Database Organization and Similarity Searching with E-State Indices

Abstract

Any approach to the quantitation of atoms or fragments within a molecule must be built upon the context and their relationships operating within this complex system. We can view each atom present in a molecule as existing in a field within a molecule in which all other atoms share and participate. The methyl group in the toluene molecule is different from the methyl group in acetic acid by virtue of its different molecular environment and connectivity, in spite of its intrinsic state as a methyl group. Quantifying the methyl group requires both an identity as a methyl group and it’s relationship to all other atoms present in the molecule in which it resides. The influence of all other atoms present in the toluene molecule makes the methyl group unique relative to other methyl groups in all other possible molecules which include a methyl group. There are also intrinsic characteristics of the methyl group which transcend its molecular context. These inner characteristics must be identified in order to correctly describe this molecular fragment in a quantitative way. We consider each of these characteristics in turn.