Journal of Applied Crystallography最新文献

{"title":"Reliability of pair distribution function analysis in <i>in situ</i> experiments.","authors":"Rasmus Baden Stubkjær, Magnus Kløve, Andreas Bertelsen, Anders Bæk Borup, Martin Roelsgaard, Bo Brummerstedt Iversen","doi":"10.1107/S1600576725001694","DOIUrl":"10.1107/S1600576725001694","url":null,"abstract":"<p><p><i>In situ</i> and <i>operando</i> pair distribution function (PDF) studies are becoming commonly used to study chemical reactions, nucleation and growth of nanoparticles, or structural changes during the operation of batteries, catalysts, thermoelectric devices <i>etc.</i> However, repeated time-resolved total scattering experiments and subsequent PDF analysis are often not prioritized due to the scarce synchrotron beam time available. This means that the experimental uncertainty and reproducibility of the experimental methods are unknown, and the full potential of <i>in situ</i> PDF experiments may not be exploited. Here, we quantify the experimental uncertainty of the PDF technique in an <i>in situ</i> study of the hydro-thermal synthesis of ZrO₂ nanoparticles. Systematic variation of the parameters used to obtain the PDF shows that the user-defined parameters can potentially affect the chemical conclusions obtained from the time-resolved experiment. We found that comparable results are best obtained using the same input parameters across different experiments. We also compare different PDF algorithms to examine whether the processing algorithm influences the chemical analysis.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"495-503"},"PeriodicalIF":6.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763416","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":"Upgrade of the KWS-2 high-intensity/extended-<i>Q</i>-range SANS diffractometer of JCNS for soft matter and biophysics: <i>in situ</i> SEC, controlled <i>in situ</i> RH/T variation and WANS detection.","authors":"Jia-Jhen Kang, Ralf Biehl, Georg Brandl, Helmut Korb, Kimio Yoshimura, Vladimir Ossovyi, Andreas Nebel, Jacqueline Lippertz, Ralf Engels, Günter Kemmerling, Alexander Zaft, Hiroki Iwase, Hiroshi Arima-Osonoi, Shin-Ichi Takata, Alexander Weber, Simon Staringer, Baohu Wu, Yue Zhao, Stefan Mattauch, Aurel Radulescu","doi":"10.1107/S160057672500158X","DOIUrl":"10.1107/S160057672500158X","url":null,"abstract":"<p><p>The KWS-2 small-angle neutron scattering (SANS) diffractometer operated by Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum, Garching, Germany, is dedicated to the investigation of mesoscopic multi-scale structures and structural changes due to rapid kinetic processes in soft condensed matter and biophysical systems. Following requests from the user community, it has been repeatedly upgraded with respect to the most important methodological parameters of an instrument of this type, namely the intensity on the sample, the instrumental resolution and the minimum scattering variable <i>Q</i> _min. Here we report on further specific improvements to the sample environment and detection capabilities which have just been completed or are being implemented. Complementary size-exclusion chromatography (SEC) for <i>in situ</i> protein purification was developed and optimized at KWS-2 to provide the instrument with biological samples of controlled quality. The instrument is also currently being equipped with a wide-angle neutron scattering (WANS) detector which will allow it to bridge the atomic and mesoscale, benefiting from the instrument's adjustable resolution down to Δλ/λ = 2%. For controlled relative humidity and temperature (RH/T) on ionic conductive samples for energy applications or biomembranes for biophysical and health applications, a precise dew point generator has recently been characterized and commissioned; this offers great versatility with regard to varying the contrast <i>in situ</i> in the beam on hydrated samples.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"581-594"},"PeriodicalIF":6.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763624","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":"Solvent-annealing-induced microphase separation in polyether polyurethane: a small-angle X-ray scattering study.","authors":"Shanshan Wang, Jiayao Song, Keping Chen, Mark Julian Henderson, Qiang Tian, László Almásy","doi":"10.1107/S1600576725001633","DOIUrl":"10.1107/S1600576725001633","url":null,"abstract":"<p><p>This study investigated the effects of solvent vapor annealing on the microphase separation structure of polyurethane (PU) using small-angle X-ray scattering (SAXS) and complementary techniques. Solvent annealing, as an alternative to thermal annealing, offers a lower-temperature method to refine the microstructure of PU. We examined the impact of methyl ethyl ketone (MEK), acetone and toluene vapors on a commercial polyether PU, focusing on changes in microphase structure, adsorption kinetics and thermal stability. The SAXS data, analyzed by a polydisperse hard-sphere model, indicated that the degree of phase separation increased upon solvent annealing, and the order of influence exerted by the solvent vapors on the microphase structure follows MEK > acetone > toluene. The <i>in situ</i> variable-temperature SAXS results showed that the solvent-annealed sample had superior thermal stability to the quenched sample. Compared with high-temperature annealing, solvent annealing induced a higher degree of phase separation but did not lead to significant growth of the hard-urethane-segment-rich domains. These findings provide valuable insights into optimizing solvent annealing processes, allowing for advanced applications of PUs where excessive heat may lead to degradation or other undesirable changes.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"564-572"},"PeriodicalIF":6.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763635","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":"Optimal <i>st</i>-PMMA/C₆₀ helical inclusion complexes via tunable energy landscapes for the application of an Ag SERS-active substrate.","authors":"Song-Yu Tsai, Wen-Tsung Tseng, Jina-Hua Su, Yu-Hao Wang, Yi-Wei Chang, Chia-Hsin Wang, U-Ser Jeng, Kuan-Yi Wu, Chien-Lung Wang, Wei-Tsung Chuang","doi":"10.1107/S1600576725001712","DOIUrl":"10.1107/S1600576725001712","url":null,"abstract":"<p><p>In bio-inspired systems, the hierarchical structures of biomolecules are mimicked to impart desired functions to self-assembled materials. However, these hierarchical architectures are based on multicomponent systems, which require not only a well defined primary structure of functional molecules but also the programming of self-assembly pathways. In this study, we investigate pathway complexity in the energy landscape of the syndiotactic poly(methyl methacrylate) (<i>st</i>-PMMA)/C₆₀/toluene complex system, where C₆₀ and toluene serve as guests in the <i>st</i>-PMMA helical host. Structural characterization revealed that <i>st</i>-PMMA preferentially wraps around C₆₀, forming a thermodynamically favorable helical inclusion complex (HIC). However, during the preparation of the <i>st</i>-PMMA/C₆₀ HIC, a lengthy guest-exchange pathway was discovered, where the <i>st</i>-PMMA/toluene HIC transformed into the <i>st</i>-PMMA/C₆₀ HIC. This pathway complexity may hinder the formation of the <i>st</i>-PMMA/C₆₀ HIC within a feasible timeframe. Given that the energy landscape can be modulated by temperature, the <i>st</i>-PMMA host can directly wrap around C₆₀ in higher temperature ranges, thereby bypassing the guest-exchange process and increasing the <i>st</i>-PMMA/C₆₀ HIC formation efficiency. Additionally, after self-assembly programming, the <i>st</i>-PMMA/C₆₀ HIC can serve as an excellent photochemical reduction site. The well dispersed nanodomains of the <i>st</i>-PMMA/C₆₀ HICs act as nanoparticle templates for surface-enhanced Raman scattering (SERS) hotspot fabrication. We successfully utilized these HIC templates to synthesize self-assembled SERS-active silver nanoparticle arrays, demonstrating their potential for use in chemical sensing applications. In summary, a clear energy landscape can guide supramolecular engineering to achieve the desired supramolecular architectures by selecting appropriate self-assembly pathways.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"553-563"},"PeriodicalIF":6.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764098","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":"A critical step toward far-field laboratory diffraction contrast tomography in Laue focusing geometry.","authors":"Yubin Zhang, Adam Lindkvist","doi":"10.1107/S1600576725001396","DOIUrl":"10.1107/S1600576725001396","url":null,"abstract":"<p><p>Recent simulations have demonstrated the promising potential of far-field laboratory diffraction contrast tomography (FF-LabDCT) in the Laue focusing geometry for 3D mapping of grain-averaged deviatoric strain tensors, achieving a strain uncertainty as low as 1 × 10^-4 [Lindkvist & Zhang (2022). <i>J. Appl. Cryst.</i> <b>55</b>, 21-32]. The present work takes a critical step towards realizing this tool. It presents the first attempt at implementing FF-LabDCT using a Zeiss Xradia 520 Versa X-ray microscope, including both hardware and software development. A new algorithm, LabDBB, which adapts the previously developed dictionary-based branch and bound (DBB) principles, is implemented for indexing FF-LabDCT data. The performance of LabDBB is evaluated by comparing the indexed grain crystallographic orientations and center of mass positions with those obtained using near-field LabDCT within the same gauge volume of a fully recrystallized iron sample. Finally, the challenges related to fitting the grain-averaged deviatoric strain tensor using the current FF-LabDCT setup are identified. The strain analysis suggests that, once these challenges are addressed, a strain uncertainty as low as 2 × 10^-4 could potentially be achieved. This work demonstrates the possibility for developing a tool capable of 3D grain-scale strain analysis with high strain precision in home laboratories.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"447-457"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764086","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":"Complete online database of maximal subgroups of subperiodic groups at the Bilbao Crystallographic Server.","authors":"Gemma de la Flor, Hans Wondratschek, Mois I Aroyo","doi":"10.1107/S1600576725001499","DOIUrl":"10.1107/S1600576725001499","url":null,"abstract":"<p><p>The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es) dedicated to subperiodic groups includes the program <i>MAXSUB</i>, which gives online access to the complete database of maximal subgroups of subperiodic groups. All maximal non-isotypic subgroups as well as all maximal isotypic subgroups of indices up to 9 are listed individually, together with the series of maximal isotypic subgroups of subperiodic groups. These data were compared with those of Litvin [(2013), <i>Magnetic group tables, 1-, 2- and 3-dimensional subperiodic groups and magnetic space groups</i>], which revealed several differences, discussed here in detail.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"622-629"},"PeriodicalIF":6.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764090","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 use of effective core potentials in Hirshfeld atom refinement: making quantum crystallography faster in <i>NoSpherA2</i>.","authors":"Florian Kleemiss, Florian Meurer, Ilya G Shenderovich, Michael Bodensteiner","doi":"10.1107/S1600576725000901","DOIUrl":"10.1107/S1600576725000901","url":null,"abstract":"<p><p>The refinement of structural models against X-ray diffraction data benefits significantly from employing non-spherical scattering factors in terms of precision and accuracy. Tailor-made scattering factors are available from quantum chemical calculations of the electron density using routine calculation packages. In this process, heavy elements in particular pose a difficulty due to their large numbers of electrons which are not involved in chemical bonding. An elegant way to circumvent this is by using effective core potentials. This work presents an approach for the treatment of these missing electrons in advanced structural refinement methods, such as Hirshfeld atom refinement. It also provides examples and benchmarks demonstrating up to a twofold reduction in refinement time without compromising on accuracy.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"374-382"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763608","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":"Probing the out-of-equilibrium dynamics of driven colloids by X-ray photon correlation spectroscopy.","authors":"Theyencheri Narayanan, William Chèvremont, Thomas Zinn","doi":"10.1107/S1600576725001244","DOIUrl":"10.1107/S1600576725001244","url":null,"abstract":"<p><p>The high brilliance of fourth-generation synchrotron sources coupled with advanced X-ray detectors enables a wide range of dynamic studies of colloids and other soft-matter systems. In particular, the higher fraction of coherent flux provided by these new sources is a major boost for X-ray photon correlation spectroscopy (XPCS). As a result, not only can equilibrium dynamics be accessed but also relatively fast out-of-equilibrium processes can be investigated by XPCS. This article briefly recalls the statistical properties of coherent scattering and then demonstrates a case study of non-equilibrium fluctuations in a driven colloidal system. A simple example is the resuspension of colloids by vigorous shaking, where the inhomogeneous flow generates local variations in number density of particles leading to strong velocity fluctuations. The Brownian motion of the particles homogenizes the suspension with time and the system gradually returns to pure diffusive dynamics. On the other hand, in a uniformly sheared suspension of particles, such concentration gradients do not form and upon cessation of shear the return to Brownian dynamics is rapid. These transient non-equilibrium effects can inadvertently influence micrometre-range particle size measurement by means of dynamic scattering methods.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"535-542"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763219","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":"Form factor of prismatic particles for small-angle scattering analysis.","authors":"Jules Marcone, Jaime Gabriel Trazo, Rahul Nag, Claire Goldmann, Nicolas Ratel-Ramond, Cyrille Hamon, Marianne Impéror-Clerc","doi":"10.1107/S1600576725000676","DOIUrl":"10.1107/S1600576725000676","url":null,"abstract":"<p><p>Since the morphology of nanoparticles directly influences many of their properties, accurately determining their shape is crucial for targeted applications. In this work, we focus on nanoprisms due to their widespread use and the limitations of direct imaging techniques in accurately describing their polygonal cross section. Specifically, we introduce a new tool for small-angle scattering (SAS) analysis of nanoprisms that requires minimal computation time compared with all-atom simulations and other form factor analyses. A key innovation in this work is the implementation of the Lebedev quadrature for isotropic averaging, which allows for accurate form factor calculations using few sampling points. This form factor model is developed for any <i>n</i>-sided prism and is compared with small-angle X-ray scattering and transmission electron microscopy experimental data for gold and/or silver nanoprisms (<i>n</i> = 3, 4, 5). For small sizes, the nanoprism form factor model is compared with the result obtained with the Debye equation from atomic coordinates, showing a very good agreement. We explore the effects of the aspect ratio and cross-sectional shape of the nanoprisms on the form factor curves and discuss the limitations of our approach. Overall, our method combines precise shape determination with rapid computation time, paving the way for detailed characterization of nanoprisms using SAS techniques, potentially even during their growth.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"543-552"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764092","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":"Benchmarking deep learning for automated peak detection on GIWAXS data.","authors":"Constantin Völter, Vladimir Starostin, Dmitry Lapkin, Valentin Munteanu, Mikhail Romodin, Maik Hylinski, Alexander Gerlach, Alexander Hinderhofer, Frank Schreiber","doi":"10.1107/S1600576725000974","DOIUrl":"10.1107/S1600576725000974","url":null,"abstract":"<p><p>Recent advancements in X-ray sources and detectors have dramatically increased data generation, leading to a greater demand for automated data processing. This is particularly relevant for real-time grazing-incidence wide-angle X-ray scattering (GIWAXS) experiments which can produce hundreds of thousands of diffraction images in a single day at a synchrotron beamline. Deep learning (DL)-based peak-detection techniques are becoming prominent in this field, but rigorous benchmarking is essential to evaluate their reliability, identify potential problems, explore avenues for improvement and build confidence among researchers for seamless integration into their workflows. However, the systematic evaluation of these techniques has been hampered by the lack of annotated GIWAXS datasets, standardized metrics and baseline models. To address these challenges, we introduce a comprehensive framework comprising an annotated experimental dataset, physics-informed metrics adapted to the GIWAXS geometry and a competitive baseline - a classical, non-DL peak-detection algorithm optimized on our dataset. Furthermore, we apply our framework to benchmark a recent DL solution trained on simulated data and discover its superior performance compared with our baseline. This analysis not only highlights the effectiveness of DL methods for identifying diffraction peaks but also provides insights for further development of these solutions.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"513-522"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764089","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}