An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

Jin Yu Xiang, Jay W. Ponder
2013 Journal of Chemical Theory and Computation  
An extensible polarizable force field for transition-metal ions was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parametrization were presented for copper(II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins.
more » ... ar dynamics (MD) simulations were performed on aqueous copper(II) ion at various temperatures as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn−Teller distortion for hexaaqua copper(II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a six-coordination first solvation shell for aqueous copper(II) ion and a 1.8 ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.
doi:10.1021/ct400778h pmid:25045338 pmcid:PMC4102146 fatcat:mfhg6eolj5f2nirvj4doq2q6fy