Journal of Applied Crystallography最新文献

{"title":"Energy-dispersive Laue diffraction analysis of the influence of statherin and histatin on the crystallographic texture during human dental enamel demineralization.","authors":"Charbel Sakr, Mohammed Al-Mosawi, Tilman A Grünewald, Philip Cook, Pieter Tack, Laszlo Vincze, Jean-Sebastien Micha, Paul Anderson, Maisoon Al-Jawad, Helga C Lichtenegger","doi":"10.1107/S1600576724007180","DOIUrl":"10.1107/S1600576724007180","url":null,"abstract":"<p><p>Energy-dispersive Laue diffraction (EDLD) is a powerful method to obtain position-resolved texture information in inhomogeneous biological samples without the need for sample rotation. This study employs EDLD texture scanning to investigate the impact of two salivary peptides, statherin (STN) and histatin-1 (HTN) 21 <i>N</i>-terminal peptides (STN21 and HTN21), on the crystallographic structure of dental enamel. These proteins are known to play crucial roles in dental caries progression. Three healthy incisors were randomly assigned to three groups: artificially demineralized, demineralized after HTN21 peptide pre-treatment and demineralized after STN21 peptide pre-treatment. To understand the micro-scale structure of the enamel, each specimen was scanned from the enamel surface to a depth of 250 µm using microbeam EDLD. Via the use of a white beam and a pixelated detector, where each pixel functions as a spectrometer, pole figures were obtained in a single exposure at each measurement point. The results revealed distinct orientations of hydroxyapatite crystallites and notable texture variation in the peptide-treated demineralized samples compared with the demineralized control. Specifically, the peptide-treated demineralized samples exhibited up to three orientation populations, in contrast to the demineralized control which displayed only a single orientation population. The texture index of the demineralized control (2.00 ± 0.21) was found to be lower than that of either the STN21 (2.32 ± 0.20) or the HTN21 (2.90 ± 0.46) treated samples. Hence, texture scanning with EDLD gives new insights into dental enamel crystallite orientation and links the present understanding of enamel demineralization to the underlying crystalline texture. For the first time, the feasibility of EDLD texture measurements for quantitative texture evaluation in demineralized dental enamel samples is demonstrated.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1514-1527"},"PeriodicalIF":6.1,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390699","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}

{"title":"The AUREX cell: a versatile <i>operando</i> electrochemical cell for studying catalytic materials using X-ray diffraction, total scattering and X-ray absorption spectroscopy under working conditions.","authors":"Sara Frank, Marcel Ceccato, Henrik S Jeppesen, Melissa J Marks, Mads L N Nielsen, Ronghui Lu, Jens Jakob Gammelgaard, Jonathan Quinson, Ruchi Sharma, Julie S Jensen, Sara Hjelme, Cecilie Friberg Klysner, Simon J L Billinge, Justus Just, Frederik H Gjørup, Jacopo Catalano, Nina Lock","doi":"10.1107/S1600576724007817","DOIUrl":"10.1107/S1600576724007817","url":null,"abstract":"<p><p>Understanding the structure-property relationship in electrocatalysts under working conditions is crucial for the rational design of novel and improved catalytic materials. This paper presents the Aarhus University reactor for electrochemical studies using X-rays (AUREX) <i>operando</i> electrocatalytic flow cell, designed as an easy-to-use versatile setup with a minimal background contribution and a uniform flow field to limit concentration polarization and handle gas formation. The cell has been employed to measure <i>operando</i> total scattering, diffraction and absorption spectroscopy as well as simultaneous combinations thereof on a commercial silver electrocatalyst for proof of concept. This combination of <i>operando</i> techniques allows for monitoring of the short-, medium- and long-range structure under working conditions, including an applied potential, liquid electrolyte and local reaction environment. The structural transformations of the Ag electrocatalyst are monitored with non-negative matrix factorization, linear combination analysis, the Pearson correlation coefficient matrix, and refinements in both real and reciprocal space. Upon application of an oxidative potential in an Ar-saturated aqueous 0.1 <i>M</i> KHCO₃/K₂CO₃ electrolyte, the face-centered cubic (f.c.c.) Ag gradually transforms first to a trigonal Ag₂CO₃ phase, followed by the formation of a monoclinic Ag₂CO₃ phase. A reducing potential immediately reverts the structure to the Ag (f.c.c.) phase. Following the electrochemical-reaction-induced phase transitions is of fundamental interest and necessary for understanding and improving the stability of electrocatalysts, and the <i>operando</i> cell proves a versatile setup for probing this. In addition, it is demonstrated that, when studying electrochemical reactions, a high energy or short exposure time is needed to circumvent beam-induced effects.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1489-1502"},"PeriodicalIF":6.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390736","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}

{"title":"Use of a confocal optical device for centring a diamond anvil cell in single-crystal X-ray diffraction experiments.","authors":"Chengdao Hu, Cameron J G Wilson, Daniel M Scully, Tobias Stuerzer, Simon Parsons","doi":"10.1107/S1600576724007829","DOIUrl":"10.1107/S1600576724007829","url":null,"abstract":"<p><p>High-pressure crystallographic data can be measured using a diamond anvil cell (DAC), which allows the sample to be viewed only along a cell vector which runs perpendicular to the diamond anvils. Although centring a sample perpendicular to this direction is straightforward, methods for centring along this direction often rely on sample focusing, measurements of the direct beam or short data collections followed by refinement of the crystal offsets. These methods may be inaccurate, difficult to apply or slow. Described here is a method based on precise measurement of the offset in this direction using a confocal optical device, whereby the cell centre is located at the mid-point of two measurements of the distance between a light source and the external faces of the diamond anvils viewed along the forward and reverse directions of the cell vector. It is shown that the method enables a DAC to be centred to within a few micrometres reproducibly and quickly.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1691-1696"},"PeriodicalIF":6.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390740","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}

{"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":"<p><p>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, <i>VESTA</i> and <i>Jmol</i>. The utility of these resources is explained and shown by several illustrative examples.</p>","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}

{"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":"<p><p>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.</p>","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}

{"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":"<p><p>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, <i>SolX 3.0</i>, which is available to download from https://12idb.xray.aps.anl.gov/solx.html.</p>","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}

{"title":"Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server.","authors":"J Gabirondo-López, I Gabirondo-López, E S Tasci, G Madariaga","doi":"10.1107/S1600576724007908","DOIUrl":"10.1107/S1600576724007908","url":null,"abstract":"<p><p>This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via <i>JSmol</i>. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1640-1649"},"PeriodicalIF":6.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390738","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}

{"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":"<p><p>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 <i>G</i>(<i>r</i>) up to 300 nm are calculated from the diffraction data. The envelope function <i>f</i> ^env of <i>G</i>(<i>r</i>) is approximated by a procedure determining the absolute maxima of <i>G</i>(<i>r</i>) in a certain interval (<i>r</i> 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.</p>","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}

{"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":"<p><p>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 <i>B</i> ₀ = 25.1 (15) GPa and its derivative <i>B</i>'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 NCN^2- complex anion. The results were corroborated using electronic structure calculation from first principles, highlighting both local structural and chemical bonding details.</p>","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}

{"title":"Low-dose electron microscopy imaging for beam-sensitive metal-organic frameworks.","authors":"Yuhang Liang, Yi Zhou","doi":"10.1107/S1600576724007192","DOIUrl":"10.1107/S1600576724007192","url":null,"abstract":"<p><p>Metal-organic frameworks (MOFs) have garnered significant attention in recent years owing to their exceptional properties. Understanding the intricate relationship between the structure of a material and its properties is crucial for guiding the synthesis and application of these materials. (Scanning) Transmission electron microscopy (S)TEM imaging stands out as a powerful tool for structural characterization at the nanoscale, capable of detailing both periodic and aperiodic local structures. However, the high electron-beam sensitivity of MOFs presents substantial challenges in their structural characterization using (S)TEM. This paper summarizes the latest advancements in low-dose high-resolution (S)TEM imaging technology and its application in MOF material characterization. It covers aspects such as framework structure, defects, and surface and interface analysis, along with the distribution of guest molecules within MOFs. This review also discusses emerging technologies like electron ptychography and outlines several prospective research directions in this field.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 5","pages":"1270-1281"},"PeriodicalIF":6.1,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390703","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}