IUCrJ最新文献

{"title":"High-accuracy measurement, advanced theory and analysis of the evolution of satellite transitions in manganese Kα using XR-HERFD","authors":"Daniel Sier ,&nbsp;Jonathan W. Dean ,&nbsp;Nicholas T. T. Tran ,&nbsp;Tony Kirk ,&nbsp;Chanh Q. Tran ,&nbsp;J. Frederick W. Mosselmans ,&nbsp;Sofia Diaz-Moreno ,&nbsp;Christopher T. Chantler ,&nbsp;V. K. Peterson (Editor)","doi":"10.1107/S2052252524005165","DOIUrl":"10.1107/S2052252524005165","url":null,"abstract":"<div><p>Here, the <em>n</em> = 2 satellite present for manganese-containing materials and across materials science has been successfully observed by applying the new technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD), developed from high-resolution resonant inelastic X-ray scattering and HERFD, and the spectra have been predicted with new advanced theory.</p></div><div><p>Here, the novel technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD) has successfully observed the <em>n</em> = 2 satellite in manganese to a high accuracy. The significance of the satellite signature presented is many hundreds of standard errors and well beyond typical discovery levels of three to six standard errors. This satellite is a sensitive indicator for all manganese-containing materials in condensed matter. The uncertainty in the measurements has been defined, which clearly observes multiple peaks and structure indicative of complex physical quantum-mechanical processes. Theoretical calculations of energy eigenvalues, shake-off probability and Auger rates are also presented, which explain the origin of the satellite from physical <em>n</em> = 2 shake-off processes. The evolution in the intensity of this satellite is measured relative to the full <em>K</em>α spectrum of manganese to investigate satellite structure, and therefore many-body processes, as a function of incident energy. Results demonstrate that the many-body reduction factor <em>S</em>₀² should not be modelled with a constant value as is currently done. This work makes a significant contribution to the challenge of understanding many-body processes and interpreting HERFD or resonant inelastic X-ray scattering spectra in a quantitative manner.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 620-633"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Chromic and dynamic: soft crystals of platinum(II) complexes pave the way for multi-responsive materials","authors":"Gonzalo Campillo-Alvarado","doi":"10.1107/S2052252524006055","DOIUrl":"10.1107/S2052252524006055","url":null,"abstract":"<div><p>The development of smart, stimuli-responsive materials has received increased attention in the past decade for their applications as sensing technologies. This commentary discusses a timely topical review by Kato [(2024). <em>IUCrJ</em>, <strong>11</strong>, 442–452] on the fabrication of multi-stimuli responsive crystals comprised of luminescent platinum(II) complexes, which exhibit intriguing chromic phenomena in response to stimuli.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 436-437"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Relating solvatochromism and solvatomorphism in organic dyes using high pressure","authors":"Elena Boldyreva","doi":"10.1107/S2052252524005773","DOIUrl":"10.1107/S2052252524005773","url":null,"abstract":"<div><p>By using complementary experimental methods including <em>in situ</em> high-pressure single-crystal X-ray diffraction and UV–Vis spectroscopy, the intricate connection between solvatochromism and solvatomorphism has been elucidated in a recent publication [Sobczak &amp; Katrusiak (2024). <em>IUCrJ</em>, <strong>11</strong>, 528–537]. The connection was demonstrated for an important pigment – Reichardt’s dye – with potential applications in nonlinear optoelectronics and molecular pressure sensor development.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 440-441"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Photoinduced bidirectional mesophase transition in vesicles containing azo­benzene amphiphiles","authors":"Svenja C. Hövelmann ,&nbsp;Ella Dieball ,&nbsp;Jule Kuhn ,&nbsp;Michelle Dargasz ,&nbsp;Rajendra P. Giri ,&nbsp;Franziska Reise ,&nbsp;Michael Paulus ,&nbsp;Thisbe K. Lindhorst ,&nbsp;Bridget M. Murphy ,&nbsp;F. Maia (Editor)","doi":"10.1107/S2052252524004032","DOIUrl":"10.1107/S2052252524004032","url":null,"abstract":"<div><p>In this work, a reversible non-invasive light-induced mesophase transition from lamellar to cubic <em>Pn</em>3<em>m</em> is observed in mixed azo­benzene-lipid and phospho­lipid vesicles using small-angle X-ray scattering.</p></div><div><p>The functionality and efficiency of proteins within a biological membrane are highly dependent on both the membrane lipid composition and the physiochemical properties of the solution. Lipid mesophases are directly influenced by changes in temperature, pH, water content or due to individual properties of single lipids such as photoswitchability. In this work, we were able to induce light- and temperature-driven mesophase transitions in a model membrane system containing a mixture of 1,2-dipalmitoyl-phosphatidylcholine phospho­lipids and azo­benzene amphiphiles. We observed reversible and reproducible transitions between the lamellar and <em>Pn</em>3<em>m</em> cubic phase after illuminating the sample for 5 min with light of 365 and 455 nm wavelengths, respectively, to switch between the <em>cis</em> and <em>trans</em> states of the azo­benzene N=N double bond. These light-controlled mesophase transitions were found for mixed complexes with up to 20% content of the photosensitive molecule and at temperatures below the gel-to-liquid crystalline phase transition temperature of 33°C. Our results demonstrate the potential to design bespoke model systems to study the response of membrane lipids and proteins upon changes in mesophase without altering the environment and thus provide a possible basis for drug delivery systems.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 486-493"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141160492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Statistical optimization of guest uptake in crystalline sponges: grading structural outcomes","authors":"Robert C. Carroll ,&nbsp;Simon J. Coles ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S2052252524004871","DOIUrl":"10.1107/S2052252524004871","url":null,"abstract":"<div><p>A statistical design of experiments approach applied to crystalline sponge analysis enables greater understanding of experimental influences and the development of a novel molecular structure quality grading system.</p></div><div><p>Investigation of the analyte soaking conditions on the crystalline sponge {[(ZnI₂)₃(tpt)₂·<em>x</em>(solvent)]_n} method using a statistical design of experiments model has provided fundamental insights into the influence of experimental variables. This approach focuses on a single analyte tested via 60 experiments (20 unique conditions) to identify the main effects for success and overall guest structure quality. This is employed as a basis for the development of a novel molecular structure grading system that enables the quantification of guest exchange quality.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 578-586"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 evolution of raw data archiving and the growth of its importance in crystallography","authors":"John R. Helliwell ,&nbsp;James R. Hester ,&nbsp;Loes M. J. Kroon-Batenburg ,&nbsp;Brian McMahon ,&nbsp;Selina L. S. Storm ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S205225252400455X","DOIUrl":"10.1107/S205225252400455X","url":null,"abstract":"<div><p>The IUCr 75th Congress in Melbourne hosted a workshop on raw data reuse, continuing efforts to promote discussions and plans within crystallography, diffraction and scattering communities. These initiatives build on earlier IUCr funded workshops, aiming to establish ground truth obtained from research results through raw data archiving potential.</p></div><div><p>The hardware for data archiving has expanded capacities for digital storage enormously in the past decade or more. The IUCr evaluated the costs and benefits of this within an official working group which advised that raw data archiving would allow ground truth reproducibility in published studies. Consultations of the IUCr’s Commissions ensued via a newly constituted standing advisory committee, the Committee on Data. At all stages, the IUCr financed workshops to facilitate community discussions and possible methods of raw data archiving implementation. The recent launch of the <em>IUCrData</em> journal’s <em>Raw Data Letters</em> is a milestone in the implementation of raw data archiving beyond the currently published studies: it includes diffraction patterns that have not been fully interpreted, if at all. The IUCr 75th Congress in Melbourne included a workshop on raw data reuse, discussing the successes and ongoing challenges of raw data reuse. This article charts the efforts of the IUCr to facilitate discussions and plans relating to raw data archiving and reuse within the various communities of crystallography, diffraction and scattering.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 464-475"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography","authors":"Leonard Michel Gabriel Chavas ,&nbsp;Fasséli Coulibaly ,&nbsp;Damià Garriga ,&nbsp;E. N. Baker (Editor)","doi":"10.1107/S205225252400513X","DOIUrl":"10.1107/S205225252400513X","url":null,"abstract":"<div><p>The 26th IUCr congress held in Melbourne brought discussions on micro-crystallization and <em>in vivo</em> crystallography within structural biology to the forefront, highlighting innovative approaches and collaborative efforts to advance macromolecular research.</p></div><div><p>A series of events underscoring the significant advancements in micro-crystallization and <em>in vivo</em> crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 476-485"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Crystallographic phase identifier of a convolutional self-attention neural network (CPICANN) on powder diffraction patterns","authors":"Shouyang Zhang ,&nbsp;Bin Cao ,&nbsp;Tianhao Su ,&nbsp;Yue Wu ,&nbsp;Zhenjie Feng ,&nbsp;Jie Xiong ,&nbsp;Tong-Yi Zhang ,&nbsp;A. Fitch (Editor)","doi":"10.1107/S2052252524005323","DOIUrl":"10.1107/S2052252524005323","url":null,"abstract":"<div><p>The development of CPICANN, a novel convolutional self-attention neural network, represents a groundbreaking approach in materials informatics. By leveraging the convolutional self-attention mechanism, CPICANN automates and significantly enhances the efficiency of crystal phase identification from whole X-ray powder diffraction patterns, marking a substantial advancement over traditional time-consuming methods.</p></div><div><p>Spectroscopic data, particularly diffraction data, are essential for materials characterization due to their comprehensive crystallographic information. The current crystallographic phase identification, however, is very time consuming. To address this challenge, we have developed a real-time crystallographic phase identifier based on a convolutional self-attention neural network (CPICANN). Trained on 692 190 simulated powder X-ray diffraction (XRD) patterns from 23 073 distinct inorganic crystallographic information files, CPICANN demonstrates superior phase-identification power. Single-phase identification on simulated XRD patterns yields 98.5 and 87.5% accuracies with and without elemental information, respectively, outperforming <em>JADE</em> software (68.2 and 38.7%, respectively). Bi-phase identification on simulated XRD patterns achieves 84.2 and 51.5% accuracies, respectively. In experimental settings, CPICANN achieves an 80% identification accuracy, surpassing <em>JADE</em> software (61%). Integration of CPICANN into XRD refinement software will significantly advance the cutting-edge technology in XRD materials characterization.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 634-642"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Analysis of COF-300 synthesis: probing degradation processes and 3D electron diffraction structure","authors":"Laurens Bourda ,&nbsp;Subhrajyoti Bhandary ,&nbsp;Sho Ito ,&nbsp;Christian R. Göb ,&nbsp;Pascal Van Der Voort ,&nbsp;Kristof Van Hecke ,&nbsp;L. Meshi (Editor)","doi":"10.1107/S2052252524003713","DOIUrl":"10.1107/S2052252524003713","url":null,"abstract":"<div><p>Detailed analysis of the influence of time and temperature on the synthesis of COF-300 showed partial linker degradation but still allowed 3D electron diffraction structure solution using optimized conditions.</p></div><div><p>Although COF-300 is often used as an example to study the synthesis and structure of (3D) covalent organic frameworks (COFs), knowledge of the underlying synthetic processes is still fragmented. Here, an optimized synthetic procedure based on a combination of linker protection and modulation was applied. Using this approach, the influence of time and temperature on the synthesis of COF-300 was studied. Synthesis times that were too short produced materials with limited crystallinity and porosity, lacking the typical pore flexibility associated with COF-300. On the other hand, synthesis times that were too long could be characterized by loss of crystallinity and pore order by degradation of the tetrakis(4-aminophenyl)methane (TAM) linker used. The presence of the degradation product was confirmed by visual inspection, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). As TAM is by far the most popular linker for the synthesis of 3D COFs, this degradation process might be one of the reasons why the development of 3D COFs is still lagging compared with 2D COFs. However, COF crystals obtained via an optimized procedure could be structurally probed using 3D electron diffraction (3DED). The 3DED analysis resulted in a full structure determination of COF-300 at atomic resolution with satisfying data parameters. Comparison of our 3DED-derived structural model with previously reported single-crystal X-ray diffraction data for this material, as well as parameters derived from the Cambridge Structural Database, demonstrates the high accuracy of the 3DED method for structure determination. This validation might accelerate the exploitation of 3DED as a structure determination technique for COFs and other porous materials.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 510-518"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 importance of definitions in crystallography","authors":"Olga Anosova ,&nbsp;Vitaliy Kurlin ,&nbsp;Marjorie Senechal ,&nbsp;D. Gratias (Editor)","doi":"10.1107/S2052252524004056","DOIUrl":"10.1107/S2052252524004056","url":null,"abstract":"<div><p>This paper proposes a rigorous definition of a periodic structure as an equivalence class of periodic sets under rigid motion, which is a composition of translations and rotations.</p></div><div><p>This paper was motivated by the articles ‘Same or different – that is the question’ in <em>CrystEngComm</em> (July 2020) and ‘Change to the definition of a crystal’ in the <em>IUCr Newsletter</em> (June 2021). Experimental approaches to crystal comparisons require rigorously defined classifications in crystallography and beyond. Since crystal structures are determined in a rigid form, their strongest equivalence in practice is rigid motion, which is a composition of translations and rotations in 3D space. Conventional representations based on reduced cells and standardizations theoretically distinguish all periodic crystals. However, all cell-based representations are inherently discontinuous under almost any atomic displacement that can arbitrarily scale up a reduced cell. Hence, comparison of millions of known structures in materials databases requires continuous distance metrics.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 453-463"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141160481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}