IUCrJ最新文献

筛选
英文 中文
Illuminating DNA repair in action: structural insights into a photocaged glycosylase complex 启发DNA修复在行动:结构洞察到光笼化糖基酶复合物。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-08-28 DOI: 10.1107/S2052252525007353
Michihiro Suga
{"title":"Illuminating DNA repair in action: structural insights into a photocaged glycosylase complex","authors":"Michihiro Suga","doi":"10.1107/S2052252525007353","DOIUrl":"10.1107/S2052252525007353","url":null,"abstract":"<div><div>Structural analysis of the co-crystal between human DNA glycosylase hOGG1 and a light-sensitive substrate analog highlights its utility as a platform for real-time observation of catalytic dynamics.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 513-514"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target? 用光笼底物重新审视DNA糖基酶的共晶结构:一个合适的时间分辨晶体学目标?
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-07-14 DOI: 10.1107/S2052252525006062
Tomoki Imura , Yuhei Hosokawa , Kai-Chun Yang , Yuki Ban , Hsuan-Yu Shih , Junpei Yamamoto , Manuel Maestre-Reyna
{"title":"Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target?","authors":"Tomoki Imura ,&nbsp;Yuhei Hosokawa ,&nbsp;Kai-Chun Yang ,&nbsp;Yuki Ban ,&nbsp;Hsuan-Yu Shih ,&nbsp;Junpei Yamamoto ,&nbsp;Manuel Maestre-Reyna","doi":"10.1107/S2052252525006062","DOIUrl":"10.1107/S2052252525006062","url":null,"abstract":"<div><div>Engineered <em>in crystallo</em> photosensitivity in a DNA-repair enzyme is carefully assessed for its suitability as a target for time-resolved crystallographic studies.</div></div><div><div>Co-crystal structures of a base-excision DNA-repair enzyme (human 8-oxo­guanine DNA glycosylase; hOgg1) in complex with a photocaged 8-oxoguanine DNA lesion were determined before and after uncaging via illumination at 2.81 and 2.48 Å resolution, respectively. The structures were carefully reassessed to rapidly expand the target repertoire of light-triggered time-resolved macromolecular crystallography. Late-intermediate cryo-trapping after uncaging revealed the partial accommodation of 8-oxoguanine in the active site with 68% occupancy, which did not induce full active-site adaptation to the catalytic state. Crystal illumination led to a light-dependent loss of diffraction power, likely due to crystal-packing collapse during the very late reaction stages. This work therefore not only demonstrates that hOgg1 is well suited for time-resolved crystallography, but also that such analysis is necessary to determine further steps in its reaction.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 515-522"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Highlighting radical sites through polarized neutron scattering from AFP-modulated polarized protons 通过极化中子散射从afp调制极化质子突出自由基位。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-08-21 DOI: 10.1107/S2052252525005871
Patrick Hautle , Oliver Zimmer , Hélène M. Jouve , Heinrich B. Stuhrmann
{"title":"Highlighting radical sites through polarized neutron scattering from AFP-modulated polarized protons","authors":"Patrick Hautle ,&nbsp;Oliver Zimmer ,&nbsp;Hélène M. Jouve ,&nbsp;Heinrich B. Stuhrmann","doi":"10.1107/S2052252525005871","DOIUrl":"10.1107/S2052252525005871","url":null,"abstract":"<div><div>Selective nuclear spin reversal by the method of adiabatic fast passage is a way to order a system of dynamically polarized nuclei. Using polarized neutron scattering, it increases the visibility of sources and sinks of proton polarization in radical proteins. Notably, Tyr369 has been confirmed as a potential radical site in bovine liver catalase.</div></div><div><div>Time-resolved neutron scattering has been used to study dynamically polarized protons in tyrosyl-doped bovine liver catalase. While the evolution of proton polarization and its inversion by the method of adiabatic fast passage (AFP) in a standard dynamic nuclear polarization (DNP) system with organic Cr(V) complexes can be well modelled and understood, the experiments with tyrosyl-doped catalase lead us into the world of extremely dilute paramagnets with only about 10<sup>17</sup> unpaired electrons per cm<sup>3</sup>. In this regime, the strength of DNP is comparable to the drift of proton polarization towards its thermal equilibrium of <em>P</em><sub>e</sub> = 0.35% at <em>T</em> = 1 K and <em>B</em> = 3.5 T. Negative DNP, which counteracts this drift, is confined to protons very close to the radical site, typically within 5 Å. In contrast, AFP reverses the polarization of protons at a larger distance from the radical. The contrast of a domain of polarized close protons giving rise to neutron scattering is considerably enhanced by AFP. Moreover, the spread of proton polarization is sensitive to magnetic inhomogeneities, like the iron of the heme of the catalase molecule. In short, polarized neutron scattering from AFP-modulated polarized samples provides an excellent tool for mapping sources and sinks of proton polarization in radical proteins.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 570-581"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Subtomogram averages of mitochondrial ATP synthase dimers from plants show a conserved extra density at the peripheral stalk 植物线粒体ATP合酶二聚体的亚断层图平均值显示,外周茎部有一个保守的额外密度。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-08-21 DOI: 10.1107/S2052252525006220
Thorsten B. Blum , Karen M. Davies , Werner Kühlbrandt
{"title":"Subtomogram averages of mitochondrial ATP synthase dimers from plants show a conserved extra density at the peripheral stalk","authors":"Thorsten B. Blum ,&nbsp;Karen M. Davies ,&nbsp;Werner Kühlbrandt","doi":"10.1107/S2052252525006220","DOIUrl":"10.1107/S2052252525006220","url":null,"abstract":"<div><div>Electron cryo-tomography of ATP synthase dimers in plant mitochondria indicates a wide dimer angle and a plant-specific subunit in the peripheral stalk.</div></div><div><div>We analyzed ATP synthase dimers in mitochondria purified from four plant species by subtomogram averaging, using <em>Saccharomyces cerevisiae</em> as a control. The purified mitochondria were plunge-frozen and broken mitochondria were examined by electron cryo-tomography. In each case, the ATP synthase dimers formed extensive rows along the tightly curved cristae ridges. ATP synthase dimer particles of each species were picked and averaged. Subtomogram averages of all four plant ATP synthases revealed an extra density at the tip of the peripheral stalk next to the OSCP hinge that is not seen in <em>S. cerevisae.</em> The dimer angle between the ATP synthase monomers is wider than in <em>Polytomella</em>, <em>S. cerevisae</em> or mammals, but less wide than in <em>Caenorhabditis elegans</em>. Slight variations in dimer angle indicate that ATP synthase dimers of plant mitochondria are more flexible than others.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 563-569"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unravelling venetoclax solvate behaviour: insights from crystal structures and computational surface analysis 解开venetoclax溶剂化行为:从晶体结构和计算表面分析的见解。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-08-28 DOI: 10.1107/S2052252525006785
Eliška Zmeškalová , Tereza Havlůjová , Martin Babor , Marcela Tkadlecová , Jaroslav Havlíček , Tomáš Pekárek , Szymon Tomczak , Luděk Ridvan , Miroslav Šoóš
{"title":"Unravelling venetoclax solvate behaviour: insights from crystal structures and computational surface analysis","authors":"Eliška Zmeškalová ,&nbsp;Tereza Havlůjová ,&nbsp;Martin Babor ,&nbsp;Marcela Tkadlecová ,&nbsp;Jaroslav Havlíček ,&nbsp;Tomáš Pekárek ,&nbsp;Szymon Tomczak ,&nbsp;Luděk Ridvan ,&nbsp;Miroslav Šoóš","doi":"10.1107/S2052252525006785","DOIUrl":"10.1107/S2052252525006785","url":null,"abstract":"<div><div>Seven venetoclax solvates were structurally characterized and studied for their desolvation behaviour, leading to the identification of two solvent-free polymorphs. Advanced crystallographic and computational analyses, including <em>Solvate Analyser</em>, <em>CSD-Particle</em>, FTIR and solid-state NMR, revealed key factors governing solvate stability and transformation. Notably, the acetone solvate exhibited exceptional stability and the desolvated forms retained the molecular arrangement of their parent solvates.</div></div><div><div>This study investigates venetoclax solvates and their nonsolvated forms through desolvation. Seven solvates were prepared and their structures solved from single-crystal X-ray diffraction data. Among these, two are cavity solvates while the remaining five are channel solvates, with three being isomorphous. De­solvation experiments led to two solvent-free crystalline polymorphs of venetoclax, forms A and B. Notably, the acetone solvate remained stable and did not convert to a nonsolvated form. Form B has a higher melting point and a faster intrinsic dissolution rate than form A. Advanced computational tools, including <em>Solvate Analyser</em> and <em>CSD-Particle</em>, provided insights into crystal surface properties and desolvation behaviour. Properties such as lattice energy, molecular interaction energy, attachment energy, surface rugosity and solvent arrangement within the crystal and on the surface were linked to solvate stability and subsequent transformation upon desolvation. A combination of FTIR, and <sup>13</sup>C and <sup>15</sup>N solid-state NMR spectroscopies showed that both short- and long-range molecular interactions and arrangements of venetoclax molecules in the desolvated forms closely resembled those in the parent solvates.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 595-609"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide 利用光笼型一氧化氮对血红素蛋白进行时间分辨连续同步加速器和连续飞秒晶体学研究。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-08-22 DOI: 10.1107/S2052252525006645
Peter Smyth , Sofia Jaho , Lewis J. Williams , Gabriel Karras , Ann Fitzpatrick , Amy J. Thompson , Sinan Battah , Danny Axford , Sam Horrell , Marina Lučić , Kotone Ishihara , Machika Kataoka , Hiroaki Matsuura , Kanji Shimba , Kensuke Tono , Takehiko Tosha , Hiroshi Sugimoto , Shigeki Owada , Michael A. Hough , Jonathan A.R. Worrall , Robin L. Owen
{"title":"Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide","authors":"Peter Smyth ,&nbsp;Sofia Jaho ,&nbsp;Lewis J. Williams ,&nbsp;Gabriel Karras ,&nbsp;Ann Fitzpatrick ,&nbsp;Amy J. Thompson ,&nbsp;Sinan Battah ,&nbsp;Danny Axford ,&nbsp;Sam Horrell ,&nbsp;Marina Lučić ,&nbsp;Kotone Ishihara ,&nbsp;Machika Kataoka ,&nbsp;Hiroaki Matsuura ,&nbsp;Kanji Shimba ,&nbsp;Kensuke Tono ,&nbsp;Takehiko Tosha ,&nbsp;Hiroshi Sugimoto ,&nbsp;Shigeki Owada ,&nbsp;Michael A. Hough ,&nbsp;Jonathan A.R. Worrall ,&nbsp;Robin L. Owen","doi":"10.1107/S2052252525006645","DOIUrl":"10.1107/S2052252525006645","url":null,"abstract":"<div><div>We demonstrate the application of a nitric oxide releasing photocage system for time-resolved serial crystallography studies of two heme containing proteins using a fixed target sample delivery system. Optimal parameters for successful photocage activation and nitric oxide release are explored.</div></div><div><div>Time-resolved X-ray crystallography is undergoing a renaissance due to the development of serial crystallography at synchrotron and XFEL beamlines. Crucial to such experiments are efficient and effective methods for uniformly initiating time-dependent processes within microcrystals, such as ligand binding, enzymatic reactions or signalling. A widely applicable approach is the use of photocaged substrates, where the photocage is soaked into the crystal in advance and then activated using a laser pulse to provide uniform initiation of the reaction throughout the crystal. This work characterizes photocage release of nitric oxide and binding of this ligand to two heme protein systems, cytochrome <em>c</em>′-β and dye-decolourizing peroxidase B using a fixed target sample delivery system. Laser parameters for photoactivation are systematically explored, and time-resolved structures over timescales ranging from 100 µs to 1.4 s using synchrotron and XFEL beamlines are described. The effective use of this photocage for time-resolved crystallography is demonstrated and appropriate illumination conditions for such experiments are determined.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 582-594"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
High-quality ultra-fast total scattering and pair distribution function data using an X-ray free-electron laser 使用x射线自由电子激光器的高质量超快速总散射和对分布函数数据。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-09-01 Epub Date: 2025-07-22 DOI: 10.1107/S205225252500538X
Adam F. Sapnik , Philip A. Chater , Dean S. Keeble , John S. O. Evans , Federica Bertolotti , Antonietta Guagliardi , Lise J. Støckler , Elodie A. Harbourne , Anders B. Borup , Rebecca S. Silberg , Adrien Descamps , Clemens Prescher , Benjamin D. Klee , Axel Phelipeau , Imran Ullah , Kárel G. Medina , Tobias A. Bird , Viktoria Kaznelson , William Lynn , Andrew L. Goodwin , David A. Keen
{"title":"High-quality ultra-fast total scattering and pair distribution function data using an X-ray free-electron laser","authors":"Adam F. Sapnik ,&nbsp;Philip A. Chater ,&nbsp;Dean S. Keeble ,&nbsp;John S. O. Evans ,&nbsp;Federica Bertolotti ,&nbsp;Antonietta Guagliardi ,&nbsp;Lise J. Støckler ,&nbsp;Elodie A. Harbourne ,&nbsp;Anders B. Borup ,&nbsp;Rebecca S. Silberg ,&nbsp;Adrien Descamps ,&nbsp;Clemens Prescher ,&nbsp;Benjamin D. Klee ,&nbsp;Axel Phelipeau ,&nbsp;Imran Ullah ,&nbsp;Kárel G. Medina ,&nbsp;Tobias A. Bird ,&nbsp;Viktoria Kaznelson ,&nbsp;William Lynn ,&nbsp;Andrew L. Goodwin ,&nbsp;David A. Keen","doi":"10.1107/S205225252500538X","DOIUrl":"10.1107/S205225252500538X","url":null,"abstract":"<div><div>This work demonstrates that high-quality ultra-fast total scattering data and pair distribution function data can be obtained from a single ∼30 fs pulse at the European XFEL, achieving a record <em>Q</em> range of up to 16.6 Å<sup>−1</sup>. These results establish XFELs as powerful tools for probing atomic scale structures on ultra-fast timescales, opening new opportunities for studying dynamic processes in disordered and complex materials.</div></div><div><div>High-quality total scattering data, a key tool for understanding atomic-scale structure in disordered materials, require stable instrumentation and access to high momentum transfers. This is now routine at dedicated synchrotron instrumentation using high-energy X-ray beams, but it is very challenging to measure a total scattering dataset in less than a few microseconds. This limits their effectiveness for capturing structural changes that occur at the much faster timescales of atomic motion. Current X-ray free-electron lasers (XFELs) provide femtosecond-pulsed X-ray beams with maximum energies of ∼24 keV, giving the potential to measure total scattering and the attendant pair distribution functions (PDFs) on femtosecond timescales. We demonstrate that this potential has been realized using the HED scientific instrument at the European XFEL and present normalized total scattering data for 0.35 Å<sup>−1</sup> &lt; <em>Q</em> &lt; 16.6 Å<sup>−1</sup> and their PDFs from a broad spectrum of materials, including crystalline, nanocrystalline and amorphous solids, liquids and clusters in solution. We analyzed the data using a variety of methods, including Rietveld refinement, small-box PDF refinement, joint reciprocal–real-space refinement, cluster refinement and Debye scattering analysis. The resolution function of the setup is also characterized. We conclusively show that high-quality data can be obtained from a single ∼30 fs XFEL pulse for multiple different sample types. Our efforts not only significantly increase the existing maximum reported <em>Q</em> range for an <em>S</em>(<em>Q</em>) measured at an XFEL but also mean that XFELs are now a viable X-ray source for the broad community of people using reciprocal-space total scattering and PDF methods in their research.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 531-547"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using multiple computer-predicted structures as molecular replacement models: application to the antiviral mini-protein LCB2 用多种计算机预测结构作为分子替代模型:在抗病毒小蛋白LCB2中的应用。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-07-01 Epub Date: 2025-06-23 DOI: 10.1107/S2052252525005123
Svetlana A. Korban , Oleg Mikhailovskii , Vladislav V. Gurzhiy , Ivan S. Podkorytov , Nikolai R. Skrynnikov
{"title":"Using multiple computer-predicted structures as molecular replacement models: application to the antiviral mini-protein LCB2","authors":"Svetlana A. Korban ,&nbsp;Oleg Mikhailovskii ,&nbsp;Vladislav V. Gurzhiy ,&nbsp;Ivan S. Podkorytov ,&nbsp;Nikolai R. Skrynnikov","doi":"10.1107/S2052252525005123","DOIUrl":"10.1107/S2052252525005123","url":null,"abstract":"<div><div>A set of crystallographic structures has been obtained for the small antiviral protein LCB2 using molecular replacement models from six different structure-prediction programs. This set of structures can be interpreted as a multiconformer ensemble, improving quality metrics and offering an interesting insight into side-chain dynamics.</div></div><div><div>In this report, we describe a set of structures of the engineered protein LCB2 that has been solved starting from different computer-predicted molecular replacement (MR) models. We found that <em>AlphaFold3</em>, <em>AlphaFold2</em>, <em>MultiFOLD</em>, <em>Rosetta</em>, <em>RoseTTAFold</em> and <em>trRosetta</em> all produced successful MR models for this three-helix bundle 58-residue protein, while some of the older predictors failed. To assign <em>B</em> factors in the MR models we used the predictor-generated confidence scores or, as a convenient alternative, the accessible surface area (ASA) values. The process of multi-start structure determination using <em>Coot</em> and <em>Phenix</em> demonstrated good convergence, leading to six structures within 0.25 Å (all-atom RMSD) of each other. Of note, structural differences between the computer-predicted MR models and the final structures can be largely attributed to a single specific crystal contact. Comparing the six structural solutions, we observe that a number of surface side chains have been solved with different conformations. Interestingly, for each individual structure the electron density is consistent with a single rotameric state and offers no direct evidence of conformational heterogeneity. Strictly speaking, this behavior constitutes a case of model bias; we argue, however, that it represents a benign side of model bias. Specifically, when we use a model where the side-chain conformation corresponds to one of the actual (significantly populated) rotameric states, this leads to an enhancement of the electron density for this particular conformation. Conversely, when we use a model with an irrelevant (low-population) side-chain conformation, it fails to produce the matching electron density. We thus conclude that the six LCB2 structures obtained in this study can be grouped into a multiconformer ensemble, where structural variations are representative of protein’s conformational dynamics. Indeed, using this six-member ensemble leads to a significant drop in <em>R</em><sub>work</sub> and <em>R</em><sub>free</sub> compared with the individual solutions. This interpretation was also supported by our MD simulations of the LCB2 crystal.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 488-501"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
High-resolution synchrotron X-ray study of icosahedrite, an icosahedral AlCuFe quasicrystal from the Khatyrka meteorite Khatyrka陨石中二十面体AlCuFe准晶体的高分辨率同步x射线研究。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-07-01 Epub Date: 2025-05-23 DOI: 10.1107/S2052252525004130
H. Takakura , K. Mizunuma , T. Yamada , A. Bosak , F. Formisano , L. Paolasini , M. de Boissieu , P. J. Steinhardt , L. Bindi
{"title":"High-resolution synchrotron X-ray study of icosahedrite, an icosahedral AlCuFe quasicrystal from the Khatyrka meteorite","authors":"H. Takakura ,&nbsp;K. Mizunuma ,&nbsp;T. Yamada ,&nbsp;A. Bosak ,&nbsp;F. Formisano ,&nbsp;L. Paolasini ,&nbsp;M. de Boissieu ,&nbsp;P. J. Steinhardt ,&nbsp;L. Bindi","doi":"10.1107/S2052252525004130","DOIUrl":"10.1107/S2052252525004130","url":null,"abstract":"<div><div>A single grain of the icosahedral AlCuFe quasicrystal extracted from the Khatyrka meteorite has been studied by means of high-resolution synchrotron X-ray diffraction at the ESRF. We found that the mineral is a phason-wave modulated icosahedral quasicrystal, a feature already observed for synthetic quasicrystals. This result might be used as a tracer to shed light on the thermal history of the meteorite.</div></div><div><div>Icosahedrite, natural icosahedral Al<sub>63</sub>Cu<sub>24</sub>Fe<sub>13</sub>, was discovered in a meteorite about 15 years ago. We have carried out a high-resolution X-ray diffraction study on a sample of this meteoritic mineral at the ESRF. The diffraction pattern turned out to be identical to an intermediate phase observed in synthetic <em>i</em>-AlCuFe during the transformation from the quasicrystalline state to a periodic rhombohedral phase. This particular natural Al<sub>63</sub>Cu<sub>24</sub>Fe<sub>13</sub> grain is an icosahedral quasicrystal on which a modulation by six cosine waves propagating along the fivefold axes is superimposed, with a wavelength of about 20 nm and a polarization in the phason/perpendicular space. By examining the thermodynamic conditions for producing this modulated icosahedral phase at high pressure in the laboratory, we may gain insights into the formation process of the Khatyrka meteorite.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 435-443"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Models of thermal motion in small-molecule crystallography 小分子晶体学中的热运动模型。
IF 3.6 2区 材料科学
IUCrJ Pub Date : 2025-07-01 Epub Date: 2025-06-06 DOI: 10.1107/S2052252525004361
Anna Hoser , Anders Ø. Madsen
{"title":"Models of thermal motion in small-molecule crystallography","authors":"Anna Hoser ,&nbsp;Anders Ø. Madsen","doi":"10.1107/S2052252525004361","DOIUrl":"10.1107/S2052252525004361","url":null,"abstract":"<div><div>This review commemorates the centenary of the Debye–Waller factor, highlighting its significance in quantifying the impact of thermal vibrations on scattering intensities as well as on crystal properties in small-molecule crystallography. It provides an introduction to thermal motion and displacement parameters, offering insights for chemists and crystallographers.</div></div><div><div>The Debye–Waller factor, introduced a century ago, remains a fundamental component in the refinement of crystal structures against X-ray, neutron and electron diffraction data. This review marks its centenary by exploring its applications in small-molecule crystallography. We provide a historical overview of the development of the Debye–Waller factor and its foundations in lattice dynamics. The review discusses the practical use of anisotropic displacement parameters and their role in accurate structure determination. We also address the challenges and advancements in modelling thermal motion and disorder, the role of multi-temperature measurements and modern computational approaches.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 421-434"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信
小红书