Molecular Modeling and Conformational Analysis

Experiment 1.O C - 2nd and 3rd Year Practical Organic Chemistry

This is an experiment which involves the use of computers for analysis of the 3D stucture of organic molecules. It is designed to improve understanding of alicyclic stereochemistry.

The experiment will involve a day's work in the Chemistry IT centre and count for one Unit, marked off in the usual way. The procedure is to book a day with Dr. Karl Harrison in the IT Centre, New Chemistry directly or by E-mail (karl.harrison@chem.ox.ac.uk).

The experiment involves the following :

1. Learning to use a standard Molecular Mechanics software.
2. Applying this to calculations on monocyclic cyclohexanes (does an axial tertiary-butyl group prefer chair to boat conformation?
3. Investigating the secondary alcohols formed by reduction of the perhydronaphthalenones shown - which is the most stable isomer and what are the full conformational possibilities?
4. Learning how to retrieve crystal structures from a database and comparing your conclusions with real structures.
5. Doing a short literature search to discover the stereochemistry of the reduction processes in practice.

An University of Oxford Chemistry IT Centre Course © Copyright 1997and 1998 John Brown & Karl Harrison