Journal of Applied Crystallography最新文献

{"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}

{"title":"If you cannot see it, is it still there?","authors":"Lukas Leitner, Jesse Hudspeth, Sebastiaan Werten, Bernhard Rupp","doi":"10.1107/S160057672500130X","DOIUrl":"10.1107/S160057672500130X","url":null,"abstract":"<p><p>Protein crystallographers rely on electron density to build atomic models of molecular structures, yet flexible regions often remain unseen in electron density and are omitted. We suggest that ensemble refinement can be used to visualize and analyse the conformational landscape of such 'invisible' protein segments, which is particularly useful in cases where molecular flexibility plays a functional role. Using ensemble refinement on multiple crystal forms of the fungal methyl-transferase PsiM as an example, we illustrate the dynamic nature of a key substrate recognition loop, demonstrating its potential role in substrate binding and release. Ensemble refinement provides a persuasive visualization of biologically relevant flexible regions and can be a powerful tool for exploring molecular plasticity and aiding the modelling of dynamic protein components.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"615-621"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764093","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":"<i>In situ</i> small-angle X-ray scattering measurement at the Very Small Angle Neutron Scattering Instrument at the China Spallation Neutron Source.","authors":"Changli Ma, Xiong Lin, Zehuan Han, Songwen Xiao, Yongcheng He, Zhenqiang He, Fangwei Wang, He Cheng, Taisen Zuo","doi":"10.1107/S1600576725001232","DOIUrl":"10.1107/S1600576725001232","url":null,"abstract":"<p><p>Small-angle X-ray and neutron scattering (SAXS and SANS) offer complementary insights into multi-scale and multiphase structures. Efforts have been made to integrate SAXS into SANS instruments, with only D22 at the Institut Laue-Langevin successfully implementing a SAXS setup; this was constrained to a horizontal geometry due to space limitations and high radiation noise. Here, we introduce an <i>in situ</i> vertical SAXS setup at beamline 14, Very Small Angle Neutron Scattering (VSANS) instrument, at the China Spallation Neutron Source. The compact vertical SAXS instrument without a beam stop, measuring 87 cm × 93 cm × 240 cm (W × L × H) and featuring a hoisting frame, can be easily installed in the VSANS sample room within 5 h. Utilizing a 50 mm-diameter neutron collimation guide, we can simultaneously detect X-rays from below and neutrons from behind, with the backboard of the SAXS chamber coated in a boron-aluminium alloy to reduce neutron background interference. Through testing with standard samples like deuterated and hydrogenated PEG, silver behenate, LaB₆, and glass carbon, we demonstrate that concurrent neutron and X-ray measurements are successful.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"573-580"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764084","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 comparison of microcrystal electron diffraction and X-ray powder diffraction for the structural analysis of metal-organic frameworks.","authors":"Erik Biehler, Silvina Pagola, Daniel Stam, Johannes Merkelbach, Christian Jandl, Tarek M Abdel-Fattah","doi":"10.1107/S1600576724012068","DOIUrl":"10.1107/S1600576724012068","url":null,"abstract":"<p><p>This study successfully implemented microcrystal electron diffraction (microED) and X-ray powder diffraction (XRPD) for the crystal structure determination of a new phase, TAF-CNU-1, Ni(C₈H₄O₄)·3H₂O, solved by microED from single microcrystals in the powder and refined at the kinematic and dynamic electron diffraction theory levels. This nickel metal-organic framework (MOF), together with its cobalt and manganese analogues with formula <i>M</i>(C₈H₄O₄)·2H₂O with <i>M</i> = Mn^II or Co^II, were synthesized in aqueous media as one-pot preparations from the corresponding hydrated metal chlorides and sodium terephthalate, as a promising 'green' synthetic route to moisture-stable MOFs. The crystal structures of the two latter materials have been previously determined <i>ab initio</i> from X-ray powder diffraction. The advantages and disadvantages of both structural characterization techniques are briefly summarized. Additional solid-state property characterization was carried out using thermogravimetric analysis, scanning electron microscopy and Fourier transform infrared spectroscopy.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 2","pages":"398-411"},"PeriodicalIF":6.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764085","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}