IUCrJ最新文献

{"title":"Scanning WAXS microscopy of regenerated cellulose fibers at mesoscopic resolution","authors":"Sara Johansson ,&nbsp;Francesco Scattarella ,&nbsp;Sebastian Kalbfleisch ,&nbsp;Ulf Johansson ,&nbsp;Christopher Ward ,&nbsp;Crispin Hetherington ,&nbsp;Herbert Sixta ,&nbsp;Stephen Hall ,&nbsp;Cinzia Giannini ,&nbsp;Ulf Olsson ,&nbsp;M. Takata (Editor)","doi":"10.1107/S205225252400383X","DOIUrl":"10.1107/S205225252400383X","url":null,"abstract":"<div><p>Scanning WAXS microscopy of a regenerated cellulose textile fiber reveals a radial gradient in the degree of orientation of the crystallite.</p></div><div><p>In this work, regenerated cellulose textile fibers, Ioncell-F, dry-wet spun with different draw ratios, have been investigated by scanning wide-angle X-ray scattering (WAXS) using a mesoscopic X-ray beam. The fibers were found to be homogeneous on the 500 nm length scale. Analysis of the azimuthal angular dependence of a crystalline Bragg spot intensity revealed a radial dependence of the degree of orientation of crystallites that was found to increase with the distance from the center of the fiber. We attribute this to radial velocity gradients during the extrusion of the spin dope and the early stage of drawing. On the other hand, the fiber crystallinity was found to be essentially homogeneous over the fiber cross section.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 570-577"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300716","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":"Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure","authors":"Ruwini S. K. Ekanayake ,&nbsp;Victor A. Streltsov ,&nbsp;Stephen P. Best ,&nbsp;Christopher T. Chantler ,&nbsp;V. K. Peterson (Editor)","doi":"10.1107/S2052252524001830","DOIUrl":"10.1107/S2052252524001830","url":null,"abstract":"<div><p>An X-ray absorption spectroscopy electrochemical cell was used to collect high-quality X-ray absorption spectroscopy measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. The geometry of binding sites for the copper binding in Aβ_4–8/12/16 and the ability of these peptides to perform redox cycles in a manner that might produce toxicity in human brains were determined.</p></div><div><p>An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer’s patients’ brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ_4–8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ_4–8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that Cu^II is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ_4–8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ_4–16 peptide. Robust investigations of XAS provide structural details of Cu^II binding with a very different <em>bis</em>-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ_4–12/16 imply that both Cu^II and Cu^III are accommodated in an ATCUN-like binding site. Hypotheses for these Cu^I, Cu^II and Cu^III geometries were proven and disproven using the novel data and statistical analysis including <em>F</em> tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 325-346"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140716153","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":"RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures","authors":"Stephen K. Burley ,&nbsp;Dennis W. Piehl ,&nbsp;Brinda Vallat ,&nbsp;Christine Zardecki ,&nbsp;E. N. Baker (Editor)","doi":"10.1107/S2052252524002604","DOIUrl":"10.1107/S2052252524002604","url":null,"abstract":"<div><p>The RCSB PDB research-focused web portal at <span>https://www.rcsb.org/</span> provides important tools and resources to search, visualize and analyze experimentally determined 3D biostructures alongside computed structure models of proteins predicted using artificial intelligence/machine-learning based tools.</p></div><div><p>The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses &gt;210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (<em>e.g.</em> approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support &gt;60 000 ‘data depositors’ (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at <span>https://www.rcsb.org/</span> (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB ‘data consumers’ access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to &gt;1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 279-286"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140717229","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":"Dynamical refinement with multipolar electron scattering factors","authors":"Barbara Olech ,&nbsp;Petr Brázda ,&nbsp;Lukas Palatinus ,&nbsp;Paulina Maria Dominiak ,&nbsp;M. Gemmi (Editor)","doi":"10.1107/S2052252524001763","DOIUrl":"10.1107/S2052252524001763","url":null,"abstract":"<div><p>Transferable aspherical atom model dynamical refinement on precession electron diffraction data for 1-methyl­uracil crystals offers superior performance compared with the independent atom model and reveals that the quality of 3D electron diffraction data and dynamical refinement is already sufficient to detect minute variations of the electrostatic potential caused by bonding and intermolecular interactions.</p></div><div><p>Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček &amp; Corrêa, (2015). <em>Acta Cryst.</em> A<strong>71</strong>, 235–244; Palatinus, Corrêa <em>et al.</em> (2015). <em>Acta Cryst.</em> B<strong>71</strong>, 740–751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza <em>et al.</em> (2020). <em>Acta Cryst.</em> A<strong>76</strong>, 92–109; Jha <em>et al.</em> (2021). <em>J. Appl. Cryst.</em> <strong>54</strong>, 1234–1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyl­uracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 309-324"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184520","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":"Biophysical and structural study of La Crosse virus endonuclease inhibition for the development of new antiviral options","authors":"Mikael Feracci ,&nbsp;Sergio Hernandez ,&nbsp;Laura Garlatti ,&nbsp;Clemence Mondielli ,&nbsp;Renaud Vincentelli ,&nbsp;Bruno Canard ,&nbsp;Juan Reguera ,&nbsp;François Ferron ,&nbsp;Karine Alvarez ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S205225252400304X","DOIUrl":"10.1107/S205225252400304X","url":null,"abstract":"<div><p>A structural analysis of several metal-ion binders that inhibit viral endonucleases is performed.</p></div><div><p>The large <em>Bunyavirales</em> order includes several families of viruses with a segmented ambisense (−) RNA genome and a cytoplasmic life cycle that starts by synthesizing viral mRNA. The initiation of transcription, which is common to all members, relies on an endonuclease activity that is responsible for cap-snatching. In La Crosse virus, an orthobunyavirus, it has previously been shown that the cap-snatching endonuclease resides in the N-terminal domain of the L protein. Orthobunyaviruses are transmitted by arthropods and cause diseases in cattle. However, California encephalitis virus, La Crosse virus and Jamestown Canyon virus are North American species that can cause encephalitis in humans. No vaccines or antiviral drugs are available. In this study, three known Influenza virus endonuclease inhibitors (DPBA, L-742,001 and baloxavir) were repurposed on the La Crosse virus endonuclease. Their inhibition was evaluated by fluorescence resonance energy transfer and their mode of binding was then assessed by differential scanning fluorimetry and microscale thermophoresis. Finally, two crystallographic structures were obtained in complex with L-742,001 and baloxavir, providing access to the structural determinants of inhibition and offering key information for the further development of <em>Bunyavirales</em> endonuclease inhibitors.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 374-383"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140664665","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":"KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography","authors":"Gabriel Biener ,&nbsp;Tek Narsingh Malla ,&nbsp;Peter Schwander ,&nbsp;Marius Schmidt ,&nbsp;T. Ishikawa (Editor)","doi":"10.1107/S2052252524002392","DOIUrl":"10.1107/S2052252524002392","url":null,"abstract":"<div><p>A kinetics-informed neural-network method (KINNTREX) is designed to analyze a time series of difference maps from a time-resolved X-ray crystallographic experiment.</p></div><div><p>Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 405-422"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140656083","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":"Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein","authors":"Chang-Yi Liu ,&nbsp;Han-Pin Cheng ,&nbsp;Chan-Pin Lin ,&nbsp;Yi-Ting Liao ,&nbsp;Tzu-Ping Ko ,&nbsp;Shin-Jen Lin ,&nbsp;Shih-Shun Lin ,&nbsp;Hao-Ching Wang ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252524003075","DOIUrl":"10.1107/S2052252524003075","url":null,"abstract":"<div><p>The first crystal structure of phytoplasma immunodominant membrane protein is reported and structural analysis revealed its potential for actin binding.</p></div><div><p>Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP–F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches’ broom phytoplasma-infected <em>Catharanthus roseus</em>. The association between IMP and PHYL1 is substantiated through <em>in vivo</em> immunoprecipitation, an <em>in vitro</em> cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 384-394"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665379","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":"Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements","authors":"Niklas B. Thompson ,&nbsp;Karen L. Mulfort ,&nbsp;David M. Tiede ,&nbsp;I. Robinson (Editor)","doi":"10.1107/S2052252524003282","DOIUrl":"10.1107/S2052252524003282","url":null,"abstract":"<div><p>Total X-ray scattering measurements of dilute solutions are uniquely well suited to address the structural basis for the effects of solvation, exemplified by the success of small-/wide-angle X-ray scattering studies of macromolecules in solution. Herein, we extend this methodology to the high-energy X-ray regime by developing a theoretical framework to describe the differential solution scattering experiment, supported by numerical simulation and experiment.</p></div><div><p>Appreciating that the role of the solute–solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems <em>in situ</em> in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime—where sub-ångström spatial resolution is achieved—remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 423-433"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140857579","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 ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo","authors":"Jason N. Busby ,&nbsp;Sarah Trevelyan ,&nbsp;Cassandra L. Pegg ,&nbsp;Edward D. Kerr ,&nbsp;Benjamin L. Schulz ,&nbsp;Irene Chassagnon ,&nbsp;Michael J. Landsberg ,&nbsp;Mitchell K. Weston ,&nbsp;Mark R. H. Hurst ,&nbsp;J. Shaun Lott ,&nbsp;A. Thorn (Editor)","doi":"10.1107/S2052252524001969","DOIUrl":"10.1107/S2052252524001969","url":null,"abstract":"<div><p>A cytotoxin encoded by an ‘orphan’ genetic locus in the insect pathogen <em>Yersinia entomophaga</em> is shown to be a functional part of an ABC toxin complex, and the structures of both the RHS-repeat-containing ‘shell’ and the free toxin alone are determined by X-ray crystallography. The structure of the toxin indicates that it most likely functions by directly modifying actin in the target cell.</p></div><div><p>Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB–TcC subcomplex that makes a hollow shell. This TcB–TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic ‘cargo’ encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from <em>Yersinia entomophaga</em>, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB–TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from <em>Salmonella typhimurium</em>. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 299-308"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184521","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":"Linking solid-state phenomena via energy differences in ‘archetype crystal structures’","authors":"B. Dittrich ,&nbsp;L. E. Connor ,&nbsp;F. P. A. Fabbiani ,&nbsp;P. Piechon ,&nbsp;A. Fitch (Editor)","doi":"10.1107/S2052252524002641","DOIUrl":"10.1107/S2052252524002641","url":null,"abstract":"<div><p>Solid-state phenomena like disorder, polymorphism but also the occurrence of high-<em>Z</em>′ crystal structures can be linked via energy differences in ‘archetype crystal structures’, which will permit better prediction of their occurrence.</p></div><div><p>Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with ‘archetype crystal structures’ bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-<em>Z</em>′ structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). <em>IUCrJ</em>, <strong>8</strong>, 305–318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder – and disappearing disorder – occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an <em>R·T</em> energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-<em>Z</em>′ structures can also be analysed energetically and understood via archetypes: high-<em>Z</em>′ structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds <em>R·T</em>, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 3","pages":"Pages 347-358"},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140694912","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}