An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties

The theory of Atoms-In-Molecules (AIM) is a partitioning of the real space of a molecule into disjoint atomic constituents as determined by the topolo gy of the electron density, rho(r), This theory identifies an atom in a mol ecule with a quantum mechanical open system and, consequently, all of the a tom's properties are unambiguously defined. AIM recovers the basic empirica l cornerstone of chemistry: that atoms and functional groups possess charac teristic and additive properties that in many cases exhibit a remarkable tr ansferability between different molecules. As a result, the theory enables the theoretical synthesis of a large molecule and the prediction of its pro perties by joining fragments that are predetermined as open systems. The pr esent article is the first of a series (in preparation) that explore this p ossibility for polypeptides by determining the transferability of the build ing blocks: the amino acid residues. Transferability of group properties re quires transferability of the electron density rho(r), which in turn requir es the transferability of the geometric parameters. This article demonstrat es that these parameters are conformation-insensitive for a representative amino acid, leucine, and that the atomic and bond properties exhibit a corr esponding transferability. The effects of hydrogen bonding are determined a nd a set of geometrical conditions for the occurrence of such bonding is id entified. The effects of transforming neutral leucine into its zwitterionic form on its atomic and bond properties are shown to be localized primarily to the sites of ionization, (C) 2000 Wiley-Liss, Inc.