Molecular Dynamics of Chain Molecules

Abstract

Molecular dynamics studies of liquids and solids composed of short chain molecules are reviewed. The factors that need to be considered in choosing a set of interaction potentials for such systems are discussed; the Hamiltonian for such systems involves two three and four-body intramolecular terms which define the flexibility of the molecule and although one or more of these can, if necessary, be eliminated by using constraints ultimately the choice of interaction potential depends on the system being studied and the properties that are of interest. In the case of fluids much can be still learned from studies using the “bead” model in which methylene groups, for instance, are treated as single interaction sites. Topics discussed here include the chemical transformation rates between gauche and trans conformers, the evidence available regarding solvent effects on molecular conformations for small molecules and also the ways in which molecular flexibility can directly influence transport properties. The need to ensure the attainment of equilibrium in such systems where there are slowly relaxing degrees of freedom will be emphasised.