IUCrJ最新文献

{"title":"Femtosecond X-ray cross-correlation analysis of disordered crystals forming in a supercooled atomic liquid","authors":"Johannes Möller ,&nbsp;Michele Caresana ,&nbsp;Alexander Schottelius ,&nbsp;Felix Lehmkühler ,&nbsp;Ulrike Boesenberg ,&nbsp;Frédéric Caupin ,&nbsp;Francesco Dallari ,&nbsp;Tiberio A. Ezquerra ,&nbsp;José M. Fernández ,&nbsp;Luca Gelisio ,&nbsp;Claudia Goy ,&nbsp;Jörg Hallmann ,&nbsp;Anton Kalinin ,&nbsp;Chan Kim ,&nbsp;Ruslan P. Kurta ,&nbsp;Dmitry Lapkin ,&nbsp;Francesco Mambretti ,&nbsp;Markus Scholz ,&nbsp;Roman Shayduk ,&nbsp;René Steinbrügge ,&nbsp;Robert E. Grisenti","doi":"10.1107/S2052252525004063","DOIUrl":"10.1107/S2052252525004063","url":null,"abstract":"<div><div>We demonstrate an advanced scattering method for accessing the 3D reciprocal space of crystalline structures forming in a rapidly supercooled noble-gas liquid using a combination of femtosecond X-ray diffraction and X-ray cross-correlation analysis.</div></div><div><div>We demonstrate an advanced scattering method for accessing the 3D reciprocal space of crystalline structures forming in a rapidly supercooled noble-gas liquid using a combination of femtosecond X-ray diffraction and X-ray cross-correlation analysis. The preservation of angular information from the scattering signal allows probing the structure factor along selected directions in reciprocal space and identifying signatures undetectable in azimuthally integrated scattering curves. Therefore, more information from serial diffraction experiments on stochastic crystallization processes can be retrieved despite the inherent variation of the crystal orientation and morphology for each single probe. We also demonstrate how different features in the correlation maps can be associated with certain forms of stacking faults, which enables studying such defects <em>in situ</em> and disentangling them from simultaneous changes in crystal size and temperature.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 462-471"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Everything you always wanted to know about the Debye–Waller factor but were afraid to ask","authors":"Richard Dronskowski","doi":"10.1107/S2052252525004968","DOIUrl":"10.1107/S2052252525004968","url":null,"abstract":"<div><div>Combining improved diffraction methods, modeling approaches and advanced computations allows for a detailed understanding of atomic thermal motions in crystals. Thus, the Topical Review by Hoser &amp; Madsen [(2025). <em>IUCrJ</em><strong>12</strong>, 421–434] covers the Debye–Waller factor, the importance of anisotropic displacement parameters, and the interplay of experiment and theory to accurately capture collective atomic vibrations in molecular crystals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 417-418"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the flexibility of the multipole model refinement. A DFT benchmark study of the tetra­kis­(μ-acetato)di­aquadicopper model system","authors":"Andrej Hlinčík ,&nbsp;Tadeáš Fülöp ,&nbsp;Peter Herich ,&nbsp;Jozef Kožíšek ,&nbsp;Karol Lušpai ,&nbsp;Lukáš Bučinský","doi":"10.1107/S2052252525003355","DOIUrl":"10.1107/S2052252525003355","url":null,"abstract":"<div><div>The refinement flexibility of the Hansen–Coppens multipole model is tested on DFT calculated structure factors for the tetra­kis­(μ-acetato)di­aquadicopper model system. The Cu scattering factor performs the best of all the options tried for most of the monitored parameters despite the Cu²⁺ nature of the complex studied. The Hansen–Coppens model performs similarly well when comparing deviations among computational chemistry methods.</div></div><div><div>In this study, the flexibility of the multipole Hansen–Coppens (HC) model refinement is investigated on calculated structure factors from a DFT reference for the tetra­kis­(μ-acetato)di­aquadicopper model system (CCDC reference 1811668). The effect of the resolution [sin(θ)/λ], the Cu scattering factor, the inclusion of anisotropic displacement parameters and the positions of the atoms in the refinement are considered in terms of statistical error analysis, residual and deformation density maps, Atoms In Molecules parameters, <em>d</em>-orbital populations, and others. The choice of the neutral Cu scattering factor in the HC refinement is found to give the most satisfactory results for most of the monitored parameters, despite the formal Cu²⁺ nature of copper in the studied complex. In order to put the difference between the HC model and the reference DFT (BLYP functional) results on the right scale, several computational chemistry methods (B3LYP, Hartree–Fock, Møller–Plesset perturbation theory and Coupled Clusters Singles and Doubles) were compared with the chosen DFT reference. Differences in the magnitudes of the structure factors and AIM parameters are presented, including considerations of relativistic effects and periodic boundary conditions, <em>i.e.</em> a comparison of a molecular crystal calculation versus an isolated molecule in the crystal.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 444-461"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Femtosecond X-rays illuminate disordered states during the early stages of crystallization","authors":"Akinobu Niozu","doi":"10.1107/S2052252525005706","DOIUrl":"10.1107/S2052252525005706","url":null,"abstract":"<div><div>Crystallization is a fundamental non-equilibrium process in materials science, yet its early transient states remain difficult to probe experimentally. Möller <em>et al.</em> [(2025). <em>IUCrJ</em><strong>12</strong>, 462–471] use femtosecond X-ray scattering and X-ray cross-correlation analysis to reveal the structural evolution of defect-containing crystals forming in a supercooled noble-gas liquid.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 419-420"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In situ high-resolution cryo-EM reconstructions from CEMOVIS","authors":"Johannes Elferich ,&nbsp;Marek Kaminek ,&nbsp;Lingli Kong ,&nbsp;Adolfo Odriozola ,&nbsp;Wanda Kukulski ,&nbsp;Benoît Zuber ,&nbsp;Nikolaus Grigorieff","doi":"10.1107/S2052252525005196","DOIUrl":"10.1107/S2052252525005196","url":null,"abstract":"<div><div>Vitreous sectioning (CEMOVIS) is an alternative to FIB milling for generating thin samples suitable for cryo-EM imaging. We show that CEMOVIS samples preserve the high-resolution structural details of macromolecular complexes such as the 60S ribosome, despite the visible macroscopic damage visible in the samples.</div></div><div><div>Cryo-electron microscopy can be used to image cells and tissue at high resolution. To ensure electron transparency, the sample thickness must not exceed 500 nm. Focused-ion-beam (FIB) milling has become the standard method for preparing thin samples (lamellae); however, the material removed by the milling process is lost, the imageable area is usually limited to a few square micrometres and the surface layers sustain damage from the ion beam. We have examined <em>c</em>ryo-<em>e</em>lectron <em>m</em>icroscopy <em>o</em>f <em>vi</em>treous <em>s</em>ections (CEMOVIS), a technique based on cutting thin sections with a knife, as an alternative to FIB milling. Vitreous sections also sustain damage, including compression, shearing and cracks. However, samples can be sectioned in series, producing many orders of magnitude more imageable area compared to lamellae, making CEMOVIS an alternative to FIB milling with distinct advantages. Using two-dimensional template matching on images of vitreous sections of <em>Saccharomyces cerevisiae</em> cells, we reconstructed the 60S ribosomal subunit at near-atomic resolution, demonstrating that, in many regions of the sections, the molecular structure of these subunits is largely intact, comparable to FIB-milled lamellae.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 502-510"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmarking quantum chemical methods with X-ray structures via structure-specific restraints","authors":"Birger Dittrich ,&nbsp;Rok Breznikar ,&nbsp;Gianluca Santarossa ,&nbsp;Pamela Whitfield ,&nbsp;Henrik Moebitz","doi":"10.1107/S2052252525004543","DOIUrl":"10.1107/S2052252525004543","url":null,"abstract":"<div><div>Single-crystal X-ray structures measured at around 20 K to high resolution were refined with structure-specific restraints from quantum chemical molecule-in-cluster and full-periodic computations, which permits benchmarking levels of theory of varying sophistication. Restraints can then ‘augment’ low-quality crystal structures, with other possible applications.</div></div><div><div>There is a need for fast, efficient and accurate solid-state structure optimization for imprecise crystal structures (‘augmentation’) for subsequent property prediction in the pharmaceutical industry. Crystal structures from single-crystal X-ray, 3D electron or powder diffraction are widely available but require augmentation to the same quality level for comparative studies. Properties can be best calculated when the level of theory is alike and the accuracy, as well as the precision, are high. Moreover, the size of molecules and the complexity of structures encountered in pharmaceutical research are increasing. Efficient procedures are thus required that can also treat structures with disorder and several molecules in the asymmetric unit of the unit cell. Hence, we investigated whether ‘molecule-in-cluster’ (MIC) computations [Dittrich <em>et al.</em> (2020). <em>CrystEngComm</em><strong>22</strong>, 7420–7431] can reach the accuracy of full-periodic (FP) computations. Selected quantum mechanical methods are assessed. The evaluation criterion is how well the structures of 22 very low temperature high-quality structures are reproduced. Computational efficiency is also considered. A novel approach to evaluating the accuracy of quantum mechanical predictions is enforcing computed structure-specific restraints in crystallographic least-squares refinements. To complement this approach, root mean square Cartesian displacements of computed and experimental structures were also compared. Analysis shows that (<em>a</em>) MIC DFT-D computations in a quantum mechanics/molecular mechanics (QM:MM) framework provide improved restraints and coordinates over earlier MIC GFN2-xTB computations, (<em>b</em>) increasing QM basis-set size in MIC QM:MM does not systematically improve computations, and (<em>c</em>) the choice of DFT functional is less important than the choice of the basis set. Overall, MIC computations are an accurate and computationally efficient tool for solid-state structure optimization that can match FP computations to augment experimental structures.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 4","pages":"Pages 472-487"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Damage before destruction? X-ray-induced changes in single-pulse serial femtosecond crystallography","authors":"Lewis J. Williams ,&nbsp;Amy J. Thompson ,&nbsp;Philipp Dijkstal ,&nbsp;Martin Appleby ,&nbsp;Greta Assmann ,&nbsp;Florian S. N. Dworkowski ,&nbsp;Nicole Hiller ,&nbsp;Chia-Ying Huang ,&nbsp;Tom Mason ,&nbsp;Samuel Perrett ,&nbsp;Eduard Prat ,&nbsp;Didier Voulot ,&nbsp;Bill Pedrini ,&nbsp;John H. Beale ,&nbsp;Michael A. Hough ,&nbsp;Jonathan A. R. Worrall ,&nbsp;Robin L. Owen","doi":"10.1107/S2052252525002660","DOIUrl":"10.1107/S2052252525002660","url":null,"abstract":"<div><div>Varied pulse-duration and pulse-intensity serial femtosecond crystallography data do not show significant signs of radiation damage under typical experimental conditions.</div></div><div><div>Serial femtosecond crystallography (SFX) exploits extremely brief X-ray free-electron laser pulses to obtain diffraction data before destruction of the crystal. However, during the pulse X-ray-induced site-specific radiation damage can occur, leading to electronic state and/or structural changes. Here, we present a systematic exploration of the effect of single-pulse duration and energy (and consequently different dose rates) on site-specific radiation damage under typical SFX room-temperature experimental conditions. For the first time in SFX we directly measured the photon pulse duration, varying from less than 10 fs to more than 50 fs, and used three pulse energies to probe in-pulse damage in two radiation-sensitive proteins: the iron-heme peroxidase DtpAa and the disulfide-rich thaumatin. While difference-map features arising from radiation damage are observed, they do not lead to significant change in refined atomic coordinates or key bond lengths. Our work thus provides experimental verification that average atomic coordinates are not significantly perturbed by radiation damage in typical SFX experiments.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 358-371"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microcrystals in structural biology: small samples, big insights","authors":"Dominik Oberthür","doi":"10.1107/S2052252525003653","DOIUrl":"10.1107/S2052252525003653","url":null,"abstract":"<div><div>Microcrystals are transforming structural biology by enabling high-resolution structures and time-resolved insights from samples once deemed too small. This commentary highlights recent advances in microfocus X-ray and MicroED methods, emphasizing their growing role as powerful and complementary tools in modern macromolecular crystallography.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 259-261"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Additive-driven microwave crystallization of tyramine polymorphs and salts: a quantum crystallography perspective","authors":"Szymon Grabowski ,&nbsp;Klaudia Nowakowska ,&nbsp;Helena Butkiewicz ,&nbsp;Anna Hoser ,&nbsp;Aleksandra Wesełucha-Birczyńska ,&nbsp;Tomasz Seidler ,&nbsp;Paulina Moskal ,&nbsp;Marlena Gryl","doi":"10.1107/S2052252525002210","DOIUrl":"10.1107/S2052252525002210","url":null,"abstract":"<div><div>This study reveals how additives and microwave radiation influence the crystallization of new tyramine polymorphs and their cocrystallization with barbital. The findings provide insights into polymorph stability and offer potential applications in molecular encapsulation and optical materials.</div></div><div><div>Polymorphism – the ability of a compound to exist in multiple crystalline forms – needs to be carefully considered in the design of functional materials, particularly in the context of cocrystallization. Tyramine, a biogenic amine, is a promising candidate for polymorph exploration due to its conformational flexibility and ability to form salts. In this study, we investigate the crystallization of tyramine polymorphs using additives and microwave-assisted techniques. Our findings reveal the formation of a new tyramine polymorph and two distinct salts, highlighting the impact of microwave radiation and additive-driven crystallization on polymorph stability and molecular encapsulation. The study demonstrates that the triclinic tyramine polymorph (T2) is thermodynamically more stable due to its lower electronic energy, whereas the monoclinic form (T1) features slightly stronger intermolecular interactions. Over time, in solution, crystals of barbital–tyramine salts (C1 and C2) begin to form, providing an opportunity to assess structural evolution. Optical properties calculations show significant maximum linear birefringence values (0.164 and 0.255) for two polymorphs of tyramine, whereas for C1, this value decreases to 0.095.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 403-416"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate temperature dependence of structure factors of l-alanine and taurine for quantum crystallography","authors":"Mibuki Hayashi ,&nbsp;Takashi Nishioka ,&nbsp;Hidetaka Kasai ,&nbsp;Eiji Nishibori","doi":"10.1107/S2052252525002647","DOIUrl":"10.1107/S2052252525002647","url":null,"abstract":"<div><div>The temperature dependence of accurate structure factors of <span>l</span>-alanine and taurine was measured at the SPring-8 BL02B1 beamline. The quality of the structure factors is evaluated by charge density and quantum crystallographic studies. The effects of small amounts of twinning on the charge density study for taurine are also described.</div></div><div><div>Multi-temperature high-quality structure factors of <span>l</span>-alanine and taurine were re-measured at the SPring-8 BL02B1 beamline for method development in quantum crystallography. The quality of the data was evaluated by comparison with previous studies. In the case of taurine, we found that the data quality was highly affected by small amounts of twinning. Residual electron density around the sulfur atoms observed in a previous study [Hibbs <em>et al.</em> (2003). <em>Chem. A Eur. J.</em><strong>9</strong>, 1075–1084] disappeared with the re-measured data. X-ray wavefunction refinements were carried out on these data. The difference electron density between the X-ray constrained wavefunction (XCW) results and the Hartree–Fock charge density showed a positive difference electron density around the nucleus and a negative difference electron density between the bonds. These features were consistent with those reported [Hupf <em>et al.</em> (2023). <em>J. Chem. Phys.</em><strong>158</strong>, 124103]. It was found that the deformation density around the nucleus and between bonds due to electron correlations and electronic polarization could be confirmed by the XCW method using the present structure factors.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 384-392"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}