Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model

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• 作者：Yang Jiang ; Haiyang Zhang ; Tianwei Tan
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2016
• 出版时间：July 12, 2016
• 年：2016
• 卷：12
• 期：7
• 页码：3250-3260
• 全文大小：547K
• 年卷期：0
• ISSN：1549-9626

文摘

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, Mg²⁺, V²⁺, Cr²⁺, Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Zn²⁺, Cd²⁺, Sn²⁺, and Hg²⁺, 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 (ΔG_sol), 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 ΔG_sol 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.