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迈向更小肽段和中等大小大环化合物的精确构象能量:MPCONF196基准能量数据集。

Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set.

作者信息

Řezáč Jan, Bím Daniel, Gutten Ondrej, Rulíšek Lubomír

机构信息

Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 Praha 6 , Czech Republic.

出版信息

J Chem Theory Comput. 2018 Mar 13;14(3):1254-1266. doi: 10.1021/acs.jctc.7b01074. Epub 2018 Mar 2.

Abstract

A carefully selected set of acyclic and cyclic model peptides and several other macrocycles, comprising 13 compounds in total, has been used to calibrate the accuracy of the DFT(-D3) method for conformational energies, employing BP86, PBE0, PBE, B3LYP, BLYP, TPSS, TPSSh, M06-2X, B97-D, OLYP, revPBE, M06-L, SCAN, revTPSS, BH-LYP, and ωB97X-D3 functionals. Both high- and low-energy conformers, 15 or 16 for each compound adding to 196 in total, denoted as the MPCONF196 data set, were included, and the reference values were obtained by the composite protocol, yielding the CCSD(T)/CBS extrapolated energies or their DLPNO-CCSD(T)/CBS equivalents in the case of larger systems. The latter was shown to be in near-quantitative (∼0.10-0.15 kcal·mol) agreement with the canonical CCSD(T), provided the TightPNO setting is used, and, therefore, can be used as the reference for larger systems (likely up to 150-200 atoms) for the problem studied here. At the same time, it was found that many D3-corrected DFT functionals provide results of ∼1 kcal·mol accuracy, which we consider as quite encouraging. This result implies that DFT-D3 methods can be, for example, safely used in efficient conformational sampling algorithms. Specifically, the DFT-D3/DZVP-DFT level of calculation seems to be the best trade-off between computational cost and accuracy. Based on the calculated data, we have not found any cheaper variant for the treatment of conformational energies, since the semiempirical methods (including DFTB) provide results of inferior accuracy (errors of 3-5 kcal·mol).

摘要

精心挑选了一组无环和环状模型肽以及其他几个大环化合物,总共13种化合物,用于校准DFT(-D3)方法计算构象能的准确性,采用了BP86、PBE0、PBE、B3LYP、BLYP、TPSS、TPSSh、M06-2X、B97-D、OLYP、revPBE、M06-L、SCAN、revTPSS、BH-LYP和ωB97X-D3等泛函。既包括高能构象异构体,也包括低能构象异构体,每种化合物有15或16个构象异构体,总共196个,记为MPCONF196数据集,并通过复合协议获得参考值,对于较大体系则得到CCSD(T)/CBS外推能或其DLPNO-CCSD(T)/CBS等效值。结果表明,只要使用TightPNO设置,后者与标准CCSD(T)的结果接近定量一致(约0.10 - 0.15 kcal·mol),因此可作为本文所研究问题中较大体系(可能多达150 - 200个原子)的参考。同时,发现许多经D3校正的DFT泛函能提供约1 kcal·mol精度的结果,我们认为这相当令人鼓舞。这一结果意味着DFT-D3方法例如可以安全地用于高效的构象采样算法。具体而言,DFT-D3/DZVP-DFT计算水平似乎是计算成本和准确性之间的最佳权衡。基于计算数据,我们未发现处理构象能更便宜的方法,因为半经验方法(包括DFTB)提供的结果准确性较差(误差为3 - 5 kcal·mol)。

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