Representation of Zn(II) complexes in polarizable molecular mechanics.: Further refinements of the electrostatic and short-range contributions.: Comparisons with parallel ab initio computations
Representation of Zn(II) complexes in polarizable molecular mechanics.: Further refinements of the electrostatic and short-range contributions.: Comparisons with parallel ab initio computations
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DOI：
10.1002/jcc.20244
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发表时间：
2005-08-01
影响因子：
3
通讯作者：
Krauss, M
中科院分区：
文献类型：
--
作者：
Gresh, N;Piquemal, JP;Krauss, M
我们提出了改进的SIBFA分子力学程序来表示Zn（II）的分子间相互作用能。两个一阶贡献，静电（E-MTP）和短程排斥（E，.，P），根据Piquemal等人的最近发展进行了改进（Piquemal等人J Phys Chem A 2003，107，9800;和Piquemal等人J Phys Chem A 2003，107，9800）。提交）。因此，E-MTP增加了一个穿透组件，E-pen，它占了一个给定的分子片段的电子密度减少的影响，由另一个相互作用的片段相互重叠时感测。E-pen适合于有限数量的选定的Zn（II）-单连接络合物，使得E-MTP和E-pen的总和从从头算Hartree-Fock能量分解程序再现库仑贡献E。用S表示相互作用单体上定域轨道之间的重叠矩阵，用R表示它们的质心之间的距离，E-rep由S-2/R项表示，现在用S-2/R-2项来表示。在选定的单配Zn（II）配合物中进行校准，以拟合从头算能量分解的相应交换排斥E-exch，并且不再像以前那样（E-c + E-exch）和E-MTP之间的差异。沿着一阶贡献的重新表述，进行了二阶贡献的有限重新校准。如在我们的原始配方（Gresh，J Comput Chem 1995，16，856）中，校准每个能量贡献的Zn（II）参数以再现其从头算HF对应物在具有N、O和S配体的单配位络合物中的径向行为。SIBFA程序随后通过与几种Zn（II）多连接络合物（包括Gal 4和P-内酰胺酶金属蛋白模型中的双核Zn（U）络合物）的并行从头计算进行比较来验证。RVS计算的最大相对误差为3%，尽管从头算相互作用能的绝对值可以高达1220 kcal/mol，但竞争结构的相对能量的排序仍得以再现。一个长期的识别SIBFA的贡献，其从头开始的同行仍然是可能的，即使是最大规模的复合物。(c)2005 Wiley Periodicals，Inc.
We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E-MTP) and short-range repulsion (E,.,P), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al.. submitted). Thus, E-MTP is augmented with a penetration component, E-pen, which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E-pen is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E-MTP and E-pen reproduces the Coulomb contribution E, from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E-rep is expressed by a S-2/R term now augmented with an S-2/R-2 one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E-exch from ab initio energy decomposition, and no longer as previously the difference between (E-c + E-exch) and E-MTP, Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(U) complexes as in models for the Gal4 and P-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes. (c) 2005 Wiley Periodicals, Inc.