Density domain bonding topology and molecular similarity measures

Abstract

A systematic description of chemical bonding and molecular shape is based on a simple density domain (DD) principle. An electronic density domain is the formal body enclosed by a molecular isodensity contour (MIDCO) surface G(a) of some density threshold a. In the Density Domain approach, chemical bonding is described by the interfacing and mutual interpenetration of local, fuzzy charge density clouds. At high density thresholds, only disjoined, local nuclear neighborhoods appear. However, at lower density thresholds the separate density domains eventually join, and gradually change into a series of topologically different bodies. By monitoring the essential topological changes of these density domains as the density threshold a is varied, a detailed description of both the bonding pattern and the molecular shape is obtained.

Various formal molecular fragments are regarded as fuzzy moieties of electron densities, dominated by one or several nuclei. A fuzzy fragment of the electron density involves a whole range of density values and consequently cannot be described by a single MIDCO. However, such a fuzzy fragment can be represented by a sequence of density domains. There are only a finite number of topologically different bodies of density domains within the chemically important range of density values. As a consequence, a simple, discrete, algebraic representation is possible. Molecular shape and chemical bonding between fragments of a molecule are characterized by a finite sequence of density domains for a range of density values, by the corresponding sequence of topological patterns of their mutual interpenetration, and by the resulting algebraic structure.