Quantum mechanical study of secondary structure formation in protected dipeptides

Abstract

An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH₂, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γ_L–γ_L(g−) and β-turn I(g+) in Ac-Gly-Phe-NH₂, and Ac-Ala-Phe-NH₂, and as the closely related γ_L(g+)–γ_L(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH₂. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH₂ the minimum energy structure corresponds to the experimentally non detected β-strand.