Computational study of hydrogen-bonding complex formation of helical polypeptides with water molecule

The structure and the binding energy of complex formation of the helical polypeptides (poly-l-alanine, poly-l-glutamic acid, poly-γ-benzyl-l-glutamate) with water molecule have been investigated by molecular mechanics, semi-empirical PM3 method, and DFT (B3LYP/6-31G(d):B3LYP/3-21G) level of the theory within the ONIOM approach. The hydrogen-bonded complexes of water molecule and polar groups of α-helical peptides were investigated. The results indicate that the long side chains aid the formation of complexes with two hydrogen bonds where water molecule bridges two polar sites of polypeptide. Mainly, it demands a significant reorientation of side chains whereas the backbone parameters change insignificantly. All used methods provide a good description of the complex geometry but PM3 slightly underestimates the energy of the hydrogen bonds and MM overestimates it comparing with DFT results.