title: Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential.
abstract: A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.
authors.affiliation: Center for Computational Research, The State University of New York at Buffalo, Buffalo, NY 14260, USA. mfrein@buffalo.edu
authors.forename: Marek
authors.initials: M
authors.lastname: Freindorf
authors.forename: Yihan
authors.initials: Y
authors.lastname: Shao
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Furlani
authors.forename: Jing
authors.initials: J
authors.lastname: Kong
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry*; D001216:Asparagine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D003198:Computer Simulation; D006639:Histidine / Q000737:chemistry; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D012694:Serine / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000081:Acetamides; D000596:Amino Acids; D011506:Proteins; D001224:Aspartic Acid; D012694:Serine; D006639:Histidine; D001216:Asparagine; D008239:Lysine; C018595:N-methylacetamide