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通过一种替代的电子密度划分提高赫希菲尔德原子精修的准确性。

Towards improved accuracy of Hirshfeld atom refinement with an alternative electron density partition.

作者信息

Chodkiewicz Michał, Woźniak Krzysztof

机构信息

Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland.

出版信息

IUCrJ. 2025 Jan 1;12(Pt 1):74-87. doi: 10.1107/S2052252524011242.

DOI:10.1107/S2052252524011242
PMID:39699305
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11707693/
Abstract

Hirshfeld atom refinement (HAR) is generally the chosen method for obtaining accurate hydrogen atom parameters from X-ray diffraction data. Still, determination can prove challenging, especially in the case of atomic displacement parameters (ADPs). We demonstrate that such a situation can occur when the ADP values of the bonding partner of the hydrogen atom are not determined accurately. Atomic electron densities partially overlap and inaccuracies in the bonding neighbour ADPs can be partially compensated for with modifications to the hydrogen ADPs. We introduce a modified version of the original Hirshfeld partition: the exponential Hirshfeld partition, parameterized with an adjustable parameter (n) to allow control of the overlap level of the atomic electron densities which, for n = 1, is equivalent to the Hirshfeld partition. The accuracy of the HAR-like procedure using the new partition (expHAR) was tested on a set of organic structures using B3LYP and MP2 electron densities. Applying expHAR improved the hydrogen atom parameters in the majority of the structures (compared with HAR), especially in cases with the highest deviations from the reference neutron values. X-H bond lengths and hydrogen ADPs improved for 9/10 of the structures for B3LYP-based refinement and 8/9 for MP2-based refinement when the ADPs were compared with a newly introduced scale-independent similarity measure.

摘要

赫希菲尔德原子精修(HAR)通常是从X射线衍射数据中获取精确氢原子参数的首选方法。然而,这种测定可能具有挑战性,尤其是在原子位移参数(ADP)的情况下。我们证明,当氢原子键合伙伴的ADP值未准确确定时,就会出现这种情况。原子电子密度会部分重叠,键合邻原子ADP中的不准确性可以通过对氢ADP进行修改来部分补偿。我们引入了原始赫希菲尔德划分的一个修改版本:指数赫希菲尔德划分,用一个可调参数(n)进行参数化,以控制原子电子密度的重叠水平,对于n = 1,它等同于赫希菲尔德划分。使用新划分(expHAR)的类HAR程序的准确性在一组有机结构上使用B3LYP和MP2电子密度进行了测试。应用expHAR在大多数结构中(与HAR相比)改善了氢原子参数,特别是在与参考中子值偏差最大的情况下。当将ADP与新引入的与比例无关的相似性度量进行比较时,基于B3LYP精修的9/10结构以及基于MP2精修的8/9结构的X-H键长和氢ADP都得到了改善。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/5fcf1bc114aa/m-12-00074-fig14.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/0f99bf501623/m-12-00074-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/fd665c0e20b0/m-12-00074-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/76d717d7c32f/m-12-00074-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/c7d15307e4d1/m-12-00074-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/309221e22443/m-12-00074-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/daf0250a9c27/m-12-00074-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/d3e70376c798/m-12-00074-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/08d2b353e766/m-12-00074-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/19a5190ee90e/m-12-00074-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/5fcce0b88eb8/m-12-00074-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/c01db6c676bb/m-12-00074-fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/a2cd8df9d6cb/m-12-00074-fig12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/52ac7d44d3c9/m-12-00074-fig13.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/5fcf1bc114aa/m-12-00074-fig14.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/0f99bf501623/m-12-00074-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/fd665c0e20b0/m-12-00074-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/76d717d7c32f/m-12-00074-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/c7d15307e4d1/m-12-00074-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/309221e22443/m-12-00074-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/daf0250a9c27/m-12-00074-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/d3e70376c798/m-12-00074-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/08d2b353e766/m-12-00074-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/19a5190ee90e/m-12-00074-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/5fcce0b88eb8/m-12-00074-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/c01db6c676bb/m-12-00074-fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/a2cd8df9d6cb/m-12-00074-fig12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/52ac7d44d3c9/m-12-00074-fig13.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8f87/11707693/5fcf1bc114aa/m-12-00074-fig14.jpg

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