Molecular mechanics and molecular shape: Part VI. The response of simple molecules to bimolecular association

Abstract

A molecular-mechanical force field, originally developed to calculate the structure and conformation of single molecules, has been applied to pairs of identical molecules lying at close proximity. The prototypes examined are very simple - short alkanes and short haloalkanes - but do include cases with conformational diversity and possible electrostatic effects. The optimized mutual orientations include the parallel alignment of linear alkanes, head-to-tail orientations of haloalkanes, as well as the head-to-head association, known from the crystallographic literature. The effect of aggregation on the conformation of the separate partners has been studied, and the intramolecular response characterized: in all cases examined, the partners contract. The computed energy gains are of the expected order of magnitude, the main contribution coming always from what molecular-mechanists label “non-bonded attraction”. Graphical representations of optimized orientations show the “protrusion-in-cleft” matching of molecular surfaces.