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基于M05 - 2X和MP2理论的Zn(II)-咪唑配合物中甲硫醇的结合强度与去质子化能:与锌酶相关的配位数和几何结构影响

Methanethiol Binding Strengths and Deprotonation Energies in Zn(II)-Imidazole Complexes from M05-2X and MP2 Theories: Coordination Number and Geometry Influences Relevant to Zinc Enzymes.

作者信息

Linder Douglas P, Rodgers Kenton R

机构信息

Department of Chemistry and Physics, Southwestern Oklahoma State University , Weatherford, Oklahoma 73096, United States.

Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108, United States.

出版信息

J Phys Chem B. 2015 Sep 17;119(37):12182-92. doi: 10.1021/acs.jpcb.5b07115. Epub 2015 Sep 4.

Abstract

Zn(II) is used in nature as a biocatalyst in hundreds of enzymes, and the structure and dynamics of its catalytic activity are subjects of considerable interest. Many of the Zn(II)-based enzymes are classified as hydrolytic enzymes, in which the Lewis acidic Zn(II) center facilitates proton transfer(s) to a Lewis base, from proton donors such as water or thiol. This report presents the results of a quantum computational study quantifying the dynamic relationship between the zinc coordination number (CN), its coordination geometry, and the thermodynamic driving force behind these proton transfers originating from a charge-neutral methylthiol ligand. Specifically, density functional theory (DFT) and second-order perturbation theory (MP2) calculations have been performed on a series of (imidazole)nZn-S(H)CH3 and (imidazole)nZn-SCH3 complexes with the CN varied from 1 to 6, n = 0-5. As the number of imidazole ligands coordinated to zinc increases, the S-H proton dissociation energy also increases, (i.e., -S(H)CH3 becomes less acidic), and the Zn-S bond energy decreases. Furthermore, at a constant CN, the S-H proton dissociation energy decreases as the S-Zn-(ImH)n angles increase about their equilibrium position. The zinc-coordinated thiol can become more or less acidic depending upon the position of the coordinated imidazole ligands. The bonding and thermodynamic relationships discussed may apply to larger systems that utilize the [(His)3Zn(II)-L] complex as the catalytic site, including carbonic anhydrase, carboxypeptidase, β-lactamase, the tumor necrosis factor-α-converting enzyme, and the matrix metalloproteinases.

摘要

锌(II)在自然界中作为数百种酶的生物催化剂,其催化活性的结构和动力学是备受关注的课题。许多基于锌(II)的酶被归类为水解酶,其中路易斯酸性锌(II)中心促进质子从水或硫醇等质子供体转移至路易斯碱。本报告展示了一项量子计算研究的结果,该研究量化了锌配位数(CN)、其配位几何结构以及源自电荷中性甲硫醇配体的这些质子转移背后的热力学驱动力之间的动态关系。具体而言,已对一系列(咪唑)ₙZn - S(H)CH₃(咪唑)ₙZn - SCH₃配合物进行了密度泛函理论(DFT)和二阶微扰理论(MP2)计算,其中CN从1变化到6,n = 0 - 5。随着与锌配位的咪唑配体数量增加,S - H质子解离能也增加(即 - S(H)CH₃酸性减弱),且Zn - S键能降低。此外,在恒定的CN下,S - H质子解离能随着S - Zn - (ImH)ₙ角围绕其平衡位置增大而降低。取决于配位咪唑配体的位置,锌配位的硫醇酸性可能增强或减弱。所讨论的键合和热力学关系可能适用于以[(His)₃Zn(II) - L]配合物作为催化位点的更大体系,包括碳酸酐酶、羧肽酶、β - 内酰胺酶、肿瘤坏死因子 - α转化酶和基质金属蛋白酶。

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