Overview of Topics in "Computational Chemistry 1"

1. Basic UNIX and Chemistry Software
   1. UNIX software
      1. getting started with LINUX
      2. basic UNIX commands
      3. vi
      4. ghostview - viewing postscript files
      5. pbs - a queueing system
   2. application software I
      1. Gaussian
         1. input files for Gaussian 03
         2. running Gaussian jobs through a queueing system
         3. 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. vibrational frequencies - practical considerations
   2. assigning vibrational frequencies
   3. the effects of isotopic substitution
5. thermochemistry I - connecting experiment and theory
   1. basic considerations
   2. reaction energetics
   3. Arrhenius and Eyring equations
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
   1. minimal basis sets (STO-xG)
   2. split valence basis sets
   3. polarization functions (p,d,f,g)
   4. diffuse basis functions
   5. extended basis sets
   6. correlation consistent basis sets
   7. the basis set superposition error (BSSE)
8. inspecting molecular orbitals
   1. from the Gaussian output file
   2. with MOLDEN
   3. with GaussView
9. 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)