Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects

During the last two decades, numerous observed data obtained by various physical techniques, also supported molecular modeling approaches, have highlighted structuring features of tripeptides, as well their aggregation properties. Herein, we focus on structural dynamics four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess stability types secondary structures, β-strand, polyproline-II (pP-II), α-helix γ-turn, which formation had been described these tripeptides. Both implicit explicit hydration effects analyzed conformational energetic trimers. It has shown that use M062X (versus B3LYP) improve intramolecular H-bonds, especially inverse γ-turn equilibrium all Explicit reflected presence five water molecules around backbone polar sites (NH3+, N–H, CO NH2) considerably changes landscapes Characteristic intermolecular interactions evidenced calculations, emphasized.