Journal of Applied Crystallography最新文献_第2页

Use of a confocal optical device for centring a diamond anvil cell in single-crystal X-ray diffraction experiments. 在单晶 X 射线衍射实验中使用共焦光学装置对金刚石砧座进行定心。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-20 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007829

Chengdao Hu, Cameron J G Wilson, Daniel M Scully, Tobias Stuerzer, Simon Parsons

引用次数: 0

Free tools for crystallographic symmetry handling and visualization. 晶体学对称性处理和可视化的免费工具。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-20 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007659

Gemma de la Flor, Mois I Aroyo, Ilaria Gimondi, Suzanna C Ward, Koichi Momma, Robert M Hanson, Leopoldo Suescun

{"title":"Free tools for crystallographic symmetry handling and visualization.","authors":"Gemma de la Flor, Mois I Aroyo, Ilaria Gimondi, Suzanna C Ward, Koichi Momma, Robert M Hanson, Leopoldo Suescun","doi":"10.1107/S1600576724007659","DOIUrl":"10.1107/S1600576724007659","url":null,"abstract":"Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1618-1639"},"PeriodicalIF":6.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Twinning and homo-epitaxy cooperation in the already rich growth morphology of CaCO₃ polymorphs. II. Calcite. CaCO3 多晶体丰富的生长形态中的孪生和同外延合作。II.方解石

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-20 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724008057

Dino Aquilano, Stefano Ghignone, Marco Bruno

{"title":"Twinning and homo-epitaxy cooperation in the already rich growth morphology of CaCO3 polymorphs. II. Calcite.","authors":"Dino Aquilano, Stefano Ghignone, Marco Bruno","doi":"10.1107/S1600576724008057","DOIUrl":"10.1107/S1600576724008057","url":null,"abstract":"The two most abundant CaCO3 polymorphs, calcite and aragonite, are universally recognized for the richness of their morphology to which different twins make relevant contributions. The epitaxial transformation calcite ↔ aragonite has long been debated. While the twinning has been thoroughly treated, the homo-epitaxy occurring within each of these minerals has, inexplicably, been overlooked to date, both experimentally and theoretically. Twinning can be deceptive to the point where it can be mistaken for homo-epitaxy, thus making the proposed growth mechanism in the crystal aggregate wrong. Within the present work, the first aim is a theoretical investigation of the homo-epitaxies among the three {10.4}-cleavage, {01.2}-steep and {01.8}-flat rhombohedra of calcite. Accordingly, the specific adhesion energies were calculated between facing crystal forms, unequivocally showing that the {01.2}/{01.8} homo-epitaxy competes with the generation of both {01.2} and {01.8} contact twins. Secondly, the calculation of the specific adhesion energy was extended to consider homo-epitaxy for the {10.4} rhombohedron. The two-dimensional geometric lattice coincidence has been tried for the {00.1} pinacoidal form as well.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1484-1488"},"PeriodicalIF":6.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications. 基于坐标的小型和大型分子组装对距离分布函数模拟：实施与应用。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-17 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007222

Xiaobing Zuo, David M Tiede

{"title":"Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.","authors":"Xiaobing Zuo, David M Tiede","doi":"10.1107/S1600576724007222","DOIUrl":"10.1107/S1600576724007222","url":null,"abstract":"X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclo-dextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0, which is available to download from https://12idb.xray.aps.anl.gov/solx.html.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1446-1455"},"PeriodicalIF":6.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server. 实现动态配置的 CIF 数据库：毕尔巴鄂晶体学服务器的新调制结构开放数据库。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-17 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007908

J Gabirondo-López, I Gabirondo-López, E S Tasci, G Madariaga

引用次数: 0

Determination of the average crystallite size and the crystallite size distribution: the envelope function approach EnvACS. 平均晶粒尺寸和晶粒尺寸分布的测定：包络函数法 EnvACS。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-17 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007362

Thorsten M Gesing, Lars Robben

{"title":"Determination of the average crystallite size and the crystallite size distribution: the envelope function approach EnvACS.","authors":"Thorsten M Gesing, Lars Robben","doi":"10.1107/S1600576724007362","DOIUrl":"10.1107/S1600576724007362","url":null,"abstract":"A procedure is presented to exactly obtain the apparent average crystallite size (ACS) of powder samples using standard in-house powder diffraction experiments without any restriction originating from the Scherrer equation. Additionally, the crystallite size distribution within the sample can be evaluated. To achieve this, powder diffractograms are background corrected and long-range radial distribution functions G(r) up to 300 nm are calculated from the diffraction data. The envelope function f env of G(r) is approximated by a procedure determining the absolute maxima of G(r) in a certain interval (r range). Fitting of an ACS distribution envelope function to this approximation gives the ACS and its distribution. The method is tested on diffractograms of LaB6 standard reference materials measured with different wavelengths to demonstrate the validity of the approach and to clarify the influence of the wavelength used. The latter results in a general description of the maximum observable average crystallite size, which depends on the instrument and wavelength used. The crystallite site distribution is compared with particle size distributions based on transmission electron microscopy investigations, providing an approximation of the average number of crystallites per particle.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1466-1476"},"PeriodicalIF":6.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multidimensional Rietveld refinement of high-pressure neutron diffraction data of PbNCN. PbNCN 高压中子衍射数据的多维里特维尔德精炼。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-05 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007635

Yannick Meinerzhagen, Katharina Eickmeier, Peter C Müller, Jan Hempelmann, Andreas Houben, Richard Dronskowski

{"title":"Multidimensional Rietveld refinement of high-pressure neutron diffraction data of PbNCN.","authors":"Yannick Meinerzhagen, Katharina Eickmeier, Peter C Müller, Jan Hempelmann, Andreas Houben, Richard Dronskowski","doi":"10.1107/S1600576724007635","DOIUrl":"10.1107/S1600576724007635","url":null,"abstract":"High-pressure neutron powder diffraction data from PbNCN were collected on the high-pressure diffraction beamline SNAP located at the Spallation Neutron Source (SNS) of Oak Ridge National Laboratory (Tennessee, USA). The diffraction data were analyzed using the novel method of multidimensional (two dimensions for now, potentially more in the future) Rietveld refinement and, for comparison, employing the conventional Rietveld method. To achieve two-dimensional analysis, a detailed description of the SNAP instrument characteristics was created, serving as an instrument parameter file, and then yielding both cell and spatial parameters as refined under pressure for the first time for solid-state cyanamides/carbodi-imides. The bulk modulus B 0 = 25.1 (15) GPa and its derivative B'0 = 11.1 (8) were extracted for PbNCN following the Vinet equation of state. Surprisingly, an internal transition was observed beyond 2.0 (2) GPa, resulting from switching the bond multiplicities (and bending direction) of the NCN2- complex anion. The results were corroborated using electronic structure calculation from first principles, highlighting both local structural and chemical bonding details.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1436-1445"},"PeriodicalIF":6.1,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Low-dose electron microscopy imaging for beam-sensitive metal-organic frameworks. 对光束敏感的金属有机框架的低剂量电子显微镜成像。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-09-05 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007192

Yuhang Liang, Yi Zhou

引用次数: 0

Coherent X-ray diffraction imaging of single particles: background impact on 3D reconstruction. 单颗粒的相干 X 射线衍射成像：背景对三维重建的影响。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-08-30 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724006101

August Wollter, Tomas Ekeberg

{"title":"Coherent X-ray diffraction imaging of single particles: background impact on 3D reconstruction.","authors":"August Wollter, Tomas Ekeberg","doi":"10.1107/S1600576724006101","DOIUrl":"10.1107/S1600576724006101","url":null,"abstract":"Coherent diffractive imaging with X-ray free-electron lasers could enable structural studies of macromolecules at room temperature. This type of experiment could provide a means to study structural dynamics on the femtosecond timescale. However, the diffraction from a single protein is weak compared with the incoherent scattering from background sources, which negatively affects the reconstruction analysis. This work evaluates the effects of the presence of background on the analysis pipeline. Background measurements from the European X-ray Free-Electron Laser were combined with simulated diffraction patterns and treated by a standard reconstruction procedure, including orientation recovery with the expand, maximize and compress algorithm and 3D phase retrieval. Background scattering did have an adverse effect on the estimated resolution of the reconstructed density maps. Still, the reconstructions generally worked when the signal-to-background ratio was 0.6 or better, in the momentum transfer shell of the highest reconstructed resolution. The results also suggest that the signal-to-background requirement increases at higher resolution. This study gives an indication of what is possible at current setups at X-ray free-electron lasers with regards to expected background strength and establishes a target for experimental optimization of the background.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1384-1391"},"PeriodicalIF":6.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Practical courses on advanced methods in macromolecular crystallization: 20 years of history and future perspectives. 大分子结晶高级方法实践课程：20 年的历史与未来展望。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-08-30 eCollection Date: 2024-10-01 DOI: 10.1107/S1600576724007106

Petra Havlickova, Jose A Gavira, Jeroen R Mesters, Anna Koutska, Barbora Kascakova, Tatyana Prudnikova, Rolf Hilgenfeld, Juan Manuel Garcia-Ruiz, Pavlina Rezacova, Ivana Kuta Smatanova

引用次数: 0