IUCrJ最新文献

{"title":"Fixed-target pump–probe SFX: eliminating the scourge of light contamination","authors":"","doi":"10.1107/S2052252524005591","DOIUrl":"10.1107/S2052252524005591","url":null,"abstract":"<div><p>Time-resolved serial femtosecond crystallography experiments can be performed with samples delivered on solid supports. Sample consumption is significantly reduced when compared with the popular crystal-delivery system via high-viscosity extrusion.</p></div><div><p>X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from <em>Chlamydomonas reinhardtii</em> were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δ<em>t</em> = 10 µs a covalent thio­ether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 749-761"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558790","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":"Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data","authors":"Michał Leszek Chodkiewicz ,&nbsp;Barbara Olech ,&nbsp;Kunal Kumar Jha ,&nbsp;Paulina Maria Dominiak ,&nbsp;Krzysztof Woźniak","doi":"10.1107/S2052252524006808","DOIUrl":"10.1107/S2052252524006808","url":null,"abstract":"<div><p>Kinematical Hirshfeld atom refinement has been applied to electron diffraction data for the first time, but the effect of using an aspherical atom model is overshadowed by dynamical scattering effects. Dynamical independent atom model refinement leads to significantly improved structures, suggesting that dynamical refinement is also necessary to obtain the full advantage of using aspherical atom models.</p></div><div><p>Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural param­eters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (I_h). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O—H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O—H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Å for HAR. The refinement results changed considerably when dynamical scattering effects were modelled – with extinction correction or with dynamical refinement. The latter led to an improvement of the O—H bond length accuracy to 0.021 Å on average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 730-736"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792562","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":"From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion","authors":"Helen W. Leung ,&nbsp;Royston C. B. Copley ,&nbsp;Giulio I. Lampronti ,&nbsp;Sarah J. Day ,&nbsp;Lucy K. Saunders ,&nbsp;Duncan N. Johnstone ,&nbsp;Paul A. Midgley","doi":"10.1107/S2052252524008121","DOIUrl":"10.1107/S2052252524008121","url":null,"abstract":"<div><p>3D electron diffraction (3DED) was used to elucidate the structure of a new ninth polymorph of indomethacin from an amorphous solid dispersion, which are product formulations used to improve the dissolution performance of active pharmaceutical ingredients with poor aqueous solubility. Insights from the structure solution allowed for a simpler crystallization route for this polymorph to be deduced, demonstrating the relevance of 3DED within drug development.</p></div><div><p>3D electron diffraction (3DED) is increasingly employed to determine molec­ular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using di­chloro­methane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 744-748"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080329","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 soft crystals based on luminescent platinum(II) complexes","authors":"Masako Kato ,&nbsp;L. R. MacGillivray (Editor)","doi":"10.1107/S2052252524003658","DOIUrl":"10.1107/S2052252524003658","url":null,"abstract":"<div><p>Platinum(II) complexes exhibit intense luminescence based on their molecular arrangement and chromic luminescence, which is a color change in response to gentle stimuli such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively control the chromic phenomenon of platinum(II) complexes.</p></div><div><p>Platinum(II) complexes of square-planar geometry are interesting from a crystal engineering viewpoint because they exhibit strong luminescence based on the self-assembly of molecular units. The luminescence color changes in response to gentle stimuli, such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively generate the chromic luminescence phenomenon of Pt(II) complexes. In this topical review, strategies for fabricating chromic luminescent Pt(II) complexes are described from a crystal design perspective, focusing on the structural regulation of Pt(II) complexes that exhibit assembly-induced luminescence via metal–metal interactions and structural control of anionic Pt(II) complexes using cations. The research progress on the evolution of various chromic luminescence properties of Pt(II) complexes, including the studies conducted by our group, are presented here along with the latest research outcomes, and an overview of the frontiers and future potential of this research field is provided.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 442-452"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300715","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":"Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure","authors":"A. Zwolenik ,&nbsp;D. Tchoń ,&nbsp;A. Makal ,&nbsp;C.-Y. Su (Editor)","doi":"10.1107/S2052252524003634","DOIUrl":"10.1107/S2052252524003634","url":null,"abstract":"<div><p>A new polymorph of 1,3-diacetylpyrene that is luminescent in the solid state and a prominent negative thermal expansion material has been obtained from its melt. A thorough structural characterization of this new crystal form was performed in a wide temperature and pressure range using single-crystal X-ray diffraction. Structural studies have been combined with steady-state UV–Vis spectroscopy and periodic density functional theory calculations. A previously published methodology of crystal placement in a diamond anvil cell has been successfully applied in predicting optimal 2°AP-β sample orientation, ensuring &gt;80% data coverage and enabling unrestrained Hirshfeld atom refinements for high-pressure structures as well as analysis of anharmonic oscillations.</p></div><div><p>A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV–Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of −55.8 (57) MK⁻¹ in the direction of C—H⋯O interactions.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 519-527"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897554","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":"A step towards 6D WAXD tensor tomography","authors":"Xiaoyi Zhao ,&nbsp;Zheng Dong ,&nbsp;Chenglong Zhang ,&nbsp;Himadri Gupta ,&nbsp;Zhonghua Wu ,&nbsp;Wenqiang Hua ,&nbsp;Junrong Zhang ,&nbsp;Pengyu Huang ,&nbsp;Yuhui Dong ,&nbsp;Yi Zhang ,&nbsp;V. T. Forsyth (Editor)","doi":"10.1107/S2052252524003750","DOIUrl":"10.1107/S2052252524003750","url":null,"abstract":"<div><p>A novel approach is reported for 6D wide-angle X-ray diffraction tensor tomography characterization based on the concept of virtual reciprocal-space scanning.</p></div><div><p>X-ray scattering/diffraction tensor tomography techniques are promising methods to acquire the 3D texture information of heterogeneous biological tissues at micrometre resolution. However, the methods suffer from a long overall acquisition time due to multi-dimensional scanning across real and reciprocal space. Here, a new approach is introduced to obtain 3D reciprocal information of each illuminated scanning volume using mathematic modeling, which is equivalent to a physical scanning procedure for collecting the full reciprocal information required for voxel reconstruction. The virtual reciprocal scanning scheme was validated by a simulated 6D wide-angle X-ray diffraction tomography experiment. The theoretical validation of the method represents an important technological advancement for 6D diffraction tensor tomography and a crucial step towards pervasive applications in the characterization of heterogeneous materials.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 502-509"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897409","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":"A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction","authors":"Xingke Fu ,&nbsp;Zhi Geng ,&nbsp;Zhichao Jiao ,&nbsp;Wei Ding ,&nbsp;T. Ishikawa (Editor)","doi":"10.1107/S2052252524004846","DOIUrl":"10.1107/S2052252524004846","url":null,"abstract":"<div><p>A modified phase-retrieval algorithm has been built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm, incorporating the π-half phase perturbation for weak reflections and the direct-methods based tangent formula for strong reflections in reciprocal space. The modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy of various forms of SAD substructure determination to facilitate automatic <em>de novo</em> macromolecular structure determination.</p></div><div><p>The success of experimental phasing in macromolecular crystallography relies primarily on the accurate locations of heavy atoms bound to the target crystal. To improve the process of substructure determination, a modified phase-retrieval algorithm built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm has been developed. Importantly, the proposed algorithm features a combination of the π-half phase perturbation for weak reflections and enforces the direct-method-based tangent formula for strong reflections in reciprocal space. The proposed algorithm is extensively demonstrated on a total of 100 single-wavelength anomalous diffraction (SAD) experimental datasets, comprising both protein and nucleic acid structures of different qualities. Compared with the standard RAAR algorithm, the modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy in SAD substructure determination, highlighting the importance of additional constraints for algorithmic performance. Furthermore, the proposed algorithm can be performed without human intervention under most conditions owing to the self-adaptive property of the input parameters, thus making it convenient to be integrated into the structural determination pipeline. In conjunction with the <em>IPCAS</em> software suite, we demonstrated experimentally that automatic <em>de novo</em> structure determination is possible on the basis of our proposed algorithm.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 587-601"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432032","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":"Chemistry and crystal engineering.","authors":"Susan A Bourne","doi":"10.1107/S2052252524006249","DOIUrl":"10.1107/S2052252524006249","url":null,"abstract":"<p><p>Recent studies published in the Chemistry and crystal engineering section of IUCrJ emphasize developments both in methodology and techniques as well as the diverse range of classes of compounds being studied and of problems being tackled.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 Pt 4","pages":"434-435"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492011","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":"Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure","authors":"Stephanie A. Wankowicz ,&nbsp;James S. Fraser ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252524005098","DOIUrl":"10.1107/S2052252524005098","url":null,"abstract":"<div><p>Traditional structural models of biomolecules typically represent only a single conformational state, even though biomolecules naturally exist in multiple states crucial for their function. Here, we propose enhancements to the macromolecular crystallographic information file (mmCIF) to better capture the complex conformational and compositional heterogeneity of biomolecules that is human- and machine-interpretable.</p></div><div><p>In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble–function predictions, analogous to the achievements of <em>AlphaFold</em> with single-structure prediction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 494-501"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492013","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":"Exploring crystal structure–physical property relationships with pressure","authors":"David R. Allan","doi":"10.1107/S205225252400602X","DOIUrl":"10.1107/S205225252400602X","url":null,"abstract":"<div><p>From its conception, X-ray crystallography has provided a unique understanding of the structure, bonding and electronic state of materials, which, in turn, unlocks a means of examining the properties and function of crystalline systems. Using state-of-the-art single-crystal X-ray diffraction, along with UV–Vis spectroscopy and DFT calculations, Zwolenik <em>et al.</em> [(2024). <em>IUCrJ</em>, <strong>11</strong>, 519–527] have provided a comprehensive study of the structure–optical property relationship of 1,3-di­acetyl­pyrene with methodologies that are increasingly accessible to non-specialist laboratories.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 438-439"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492015","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}