The first priority is to get a reasonable idea of the principles of Molecular
Mechanics, which uses Newtonian mechanics to determine the geometry and enthalpy
of organic molecules. More details can be obtained from the CAChe applications
manual, but the computational procedure, involves starting with a fixed set
of atomic positions, which may be derived from a drawing of the molecule, and
measuring bond lengths, bond angles, interatomic non-bonded interactions and
torsional angles for that structure. These are assessed in comparison to an
"ideal" structure which provides the best trade-off between the different
types of strain -
The programme then iterates small changes in atomic positions and accumulates those which diminish the total strain energy, finding "descent gradients" on the overall energy surface. When a minimum is reached the computation stops. Of course there is a danger of encountering false minima, and depending on how sophisticated the computational procedure, depends the reliability of the final result.
For desktop computers the CAChe system is about as good as is available.
An University of Oxford Chemistry IT Centre Course © Copyright 1997 John Brown & Karl Harrison