An accurate DFT study within conformational survey of the d-form serine−alanine protected dipeptide

The conformational analysis of n-formyl-d-serine-d-alanine-NH(2) dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in β(L), γ(D), γ(L) and the alanine in γ(L) and γ(D) configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γ(D)(–)γ(L), is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γ(D)(–)γ(L) includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n(*) of intra‒ligand alanine moiety of dipeptide structure. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13065-023-01051-9.