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利用色散校正密度泛函理论(DFT-D)从粉末衍射数据验证分子晶体结构。

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

作者信息

van de Streek Jacco, Neumann Marcus A

机构信息

Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.

Avant-garde Materials Simulation Deutschland GmbH, Merzhauser Strasse 177, D-79100 Freiburg, Germany.

出版信息

Acta Crystallogr B Struct Sci Cryst Eng Mater. 2014 Dec;70(Pt 6):1020-32. doi: 10.1107/S2052520614022902. Epub 2014 Dec 1.

Abstract

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

摘要

2010年,我们使用色散校正密度泛函理论(DFT-D)对225个高质量单晶(SX)结构进行了能量最小化处理,以建立一个定量基准。对于当前这篇论文,我们对215个由X射线粉末衍射(XRPD)数据确定并发表在国际晶体学联盟(IUCr)期刊上的有机晶体结构进行了DFT-D能量最小化处理,并与SX基准进行了比较。XRPD结构中平均精度略低的原子坐标,在能量最小化后确实会导致均方根笛卡尔位移(RMSCD)值系统地高于SX结构,但RMSCD值仍然是检测值得进一步研究的结构的一个良好指标。正确结构的RMSCD上限必须从SX结构的0.25 Å提高到XRPD结构的0.35 Å;灰色区域必须从0.30 Å扩展到0.40 Å。基于能量最小化,对三个结构进行了重新精修,以给出更精确的原子坐标。对于六个结构,我们的计算提供了H原子缺失的位置,对于五个结构,提供了一些H原子的校正位置。七个晶体结构显示一个非H原子存在小错误。对于五个结构,能量最小化表明具有更高的空间群对称性。对于225个SX结构,在能量最小化过程中观察到的唯一偏差是三个与H原子相关的小问题。择优取向是问题的最重要原因。择优取向校正是唯一一种修改实验数据以拟合模型的校正方法。我们得出结论,发表在IUCr期刊上的由粉末衍射数据确定的分子晶体结构质量很高,非H原子存在错误的结构不到4%。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23a0/4468513/368940aed793/b-70-01020-fig1.jpg

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