High-quality Diffraction Research Articles

In-situ cryogenic X-ray diffraction analysis of Poly(dimethylsiloxane) oil and film

Understanding the phase transitions and crystallographic characteristics of polysiloxane materials poses a significant challenge. To address this issue, a custom cryogenic chamber has been developed and integrated with a laboratory X-ray diffraction apparatus, enabling the execution of in-situ temperature-dependent X-ray diffraction (XRD) analyses across the cooling and heating cycles. Through the utilization of diverse sample holders, the real-time monitoring of crystallization and melting phenomena in both linear poly(dimethylsiloxane) (PDMS) oil and crosslinked PDMS film has been made feasible. Notably, high-quality X-ray diffraction data, encompassing 13 diffraction lines, are successfully acquired for the first time for linear PDMS oil at 153K. Subsequent crystallographic examination has revealed a tetragonal unit cell characterized by lattice parameters a = b = 8.3379 Å, c = 11.9284 Å, and space group I 41, suggesting the adoption of a fourfold helical conformation by two polymer chains, each comprising four monomer units, within the lattice structure. This improved and versatile X-ray instrumentation presents clear advantages over conventional commercial powder X-ray diffractometers, which is anticipated to provide a promising in-situ characterization approach for investigating the low-temperature behaviors of liquid or oil materials.

Development of a laser-driven shock compression platform for time-resolved XRD experiments at the ID09 beamline of the European Synchrotron Radiation Facility

ABSTRACT We present a newly developed laser-driven shock compression platform at the ID09 beamline of the European Synchrotron Radiation Facility (ESRF). This platform combines a custom high-power EKSPLA laser with ESRF's high-energy X-ray pulses to perform in situ, time-resolved X-ray diffraction (XRD) measurements in materials under well characterized, moderate pressure (up to 1 Mbar) and short-duration shock waves. Its purpose is to serve as a shock driver to study materials under dynamic pressure, focusing on phase transitions in condensed matter. We provide a detailed description of this platform's design and functionalities, along with preliminary experimental results obtained from iron and tin samples subjected to shock compression. These results not only demonstrate the platform's ability to acquire high-quality X-ray diffraction data but also highlight its potential for advancing research in material science and high-energy-density physics.

4D-STEM Mapping of Nanocrystal Reaction Dynamics and Heterogeneity in a Graphene Liquid Cell.

Chemical reaction kinetics at the nanoscale are intertwined with heterogeneity in structure and composition. However, mapping such heterogeneity in a liquid environment is extremely challenging. Here we integrate graphene liquid cell (GLC) transmission electron microscopy and four-dimensional scanning transmission electron microscopy to image the etching dynamics of gold nanorods in the reaction media. Critical to our experiment is the small liquid thickness in a GLC that allows the collection of high-quality electron diffraction patterns at low dose conditions. Machine learning-based data-mining of the diffraction patterns maps the three-dimensional nanocrystal orientation, groups spatial domains of various species in the GLC, and identifies newly generated nanocrystallites during reaction, offering a comprehensive understanding on the reaction mechanism inside a nanoenvironment. This work opens opportunities in probing the interplay of structural properties such as phase and strain with solution-phase reaction dynamics, which is important for applications in catalysis, energy storage, and self-assembly.

Influence of Al Doping on the Structural, Optical, and Electrical Characteristics of ZnMn2O4

Doped zinc manganite samples were synthesized using the sol-gel method, incorporating varying amounts of aluminum (ZnMn2-xAlxO4, x = 0, 0.03, 0.05, 0.07, 0.1). High quality X-ray diffraction data enabled detection and accurate quantification of the predominant phase ZnMn2O4 (ZMO) and minor phase ZnO. The structure and microstructure of developed phases were investigated applying the Rietveld refinement method. The nanoscale nature of the samples was examined by High-resolution transmission electron microscopy (HRTEM); the incorporation of Al into the ZMO matrix and the oxidation states of various cations were studied through X-ray photoelectron spectroscopy (XPS). The introduction of Al has resulted in a modification of the light-absorption characteristics of the ZMO sample. Specifically, the direct optical band gap energy of ZMO decreased from 2.45 to 2.25 eV with an increase in the amount of Al doping to 0.1. Moreover, an investigation was conducted into the impact of Al doping amount, frequency, and temperature on the dielectric constant, dielectric tangent loss, ac conductivity, complex impedance, and complex electric modulus. It was observed that all samples, except for the sample with x = 0.05, exhibited ferroelectric features. The activation energies for the samples with x = 0, 0.03, 0.05, 0.07, and 0.1 were determined to be 0.274, 0.456, 0.099, 0.103, and 0.152 eV, respectively. The conduction mechanism type in the different samples was identified. The obtained changes of dielectric properties indicated the capability of improving the ZMO characteristics for various applications via controlling the doping content of Al.

Generational assessment of EBSD detectors for cross-correlation-based analysis: From scintillators to direct detection

Introduced over ten years ago, cross-correlation-based electron backscatter diffraction has enabled high precision measurements of crystallographic rotations and elastic strain gradients at high spatial resolution. Since that time, there have been remarkable improvements in electron detector technology, including the advent of ultra-high speed detectors and the commercialization of direct detectors. In this study, we assess the efficacy of multiple generations of electron detectors for cross-correlation-based analysis using a single crystal Si sample as a reference. We show that, while improvements in precision are modest, there have been significant gains in the rate at which high-quality diffraction patterns can be collected. This has important implications in the size of datasets that can be collected and reduces the impact of drift and sample contamination.

Experimental electron density distribution of KZnB3O6 constructed by maximum-entropy method

The dynamic charge density of KZnB3O6, which contains edge-sharing BO4 units, has been characterized using laboratory and synchrotron X-ray diffraction techniques. The experimental electron density distribution (EDD) was constructed using the maximum-entropy method (MEM) from single crystal diffraction data obtained at 81 and 298 K. Additionally, MEM-based pattern fitting (MPF) method was employed to refine the synchrotron powder diffraction data obtained at 100 K. Both the room-temperature single crystal diffraction data and the cryogenic synchrotron powder diffraction data reveal an intriguing phenomenon: the edge-shared B2O2 ring exhibits a significant charge density accumulation between the O atoms. Further analysis of high-quality single crystal diffraction data collected at 81 K, with both high resolution and large signal-to-noise ratio, reveals no direct O–O bonding within the B2O2 ring. The experimental EDD of KZnB3O6 obtained aligns with the results obtained from ab-initio calculations. Our work underscores the importance of obtaining high-quality experimental data to accurately determine EDDs.

Towards a compact all-optical terahertz-driven electron source

In this study, we propose a physical design of a compact all-optical terahertz (THz)-driven electron source. The 300-mm accelerator beamline, powered by a Joule-level laser system, can be easily integrated into the tabletop scale. A THz-driven electron gun, a tapered dielectric-loaded cylindrical waveguide, THz-driven bunch compressors, and permanent magnetic solenoids (PMSs) have been designed and optimized. Dynamic simulations show that the electron source can deliver 19 fC electron beams at 3 MeV, with a normalized transverse emittance of 0.079 π.mm.mrad. A minimum relative energy spread of 0.04% or a minimum root-mean-square (RMS) bunch length of 6.1 fs can be achieved. Sensitivity analysis shows that the THz-driven electron source can effectively work with a laser power jitter within 1.5%. Simulation studies also reveal the potential of the designed THz-driven electron source for achieving high-quality ultrafast electron diffraction (UED). Prototype THz-driven electron guns have been fabricated and are currently under testing, and more comprehensive results will be reported in future works.

Crystal Structure Determination of Nucleotide-sugar Binding Domain of Human UDP-glucuronosyltransferases 2B10.

UDP-glucuronosyltransferases (UGTs) play a crucial role in maintaining endobiotic homeostasis and metabolizing xenobiotic compounds, particularly clinical drugs. However, the detailed catalytic mechanism of UGTs has not been fully elucidated due to the limited availability of reliable protein structures. Determining the catalytic domain of human UGTs has proven to be a significant challenge, primarily due to the difficulty in purifying and crystallizing the full-length protein. This study focused on the human UGT2B10 C-terminal cofactor binding domain, aiming to provide structural insights into the fundamental catalytic mechanisms. In this study, the C-terminal sugar-donor binding domain of human UGT2B10 was purified and crystallized using the vapor-diffusion method. The resulting UGT2B10 CTD crystals displayed high-quality diffraction patterns, allowing for data collection at an impressive resolution of 1.53 Å using synchrotron radiation. Subsequently, the structure of the UGT2B10 CTD was determined using the molecule replacement method with a homologous structure. The crystals were monoclinic, belonging to the space C2 with unit-cell parameters a = 85.90 Å, b = 58.39 Å, c = 68.87 Å, α = γ = 90°, and β = 98.138°. The Matthews coefficient VM was determined to be 2.24 Å3 Da-1 (solvent content 46.43%) with two molecules in the asymmetric unit. The crystal structure of UGT2B10 CTD was solved at a high resolution of 1.53 Å, revealing a conserved cofactor binding pocket. This is the first study determining the C-terminal cofactor binding domain of human UGT2B10, which plays a key role in additive drug metabolism.

Unlocking the secrets of doxepin hydrochloride's crystal structure: Insights from high-quality powder diffraction analysis

Doxepin hydrochloride, a versatile pharmaceutical compound, has been the subject of extensive research aimed at elucidating its crystal structure and solid-state characteristics. In this manuscript, we explore the significance of high-quality powder diffraction data in unveiling the intricate details of doxepin hydrochloride's crystal lattice. By examining the refined atom coordinates, density functional theory (DFT) optimization, and intermolecular interactions, we gain valuable insights into its structural conformation. This knowledge highlights the importance of precise crystallographic data in advancing our understanding of complex compounds and their pharmaceutical applications.

ABCG5/G8 Crystallization in a Lipidic Bicelle Environment for X-Ray Crystallography.

ATP-binding cassette (ABC) transporters constitute lipid-embedded membrane proteins. Extracting these membrane proteins from the lipid bilayer to an aqueous environment is typically achieved by employing detergents. These detergents disintegrate the lipid bilayer and solubilize the proteins. The intrinsic habitat of membrane proteins within the lipid bilayer poses a challenge in maintaining their stability and uniformity in solution for structural characterization. Bicelles, which comprise a blend of long and short-chain phospholipids and detergents, replicate the natural lipid structure. The utilization of lipid bicelles and detergents serves as a suitable model system for obtaining high-quality diffraction crystals, specifically to determine the high-resolution structure of membrane proteins. Through these synthetic microenvironments, membrane proteins preserve their native conformation and functionality, facilitating the formation of three-dimensional crystals. In this approach, the detergent-solubilized heterodimeric ABCG5/G8 was reintegrated into DMPC/CHAPSO bicelles, supplemented with cholesterol. This setup was employed in the vapor diffusion experimental procedure for protein crystallization.

Neutron diffraction probing hydrogen in monoclinic H2VOPO4

Light hydrogen atoms are resolvable with neutrons; however, the massive incoherent background inhibits the diffraction quality. To improve the signal, isotope treatment by deuteration becomes a prerequisite for a successful crystallographic understanding of hydrogen-containing materials by neutron diffraction. Thanks to the low-background and high-resolution time-of-flight neutron diffractometer, this work demonstrates a direct and successful measurement of high-quality neutron diffraction patterns of H2VOPO4 powders, a precursor of a high-capacity alkali-ion battery cathode. The Rietveld refinement identifies the hydrogen coordinates, occupancy, and thermal parameters in the H2VOPO4 lattice. The result highlights the unique capability of neutron diffraction for the structure characterization of hydrogen-containing materials, potentially without requiring costly and possibly artifact-inducing deuteration for neutron diffraction.

Experimental synthesis and crystal structure refinement of a new ternary intermetallic compound Al3GaCu9

A new ternary intermetallic compound Al3GaCu9 was synthesized experimentally. A high-quality powder diffraction pattern of the compound was collected by an X-ray diffractometer, and its crystal structure was determined using the Rietveld refinement method. Results show that the compound has a cubic cell with the Al4Cu9 structure type (space group $P\bar{4}3m$ and Pearson symbol cP52). The lattice parameter a = 8.7132(3) Å, unit-cell volume V = 661.52 Å3, calculated density Dcalc = 7.26 g/cm3, and Z = 4. The residual factors converge to Rp = 2.96%, Rwp = 4.06%, and Rexp = 2.57%. The experimentally obtained reference intensity ratio value is 7.04.

Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.

X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high-quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X-ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X-rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high-resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal-, phosphorus- and sulfur-containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics.

DMD maskless digital lithography based on stepwise rotary stitching

Diffractive optical elements (DOEs) with rotationally symmetric phase distribution are mainly produced by laser direct writing technique in a polar coordinate system, which has slow processing speed and limited fabrication area. In this paper, we propose a digital micro-mirror device maskless digital lithography technique based on stepwise rotary stitching. DOEs with rotationally symmetric phase distribution are fabricated by exposure of stitching units and rotation of rotary tables. Then, different stitching units are designed to compensate for the errors caused by the accuracy of the rotary table. Finally, the high quality DOEs are produced by the double-exposure method. When increasing the fabrication area, significantly improves the saw-tooth of the lithography pattern edge while reducing misalignment and overlap of stitching caused by residual errors. The diameter of the fabricated Fresnel zone plate was increased from 5.25 mm to 11.40 mm, and the fabrication area was 4.72 times larger than conventional lithography. The stitching error of 18.95 μm has been eliminated after optimization, and the pixelization has been smoothed. The diffraction results show that the method not only can produce large area and high-quality diffraction elements but also greatly reduce the processing cost.

Ferrimagnetic Ordering and Spin-Glass State in Diluted GdFeO3-Type Perovskites (Lu0.5Mn0.5)(Mn1-xTix)O3 with x = 0.25, 0.50, and 0.75.

ABO3 perovskite materials with small cations at the A site, especially those with ordered cation arrangements, have attracted a great deal of interest because they show unusual physical properties and deviations from the general characteristics of perovskites. In this work, perovskite solid solutions (Lu0.5Mn0.5)(Mn1-xTix)O3 with x = 0.25, 0.50, and 0.75 were synthesized by means of a high-pressure, high-temperature method at approximately 6 GPa and approximately 1550 K. All the samples crystallize in the GdFeO3-type perovskite structure (space group Pnma) and have random distributions of the small Lu3+ and Mn2+ cations at the A site and Mn4+/3+/2+ and Ti4+ cations at the B site, as determined by Rietveld analysis of high-quality synchrotron X-ray powder diffraction data. Lattice parameters are a = 5.4431 Å, b = 7.4358 Å, c = 5.1872 Å (for x = 0.25); a = 5.4872 Å, b = 7.4863 Å, c = 5.2027 Å (for x = 0.50); and a = 5.4772 Å, b = 7.6027 Å, c = 5.2340 Å (for x = 0.75). Despite a significant dilution of the A and B sublattices by non-magnetic Ti4+ cations, the x = 0.25 and 0.50 samples show long-range ferrimagnetic order below TC = 89 K and 36 K, respectively. Mn cations at both A and B sublattices are involved in the long-range magnetic order. The x = 0.75 sample shows a spin-glass transition at TSG = 6 K and a large frustration index of approximately 22. A temperature-independent dielectric constant was observed for x = 0.50 (approximately 32 between 5 and 150 K) and for x = 0.75 (approximately 50 between 5 and 250 K).

Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.

Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca2+ binding site configurations and altered rotameric distributions. These insights emphasize the value and need for multiconformer model refinement to extract ensemble information from diffraction data and to understand ensemble-function relationships.

3-D pre-stack diffraction separation by extending the PWD method with parametrized local slope

SUMMARY Diffractions comprise the seismic response of subsurface geological discontinuities and thus can provide detailed geological information during 3-D seismic exploration. The separation of weak diffractions from specular reflections is challenging, especially when the diffractions and reflections have similar kinematical characteristics in the 3-D pre-stack case. Conventional separation methods often estimate the local slope based on optimization or the Hilbert transform, which directly depends on the distribution behaviour of seismic events and may lead to the aliasing effects of the hyperbolic reflected and diffracted slopes in the shot domain. In this study, a different method is employed: local slopes are parametrized and constrained to the normal moveout velocity and ray parameter, which can distinguish reflections and diffractions in the shot domain and enhance the stability and accuracy of local slopes. Interestingly, when the receiver line and the geological edge are coplanar, the corresponding edge diffractions and reflections exhibit extremely similar behaviour, rendering them indistinguishable. Considering this phenomenon, a 3-D pre-stack diffraction separation strategy is proposed based on the estimation of the local slopes in two orthogonal directions. Thus, the accurate local slope can be used for plane-wave destruction when separating diffractions in the 3-D pre-stack domain. Synthetic and field data applications demonstrate that the proposed separation strategy is effective and can obtain high-quality diffraction wavefields for detecting the subsurface discontinuous structure.

Theoretical study of the enhancement of saturable absorption of Kr under x-ray free-electron laser

The generation of hollow atoms will reduce the probability of light absorption and provide a high-quality diffraction image in the experiment. In this paper, we calculated the ionization rate of the Kr atom under x-ray free-electron laser (XFEL) using Hartree–Fock–Slater model and simulated the ionization model of Kr atom using Monte–Carlo method to determine the response of the hollow atom of Kr atom to the XFEL photon energy. Calculating the correlation between the total photoionization cross-section of the ground state of Kr atom and the photon energy, we determined three particular photon energies of 1.75 keV, 1.90 keV, and 14.30 keV. The dynamics simulation under the experimental condition’s 17.50 keV photon energy was achieved by implementing the Monte–Carlo method and calibrating the photon flux modeling parameters. Consequently, our calculated data are more consistent with experimental phenomena than previous theoretical studies. The saturable absorption of Kr at 1.75 keV, 1.90 keV, 14.30 keV, and 17.50 keV energies was further investigated by using the optimized photon flux model theory. We compared the statistics on main ionization paths under those four specific photon energies and calculated the population changes of various Kr hollow atoms with different configurations. The results demonstrate that the population of hollow atoms produced at the critical ionization photon energy is high. Furthermore, the change of population with respect to position is smooth, which shows a significant difference between the generation mode of ions with low and high photon energies. The result is important for the study of medium- and high-Z element hollow atoms, which has substantial implications for the study of hollow atoms with medium and high charge states, as well as for the scaling of photon energy of free electron lasers.

Effective diffraction separation using the improved optimal rank-reduction method

Seismic diffractions encoding subsurface small-scale geologic structures have great potential for high-resolution imaging of subwavelength information. Diffraction separation from the dominant reflected wavefields still plays a vital role because of the weak energy characteristics of the diffractions. Traditional rank-reduction (RR) methods based on the low-rank assumption of reflection events have been commonly used for diffraction separation. However, these methods using truncated singular-value decomposition (TSVD) suffer from the problem of reflection-rank selection by singular-value spectrum analysis, especially for complicated seismic data. In addition, the separation problem for the tangent wavefields of reflections and diffractions is challenging. To alleviate these limitations, we have developed an effective diffraction separation strategy using an improved optimal RR (ORR) method to remove the dependence on the reflection rank and improve the quality of separation results. The improved RR method adaptively determines the optimal singular values from the input signals by directly solving an optimization problem that minimizes the Frobenius-norm difference between the estimated and exact reflections instead of the TSVD operation. This improved method can effectively overcome the problem of reflection-rank estimation in the global and local RR methods and adjusts to the diversity and complexity of seismic data. The adaptive data-driven algorithms indicate good performance in terms of the trade-off between high-quality diffraction separation and reflection suppression for the ORR operation. Applications of our strategy to synthetic and field examples demonstrate the superiority of diffraction separation in detecting and revealing subsurface small-scale geologic discontinuities and inhomogeneities.

A crystal-processing machine using a deep-ultraviolet laser: application to long-wavelength native SAD experiments.

While native SAD phasing is a promising method for next-generation macromolecular crystallography, it requires the collection of high-quality diffraction data using long-wavelength X-rays. The crystal itself and the noncrystalline medium around the crystal can cause background noise during long-wavelength X-ray data collection, hampering native SAD phasing. Optimizing the crystal size and shape or removing noncrystalline sample portions have thus been considered to be effective means of improving the data quality. A crystal-processing machine that uses a deep-UV laser has been developed. The machine utilizes the pulsed UV laser soft ablation (PULSA) technique, which generates less heat than methods using infrared or visible lasers. Since protein crystals are sensitive to heat damage, PULSA is an appropriate method to process them. Integration of a high-speed Galvano scanner and a high-precision goniometer enables protein crystals to be shaped precisely and efficiently. Application of this crystal-processing machine to a long-wavelength X-ray diffraction experiment significantly improved the diffraction data quality and thereby increased the success rate in experimental phasing using anomalous diffraction from atoms.