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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↗

DOE OSTI2015

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

New regions of diffraction reflection in apodized one-dimensional photonic crystals with a large modulation depth

Particular features of the band structure of one-dimensional apodized photonic crystals based on metamaterials are studied in the case in which the medium is simultaneously inhomogeneous with respect to both the dielectric and the magnetic properties. It is shown that in the case of oblique incidence of light at large values of the modulation depth, a new region of diffraction reflection appears. This new region of diffraction reflection is also observed at magnetic permeability μ = const = 1. The particular features of the absorption and localization of light in these structures are examined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Peculiarities of Forming a Multiband Transmission Function Based on Multifrequency Acousto-Optic Diffraction

An analytical solution for the transmission function of noncoherent wideband radiation is obtained under acousto-optic (AO) filtering using a discrete set of monochromatic AO waves with a small spectral overlap. We studied characteristics of the AO transformation of a continuous spectrum of noncoherent radiation into a given set of discrete narrow bands of spectral transmission by excitation of a discrete set of sound frequencies. We carried out the analysis of transmission functions of individual channels taking into account a partial overlap of their spectra and possible intermodulation distortions. It is shown that a stationary value of the root-mean-square light power is found at the electronic output due to the photoelectric transformation and detecting diffracted light. Based on this, a necessary stationary, multiband, and nearly equidistant transmission function of a device can be formed by using a relevant spectrum of acoustic excitation. Peculiarities of this way of forming the multiband transmission function are revealed: the limitation of diffraction efficiency for an individual channel, the possibility of decoupling side lobes of adjacent channels, etc. A multiband acousto-optic filter (MAOF) was simulated that was based on a paratellurite monocrystal (TeO{sub 2}), which was previously used for experimental optical encoding. The theoretical and experimental results are in gratifying agreement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Harmonic Kinoform Lens: Diffraction Efficiency and Chromatism

Sawtooth microstructures with a relief depth significantly exceeding the central wavelength of the working spectral range are studied within the scalar and strict diffraction theories. The possibility of maintaining high diffraction efficiency, irrespective of the working spectral bandwidth and at allowed angles of incidence, which can reach 45° or more, is shown. It is also shown that the chromatism of such lenses is controlled in a very wide range and can be less than that of the lightest crown glasses.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2013

Study of structural order in porphyrin-fullerene dyad ZnDHD6ee monolayers by electron diffraction and atomic force microscopy

The structure of porphyrin-fullerene dyad ZnDHD6ee monolayers formed on the surface of aqueous subphase in a Langmuir trough and transferred onto solid substrates has been studied. The data obtained are interpreted using simulation of the structure of isolated molecules and their packing in monolayer and modeling of diffraction patterns from molecular aggregates having different sizes and degrees of order. Experiments on the formation of condensed ZnDHD6ee monolayers are described. The structure of these monolayers on a water surface is analyzed using {pi}-A isotherms. The structure of the monolayers transferred onto solid substrates is investigated by electron diffraction and atomic force microscopy. The unit-cell parameters of two-dimensional domains, which are characteristic of molecular packing in monolayers and deposited films, are determined. Domains are found to be organized into a texture (the molecular axes are oriented by the [001] direction perpendicular to the substrate). The monolayers contain a limited number of small 3D domains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

Generalization of the nonstandard approach in the dynamic theory of diffraction for deformed crystals

The nonstandard theory of X-ray scattering in a deformed crystal has been generalized. The vector of atomic-plane displacement is introduced into the crystal polarizability model like in the generalized Takagi dynamic theory. The solution to the wave equation is sought for using the procedure of expanding the field amplitude and vector operators in the Fourier components of polarizability χ{sub H} in a series according to the multiscale method. It is shown that considering lattice strain generally calls for introducing various characteristic spatial regions for the diffraction equation, which is in complete agreement with the main concept of the multiscale method. A particular case of a strain field depending on one scale is considered. If a relative change in strain occurs at a length on the order of the extinction length, one can obtain equations generalizing the Takagi equations to the case of arbitrary diffraction geometries.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

X-ray diffraction study of defects in zinc-diffusion-doped silicon

Samples of CZ n-Si〈Zn〉(111) are prepared by high-temperature zinc-diffusion annealing followed by quenching and are studied by X-ray diffraction. The silicon contains an initial phosphorus impurity and zinc-compensating admixture at concentrations N{sub P} = 1.5 × 10{sup 14} cm{sup −3} and N{sub Zn} = 1 × 10{sup 14} cm{sup −3}; i.e., the relation N{sub P}/2 < N{sub Zn} < N{sub P} is fulfilled. Microdefects are studied by double- and triple-crystal X-ray diffraction in the dispersion free modes (n, −n) and (n, −n, +n). The samples are found to contain microdefects with two characteristic sizes (average sizes of about 1 μm and 70 nm). The interplanar distance in the near-surface layer with a thickness of 0.1 μm is smaller than this parameter in the remaining matrix, the difference being equal to d{sub 0} Δd/d{sub 0} ≈ 2 × 10{sup −5}. This layer contains mainly vacancy-type microdefects. The angle between the reflecting planes and the local surface relief is Δψ = (7 ± 1) arcmin.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Specific features of two diffraction schemes for a widely divergent X-ray beam

We investigated the specific features of two diffraction schemes for a widely divergent X-ray beam that use a circular diaphragm 30–50 μm in diameter as a point source of characteristic radiation. In one of the schemes, the diaphragm was set in front of the crystal (the diaphragm-crystal (d-c) scheme); in the other, it was installed behind the crystal (the crystal-diaphragm (c-d) scheme). It was established that the diffraction image in the c-d scheme is a topographic map of the investigated crystal area. In the d-c scheme at L = 2l (l and L are the distances between the crystal and the diaphragm and between the photographic plate and the diaphragm, respectively), the branches of hyperbolas formed in this family of planes (hkl) by the characteristic K{sub α} and K{sub β} radiations, including higher order reflections, converge into one straight line. It is experimentally demonstrated that this convergence is very sensitive to structural inhomogeneities in the crystal under study.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Crystallization and preliminary X-ray diffraction study of porcine carboxypeptidase B

Crystals of porcine pancreatic carboxypeptidase B have been grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction study showed that the crystals belong to sp. gr. P4{sub 1}2{sub 1}2 and have the following unit-cell parameters: a = b = 79.58 Å, c = 100.51 Å; α = β = γ = 90.00°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one of the grown crystals at the SPring 8 synchrotron facility to 0.98 Å resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6{sub 3}22 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

X-ray third-order nonlinear dynamical diffraction in a crystal

The dynamic diffraction of an X-ray wave in a crystal with a third-order nonlinear response to external field strength has been theoretically investigated. General equations for the wave propagation in crystal and nonlinear Takagi equations for both ideal and deformed crystals are derived. Integrals of motion are determined for the nonlinear problem of dynamic diffraction. The results of the numerical calculations of reflectivity in the symmetric Laue geometry for an incident plane wave and the intensity distributions on the output crystal surface for a point source are reported as an example.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗