Computational Chemistry and
Molecular Modeling (CH504/628)
I. Introduction
A. Historical aspects of
theoretical chemistry
B. Thermodynamics and kinetics
II. Thermodynamic quantities from group
equivalents
A. Strain energies
B. Limitations of methods based on group
equivalents
III. Geometry and energy
A. Geometries from Z
Matrices
B. Computer graphics and geometries
C. Overview of computational methods
1. Molecular Mechanics vs.
Quantum Mechanics
D. Problems associated with energy
minimizations
IV. Molecular Mechanics Calculations
A. Force fields for MM
calculations
Force Field References
B. Examples of molecular mechanics
calculations
1. Analysis of output
2. Treatment of conjugated pi
systems
3. Hydrogen bonding
C. The local minima problem
D. Examples of the Prediction of Reaction
Products Using Molecular Mechanics
V. Qualitative molecular orbital
theory
A. The concept of molecular orbitals
1. Orbital
symmetries
B. Group orbitals
1. Molecular orbitals from
group orbitals
C. Frontier molecular orbital theory
VI. Semi-empirical calculations
A. The Schrödinger
equation
B. Simple Huckel calculations
1. HOMOs and LUMOs
2. The concept of aromaticity
C. Extended Huckel calculations
1. Used to obtain orbital
Symmetries
2. Correlation diagrams
D. SCF calculations
E. Semi-empirical calculations including
SCF
1. Introduction to various
methods (MNDO, AM-1, PM3, etc)
2. The Output of a MOPAC or AMPAC
Calculation
a. Optimized geometry, heat of
formation, ionization potential, molecular orbitals, atomic electron
densities and charges, dipole moment, bond orders
3. Semi-empirical calculations on open
shell systems
4. Examples of the use of semi-empirical
calculations
VII. Ab initio molecular orbital theory
A. Basis sets available
1. The concept of Gaussian
orbitals
2. Minimal basis sets
3. Split valence basis sets
a. Addition of d
orbitals
B. Electron correlation
C. Density functional theory
D. The output of a Gaussian
calculation
E. Comparisons between semi-empirical and
ab initio calculations
VIII. Energies and geometries of transition
states
A. Defining a transition
state
B. Estimation of transition state energies
using qualitative MO theory
1. FMO theory and correlation
diagrams
C. Quantum mechanical calculations of
transition state energies
1. Example: the Diels-Alder
reaction
D. Molecular mechanics treatment of
transition states
1. The Diels-Alder
reaction
2. Cyclization of 5-hexenyl radicals
E. Transition state spectroscopy - theory
and experiment in concert
IX. The role of solvent in molecular
modeling studies
A. Differences in gas phase vs.
solution
1. Calculation of dipole
moments and heats of solution
2. Treatment of biological molecules
B. The SN2 Reaction as an illustrative
example of solvent effects
X. Molecular Dynamics Calculations
A. Conformations of small
molecules
B. Molecular dynamics and experiments in
determining the structures of macromolecules.
XI. Examples of the use of computational
chemistry to solve chemical problems