계산화학. Zipse 교수의 강의 노트

Zipse 교수의 계산화학 강의 노트.
계산화학과 관련해서 UNIX 명령어와 vi 편집기에 대한 내용에서 시작해서 solvent effect에 관련한 내용까지 비교적 세심하게 정리되어 있다.
http://www.cup.uni-muenchen.de/oc/zipse/lv18099/topics.html

Table of contents

Overview of Topics in "Computational Chemistry"

summer semester

1. Basic UNIX and Chemistry Software
   1. UNIX software
      1. basic UNIX commands
      2. vi
      3. ghostview - viewing postscript files
      4. pbs - a queueing system
   2. application software I
      1. Gaussian
         1. input files for Gaussian 98
         2. running Gaussian jobs through a queueing system
         3. output files generated by Gaussian 98
      2. GaussView
      3. Molden
   
   
2. geometry optimization - what is the preferred structure of molecules?
   1. geometry definition in Gaussian 98
   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. 2nd derivatives - calculating molecular vibrations
   1. vibrational frequencies - practical considerations
   2. assigning vibrational frequencies
   3. the effects of isotopic substitution
   
   
4. thermochemistry I - connecting experiment and theory
   1. basic considerations
   2. reaction energetics
   3. Arrhenius and Eyring equations
   
   
5. theoretical methods I - 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

winter semester

6. theoretical methods II - where does the energy come from?
   1. correlated methods
      1. overview
      2. some output examples
   2. force field methods
   3. force field calculations in Gaussian 98
   4. Application software III: MacroModel
   
   
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. effective core potentials
   8. 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 Population Analysis analysis (NPA)
    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)
    
    
11. solvation effects - how does the solvent affect molecular system?
    1. Onsager reaction field theory
    2. the polarizable continuum model (PCM)
    3. SCIPCM
    4. the supermolecule approach