Journal of Applied Crystallography最新文献

The crystallographic challenge of structure determination is nowadays effectively supported by advanced computational methods, such as direct methods and Patterson techniques, implemented in sophisticated software. With the rapid expansion of artificial intelligence (AI) across diverse scientific domains, exploring its potential contribution to structure solution and its ability to overcome the limitations of traditional approaches has become increasingly compelling. This work builds upon and extends the findings of two recent studies on AI-driven phasing. The first, by Larsen et al. [Science (2024), 385, 522-528], focused on designing and applying a neural network architecture to solve small structures (with unit-cell volumes up to 1000 ų), primarily within the most common centrosymmetric space group P2₁/c. The second, by Carrozzini et al. [Acta Cryst. (2025), A81, 188-201], introduced a novel phase-seeding method applicable to both centro-symmetric and non-centrosymmetric crystal structures of varying complexity, from small molecules to proteins. Although designed with AI integration in mind, this latter method had not yet been tested within an AI framework. In this paper, we apply the method proposed by Carrozzini et al. to cases where seed phases are generated by the AI network developed by Larsen et al. We demonstrate that this combined approach, termed AI-PhaSeed, successfully extends the applicability of Larsen's neural network to structures with unit-cell volumes exceeding 1000 ų, even under conditions of limited experimental resolution. The proposed procedure has been extensively tested on a set of structures taken from the Crystallography Open Database, proving it to be a powerful and reliable tool for structure solution. We also provide insights into the use of AI for crystallographic phasing and introduce statistical tools to evaluate the robustness of the solution process based on AI-calculated phases.

This study investigates the effect of relative humidity (RH) on the crystal structures of human insulin (HI) complexes with organic ligands, m-cresol and m-nitro-phenol, using in situX-ray powder diffraction (XRPD) with a controlled-humidity chamber. Co-crystallization at pH 7.5 produced hexagonal microcrystals (space group R3) for both protein-ligand complexes. The corresponding single-crystal X-ray diffraction structures were solved: HI-m-cresol (PDB entry 9ibb, 1.84 Å) and HI-m-nitro-phenol (PDB entry 9qld, 2.55 Å). Pawley analysis of the in situ XRPD data revealed structural stability up to 70% RH, with no phase transitions observed. At lower humidity levels, reduced diffraction intensities indicated loss of crystallinity, which was fully restored upon rehydration to 95% RH. Notably, each complex exhibited distinct changes in unit-cell parameters during dehydration-rehydration cycles. These results highlight the critical role of controlling environmental factors in structure-based drug design and pharmaceutical manufacturing, and demonstrate how organic ligands can enhance the stability of protein crystals, offering valuable insights for pharmaceutical development.

Dypingite, a hydrated magnesium carbonate hydroxide mineral [Mg₅(CO₃)₄(OH)₂·XH₂O, X = 5-6], exhibits promising catalytic and purification properties. Although it was discovered 55 years ago, the crystal structure of this compound has remained unknown due to its aggregated morphology and structural disorder. This work investigates the origin of this phenomenon through a systematic analysis of synthetic and natural mineral samples, using synchrotron powder X-ray diffraction, thermogravimetric analysis and transmission electron microscopy. The findings reveal that ambient humidity significantly influences dypingite's structural properties at room temperature. High humidity (80% relative humidity at 22 °C) causes inhomogeneous expansion of the unit cell along the crystallographic c axis, leading to long-range structural disorder. Conversely, at 20% relative humidity at 22 °C, the mineral structure exhibits a shorter c lattice constant and reduced structural disorder. Chemical analysis reveals that samples kept at 80% and 20% relative humidity for 10 days differ by one molecule of water of hydration, yielding Mg₅(CO₃)_4.5(2)(OH)_0.96(3)·6.0(2)H₂O and Mg₅(CO₃)_4.5(2)(OH)_1.02(4)·5.0(2)H₂O, respectively. The results obtained demonstrate that the crystal structure of dehydrated dypingite [Mg₅(CO₃)_4.5(2)(OH)_1.02(4)·5.0(2)H₂O] derives from hydro-magnesite's unit cell tripled along the a axis. The analysis of the mineral crystal structure provides insight into the role of humidity on the structural properties of dypingite, including unit-cell dimensions and long-range disorder.

The development of 3D non-destructive X-ray characterization techniques in home laboratories is essential for enabling many more researchers to perform 3D characterization daily, overcoming the limitations imposed by competitive and scarce access to synchrotron facilities. Recent efforts have focused on techniques such as laboratory diffraction contrast tomography (LabDCT). LabDCT allows 3D characterization of recrystallized grains with sizes larger than 15-20 µm, offering a boundary resolution of approximately 5 µm using commercial X-ray computed tomography (CT) systems. To enhance the capa-bil-ities of laboratory instruments, we have developed a new laboratory-based 3D X-ray micro-beam diffraction (Lab-3DµXRD) technique. Lab-3DµXRD combines the use of a focused polychromatic beam with a scanning-tomographic data acquisition routine to enable depth-resolved crystallographic orientation characterization. This work presents the first realization of Lab-3DµXRD, including hardware development through the integration of a newly developed Pt-coated twin paraboloidal capillary X-ray focusing optics into a conventional X-ray micro-computed tomography (µCT) system, as well as the development of data acquisition and processing software. The results are validated through comparisons with LabDCT and synchrotron phase contrast tomography. The findings clearly demonstrate the feasibility of Lab-3DµXRD, particularly in detecting smaller grains and providing intragranular information. Finally, we discuss future directions for developing Lab-3DµXRD into a versatile tool for studying materials with smaller grain sizes and high defect densities, including the potential of combining it with LabDCT and µCT for multiscale and multimodal microstructural characterization.

A scattering geometry for depth-resolved energy-dispersive X-ray stress analysis on polycrystalline materials is introduced. Via simultaneous data acquisition during a sin² ψ measurement using two detectors arranged in the horizontal diffraction plane, it aims to extend the accessible information depth to the free surface as well as deeper material zones. While data acquisition with the first detector takes place in a symmetrical configuration with regard to the incident and exit angles, α_i and α_e, respectively, the second detector runs in an asymmetrical mode, defined by α_i < α_e. Therefore, the scattering vectors assigned to the two diffraction geometries run in different tilt planes during a χ scan of the sample performed in the Eulerian cradle. Treatment of the data recorded in the asymmetric diffraction mode requires modifications of the fundamental equation of X-ray stress analysis, which are discussed using the example of measurements performed on a unidirectionally ground ferritic steel sample.

A nanocrystalline Fe-1.8%Cr steel powder was tested as a reference material on more than five powder diffraction instruments and configurations, as well as with different data-analysis methodologies. The material, commercially available at low cost, was ground in a high-energy planetary mill to obtain homogeneous crystalline domain dimensions of 10 (2) nm, with size dispersion of 5 (1) nm and a nominal dislocation density of the order of 2.90 (2) × 10¹⁶ m^-2. The powder is stable, easy to handle and suitable for preparing samples in any measurement geometry. It is well suited for testing the modelling of diffraction peak profiles, either individually or across the entire diffraction pattern, as in the Rietveld method. This paper reports the simple details for the production of the material and the analysis of the diffraction patterns collected with both laboratory and synchrotron beamline instruments, using X-rays of different energies. In particular, the screening of the data based on integral breadths (Williamson-Hall method), the analysis by whole powder pattern modelling and the analysis by the Rietveld method are shown. Aspects related to diffuse scattering and pair distribution function analysis are also discussed.

In the present work, the role of microstrain developing in the temperature range above the structural transition in Fe-based superconductors is analysed in depth. Reviewing the results obtained from different compositions, a similar behaviour emerges in all cases. In particular, using an accurate diffraction line broadening analysis it is demonstrated that the tetragonal-to-orthorhombic structural transition occurring on cooling is anticipated by a symmetry breaking developing on the local scale in the tetragonal plane. The increase in microstrain with decreasing temperature in the stability field of the tetragonal phase qualitatively mirrors the development of anisotropy measured in some physical properties, a behaviour ascribed to nematicity. These results demonstrate the tight and delicate interplay correlating structural features on the local scale with transport and magnetic properties.

The DXRD program suite consisting of a series of dynamical theory programs is introduced for computing dynamical X-ray diffraction from single crystals. Its interactive graphical user interfaces (GUIs) allow general users to make complicated calculations with minimal effort. It can calculate plane-wave Darwin curves of single crystals (or multiple crystals) for both the Bragg and Laue cases, including grazing-incidence diffraction and backward diffraction (with Bragg angles approaching 90°). It is also capable of simulating rocking curves for divergent incident X-ray beams with finite bandwidths. A unique feature of DXRD is that it provides a convenient GUI-based multiple-beam diffraction program that can accurately compute arbitrary N-beam diffraction of any geometry using a universal 4N × 4N matrix method. DXRD also provides a mapping program for plotting all the multiple-beam diffraction lines (monochromator glitches) in the azimuth-energy coordinate system. All these functions make DXRD a convenient and powerful software tool for designing crystal-based synchrotron/X-ray optics (monochromators, analyzers, polarizers, phase plates etc.) and for crystal characterization, X-ray spectroscopy and X-ray diffraction teaching.

We present a method for achieving high-quality anomalous X-ray powder diffraction, interleaved with transmission X-ray absorption spectroscopy, using a flat-panel imaging detector scanned over a large angular range. Anomalous X-ray powder diffraction is a technique that enables the highlighting of specific elements within a crystal structure and pinpointing the nature of active (or inactive) sites involved in specific reactions in situ or in an operando manner. This approach enables the collection of a Q range that is not attainable using static flat-panel detectors in the absorption energy regimes used (8.94-17.5 keV). We consider the advantages and limitations of such an approach compared with alternative methods and describe in detail how it is achieved, along with the data processing and workflow required for an accurate restoration of conventional X-ray powder diffraction and anomalous X-ray powder diffraction data from sequentially acquired images. We demonstrate the applicability and capacity of this method for the in situ/operando restoration of the positions and atomic arrangement of copper atoms in the elevated-temperature aerobic activation of a copper-ion-exchanged zeolite, Cu-mazzite.

The study of crystallography and the introduction to X-ray structure analysis are generally regarded as tasks for universities and, even then, usually only in graduate studies. However, analysis of crystal structures in science classes at high schools offers a wide range of opportunities for illustrating and improving understanding of fundamental structural chemistry concepts. This article attempts to share some experiences with crystallographers who want to work with high school students on crystallographic topics. After presenting some preconditions for introducing students to crystallographic topics, such as the curricular situation, two levels of didactical reduction are suggested. Examples of the use of database structures from the Protein Data Bank and the Teaching Subset of the Cambridge Structural Database in chemistry lessons are presented. In the Göttingen experimental laboratory for young people, XLAB, high school students can carry out the essential steps of structure determination, structure solution and refinement of X-ray diffraction data themselves, using aspirin or citric acid as examples. Finally, a network scheme for promoting crystallographic topics in the classroom is proposed.