在晶体结构预测的第七次盲测中,分子 XXXI 和 XXXII 的构象行为截然不同。

Gregory J O Beran, Cameron J Cook, Pablo A Unzueta
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引用次数: 0

摘要

构象能量的精确建模是构象多晶体晶体结构预测的关键。本研究以第七次晶体结构预测盲测中的分子 XXXI 和 XXXII 为研究对象,采用了各种电子结构方法,包括域-局域对自然轨道耦合簇单倍和双倍扰动三倍[DLPNO-CCSD(T1)]方法,对构象能量进行了基准测试,并评估了它们对晶体能谱的影响。事实证明,分子 XXXI 是一个相对简单的例子,当使用 PBE0-D4、ωB97M-V 和 revDSD-PBEP86-D4、弥散校正二阶默勒-普利塞特扰动理论(SCS-MP2D)或 DLPNO-CCSD(T1)等更先进的密度函数时,广义梯度近似(GGA)函数 B86bPBE-XDM 的构象能变化不大。相比之下,分子 XXXII 的构象能很难可靠地确定,而且计算出的构象能的变化对晶体能谱有明显的影响。即使是高级方法,如 revDSD-PBEP86-D4 和 SCS-MP2D,在 XXXII 分子上也与 DLPNO-CCSD(T1)基准存在明显差异,这突出表明了预测复杂的类药物分子构象能的难度。这里得到的 XXXII 分子的最佳合并预测晶体能谱与实验推断的固体形态能谱有很大差异。计算中发现的局限性可能不足以解释 XXXII 分子理论与实验之间的差异,因此进一步研究实验中的固体形态景观将是非常有价值的。最后,对几种半经验方法的评估发现 r2SCAN-3c 是最有前途的方法,其构象能量精度介于 GGA 和混合函数之间,计算成本较低。
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Contrasting conformational behaviors of molecules XXXI and XXXII in the seventh blind test of crystal structure prediction.

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 r2SCAN-3c to be the most promising, with conformational energy accuracy intermediate between the GGA and hybrid functionals and a low computational cost.

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来源期刊
Acta crystallographica Section B, Structural science, crystal engineering and materials
Acta crystallographica Section B, Structural science, crystal engineering and materials CHEMISTRY, MULTIDISCIPLINARYCRYSTALLOGRAPH-CRYSTALLOGRAPHY
CiteScore
3.60
自引率
5.30%
发文量
0
期刊介绍: Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials publishes scientific articles related to the structural science of compounds and materials in the widest sense. Knowledge of the arrangements of atoms, including their temporal variations and dependencies on temperature and pressure, is often the key to understanding physical and chemical phenomena and is crucial for the design of new materials and supramolecular devices. Acta Crystallographica B is the forum for the publication of such contributions. Scientific developments based on experimental studies as well as those based on theoretical approaches, including crystal-structure prediction, structure-property relations and the use of databases of crystal structures, are published.
期刊最新文献
Assessment of the exchange-hole dipole moment dispersion correction for the energy ranking stage of the seventh crystal structure prediction blind test. Contrasting conformational behaviors of molecules XXXI and XXXII in the seventh blind test of crystal structure prediction. Crystal structure of the incommensurate modulated high-pressure phase of the potassium guaninate monohydrate. From `crystallographic accuracy' to `thermodynamic accuracy': a redetermination of the crystal structure of calcium atorvastatin trihydrate (Lipitor®). Polymorph sampling with coupling to extended variables: enhanced sampling of polymorph energy landscapes and free energy perturbation of polymorph ensembles.
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