A QM/MM approach with effective fragment potentials applied to the dipeptide-water structures

Abstract An application of the hybrid quantum mechanical and molecular mechanical (QM/MM) model to calculations of the structures of the hydrogen-bonded complex of the dipeptide N-acetyl- l -alanine N′-methylamide with water molecules is described. This particular approach is essentially based on the effective fragment potential theory [J. Phys. Chem. A 105 (2001) 293]. We discuss both options in the QM/MM treatment of the system, considering once the dipeptide as a quantum part and water molecules as a MM subsystem, and vice versa, taking the dipeptide as a collection of effective fragments, while water molecules constitute a QM part. The first method is realized in the gamess program, in the second case a new version, combining quantum chemical and molecular mechanical packages is required. Our approach assumes that the MM subsystem is viewed as a flexible composition of effective fragments while fragment–fragment interactions are replaced by the MM force fields. It is shown that these QM/MM models correctly describe the conformational properties of dipeptide, namely, the changes in the backbone angles φ and ψ due to complexation with water.