Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.
Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.
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DOI：
10.1021/ct100091j
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发表时间：
2010-07-13
影响因子：
5.5
通讯作者：
Ren, Pengyu
中科院分区：
文献类型：
--
作者：
Wu, Johnny C.;Piquemal, Jean-Philip;Chaudret, Robin;Reinhardt, Peter;Ren, Pengyu
在分子动力学模拟中，利用极化力场研究了锌二价阳离子的水合自由能、结构和动力学。Zn 2+的参数来自气相从头计算的Zn 2 +-水二聚体。基于约束空间轨道变化（CSOV）的计算调整基于托尔的偶极子极化，同时还讨论了对称自适应微扰理论（SAPT）的方法。通过比较AMOEBA Zn ~（2+）-水的二聚化能与几个理论水平和基组在一定距离范围内的结果，得到了Zn ~（2+）的vdW参数。随后进行了分子动力学模拟的Zn 2+溶剂化在散装水与极化力场。计算得到的第一壳层水配位数、水停留时间和水化自由能与实验值和前人的理论值一致。该研究补充了广泛的约化变分空间（RVS）和电子局域化函数（ELF）的计算，以解开在Zn 2+（H2O）n（n= 1，6）配合物的成键的性质，并分析电荷转移的复合物的贡献。结果表明，由于反协同效应和金属-配体键性质的变化，电荷转移的重要性随着Zn-水簇合物尺寸的增大而减小。当体系接近凝聚相时，Zn（II）-水相互作用中的共价效应被消除，体系的诱导作用主要由极化决定。为了构造一个“有效的”经典极化电位的Zn 2+在散装水，因此，应该避免过度拟合的从头算电荷转移能量的Zn 2 +-水二聚体。事实上，为了避免高估凝聚相多体效应，这是至关重要的可极化的分子动力学的可转移性，电荷转移不应该包括在经典的极化贡献，并应优选地被纳入成对的货车范德华贡献或明确处理。
The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn2+ are derived from gas-phase ab initio calculation of Zn2+-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn2+ have been obtained by comparing the AMOEBA Zn2+-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn2+ solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn2+(H2O)n (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an “effective” classical polarizable potential for Zn2+ in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn2+-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.
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影响因子：
4.1
作者：
BENNETT, CH
通讯作者：
BENNETT, CH
影响因子：
3
作者：
Gresh, N;Piquemal, JP;Krauss, M
通讯作者：
Krauss, M
影响因子：
2.8
作者：
CAMINITI, R;LICHERI, G;PINNA, G
通讯作者：
PINNA, G
影响因子：
5.5
作者：
de Courcy, B.;Pedersen, L. G.;Parisel, O.;Gresh, N.;Silvi, B.;Pilme, J.;Piquemal, J. -P.
通讯作者：
Piquemal, J. -P.
影响因子：
4.4
作者：
BECKE, AD;EDGECOMBE, KE
通讯作者：
EDGECOMBE, KE