Atomic properties of selected biomolecules: quantum topological atom types of carbon occurring in natural amino acids and derived molecules.

Abstract

We seek to recover rigorous atom types from amino acid wave functions. The atom types emerge from a cluster analysis operating on a set of seven atomic properties, including kinetic energy, volume, population, and dipole, quadrupole, octupole, and hexadecapole moments. These properties are acquired by partitioning the molecular electron density into quantum topological atoms. Wave functions are generated at the B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for a sensible conformation of each of the 20 naturally occurring amino acids and smaller derived molecules, which together constitute a data set of 57 molecules. From this set 213 unique quantum topological carbons are obtained, which are linked according to the similarity of their properties. After introducing a statistical separation criterion, our cluster analysis proposes two representations: a cruder one with 5 atom types and a finer one with 21 atom types. The immediate coordination of the central carbon plays a major role in labeling the atom types.