Pub Date : 2023-07-07DOI: 10.1107/s2053273323099059
Christina Hoffmann, Xiaoping Wang, S. Latturner
{"title":"Where the H is the interstitial: single-crystal neutron diffraction studies of complex metal hydrides","authors":"Christina Hoffmann, Xiaoping Wang, S. Latturner","doi":"10.1107/s2053273323099059","DOIUrl":"https://doi.org/10.1107/s2053273323099059","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323099254
Matthew L. Brown
{"title":"When is PXRD data good enough, or when should I stop trying to resolve those tiny peaks out of the baseline?","authors":"Matthew L. Brown","doi":"10.1107/s2053273323099254","DOIUrl":"https://doi.org/10.1107/s2053273323099254","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098169
Andrzej Joachimiak
The exponential growth of genomics sequence information in the 1990s led to significant knowledge gaps in our understanding of biological systems. It was true then, and it is still true now that the sequence information bore little insights about the functions encoded in the genomes. The fi eld of Structural Genomics (SG) arose to address these gaps. The mission of SG programs was to facilitate rapid de novo structure determination for proteins representing new protein families to provide meaningful structural coverage of the genomes. There were significant challenges to advance technologies for the prepara tion of thousands of proteins and for their structural and functional characterization. The SG programs quickly addressed barriers, and deficiencies, improved effectiveness, and reproducibility, and created highly integrated and cost - effective pipelines for p rotein production and structure determination. The improvements in experimental methods developed by the SG consortia resulted in fast progress in molecular and structural biology, enhanced structure quality, and significantly benefitted biological and biomedical research, providing insights into novel structural and functional space. The experimental three - dimensional models were promptly made public through the Protein Data Bank structure repository, facilitating the structure determination of other m embers of the family, and helping to understand their molecular and biochemical functions. The light sources and dedicated macromolecular crystallography beamlines, advanced software, and computing resources have contributed to SG success and expanded biology community competence in determining protein structures. Structural biology research was set to undergo a major transformation. The advancements resulted in the determination of thousands of protein structures, mostly from unique protein families, and increased structural coverage of the rapidly expanding protein universe. These structures contributed to AlphaFold/RozeTTAFold AI algorithms allowing accurate structure prediction of millions of proteins. In principle, the original goal propo sed by the National Institutes of Health Protein Structure Initiative, that structures of all proteins should be available to the community experimentally or computationally, has been accomplished. At
{"title":"Structural genomics: past, present and future","authors":"Andrzej Joachimiak","doi":"10.1107/s2053273323098169","DOIUrl":"https://doi.org/10.1107/s2053273323098169","url":null,"abstract":"The exponential growth of genomics sequence information in the 1990s led to significant knowledge gaps in our understanding of biological systems. It was true then, and it is still true now that the sequence information bore little insights about the functions encoded in the genomes. The fi eld of Structural Genomics (SG) arose to address these gaps. The mission of SG programs was to facilitate rapid de novo structure determination for proteins representing new protein families to provide meaningful structural coverage of the genomes. There were significant challenges to advance technologies for the prepara tion of thousands of proteins and for their structural and functional characterization. The SG programs quickly addressed barriers, and deficiencies, improved effectiveness, and reproducibility, and created highly integrated and cost - effective pipelines for p rotein production and structure determination. The improvements in experimental methods developed by the SG consortia resulted in fast progress in molecular and structural biology, enhanced structure quality, and significantly benefitted biological and biomedical research, providing insights into novel structural and functional space. The experimental three - dimensional models were promptly made public through the Protein Data Bank structure repository, facilitating the structure determination of other m embers of the family, and helping to understand their molecular and biochemical functions. The light sources and dedicated macromolecular crystallography beamlines, advanced software, and computing resources have contributed to SG success and expanded biology community competence in determining protein structures. Structural biology research was set to undergo a major transformation. The advancements resulted in the determination of thousands of protein structures, mostly from unique protein families, and increased structural coverage of the rapidly expanding protein universe. These structures contributed to AlphaFold/RozeTTAFold AI algorithms allowing accurate structure prediction of millions of proteins. In principle, the original goal propo sed by the National Institutes of Health Protein Structure Initiative, that structures of all proteins should be available to the community experimentally or computationally, has been accomplished. At","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323096274
Silvia Russi, Derek A. Mendez
{"title":"The Structural Molecular Biology program at the Stanford Synchrotron Radiation Lightsource","authors":"Silvia Russi, Derek A. Mendez","doi":"10.1107/s2053273323096274","DOIUrl":"https://doi.org/10.1107/s2053273323096274","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s205327332309873x
Thomas Albrecht-Schoenzart
{"title":"A race against time: crystallization and characterization of berkelium and californium compounds","authors":"Thomas Albrecht-Schoenzart","doi":"10.1107/s205327332309873x","DOIUrl":"https://doi.org/10.1107/s205327332309873x","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323096778
Qiu Zhang, Honghai Zhang, Matthew J Keller, Wellington Leite, Shuo Qian, Robert L Hettich, Hugh O'Neill
Membrane proteins play crucial roles in many cellular processes, however, studying membrane proteins is challenging because of their complex structure and fragility when isolated from their native environment. One solution is to embed membrane proteins in a membrane-mimic to provide a more native environment to facilitate their characterization. Small-angle neutron scattering (SANS) is an ideal technique to obtain structural information on biomacromolecules under physiologically relevant conditions. With this technique, deuterated phospholipids need be used to suppress their 1H signal in SANS measurements. Currently, there are three ways to obtain deuterated phospholipids; extraction of native lipids from cells produced in deuterated media, chemical synthesis, or semi -synthetic approaches that combine both routes. In this study, we report on producing deuterated phosphatidylethanolamine (PE) by extraction and fractionation from native Escherichia coli extracts, and phosphatidylcholine (PC) from an engineered E. coli strain. The PC synthase (PCs) pathway was introduced into E. coli to produce par tially deuterated and perdeuterated PC by feeding deuterated E. coli cultures with hydrogenated or deuterated choline chloride. The isolated PC product was confirmed by 1 H Nuclear Magnetic Resonance (NMR) and Liquid Chromatography - Mass Spectrometry (LC-MS) was used to determine the deuteration level of PC produced under different growth conditions. These materials can be used for neutron scattering studies with micelles, bicelles, liposomes, styrene-maleic acid lipid particles (SMALPs), and Membrane Scaffold Protein (MSP) -based lipid nanodiscs to produce a membrane-mimicking environment for studying membrane proteins, and can be used for deuterated lipids for NMR studies as well.
膜蛋白在许多细胞过程中发挥着至关重要的作用，然而，由于膜蛋白结构复杂，从其原生环境中分离出来时非常脆弱，因此研究膜蛋白具有挑战性。一种解决方案是将膜蛋白嵌入膜模拟物中，以提供更原生的环境，从而促进其表征。小角中子散射（SANS）是在生理相关条件下获取生物大分子结构信息的理想技术。使用这种技术时，需要使用氚代磷脂来抑制 SANS 测量中的 1H 信号。目前，有三种方法可以获得氚代磷脂：从氚介质培养的细胞中提取原生脂质、化学合成或结合两种途径的半合成方法。在本研究中，我们报告了通过从原生大肠杆菌提取物中提取和分馏生产氚代磷脂酰乙醇胺（PE）以及从工程大肠杆菌菌株中提取磷脂酰胆碱（PC）的情况。将 PC 合成酶（PCs）途径引入大肠杆菌，通过给氚化大肠杆菌培养物喂食氢化或氚化氯化胆碱来生产部分氚化和过氚化 PC。分离出的 PC 产物通过 1 H 核磁共振（NMR）和液相色谱-质谱法（LC-MS）进行确证，以确定在不同生长条件下产生的 PC 的氘化水平。这些材料可用于胶束、双胞、脂质体、苯乙烯-马来酸脂质颗粒（SMALPs）和基于膜脆性蛋白（MSP）的脂质纳米盘的中子散射研究，以产生膜模拟环境来研究膜蛋白，也可用于氚化脂质的核磁共振研究。
{"title":"Biosynthesis of deuterated lipids for structural and biophysical characterization of biomembranes and membrane proteins","authors":"Qiu Zhang, Honghai Zhang, Matthew J Keller, Wellington Leite, Shuo Qian, Robert L Hettich, Hugh O'Neill","doi":"10.1107/s2053273323096778","DOIUrl":"https://doi.org/10.1107/s2053273323096778","url":null,"abstract":"Membrane proteins play crucial roles in many cellular processes, however, studying membrane proteins is challenging because of their complex structure and fragility when isolated from their native environment. One solution is to embed membrane proteins in a membrane-mimic to provide a more native environment to facilitate their characterization. Small-angle neutron scattering (SANS) is an ideal technique to obtain structural information on biomacromolecules under physiologically relevant conditions. With this technique, deuterated phospholipids need be used to suppress their 1H signal in SANS measurements. Currently, there are three ways to obtain deuterated phospholipids; extraction of native lipids from cells produced in deuterated media, chemical synthesis, or semi -synthetic approaches that combine both routes. In this study, we report on producing deuterated phosphatidylethanolamine (PE) by extraction and fractionation from native Escherichia coli extracts, and phosphatidylcholine (PC) from an engineered E. coli strain. The PC synthase (PCs) pathway was introduced into E. coli to produce par tially deuterated and perdeuterated PC by feeding deuterated E. coli cultures with hydrogenated or deuterated choline chloride. The isolated PC product was confirmed by 1 H Nuclear Magnetic Resonance (NMR) and Liquid Chromatography - Mass Spectrometry (LC-MS) was used to determine the deuteration level of PC produced under different growth conditions. These materials can be used for neutron scattering studies with micelles, bicelles, liposomes, styrene-maleic acid lipid particles (SMALPs), and Membrane Scaffold Protein (MSP) -based lipid nanodiscs to produce a membrane-mimicking environment for studying membrane proteins, and can be used for deuterated lipids for NMR studies as well.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"373 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098133
L. Fan, Yun-Xing Wang
Small-angle X - ray scattering (SAXS) is a complementary technique to Macromolecular Crystallography, NMR and Cryo -EM techniques and is becoming more widely used in structural biology. Crystallography requires good crystals and NMR has a size limitation. Cryo - EM studies biomolecules under a frozen condition. SAXS, on the other hand, allows for the study of the structure and dynamics of macrobiomolecules and their complexes in solution and under various buffer conditions such as salt concentration, pH, with or without ligand as well as under changing sample environments such as temperature and pressure. SAXS provides insight not only into global information about size and shape of biomacrobiomolecules, but also the information about flexibility and an ensemble of conformers. SAXS data can also be used in tandem with other biophysical methods (including crystallography, NMR, AFM and cryo-EM) by providing additional restraints that further improve simulations, validate structural models as well as fi nd missing fragments. The SAXS Facility of the Natio nal Cancer Institute (NCI) opens to all intramural and extramural research communities. The mission of the SAXS Core Facility is to provide support to the user communities with expertise in experimental design, data collection, processing, analysis, and in terpretation. The research fi eld includes but is not limited to structural studies of nucleic acids, proteins, protein assemblies, virus particles, lipid membranes and membrane-protein/DNA complexes. This presentation gives a brief introduction to the NCI SAXS facility and highlights recent scientific achievements in structural biology produced by NCI SAXS core users. NCI SAXS Core website: https://ccr.cancer.gov/center - for -structural-biology/saxs-core-facility
小角 X 射线散射（SAXS）是大分子晶体学、核磁共振（NMR）和低温电子显微镜（Cryo-EM）技术的补充技术，在结构生物学中的应用越来越广泛。晶体学需要良好的晶体，而核磁共振则有尺寸限制。低温电磁技术研究冷冻状态下的生物分子。另一方面，SAXS可以研究溶液中的大生物分子及其复合物的结构和动力学，以及在盐浓度、pH值、有配体或无配体等各种条件下，以及在温度和压力等不断变化的样品环境中的结构和动力学。SAXS 不仅能提供有关生物大分子大小和形状的总体信息，还能提供有关其流动性和构象组合的信息。SAXS 数据还可与其他生物物理方法（包括晶体学、核磁共振、原子力显微镜和低温电子显微镜）配合使用，提供额外的约束条件，进一步改进模拟、验证结构模型以及查找缺失的片段。美国国家癌症研究所（NCI）的 SAXS 设施向所有校内和校外研究团体开放。SAXS 核心设施的任务是为用户群体提供实验设计、数据收集、处理、分析和解释方面的专业知识支持。研究领域包括但不限于核酸、蛋白质、蛋白质组装体、病毒颗粒、脂质膜和膜蛋白/DNA 复合物的结构研究。本报告简要介绍了 NCI SAXS 设施，并重点介绍了 NCI SAXS 核心用户最近在结构生物学领域取得的科学成就。NCI SAXS 核心网站：https://ccr.cancer.gov/center - for -structural-biology/saxs-core-facility
{"title":"Small-angle X-ray scattering applications in structural biology","authors":"L. Fan, Yun-Xing Wang","doi":"10.1107/s2053273323098133","DOIUrl":"https://doi.org/10.1107/s2053273323098133","url":null,"abstract":"Small-angle X - ray scattering (SAXS) is a complementary technique to Macromolecular Crystallography, NMR and Cryo -EM techniques and is becoming more widely used in structural biology. Crystallography requires good crystals and NMR has a size limitation. Cryo - EM studies biomolecules under a frozen condition. SAXS, on the other hand, allows for the study of the structure and dynamics of macrobiomolecules and their complexes in solution and under various buffer conditions such as salt concentration, pH, with or without ligand as well as under changing sample environments such as temperature and pressure. SAXS provides insight not only into global information about size and shape of biomacrobiomolecules, but also the information about flexibility and an ensemble of conformers. SAXS data can also be used in tandem with other biophysical methods (including crystallography, NMR, AFM and cryo-EM) by providing additional restraints that further improve simulations, validate structural models as well as fi nd missing fragments. The SAXS Facility of the Natio nal Cancer Institute (NCI) opens to all intramural and extramural research communities. The mission of the SAXS Core Facility is to provide support to the user communities with expertise in experimental design, data collection, processing, analysis, and in terpretation. The research fi eld includes but is not limited to structural studies of nucleic acids, proteins, protein assemblies, virus particles, lipid membranes and membrane-protein/DNA complexes. This presentation gives a brief introduction to the NCI SAXS facility and highlights recent scientific achievements in structural biology produced by NCI SAXS core users. NCI SAXS Core website: https://ccr.cancer.gov/center - for -structural-biology/saxs-core-facility","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323097206
Jessica Bruhn
Here I will present a recently determined crystal structure of ipragliflozin L - proline, a pharmaceutical drug used for the treatment of type 2 diabetes. Due to the small crystal size, MicroED was used to determine this structure. Initial phasing was carried out in the orthorhombic space group P 212121, but refinement in this space group proved to be challenging. Subsequent reduction in symmetry to P 21 produced a structure that could be refined
在这里，我将介绍最近测定的ipragliflozin L - proline的晶体结构，这是一种用于治疗2型糖尿病的药物。由于晶体尺寸较小，因此使用 MicroED 来确定该结构。最初在正交空间群 P 212121 中进行了分相，但事实证明在该空间群中重新分相具有挑战性。随后将对称性降低到 P21，得到了一种可以重新定型的结构
{"title":"What to do when h, k and l do not describe all the reflections in the diffraction?","authors":"Jessica Bruhn","doi":"10.1107/s2053273323097206","DOIUrl":"https://doi.org/10.1107/s2053273323097206","url":null,"abstract":"Here I will present a recently determined crystal structure of ipragliflozin L - proline, a pharmaceutical drug used for the treatment of type 2 diabetes. Due to the small crystal size, MicroED was used to determine this structure. Initial phasing was carried out in the orthorhombic space group P 212121, but refinement in this space group proved to be challenging. Subsequent reduction in symmetry to P 21 produced a structure that could be refined","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"118 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098108
K. Woźniak, M. Chodkiewicz, R. Gajda, V. Prakapenka, Przemyslaw Dera
Background. 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 and spectroscopic measurements have suggested existence for additional as of yet 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 atomic displacement parameters. Methods. We applied a new way of refinement of single crystal high pressure X - ray synchrotron and laboratory X -ray and electron diffraction data called Hirshfeld Atom Refinement. This method utilizes aspherical atomic scattering factors (X - rays), and aspherical atomic electrostatic potentials (ED), based on so called stockholder (Hirshfeld) partition and is especially effective in the case of refinement of crystals of H -rich compounds. Results. Here we present accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI and ice VII obtained by Hirshfeld Atom Refinement (HAR) against high pressure single crystal synchrotron and laboratory X - ray diffraction data as well as results of refinement of hexagonal ice obtained by HAR against electron diffraction data. It was possible to obtain O - H bond lengths and anisotropic atomic displacement parameters for disordered hydrogen atoms which are in good agreement with the corresponding results of single crystal neutron diffraction data.[1] Conclusions. Our results show that Hirshfeld atom refinement against X - ray diffraction and electron diffraction data is a tool which can
背景。水是生物体内不可或缺的化合物，目前已知有二十种不同的晶体固体形态（冰）。然而，这些结构仍存在许多基本问题，如确定氢原子的正确位置和热运动。由于 DFT 计算和光谱测量表明还存在其他未知物相，因此冰结构清单还不完整。在许多冰结构中，无论是中子衍射法、DFT 计算法还是 X 射线衍射法，都无法轻松解决氢原子无序问题或准确确定其原子位移参数。方法。我们对单晶高压 X 射线同步加速器和实验室 X 射线与电子衍射数据采用了一种新的重构方法，称为 "Hirshfeld 原子重构"。这种方法利用非球面原子散射系数（X 射线）和非球面原子静电位（ED），以所谓的股东（Hirshfeld）分区为基础，在富含 H - 化合物晶体的再注塑中尤为有效。结果。在此，我们展示了利用希什菲尔德原子重整（HAR）技术获得的 H2O、D2O 和混合（50%H2O/50%D2O）冰 VI 和冰 VII 的精确晶体结构与高压单晶同步加速器和实验室 X 射线二重衍射数据的对比结果，以及利用 HAR 技术获得的六方冰重整与电子二重衍射数据的对比结果。我们得到了无序氢原子的 O - H 键长度和各向异性原子位移参数，这与单晶中子衍射数据的相应结果非常吻合。我们的研究结果表明，根据 X 射线衍射和电子衍射数据对 Hirshfeld 原子进行重新标定是一种可以
{"title":"Accurate crystal structures of ices from X-ray and ED with Hirshfeld atom refinement","authors":"K. Woźniak, M. Chodkiewicz, R. Gajda, V. Prakapenka, Przemyslaw Dera","doi":"10.1107/s2053273323098108","DOIUrl":"https://doi.org/10.1107/s2053273323098108","url":null,"abstract":"Background. 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 and spectroscopic measurements have suggested existence for additional as of yet 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 atomic displacement parameters. Methods. We applied a new way of refinement of single crystal high pressure X - ray synchrotron and laboratory X -ray and electron diffraction data called Hirshfeld Atom Refinement. This method utilizes aspherical atomic scattering factors (X - rays), and aspherical atomic electrostatic potentials (ED), based on so called stockholder (Hirshfeld) partition and is especially effective in the case of refinement of crystals of H -rich compounds. Results. Here we present accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI and ice VII obtained by Hirshfeld Atom Refinement (HAR) against high pressure single crystal synchrotron and laboratory X - ray diffraction data as well as results of refinement of hexagonal ice obtained by HAR against electron diffraction data. It was possible to obtain O - H bond lengths and anisotropic atomic displacement parameters for disordered hydrogen atoms which are in good agreement with the corresponding results of single crystal neutron diffraction data.[1] Conclusions. Our results show that Hirshfeld atom refinement against X - ray diffraction and electron diffraction data is a tool which can","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"2013 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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