Conformational analyses for alanine oligomer during hydration by quantum chemical calculation (QCC)

The structure and association energy of hydrated l-alanine pentamers at the hydration rate (h) of 0–1 were calculated by quantum chemical calculation (QCC) using the density functional theory [B3LYP/6-31G(d, p)] method for three kinds of stable conformers (β-extended: t−/t+, PP_II-like: g−/g+, α-helix: g−/g−) converged by convergent calculations from l-alanine pentamers in gas phase. Water molecules are mainly inserted between intramolecular hydrogen bond of CO–HN in PP_II-like and α-helix conformers and attached to the CO group in β-extended conformer. α-Helix conformer turns to PP_II-like conformer at higher hydration rate. The association energy decreased with the increase of the hydration rate, indicating that the conformers were stabilized by the hydration. It was found that PP_II-like conformer, which was the most stable in the anhydrate state, was also the most stable in the hydrate state. This structure corresponds to a middle structure of PP_II (g−/t+) and β-extended (t−/t+) structures. These results obtained by energy calculation using QCC support the experimental results by Eker et al. and Graf et al., who reported that alanine oligomer exhibited a mixture of PP_II and β-extended structure in aqueous solution.