Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Abstract

The geometries of the 20 genetically encoded amino acids were optimized at the restricted Hartree-Fock level of theory using the 6-31+G* basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X-ray crystallography. The study demonstrated that the geometric parameters for the main-chain group and for the bonds and common functional groups of the side-chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the Calpha-N bond length in a peptide being shorter than in the charged species Calpha-NH3+ is resolved when the charge separation is gauged by the differences in the charges of the Calpha and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted IUPAC-IUB rules, is proposed to uniquely identify every atom and bond in the amino acids.

Quantum chemical analysis of ATP, GTP and related compounds in gas phase

“…The quantum theory of atoms in molecules is based on the analysis of electronic density topology and identifies chemical bond as a bond critical point (BCP) and corresponding bond paths (BP). Because of flexibility and reliability of this method, many researches have been devoted to obtain chemical bond strength and nature in both organic and inorganic chemistry, via QTAIM analysis [17][18][19]. What distinguishes this research from others is the characterization of terminal P-O bond in terms of QTAIM parameters and analysis of the effect of different segments on the strength of such a P-O bond.…”

An Introduction to the Quantum Theory of Atoms in Molecules

“…Atomic properties have also been used empirically to predict several experimental properties including for example, the pK a of weak acids from the atomic energy of the acidic hydrogen [96], a wide array of biological and physicochemical properties of the amino acids, including the genetic code itself, and the effects of mutation on protein stability [60], protein retention times [97], HPLC column capacity factors of high-energy materials [98], NMR spin-spin coupling constants from the electron delocalization indices [99,100], simultaneous consistent prediction of five bulk properties of liquid HF in MD simulation [101], classification of atom types in proteins with future potential applications in force-field design [60,[102][103][104], reconstructing large molecules from transferable fragments or atoms in molecules [60,[105][106][107][108][109][110][111][112][113][114][115][116][117][118][119] (see also Chapters 11 and 12), atomic partitioning of the molecular electrostatic potential [120][121][122], prediction of hydrogenbond donor capacity [123] and basicity [124], and to provide an atomic basis for curvature-induced polarization in carbon nanotubes and nanoshells [125].…”

Fragment Transferability Studied Theoretically and Experimentally with QTAIM – Implications for Electron Density and Invariom Modeling

“…Bader and Matta have published complete topological data on all twenty amino acids based on theoretical calculations [16][17][18] and experimental studies on sixteen of the twenty amino acids have been performed by different groups, as detailed in Table 12.1. This class of compounds is thus the first for which a complete set of theoretical electron-density data is available and for which the corresponding experimental studies are approaching completeness.…”