Journal of Applied Crystallography最新文献

We introduce a new approach to calculating small-angle X-ray scattering (SAXS) profiles from high-resolution atomic structures, which is realized in the open-source software AUSAXS. We employ an efficient implementation of the Debye equation, incorporating both accurate excluded volume models and a novel hydration shell model based on explicit dummy atoms. Two new excluded volume models are presented: (i) a simple, heterogeneous equivalent atom model, and (ii) a grid-based model. The two approaches reduce the risk of overfitting by either eliminating fitting parameters or introducing a safer volume scaling method. These models are compared with the traditional Gaussian sphere method, which is widely used in existing software. The comparisons reveal significant shortcomings in previously accepted methods, suggesting they may be more prone to overfitting than previously thought. This underscores the importance of a well tested and openly accessible baseline implementation like AUSAXS. AUSAXS is freely available at https://github.com/AUSAXS/AUSAXS.

We have produced superstable compound liquid microjets with a 3D-printed coaxial flow-focusing injector. The aqueous jet core is surrounded by a shell, a few hundred nanometres in thickness, of a low-concentration aqueous solution of a low-molecular-weight polymer. Due to the stabilizing effect of the polymeric shell, the minimum liquid flow rate leading to stable flow-focusing is decreased by one order of magnitude, resulting in much thinner and longer jets. Possible applications of this technique for serial femtosecond X-ray crystallography are discussed.

The mechanisms of crystal growth from solution are more complicated than those from vapor or melt growth. These mechanisms are important in bio-mineralization (bones, teeth, shells) and in the characterization of optically non-linear crystals, perfectly crystallized proteins, nucleic acids and complex viruses. This motivated studies on new basic phenomena, including the crystal interfaces of biological macromolecules and those of low-solubility inorganic salts. Generalization of the Gibbs-Thomson effect has been questioned when describing isotropic (circular) or anisotropic (polygonized) spiral steps spreading onto a crystal face. This work focuses on the brushite crystal (CaHPO₄·2H₂O) since it can grow freely or as a deposit on a gypsum (CaSO₄·2H₂O) substrate. Brushite looks like a 2D crystal built by a flat {010} form limited by {h0l} polar and thin faces running as straight steps. Moreover, it is worth investigating the {010} gypsum to {010} brushite transformation since mineralogy and geochemistry play an important role in the crystal growth. Here, we study the freely growing brushite and, subsequently, its {010} form arising from gypsum. The epitaxy {010} gypsum/{010} brushite is also examined because brushite twins are involved. A new way of thinking about the epi-relations is proposed, along with more rigorous constraints; this new approach emphasizes the physical importance of the adhesion energy connected to every epitaxy.

Understanding molecular adsorption on ionic surfaces is crucial for a variety of chemical applications, from heterogeneous catalysis to prebiotic chemistry. Traditional approaches for identifying adsorption sites often rely on computationally expensive methods such as density functional theory (DFT), which limits their applicability to chemically complex surfaces. In this work, we propose an automated high-throughput approach to obtain a complete picture of the adsorbate-surface interaction by means of pairwise Coulomb and Lennard-Jones potentials. Using a grid-based surface scan to calculate per-site potential energies of adsorption, this method efficiently predicts global adsorption minima and all potential binding modes of a surface-adsorbate system, with the only user input being the surface CIF. Our approach is validated by studying formaldehyde (H₂CO) adsorption on forsterite (Mg₂SiO₄), a common silicate, and l-cysteine adsorption on cadmium sulfide (CdS). The predicted adsorption configurations and energies are compared with DFT values in the literature, showing good agreement and confirming the accuracy of our method. Our workflow provides a rapid means of exploring large configurational spaces and identifying stable adsorption structures, making it particularly useful for complex surfaces with multiple interaction sites. The simplicity of the model, combined with its accuracy, suggest it could be employed to discover new catalytic pathways on chemically complex ionic surfaces.

Nanobeam X-ray diffraction (nanoXRD) is a powerful tool for collecting in situ crystal structure information with high spatial resolution and data acquisition rate. However, analyzing the enormous amount of data produced by these high-throughput experiments for defect recognition or discovering hidden structural features becomes challenging. Machine learning (ML) methods have become attractive recently due to their outstanding performance in analyzing large data sets. This research utilizes an ML algorithm, uniform manifold approximation and projection (UMAP), to enhance the nanoXRD-based crystal structure analysis of a cross-sectional hydride vapor-phase epitaxy GaN wafer. Compared with the results obtained by conventional fitting, UMAP gives a more precise categorization of crystal structure based on the raw three-dimensional ω-2θ-φ diffraction patterns. The property that UMAP embeds the high-dimensional data while retaining the data structure is valuable in guiding the analysis of nanoXRD profiles. This research also demonstrates the capability of UMAP in analyzing other spectroscopic or diffraction data sets to guide crystal structure investigations.

This study focuses on the kinetics of light-induced mesophase transitions in lyotropic liquid crystals containing a mixture of phospho-lipids and azo-benzene amphiphiles. Lipid membranes organize in a wide range of morphologies, directly influencing their functionality and the efficiency of associated components such as proteins. Transitions between mesophases occur naturally during membrane fusion and can also be triggered by multiple factors, such as pH, salinity, temperature and light. Employing light to isomerize artificial photoswitchable lipids in mixed model membranes containing 1,2-dipalmitoyl-phos-pha-tidylcholine or 1,2-didecanoyl-phosphatidylcholine revealed light-induced structural changes including mesophase transitions from a lamellar to a cubic Pn3m phase. Performing time-resolved small-angle X-ray scattering measurements, the kinetics of the change in membrane repeat distance and the transition from a lamellar to a bicontinuous cubic phase could be captured on the timescale of tens of seconds. The results demonstrate new possibilities for investigating intermediate states during mesophase transitions that are important to understand membrane fusion, and they highlight the potential of photoswitchable lipids for designing bespoke drug delivery systems.

Human transthyretin (TTR) is a homotetrameric protein involved in transporting thyroxine (T4) and retinol-binding protein within serum and cerebrospinal fluid. The disassociation of TTR's tetrameric structure can lead to the formation of biologically toxic TTR amyloid fibrils. Tolcapone, a small molecule currently under clinical trial, has shown potential as a TTR stabilizer and may act as an alternative to tafamidis, the conventional therapeutic agent used to prevent TTR dissociation. Using size-exclusion-chromatography-based small- and wide-angle X-ray scattering (SEC-SWAXS) complemented by nuclear magnetic resonance (NMR) spectroscopy, this study reveals the solution conformations of Apo-TTR and TTR complexed with tolcapone and tafamidis. Our results indicate that both compounds can bind similarly to the two T4 sites of TTR, leading to a small increase in the radius of gyration from 24.3 ± 0.1 Å (Apo-TTR) to 25.8 ± 0.1 Å. Consequently, both compounds largely stabilize the TTR against dissociation, denaturation and oligomerization up to 8 M urea, whereas Apo-TTR starts to denature at this concentration and forms larger oligomers at 8 M urea. Additionally, under a reduced TTR-drug mixing ratio of 1:1, which targets only one T4 site, tafamidis more effectively stabilizes the TTR tetrameric conformation at 8 M urea, a difference attributed to its higher affinity for the first T4 site. These results illustrate an effective strategy for investigating protein-drug interactions by examining the solution conformations of protein-drug complexes under physiological conditions, providing structural hints to the design of therapeutic agents targeting TTR.

Peptide-based nanotubes are bio-based self-assembled nanostructures with intriguing structural and functional properties. The structure of such nanotubes can be probed in detail using small-angle scattering experiments due to the typical length scales, i.e. diameter and wall thickness of the nanotubes, which span the range accessible in small-angle X-ray scattering (SAXS) or small-angle neutron scattering (SANS) studies. Here, we present SAXS data for several classes of peptide and lipopeptide systems previously studied by our group, as well as newly reported data for model short lysine-sequence lipopeptides. Previous data are re-examined using more accurate models for data plotted on Kratky plots, which emphasizes fine details of nanotube structure. In some cases, consideration of structure-factor effects is necessary to allow for the coexisting structures, and a lamellar structure factor is used to describe this. In other cases, such as several examples of surfactant-like peptides, only a form factor has to be considered to accurately fit the measured SAXS data. In these cases, a form factor for hollow nanotubes with a Gaussian bilayer profile to represent the layered peptide ordering in the nanotube walls is used to model the data. A general expression for the cross section scattering form factor is provided, which can be used for any scattering density profile (electron density for SAXS or scattering length density for SANS) across the wall. This is analysed along with the form factor for multishell (multiwall) nanotube structures with a series of slabs to represent the scattering density profile. For lipopeptides C₁₆-KFK and C₁₆-K (C₁₆ indicates a hexa-decyl lipid chain), SAXS data show aperiodicity in the form-factor oscillations, as well as apparent broad structure-factor peaks. These features cannot be fitted using solely nanotube form-factor models, this being ascribed to the presence of coexisting structures. Lastly, for comparison, the form factors for helical ribbon and cochleate (scroll) structures are evaluated for several examples, since in many cases electron microscopy of peptide- and lipopeptide-based nanotube systems reveals the coexistence of nanotubes with such structures, related to nanotubes.

Visual Studio Code (VS Code) is a popular text editor and integrated development environment commonly used in software development. The crystallographic information file (CIF) language extension makes syntax highlighting, auto completion, error checking and hover information available for crystallographers reading and editing CIFs. The language extension features are available for all files following the CIF syntax, including CIF dictionary files. The design and features of the VS Code CIF extension are presented.

We report the latest advances of the iMATERIA instrument, namely, time-of-flight small-angle neutron scattering (SANS) specifically for measurements in the manufacturing and energy industries. Observations are available that are multi-scale (from a minimum q _min = 0.007 Å^-1 to a maximum q = 30 Å^-1), multi-time domain (>0.5 s) and multi-contrast by dynamical nuclear polarization. Multi-angle (or stereo) observation of film specimens can bridge between conventional SANS and reflectivity measurements. For multi-analysis, we have developed real-time simultaneous SANS and neutron radiography (NR), targeting polymer electrolyte fuel cells. In the future, we plan to establish simultaneous triple-analysis combining SANS, NR and prompt γ-ray analysis. By scanning with a beam of 1 mm² in size, such analysis enables the mapping of structural parameters determined by SANS and elemental composition determined by prompt γ-ray analysis on the image obtained by NR.