An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide.

ABSTRACT: The conformational analysis of N-formyl-D-serine-D-alanine-NH₂ 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.

SUBMITTER: Chahkandi B 

PROVIDER: S-EPMC10571400 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature