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

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.