一刀切?用于测试计算建模方法的cpos209实验和假设多态数据集的开发。

IF 3.2 2区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Crystal Growth & Design Pub Date : 2025-04-28 eCollection Date: 2025-05-07 DOI:10.1021/acs.cgd.5c00255
Louise S Price, Matteo Paloni, Matteo Salvalaglio, Sarah L Price
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引用次数: 0

摘要

有机晶体结构预测(CSP)的研究导致了预测已知晶体结构和计算机生成晶体结构相对能量的方法的快速发展。在理论处理的水平、它在不同类型有机系统中的可靠性、它的准确性如何取决于单体细胞的大小和形状、以及在可承受的计算成本下可以建模的结构的大小和数量之间存在妥协。我们利用我们的晶体结构预测研究数据库,通常作为实验筛选的补充,为20个有机分子生产了包含6到15个晶体结构的集合,包括已知的多晶型,观察到的密切相关分子的包装,以及csp产生的能量竞争但不同的结构。选择这些来说明在任何晶格能量方法中需要考虑的一些问题,寻求普遍适用于中等大小的有机分子,包括小药物分子。我们收录了报道的实验晶型的结晶方法。在所有的例子中,原始的CSP使用分子的电子结构计算来给出构象能,并使用各向异性原子-原子模型来给出静电分子间能,结合经验的“exp-6”排斥色散模型来给出分子间晶格能。将晶格能量和结构与使用周期平面波色散校正密度泛函理论(特别是使用TS色散校正的PBE)和使用多体色散(MBD)色散校正的单点能量进行再优化得到的晶格能量和结构进行比较,作为广泛使用的“主力”方法的一个例子。该数据集用于两个机器学习基础模型MACE-MP-0和MACE-OFF23的建模方法的初步测试。在对一系列分子、其能量和可能与实验数据一致的水平进行假设和观察的多晶型建模时所面临的挑战进行了说明。非常相似的分子在观察到的多晶态上可能存在显著差异,这仅部分反映了所使用的多晶型筛选实验的范围以及基于纯粹热力学范式的CSP方法产生的能量竞争结构。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
One Size Fits All? Development of the CPOSS209 Data Set of Experimental and Hypothetical Polymorphs for Testing Computational Modeling Methods.

Organic crystal structure prediction (CSP) studies have led to the rapid development of methods for predicting the relative energies of known and computer-generated crystal structures. There is a compromise between the level of theoretical treatment, its reliability across different types of organic systems, how its accuracy depends on the size and shape of the unit cell, and the size and the number of structures that can be modeled at an affordable computational cost. We have used our database of crystal structure prediction studies, often performed as a complement to experimental screening, to produce sets comprising 6 to 15 crystal structures, covering known polymorphs, observed packings of closely related molecules, and CSP-generated energetically competitive but distinct structures, for 20 organic molecules. These have been chosen to illustrate some of the issues that need consideration in any lattice energy method, seeking to be generally applicable to moderate-sized organic molecules, including small drug molecules. We included the methods of crystallization reported for the experimental polymorphs. In all of the examples, the original CSP used electronic structure calculations on the molecule to give the conformational energy and an anisotropic atom-atom model for the electrostatic intermolecular energy, combined with an empirical "exp-6" repulsion dispersion model to give the intermolecular lattice energy. The lattice energies and structures are compared with those obtained by reoptimizing with periodic, plane-wave, dispersion-corrected density functional theory, specifically PBE with the TS dispersion correction, and with single point energies where the many body dispersion (MBD) dispersion correction is applied, as an example of a widely used "workhorse" method. The use of this data set for a preliminary test of modeling methods is illustrated for two Machine Learned Foundation Models, MACE-MP-0 and MACE-OFF23. The challenges in modeling the putative and observed polymorphs for a range of molecules, their energies, and the possible level of agreement with experimental data are illustrated. Very similar molecules can differ significantly in the polymorphs observed, only partially reflecting the range of polymorph screening experiments used and the energetically competitive structures produced by CSP approaches based on a purely thermodynamic paradigm.

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来源期刊
Crystal Growth & Design
Crystal Growth & Design 化学-材料科学:综合
CiteScore
6.30
自引率
10.50%
发文量
650
审稿时长
1.9 months
期刊介绍: The aim of Crystal Growth & Design is to stimulate crossfertilization of knowledge among scientists and engineers working in the fields of crystal growth, crystal engineering, and the industrial application of crystalline materials. Crystal Growth & Design publishes theoretical and experimental studies of the physical, chemical, and biological phenomena and processes related to the design, growth, and application of crystalline materials. Synergistic approaches originating from different disciplines and technologies and integrating the fields of crystal growth, crystal engineering, intermolecular interactions, and industrial application are encouraged.
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