Organic Molecular Modeling

Organic Molecular Modeling



2016/03/20 revised
Lab coat and goggle are not necessary
Self-prepare digital camera
Download Avogadro and Chemsketch free software
(reference expt.)
Collect and check contents: MOLYMOLD Organic Set
White ball: 20
Green ball: 4
Black ball: 12
Yellow ball: 2
Red ball: 6
Grey ball: 1
Blue ball: 4
Purple ball: 1
Short white link: 26
Medium grey link: 26
Long grey link: 12
Link remover: 1
1
Purpose
 Construct and learn spatial arrangement of organic
molecules
 Use MOLYMOLD organic set to build
 Ball-and-stick model
 Observe the conformers and isomers
 Use free software to sketch the chemical
structures (reference expt.)
 Chemsketch
 Avogadro
2
Chemical Structure of
Organic Compound
 Lewis structure
H
H C H
H
Wedgeand-dash
H
C
H
H
H
 Ball-and-stick
 Space-filling
3
MOLYMOLD Organic Set
Ball-and-stick
Specific color for element
C
H
O
Single Multiple
bond
bond
N
Cl
Space-filling
Link remover
4
Flow Chart I. Organic
Molecular Modeling
MOLYMOD ball-and-stick model
Check the contents in the
set
Draw chemical structures
MOLYMOD organic set
Construct ball-and-stick model
Compare and take picture
After lab, recheck the set
Ball-and-stick model
5
I. Newman Projection
 For ethane, C2H6
Newman Projection
1. Staggered
1
2
1
2
2
1
2
1
1
2. Eclipsed
1
2
1
2
1
6
II. Conformation
 Conformation

Rotate single bond to change the spatial arrangement
Staggered, lower energy
2
Eclipsed, higher energy
2
More stable
1
1
7
II. Chair and Boat Form of
Cyclohexane
 Cyclohexane, C6H12: chair and boat form
Chair form
6
4
3
1
4
3
2
Boat form
2
5
6
1
5
More stable
H
H
H
H
H
H
H
H
H
H
H
H
H
8
III. Isomers
Same formula, but
different structures
Isomers
Different
skeleton
Functional
group
isomers
Structural
isomers
Skeletal
isomers
Positional
isomers
Geometric
isomers
Same skeleton,
but different spatial
arrangement
Enantiomers
Cl
CH3OCH
CH3CH2OH
Stereoisomers
Cl
Cl
Cl
Cl
Cl
9
Geometric Isomers
Geometric isomers (cis, trans-isomers)
 Molecule with C=C double bond or ring structure
 cis: on the same side
 trans: on the other side
H
H
C
C
C
Cl
Cl
Cis-form
Cl
H
C
Cl
H
Trans-form
1,2-Dichloroethene
Cis-form
Trans-form
1,4-dimethylcyclohexane
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Enantiomers
 Chiral carbon


Carbon with four different substituents
Labeled as C*
*
Chiral
carbon
*
 Enantiomers (optical isomers)


Molecule with chiral carbon is non-superimposable with its
mirror image, named enantiomers
Enantiomers could rotate plane-polarized light with same
angle but different direction, and named optical isomers
• Rotate clockwise, i.e. dextrorotatory, represent as (+) or d• Rotate counterclockwise, i.e. levorotatory, represent as (-) or l-
11
Naming StereocentersThe R, S System
Priority rules:
 Higher atomic number with higher priority (assign 1)
2
2
4
4
1
3
Counterclockwise
1
3
Clockwise
Enantiomers of 2-butanol
 OH
S-
[]25
D +13.52
OH 
C* H 
 H3C
CH2CH3 
[ ]25
D -13.52
(S)-(＋)-2-Butanol
(R)-(－)-2-Butanol

*
H C CH
3 
 CH CH
3
2
IUPAC
R-
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Compare the Enantiomers
1. Assemble the molecules
2. Compare and take picture
3. Determine the R- or S- configurations
13
Notice
 Construct the molecules and take pictures in the lab
 Use link remover to take the constructed model apart to
avoid breaking the links
 After lab, check the contents of MOLYMOD set, hand-in
and rechecked by GTA
 Hand-in lab report with IUPAC systematic names, the
chemical structures and pictures of modeling next week
Hand-writing or
draw by software
14
Flaw Chart II: Free Software for
Chemical Structures (Reference)
 Chemsketch
http://www.youtube.com/watch?v=5kaU5iEqifQ
 Draw chemical structure
CH2
H3C
 Avogadro
http://www.youtube.com/watch?v=ohdMhGaaP68
 Show three-dimensional structure
 Calculate bond-angle, bond-length, and bond
energy
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