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DOE OSTI2024

Extending the Takagi-Taupin equations for x-ray nanobeam Bragg coherent diffraction

We present an approach for simulating x-ray nanobeam Bragg coherent diffraction patterns based on the Takagi-Taupin equations. Compared to conventional methods, the current approach can be universally applied to any weakly strained system including semi-infinite crystals that diffract dynamically. It addresses issues such as the curved wave front and redivergence of the focused incident beam. In conclusion, we show excellent agreement with experimental data for a strained La 0.7 ⁢Sr 0.3⁢ MnO 3 thin film on a SrTiO 3 substrate and a path to extracting physical information using automatic differentiation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Ultrafast X-Ray Diffraction Studies of the Phase Transitions and Equation of State of Scandium Shock Compressed to 82 GPa

Using x-ray diffraction at the Linac Coherent Light Source x-ray free-electron laser, we have determined simultaneously and self-consistently the phase transitions and equation of state (EOS) of the lightest transition metal, scandium, under shock compression. On compression scandium undergoes a structural phase transition between 32 and 35 GPa to the same bcc structure seen at high temperatures at ambient pressures, and then a further transition at 46 GPa to the incommensurate host-guest polymorph found above 21 GPa in static compression at room temperature. Furthermore, shock melting of the host-guest phase is observed between 53 and 72 GPa with the disappearance of Bragg scattering and the growth of a broad asymmetric diffraction peak from the high-density liquid.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Imaging the Progression of Radiolytic Damage in Molecular Crystals with Scanning Nanobeam Electron Diffraction

Almost every electron microscopy experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive materials. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space movies of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting domains undergoes internal rearrangement as a function of accumulating electron fluence, causing the intensities of some associated Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the isotropic propagation of delocalized radiolytic damage well beyond the direct footprint of the incident beam. We refer to these expanding tides of amorphization as “impact craters.”

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Autoindexing diffraction images with iMosflm

The principles of one-dimensional FFT-based autoindexing of diffraction images are described together with practical issues that may arise. A procedure for indexing multiple lattices as implemented in iMosflm is presented. An overview of autoindexing diffraction images based on one-@@dimensional fast Fourier transforms is presented. The implementation of the algorithm in the Mosflm/iMosflm program suite is described with a discussion of practical issues that may arise and ways of assessing the success or failure of the procedure. Recent developments allow indexing of images that show multiple lattices, and several examples demonstrate the success of this approach in real cases.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

dxtbx : the diffraction experiment toolbox

Data formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Extraction of Plutonium-Containing Microcrystals from Hanford Soil using a Focused Ion Beam for Single-Crystal X-ray Diffraction Analysis

Herein we report the successful use of a focused ion beam/scanning electron microscope (FIB/SEM) to prepare microsamples of radioactive single-crystals for X-ray diffraction analysis. This technique was used to extract and analyze crystalline Pu-containing particles as small as 28 µm3 from Hanford soil taken from the 216-Z-9 waste crib which were then crystallographically characterized using single-crystal X-ray diffraction (SCXRD) to confirm the cubic structure of PuO2. As a systematic proof of concept, the technique was first tested using UO2 crystals milled into cubic shapes with approximate volumes 4620, 1331, 125, 8 and 1 µm3, respectively, in order to empirically determine the crystal size limits for characterization by a laboratory-based diffractometer with a sealed tube Mo or Ag anode X-ray source and a charge-coupled device (CCD) detector.

microcrystals, Plutomium, focused ion beam/scannin↗

DOE OSTI2021

Dislocation contrast on X-ray topographs under weak diffraction conditions

The contrast of dislocations in 4H-SiC crystals shows distinctive features on grazing-incidence X-ray topographs for diffraction at different positions on the operative rocking curve. Ray-tracing simulations have previously been successfully applied to describe the dislocation contrast at the peak of a rocking curve.The present work shows that the dislocation images observed under weak diffraction conditions can also be simulated using the ray-tracing method. Furthermore, these simulations indicate that the contrast of the dislocations is dominated by orientation contrast. Analysis of the effective misorientation reveals that the dislocation contrast in weak-beam topography is more sensitive to the local lattice distortion, consequently enabling information to be obtained on the dislocation sense which cannot be obtained from the peak.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector

The effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO 2 , including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Machine-learning-assisted automation of single-crystal neutron diffraction

Neutron scattering is a powerful but expensive technique to study materials and discover new matter. Advanced detector technology has significantly improved the efficiency of neutron experiments, increasing the complexity of neutron data reduction and analysis. Machine learning (ML) brings new directions for neutron diffraction data reduction and experiment operation. Here, this work presents an ML-assisted data reduction and analysis method for precise recognition of Bragg peaks and the corresponding regions of interest; it can then automatically screen and align a measured crystal using the recognized peaks, and subsequently plan and optimize the data collection with user-provided information and uncertainty quantification values of detected peaks. This method shows robust performance in different complex sample environments and enables automated single-crystal neutron diffraction.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Solid structure of Li 2 BeF 4 (FLiBe) from room temperature to melting studied by neutron and X-ray diffraction

Molten fluoride salts such as Li 2 BeF 4 (FLiBe) are used in molten salt reactors, fluoride-salt-cooled high-temperature reactors and fusion reactors as a fuel solvent, coolant and/or tritium breeding medium. In engineered systems that use molten salt, solid-state material will be present during melting and freezing scenarios, and therefore the temperature-dependent properties of the solid and solid/liquid phase transition merit investigation. To observe the behavior of the solid state of Li 2 BeF 4 from room temperature to melting, this work used neutron and X-ray diffraction to measure the changes in the lattice parameters and volume of the crystalline unit cell and compared the results with prior low-temperature data for solid Li 2 BeF 4 . From neutron diffraction data it is also possible to identify anisotropy: centimetre-scaled crystals align preferentially with the a axes parallel to the direction of freezing front propagation, and the c axes expand 54% more than the a axes. This work provides the lattice constants as a function of temperature, quantifies the thermal expansion, and determines the equation describing the change in density for solid Li 2 BeF 4 from room temperature to 459°C to be ρ solid (kg m −3 ) = 2182 (3) − 0.115 (2) T (°C) and the volume expansion upon melting to be less than 5%. This density changes depending on molecular weight and enrichment.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Novel silica stabilization method for the analysis of fine nanocrystals using coherent X-ray diffraction imaging

High-energy X-ray Bragg coherent diffraction imaging (BCDI) is a well established synchrotron-based technique used to quantitatively reconstruct the three-dimensional morphology and strain distribution in nanocrystals. The BCDI technique has become a powerful analytical tool for quantitative investigations of nanocrystals, nanotubes, nanorods and more recently biological systems. BCDI has however typically failed for fine nanocrystals in sub-100?nm size regimes ? a size routinely achievable by chemical synthesis ? despite the spatial resolution of the BCDI technique being 20?30?nm. The limitations of this technique arise from the movement of nanocrystals under illumination by the highly coherent beam, which prevents full diffraction data sets from being acquired. A solution is provided here to overcome this problem and extend the size limit of the BCDI technique, through the design of a novel stabilization method by embedding the fine nanocrystals into a silica matrix. Chemically synthesized FePt nanocrystals of maximum dimension 20?nm and AuPd nanocrystals in the size range 60?65?nm were investigated with BCDI measurement at beamline 34-ID-C of the APS, Argonne National Laboratory. Novel experimental methodologies to elucidate the presence of strain in fine nanocrystals are a necessary pre-requisite in order to better understand strain profiles in engineered nanocrystals for novel device development.

36 MATERIALS SCIENCE↗

DOE OSTI2018

In situ observation of phase changes of a silica-supported cobalt catalyst for the Fischer–Tropsch process by the development of a synchrotron-compatible in situ/operando powder X-ray diffraction cell

In situ characterization of catalysts gives direct insight into the working state of the material. Here, the design and performance characteristics of a universal in situ synchrotron-compatible X-ray diffraction cell capable of operation at high temperature and high pressure, 1373 K, and 35 bar, respectively, are reported. Its performance is demonstrated by characterizing a cobalt-based catalyst used in a prototypical high-pressure catalytic reaction, the Fischer–Tropsch synthesis, using X-ray diffraction. Cobalt nanoparticles supported on silica were studied in situ during Fischer–Tropsch catalysis using syngas, H 2 and CO, at 723 K and 20 bar. Post reaction, the Co nanoparticles were carburized at elevated pressure, demonstrating an increased rate of carburization compared with atmospheric studies.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2023

At-wavelength characterization of X-ray wavefronts in Bragg diffraction from crystals

The advent of next-generation synchrotron radiation sources and X-ray free-electron lasers calls for high-quality Bragg-diffraction crystal optics to preserve the X-ray beam coherence and wavefront. This requirement brings new challenges in characterizing crystals in Bragg diffraction in terms of Bragg-plane height errors and wavefront phase distortions. Here, a quantitative methodology to characterize crystal optics using a state-of-the-art at-wavelength wavefront sensing technique and statistical analysis is proposed. The method was tested at the 1-BM-B optics testing beamline at the Advanced Photon Source for measuring silicon and diamond crystals in a self-referencing single-crystal mode and an absolute double-crystal mode. The phase error sensitivity of the technique is demonstrated to be at the λ/100 level required by most applications, such as the characterization of diamond crystals for cavity-based X-ray free-electron lasers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Experimental 3D coherent diffractive imaging from photon-sparse random projections

The routine atomic resolution structure determination of single particles is expected to have profound implications for probing structure–function relationships in systems ranging from energy-storage materials to biological molecules. Extremely bright ultrashort-pulse X-ray sources – X-ray free-electron lasers (XFELs) – provide X-rays that can be used to probe ensembles of nearly identical nanoscale particles. When combined with coherent diffractive imaging, these objects can be imaged; however, as the resolution of the images approaches the atomic scale, the measured data are increasingly difficult to obtain and, during an X-ray pulse, the number of photons incident on the 2D detector is much smaller than the number of pixels. This latter concern, the signal `sparsity', materially impedes the application of the method. An experimental analog using a conventional X-ray source is demonstrated and yields signal levels comparable with those expected from single biomolecules illuminated by focused XFEL pulses. The analog experiment provides an invaluable cross check on the fidelity of the reconstructed data that is not available during XFEL experiments. Using these experimental data, it is established that a sparsity of order 1.3 × 10 −3 photons per pixel per frame can be overcome, lending vital insight to the solution of the atomic resolution XFEL single-particle imaging problem by experimentally demonstrating 3D coherent diffractive imaging from photon-sparse random projections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet–triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain ADP

The amidase domain of the allophanate hydrolase AtzF from Pseudomonas sp. strain ADP has been crystallized and preliminary X-ray diffraction data have been collected. The allophanate hydrolase from Pseudomonas sp. strain ADP was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50 kDa construct retained amidase activity and was crystallized. The crystals diffracted to 2.5 Å resolution and adopted space group P2{sub 1}, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6 Å, β = 106.6°.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase

A crystal was obtained of the complex between reduced terminal oxygenase and oxidized ferredoxin components of carbazole 1,9a-dioxygenase. The crystal belonged to space group P2{sub 1} and diffracted to 2.25 Å resolution. The initial reaction in bacterial carbazole degradation is catalyzed by carbazole 1,9a-dioxygenase, which consists of terminal oxygenase (Oxy), ferredoxin (Fd) and ferredoxin reductase components. The electron-transfer complex between reduced Oxy and oxidized Fd was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant under anaerobic conditions. The crystal diffracted to a maximum resolution of 2.25 Å and belonged to space group P2{sub 1}, with unit-cell parameters a = 97.3, b = 81.6, c = 116.2 Å, α = γ = 90, β = 100.1°. The V{sub M} value is 2.85 Å{sup 3} Da{sup −1}, indicating a solvent content of 56.8%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)

The use of truncation and RNA-binding mutations of caffeine induced death suppressor protein 1 (Cid1) as a means to enhance crystallogenesis leading to an improvement of X-ray diffraction resolution by 1.5 Å is reported. The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallo@@graphic studies of this TUT system to be initiated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗