Geometry and vibrational frequencies of the helical polypeptide complexes with ligand molecules

The complexes of alpha helical polypeptides and individual molecules of water, acetonitrile, and 1,4-dioxane have been investigated. We used 16-mer of polyalanine (PA), polyglutamic acid (PGA) and poly-γ-benzyl-L-glutamate (PBG). Full geometry optimization was performed for polypeptides and their complexes with ligands, each structure has been characterized by the vibrational analysis and the interaction energy including the correction for zero point vibrational energy. Polyalanine creates by single complex with water molecule, acetonitrile, and dioxane. Polyglutamic acid forms five different complexes with water molecule, and three complexes with acetonitrile and two complexes with dioxane. Two complexes of poly-γ-benzyl-L-glutamate with each ligand were found. Carbonyl oxygen of PGA and PBG confirms its strong acceptor character by participation in formation of all obtained complexes with water and acetonitrile. The long side chains of PGA and PBG aid the formation of complexes with two hydrogen bonds where ligand molecule bridges two polar sites of polypeptide. Most of complexes of dioxane with polypeptides are produced due to weak hydrogen bonds of type CH···O. Strong shifts for the stretching vibrations of the interacting group of polypeptides and ligands under the complex formation are detected. Obtained frequencies are in a good agreement with known experimental data. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011