title: An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties.
abstract: 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 topology of the electron density, rho(r). This theory identifies an atom in a molecule with a quantum mechanical open system and, consequently, all of the atom's properties are unambiguously defined. AIM recovers the basic empirical cornerstone of chemistry: that atoms and functional groups possess characteristic and additive properties that in many cases exhibit a remarkable transferability between different molecules. As a result, the theory enables the theoretical synthesis of a large molecule and the prediction of its properties by joining fragments that are predetermined as open systems. The present article is the first of a series (in preparation) that explore this possibility for polypeptides by determining the transferability of the building blocks: the amino acid residues. Transferability of group properties requires transferability of the electron density rho(r), which in turn requires the transferability of the geometric parameters. This article demonstrates that these parameters are conformation-insensitive for a representative amino acid, leucine, and that the atomic and bond properties exhibit a corresponding transferability. The effects of hydrogen bonding are determined and a set of geometrical conditions for the occurrence of such bonding is identified. The effects of transforming neutral leucine into its zwitter-ionic form on its atomic and bond properties are shown to be localized primarily to the sites of ionization.
authors.affiliation: Chemistry Department, McMaster University, Hamilton, Ontario, Canada.
authors.forename: C F
authors.initials: CF
authors.lastname: Matta
authors.forename: R F
authors.initials: RF
authors.lastname: Bader
mesh_terms: D000596:Amino Acids / Q000737:chemistry* / Q000235:genetics*; D003198:Computer Simulation; D004583:Electrons; D007930:Leucine / Q000737:chemistry; D008956:Models, Chemical; D015233:Models, Statistical; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry
chemical_list: D000596:Amino Acids; D012694:Serine; D007930:Leucine