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精修天青蛋白的QM/MM 模型的融合结构和光谱性质。

Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin.

机构信息

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

出版信息

Inorg Chem. 2021 May 17;60(10):7399-7412. doi: 10.1021/acs.inorgchem.1c00640. Epub 2021 May 3.

Abstract

Blue copper proteins continue to challenge experiment and theory with their electronic structure and spectroscopic properties that respond sensitively to the coordination environment of the copper ion. In this work, we report state-of-the art electronic structure studies for geometric and spectroscopic properties of the archetypal "Type I" copper protein azurin in its Cu(II) state. A hybrid quantum mechanics/molecular mechanics (QM/MM) approach is used, employing both density functional theory (DFT) and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) methods for the QM region, the latter method making use of the domain-based local pair natural orbital (DLPNO) approach. Models of increasing QM size are employed to investigate the convergence of critical geometric parameters. It is shown that convergence is slow and that a large QM region is critical for reproducing the short experimental Cu-SCys112 distance. The study of structural convergence is followed by investigation of spectroscopic parameters using both DFT and DLPNO-CC methods and comparing these to the experimental spectrum using simulations. The results allow us to examine for the first time the distribution of spin densities and hyperfine coupling constants at the coupled cluster level, leading us to revisit the experimental assignment of the S hyperfine splitting. The wavefunction-based approach to obtain spin-dependent properties of open-shell systems demonstrated here for the case of azurin is transferable and applicable to a large array of bioinorganic systems.

摘要

蓝色铜蛋白的电子结构和光谱性质对铜离子的配位环境敏感,这使其不断挑战实验和理论。在这项工作中,我们报告了典型“I 型”铜蛋白蓝铜蛋白在其 Cu(II)状态下的几何和光谱性质的最先进的电子结构研究。采用混合量子力学/分子力学 (QM/MM) 方法,在 QM 区域中同时使用密度泛函理论 (DFT) 和包含单重态、双重态和微扰三重态的耦合簇 (CCSD(T)) 方法,后者方法利用基于域的局部对自然轨道 (DLPNO) 方法。采用越来越大的 QM 尺寸模型来研究关键几何参数的收敛性。结果表明,收敛速度较慢,并且需要一个大的 QM 区域才能重现实验测定的短 Cu-SCys112 距离。在研究结构收敛性之后,使用 DFT 和 DLPNO-CC 方法研究了光谱参数,并使用模拟与实验光谱进行了比较。结果使我们首次能够在耦合簇水平上检查自旋密度和超精细耦合常数的分布,从而重新审视 S 超精细分裂的实验分配。这里针对蓝铜蛋白的情况展示了基于波函数的方法来获得开壳体系的自旋相关性质,该方法可转移并适用于大量生物无机体系。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8304/8154437/ccf08fa864d0/ic1c00640_0002.jpg

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