物改造工具
具—Topomer CoMFA 和 Topomer Search。Topom
mer 技术的应
应
用使分子的三
三维构象生成
成、叠合完全
全自动完成；Topomer Co
oMFA 使药物
物化学家能够
够在几分钟内
内建立起高质
质
量的 3D-QSA
AR 模型，所得
得模型可以用
用来筛选数据
据库，使 CoM
MFA 模型的实
实用性产生了
了质的飞跃；
基于
基 Topomer
技术进行的相
相似性搜索，
，速度快、命
命中率高，非
非常适用于先
先导化合物的
的优化和改造
造（包括 R 基团和骨架跃
基
跃
迁），使药物
物改造这一艰
艰巨的工作变
变得有章可循
循且更富效率
率。
好的为中国用
用户提供服务
务，Tripos 和源资信息科
和
科技联合举办系
系列课程，希
希望帮助学术
术界及产业界
界
为了更好
进行人才的培
培育；同时也
也将与国内的
的大专院校合
合作，定期邀
邀请国内外相
相关领域的学
学者进行研讨及授课。
我们关心您的研究需要，
，欢迎您与我
我们联系！
303

hai Jiao

Transcription

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