Computational Chemistry: Catalysis in Chemical and Biological Systems

Course hours:
Kleiner Hörsaal (4.07), Physikal. Chemie, Klingelbergstrasse 80

Lectures
Tue: 10-12 and Thu: 16-17 (Nov 9, Dec 21)

Exercises:
Thu: 16-18 (Computer Laboratory, Ground Floor, Nov 16, 30, Dec 7)

Information:
The course is in English and is suited for undergraduate and graduate students interested in the use of computational methods to understand chemical, physical and biophysical processes.

Content:

  1. Introduction/Historical Overview
  2. Electronic Structure Theory: Hartree-Fock and Correlated Methods
  3. Intermolecular Interactions, Force Fields
  4. Optimization Techniques (Non-Gradient, Gradient) and Saddle Points
  5. Harmonic Analysis
  6. Classical Dynamics
  7. Molecular Dynamics (MD) Simulations
  8. Monte Carlo (MC) Simulations
  9. Analysis of Data
  10. Application I: Protein-Ligand Binding
  11. Application II: Peptide and Protein Folding
  12. Advanced Topics

During the course a number of "hands-on" exercises are treated and solved. They are essential to take as much advantage as possible from the course. You should be prepared to interact with the computer and be willing to use it as a means to understand a chemical, physical and biophysical process.

Link to UNIX Introduction from University of Surrey
Introduction to UNIX (Tutorials 1 and 2)

Overheads for electronic structure part based on Szabo and Ostlund

Density Functional Theory Based on lectures from David Tozer (http://www.dur.ac.uk/d.j.tozer/)

Source code for calculation of HeH+ with minimal (STO-nG) basis set; from Szabo and Ostlund (Modern Quantum Chemistry). Compile e.g. with "gfortran -o hehp hehp.f".

Handout accompanying hehp.f compiled from Szabo and Ostlund

Atomistic Simulations Molecular Dynamics, Force Fields and Monte Carlo

Tech Support for
Gaussian Keywords


Instructions and Input Files:

Exercise for Gaussian Calculations

Input file QST2 Test input file for QST2 calculation (SiH2 + H2 -> SiH4)

Input file IRC Test input file for IRC calculation (path from transition state of the above reaction towards product - SiH4 - and educt - SiH2 + H2)

Input file QST2 Input files for qst2 calculation for TS of cis- to trans-HONO and corresponding IRC calculation.

Exercise 2 Instructions for molecular dynamics simulation

Myoglobin A set of instructions and input files for MD simulations of ligands in myoglobin. Read instructions.txt and the accompanying manuscript before starting.

Normal Modes A set of instructions and input files for normal mode analysis of small molecules. Read instructions.txt and the accompanying manuscript before starting.

Free Energy Calculations A set of instructions and input files for free energy calculations. Read instructions.txt and the accompanying manuscript before starting.

Minimum Energy Paths A set of instructions and input files for minimum energy paths and transition state calculations. Read instructions.txt and the accompanying manuscript before starting.