Syllabus for Chemistry 380.37 - Computational
Chemistry
Course Description: Chemistry 380.37 provides an introduction to common
techniques employed in computational chemistry. Emphasis is placed on molecular
mechanics and molecular dynamics, along with methods of molecular orbital theory.
Students will gain experience running major computational chemistry packages
on a UNIX-based graphics workstation.
COURSE SYLLABUS
I. Introduction to the Computing Environment
Hardware: SGI Personal Iris 4D/35
Operating system, basic UNIX commands
X Window System graphical user interface
A simple text editor: asedit
II. Introduction to Molecular Modeling
What is molecular modeling?
Types of molecular modeling techniques
Using molecular modeling to predict and explain experiments
How to choose the right technique for the system
III. Molecular Mechanics
Molecular potential energy surfaces
Conformations: global vs. local
Force fields: expressions for stretch, bend, torsion, etc.
Description of various force fields: MM3, Dreiding, AMBER, CHARMM, etc.
Methods for minimizing the energy
IV. Molecular Dynamics
Newton's equations for many particles
Verlet and related algorithms
Types of dynamics simulations: adiabatic, constant T, annealed, etc.
Conformational searching using MD and other methods
Free energy calculations
V. Numerical Techniques
VI. Quantum Mechanics Review
Time-independent Schrödinger equation
Operators
Wavefunctions
Electron spin
The variation principle
VII. Molecular Orbital Techniques
Basis sets
Hartree-Fock equations
Properties: Dipole moment, vibrations, etc.
Molecular orbitals and visualization
Determination of equilibrium geometries
Chemical reactions and transition states
Correlation energy
Semiempirical methods
Return to
Computational Science Courses
|