Michał Chodkiewicz , Leonid Patrikeev , Sylwia Pawlędzio , Krzysztof Woźniak , P. Lightfoot (Editor)
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In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to <em>l</em> = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). 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引用次数: 0
摘要
基于非球面原子电子密度模型的形式因子极大地提高了从 X 射线晶体结构细化中得出的氢原子参数的精确度。目前,此类模型主要有两类,一类是使用汉森-科普斯多极模型参数化的可转移原子密度库,可快速评估原子形式因子;另一类是与希尔施菲尔德原子细化(HAR)相关的方法,通常更为精确,但速度也较慢。在这项工作中,我们测试了一种结合了这两种方法的模型。该模型使用基于 Hirshfeld 电子密度分区的原子电子密度,这些电子密度是预先计算并存储在数据库中的。该模型还被应用于五种小分子结构的细化。将得出的氢原子参数与中子衍射数据得出的氢原子参数进行比较后发现,氢原子参数比基于汉森-科普斯数据库得出的氢原子参数更加精确,而比忽略晶体环境的 HAR 版本得出的氢原子参数精确度略低。如果将环境的影响考虑在内,使用 HAR 的优势就会更加明显。为了加快计算速度,使用数值径向函数(与 Hansen-Coppens 模型采用的方法不同),用球面谐波多极扩展来表示原子密度,最大可达 l=7。使用 12 个 CPU 内核计算小型蛋白质 crambin 的原子形式因子(分辨率为 0.73 Å)仅用了 68 秒。
Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors
A databank of atomic densities calculated using Hirshfeld partition has been developed which allows for refinement with similar accuracy to Hirshfeld atom refinement without the need for time-consuming wavefunction calculations.
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.
期刊介绍:
IUCrJ is a new fully open-access peer-reviewed journal from the International Union of Crystallography (IUCr).
The journal will publish high-profile articles on all aspects of the sciences and technologies supported by the IUCr via its commissions, including emerging fields where structural results underpin the science reported in the article. Our aim is to make IUCrJ the natural home for high-quality structural science results. Chemists, biologists, physicists and material scientists will be actively encouraged to report their structural studies in IUCrJ.