HRSMC Course "Molecular Modeling"

May 2008
Introduction

The goal of the standard exercises is for the participants to get started with the modeling programs PCSpartan, Gaussian, ADF and Maestro. Depending on previous experience it may not be necessary for all participants to carry out all exercises. In the first session simple tasks are to be performed, such as structure building and energy minimization. Practical problems are to be overcome such as connecting to the compute server, handling data files on unix systems, simple text editing, file transfer between computers and conversion between the data formats associated with the different programs. A list of the most basic commands and some useful links can be found here.

Of each exercise, a report will be prepared as soon as possible, showing the results and the conclusion in max. 4 powerpoint slides.

Standard Exercises

1. Molecular Structure, theory vs. experiment

Experimentally determined molecular structures (extracted from the Cambridge Structural Database) will be provided (mol2 structure files; pdf documents describing the crystal structure determination and bibliographical information). Download the mol2 file and import the structure into the program to be used.

a. optimize the structures with three of the following methods:

MMFF94s force field (Macromodel, via Maestro)
semi-empirical AM1 (PCSpartan)
HF/6-31G* (Gaussian)
any functional, DZP basis set (ADF)
b. collect the bond lengths and other relevant structural parameters in an Excel spreadsheet use this template ). For each bond give the atom types (see original mol2 file) in alphabetical order (e.g C.2 - C.3 not C.3 - C.2) and the distances in the experimental and computed structures.

Points of interest for the discussion:

Add relevant experimental details to the report (see the pdf file from the CSD search)
Have the hydrogen atom positions been determined with sufficient accuracy?
In evaluating the quality of the computational methods also consider other chemically relevant aspects, e.g. dihedral angles or intramolecular hydrogen bonds
What is the meaning of the different energies produced by the different calculations?

each team can select one of the following molecules for this exercise