Structure and stability of alanine, glycine and serine conformers and effects of explicit water molecules: A quantum mechanical study

The explicit atomic interactions of various dipeptide conformations are investigated by quantum mechanical calculations using density functional theory and ab initio molecular orbital theory. The structure and stability of three amino acid systems are analyzed: (1) gas phase, one water and two water alanine dipeptide; (2) gas phase glycine dipeptide and tripeptide; and (3) gas phase serine dipeptide. It is found that without water, six alanine dipeptide conformers exist with relative energies of less than 7 kcal mol-1. Addition of explicit water molecules initiates the collapse of several conformers to the more stable C7eq and C5, with respective energies of 0.0 and 0.2 kcal/mol. Only three unique glycine dipeptide conformers, C7eq, C5 and beta2, are found to exist in the gas phase. Geometry optimization of thirteen glycine tripeptide moieties results in the C5-C5 conformer having the greatest stability, Also competitive are the C7eq-C7eq and C7eq-C7eq(-) conformations, which are within 1 kcal/mol. (Abstract shortened by UMI.).