Toward a computed structure database: methodology for effective molecular orbital computations

This work provides a concise description and presentation of selected results emerging from the application of an established modular definition of molecular structure to molecular orbital computations. Perturbations in the relative spatial orientation of the constituent phenyl ring carbon nuclei in benzene, phenol and conformers of Ac-Phenylalanine-NH2, Ac-Phenylalanine-NHMe and Ac-Tyrosine-NHMe, each geometry optimized at the B3LYP/6-31G(d) level of ab initio theory, were investigated. Several stable conformers were selected for the peptide models. The influence of basis-set refinement was investigated using the Ac-Phenylalanine-NH2 system, applying the 6-31G(d,p) and 6-31+G(d) levels of theory. The deviation of the phenyl structural elements from that of benzene was statistically negligible in all cases, with standard deviations of approximately 0.001 Å, 0.15°, 0.20°, for the phenyl ring carbon bond lengths, bond angles, dihedral angles, respectively. Total and relative energies are also presented, showing that the phenyl ring structures of high energy model peptide conformers are also immune to perturbation.