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.

Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine

“…They found trans;exp (% bcp ) = 0.09 e Å À3 and trans;exp (r 2 % bcp ) = 3.5 e Å À5 . As a first extensive work on transferability from theoretical calculations, Matta and Bader carried out a pilot study for all 20 genetically encoded amino acids (Matta & Bader, 2000, 2002, 2003. The transferability indices they found for the mean values of the density %(r) and the Laplacian r 2 %(r) at the bond-critical point of all common bonds are trans;theo (% bcp ) = 0.02 e Å À3 and trans;theo (r 2 % bcp ) = 0.5 e Å À5 .…”

Molecular and crystal properties of ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate from experimental and theoretical electron densities

“…All recently undertaken studies of the electron density in peptides, biomolecules and related compounds eventually face the question 'how transferable are the characteristics of the electron density in a series of similar compounds as well as among different conformers of the same molecule?'. Some workers suggest using the multipole-model parameters as the transferable moieties (Pichon-Pesme et al, 1995;Jelsch et al, 2000;Pichon-Pesme et al, 2004;Koritsanszky et al, 2002;Lecomte et al, 2005), while others (Chang & Bader, 1992;Popelier & Bader, 1994;Breneman & Rhem, 1997;Popelier, 1999;O'Brien & Popelier, 1999Matta & Bader, 2000, 2002Dittrich et al, 2002;Whitehead et al, 2003;Popelier & Aicken, 2003;Dittrich et al, 2003;Cortes-Guzman & Bader, 2004) deal with characteristics arising from Bader's (1990Bader's ( , 2005 Quantum Theory of Atoms in Molecules and Crystals (QTAMC). The question of whether experimental or theoretical electron densities provide the most reliable basis for such an analysis is also the subject of some discussion (Pichon-Pesme et al, 2004; Volkov, Korit-sanszky, Li .…”

When does a hydrogen bond become avan der Waalsinteraction? a topological answer

“…Thus, it appears that for both classical and nonclassical H‐bond systems, the SF is able to determine and reveal the consequences of chemical transferability, confirming again to be a robustness descriptor.…”