A complete conformational study of N-formyl-D-serine-D-alanine-NH2 dipeptide

Abstract

Abstract The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was comprehensively studied using the density functional theory methods in the gas and solution phases. The all-expected 35=243 stable conformers were explored, where 91 conformers were located, and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model with the serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side-chain–backbone interactions revealed that the most stable conformer, γD–γL, is in the β − turn region of the Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β − turn conformation. QTAM consideration of the intramolecular hydrogen bonding in β-turns disclosed the highest stable conformer as γD–γL includes the three hydrogen bonds. The computed UV-Vis spectrum alongside of NBO calculation showed and explained the five main electronic transition bands derived of n→ n* of intra-ligand alanine moiety of dipeptide structure.