A reconnaissance DFT study of the full conformational analysis of N-formyl-L-serine-L-alanine-NH2 dipeptide.

Abstract

Theoretical conformational analysis of N-formyl-L-serine-L-alanine-NH2 dipeptide model was investigated using B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) calculations. In this research, 243 total possible conformations of the dipeptide model were optimized including 87 stable conformers and the other disappeared ones migrated to more stable geometries. Migration pattern suggests more stability of the dipeptide model with the serine (ser) in βL, γL, and γD and the alanine (ala) in γD and γL configurations, along with 26 of the found conformers having β-turn structures. Our calculations reveal that the most stable conformer, γL+γD, is in β-turn region of Ramachandran map; therefore, serine-alanine (ser-ala) dipeptide model should be adopted with a β-turn conformation. The atoms in molecules (AIM) topological analysis was carried out to characterize the nature of the intramolecular hydrogen bonding in β-turn structures. The γL+γD, including three hydrogen bonds, has the highest stability, while αLaγL as the most unstable β-turn conformer bears two and one hydrogen bonds at the B3LYP/6-311+G(d,p) and M06-2X/6-311+G(d,p) levels of theory, respectively. Graphical abstract.