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探索用于酶催化反应中密度泛函理论(DFT)方法基准测试的CPS外推DLPNO-CCSD(T)参考值。

Exploring CPS-Extrapolated DLPNO-CCSD(T) Reference Values for Benchmarking DFT Methods on Enzymatically Catalyzed Reactions.

作者信息

Wappett Dominique A, Goerigk Lars

机构信息

School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia.

出版信息

J Phys Chem A. 2024 Jan 11;128(1):62-72. doi: 10.1021/acs.jpca.3c05086. Epub 2023 Dec 20.

Abstract

Domain-based local pair natural orbital coupled-cluster singles doubles with perturbative triples [DLPNO-CCSD(T)] is regularly used to calculate reliable benchmark reference values at a computational cost significantly lower than that of canonical CCSD(T). Recent work has shown that even greater accuracy can be obtained at only a small additional cost through extrapolation to the complete PNO space (CPS) limit. Herein, we test two levels of CPS extrapolation, CPS(5,6), which approximates the accuracy of standard TightPNO, and CPS(6,7), which surpasses it, as benchmark values to test density functional approximations (DFAs) on a small set of organic and transition-metal-dependent enzyme active site models. Between the different reference levels of theory, there are changes in the magnitudes of the absolute deviations for all functionals, but these are small and there is minimal impact on the relative rankings of the tested DFAs. The differences are more significant for the metalloenzymes than the organic enzymes, so we repeat the tests on our entire ENZYMES22 set of organic enzyme active site models [Wappett, D. A.; Goerigk, L. 2019, 123, 7057-7074] to confirm that using the CPS extrapolations for the reference values has negligible impact on the benchmarking outcomes. This means that we can particularly recommend CPS(5,6) as an alternative to standard TightPNO settings for calculating reference values, increasing the applicability of DLPNO-CCSD(T) in benchmarking reaction energies and barrier heights of larger models of organic enzymes. DLPNO-CCSD(T)/CPS(6,7) energies for ENZYMES22 are finally presented as updated reference values for the set, reflecting the recent improvements in the method.

摘要

基于域的定域对自然轨道耦合簇单双激发微扰三激发 [DLPNO-CCSD(T)] 常用于以远低于正则CCSD(T) 的计算成本来计算可靠的基准参考值。最近的研究表明,通过外推到完整的PNO空间(CPS)极限,只需少量额外成本就能获得更高的精度。在此,我们测试了两个CPS外推水平,即近似标准TightPNO精度的CPS(5,6) 和超越其精度的CPS(6,7),以此作为基准值,在一小部分有机和过渡金属依赖性酶活性位点模型上测试密度泛函近似(DFA)。在不同的理论参考水平之间,所有泛函的绝对偏差大小都有变化,但这些变化很小,对所测试DFA的相对排名影响极小。金属酶的差异比有机酶更显著,因此我们在整个有机酶活性位点模型的ENZYMES22数据集上重复测试 [Wappett, D. A.; Goerigk, L. 2019, 123, 7057 - 7074],以确认使用CPS外推的参考值对基准测试结果的影响可忽略不计。这意味着我们特别推荐将CPS(5,6) 作为计算参考值的标准TightPNO设置的替代方法,从而提高DLPNO-CCSD(T) 在基准测试更大有机酶模型的反应能量和势垒高度方面的适用性。最后给出了ENZYMES22的DLPNO-CCSD(T)/CPS(6,7) 能量,作为该数据集的更新参考值,反映了该方法的最新改进。

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