Molecular conformations and molecular shape: A discrete characterization of continua of van der Waals surfaces

A characterization of molecular model surfaces is proposed. It is based on a graph associated with the van der Waals surface, defined by the detailed information on the interpenetration of van der Waals spheres of the constituent atoms. This “van der Waals graph” describes the three-dimensional body of the molecule, and it does not coincide in general with the less informative bond graph obtainable from the molecular skeleton. The description in terms of the graph reveals clearly the changes in molecular shape induced by conformational rearrangements. The nuclear configurations can be classified by the graph associated with the molecular surface, and the graph-theoretical analysis provides a rigorous partitioning of the configurational space based on shape properties.

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