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通过 Hirshfeld 原子精修利用 X 射线衍射得到的冰 VI 的精确晶体结构。

Accurate crystal structure of ice VI from X-ray diffraction with Hirshfeld atom refinement.

作者信息

Chodkiewicz Michal L, Gajda Roman, Lavina Barbara, Tkachev Sergey, Prakapenka Vitali B, Dera Przemyslaw, Wozniak Krzysztof

机构信息

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

Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA.

出版信息

IUCrJ. 2022 Jul 16;9(Pt 5):573-579. doi: 10.1107/S2052252522006662. eCollection 2022 Sep 1.

DOI:10.1107/S2052252522006662
PMID:36071798
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9438488/
Abstract

Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations have suggested the existence of additional and - to date - unknown phases. In many ice structures, neither neutron diffraction nor DFT calculations nor X-ray diffraction methods can easily solve the problem of hydrogen atom disorder or accurately determine their anisotropic displacement parameters (ADPs). Here, accurate crystal structures of HO, DO and mixed (50%HO/50%DO) ice VI obtained by Hirshfeld atom refinement (HAR) of high-pressure single-crystal synchrotron and laboratory X-ray diffraction data are presented. It was possible to obtain O-H/D bond lengths and ADPs for disordered hydrogen atoms which are in good agreement with the corresponding single-crystal neutron diffraction data. These results show that HAR combined with X-ray diffraction can compete with neutron diffraction in detailed studies of polymorphic forms of ice and crystals of other hydrogen-rich compounds. As neutron diffraction is relatively expensive, requires larger crystals which can be difficult to obtain and access to neutron facilities is restricted, cheaper and more accessible X-ray measurements combined with HAR can facilitate the verification of the existing ice polymorphs and the quest for new ones.

摘要

水是生物体必需的化合物,已知其有20种不同的晶体固态形式(冰)。然而,这些结构仍存在许多基本问题,比如确定氢原子的正确位置和热运动。由于密度泛函理论(DFT)计算表明存在其他尚未知晓的相,冰结构的列表尚未完整。在许多冰结构中,中子衍射、DFT计算以及X射线衍射方法都难以解决氢原子无序问题,也无法准确确定其各向异性位移参数(ADPs)。在此,本文展示了通过对高压单晶同步加速器和实验室X射线衍射数据进行 Hirshfeld 原子精修(HAR)获得的HO、DO以及混合(50%HO/50%DO)冰VI的精确晶体结构。对于无序氢原子,能够获得与相应单晶中子衍射数据高度吻合的O-H/D键长和ADPs。这些结果表明,在对冰的多晶型形式以及其他富氢化合物晶体的详细研究中,HAR结合X射线衍射能够与中子衍射相媲美。由于中子衍射相对昂贵,需要更大的晶体(而这可能难以获得),并且使用中子设施受到限制,结合HAR的更廉价且更易获取的X射线测量能够促进对现有冰多晶型的验证以及对新多晶型的探索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/5edee02254cd/m-09-00573-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/e5f41e403ff7/m-09-00573-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/686e89696ec3/m-09-00573-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/5edee02254cd/m-09-00573-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/e5f41e403ff7/m-09-00573-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/686e89696ec3/m-09-00573-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64f9/9438488/5edee02254cd/m-09-00573-fig3.jpg

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