Journal of Applied Crystallography最新文献

{"title":"Normalized radial distribution as a crystal structure descriptor: applications in comparative crystal chemistry and the 'search match' problem","authors":"Sergey Rashchenko","doi":"10.1107/S1600576726002797","DOIUrl":"https://doi.org/10.1107/S1600576726002797","url":null,"abstract":"<p>A crystal structure descriptor (`fingerprint function') based on a normalized radial distribution function is presented. Unlike earlier prototypes developed mainly for use in crystal structure prediction, data mining and machine-learning workflows, the presented approach is focused on applications in the field of comparative crystal chemistry. Its prospective applications include the classification of large datasets of chemically heterogeneous crystal structures or `search match' problems, when structures homeotypic to a given structure are searched for throughout a database. Practical aspects of the proposed approach are illustrated with real-life examples from the Crystallography Open Database.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"901-909"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148117547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Normalized radial distribution as a crystal structure descriptor: applications in comparative crystal chemistry and the 'search match' problem","authors":"Sergey Rashchenko","doi":"10.1107/S1600576726002797","DOIUrl":"https://doi.org/10.1107/S1600576726002797","url":null,"abstract":"<p>A crystal structure descriptor (`fingerprint function') based on a normalized radial distribution function is presented. Unlike earlier prototypes developed mainly for use in crystal structure prediction, data mining and machine-learning workflows, the presented approach is focused on applications in the field of comparative crystal chemistry. Its prospective applications include the classification of large datasets of chemically heterogeneous crystal structures or `search match' problems, when structures homeotypic to a given structure are searched for throughout a database. Practical aspects of the proposed approach are illustrated with real-life examples from the Crystallography Open Database.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"901-909"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148117549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conical diffraction of a synchrotron beam to probe the efficiency and morphology of blazed gratings","authors":"K. V. Nikolaev,&nbsp;L. I. Goray,&nbsp;P. S. Savchenkov,&nbsp;A. V. Rogachev,&nbsp;A. A. Chouprik,&nbsp;T. N. Berezovskaya,&nbsp;D. V. Mokhov,&nbsp;S. A. Garakhin,&nbsp;N. I. Chkhalo,&nbsp;A. D. Bouravleuv,&nbsp;S. N. Yakunin","doi":"10.1107/S1600576726002372","DOIUrl":"https://doi.org/10.1107/S1600576726002372","url":null,"abstract":"<p>This study explores the use of synchrotron measurements as a nanometrology tool for blazed gratings. In grazing-incidence geometry, one can measure both the conical diffraction and the diffuse scattering on the grating simultaneously in a single scattering pattern. The sensitivity of scattering patterns to the structure of blazed gratings is evaluated. The diffraction component of the pattern is shown to be sensitive to the average groove profile of the gratings, while the diffuse scattering depends on the roughness morphology of the reflective surface of the blazed gratings. These findings are supported by numerical simulations. The simulations were performed using several rigorous solvers for the Helmholtz equations and with perturbation theory. The analysis relies on synchrotron data, as well as on data from atomic force microscopy and scanning electron microscopy. The aim of this article is to draw the attention of the optical community to synchrotron measurements as a nanometrology tool for modern optical elements.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"737-750"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148118214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computation and sensitivity analysis of the deformation gradient tensor reconstruction in dark-field X-ray microscopy","authors":"Brinthan Kanesalingam,&nbsp;Darshan Chalise,&nbsp;Carsten Detlefs,&nbsp;Leora Dresselhaus-Marais","doi":"10.1107/S1600576726001226","DOIUrl":"https://doi.org/10.1107/S1600576726001226","url":null,"abstract":"<p>Spatially resolved strain measurements are crucial to understanding the properties of engineering materials. Although strain measurements utilizing techniques such as transmission electron microscopy and electron backscatter diffraction offer high spatial resolution, they are limited to surface or thin samples. X-ray diffraction methods, including Bragg coherent diffraction imaging and X-ray topography, enable strain measurements deep inside bulk materials but face challenges in simultaneously achieving both high spatial resolution and large fields of view. Dark-field X-ray microscopy (DFXM) offers a promising solution, with its ability to image bulk crystals at the nanoscale while offering a field of view approaching a few hundred micrometres. However, an inverse modelling framework to relate the angular shifts in DFXM explicitly to the strain and lattice rotation tensors is lacking. In this paper, we develop such an inverse modelling formalism. Using the oblique diffraction geometry for DFXM, enabling access to non-coplanar symmetry-equivalent reflections, we demonstrate that the reconstruction of the full deformation gradient tensor <b>F</b>^(g), and consequently the strain and lattice rotation matrices, is possible. In addition to the formalism, we develop a computational framework that both forward calculates the anticipated angular shifts and reconstructs the average <b>F</b>^(g) for an individual pixel from DFXM experiments. Finally, utilizing the established formalism and computational framework, we present methods for sensitivity analysis to relate individual components of the rotation or strain tensor to specific angles of DFXM. The developed sensitivity analysis also enables explicit computation of the errors associated with the reconstruction of each component. The formalism, the computational framework and the sensitivity analysis established in this paper should assist both the interpretation of past DFXM experiments and the design of future DFXM experiments.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"716-736"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148119278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM–microcrystal electron diffraction structural elucidation of cefadroxil: nanocrystallographic and neurotherapeutic insights into a β-lactam antibiotic","authors":"Saleem Iqbal,&nbsp;Bairong Shen","doi":"10.1107/S1600576726003250","DOIUrl":"https://doi.org/10.1107/S1600576726003250","url":null,"abstract":"<p>Atomic-resolution structure determination is central to understanding the intrinsic conformational properties of pharmaceutical small molecules. In this study, we report the first cryo-enabled microcrystal electron diffraction (cryo-MicroED) structure of the β-lactam antibiotic cefadroxil, providing a high-fidelity nanocrystallographic characterization of its molecular geometry, stereochemistry and intermolecular interactions. The structure was resolved in the orthorhombic <i>P</i>2₁2₁2₁ space group, enabling unambiguous assignment of relative stereochemistry and confirmation of the known absolute configuration at all stereogenic centers and crystal packing motifs. This MicroED-derived structure establishes a robust atomic-level reference for cefadroxil and related β-lactam scaffolds, highlighting the capability of cryo-MicroED to resolve complex pharmaceutical compounds beyond the limits of conventional X-ray crystallography. To demonstrate the functional relevance of the experimentally determined structure, complementary long-timescale molecular dynamics simulations were performed using the MicroED coordinates, revealing a structurally stable and conformationally coherent interaction profile under biologically relevant conditions. Overall, this work highlights MicroED as a powerful and versatile crystallographic technique for small-molecule structural chemistry, providing precise structural benchmarks that can be extended to downstream modeling and structure-guided applications. The study illustrates a generalizable workflow for integrating cryo-MicroED crystallography with computational analysis, advancing the structural characterization of legacy drug molecules.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"869-878"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148117545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computation and sensitivity analysis of the deformation gradient tensor reconstruction in dark-field X-ray microscopy","authors":"Brinthan Kanesalingam,&nbsp;Darshan Chalise,&nbsp;Carsten Detlefs,&nbsp;Leora Dresselhaus-Marais","doi":"10.1107/S1600576726001226","DOIUrl":"https://doi.org/10.1107/S1600576726001226","url":null,"abstract":"<p>Spatially resolved strain measurements are crucial to understanding the properties of engineering materials. Although strain measurements utilizing techniques such as transmission electron microscopy and electron backscatter diffraction offer high spatial resolution, they are limited to surface or thin samples. X-ray diffraction methods, including Bragg coherent diffraction imaging and X-ray topography, enable strain measurements deep inside bulk materials but face challenges in simultaneously achieving both high spatial resolution and large fields of view. Dark-field X-ray microscopy (DFXM) offers a promising solution, with its ability to image bulk crystals at the nanoscale while offering a field of view approaching a few hundred micrometres. However, an inverse modelling framework to relate the angular shifts in DFXM explicitly to the strain and lattice rotation tensors is lacking. In this paper, we develop such an inverse modelling formalism. Using the oblique diffraction geometry for DFXM, enabling access to non-coplanar symmetry-equivalent reflections, we demonstrate that the reconstruction of the full deformation gradient tensor <b>F</b>^(g), and consequently the strain and lattice rotation matrices, is possible. In addition to the formalism, we develop a computational framework that both forward calculates the anticipated angular shifts and reconstructs the average <b>F</b>^(g) for an individual pixel from DFXM experiments. Finally, utilizing the established formalism and computational framework, we present methods for sensitivity analysis to relate individual components of the rotation or strain tensor to specific angles of DFXM. The developed sensitivity analysis also enables explicit computation of the errors associated with the reconstruction of each component. The formalism, the computational framework and the sensitivity analysis established in this paper should assist both the interpretation of past DFXM experiments and the design of future DFXM experiments.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"716-736"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148119291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conical diffraction of a synchrotron beam to probe the efficiency and morphology of blazed gratings","authors":"K. V. Nikolaev,&nbsp;L. I. Goray,&nbsp;P. S. Savchenkov,&nbsp;A. V. Rogachev,&nbsp;A. A. Chouprik,&nbsp;T. N. Berezovskaya,&nbsp;D. V. Mokhov,&nbsp;S. A. Garakhin,&nbsp;N. I. Chkhalo,&nbsp;A. D. Bouravleuv,&nbsp;S. N. Yakunin","doi":"10.1107/S1600576726002372","DOIUrl":"https://doi.org/10.1107/S1600576726002372","url":null,"abstract":"<p>This study explores the use of synchrotron measurements as a nanometrology tool for blazed gratings. In grazing-incidence geometry, one can measure both the conical diffraction and the diffuse scattering on the grating simultaneously in a single scattering pattern. The sensitivity of scattering patterns to the structure of blazed gratings is evaluated. The diffraction component of the pattern is shown to be sensitive to the average groove profile of the gratings, while the diffuse scattering depends on the roughness morphology of the reflective surface of the blazed gratings. These findings are supported by numerical simulations. The simulations were performed using several rigorous solvers for the Helmholtz equations and with perturbation theory. The analysis relies on synchrotron data, as well as on data from atomic force microscopy and scanning electron microscopy. The aim of this article is to draw the attention of the optical community to synchrotron measurements as a nanometrology tool for modern optical elements.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"737-750"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148118220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM–microcrystal electron diffraction structural elucidation of cefadroxil: nanocrystallographic and neurotherapeutic insights into a β-lactam antibiotic","authors":"Saleem Iqbal,&nbsp;Bairong Shen","doi":"10.1107/S1600576726003250","DOIUrl":"https://doi.org/10.1107/S1600576726003250","url":null,"abstract":"<p>Atomic-resolution structure determination is central to understanding the intrinsic conformational properties of pharmaceutical small molecules. In this study, we report the first cryo-enabled microcrystal electron diffraction (cryo-MicroED) structure of the β-lactam antibiotic cefadroxil, providing a high-fidelity nanocrystallographic characterization of its molecular geometry, stereochemistry and intermolecular interactions. The structure was resolved in the orthorhombic <i>P</i>2₁2₁2₁ space group, enabling unambiguous assignment of relative stereochemistry and confirmation of the known absolute configuration at all stereogenic centers and crystal packing motifs. This MicroED-derived structure establishes a robust atomic-level reference for cefadroxil and related β-lactam scaffolds, highlighting the capability of cryo-MicroED to resolve complex pharmaceutical compounds beyond the limits of conventional X-ray crystallography. To demonstrate the functional relevance of the experimentally determined structure, complementary long-timescale molecular dynamics simulations were performed using the MicroED coordinates, revealing a structurally stable and conformationally coherent interaction profile under biologically relevant conditions. Overall, this work highlights MicroED as a powerful and versatile crystallographic technique for small-molecule structural chemistry, providing precise structural benchmarks that can be extended to downstream modeling and structure-guided applications. The study illustrates a generalizable workflow for integrating cryo-MicroED crystallography with computational analysis, advancing the structural characterization of legacy drug molecules.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"869-878"},"PeriodicalIF":2.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148117548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"889-900"},"PeriodicalIF":2.8,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148117539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"59 3","pages":"879-888"},"PeriodicalIF":2.8,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148116614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}