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Molecular Visualization and Simulation with HyperChem Thomas K. Green Department of Chemistry University of Alaska Fairbanks Is the Time Right? “Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational

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molecular visualization and simulation with hyperchem

Molecular Visualizationand Simulation with HyperChem

Thomas K. Green

Department of Chemistry

University of Alaska Fairbanks

is the time right
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

slide3

“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

features of molecular modeling
Features of Molecular Modeling
  • Structure
  • Stability
  • Reactivity
  • Properties
structural models
Structural Models
  • 2-D Drawing Ethanol
  • 3-D Models of HyperChem

Sticks

Tubes

Ball and Stick

Space-Filling

CH3CH2OH

computational methods
Computational Methods
  • Molecular Mechanics
  • Semi-Empirical
  • abinitio
molecular mechanics
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.
semi empirical method
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.
ab initio methods
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

stability and geometry optimization
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.
conformational analysis of cyclohexane
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

bond rotation of butadiene
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

600

300

S-Cis 00

3.40 kcal/mol

2.80 kcal/mol

3.46 kcal/mol

slide31

S-Cis

S-Trans

slide32

Space-Filling Model of S-Cis Conformation

Steric Repulsion

of Hydrogen Atoms

stability of benzyl carbocation
Stability of Benzyl Carbocation

900

Planar

Hf 222 kcal/mol

Perpendicular

Hf 253 kcal/mol

molecular orbitals of planar benzyl carbocation
Molecular Orbitals of Planar Benzyl Carbocation
  • Molecular Orbital is where the electrons are located
  • Lowest Unoccupied Molecular Orbital represents distribution of positive charge.
electrostatic potential of ammonia
Electrostatic Potentialof Ammonia
  • Electrostatic potential reveals site of protonation in acid-base reaction.

:NH3 + H+ NH4+