title: Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model.
abstract: A nonbonded dummy model for metal ions is highly imperative for the computation of complex biological systems with for instance multiple metal centers. Here we present nonbonded dummy parameters of 11 divalent metallic cations, namely, Mg(2+), V(2+), Cr(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), Sn(2+), and Hg(2+), that are optimized to be compatible with three widely used water models (TIP3P, SPC/E, and TIP4P-EW). The three sets of metal parameters reproduce simultaneously the solvation free energies (ΔGsol), the ion-oxygen distance in the first solvation shell (IOD), and coordination numbers (CN) in explicit water with a relative error less than 1%. The main sources of errors to ΔGsol that arise from the boundary conditions and treatment of electrostatic interactions are corrected rationally, which ensures the independence of the proposed parameters on the methodology used in the calculation. This work will be of great value for the computational study of metal-containing biological systems.
authors.affiliation: Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China.
authors.forename: Tianwei
authors.initials: T
authors.lastname: Tan