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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

    Computer representation of floating point numbers

    Round-off errors

    Numerical differentiation

    Numerical integration

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



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