Jiang Yang, Zhang Haiyang, Tan Tianwei
Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China.
Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China.
J Chem Theory Comput. 2016 Jul 12;12(7):3250-60. doi: 10.1021/acs.jctc.6b00223. Epub 2016 Jun 7.
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.
对于具有多个金属中心等复杂生物系统的计算而言，用于金属离子的非键合虚拟模型极为必要。在此，我们给出了11种二价金属阳离子，即Mg(2+)、V(2+)、Cr(2+)、Mn(2+)、Fe(2+)、Co(2+)、Ni(2+)、Zn(2+)、Cd(2+)、Sn(2+)和Hg(2+)的非键合虚拟参数，这些参数经过优化，可与三种广泛使用的水模型（TIP3P、SPC/E和TIP4P-EW）兼容。这三组金属参数在显式水中同时再现了溶剂化自由能（ΔGsol）、第一溶剂化层中的离子 - 氧距离（IOD）和配位数（CN），相对误差小于1%。合理校正了由边界条件和静电相互作用处理引起的ΔGsol误差的主要来源，这确保了所提出参数与计算中使用的方法无关。这项工作对于含金属生物系统的计算研究具有重要价值。
