Molecular bonding profiles

We present a refinement of recently proposed characterization of molecules based on a sequence of powers of interatomic separations referred to as molecular profiles. The molecular profiles and closely related shape profiles were based on the averaging contributions arising from different powers of interatomic distances for atoms in a molecule or atoms at the molecular periphery, respectively. Consequently, molecular models in which atoms have the same set of coordinates but different bonding patterns will result in identical molecular profiles. In this article we outline a refinement of molecular profiles in which the bonding pattern in a molecule is fully acknowledged. This is accomplished by adding “ghost” sites along chemical bonds. The distance-based invariants of the augmented matrix reflect the bonding pattern of a structure giving different molecular profiles for molecules having the same atomic coordinates but different bondings. The procedure is general and applies to two-dimensional and three-dimensional molecular skeletons. Equally, the approach can be applied to van der Waals-type molecular surfaces and molecular contours of equal electron densities in order to obtain characterization of more realistic molecular models.

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