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在晶体结构预测的第七次盲测中分子XXXI和XXXII的对比构象行为

Contrasting conformational behaviors of molecules XXXI and XXXII in the seventh blind test of crystal structure prediction.

作者信息

Beran Gregory J O, Cook Cameron J, Unzueta Pablo A

机构信息

Department of Chemistry, University of California, Riverside, CA 92521, USA.

出版信息

Acta Crystallogr B Struct Sci Cryst Eng Mater. 2024 Dec 1;80(Pt 6):606-19. doi: 10.1107/S2052520624005043.

Abstract

Accurate modeling of conformational energies is key to the crystal structure prediction of conformational polymorphs. Focusing on molecules XXXI and XXXII from the seventh blind test of crystal structure prediction, this study employs various electronic structure methods up to the level of domain-local pair natural orbital coupled cluster singles and doubles with perturbative triples [DLPNO-CCSD(T1)] to benchmark the conformational energies and to assess their impact on the crystal energy landscapes. Molecule XXXI proves to be a relatively straightforward case, with the conformational energies from generalized gradient approximation (GGA) functional B86bPBE-XDM changing only modestly when using more advanced density functionals such as PBE0-D4, ωB97M-V, and revDSD-PBEP86-D4, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D), or DLPNO-CCSD(T1). In contrast, the conformational energies of molecule XXXII prove difficult to determine reliably, and variations in the computed conformational energies appreciably impact the crystal energy landscape. Even high-level methods such as revDSD-PBEP86-D4 and SCS-MP2D exhibit significant disagreements with the DLPNO-CCSD(T1) benchmarks for molecule XXXII, highlighting the difficulty of predicting conformational energies for complex, drug-like molecules. The best-converged predicted crystal energy landscape obtained here for molecule XXXII disagrees significantly with what has been inferred about the solid-form landscape experimentally. The identified limitations of the calculations are probably insufficient to account for the discrepancies between theory and experiment on molecule XXXII, and further investigation of the experimental solid-form landscape would be valuable. Finally, assessment of several semi-empirical methods finds rSCAN-3c to be the most promising, with conformational energy accuracy intermediate between the GGA and hybrid functionals and a low computational cost.

摘要

准确模拟构象能量是构象多晶型物晶体结构预测的关键。本研究聚焦于晶体结构预测第七次盲测中的分子XXXI和XXXII,采用了各种电子结构方法,直至域局域对自然轨道耦合簇单双激发并微扰三激发[DLPNO - CCSD(T1)]水平,以对构象能量进行基准测试,并评估它们对晶体能量景观的影响。分子XXXI被证明是一个相对简单的例子,当使用更先进的密度泛函如PBE0 - D4、ωB97M - V和revDSD - PBEP86 - D4、色散校正二阶Møller - Plesset微扰理论(SCS - MP2D)或DLPNO - CCSD(T1)时,广义梯度近似(GGA)泛函B86bPBE - XDM的构象能量变化不大。相比之下,分子XXXII的构象能量难以可靠确定,计算得到的构象能量变化对晶体能量景观有明显影响。即使是像revDSD - PBEP86 - D4和SCS - MP2D这样的高水平方法,对于分子XXXII也与DLPNO - CCSD(T1)基准存在显著差异,凸显了预测复杂类药物分子构象能量的困难。这里为分子XXXII获得的最佳收敛预测晶体能量景观与实验推断的固态形式景观有显著差异。计算中确定的局限性可能不足以解释分子XXXII理论与实验之间的差异,对实验固态形式景观的进一步研究将很有价值。最后,对几种半经验方法的评估发现rSCAN - 3c最有前景,其构象能量精度介于GGA和杂化泛函之间,且计算成本较低。

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