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评估 DLPNO-CCSD(T) 在计算普遍存在的酶反应的活化能和反应能中的有效性。

Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions.

机构信息

LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.

出版信息

J Comput Chem. 2020 Nov;41(29):2459-2468. doi: 10.1002/jcc.26401. Epub 2020 Sep 3.

Abstract

The domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) method was employed to portray the activation and reaction energies of four ubiquitous enzymatic reactions, and its performance was confronted to CCSD(T)/complete basis set (CBS) to assess its accuracy and robustness in this specific field. The DLPNO-CCSD(T) results were also confronted to those of a set of density functionals (DFs) to understand the benefit of implementing this technique in enzymatic quantum mechanics/molecular mechanics (QM/MM) calculations as a second QM component, which is often treated with DF theory (DFT). On average, the DLPNO-CCSD(T)/aug-cc-pVTZ results were 0.51 kcal·mol apart from the canonic CCSD(T)/CBS, without noticeable biases toward any of the reactions under study. All DFs fell short to the DLPNO-CCSD(T), both in terms of accuracy and robustness, which suggests that this method is advantageous to characterize enzymatic reactions and that its use in QM/MM calculations, either alone or in conjugation with DFT, in a two-region QM layer (DLPNO-CCSD(T):DFT), should enhance the quality and faithfulness of the results.

摘要

采用基于域的局部对自然轨道耦合簇方法,包括单、双和微扰三重激发(DLPNO-CCSD(T)),描绘了四种常见酶促反应的活化能和反应能,并将其性能与 CCSD(T)/完全基组(CBS)进行对比,以评估其在该特定领域的准确性和稳健性。还将 DLPNO-CCSD(T)的结果与一组密度泛函(DFs)进行对比,以了解在酶学量子力学/分子力学(QM/MM)计算中作为第二 QM 组件实施该技术的好处,该组件通常用 DF 理论(DFT)处理。平均而言,DLPNO-CCSD(T)/aug-cc-pVTZ 结果与规范 CCSD(T)/CBS 相差 0.51 kcal·mol,对所研究的反应没有明显的偏差。所有 DFs 在准确性和稳健性方面都不如 DLPNO-CCSD(T),这表明该方法有利于描述酶促反应,并且其在 QM/MM 计算中的应用,无论是单独使用还是与 DFT 结合使用,在两层 QM 区域(DLPNO-CCSD(T):DFT)中,都应该提高结果的质量和可信度。

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