Computational Chemistry

## Overview of Topics in

"Computational Chemistry"

- Basic UNIX and Chemistry Software
- UNIX software
- getting started with LINUX
- basic UNIX commands
- vi
- ghostview - viewing postscript files
- pbs - a queueing system

- application software I
- Gaussian
- input files for Gaussian 03
- running Gaussian jobs through a queueing system
- output files generated by Gaussian 03

- GaussView
- Molden

- geometry optimization - what is the preferred structure of molecules?
- geometry definition in Gaussian 03
- coordinate systems
- using symmetry
- internal coordinates
- cartesian coordinates
- redundant internal coordinates
- geometry optimization - basic considerations
- Newton-Raphson (NR) optimization
- comparative examples

- transition state optimization
- scanning bond distances, bond angles, and dihedral angles
- eigenvector following with the Berny algorithm
- global search algorithms: STQN

- reaction path following
- following the reaction pathway - choosing direction, stepsize, and convergence parameters
- a worked example
- choosing a coordinate system

- Searching conformational space with Force Field methods
- force field methods
- force field calculation with TINKER
- force field calculations in
*Gaussian 03*

- 2nd derivatives - calculating molecular vibrations
- vibrational frequencies - practical considerations
- assigning vibrational frequencies
- the effects of isotopic substitution

- thermochemistry I - connecting experiment and theory
- basic considerations
- reaction energetics
- Arrhenius and Eyring equations

- theoretical methods - where does the energy come from?
- Hartree-Fock (HF) theory
- basic considerations
- treating open shell systems: RHF, UHF, ROHF
- convergence of SCF calculations
- stability of wavefunctions
- performance considerations

- density functional theory (DFT)
- semiempirical methods
- Application software II: MOPAC

- basis sets for molecular system
- minimal basis sets (STO-xG)
- split valence basis sets
- polarization functions (p,d,f,g)
- diffuse basis functions
- extended basis sets
- correlation consistent basis sets
- effective core potentials
- the basis set superposition error (BSSE)

- thermochemistry II - increasing accuracy
- Gaussian Theories: G2 and G3
- isodesmic reactions

- inspecting molecular orbitals
- from the
*Gaussian* output file
- with MOLDEN
- with GaussView

- population analysis - where really are these electrons?
- the Mulliken population analysis
- the Natural Population Analysis analysis (NPA)
- inspecting the molecular electrostatic potential
- fitting the molecular electrostatic potential I: CHELPG
- fitting the molecular electrostatic potential II: Merz-Singh-Kollman (MK)
- the Atoms in Molecules analysis (AIM)
- calculating the (Pauling bond order )

- solvation effects - how does the solvent affect molecular system?
- Onsager reaction field theory
- the polarizable continuum model (PCM)
- SCIPCM
- the supermolecule approach

` Questions & Comments to: suleechem@skku.edu
`