Molecular Visualization and Simulation with HyperChem

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Molecular Visualizationand Simulation with
HyperChem

• Thomas K. Green
• Department of Chemistry
• University of Alaska Fairbanks

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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
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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
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Features of Molecular Modeling

• Structure
• Stability
• Reactivity
• Properties

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Structural Models

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

CH3CH2OH
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Periodic Table
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Ethanol HOCH2CH3
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Tubes
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Ball and Stick
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Space-filling
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Nucleic Acids
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DNA
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Amino Acids
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Protein
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Computational Methods

• Molecular Mechanics
• Semi-Empirical
• ab initio

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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.

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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.

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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?
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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.

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Energy Minima
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Saddle Point
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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
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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
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S-Cis
S-Trans
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Space-Filling Model of S-Cis Conformation
Steric Repulsion of Hydrogen Atoms
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Stability of Benzyl Carbocation
900
Planar Hf ? 222 kcal/mol
Perpendicular Hf? 253 kcal/mol
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Resonance Stabilizationof Benzyl Carbocation
More Stable
Less Stable
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Molecular Orbitals of Planar Benzyl Carbocation

• Molecular Orbital is where the electrons are
  located
• Lowest Unoccupied Molecular Orbital represents
  distribution of positive charge.

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Perpendicular Benzyl Carbocation
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Spin Density of Allyl Radical
Unpaired electron
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Electrostatic Potentialof Ammonia

• Electrostatic potential reveals site of
  protonation in acid-base reaction.

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