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Molecular Visualization and Simulation with HyperChem

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Title: Molecular Visualization and Simulation with HyperChem


1
Molecular Visualizationand Simulation with
HyperChem
  • Thomas K. Green
  • Department of Chemistry
  • University of Alaska Fairbanks

2
Is the Time Right?
Every attempt to employ mathematical methods in
the study of chemical questions must be
considered profoundly irrational and contrary to
the spirit of chemistry. It would occasion a
rapid and widespread degeneration of that
science A.
Compte 1798-1857
3
The more progress physical sciences make the
more they tend to enter the domain
of mathematics, which is a kind of centre
to which they all converge. We may judge the
degree of perfection to which a science has
arrived by the facility with which it may be
submitted to calculation.
Adolphe Quetelet 1796-1874
4
Features of Molecular Modeling
  • Structure
  • Stability
  • Reactivity
  • Properties

5
Structural Models
  • 2-D Drawing Ethanol
  • 3-D Models of HyperChem
  • Sticks
  • Tubes
  • Ball and Stick
  • Space-Filling

CH3CH2OH
6
Periodic Table
7
Ethanol HOCH2CH3
8
Tubes
9
Ball and Stick
10
Space-filling
11
Nucleic Acids
12
DNA
13
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14
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15
Amino Acids
16
Protein
17
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18
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19
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20
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21
Computational Methods
  • Molecular Mechanics
  • Semi-Empirical
  • ab initio

22
Molecular Mechanics
  • Describes the energy of molecule in terms of
    distortions of bond distances and angles away
    from idealized values, with contributions from
    nonbonded interactions.
  • Provides equilibrium geometry very quickly.
  • Does not provide reliable relative energies of
    isomers or of reaction energies.

23
Semi-Empirical Method
  • Based on more sophisticated quantum mechanical
    methods but with time-saving approximations ,
    including incorporation of experimentally-derived
    parameters.
  • Provides good account of equilibrium structures
    but less satisfactory for reaction
    thermochemistry than ab initio method.
  • AM1 method is most popular present-generation
    method.

24
ab initio Methods
  • Quantum Mechanical methods successful in
    providing equilibrium and transition state
    geometries
  • Relative computation times are much longer than
    semi-empirical methods and therefore more costly.
  • 3-21G and 6-31G are most popular.

H?? E?
25
Stability and Geometry Optimization
  • Geometry optimization alters molecular geometry
    to lower the energy of the system to yield a more
    stable conformation.
  • Derivative of the energy with respect to all
    coordinates, called the gradient, is near zero.
  • Several different minima are possible.

26
Energy Minima
27
Saddle Point
28
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29
Conformational Analysis of Cyclohexane
Chair Global Minimum
Twist Boat Local Minimum
1.33 kcal/mol
7.22 kcal/mol
Boat Saddle point
8.31 kcal/mol
30
Bond Rotation of Butadiene
S-Trans S-Cis
S-Trans 1800 0.0 kcal/mol
1500
900
1.62 kcal/mol
5.35 kcal/mol
S-Cis 00
600
300
3.40 kcal/mol
2.80 kcal/mol
3.46 kcal/mol
31
S-Cis
S-Trans
32
Space-Filling Model of S-Cis Conformation
Steric Repulsion of Hydrogen Atoms
33
Stability of Benzyl Carbocation
900
Planar Hf ? 222 kcal/mol
Perpendicular Hf? 253 kcal/mol
34
Resonance Stabilizationof Benzyl Carbocation
More Stable
Less Stable
35
Molecular Orbitals of Planar Benzyl Carbocation
  • Molecular Orbital is where the electrons are
    located
  • Lowest Unoccupied Molecular Orbital represents
    distribution of positive charge.

36
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37
Perpendicular Benzyl Carbocation
38
Spin Density of Allyl Radical
Unpaired electron
39
Electrostatic Potentialof Ammonia
  • Electrostatic potential reveals site of
    protonation in acid-base reaction.

NH3 H NH4
40
Infrared Spectrum of Ethanol
41
The O-H Stretch
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