Overview of Topics in "Computational Chemistry"

  1. Basic UNIX/WINDOWS and Chemistry Software
    1. UNIX software
      1. getting started with LINUX
      2. basic UNIX commands
      3. vi
      4. ghostview - viewing postscript files
      5. a queueing system
    2. WINDOWS software
      1. getting started with WINDOWS
      2. text editor


     3. application software I

    1. Gaussian
      1. input files for Gaussian 03
      2. running Gaussian jobs through a queueing system under UNIX/LINUX
      3. running Gaussian jobs under WINDOS
      4. output files generated by Gaussian 03
    2. GaussView
    3. Molden

  2. geometry optimization - what is the preferred structure of molecules?
    1. geometry definition in Gaussian 03
    2. coordinate systems
      1. using symmetry
      2. internal coordinates
      3. cartesian coordinates
      4. redundant internal coordinates
      5. geometry optimization - basic considerations
      6. Newton-Raphson (NR) optimization
      7. comparative examples
    3. transition state optimization
      1. scanning bond distances, bond angles, and dihedral angles
      2. eigenvector following with the Berny algorithm
      3. global search algorithms: STQN
    4. reaction path following
      1. following the reaction pathway - choosing direction, stepsize, and convergence parameters
      2. a worked example
      3. choosing a coordinate system

  3. Searching conformational space with Force Field methods
    1. force field methods
    2. force field calculations in Gaussian 03
    3. force field calculation with TINKER

  4. 2nd derivatives - calculating molecular vibrations
    1. overview and theorie
    2. vibrational frequencies - practical considerations
    3. assigning vibrational frequencies
    4. the effects of isotopic substitution

  5. thermochemistry I - connecting experiment and theory
    1. basic considerations
    2. reaction energetics
    3. Arrhenius and Eyring equations
    4. Activation barriers, velocities and Half-times 

  6. theoretical methods - where does the energy come from?
    1. Hartree-Fock (HF) theory
      1. basic considerations
      2. treating open shell systems: RHF, UHF, ROHF
      3. convergence of SCF calculations
      4. stability of wavefunctions
      5. performance considerations
    2. density functional theory (DFT)
    3. semiempirical methods
    4. Application software II: MOPAC
    5. correlated methods

  7. basis sets for molecular system (whole document as pdf file)
    1. Introduction
    2. minimal basis sets (STO-xG)
    3. split valence basis sets
    4. polarization functions (p,d,f,g)
    5. diffuse basis functions
    6. extended basis sets
    7. correlation consistent basis sets
    8. effective core potentials
    9. practical considerations
    10. the basis set superposition error (BSSE)

  8. thermochemistry II - increasing accuracy
    1. Gaussian Theories: G2 and G3
    2. isodesmic reactions

  9. inspecting molecular orbitals
    1. from the Gaussian output file
    2. with MOLDEN
    3. with GaussView

  10. population analysis - where really are these electrons?
    1. the Mulliken population analysis
    2. the Natural Bond Orbital (NBO) Analysis
    3. inspecting the molecular electrostatic potential
    4. fitting the molecular electrostatic potential I: CHELPG
    5. fitting the molecular electrostatic potential II: Merz-Singh-Kollman (MK)
    6. the Atoms in Molecules analysis (AIM)
    7. calculating the (Pauling bond order )
    8. Advanced exercise and theory

  11. solvation effects - how does the solvent affect molecular systems?
    1. Onsager reaction field theory
    2. the polarizable continuum model (PCM)
    3. SCIPCM
    4. the supermolecule approach