Applications of HPC to Materials Chemistry
Transcription
Applications of HPC to Materials Chemistry
MSc in High Performance Computing: Guest Lecture 21/1/2011 Applications of HPC to Materials Chemistry Research Highlights Of The Materials Chemistry Consortium (e05) [email protected] http://www.ucl.ac.uk/klmc/mcc Strategic Vision Statement The HPC Materials Chemistry Consortium exploits the latest developments in HPC technologies, in a wide ranging programme of development, optimisation and applications studies aimed at modelling and predicting the structures, properties and reactivities of functional materials, including catalysts, ceramics, minerals and molecular materials. The programme embraces both large scale simulations based on force-fields and electronic structure techniques employing both Density Functional Theory, Hartree Fock and hybrid techniques. Strong emphasis is placed on code development and optimisation for MPP platforms while several applications highlight systems of industrial importance. There is strong symbiosis between the modelling studies of the consortium and experimental programmes. Consortium Members* Prof Richard Catlow, Dr Samuel A. French, Mr Said Hamad, Dr Erika J Palin, Dr Alexey A Sokol, Miss Eleonora Spano‚ Ms Judy To, Mr Dan Wilson, Dr Scott M Woodley Prof Nicholas M Harrison, Mr Amit Agarwal, Dr Ian J. Bush, Miss Jennifer A Chan, Dr. Xiao-Bing Feng, Mr Matthew Habgood, Dr Giuseppe Mallia, Dr Barbara Montanari, Dr. Sanghamitra Mukhopadhyay, Ms Jessica J Scaranto, Dr Barry G Searle Dr Ben Slater, Ms Kat F Austen, Ms Dervishe Salih Dr Emilio Artacho, Dr Miguel Pruneda, Mr Jon Wakelin, Mr Andrew D Walkingshaw, Dr. Toby O H White Dr Fernando Bresme, Mr Luis Gomez Camara, Dr Minerva Gonzalez, Mr Kafui K Tay Prof Julian Clarke, Dr Steven Y Liem, Ms Beatrice Nikolaidi Dr Martin T Dove, Dr Mark Calleja, Dr Guillaume Ferlat, Miss Marivi Fernandez-Serra, Dr Ilian T. Todorov, Dr Kostya Trachenko Prof Julian D. Gale Prof Michael Gillan, Dr Dario Alfe, Dr. Maria Alfredsson, Dr Louise Dash Prof John Harding, Dr Dorothy M Duffy, Dr Duncan J Harris Dr Saiful Islam, Dr Julian R Tolchard Dr Lev Kantorovich, Mr Chris L Hobbs, Mr Ross E A Kelly, Dr Natalia Martsinovich, Mr Thomas P Trevethan Prof Moti Lal, Bill Smith, Dr Martin Plummer Dr Nora H. de Leeuw , Mr Ricardo Grau-Crespo, Dr Antonio Tilocca Dr Phil P Lindan, Dr Elena Bichoutskaia, Miss Elizabeth J Duplock, Miss Samantha Lister, Dr Changjun C Zhang Dr William W C Mackrodt Prof Steve Parker, Mr David DJ Cooke, Mr Sebastien SN Kerisit, Dr Arnaud Marmier, Mr Dino Spagnoli Prof N Quirke, Dr David Cubero, Mr Antoni Homs-Corbera Prof Mark PM Rodger, Mr Robert Hawtin, Dr Changman Moon Prof Sasha Shluger, Mr Andrey Y Gal, Dr Jacob L. Gavartin, Dr David Munoz Ramo, Ms Dervishe Salih, Dr. Peter P.V. Sushko, Dr Matthew B Watkins Dr Graeme W Watson, Miss Joanne Fearon, Dr. Michael J Nolan Dr David J Willock, Mr Rudy Coquet, Mr Edward Jeffery Dr Kate Wright, Mr Andrew M Walker Dr Stephen S A Wells * Registered on either HPCx or CSAR Consortium Members* Prof Richard Catlow, Chemistry, University College London Dr Dorothy Duffy, Physics, University College London Miss Xin Xia, Dr Gargi Dutta, Mr Alastair Smith, Mr Ludovic Briquet, Miss Martina Miskufova, Dr Alexey A Sokol, Dr Aron Walsh, Miss Hsin-Yi Tiffany Chen, Mr Crispin S Cooper, Miss Elisabeth Krizek Mr Jack Mulroue Prof Nic Harrison, Chemistry, Imperial College London Dr Giuseppe Mallia, Dr Leandro Liborio, Dr. Sanghamitra Mukhopadhyay, Dr Leonardo Bernasconi, Dr Ruth Martinez-Casado, Mr Ehsan A Ahmad, Miss Su Chuen Chew, Miss Romi Kaur Dr Ricardo Grau Crespo, Chemistry, University College London Prof Claire Grey, Chemistry, University of Cambridge Dr Derek S Middlemiss Prof Roy L. Johnston, Chemistry, University of Birmingham Mr. Lauro Oliver Paz Borbon Prof M Saiful Islam, Chemistry, University of Bath Prof Lev Kantorovich, Physics, Kings College London Dr Pooja Panchmatia, Dr Corinne Arrouvel, Mr Paul J Weaver, Mr Jesse Dufton, Dr Chris Eames, Mr Grahame R Gardiner Miss Manuela M Mura, Mr Dawid D Toton, Mr Joseph Bamidele Prof Nora de Leeuw, Chemistry, University College London Mr Anthony J Devey, Mr Thomas D Daff, Miss Emilia Tang, Dr Devis Di Tommaso, Dr Iman Saadoune, Ms Neyvis Almora Barrios, Dr Zhimei Du, Dr Hasani HR Chauke, Dr Simona Irrera, Dr Ian Streeter, Miss Saima Haider, Dr Glenn Jones, Dr Mariette M Wolthers, Mr Richard I Ainsworth, Alberto A Roldan-Martinez, Mr Nelson Y Dzade Kostya Trachenko, Physics, Queen Mary London Prof Angelos Michaelides, Chemistry, University College London Mr Xiaoliang Hu, Mr Jiri Klimes, Dr Limin Liu Liu, Mr Ding Pan, Mr Erlend Davidson, Dr Brent G Walker, Dr Xinzheng Li Dr Barbara Montanari, Daresbury Laboratory Prof Alex Shluger, Physics, University College London Miss Christine L Bailey, Mr Naunidh S Virk Dr Keith P McKenna, Dr David Munoz Ramo, Dr Matthew B Watkins, Mr Matthew Wolf, Dr Gilberto Teobaldi,Dr Niri Govind, Miss Natalie N C Moore, Dr Thomas Trevethan Dr Arash A Mostofi, Materials and Physics, Imperial College London Dr Ben Slater, Chemistry, University College London Prof Stephen Parker, Chemistry, University of Bath Mr Iain A Bethune, Mr Raimondas Galvelis, Mr Florian Schiffmann, Mr Zamaan Raza Mr Wojciech Gren, Mr Jeremy P Allen, Mr Tom V Shapley, Dr Marco Molinari Dr David J Willock, Chemistry, University of Cardiff Dr Martin M Plummer, Daresbury Laboratory Mr Adam Thetford, Miss Kara Howard, Mr Christopher A Lee Dr Paul Popelier, Chemistry, University of Manchester Prof John Harding, Materials, University of Sheffield Dr Majeed S Shaik, Dr Yongna Yuan, Mr Matthew J Mills Dr Colin C L Freeman, Mr Hung-Ru Chen Dr Peter Sushko, Physics, University College London Dr Jochen Blumberger, Physics, University College London Mr Clyde JA Fare, Dr Anna Kimmel, Dr Antonio AT Torrisi Mr Marian Breuer Dr Antonio Tilocca, Chemistry, University College London Dr George Darling, Chemistry, University of Liverpool Dr Jamieson Christie Dr Matthew S Dyer, Miss Kim Jelfs, Dr Jeremy Rabone, Mr Geoff Thomas, Mr Christopher M Collins, Dr Abbie E Trewin Dr Scott M Woodley, Chemistry, University College London Prof Martin Dove, Earth Sciences, University of Cambridge Dr Helen F Chappell Mr Fabiano Corsetti Dr Asimina AM Maniopoulou, Mr Russell Woolley, Dr Andrew R Turner, Mr Mohamed K Matar, Dr Regina R Maphanga Dr Martinus A Zwijnenburg, Chemistry, University College London * Registered on HECToR Management of Resources All-day meeting held every six months Key points: Morning devoted to talks (on research and HPC issues) by members who were allocated major HPC-time for the last six months, as well as ocasional guest speakers. HPC-time proposals for the next 6 months distributed among members > 1 week beforehand. Interim proposals are considered outside meetings for smaller HPC requests. Open management system As well as using email for collecting/distributing information, key information is stored on our website http://www.ucl.ac.uk/klmc/mcc Information includes: All sub-project proposals, Allocation and usage reports (by user, sub-group, sub-project and theme), Highlights of our research, list and photographs of members, Notes for new users, Final Report to EPSRC, Minutes of our meetings. One day seminars E.g. workshop for new and experienced users of relevant codes utilised by consortium The Seven Themes Surfaces and Interfaces Biomaterials Materials for Power Nano and Defect Chemistry Reactivity Environmental Materials Quantum Devices Reactivity Publication on Website text removed Nano and Defects Publication on Website text removed Surfaces and Interfaces Publication on Website text removed Materials for energy technology Publication on Website text removed Biomaterials Environmental Materials Publication on Website text removed Publication on Website text removed Key Research Highlights (1) The first theoretical study of the influence of polymer weight, tacticity and conformation on inhibitor activity, which also showed that kinetic inhibitors can actually promote nanocrystal growth RW Hawtin, PM Rodger, J. Mater. Chem. 16 1934 (2006) Development of a comprehensive model of the first thermally stable inorganic electride based on the complex oxide 12CaO.7Al2O3, which can be used in a variety of applications such as a cold electron emitter and as an effective reducing agent in catalysis PV Sushko, AL Shluger, M Hirano, H Hosono, J. Am. Chem. Soc. 129 942 (2007) Development of a new microscopic interpretation of the origin of the hydration force, which is connected to the anomalous dielectric behaviour of water under confinement conditions J Faraudo, F Bresme, Phys Rev. Lett. 7 94 (2005) The elucidation by dynamical simulations of the mechanisms of pre-nucleation in crystal growth of both inorganic and molecular materials; pre-nucleation phenomena can control the polymorphic outcome in crystallisation. ZnS: S Hamad, S Cristol, CRA Catlow, J. Amer. Chem. Soc. 127 2580 (2005) 5-fluoruracil: S Hamad, C Moon, CRA Catlow, AT Hulme, SL Price, J. Phys. Chem. B 110 3323 (2006) Determination of the electronic and magnetic structure of the partial oxidation catalyst FeSbO4 and of the relevant redox processes, as a function of surface composition and chemical potential R Grau Crespo, CRA Catlow, NH de Leeuw, J. Catal. 248 77 (2007) The blind structure prediction of the new ice XIV phase GA Tribello, B Slater, CG Salzmann, J. Amer. Chem. Soc. 128 12594 (2006) Key Research Highlights (2) Demonstration that graphitic ribbons support very long-range ferromagnetic interactions and are thus of great interest for spintronics applications L Pisani, JA Chan, B Montanari, NM Harrison, Phys. Rev. B 75 064418 (2007) On investigating an archetypal interface formed by the LaAlO3 film growth on SrTiO3 (001) surface, discovered that intermixing of all four metal species and formation of a quaternary oxide region is energetically preferable to the interface. This finding calls for a rethink of the origin of the two-dimensional electron gas associated with this interface. L Qiao, TC Droubay, V Shutthanandan, Z Zhu, PV Sushko, SA Chambers, J Phys: Condense Matter 22, 312201 (2010) Employed ab initio simulations to create the first atomic-scale model of stoichio-metric and oxygen deficient novel oxide 12CaO.7Al2O3, which has intriguing properties and is promising for applications in chemistry and electronics. PV Sushko, AL Shluger, Y Toda, M Hirano, H Hosono, Proc. R. Soc. A, in press. State-of-the-art DFT calculations with self-consistent incorporation of the van der Waals (vdW) interaction explained the existing controversy concerning a flat surface potential on the one hand and strong binding of flat organic molecules to the Au(111) surface on the other. M Mura, A Gulans, T Thonhauser, L Kantorovich, Phys. Chem. Chem. Phys. 12 4759 (2010) Surfaces and Interfaces Influence of pH on crystal growth of silica Steve Parker, Chemistry, University of Bath Ice formation on surfaces and in the upper atmosphere Angelos Michaelides, LCN, University College London Influence of pH on crystal growth of silica Steve Parker, Chemistry, University of Bath Publication on Website Slides Removed Nanoscale water film on salt Large scale ab initio molecular dynamics simulations of liquid solid interfaces: e.g. a nanoscale water film on salt: For more information see: www.chem.ucl.ac.uk/ice Liu et al. J. Am. Chem. Soc. 130, 8572 (2008) The smallest particle of ice imaged with STM and DFT For more information see: www.chem.ucl.ac.uk/ice Michaelides and Morgenstern, Nature Mater. 6, 597 (2007) Upper atmosphere - Ice formation 高岭石: Kaolinite Ice Nucleation: Without impurities water can become very cold (001) 500nm 200nm Common ice nucleating agents & their “ice nucleation threshold” top side bottom • Clays: -5 to -12 °C • AgI:-3 to -6 °C • Metals, Metal oxides: -5 to -12 °C • Cholesterol = -1 to -2 °C Ice formation in the upper atmosphere First principles calculations predict the formation of a 2D ice-like overlayer that is equally stable to bulk ice. 0 1/6 1/3 1/2 3/4 5/6 1 7/6 3/2 Coverage X. L. Hu and A. Michaelides, Surf. Sci. 601, 5378 (2007) X. L. Hu and A. Michaelides, Surf. Sci. 602, 960 (2008) The surface of proton disordered ice Ih The surface of proton disordered ice Ih is proton ordered a first principles prediction. Electrostatic repulsion between protons at the surface cause them to line up, effectively making the surface superchilled. This insight into the ice surface is likely to have implications for the equilibrium crystal shape of ice crystals or catalytic reactions which take place on their surfaces. Pan et al. Phys. Rev. Lett. 101, 155709 (2008) Wetting layer structures To wet or not to wet: Dispersion forces tip the balance for water-ice on metals Standard density functionals predict that water-ice should not wet metals, but form 3 dimensional nonwetting ice crystals. Accounting for dispersion forces rectifies this problem. Results agree with experiment. water on Cu(110): most well-characterized water on Ru(0001) most widely investigated For more information see: www.chem.ucl.ac.uk/ice Carrasco et al. Phys. Rev. Lett. 106, 126101 (2011) Materials for energy technology Solid oxide fuel cells, Cathode and Anode Materials Saiful Islam, Chemistry, University of Bath Hydrogen Storage Materials: MgH2 Ricardo Grau-Crespo, Chemistry, University College London Cathode Materials Claire Grey, Chemistry, University of Cambridge Solid Oxide Fuel Cells SOFC Space heater Energy conversion device – local heat & power generation New or improved materials are key to major advances Fuel Cell: Novel Ionic Conductor LaBaGaO4 Is a good O2- conductor Has complex structure with tetrahedral Ga - Conduction mechanism? - MD/atomistic simulations GaO4 La Ba LaBaGaO4 : Conduction Mechanism? • Unusual co-operative mechanism breaking and re-forming Ga2O7 from neighbouring GaO4 units • Ga2O7 Flexible structure GaO4 • Related oxides with tetrahedra? Nature Mater. 6, 871 (2007) Cathode and Anode Materials Saiful Islam, Chemistry, University of Bath Publication on Website Slides Removed Hydrogen Storage Materials: MgH2 Ricardo Grau-Crespo, Chemistry, University College London Publication on Website Slides Removed Cathode Materials Claire Grey, Chemistry, University of Cambridge Publication on Website Slides Removed Quantum Devices Sc Spin Qubits in Carbon Peapods Barbara Montanari, University of Oxford & Daresbury Lab Lifting the C60 Molecule with a SPM Tip Lev N. Kantorovich, Physics, King’s College London Charge Rearrangement in Peapods L Ge, B Montanari, J Jefferson et al PRB 77 235416 2008 J Warner, A Watt, L Ge, Nano Lett 8 (4) 1005 2008 How Spin Qubits Align in Peapods Lifting the C60 Molecule with a SPM Tip Using only the chemical tip-molecule interaction C60 in a stable adsorption configuration C60 at a pivoting point (2 Si-C bonds) lift next stable adsorption configuration deposit carry the C60 (attached only to the tip) C60 can be lifted from the surface thanks to the tip-C60 chemical bonding, without applying bias voltage The C60 needs to be brought to a suitable adsorption configuration (precursor state) with minimised bonding to the substrate a combination of lateral and vertical manipulation The precursor mechanism may be generally valid for vertical manipulation of adsorbates 0 -1 unsuccessful Binding energy, eV Lateral manipulation successful -2 -3 Barrier 2 eV Tip height, Å Environmental Materials Radiation damage effects in nuclear and thermonuclear power applications Kostya Trachenko, Physics, Queen Mary, Martin Dove, Materials, Cambridge Ilian Todorov, Daresbury Laboratory, Dorothy Duffy, Physics, UCL Electronic effects in radiation damage simulations Dorothy Duffy, LCN, University College London Radiation damage effects in nuclear and thermonuclear power applications Kostya Trachenko, Physics, Queen Mary, Martin Dove, Materials, Cambridge Ilian Todorov, Daresbury Laboratory, Dorothy Duffy, Physics, UCL Publication on Website Slides Removed Electronic effects in radiation damage simulations Dorothy Duffy, LCN, University College London Publication on Website Slides Removed Reactivity DFT+U applied to supported Au/Fe2O3 catalysts Dave J Willock, Chemistry, Cardiff University Challenges to Methanol Synthesis Alexey Sokol, Richard Catlow, Gargi Dutta, Chemistry, UCL DFT+U applied to supported Au/Fe2O3 catalysts • • • Experiments identified particles containing around 10 Au atoms as most active.1 Calculations show that dissociation of O2 is found to be favourable at metal/oxide interface but not on an isolated cluster. Further experiments/calculations have shown these catalysts may also break the CO bond.2 200 Au10 150 Energy / kJ mol-1 High activity O2 gas 100 50 0 Au10 on Fe2O3 -50 -100 -150 -200 -250 -300 0 0.5 1 1.5 2 2.5 3 3.5 4 O...O / Å 4.5 1. G. Hutchings, C. Kiely et al., Science, 2008, 321, 1331 2. G. Hutchings, D.J. Willock et al., Phys. Chem. Chem. Phys., 2011, Advanced Article, DOI: 10.1039/C0CP01852J. ZnO (000-1)-O ZnO (0001)-Zn Surface hydrogenation Methanol – Catalytic cycle Copper anchoring Identification of Vibrational Modes AZn BZn 1507cm-1 (BZn) 1745cm-1 (BO) (AO) (AZn) SA French et al, J Chem Phys 118 (2003) 317 Zinc Hydride Vibrational Modes Type I ̶ reversible Zn – H 1745cm-1 expt. 1710cm-1 Type II ̶ irreversible Zn – H 1507cm-1 expt. 1475cm-1 Surface Defects Intrinsic surface vacancy traps electron AA Sokol et al, Int J Quant Chem 99 (2004) 695 Challenges to Methanol Synthesis Alexey Sokol, Richard Catlow, Gargi Dutta, Chemistry, UCL Publication on Website Some Slides Removed Biomaterials Peptide Influence on the (1 0 4) Calcite Surface John Harding, Chemistry, University of Sheffield Mark Rodger, Physics, University of Warwick Interaction of Bio-molecules with Apatite Mineral Surfaces Nora de Leeuw, Chemistry, UCL Bio-inspired (Fe,Ni)S nano-catalysts for CO2 activation Nora de Leeuw, Chemistry, UCL Bio-inspired (Fe,Ni)S nano-catalysts for CO2 activation Nora de Leeuw, Chemistry, UCL Publication on Website Slides Removed Surface morphology - Influence of proteins How do peptides influence the morphology of calcite and the (1 0 4) calcite surface in water? water solution Chosen peptides mimic the proteins in egg shells. (1 0 4) calcite surface peptide MD simulations Collagen Structure c Adsorption to hydroxy-apatite Adsorption of Proline Hydroxyproline Glycine to hydroxy-apatite SIESTA calculations Glycine adsorption (0001) (1010) H from –COOH group migrates to surface OH, forming trapped water molecule Proline adsorption (0001) (1010) H from –COOH group migrates to -NH2 group then to surface PO4 group Hydroxy-proline adsorption (0001) (1010) H from –COOH group migrates to surface PO4 group. Extra flexible –OH group strengthens interactions Adsorption of amino acids at HA surfaces Adsorption energies (kJ mol-1) HA Surface Glycine Proline Hydroxyproline (0 0 0 1) -77.05 -70.58 -106.73 (0 1-1 0) -359.92 -509.77 -609.79 All amino acids form multiple interactions with surface species, particularly if they can bridge between two surface calcium ions Physisorption to (0001) surface with few dangling bonds Strong interactions with less stable (01.0) surface, involving changes in chemical bonding Glycine more flexible but less adhesive Collagen should provide favourable nucleation sites for growth of hydroxyapatite (01.0) surface Nano and Defects The electronic structure and properties of a novel complex oxide 12CaO.7Al2O3 Peter Sushko, Alex Shluger, Physics, University College London Structure Prediction and Optical Properties of Doped Nanoparticles Scott Woodley, Shephen Shevlin, Chemistry, University College London The electronic structure and properties of a novel complex oxide 12CaO.7Al2O3 Peter Sushko, Alex Shluger, Physics, University College London Publication on Website Some Slides Removed Photoactive H-doped C12A7 UV light H2 + O2– H– + OH– H– H0 + e– H0 H2 O2– H0 + O2– OH– + e– O2– O2– K. Hayashi et al., Nature 419, 462, (2002) Matsuishi et al., JACS, 127, 12454 (2005) H– O2– OH– e– e– P. V. Sushko et al., APL 86, 092101, (2005) P. V. Sushko et al., PRB 73, 045120, (2006) e– Structure Prediction and Optical Properties of Doped Nanoparticles Scott Woodley, Shephen Shevlin, Chemistry, University College London Publication on Website Some Slides Removed Photocatalyst H2 production via heterolytic dissociation of water H2O → H2 + ½O2 Titania (TiO2)n Pros: Stable and non-toxic Con: Band-gap rather large 3.03 eV for rutile 3.18 eV for anatase only a small part of the solar spectrum can be harvested Anion doping: reduce the bandgap increase photoactivity. Smaller particles: greater surface area dopants closer to H2O reduces HOMO-LUMO gap Photocatalyst 6 7 LUMO+1 LUMO HOMO HOMO–1 10 HOMO residing solely on the O(2p) states LUMO residing solely on the Ti(3d) states Titania (TiO2)n 13 Photocatalyst × CO × NO × SO 6 6 10 10 × CO Doped Titania (TiO2)n × NO × SO Photocatalyst All of the dopants reduce the transition energy × CO 6 10 × NO × SO LUMO HOMO carbon and sulphur dopants nitrogen-doping transition energies that are close to the peak in the solar spectrum (~2.5 eV) transition energy that is too low (~ 1.0 eV) for water-splitting applications thus are more efficient at photoconversion than undoped nanoparticles. 2010 13-17 Acknowledgements HPC Materials Chemistry Consortium Funded by EPSRC Lead by Richard Catlow Driven by HECToR All Members of the HPC Material Chemistry Consortium Publications Journal of Materials Chemistry 2006 (vol.16 iss. 20) Royal Society Proc A 2011(in press) [email protected]