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TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data.
Acta Crystallographica Section B ( IF 2.684 ) Pub Date : 2020-04-15 , DOI: 10.1107/s2052520620002917
Kunal Kumar Jha 1 , Barbara Gruza 1 , Prashant Kumar 1 , Michal Leszek Chodkiewicz 1 , Paulina Maria Dominiak 1
Affiliation  

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X‐ray diffraction is the most common method for structure determination. It depends on scattering of X‐rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X‐ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X‐ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non‐hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user‐friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

中文翻译:

TAAM:使用常规X射线衍射数据进行氢原子定位的可靠且用户友好的工具。

氢几乎存在于生物的所有分子中。它具有很高的反应性,可与大多数元素形成键,从而终止其化合价并增强其化学性质。X射线衍射是确定结构的最常用方法。这取决于电子密度对X射线的散射,这意味着难以检测到氢的单个电子。通常,中子衍射数据用于确定氢原子的准确位置。但是,对高​​质量单晶的要求,昂贵的维护费用以及中子衍射设备的数量有限,意味着这类结果很少获得。X -H键长,并使它们与平均中子键长相当。从伪原子数据库构建的TAAM用于确定75个有机分子晶体数据集上的X -H键长。使用通过DiSCaMB软件库应用的经过修改的伪原子的布法罗大学数据库(UBDB)提供的TAAM参数设置。通过TAAM精细化方法与原子分辨率的X射线衍射数据确定的平均键长(d min≤0.83Å)与中子数据非常吻合,主要在一个样品标准偏差内,非常类似于Hirshfeld原子精炼(HAR)。通过精炼获得的氢原子和非氢原子的原子位移与IAM结果系统地不同。与IAM相比,总体TAAM更适合标准分辨率的实验数据。这项研究还伴随着软件的开发,该软件旨在提供用户友好的工具,以非球面原子模型来提纯有机分子,其速度可与基于球形原子模型的常规提纯相提并论。
更新日期:2020-04-15
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