Structure Evolution of BaTiO3 on Co Doping: X-ray diffraction and Raman study

NASA Astrophysics Data System (ADS)

Mansuri, Amantulla; Mishra, Ashutosh

2016-10-01

In the present study, we have synthesize polycrystalline samples of BaTi1-xCoxO3 (x = 0, 0.05 and 0.1) with standard solid state reaction technique. The obtained samples are characterized by X-ray diffraction (XRD) and Raman spectroscopy. The detail structural analysis has been performed by Rietveld refinement using Fullprof program. The structural analysis reveal the samples are chemical pure and crystallize in tetragonal phase with space group Pm3m. We observe an increase in lattice parameters which results due to substitution of Co2+ with large ionic radii (0.9) for smaller ionic radii (0.6) Ti4+. Moreover peak at 45.5° shift to 45° on Co doping, which is due to structure phase transition from tetragonal to cubic. Raman study infers that the intensity of characteristic peaks decreases and linewidth increases with Co doping. The bands linked with the tetragonal structure (307 cm1) decreased due to the tetragonal-towards-cubic phase transition with Co doping. Our structural study reveals the expansion of BTO unit cell and tetragonal-to-cubic phase transformation takes place, results from different characterization techniques are conclusive and show structural evolution with Co doping.

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.

2014-10-01

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

X-ray transparent microfluidic chip for mesophase-based crystallization of membrane proteins and on-chip structure determination

DOE PAGES

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; ...

2014-08-21

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. In addition, we validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature.

PubMed

Ishigami, Izumi; Zatsepin, Nadia A; Hikita, Masahide; Conrad, Chelsie E; Nelson, Garrett; Coe, Jesse D; Basu, Shibom; Grant, Thomas D; Seaberg, Matthew H; Sierra, Raymond G; Hunter, Mark S; Fromme, Petra; Fromme, Raimund; Yeh, Syun-Ru; Rousseau, Denis L

2017-07-25

Cytochrome c oxidase (C c O), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C c O (bC c O) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a 3 iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near Cu B , which, in turn, moves closer to the heme a 3 iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3 , thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.

X-ray scattering study of pyrochlore iridates: Crystal structure, electronic, and magnetic excitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clancy, J. P.; Gretarsson, H.; Lee, E. K. H.

2016-07-06

We have investigated the structural, electronic, and magnetic properties of the pyrochlore iridates Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using a combination of resonant elastic x-ray scattering, x-ray powder diffraction, and resonant inelastic x-ray scattering (RIXS). The structural parameters of Eu 2Ir 2O 7 have been examined as a function of temperature and applied pressure, with a particular emphasis on regions of the phase diagram where electronic and magnetic phase transitions have been reported. We find no evidence of crystal symmetry change over the range of temperatures (~6 to 300 K) and pressures (~0.1 to 17 GPa)more » studied. We have also investigated the electronic and magnetic excitations in single-crystal samples of Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using high-resolution Ir L- 3-edge RIXS. In spite of very different ground state properties, we find that these materials exhibit qualitatively similar excitation spectra, with crystal field excitations at ~3-5 eV, spin-orbit excitations at ~ 0.5-1 eV, and broad low-lying excitations below ~0.15 eV. In single-crystal samples of "Eu-rich" Eu 2Ir 2O 7 (found to possess an actual stoichiometry of Eu 2.18Ir 1.82O 7.06) we observe highly damped magnetic excitations at ~45 meV, which display significant momentum dependence. Here, we compare these results with recent dynamical structure factor calculations« less

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

PubMed

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-11-01

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frank, Matthias; Carlson, David B.; Hunter, Mark

2014-02-28

Here we present femtosecond x-ray diffraction patterns from two-dimensional (2-D) protein crystals using an x-ray free electron laser (XFEL). To date it has not been possible to acquire x-ray diffraction from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permits a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy methodology at the Linac Coherent Light Source, we observed Bragg diffraction to better than 8.5 Å resolution for two different 2-D protein crystal samples that were maintained at room temperature. These proof-of-principle results show promisemore » for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.« less

Synthesis and crystal structure of the solid solution Co3(SeO3)3-x(PO3OH)x(H2O) involving crystallographic split positions of Se4+ and P5+.

PubMed

Zimmermann, Iwan; Johnsson, Mats

2013-10-21

Three new cobalt selenite hydroxo-phosphates laying in the solid solution Co3(SeO3)3-x(PO3OH)x(H2O), with x = 0.8, x = 1.0, and x = 1.2 are reported. Single crystals were obtained by hydrothermal synthesis and the crystal structure was determined by single crystal X-ray diffraction. The structure can be described as a 3D framework having selenite and hydroxo-phosphate groups protruding into channels in the crystal structure. Se(4+) and P(5+) share a split position in the structure so that either SeO3 groups having a stereochemically active lone pair or tetrahedrally coordinated PO3OH groups are present. The OH-group is thus only present when the split position is occupied by P(5+). The crystal water is coordinated to a cobalt atom and TG and IR measurements show that the water and hydroxyl groups leave the structure at unusually high temperatures (>450 °C). Magnetic susceptibility measurements show antiferromagnetic coupling below 16 K and a magnetic moment of 4.02(3) μB per Co atom was observed.

Crystal structure and electronic states of Co and Gd ions in a Gd0.4Sr0.6CoO2.85 single crystal

NASA Astrophysics Data System (ADS)

Platunov, M. S.; Dudnikov, V. A.; Orlov, Yu. S.; Kazak, N. V.; Solovyov, L. A.; Zubavichus, Ya. V.; Veligzhanin, A. A.; Dorovatovskii, P. V.; Vereshchagin, S. N.; Shaykhutdinov, K. A.; Ovchinnikov, S. G.

2016-02-01

X-ray diffraction and X-ray absorption near edge structure (XANES) spectra have been measured at the Co K-edge and Gd L 3-edge in GdCoO3 and Gd0.4Sr0.6CoO2.85 cobaltites. The effect of Sr substitution on the crystal structure and electronic and magnetic states of Co3+ ions in a Gd0.4Sr0.6CoO2.85 single crystal has been analyzed. The XANES measurements at the Co K-edge have not showed a noticeable shift of the absorption edge with an increase in the concentration of Sr. This indicates that the effective valence of cobalt does not change. An increase in the intensity of absorption at the Gd L 3-edge is due to an increase in the degree of hybridization of the Gd(5 d) and O(2 p) states. The effect of hole doping on the magnetic properties results in the appearance of the ferromagnetic component and in a significant increase in the magnetic moment.

Single crystal X-ray structure of the artists' pigment zinc yellow

NASA Astrophysics Data System (ADS)

Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

2017-08-01

The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

Biological Evaluation and X-ray Co-crystal Structures of Cyclohexylpyrrolidine Ligands for Trypanothione Reductase, an Enzyme from the Redox Metabolism of Trypanosoma.

PubMed

De Gasparo, Raoul; Brodbeck-Persch, Elke; Bryson, Steve; Hentzen, Nina B; Kaiser, Marcel; Pai, Emil F; Krauth-Siegel, R Luise; Diederich, François

2018-05-08

The tropical diseases human African trypanosomiasis, Chagas disease, and the various forms of leishmaniasis are caused by parasites of the family of trypanosomatids. These protozoa possess a unique redox metabolism based on trypanothione and trypanothione reductase (TR), making TR a promising drug target. We report the optimization of properties and potency of cyclohexylpyrrolidine inhibitors of TR by structure-based design. The best inhibitors were freely soluble and showed competitive inhibition constants (K i ) against Trypanosoma (T.) brucei TR and T. cruzi TR and in vitro activities (half-maximal inhibitory concentration, IC 50 ) against these parasites in the low micromolar range, with high selectivity against human glutathione reductase. X-ray co-crystal structures confirmed the binding of the ligands to the hydrophobic wall of the "mepacrine binding site" with the new, solubility-providing vectors oriented toward the surface of the large active site. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, structure and properties of blödite-type solid solutions, Na2Co1-x Cu x (SO4)2·4H2O (0 < x ≤ 0.18), and crystal structure of synthetic kröhnkite, Na2Cu(SO4)2·2H2O

NASA Astrophysics Data System (ADS)

Marinova, Delyana; Wildner, Manfred; Bancheva, Tsvetelina; Stoyanova, Radostina; Georgiev, Mitko; Stoilova, Donka G.

2018-03-01

Based on different experimental methods—crystallization processes in aqueous solutions, infrared spectroscopy, single-crystal X-ray diffraction, electron paramagnetic resonance (EPR) and TG-DTA-DSC measurements—it has been established that copper ions are included in sodium cobalt sulfate up to about 18 mol%, thus forming limited solid solutions Na2Co1-x Cu x (SO4)2·4H2O (0 < x ≤ 0.18) with a blödite-type structure. In contrast, cobalt ions are not able to accept the coordination environment of the copper ions in the strongly distorted Cu(H2O)2O4 octahedra, thus resulting in the crystallization of Co-free kröhnkite. The solid solutions were characterized by vibrational and EPR spectroscopy. DSC measurements reveal that the copper concentration increase leads to increasing values of the enthalpy of dehydration (ΔH deh) and decreasing values of the enthalpy of formation (ΔH f). The crystal structures of synthetic kröhnkite, Na2Cu(SO4)2·2H2O, as well as of three Cu2+-bearing mixed crystals of Co-blödite, Na2Co1-x Cu x (SO4)2·4H2O with x (Cu) ranging from 0.03 to 0.15, have been investigated from single-crystal X-ray diffraction data. The new data for the structure of synthetic kröhnkite facilitated to clarify structural discrepancies found in the literature for natural kröhnkite samples, traced back to a mix-up of lattice parameters. The crystal structures of Co-dominant Na2Co1-x Cu x (SO4)2·4H2O solid solutions reveal a comparatively weak influence of the Jahn-Teller-affected Cu2+ guest cations up to the maximum content of x (Cu) = 0.15. The response of the MO2(H2O)4 octahedral shape by increased bond-length distortion with Cu content is clear cut (but limited), mainly concerning the M-OH2 bond lengths, whereas other structural units are hardly affected. However, the specific type of imposed distortion seems to play an important role impeding higher Cu/Co replacement ratios.

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishigami, Izumi; Zatsepin, Nadia A.; Hikita, Masahide

Here, cytochrome c oxidase (C cO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C cO (bC cO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-raymore » crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near Cu B, which, in turn, moves closer to the heme a 3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

DOE PAGES

Ishigami, Izumi; Zatsepin, Nadia A.; Hikita, Masahide; ...

2017-07-11

Here, cytochrome c oxidase (C cO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine C cO (bC cO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-raymore » crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near Cu B, which, in turn, moves closer to the heme a 3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a 3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a 3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less

Curved focusing crystals for hard X-ray astronomy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferrari, C., E-mail: ferrari@imem.cnr.it; Buffagni, E.; Bonnini, E.

A lens made by a properly arranged array of crystals can be used to focus x-rays of energy ranging from 30 to 500 keV for x-ray astronomy. Mosaic or curved crystals can be employed as x-ray optical elements. In this work self standing curved focusing Si and GaAs crystals in which the lattice bending is induced by a controlled damaging process on one side of planar crystals are characterized. Diffraction profiles in Laue geometry have been measured in crystals at x-ray energies E = 17, 59 and 120 keV. An enhancement of diffraction efficiency is found in asymmetric geometries.

Increasing dissolution of trospium chloride by co-crystallization with urea

NASA Astrophysics Data System (ADS)

Skořepová, Eliška; Hušák, Michal; Čejka, Jan; Zámostný, Petr; Kratochvíl, Bohumil

2014-08-01

The search for various solid forms of an active pharmaceutical ingredient (API) is an important step in drug development. Our aim was to prepare co-crystals of trospium chloride, an anticholinergic drug used for the treatment of incontinence, and to investigate if they have advantageous properties for drug formulation. Phase identification was done by powder X-ray diffraction and single-crystal X-ray diffraction. The chemical composition was verified by solution NMR and the dissolution rate of the prepared phases was studied by IDR (intrinsic dissolution rate). For further analysis of phase stability and transitions, combined thermal analysis and temperature-resolved X-ray powder diffraction were used. Urea was selected as a co-crystallization partner. Trospium chloride urea (1:1) co-crystal was prepared by a solvent evaporation. From single-crystal data, the co-crystal structure was solved in a space group P21/c and compared to previously published structures of trospium chloride. Intrinsic dissolution rate revealed that the co-crystal dissolves 32% faster than pure API. However, its low thermal and pressure stability makes it a challenging choice for the final drug formulation.

X-Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muckelbauer, Jodi; Sack, John S.; Ahmed, Nazia

Bone marrow kinase in the X chromosome, a member of the Tec family of tyrosine kinases, plays a role in both monocyte/macrophage trafficking as well as cytokine secretion. Although the structures of Tec family kinases Bruton's tyrosine kinase and IL-2-inducible T-cell kinase are known, the crystal structures of other Tec family kinases have remained elusive. We report the X-ray crystal structures of bone marrow kinase in the X chromosome in complex with dasatinib at 2.4 {angstrom} resolution and PP2 at 1.9 {angstrom} resolution. The bone marrow kinase in the X chromosome structures reveal a typical kinase protein fold; with well-orderedmore » protein conformation that includes an open/extended activation loop and a stabilized DFG-motif rendering the kinase in an inactive conformation. Dasatinib and PP2 bind to bone marrow kinase in the X chromosome in the ATP binding pocket and display similar binding modes to that observed in other Tec and Src protein kinases. The bone marrow kinase in the X chromosome structures identify conformational elements of the DFG-motif that could potentially be utilized to design potent and/or selective bone marrow kinase in the X chromosome inhibitors.« less

Forming a structure of the CoNiFe alloys by X-ray irradiation

NASA Astrophysics Data System (ADS)

Valko, Natalia; Kasperovich, Andrey; Koltunowicz, Tomasz N.

The experimental data of electrodeposition kinetics researches and structure formation of ternary CoNiFe alloys deposited onto low-carbon steel 08kp in the presence of X-rays are presented. Relations of deposit rate, current efficiencies, element and phase compositions of CoNiFe coatings formed from sulfate baths with respect to cathode current densities (0.5-3A/dm2), electrolyte composition and irradiation were obtained. It is shown that, the CoNiFe coatings deposited by the electrochemical method involving exposure of the X-rays are characterized by more perfect morphology surfaces with less developed surface geometry than reference coatings. The effect of the X-ray irradiation on the electrodeposition of CoNiFe coatings promotes formatting of alloys with increased electropositive component and modified phase composition.

X-ray driven channeling acceleration in crystals and carbon nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Young-Min; Still, Dean A.; Shiltsev, Vladimir

2013-12-01

Acceleration of particles channeling in a crystal by means of diffracted x-rays via Bormann anomalous transmission was conceived for heavy ions and muons by Tajima and Cavenago [Phys. Rev. Lett. 59, 1440 (1987)], which potentially offers an appreciably high field gradient on the order of GV/cm. The theoretical model of the high gradient acceleration has been studied in two kinds of atomic structure, crystals and carbon nanotubes (CNTs), with analytic calculations and electromagnetic eigenmode simulations. A range of acceleration gradients and cutoffs of the x-ray power (the lowest power limit to overcome the Bremsstrahlung radiation losses) are characterized in termsmore » of the lattice constants, unit cell sizes, and photon energies. The parametric analysis indicates that the required x-ray power can be reduced to an order of megawatt by replacing crystals with CNTs. Eventually, the equivalent dielectric approximation of a multi-wall nanotube shows that 250–810 MeV muons can be synchronously coupled with x-rays of 0.65–1.32 keV in the accelerating structure.« less

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

PubMed Central

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Ke, Jiyuan; Eileen Tan, M. H.; Zhang, Chenghai; Moeller, Arne; West, Graham M.; Pascal, Bruce; Van Eps, Ned; Caro, Lydia N.; Vishnivetskiy, Sergey A.; Lee, Regina J.; Suino-Powell, Kelly M.; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A.; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P.; Katritch, Vsevolod; Gurevich, Vsevolod V.; Griffin, Patrick R.; Hubbell, Wayne L.; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2015-01-01

G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology. PMID:26200343

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

PubMed

Kang, Yanyong; Zhou, X Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Ke, Jiyuan; Tan, M H Eileen; Zhang, Chenghai; Moeller, Arne; West, Graham M; Pascal, Bruce D; Van Eps, Ned; Caro, Lydia N; Vishnivetskiy, Sergey A; Lee, Regina J; Suino-Powell, Kelly M; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie E; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P; Katritch, Vsevolod; Gurevich, Vsevolod V; Griffin, Patrick R; Hubbell, Wayne L; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2015-07-30

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

X-Ray Structure determination of the Glycine Cleavage System Protein H of Mycobacterium tuberculosis Using An Inverse Compton Synchrotron X-Ray Source

PubMed Central

Abendroth, Jan; McCormick, Michael S.; Edwards, Thomas E.; Staker, Bart; Loewen, Roderick; Gifford, Martin; Rifkin, Jeff; Mayer, Chad; Guo, Wenjin; Zhang, Yang; Myler, Peter; Kelley, Angela; Analau, Erwin; Hewitt, Stephen Nakazawa; Napuli, Alberto J.; Kuhn, Peter; Ruth, Ronald D.; Stewart, Lance J.

2010-01-01

Structural genomics discovery projects require ready access to both X-ray and NMR instrumentation which support the collection of experimental data needed to solve large numbers of novel protein structures. The most productive X-ray crystal structure determination laboratories make extensive frequent use of tunable synchrotron X-ray light to solve novel structures by anomalous diffraction methods. This requires that frozen cryo-protected crystals be shipped to large government-run synchrotron facilities for data collection. In an effort to eliminate the need to ship crystals for data collection, we have developed the first laboratory-scale synchrotron light source capable of performing many of the state-of-the-art synchrotron applications in X-ray science. This Compact Light Source is a first-in-class device that uses inverse Compton scattering to generate X-rays of sufficient flux, tunable wavelength and beam size to allow high-resolution X-ray diffraction data collection from protein crystals. We report on benchmarking tests of X-ray diffraction data collection with hen egg white lysozyme, and the successful high-resolution X-ray structure determination of the Glycine cleavage system protein H from Mycobacterium tuberculosis using diffraction data collected with the Compact Light Source X-ray beam. PMID:20364333

Thermal expansion behavior study of Co nanowire array with in situ x-ray diffraction and x-ray absorption fine structure techniques

NASA Astrophysics Data System (ADS)

Mo, Guang; Cai, Quan; Jiang, Longsheng; Wang, Wei; Zhang, Kunhao; Cheng, Weidong; Xing, Xueqing; Chen, Zhongjun; Wu, Zhonghua

2008-10-01

In situ x-ray diffraction and x-ray absorption fine structure techniques were used to study the structural change of ordered Co nanowire array with temperature. The results show that the Co nanowires are polycrystalline with hexagonal close packed structure without phase change up until 700 °C. A nonlinear thermal expansion behavior has been found and can be well described by a quadratic equation with the first-order thermal expansion coefficient of 4.3×10-6/°C and the second-order thermal expansion coefficient of 5.9×10-9/°C. The mechanism of this nonlinear thermal expansion behavior is discussed.

Analysis of synthetic diamond single crystals by X-ray topography and double-crystal diffractometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prokhorov, I. A., E-mail: igor.prokhorov@mail.ru; Ralchenko, V. G.; Bolshakov, A. P.

2013-12-15

Structural features of diamond single crystals synthesized under high pressure and homoepitaxial films grown by chemical vapor deposition (CVD) have been analyzed by double-crystal X-ray diffractometry and topography. The conditions of a diffraction analysis of diamond crystals using Ge monochromators have been optimized. The main structural defects (dislocations, stacking faults, growth striations, second-phase inclusions, etc.) formed during crystal growth have been revealed. The nitrogen concentration in high-pressure/high-temperature (HPHT) diamond substrates is estimated based on X-ray diffraction data. The formation of dislocation bundles at the film-substrate interface in the epitaxial structures has been revealed by plane-wave topography; these dislocations are likelymore » due to the relaxation of elastic macroscopic stresses caused by the lattice mismatch between the substrate and film. The critical thicknesses of plastic relaxation onset in CVD diamond films are calculated. The experimental techniques for studying the real diamond structure in optimizing crystal-growth technology are proven to be highly efficient.« less

X-ray Microscopic Characterization of Protein Crystals

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Holmes, A.; Thomas, B.R.; Chernov, a. A.; Chu, Y. S.; Lai, B.

2004-01-01

The microscopic mapping of the variation in degree of perfection and in type of defects in entire protein crystals by x-rays may well be a prerequisite for better understanding causes of lattice imperfections, the growth history, and properties of protein crystals. However, x-ray microscopic characterization of bulk protein crystals, in the as-grown state, is frequently more challenging than that of small molecular crystals due to the experimental difficulties arising largely from the unique features possessed by protein crystals. In this presentation, we will illustrate ssme recent activities in employing coherence-based phase contrast x-ray imaging and high-angular-resolution diffraction techniques for mapping microdefects and the degree of perfection of protein crystals, and demonstrate a correlation between crystal perfection, diffraction phenomena., and crystallization conditions. The observed features and phenomena will be discussed in context to gain insight into the nature of defects, nucleation and growth, and the properties of protein crystals.

X-ray Diffraction Crystal Calibration and Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michael J. Haugh; Richard Stewart; Nathan Kugland

2009-06-05

National Security Technologies’ X-ray Laboratory is comprised of a multi-anode Manson type source and a Henke type source that incorporates a dual goniometer and XYZ translation stage. The first goniometer is used to isolate a particular spectral band. The Manson operates up to 10 kV and the Henke up to 20 kV. The Henke rotation stages and translation stages are automated. Procedures have been developed to characterize and calibrate various NIF diagnostics and their components. The diagnostics include X-ray cameras, gated imagers, streak cameras, and other X-ray imaging systems. Components that have been analyzed include filters, filter arrays, grazing incidencemore » mirrors, and various crystals, both flat and curved. Recent efforts on the Henke system are aimed at characterizing and calibrating imaging crystals and curved crystals used as the major component of an X-ray spectrometer. The presentation will concentrate on these results. The work has been done at energies ranging from 3 keV to 16 keV. The major goal was to evaluate the performance quality of the crystal for its intended application. For the imaging crystals we measured the laser beam reflection offset from the X-ray beam and the reflectivity curves. For the curved spectrometer crystal, which was a natural crystal, resolving power was critical. It was first necessary to find sources of crystals that had sufficiently narrow reflectivity curves. It was then necessary to determine which crystals retained their resolving power after being thinned and glued to a curved substrate.« less

Structural changes that occur upon photolysis of the Fe(II)a3 - CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB

PubMed Central

Liu, Bin; Zhang, Yang; Sage, J. Timothy; Soltis, S. Michael; Doukov, Tzanko; Chen, Ying; Stout, C. David; Fee, James A.

2012-01-01

The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a3 moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba3-oxidase from Thermus thermophilus, determined at ~ 2.8 – 3.2 Å resolution, reveal a Fe-C distance of ~2.0 Å, a Cu-O distance of 2.4 Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100 K, X-ray structures indicate loss of Fea3-CO and appearance of CuB-CO having a Cu-C distance of ~1.9 Å and an O-Fe distance of ~2.3 Å. Absolute FTIR spectra recorded from single crystals of reduced ba3–CO that had not been exposed to X-ray radiation, showed several peaks around 1975 cm−1; after photolysis at 100 K, the absolute FTIR spectra also showed a significant peak at 2050 cm−1. Analysis of the “light’ minus ‘dark’ difference spectra showed four very sharp CO stretching bands at 1970 cm−1, 1977 cm−1, 1981 cm−1, and 1985 cm−1, previously assigned to the Fea3-CO complex, and a significantly broader CO stretching band centered at ~2050 cm−1, previously assigned to the CO stretching frequency of CuB bound CO. As expected for light propagating along the tetragonal axis of the P43212 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba3 crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO2 at 2337 cm−1 and one from traces of CO at 2133 cm−1; while bands associated with CO bound to either Fea3 or to CuB in “light” minus “dark” FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2 Å and FTIR spectra support the long-held position that photolysis of Fea3-CO in cytochrome c oxidases leads to significant

X-ray and dielectric characterization of Co doped tetragonal BaTiO3 ceramics

NASA Astrophysics Data System (ADS)

Bujakiewicz-Koronska, R.; Vasylechko, L.; Markiewicz, E.; Nalecz, D. M.; Kalvane, A.

2017-01-01

The crystal structure modifications of BaTiO3 induced by cobalt doping were studied. The polycrystalline (1 - x)BaTiO3 + xCo2O3 samples, with x ≤ 10 wt.%, were prepared by high temperature sintering conventional method. According to X-ray phase and structural characterization, performed by full-profile Rietveld refinement technique, all synthesized samples showed tetragonal symmetry perovskite structure with minor amount of parasitic phases. Pure single-phase composition has been detected only in the low level of doping BaTiO3. It was indicated that substitution of Co for the Ti sites in the (1 - x)BaTiO3 + xCo2O3 series led to decrease of tetragonality (c/a) of the BaTiO3 perovskite structure. This effect almost vanished in the (1 - x)BaTiO3 + xCo2O3 samples with nominal Co content higher than ∼1 wt.%, in which precipitation of parasitic Co-containing phases CoO and Co2TiO4 has been observed. Based on the results, the solubility limit of Co in Ti sub-lattice in the (1 - x)BaTiO3 + xCo2O3 series is estimated as x = 0.75 wt.%.

Diamond drumhead crystals for X-ray optics applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolodziej, Tomasz; Vodnala, Preeti; Terentyev, Sergey

2016-07-14

Thin (<50 µm) and flawless diamond single crystals are essential for the realization of numerous advanced X-ray optical devices at synchrotron radiation and free-electron laser facilities. The fabrication and handling of such ultra-thin components without introducing crystal damage and strain is a challenge. Drumhead crystals, monolithic crystal structures composed of a thin membrane furnished with a surrounding solid collar, are a solution ensuring mechanically stable strain-free mounting of the membranes with efficient thermal transport. Diamond, being one of the hardest and most chemically inert materials, poses significant difficulties in fabrication. Reported here is the successful manufacture of diamond drumhead crystalsmore » in the [100] orientation using picosecond laser milling. Subsequent high-temperature treatment appears to be crucial for the membranes to become defect free and unstrained, as revealed by X-ray topography on examples of drumhead crystals with a 26 µm thick (1 mm in diameter) and a 47 µm thick (1.5 × 2.5 mm) membrane.« less

Photonic crystals at visible, x-ray, and terahertz frequencies

NASA Astrophysics Data System (ADS)

Prasad, Tushar

Photonic crystals are artificial structures with a periodically varying refractive index. This property allows photonic crystals to control the propagation of photons, making them desirable components for novel photonic devices. Photonic crystals are also termed as "semiconductors of light", since they control the flow of electromagnetic radiation similar to the way electrons are excited in a semiconductor crystal. The scale of periodicity in the refractive index determines the frequency (or wavelength) of the electromagnetic waves that can be manipulated. This thesis presents a detailed analysis of photonic crystals at visible, x-ray, and terahertz frequencies. Self-assembly and spin-coating methods are used to fabricate colloidal photonic crystals at visible frequencies. Their dispersion characteristics are examined through theoretical as well as experimental studies. Based on their peculiar dispersion property called the superprism effect, a sensor that can detect small quantities of chemical substances is designed. A photonic crystal that can manipulate x-rays is fabricated by using crystals of a non-toxic plant virus as templates. Calculations show that these metallized three-dimensional crystals can find utility in x-ray optical systems. Terahertz photonic crystal slabs are fabricated by standard lithographic and etching techniques. In-plane superprism effect and out-of-plane guided resonances are studied by terahertz time-domain spectroscopy, and verified by numerical simulations.

Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

DOEpatents

Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

2015-04-14

A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

DOE PAGES

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; ...

2015-07-22

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Highly magnetic Co nanoparticles fabricated by X-ray radiolysis

NASA Astrophysics Data System (ADS)

Clifford, Dustin M.; Castano, Carlos E.; Rojas, Jessika V.

2018-03-01

Advanced routes for the synthesis of nanomaterials, such as ferromagnetic nanoparticles, are being explored that are easy to perform using cost-effective and non-toxic precursors. Radiolytic syntheses based on the use of X-rays as ionizing radiation are promising towards this effort. X-rays were used to produce highly magnetic cobalt nanoparticles (NPs), stable in air up to 200 °C, from the radiolysis of water. Crystal structure analysis by XRD indicates a mixture of Cofcc, 63%, and Cohcp, 37%, phases. Magnetic analysis by VSM gave a saturation magnetization (Ms) 136 emu/g at 1 T and coercivity (Hc) = 325 Oe when the reaction solution was purged with N2 while an air-purged treatment resulted in Co NPs having 102 emu/g with a coercivity (Hc) 270 Oe. Overall, the reduction of Co2+ occurred in an aqueous reaction environment without addition of chemical reductants resulting in Co NPs with size distribution from 20 to 140 nm. This clean approach at ambient temperature produced highly magnetic Co NPs that may be used for switching devices (i.e. reed switches) or as additives for alloys that require high Curie points.

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.

2016-05-15

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer ofmore » the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.« less

Single crystal growth and structural evolution across the 1st order valence transition in (Pr 1–yY y) 1–xCa xCoO 3-δ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schreiber, N. J.; Zhang, Junjie; Zheng, Hong

Here, praseodymium-containing cobalt perovskites, such as (Pr 1-yY y) 1-xCa xCoO 3-δ, have been argued to undergo a first-order charge shift between Pr and hybridized Co-O orbitals that leads to a metal-insulator transition at a temperature, T VT. Magnetization and x-ray absorption spectroscopy measurements on single crystals of (Pr 0.85Y 0.15) 0.7Ca 0.3CoO 3-δ grown in an IR image furnace under 40-60 bar of oxygen confirm the presence of this valence transition. Single crystal x-ray synchrotron diffraction measurements are consistent with an isomorphic phase transition at T VT. No evidence of charge ordering was revealed by the single crystal diffraction.more » Dissimilar to analytical transmission electron microscopy measurements performed on a grain from a polycrystalline sample that revealed an oxygen vacancy order-disorder transition at T VT, the present single-crystal measurements did not evidence such a transition, likely reflecting a lower density of oxygen vacancies in the high-pO 2 grown single crystals.« less

Single crystal growth and structural evolution across the 1st order valence transition in (Pr 1–yY y) 1–xCa xCoO 3-δ

DOE PAGES

Schreiber, N. J.; Zhang, Junjie; Zheng, Hong; ...

2017-06-27

Here, praseodymium-containing cobalt perovskites, such as (Pr 1-yY y) 1-xCa xCoO 3-δ, have been argued to undergo a first-order charge shift between Pr and hybridized Co-O orbitals that leads to a metal-insulator transition at a temperature, T VT. Magnetization and x-ray absorption spectroscopy measurements on single crystals of (Pr 0.85Y 0.15) 0.7Ca 0.3CoO 3-δ grown in an IR image furnace under 40-60 bar of oxygen confirm the presence of this valence transition. Single crystal x-ray synchrotron diffraction measurements are consistent with an isomorphic phase transition at T VT. No evidence of charge ordering was revealed by the single crystal diffraction.more » Dissimilar to analytical transmission electron microscopy measurements performed on a grain from a polycrystalline sample that revealed an oxygen vacancy order-disorder transition at T VT, the present single-crystal measurements did not evidence such a transition, likely reflecting a lower density of oxygen vacancies in the high-pO 2 grown single crystals.« less

Ionothermal synthesis, crystal structure, and magnetic study of Co2PO4OH isostructural with caminite.

PubMed

Wang, Guangmei; Valldor, Martin; Spielberg, Eike T; Mudring, Anja-Verena

2014-03-17

A new framework cobalt(II) hydroxyl phosphate, Co2PO4OH, was prepared by ionothermal synthesis using 1-butyl-4-methyl-pyridinium hexafluorophosphate as the ionic liquid. As the formation of Co2PO4F competes in the synthesis, the synthesis conditions have to be judiciously chosen to obtain well-crystallized, single phase Co2PO4OH. Single-crystal X-ray diffraction analyses reveal Co2PO4OH crystallizes with space group I41/amd (a = b = 5.2713(7) Å, c = 12.907(3) Å, V = 358.63(10) Å(3), and Z = 4). Astonishingly, it does not crystallize isotypically with Co2PO4F but rather isotypically with the hydroxyl minerals caminite Mg1.33[SO4(OH)0.66(H2O)0.33] and lipscombite Fe(2–y)PO4(OH) (0 ≤ y ≤ 2/3). Phosphate tetrahedra groups interconnect four rod-packed face-sharing ∞(1){CoO(6/2)} octahedra chains to form a three-dimensional framework structure. The compound Co2PO4OH was further characterized by powder X-ray diffraction, Fourier transform–infrared, and ultraviolet–visible spectroscopy, confirming the discussed structure. The magnetic measurement reveals that Co2PO4OH undergoes a magnetic transition and presents at low temperatures a canted antiferromagnetic spin order in the ground state.

Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.

2005-10-01

The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombicmore » space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

PubMed

Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

2014-12-11

The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

X-ray diffraction analysis of LiCu2O2 crystals with additives of silver atoms

NASA Astrophysics Data System (ADS)

Sirotinkin, V. P.; Bush, A. A.; Kamentsev, K. E.; Dau, H. S.; Yakovlev, K. A.; Tishchenko, E. A.

2015-09-01

Silver-containing LiCu2O2 crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1- x)CuO · 20 x AgNO3 · 20Li2CO3 (0 ≤ х ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu2O2 structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter с of the LiCu2O2 rhombic unit cell, a slight increase in parameter а, and a slight decrease in parameter b.

A graphite crystal polarimeter for stellar X-ray astronomy.

NASA Technical Reports Server (NTRS)

Weisskopf, M. C.; Berthelsdorf, R.; Epstein, G.; Linke, R.; Mitchell, D.; Novick, R.; Wolff, R. S.

1972-01-01

The first crystal X-ray polarimeter to be used for X-ray astronomy is described. Polarization is measured by modulation of the X rays diffracted at an average 45 deg glancing angle from large, curved graphite crystal panels as these rotate about an axis parallel to the incident X-ray flux. Arrangement of the crystal panels, the design of the detector, and the signal-processing circuitry were optimized to minimize systematic effects produced by off-axis pointing of the rocket and cosmic ray induced events. The in-flight performance of the instrument in relation to the observed background signal is discussed.

Influence of crystal structure on the Co{sup II} diffusion behavior in the Zn{sub 1-x}Co{sub x}O system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peiteado, M.; Makovec, D.; Villegas, M.

2008-09-15

The solid state interaction of the Zn{sub 1-x}Co{sub x}O nominal system is investigated by means of diffusion couples and analysis of co-precipitated samples. The formation of a homogeneous Co:ZnO solid solution is found to be determined by the crystal structure from which Co{sup II} ions diffuse into the wurtzite lattice. No diffusion is observed whenever the CoO rock-salt structure is formed from the Co{sup II} precursor. On the contrary, the diffusion from the Co{sub 3}O{sub 4} spinel phase is feasible but has a limited temperature range defined by the reduction at a high temperature of Co{sup III}-Co{sup II}, since thismore » process again leads to the formation of the rock-salt structure. However, when using a highly reactive and homogeneous co-precipitated starting powder, neither the spinel phase nor the rock-salt structure is formed, and a Co{sup II}:ZnO solid solution is obtained, which remains stable up to high temperatures. - Graphical abstract: Maximum diffusion distance for the ZnO-CoO{sub x} couple as a function of temperature. Dashed gray lines represent the temperature values at which the transformations between CoO and Co{sub 3}O{sub 4} compounds take place.« less

X-ray crystallography

NASA Technical Reports Server (NTRS)

2001-01-01

X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

Cationic metal complex, carbonatobis(1,10-phenanthroline)cobalt(III) as anion receptor: Synthesis, characterization, single crystal X-ray structure and packing analysis of [Co(phen) 2CO 3](3,5-dinitrobenzoate)·5H 2O

NASA Astrophysics Data System (ADS)

Sharma, Raj Pal; Singh, Ajnesh; Brandão, Paula; Felix, Vitor; Venugopalan, Paloth

2009-03-01

To explore the potential of [Co(phen) 2CO 3] + as anion receptor, red coloured single crystals of [Co(phen) 2CO 3](dnb)·5H 2O (dnb = 3,5-dinitrobenzoate) were obtained by recrystallizing the red microcrystalline product synthesised by the reaction of carbonatobis (1,10-phenanthroline)cobalt(III)chloride with sodium salt of 3,5-dinitrobenzoic acid in aqueous medium (1:1 molar ratio). The newly synthesized complex salt has been characterized by elemental analysis, spectroscopic studies (IR, UV/visible, 1H and 13C NMR), solubility and conductance measurements. The complex salt crystallizes in the triclinic crystal system with space group P1¯, having the cell dimensions a = 10.3140(8), b = 12.2885(11), c = 12.8747(13), α = 82.095(4), β = 85.617(4), γ = 79.221(4)°, V = 1585.6(2) Å 3, Z = 2. Single crystal X-ray structure determination revealed ionic structure consisting of cationic carbonatobis(1,10-phenanthroline)cobalt(III), dnb anion and five lattice water molecule. In the complex cation [Co(phen) 2CO 3] +, the cobalt(III) is bonded to four nitrogen atoms, originating from two phenanthroline ligands and two oxygen atoms from the bidentate carbonato group showing an octahedral geometry around cobalt(III) center. Supramolecular networks between ionic groups [ CHphen+⋯Xanion-] by second sphere coordination i.e. C sbnd H⋯O (benzoate), C sbnd H⋯O (nitro), C sbnd H⋯O (water) besides electrostatic forces of attraction alongwith π-π interactions stabilize the crystal lattice.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

Research of X-ray curved crystals analyzer

NASA Astrophysics Data System (ADS)

Xiao, Shali; Xong, Xian-cai; Qian, Jia-yu; Zhong, Xian-xin; Yan, Guo-hong; Liu, Zhong-li; Ding, Yong-kun

2005-08-01

X-ray spectrograph has long been used as a means of diagnosing conditions of laser-produced plasmas, as information concerning both the temperature and density can be extracted from the emitted radiation. For the measurement of X-ray lines in the energy range of 0.6-6 keV, A curved crystal X-ray spectrometer of reflection type elliptical geometry is required. In order to obtain both high resolution and collection efficiency the elliptical geometry is more advantageous than the flat configurations. Elliptical curved crystals spectrograph with a relatively wide spectral range are of particular use for deducing electron temperatures by measurement of the ratios of lines associated with different charge states. Curved crystals analyzer was designed and manufactured for use on an experiment to investigate the properties of laser produced plasmas. The spectrograph has 1350mm focal length and for these measurements, utilized PET, LIF, KAP and MICA crystal bent onto an elliptical substrate. This crystal analyzer covers the Bragg angel range from 30 to 67.5. The analyzer based on elliptically geometrical principle, which has self-focusing characteristics. The experiment was carried out on Shanghai Shengguang-II Facility and aimed to investigate the characteristics of a high density plasma. Experimental results using Curved crystal analyzer are described which show spectrum of Ti, Au laser-plasma. The focusing crystal analyzer clearly gave an increase in sensitivity over a flat crystal. Spectra showing the main resonance line were recorded with X-ray CCD and with laser energies 150J laser wavelength 350nm. The calculated wavelength resolution is about 500-1000.

Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiMattia,M.; Govindasamy, L.; Levy, H.

2005-01-01

Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Angstroms resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c =more » 629.7 Angstroms. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Effect of Sr doping on structural and magnetic behavior of SmBa1-xSrxCo2O5+δ (x = 0 and 1)

NASA Astrophysics Data System (ADS)

Kumari, Archana; Dhanasekhar, C.; Das, A. K.

2018-05-01

Layered double perovskite, SmBa1-xSrxCo2O5+δ (x = 0, δ = 0.5 and x = 1, δ = 1) samples were prepared by solid state reaction method. X-ray diffraction studies show that the SmBaCo2O5.5 sample crystallizes in the orthorhombic crystal structure with Pmmm space group, whereas SmSrCo2O6 sample crystallizes in the orthorhombic crystal structure with Pnma space group. The temperature dependent magnetization of the SmBaCo2O5.5 sample shows a paramagnetic (PM)-ferromagnetic (FM) and a FM-antiferromagnetic (AFM) transitions at TC = 267 K and TN = 221 K, respectively. In contrast, the SmSrCo2O6 sample shows a PM-FM transition at TC = 175 K. According to Goodenough-Kanamori-Anderson rules, the ferromagnetic behavior in SmSrCo2O6 can be understood from the super exchange interaction between the intermediate spin Co3+ and low spin Co4+ via O2- (IS Co3+ -O2- - LS Co4+). The change in magnetic entropy (ΔSMmax) is found to be maximum for the SmSrCo2O6 sample.

Radiation coloring of nonstoichiometric M(1-x)R(x)F(2+x) single crystals with a fluorite defect structure

NASA Astrophysics Data System (ADS)

Rustamov, Ia.; Tavshunskii, G. A.; Khabibullaev, P. K.; Bessonova, T. S.; Sobolev, B. P.

1985-06-01

Experimental results are reported concerning the radiation coloring of nonstoichiometric crystals of the M(1-x)R(x)F(2+x) type in the presence of fluorite defects. Samples of the crystals are cut using the Stockbarger technique in a chemically active fluoridating atmosphere generated by pyrolysis of tetrafluoroethylene. The samples were irradiated at 77 and 300 K using a Co-60 gamma-ray source and the total doses were in the range 10 to the 6th to 10 to the 7th roentgen. Absorption spectra of the crystals were analogous spectra for MF2-RF3 single crystals with RF 3 contents of less than 1 mole percent. It is shown that the properties of radiation coloring of the two types of crystal are very different: F-centers formed at 300 K in Ca(1-x)R(x) F(2+x), but not at 77 K. Complex color centers were observed at 77 K in Ca(1-x)R(x)F(2+x) single crystals and the intensity of the centers was determined by the competition among the electron trapping processes involving the r3(+) ions. It is concluded that the coloring characteristics of the M(1-x)R(x)F(2+x) crystals are related to their structural characteristics as compared with the MF2-RF3 crystals.

Dynamic X-ray diffraction sampling for protein crystal positioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction,more » significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by usingin situtwo-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure

Dynamic X-ray diffraction sampling for protein crystal positioning

PubMed Central

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye; Kissick, David J.; Zhang, Shijie; Newman, Justin A.; Sheedlo, Michael J.; Chowdhury, Azhad U.; Fischetti, Robert F.; Das, Chittaranjan; Buzzard, Gregery T.; Bouman, Charles A.; Simpson, Garth J.

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by

Dynamic X-ray diffraction sampling for protein crystal positioning.

PubMed

Scarborough, Nicole M; Godaliyadda, G M Dilshan P; Ye, Dong Hye; Kissick, David J; Zhang, Shijie; Newman, Justin A; Sheedlo, Michael J; Chowdhury, Azhad U; Fischetti, Robert F; Das, Chittaranjan; Buzzard, Gregery T; Bouman, Charles A; Simpson, Garth J

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by

Dynamic X-ray diffraction sampling for protein crystal positioning

DOE PAGES

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye; ...

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction,more » significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by usingin situtwo-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering.

PubMed

Cho, Hyun Sun; Dashdorj, Naranbaatar; Schotte, Friedrich; Graber, Timothy; Henning, Robert; Anfinrud, Philip

2010-04-20

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02-2.5 A(-1), thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 A), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 A(3) volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume approximately 2 A(3) larger than MbCO within approximately 10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

DOE PAGES

Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; ...

2015-06-27

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here in this study, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallizationmore » conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.« less

A short working distance multiple crystal x-ray spectrometer

USGS Publications Warehouse

Dickinson, B.; Seidler, G.T.; Webb, Z.W.; Bradley, J.A.; Nagle, K.P.; Heald, S.M.; Gordon, R.A.; Chou, I.-Ming

2008-01-01

For x-ray spot sizes of a few tens of microns or smaller, a millimeter-sized flat analyzer crystal placed ???1 cm from the sample will exhibit high energy resolution while subtending a collection solid angle comparable to that of a typical spherically bent crystal analyzer (SBCA) at much larger working distances. Based on this observation and a nonfocusing geometry for the analyzer optic, we have constructed and tested a short working distance (SWD) multicrystal x-ray spectrometer. This prototype instrument has a maximum effective collection solid angle of 0.14 sr, comparable to that of 17 SBCA at 1 m working distance. We find good agreement with prior work for measurements of the Mn K?? x-ray emission and resonant inelastic x-ray scattering for MnO, and also for measurements of the x-ray absorption near-edge structure for Dy metal using L??2 partial-fluorescence yield detection. We discuss future applications at third- and fourth-generation light sources. For concentrated samples, the extremely large collection angle of SWD spectrometers will permit collection of high-resolution x-ray emission spectra with a single pulse of the Linac Coherent Light Source. The range of applications of SWD spectrometers and traditional multi-SBCA instruments has some overlap, but also is significantly complementary. ?? 2008 American Institute of Physics.

Structure and magnetism in Co/X, Fe/Si, and Fe/(FeSi) multilayers

NASA Astrophysics Data System (ADS)

Franklin, Michael Ray

Previous studies have shown that magnetic behavior in multilayers formed by repeating a bilayer unit comprised of a ferromagnetic layer and a non-magnetic spacer layer can be affected by small structural differences. For example, a macroscopic property such as giant magnetoresistance (GMR) is believed to depend significantly upon interfacial roughness. In this study, several complimentary structural probes were used to carefully characterize the structure of several sputtered multilayer systems-Co/Ag, Co/Cu, Co/Mo, Fe/Si, and Fe//[FeSi/]. X-ray diffraction (XRD) studies were used to examine the long-range structural order of the multilayers perpendicular to the plane of the layers. Transmission electron diffraction (TED) studies were used to probe the long-range order parallel to the layer plane. X-ray Absorption Fine Structure (XAFS) studies were used to determine the average local structural environment of the ferromagnetic atoms. For the Co/X systems, a simple correlation between crystal structure and saturation magnetization is discovered for the Co/Mo system. For the Fe/X systems, direct evidence of an Fe-silicide is found for the /[FeSi/] spacer layer but not for the Si spacer layer. Additionally, differences were observed in the magnetic behavior between the Fe in the nominally pure Fe layer and the Fe contained in the /[FeSi/] spacer layers.

Crystals for astronomical X-ray spectroscopy

NASA Technical Reports Server (NTRS)

Burek, A.

1976-01-01

Crystal spectrometric properties and the factors that affect their measurement are discussed. Theoretical and experimental results on KAP are summarized and theoretical results based on the dynamical theory of X-ray diffraction are given for the acid phthalates as well as for the commonly used planes of ADP, PET and EDDT. Anomalous dispersion is found to be important for understanding the details of crystal Bragg reflection properties at long X-ray wavelengths and some important effects are pointed out. The theory of anomalous dispersion is applied to explain the anomalous reflectivity exhibited by KAP at 23.3 A.

X-ray Scintillation in Lead Halide Perovskite Crystals

PubMed Central

Birowosuto, M. D.; Cortecchia, D.; Drozdowski, W.; Brylew, K.; Lachmanski, W.; Bruno, A.; Soci, C.

2016-01-01

Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (EDBE)PbCl4 hybrid perovskite crystals. X-ray excited thermoluminescence measurements indicate the absence of deep traps and a very small density of shallow trap states, which lessens after-glow effects. All perovskite single crystals exhibit high X-ray excited luminescence yields of >120,000 photons/MeV at low temperature. Although thermal quenching is significant at room temperature, the large exciton binding energy of 2D (EDBE)PbCl4 significantly reduces thermal effects compared to 3D perovskites, and moderate light yield of 9,000 photons/MeV can be achieved even at room temperature. This highlights the potential of 2D metal halide perovskites for large-area and low-cost scintillator devices for medical, security and scientific applications. PMID:27849019

Studies on the syntheses, structural Characterization, antimicrobial of the CO-CRYSTAL 1,10-phenanthrolin-1-IUM(1,10-phenH+)-caffeine(caf)-hexafluorophosphate

NASA Astrophysics Data System (ADS)

El Hamdani, H.; El Amane, M.; Duhayon, C.

2018-03-01

Co-crystal of 1,10-phenanthrolin-1-ium-caffeine-hexafluorophosphate was synthesized, studied by FTIR, 1H, 13C NMR, DSC and X-ray structure and crystallized in the monoclinic space group C2/c. The unit cell parameters are a = 19.3761 (3), b = 17.9548 (3), c = 13.8074 (3) with β = 117.8132 (10). The final R value is 0.069 for 29,522 measured reflections. The co-crystal structure analysis indicate the 1,10-phenanthroline is protonated by one nitrogen atom and formed the 1,10-phenanthrolin-1-ium cation, which is stabilized by hydrogen bonds N+-H…Odbnd C interaction with carbonyl and imidazol ring in caffeine molecule. The intermolecular hydrogen bonds: Csbnd H...O, Csbnd H...N, Nsbnd H...O, Csbnd H...F and intramolecular hydrogen bond: C1sbnd H12...O14, together play a vital role in stabilizing the structure of co-crystal. The X-ray structural analysis confirm the assignments of the structure from infrared, 1H, 13C NMR, spectroscopic data DSC and molar conductivity analysis. The antimicrobial activity of the co-crystal was studied.

Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment.

PubMed

Panjikar, Santosh; Parthasarathy, Venkataraman; Lamzin, Victor S; Weiss, Manfred S; Tucker, Paul A

2005-04-01

The EMBL-Hamburg Automated Crystal Structure Determination Platform is a system that combines a number of existing macromolecular crystallographic computer programs and several decision-makers into a software pipeline for automated and efficient crystal structure determination. The pipeline can be invoked as soon as X-ray data from derivatized protein crystals have been collected and processed. It is controlled by a web-based graphical user interface for data and parameter input, and for monitoring the progress of structure determination. A large number of possible structure-solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. The processes have been optimized for speed so that the pipeline can be used effectively for validating the X-ray experiment at a synchrotron beamline.

Detailed transient heme structures of Mb-CO in solution after CO dissociation: an X-ray transient absorption spectroscopic study.

PubMed

Stickrath, Andrew B; Mara, Michael W; Lockard, Jenny V; Harpham, Michael R; Huang, Jier; Zhang, Xiaoyi; Attenkofer, Klaus; Chen, Lin X

2013-04-25

Although understanding the structural dynamics associated with ligand photodissociation is necessary in order to correlate structure and function in biological systems, few techniques are capable of measuring the ultrafast dynamics of these systems in solution-phase at room temperature. We present here a detailed X-ray transient absorption (XTA) study of the photodissociation of CO-bound myoglobin (Fe(II)CO-Mb) in room-temperature aqueous buffer solution with a time resolution of 80 ps, along with a general procedure for handling biological samples under the harsh experimental conditions that transient X-ray experiments entail. The XTA spectra of (Fe(II)CO-Mb) exhibit significant XANES and XAFS alterations following 527 nm excitation, which remain unchanged for >47 μs. These spectral changes indicate loss of the CO ligand, resulting in a five-coordinate, domed heme, and significant energetic reorganization of the 3d orbitals of the Fe center. With the current experimental setup, each X-ray pulse in the pulse train, separated by ~153 ns, can be separately discriminated, yielding snapshots of the myoglobin evolution over time. These methods can be easily applied to other biological systems, allowing for simultaneous structural and electronic measurements of any biological system with both ultrafast and slow time resolutions, effectively mapping out all of the samples' relevant physiological processes.

Implications of room temperature oxidation on crystal structure and exchange bias effect in Co/CoO nanoparticles

DOE PAGES

Feygenson, Mikhail; Formo, Eric V.; Freeman, Katherine; ...

2015-11-02

In this study, we describe how the exchange bias effect in Co/CoO nanoparticles depends on the size focusing and temperature treatment of precursor Co nanoparticles before oxidation at ambient conditions. By appealing to magnetization, microscopy, neutron and synchrotron x-ray measurements we found that as-synthesized Co nanoparticles readily oxidize in air only after 20 days. The highest exchange bias field of 814 Oe is observed at T = 2K. When the same nanoparticles are centrifuged and annealed at 70 °C in vacuum prior to oxidation, the exchange bias field is increased to 2570 Oe. Annealing of Co nanoparticles in vacuum improvesmore » their crystallinity and prevents complete oxidation, so that Co-core/CoO-shell structure is preserved even after 120 days. The crystal structure of CoO shell in both samples is different from its bulk counterpart. Implications of such distorted CoO shells on exchange bias are discussed. Coating of Co nanoparticles with amorphous silica shell makes them resistant to oxidation, but ultimately modifies the crystal structure of both Co core and SiO 2 shell.« less

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

PubMed Central

Anfinrud, Philip

2010-01-01

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them. PMID:20406909

Perfectly Cold Crystals: What Happens When They Are X-rayed?

NASA Technical Reports Server (NTRS)

vanderWoerd, Mark; Ferree, Darren S.; Snell, Edward H.

2003-01-01

For many macromolecular crystals the cryo-preservation of these crystals during X-ray data collection is of crucial importance, particularly at synchrotron facilities where the crystals rapidly receive a high dose of radiation. A practical variable to ensure adequate preservation is the variation of the cryo-protectant present when the crystal is preserved. Our initial approach to study X-ray diffraction data quality as a function of cryo-protectant present when preserving a xylose isomerase crystal shows that the data quality can be tremendously improved by recipe adjustment. Guided by crystal mosaicity estimates, we optimized crystal growth conditions to obtain cryo-preserved xylose isomerase crystals that withstand a very high dose of X-rays, with only the smallest amount of radiation damage at ultra-high resolution (1.2Angstroms). The rate at which damage occurs allowed us to collect a series of complete data sets, which show how the data degradation proceeds over time. We are here presenting data for the xylose isomerase crystallization recipe improvement and our interpretation of the crystal degradation process during X-ray data collection.

Growth and luminescent properties of Yb:YAG and Ca co-doped Yb:YAG ultrafast scintillation crystals

NASA Astrophysics Data System (ADS)

Zhu, Maodong; Qi, Hongji; Pan, Mingyan; Hou, Qing; Jiang, Benxue; Jin, Yaxue; Han, Hetong; Song, Zhaohui; Zhang, Hui

2018-05-01

In this work, Yb-doped Y3Al5O12 [yttrium aluminum garnet (YAG)] crystals and Ca co-doped Yb:YAG crystals were grown by the Czochralski (CZ) method. The chemical formulas of the two crystals are (Yb0.1Y0.9)3Al5O12 and (Ca0.001Yb0.1Y0.899)3Al5O12, respectively. The structural, optical and luminescent properties of the Yb:YAG and Ca, Yb:YAG crystals were investigated by X-ray rocking curve, X-ray diffraction, Raman spectra, UV-Visble-NIR absorption spectra and X-ray fluorescence. X-ray fluorescence spectrum with two emission peaks at 330 nm and 490 nm were observed in the two kinds of crystals, which would increase slightly after the annealing. Comparing to the Yb:YAG crystal, Ca co-doped Yb:YAG crystal behaved the better luminescent intensity without changing the crystal structure and vibrational modes. This indicates that by doping Ca2+ in Yb:YAG crystal may be an appropriate way to enhance the luminescent property of the scintillation crystal.

Correlation between the structural distortions and thermoelectric characteristics in La(1-x)A(x)CoO(3) (A = Ca and Sr).

PubMed

Wang, Yang; Sui, Yu; Ren, Peng; Wang, Lan; Wang, Xianjie; Su, Wenhui; Fan, Hong Jin

2010-04-05

Detailed structures and thermoelectric (TE) properties are investigated for the perovskite La(1-x)Ca(x)CoO(3) and La(1-x)Sr(x)CoO(3) with 0 x crystal structures for all samples are refined from powder X-ray diffraction, which reveals that the La(1-x)Sr(x)CoO(3) series has smaller global distortions but larger local distortions. The different structural distortions strongly influence the transport and TE properties in terms of resistivity, thermopower, thermal conductivity, bandwidth, and effective mass as well as electronic correlation. These results unambiguously demonstrate a close correlation between the structural distortions and TE characteristics in this family. Furthermore, a new approach is suggested to improve the TE performance by controlling the structure factors in such strongly correlated oxide systems. The effects of the spin-state transition of Co ions on the TE properties are also discussed.

Single crystal growth and structural evolution across the 1st order valence transition in (Pr1-yYy)1-xCaxCoO3-δ

NASA Astrophysics Data System (ADS)

Schreiber, N. J.; Zhang, Junjie; Zheng, Hong; Freeland, J. W.; Chen, Yu-Sheng; Mitchell, J. F.; Phelan, D.

2017-10-01

Praseodymium-containing cobalt perovskites, such as (Pr1-yYy)1-xCaxCoO3-δ, have been argued to undergo a first-order charge shift between Pr and hybridized Co-O orbitals that leads to a metal-insulator transition at a temperature, TVT. Magnetization and x-ray absorption spectroscopy measurements on single crystals of (Pr0.85Y0.15)0.7Ca0.3CoO3-δ grown in an IR image furnace under 40-60 bar of oxygen confirm the presence of this valence transition. Single crystal x-ray synchrotron diffraction measurements are consistent with an isomorphic phase transition at TVT. No evidence of charge ordering was revealed by the single crystal diffraction. Dissimilar to analytical transmission electron microscopy measurements performed on a grain from a polycrystalline sample that revealed an oxygen vacancy order-disorder transition at TVT, the present single-crystal measurements did not evidence such a transition, likely reflecting a lower density of oxygen vacancies in the high-pO2 grown single crystals.

Soft X-ray photoemission study of Co2(Cr1-xFex)Ga Heusler compounds

NASA Astrophysics Data System (ADS)

Tsunekawa, Masanori; Hattori, Yoshiro; Sekiyama, Akira; Fujiwara, Hidenori; Suga, Shigemasa; Muro, Takayuki; Kanomata, Takeshi; Imada, Shin

2015-08-01

We have performed soft X-ray photoemission spectroscopy (SXPES) and X-ray absorption spectroscopy (XAS) of the Co-based Heusler compounds Co2(Cr1-xFex)Ga (x = 0.0, 0.4, and 1.0) in order to study their electronic structures. Band-structure calculation was carried out and compared with the experimental results. SXPES spectra show hν-dependence, revealing the contributions of the Co, Cr, and Fe 3d electronic states in the valence band. The band width observed by the SXPES seems to be narrower than that predicted by the band-structure calculation. XAS spectra depend strongly on the the value of x in Co2(Cr1-xFex)Ga. The electron correlation effects are found to be stronger as x changes from 0.0 to 1.0.

Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

PubMed Central

Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

2016-01-01

For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties. PMID:27087141

Evolution of the magnetic and structural properties of Fe 1 - x Co x V 2 O 4

DOE PAGES

Sinclair, R.; Ma, Jie; Cao, H. B.; ...

2015-10-12

The magnetic and structural properties of single-crystal Fe 1-xCo xV 2O 4 samples have been investigated by performing specific heat, susceptibility, neutron diffraction, and x-ray diffraction measurements. As the orbital-active Fe 2+ ions with larger ionic size are gradually substituted by the orbital-inactive Co 2+ ions with smaller ionic size, the system approaches the itinerant electron limit with decreasing V-V distance. Then, various factors such as the Jahn-Teller distortion and the spin-orbital coupling of the Fe 2+ ions on the A sites and the orbital ordering and electronic itinerancy of the V 3+ ions on the B sites compete withmore » each other to produce a complex magnetic and structural phase diagram. Finally, this phase diagram is compared to those of Fe 1-xMn xV 2O 4 and Mn 1-xCo xV 2O 4 to emphasize several distinct features.« less

Local structure and X-ray magnetic circular dichroism of Au in Au-Co nanoalloys

NASA Astrophysics Data System (ADS)

Maurizio, C.; Michieli, N.; Kalinic, B.; Mattarello, V.; Bello, V.; Wilhelm, F.; Ollefs, K.; Mattei, G.

2018-03-01

Coupling a plasmonic metal with a magnetic one in thin films and nanostructures is very interesting for the emerging field of magnetoplasmonics. In particular, coupling through alloying is a promising strategy to induce a magnetic moment on the plasmonic metal atoms, in a way that is intimately related to the local structure of the (metastable) alloy material. In this framework, Au:Co bimetallic films have been produced via magnetron co-sputtering deposition. X-ray absorption spectroscopy (XAS) at both Au- and Co-edges clearly indicates the formation of a full-metallic layer composed for the major part of a binary AuxCo1-x alloy, with x = 0.7-0.8. XAS and transmission electron microscopy analyses suggest the presence of a minor fraction of segregated metals. X-ray magnetic circular dichroism (XMCD) analysis at Au L2,3 edges detected a net magnetic moment of Au atoms (μ = 0.06 μB), significantly larger (≈3.5 times) that the one for Au-capped Co nanoclusters and comparable to the one for a Co-rich Au/Co multilayer, despite the 4 times larger concentration of Co with respect to the present case. This Au-Co magnetic coupling is favored by a high degree of mixing of the two metals in the alloy.

X-ray Crystallography Facility

NASA Technical Reports Server (NTRS)

2000-01-01

Edward Snell, a National Research Council research fellow at NASA's Marshall Space Flight Center (MSFC), prepares a protein crystal for analysis by x-ray crystallography as part of NASA's structural biology program. The small, individual crystals are bombarded with x-rays to produce diffraction patterns, a map of the intensity of the x-rays as they reflect through the crystal.

X-ray characterization of curved crystals for hard x-ray astronomy

NASA Astrophysics Data System (ADS)

Buffagni, Elisa; Bonnini, Elisa; Ferrari, Claudio; Virgilli, Enrico; Frontera, Filippo

2015-05-01

Among the methods to focus photons the diffraction in crystals results as one of the most effective for high energy photons. An assembling of properly oriented crystals can form a lens able to focus x-rays at high energy via Laue diffraction in transmission geometry; this is a Laue lens. The x-ray diffraction theory provides that the maximum diffraction efficiency is achieved in ideal mosaic crystals, but real mosaic crystals show diffraction efficiencies several times lower than the ideal case due to technological problems. An alternative and convenient approach is the use of curved crystals. We have recently optimized an efficient method based on the surface damage of crystals to produce self-standing uniformly curved Si, GaAs and Ge tiles of thickness up to 2-3 mm and curvature radii R down to a few meters. We show that, for curved diffracting planes, such crystals have a diffraction efficiency nearly forty times higher than the diffraction efficiency of perfect similar flat crystals, thus very close to that of ideal mosaic crystals. Moreover, in an alternative configuration where the diffracting planes are perpendicular to the curved ones, a focusing effect occurs and will be shown. These results were obtained for several energies between 17 and 120 keV with lab sources or at high energy facilities such as LARIX at Ferrara (Italy), ESRF at Grenoble (France), and ANKA at Karlsruhe (Germany).

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

PubMed Central

Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Wan, Frank; Sheraden, Paige N.; Broecker, Jana; Ernst, Oliver P.; Gennis, Robert B.

2017-01-01

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å. PMID:28469762

Long Periodic Structure of a Room-Temperature Ionic Liquid by High-Pressure Small-Angle X-Ray Scattering and Wide-Angle X-Ray Scattering: 1-Decyl-3-Methylimidazolium Chloride.

PubMed

Abe, Hiroshi; Hamaya, Nozomu; Koyama, Yoshihiro; Kishimura, Hiroaki; Takekiyo, Takahiro; Yoshimura, Yukihiro; Wakabayashi, Daisuke; Funamori, Nobumasa; Matsuishi, Kiyoto

2018-04-23

The Bragg reflections of 1-decyl-3-methylimidazolium chloride ([C 10 mim][Cl]), a room-temperature ionic liquid, are observed in a lowly scattered wavevector (q) region using high-pressure (HP) small-angle X-ray scattering methods. The HP crystal of [C 10 mim][Cl] was characterized by an extremely long periodic structure. The peak position at the lowest q (1.4 nm -1 ) was different from that of the prepeak observed in the liquid state (2.3 nm -1 ). Simultaneously, Bragg reflections at high-q were detected using HP wide-angle X-ray scattering. The longest lattice constant was estimated to be 4.3 nm using structural analysis. The crystal structure of HP differed from that of the low-temperature (LT) crystal and the LT liquid crystal. With increasing pressure, Bragg reflections in the high-q component became much broader, and were accompanied by phase transition, although those in the low-q component were observed to be relatively sharp. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated β-lactam antibiotic

DOE PAGES

Lewandowski, Eric M.; Skiba, Joanna; Torelli, Nicholas J.; ...

2015-03-02

We have determined a 1.18 Å resolution X-ray crystal structure of a novel ruthenocenyle-6-aminopenicillinic acid in complex with CTX-M β-lactamase, showing unprecedented details of interactions between ruthenocene and protein. As the first product complex with an intact catalytic serine, the structure also offers insights into β-lactamase catalysis and inhibitor design.

X-ray diffraction analysis of LiCu{sub 2}O{sub 2} crystals with additives of silver atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirotinkin, V. P., E-mail: irotinkin.vladimir@mail.ru; Bush, A. A.; Kamentsev, K. E.

2015-09-15

Silver-containing LiCu{sub 2}O{sub 2} crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20{sub x}AgNO{sub 3} · 20Li{sub 2}CO{sub 3} (0 ≤ x ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu{sub 2}O{sub 2} structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter c of the LiCu{sub 2}O{submore » 2} rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b.« less

Crystal structure and magnetic properties of Mn substituted ludwigite Co 3O 2BO 3

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Ivanova, N. B.; Kazak, N. V.; Platunov, M. S.; Bezmaternykh, L. N.; Velikanov, D. А.; Vasiliev, А. D.; Ovchinnikov, S. G.; Yurkin, G. Yu.

2012-03-01

The needle shape single crystals Co3-x MnxO2BO3 with ludwigite structure have been prepared. According to the X-ray diffraction data the preferable character of distinct crystallographic positions occupation by Mn ions is established. Magnetization field and temperature dependencies are measured. Paramagnetic Curie temperature value Θ=-100 K points out the predominance of antiferromagnetic interactions. Spin-glass magnetic ordering takes the onset at TN=41 K. The crystallographic and magnetic properties of Co3O2BO3:Mn are compared with the same for the isostructural analogs Co3O2BO3 and CoO2BO3:Fe.

Synthesis and X-ray crystal structure determination of N- p-methylphenyl-4-benzoyl-3,4-diphenyl-2-azetidinone

NASA Astrophysics Data System (ADS)

Kabak, Mehmet; Şenöz, Hülya; Elmali, Ayhan; Adar, Vildan; Svoboda, Ingrid; Dušek, Michal; Fejfarová, Karla

2010-12-01

The title compound, C29H23NO2, has been characterized by single-crystal X-ray diffraction at two different temperatures (303 K and 120 K) and wavelengths (Mo K α and Cu K α). The non-centrosymmetric hexagonal crystal structure contains four-membered planar β-lactam ring with an unusually long C-C bond. The β-lactam ring is almost planar.

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

X-ray evaluation of crystals for stellar spectrometers

NASA Technical Reports Server (NTRS)

Alexandropolos, N. G. (Editor)

1974-01-01

The report consists of three parts. The first part is an analysis of the principles involved in X-ray crystal evaluation and how they are applied to a number of crystals. The principles of crystal evaluation analysis as they apply to the special problems of X-ray astronomy are presented. A number of crystals were evaluated, and the energy dependence of the diffraction properties of (002) PET, (111) Ge, (101) ADP, (001) KAP, and (001) RAP are reported. The second part is a compilation of the diffraction properties of a number of crystals as reported by other authors. In the third part some technical details of a triple crystal spectrometer built by the author at Polytechnic Institute of Brooklyn are given. This spectrometer seems to be a most appropriate instrument for evaluation of crystal properties. (Modified author abstract)

Structural, quantum chemical, vibrational and thermal studies of a hydrogen bonded zwitterionic co-crystal (nicotinic acid: pyrogallol)

NASA Astrophysics Data System (ADS)

Prabha, E. Arockia Jeya Yasmi; Kumar, S. Suresh; Athimoolam, S.; Sridhar, B.

2017-02-01

In the present work, a new co-crystal of nicotinic acid with pyrogallol (NICPY) has been grown in the zwitterionic form and the corresponding structural, vibrational, thermal, solubility and anti-cancer characteristics have been reported. The single crystal X-ray diffraction analysis confirms that the structural molecular packing of the crystal stabilized through N-H⋯O and O-H⋯O hydrogen bond. The stabilization energy of the hydrogen bond motifs were calculated in the solid state. Vibrational spectral studies such as Fourier transform-infrared (FT-IR) and FT-Raman were adopted to understand the zwitterionic co-crystalline nature of the compound, which has been compared with theoretically calculated vibrational frequencies. The thermal stability of the grown co-crystal was analyzed by TG/DTA study. The solubility of the NICPY co-crystal was investigated in water at different temperature and compared with that of the nicotinic acid, which is the parent compound of NICPY co-crystal. The grown crystals were treated with human cervical cancer cell line (HeLa) to analyze the cytotoxicity of NICPY crystals and compared with the parent compound, which shows that NICPY has moderate activity against human cervical cancer cell line.

Protein crystallization: Eluding the bottleneck of X-ray crystallography

PubMed Central

Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

2017-01-01

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

Single-crystal sapphire microstructure for high-resolution synchrotron X-ray monochromators

DOE PAGES

Asadchikov, Victor E.; Butashin, Andrey V.; Buzmakov, Alexey V.; ...

2016-03-22

We report on the growth and characterization of several sapphire single crystals for the purpose of x-ray optics applications. Structural defects were studied by means of laboratory double-crystal X-ray diffractometry and white beam synchrotron-radiation topography. The investigations confirmed that the main defect types are dislocations. The best quality crystal was grown using the Kyropoulos technique with a dislocation density of 10 2-10 3 cm -2 and a small area with approximately 2*2 mm 2 did not show dislocation contrast in many reflections and has suitable quality for application as a backscattering monochromator. As a result, a clear correlation between growthmore » rate and dislocation density is observed, though growth rate is not the only parameter impacting the quality.« less

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis.

PubMed

Suganuma, Masatoshi; Teh, Aik Hong; Makino, Masatomo; Shimizu, Nobutaka; Kaneko, Tomonori; Hirata, Kunio; Yamamoto, Masaki; Kumasaka, Takashi

2009-11-01

RsbX from Bacillus subtilis is a manganese-dependent PPM phosphatase and negatively regulates the signal transduction of the general stress response by the dephosphorylation of RsbS and RsbR, which are activators of the alternative RNA polymerase sigma factor SigB. In order to elucidate the structural-functional relationship of its Ser/Thr protein-phosphorylation mechanism, an X-ray crystallographic diffraction study of RsbX was performed. Recombinant RsbX was expressed in Escherichia coli, purified and crystallized. Crystals were obtained using the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 1.06 angstrom resolution with an R(merge) of 8.1%. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 33.3, b = 41.7, c = 68.6 angstrom , alpha = 98.8, beta = 90.0, gamma = 108.4 degrees.

Magnetic properties of Co 2 2+ Co 1 - x 3+ Fe x 3+ BO5 ( x = 0.10) single crystals with a ludwigite structure

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Kazak, N. V.; Bayukov, O. A.; Platunov, M. S.; Velikanov, D. A.; Bezmaternykh, L. N.; Ivanova, N. B.; Ovchinnikov, S. G.

2017-04-01

The investigation of mixed Co-Fe ludwigite single crystals shows that their magnetic properties are close to the magnetic properties of Fe3BO5 despite the predominance of cobalt ions. The magnetic properties of Co3 - x Fe x BO5 single crystals with x = 0.10 are studied in detail. Magnetometric measurements demonstrate a strong magnetic anisotropy with easy magnetization axis b, and the orbital magnetic moment of cobalt is in a frozen state. The detected temperature dependence of the absorption of Mössbauer spectra allowed us to determine the magnetic ordering temperature, which agrees with the results of magnetization measurements ( T C = 84 K).

Crystal structure and magnetism of the FexNi8-xSi3 materials, 0 ≤ x ≤ 8

NASA Astrophysics Data System (ADS)

Gallus, Simone; Haddouch, Mohammed Ait; Chikovani, Mamuka; Perßon, Jörg; Voigt, Jörg; Friese, Karen; Senyshyn, Anatoliy; Grzechnik, Andrzej

2018-02-01

The crystal structure and magnetic properties of the materials FexNi8-xSi3 with 0 ≤ x ≤ 8 have been investigated to estimate any possible magnetocaloric effect and compare it to that in known magnetocalorics. Two structural ranges could be identified in this system by X-ray and neutron diffraction. The structure of the samples with 0 ≤ x ≤ 4 is related to the trigonal structure of Ni31Si12. Doubled c lattice parameters compared to the one in Ni31Si12 are observed in the samples with x = 2 and x = 3. The average structure of Fe2Ni6Si3 has been determined by X-ray single-crystal diffraction. The compounds with the compositions 5 ≤ x ≤ 8 crystallize in cubic Fe3Si-type structure. Magnetic measurements have shown that the compound Fe3Ni5Si3 displays a phase transition close to room temperature. However, its magnetocaloric effect is much smaller than the one in the promising magnetocaloric materials.

X-ray rocking curve measurements of bent crystals. [used in High Resolution Spectrometer in Advanced X-ray Astrophysics Facility

NASA Technical Reports Server (NTRS)

Hakim, M. B.; Muney, W. S.; Fowler, W. B.; Woodgate, B. E.

1988-01-01

A three-crystal laboratory X-ray spectrometer is used to measure the Bragg reflection from concave cylindrically curved crystals to be used in the high-resolution X-ray spectrometer of the NASA Advanced X-ray Astrophysics Facility (AXAF). The first two crystals, in the dispersive (1.1) arrangement, select a narrow collimated monochromatic beam in the Cu K-alpha(1) line at 1.5 A (8.1 keV), which illuminates the test crystal. The angular centroids of rocking curves measured along the surface provide a measure of the conformity of the crystal to the desired radius of curvature. Individual and combined rocking-curve widths and areas provide a measure of the resolution and efficiency at 1.54 A. The crystals analyzed included LiF(200), PET, and acid phthalates such as TAP.

Two-dimensional single crystal diamond refractive x-ray lens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antipov, S., E-mail: s.antipov@euclidtechlabs.com; Baryshev, S. V.; Butler, J. E.

2016-07-27

The next generation light sources such as diffraction-limited storage rings and high repetition rate x-ray free-electron lasers will generate x-ray beams with significantly increased brilliance. These future machines will require X-ray optical components that are capable of handling higher instantaneous and average power densities while tailoring the properties of the x-ray beams for a variety of scientific experiments. Single crystal diamond is one of the best bulk materials for this application, because it is radiation hard, has a suitable uniform index of refraction and the best available thermal properties. In this paper we report on fabrication and experimental testing ofmore » a two-dimensional (2D) single crystal diamond compound refractive X-ray lenses (CRL). These lenses were manufactured using femto-second laser cutting and tested at the Advanced Photon Source of Argonne National Laboratory.« less

Production, purification, crystallization and preliminary X-ray analysis of adeno-associated virus serotype 8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, Michael Douglas; Nam, Hyun-Joo; Padron, Eric

2005-06-01

The production, purification, crystallization and preliminary X-ray crystallographic analysis of adeno-associated virus serotype 8 is reported. Adeno-associated viruses (AAVs) are actively being developed for clinical gene-therapy applications and the efficiencies of the vectors could be significantly improved by a detailed understanding of their viral capsid structures and the structural determinants of their tissue-transduction interactions. AAV8 is ∼80% identical to the more widely studied AAV2, but its liver-transduction efficiency is significantly greater than that of AAV2 and other serotypes. The production, purification, crystallization and preliminary X-ray crystallographic analysis of AAV8 viral capsids are reported. The crystals diffract X-rays to 3.0 Åmore » resolution using synchrotron radiation and belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = 257.5, c = 443.5 Å. The unit cell contains two viral particles, with ten capsid viral protein monomers per crystallographic asymmetric unit.« less

Covering complete proteomes with X-ray structures: A current snapshot

DOE PAGES

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

2014-10-23

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

3D coherent X-ray diffractive imaging of an Individual colloidal crystal grain

NASA Astrophysics Data System (ADS)

Shabalin, A.; Meijer, J.-M.; Sprung, M.; Petukhov, A. V.; Vartanyants, I. A.

Self-assembled colloidal crystals represent an important model system to study nucleation phenomena and solid-solid phase transitions. They are attractive for applications in photonics and sensorics. We present results of a coherent x-ray diffractive imaging experiment performed on a single colloidal crystal grain. The full three-dimensional (3D) reciprocal space map measured by an azimuthal rotational scan contained several orders of Bragg reflections together with the coherent interference signal between them. Applying the iterative phase retrieval approach, the 3D structure of the crystal grain was reconstructed and positions of individual colloidal particles were resolved. We identified an exact stacking sequence of hexagonal close-packed layers including planar and linear defects. Our results open up a breakthrough in applications of coherent x-ray diffraction for visualization of the inner 3D structure of different mesoscopic materials, such as photonic crystals. Present address: University of California - San Diego, USA.

Crystal structure and X-ray photoemission spectroscopic study of A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, Alo, E-mail: alo_dutta@yahoo.com; Saha, Sujoy; Kumari, Premlata

2015-09-15

The X-ray photoemission spectroscopic (XPS) study of the double perovskite oxides A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta] synthesized by the solid-state reaction technique has been carried out to investigate the nature of the chemical state of the constituent ions and the bonding between them. The Rietveld refinement of the X-ray diffraction patterns suggests the monoclinic crystal structure of all the materials at room temperature. The negative and positive chemical shifts of the core level XPS spectrum of O-1s and Nb-3d{sub 3/2}/Ta-4f{sub 5/2} respectively suggest the covalent bonding between Nb/Ta cations and O ion. The change of the bonding strengthmore » between the anion and the cations from one material to another has been analyzed. The vibrational property of the materials is investigated using the room temperature Raman spectra. A large covalency of Ta-based compound than Nb compound is confirmed from the relative shifting of the Raman modes of the materials. - Graphical abstract: Crystal structure of two perovskite oxides CLN and CLT is investigated. XPS study confirms the two different co-ordination environments of Ca and covalent bonding between B-site cations and O-ion. - Highlights: • Ordered perovskite structure obtained by Rietveld refinement of XRD patterns. • Study of nature of chemical bonding by X-ray photoemission spectroscopy. • Opposite chemical shift of d-states of Nb/Ta with respect to O. • Covalent bonding between d-states of Nb/Ta and O. • Relative Raman shifts of CLN and CLT substantiate the more covalent character of Ta than Nb.« less

Correct interpretation of diffraction properties of quartz crystals for X-ray optics applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Xian-Rong; Gog, Thomas; Kim, Jungho

Quartz has hundreds of strong Bragg reflections that may offer a great number of choices for making fixed-angle X-ray analyzers and polarizers at virtually any hard X-ray energies with selectable resolution. However, quartz crystals, unlike silicon and germanium, are chiral and may thus appear in two different forms of handedness that are mirror images. Furthermore, because of the threefold rotational symmetry along thecaxis, the {h 1h 2h 3L} and {h 2h 1h 3L} Bragg reflections may have quite different Darwin bandwidth, reflectivity and angular acceptance, although they have the same Bragg angle. The design of X-ray optics from quartz crystalsmore » therefore requires unambiguous determination of the orientation, handedness and polarity of the crystals. The Laue method and single-axis diffraction technique can provide such information, but the variety of conventions used in the literature to describe quartz structures has caused widespread confusion. The current studies give detailed guidelines for design and fabrication of quartz X-ray optics, with special emphasis on the correct interpretation of Laue patterns in terms of the crystallography and diffraction properties of quartz. Meanwhile, the quartz crystals examined were confirmed by X-ray topography to have acceptably low densities of dislocations and other defects, which is the foundation for developing high-resolution quartz-based X-ray optics.« less

Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

DOE PAGES

Dao, E. Han; Sierra, Raymond G.; Laksmono, Hartawan; ...

2015-04-30

In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecondmore » X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.« less

Acemetacin cocrystal structures by powder X-ray diffraction.

PubMed

Bolla, Geetha; Chernyshev, Vladimir; Nangia, Ashwini

2017-05-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p -aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM-NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid-amide dimer three-point synthon R 3 2 (9) R 2 2 (8) R 3 2 (9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM-NAM, ACM-NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study.

Acemetacin cocrystal structures by powder X-ray diffraction

PubMed Central

Bolla, Geetha

2017-01-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R 3 2(9)R 2 2(8)R 3 2(9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study. PMID:28512568

The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

PubMed

Guizard, C; Chanzy, H; Sarko, A

1985-06-05

The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

PubMed Central

Sawaya, Michael R.; Cascio, Duilio; Gingery, Mari; Rodriguez, Jose; Goldschmidt, Lukasz; Colletier, Jacques-Philippe; Messerschmidt, Marc M.; Boutet, Sébastien; Koglin, Jason E.; Williams, Garth J.; Brewster, Aaron S.; Nass, Karol; Hattne, Johan; Botha, Sabine; Doak, R. Bruce; Shoeman, Robert L.; DePonte, Daniel P.; Park, Hyun-Woo; Federici, Brian A.; Sauter, Nicholas K.; Schlichting, Ilme; Eisenberg, David S.

2014-01-01

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information. PMID:25136092

Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santos-Silva, Teresa; Trincão, José; Carvalho, Ana L.

2005-11-01

Superoxide reductase is a non-haem iron-containing protein involved in resistance to oxidative stress. The oxidized form of the protein has been crystallized and its three-dimensional structure solved. A highly redundant X-ray diffraction data set was collected on a rotating-anode generator using Cu Kα X-ray radiation. Four Fe atoms were located in the asymmetric unit corresponding to four protein molecules arranged as a dimer of homodimers. Superoxide reductase is a 14 kDa metalloprotein containing a catalytic non-haem iron centre [Fe(His){sub 4}Cys]. It is involved in defence mechanisms against oxygen toxicity, scavenging superoxide radicals from the cell. The oxidized form of Treponemamore » pallidum superoxide reductase was crystallized in the presence of polyethylene glycol and magnesium chloride. Two crystal forms were obtained depending on the oxidizing agents used after purification: crystals grown in the presence of K{sub 3}Fe(CN){sub 6} belonged to space group P2{sub 1} (unit-cell parameters a = 60.3, b = 59.9, c = 64.8 Å, β = 106.9°) and diffracted beyond 1.60 Å resolution, while crystals grown in the presence of Na{sub 2}IrCl{sub 6} belonged to space group C2 (a = 119.4, b = 60.1, c = 65.6 Å, β = 104.9°) and diffracted beyond 1.55 Å. A highly redundant X-ray diffraction data set from the C2 crystal form collected on a copper rotating-anode generator (λ = 1.542 Å) clearly defined the positions of the four Fe atoms present in the asymmetric unit by SAD methods. A MAD experiment at the iron absorption edge confirmed the positions of the previously determined iron sites and provided better phases for model building and refinement. Molecular replacement using the P2{sub 1} data set was successful using a preliminary trace as a search model. A similar arrangement of the four protein molecules could be observed.« less

Synthesis, X-ray crystal structures and thermal analyses of some new antimicrobial zinc complexes: New configurations and nano-size structures.

PubMed

Masoudiasl, A; Montazerozohori, M; Naghiha, R; Assoud, A; McArdle, P; Safi Shalamzari, M

2016-04-01

Some new five coordinated ZnLX2 complexes, where L is N3-Schiff base ligand obtained by condensation reaction between diethylenetriamine and (E)-3-(2-nitrophenyl)acrylaldehyde and X (Cl(-), Br(-), I(-), N3(-) and NCS(-)), were synthesized and characterized by FT-IR, (1)H and (13)CNMR, UV-visible, ESI-mass spectra and molar conductivity measurements. The structures of zinc iodide and thiocyanate complexes were determined by X-ray crystallographic analysis. The X-ray results showed that the Zn (II) center in these complexes is five-coordinated in a distorted trigonal-bipyramidal configuration. Zinc iodide and thiocyanate complexes crystallize in the monoclinic and triclinic systems with space groups of C2/c and P1- with eight and two molecules per unit cell respectively. The crystal packing of the complexes consists of intermolecular interactions such as C-H(…)O and C-H(…)I, C-H(···)S, N(…)O, together with π-π stacking and some other unexpected interactions. The mentioned interactions cause three-dimensional supramolecular structure in the solid state. Zinc complexes were also prepared in nano-structure by sonochemical method confirmed by XRD, SEM and TEM analyses. Moreover, ZnO nanoparticles were synthesized by direct thermolysis of zinc iodide complex. Furthermore, antimicrobial and thermal properties of the compounds were completely investigated. Copyright © 2016 Elsevier B.V. All rights reserved.

Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.

PubMed

Du, Wen-Ge Han; Noodleman, Louis

2013-12-16

Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.

A multi-cone x-ray imaging Bragg crystal spectrometer

DOE PAGES

Bitter, M.; Hill, K. W.; Gao, Lan; ...

2016-08-26

This article describes a new x-ray imaging Bragg crystal spectrometer, which—in combination with a streak camera or a gated strip detector—can be used for time-resolved measurements of x-ray line spectra at the National Ignition Facility and other high power laser facilities. The main advantage of this instrument is that it produces perfect images of a point source for each wavelength in a selectable spectral range and that the detector plane can be perpendicular to the crystal surface or inclined by an arbitrary angle with respect to the crystal surface. Furthermore, these unique imaging properties are obtained by bending the x-raymore » diffracting crystal into a certain shape, which is generated by arranging multiple cones with different aperture angles on a common nodal line.« less

Hydrothermal Synthesis, Crystal Structure, and Photoluminescent Properties of Li[UO2(CH3COO)3]3[Co(H2O)6

NASA Astrophysics Data System (ADS)

AlDamen, Murad A.; Juwhari, Hassan K.; Al-zuheiri, Aya M.; Alnazer, Louy A.

2017-12-01

Single crystal of Li[UO2(CH3COO)3]3[Co(H2O)6] was prepared and found to crystallize in the monoclinic crystal system in the sp. gr. C2/ c, with Z = 2, and unit cell parameters a = 22.1857(15) Å, b = 13.6477(8) Å, c = 15.6921(10) Å, β = 117.842(9)°, V = 4201.3(4) Å3. The crystal was characterized by X-ray diffraction, Fourier transform infrared spectroscopy, and differential scanning calorimetry. The single crystal X-ray diffraction analysis revealed that the crystal has a lamellar structure in which a cobalt hydrate is sandwiched within the Li[UO2(CH3COO)3]3 2- chains. Furthermore, the room temperature photoluminescence spectrum of the complex was investigated in the solid state.

Cu{sub 2}Mn{sub 1-x}Co{sub x}SnS{sub 4}: Novel keesterite type solid solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez-Vergara, F., E-mail: fer_martina@u.uchile.cl; Galdamez, A., E-mail: agaldamez@uchile.cl; Manriquez, V.

2013-02-15

A new family of Cu{sub 2}Mn{sub 1-x}Co{sub x}SnS{sub 4} chalcogenides has been synthesized by conventional solid-state reactions at 850 Degree-Sign C. The reactions products were characterized by powder X-ray diffraction (XRD), energy-dispersive X-ray analysis (SEM-EDS), Raman spectroscopy and magnetic susceptibility. The crystal structures of two members of the solid solution series Cu{sub 2}Mn{sub 0.4}Co{sub 0.6}SnS{sub 4} and Cu{sub 2}Mn{sub 0.2}Co{sub 0.8}SnS{sub 4} have been determined by single-crystal X-ray diffraction. Both phases crystallize in the tetragonal keesterite-type structure (space group I4{sup Macron }). The distortions of the tetrahedral volume of Cu{sub 2}Mn{sub 0.4}Co{sub 0.6}SnS{sub 4} and Cu{sub 2}Mn{sub 0.2}Co{sub 0.8}SnS{sub 4}more » were calculated and compared with the corresponding differences in the Cu{sub 2}MnSnS{sub 4} (stannite-type) end-member. The compounds show nearly the same Raman spectral features. Temperature-dependent magnetization measurements (ZFC/FC) and high-temperature susceptibility indicate that these solid solutions are antiferromagnetic. - Graphical abstract: View along [100] of the Cu{sub 2}Mn{sub 1-x}Co{sub x}SnS{sub 4} structure showing tetrahedral units and magnetic measurement ZFC-FC at 500 Oe. The insert shows the 1/{chi}-versus-temperature plot fitted by a Curie-Weiss law. Highlights: Black-Right-Pointing-Pointer Cu{sub 2}Mn{sub 1-x}Co{sub x}SnS{sub 4} solid solutions belong to the family of compounds adamantine. Black-Right-Pointing-Pointer Resolved single crystals of the solid solutions have space group I4{sup Macron }. Black-Right-Pointing-Pointer The distortion of the tetrahedral volume of Cu{sub 2}Mn{sub 1-x}Co{sub x}SnS{sub 4} were calculated. Black-Right-Pointing-Pointer These solid solutions are antiferromagnetic.« less

X-ray Spectropolarimetry of Z-pinch Plasmas with a Single-Crystal Technique

NASA Astrophysics Data System (ADS)

Wallace, Matt; Haque, Showera; Neill, Paul; Pereira, Nino; Presura, Radu

2017-10-01

When directed beams of energetic electrons exist in a plasma the resulting x-rays emitted by the plasma can be partially polarized. This makes plasma x-ray polarization spectroscopy, spectropolarimetry, useful for revealing information about the anisotropy of the electron velocity distribution. X-ray spectropolarimetry has indeed been used for this in both space and laboratory plasmas. X-ray polarization measurements are typically performed employing two crystals, both at a 45° Bragg angle. A single-crystal spectropolarimeter can replace two crystal schemes by utilizing two matching sets of internal planes for polarization-splitting. The polarization-splitting planes diffract the incident x-rays into two directions that are perpendicular to each other and the incident beam as well, so the two sets of diffracted x-rays are linearly polarized perpendicularly to each other. An X-cut quartz crystal with surface along the [11-20] planes and a paired set of [10-10] planes in polarization-splitting orientation is now being used on aluminum z-pinches at the University of Nevada, Reno. Past x-ray polarization measurements have been reserved for point-like sources. Recently a slotted collimating aperture has been used to maintain the required geometry for polarization-splitting enabling the spectropolarimetry of extended sources. The design of a single-crystal x-ray spectropolarimeter and experimental results will be presented. Work was supported by U.S. DOE, NNSA Grant DE-NA0001834 and cooperative agreement DE-FC52-06NA27616.

Enhanced light extraction of scintillator using large-area photonic crystal structures fabricated by soft-X-ray interference lithography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Zhichao; Wu, Shuang; Liu, Bo, E-mail: lbo@tongji.edu.cn

2015-06-15

Soft-X-ray interference lithography is utilized in combination with atomic layer deposition to prepare photonic crystal structures on the surface of Bi{sub 4}Ge{sub 3}O{sub 12} (BGO) scintillator in order to extract the light otherwise trapped in the internal of scintillator due to total internal reflection. An enhancement with wavelength- and emergence angle-integration by 95.1% has been achieved. This method is advantageous to fabricate photonic crystal structures with large-area and high-index-contrast which enable a high-efficient coupling of evanescent field and the photonic crystal structures. Generally, the method demonstrated in this work is also suitable for many other light emitting devices where amore » large-area is required in the practical applications.« less

Crystallization and preliminary X-ray analysis of copper amine oxidase from Escherichia coli K-12.

PubMed

Roh, J H; Suzuki, H; Kumagai, H; Yamashita, M; Azakami, H; Murooka, Y; Mikami, B

1994-05-13

Copper-containing monoamine oxidase (MAO) from Escherichia coli was overproduced in the periplasmic space by expression of the cloned gene. The purified MAO has been crystallized by means of the hanging drop technique using sodium citrate as a precipitant. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit cell dimensions of a = 136.1 A, b = 168.4 A and c = 81.6 A. The asymmetric unit contains one molecule of MAO, with a crystal volume per protein mass (Vm) of 2.88 A3/Da and a solvent content of 58% by volume. The crystals diffract X-rays to a resolution limit of at least 2.7 A and are resistant to X-ray radiation damage. They appear to be suitable for X-ray structure analysis.

X-ray absorption fine structure (XAFS) spectroscopy using synchrotron radiation

NASA Astrophysics Data System (ADS)

Shrivastava, B. D.

2012-05-01

The X-ray absorption fine structure (XAFS) spectra are best recorded when a highly intense beam of X-rays from a synchrotron is used along with a good resolution double crystal or curved crystal spectrometer and detectors like ionization chambers, scintillation counters, solid state detectors etc. Several synchrotrons around the world have X-ray beamlines dedicated specifically to XAFS spectroscopy. Fortunately, the Indian synchrotron (Indus-2) at Raja Ramanna Centre for Advanced Technology (RRCAT) at Indore has started operation. A dispersive type EXAFS beamline called BL-8 has been commissioned at this synchrotron and another beamline having double crystal monochromator (DCM) is going to be commissioned shortly. In Indian context, in order that more research workers use these beamlines, the study of XAFS spectroscopy using synchrotron radiation becomes important. In the present work some of the works done by our group on XAFS spectroscopy using synchrotron radiation have been described.

Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyashenko, Andrey V.; Zhukhlistova, Nadegda E.; Gabdoulkhakov, Azat G.

2006-10-01

The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccasemore » structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R{sub free} = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO{sub 2} substituents.« less

Crystal and Vibrational Structure of Energetic 3,5-dinitro 1,3,5-oxadiazinane (DOD) by Single Crystal X-ray Diffractometry and Raman Spectroscopy

DTIC Science & Technology

2018-03-19

calculations using a temperature of 298 K. 15. SUBJECT TERMS 3,5-dinitro-1,3,5-oxadiazinane (DOD), X-ray crystallography , Raman, energetic material...X-ray analysis. 2.2 Characterization X-ray Crystallography . DOD crystals were characterized with a SuperNova, Dualflex, EosS2 diffractometer using

Crystal defect studies using x-ray diffuse scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, B.C.

1980-01-01

Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation intomore » dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above.« less

Effect of reducing atmosphere on the magnetism of Zn(1-x)Co(x)O (0≤x≤0.10) nanoparticles.

PubMed

Naeem, M; Hasanain, S K; Kobayashi, M; Ishida, Y; Fujimori, A; Buzby, Scott; Shah, S Ismat

2006-05-28

We report the crystal structure and magnetic properties of Zn(1-x)Co(x)O (0≤x≤0.10) nanoparticles synthesized by heating metal acetates in organic solvent. The nanoparticles were crystallized in the wurtzite ZnO structure after annealing in air and in a forming gas (Ar95% + H5%). The x-ray diffraction and x-ray photoemission spectroscopy (XPS) data for different Co content show clear evidence for the Co(2+) ions in tetrahedral symmetry, indicating the substitution of Co(2+) in the ZnO lattice. However, samples with x = 0.08 and higher cobalt content also indicate the presence of Co metal clusters. Only those samples annealed in the reducing atmosphere of the forming gas, that showed the presence of oxygen vacancies, exhibited ferromagnetism at room temperature. The air annealed samples remained non-magnetic down to 77 K. The essential ingredient in achieving room temperature ferromagnetism in these Zn(1-x)Co(x)O nanoparticles was found to be the presence of additional carriers generated by the presence of the oxygen vacancies.

Role of Molecular Structure on X-ray Diffraction in Thermotropic Uniaxial and Biaxial Nematic Liquid Crystal Phases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-08-27

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Role of Molecular Structure on X-ray Diffraction in Uniaxial and Biaxial Phases of Thermotropic Liquid Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-04-29

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Na, K, Rb, and Cs Exchange in Heulandite Single-Crystals: X-Ray Structure Refinements at 100 K

NASA Astrophysics Data System (ADS)

Yang, Ping; Armbruster, Thomas

1996-04-01

The crystal structures of Na-, K-, Rb-, and Cs-exchanged varieties of the zeolite heulandite with the simplified compositionM+9Al9Si27O72·nH2O were studied by single-crystal X-ray diffraction at 100 K. The structure refinements of Na-, K-, and Rb-exchanged heulandite were performed in space groupC2/mwith resultantRvalues of 3.8, 3.0, and 4.9%, respectively. Cs-exchanged heulandite was refined in space groupC[formula], yielding anRvalue of 3.4%. X-ray single-crystal data of the Cs-exchanged variety indicated that many reflections of typeh k lwere not equivalent toh -k las expected for monoclinic symmetry. With increasing radius of the incorporated channel cations, thebaxis increases from 17.93 to 18.09 Å leading to a slight widening of the channels. The number of H2O molecules also decreases with increasing cation radius due to space limitations. Three general cation positions (II-1,C3, andB4) were found in the four exchanged heulandite samples. For Rb- and Cs-exchanged crystals, the additional cation siteA2 occurs. In Cs-exchanged heulandite symmetry lowering is due to partial Si, Al ordering in the framework accompanied with a more asymmetric arrangement of channel Cs. Only if heavy elements in the channels are present the symmetry information of the framework is enforced, thus partial Si, Al ordering can be resolved.

Crystal structures and magnetic properties of two-dimensional antiferromagnets Co{sub 1-x}Zn{sub x}TeMoO{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doi, Yoshihiro, E-mail: doi@sci.hokudai.ac.j; Suzuki, Ryo; Hinatsu, Yukio

2009-12-15

Crystal structures and magnetic properties of metal telluromolybdates Co{sub 1-x}Zn{sub x}TeMoO{sub 6} (x=0.0, 0.1,...,0.9) are reported. All the compounds have an orthorhombic structure with space group P2{sub 1}2{sub 1}2 and a charge configuration of M{sup 2+}Te{sup 4+}Mo{sup 6+}O{sub 6}. In this structure, M ions form a pseudo-two-dimensional lattice in the ab plane. Their magnetic susceptibility measurements have been performed in the temperature range between 1.8 and 300 K. The end member CoTeMoO{sub 6} shows a magnetic transition at 24.4 K. The transition temperature for solid solutions rapidly decreases with increasing x and this transition disappears between x=0.4 and 0.5, whichmore » is corresponding to the percolation limit for the square-planer lattice. From the magnetization, specific heat, and powder neutron diffraction measurements, it is found that the magnetic transition observed in the CoTeMoO{sub 6} is a canted antiferromagnetic ordering of Co{sup 2+} ions. The antiferromagnetic component of the ordered magnetic moment (3.12(3)mu{sub B} at 10 K) is along the b-axis. In addition, there exists a small ferromagnetic component (0.28(3)mu{sub B}) along the a-axis. - Graphical abstract: The metal telluromolybdates Co{sub 1-x}Zn{sub x}TeMoO{sub 6} have an orthorhombic structure with space group P2{sub 1}2{sub 1}2. In this structure, M ions form a pseudo-square-planer lattice in the ab plane. These compounds show a low-dimensional magnetism reflecting this structural feature. The magnetic transition observed in the CoTeMoO{sub 6} is a canted antiferromagnetic ordering of Co{sup 2+} ions, and the figure is the magnetic structure.« less

X-ray Crystallography Facility

NASA Technical Reports Server (NTRS)

1999-01-01

University of Alabama engineer Lance Weiss briefs NASA astronaut Dr. Bornie Dunbar about the design and capabilities of the X-ray Crystallography Facility under development at the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, AL, April 21, 1999. The X-ray Crystallography Facility is designed to speed the collection of protein structure information from crystals grown aboard the International Space Station. By measuring and mapping the protein crystal structure in space, researchers will avoid exposing the delicate crystals to the rigors of space travel and make important research data available to scientists much faster. The X-ray Crystallography facility is being designed and developed by the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, a NASA Commercial Space Center.

X-ray Crystallography Facility

NASA Technical Reports Server (NTRS)

1999-01-01

University of Alabama engineer Stacey Giles briefs NASA astronaut Dr. Bornie Dunbar about the design and capabilities of the X-ray Crystallography Facility under development at the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, AL, April 21, 1999. The X-ray Crystallography Facility is designed to speed the collection of protein structure information from crystals grown aboard the International Space Station. By measuring and mapping the protein crystal structure in space, researchers will avoid exposing the delicate crystals to the rigors of space travel and make important research data available to scientists much faster. The X-ray Crystallography facility is being designed and developed by the Center for Macromolecular Crystallography of the University of Alabama at Birmingham, a NASA Commercial Space Center.

Structural and magnetic properties of (Co1-xNix)Cr2O4 (x = 0.5, 0.25) nanoparticles

NASA Astrophysics Data System (ADS)

Mohanty, P.; Prinsloo, A. R. E.; Doyle, B. P.; Carleschi, E.; Sheppard, C. J.

2018-05-01

Nanoparticles of (Co1-xNix)Cr2O4, with x = 0.5 and 0.25, were prepared utilizing the sol-gel technique, in order to investigate the effect of Ni substitution at the Co site. The crystal structure of the prepared samples was identified using X-ray diffraction. Transmission electron microscopy images indicate a non-uniform distribution in particle sizes. Temperature dependent magnetization measurements as a function of probing field demonstrate different magnetic transition temperatures to that of both the parent compounds. The magnetization as a function of applied magnetic field shows a wasp-waist like feature for (Co0.5Ni0.5)Cr2O4 nanoparticles measured at 10 K, which is absent in both NiCr2O4 and CoCr2O4. This feature diminished for other measurement temperatures below the Curie temperature and was also absent at all temperatures for the (Co0.75Ni0.25)Cr2O4 nanoparticles. X-ray photoemission spectroscopy results show that the Ni cations prefers the 3+ and Co the 2+ oxidation states, while that of Cr was found to be 3+. However, mixed oxidation states were observed for Ni and Co in both samples, which can influence the magnetic properties.

X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin.

PubMed Central

Ishida, T; Kenmotsu, M; Mino, Y; Inoue, M; Fujiwara, T; Tomita, K; Kimura, T; Sakakibara, S

1984-01-01

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4'-bromo)Phe4, Leu5]-, [(4'-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4'-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4'-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors. PMID:6721829

Crystal growth of carbonate apatite using a CaCO3 flux.

PubMed

Suetsugu, Y; Tanaka, J

1999-09-01

Single crystals of carbonate apatite were grown using a CaCO3 flux under an Ar gas pressure of 55 MPa. The crystals obtained were observed by scanning electron microscopy, optical microscopy and X-ray diffraction. Electron probe microanalyses and thermal analyses were performed. CO3 ions in planar triangle form replaced both OH sites and PO4 tetrahedral sites in the apatite structure: in particular, the OH sites were perfectly substituted by CO3 ions using this method.

The crystal structure of galgenbergite-(Ce), CaCe2(CO3)4•H2O

NASA Astrophysics Data System (ADS)

Walter, Franz; Bojar, Hans-Peter; Hollerer, Christine E.; Mereiter, Kurt

2013-04-01

Galgenbergite-(Ce) from the type locality, the railroad tunnel Galgenberg between Leoben and St. Michael, Styria, Austria, was investigated. There it occurs in small fissures of an albite-chlorite schist as very thin tabular crystals building rosette-shaped aggregates associated with siderite, ancylite-(Ce), pyrite and calcite. Electron microprobe analyses gave CaO 9.49, Ce2O3 28.95, La2O3 11.70, Nd2O3 11.86, Pr2O3 3.48, CO2 30.00, H2O 3.07, total 98.55 wt.%. CO2 and H2O calculated by stoichiometry. The empirical formula (based on Ca + REE ∑3.0) is C{{a}_{1.00 }}{{( {C{{e}_{1.04 }}L{{a}_{0.42 }}N{{d}_{0.42 }}P{{r}_{0.12 }}} )}_{2.00 }}{{( {C{{O}_3}} )}_4}\\cdot {{H}_2}O , and the simplified formula is CaC{{e}_2}{{( {C{{O}_3}} )}_4}\\cdot {{H}_2}O . According to X-ray single crystal diffraction galgenbergite-(Ce) is triclinic, space group Poverline{1},a=6.3916(5) , b = 6.4005(4), c = 12.3898(9) Å, α = 100.884(4), β = 96.525(4), γ = 100.492(4)°, V = 483.64(6) Å3, Z = 2. The eight strongest lines in the powder X-ray diffraction pattern are [ d calc in Å/( I)/ hkl]: 5.052/(100)/011; 3.011/(70)/0-22; 3.006/(66)/004; 5.899/(59)/-101; 3.900/(51)/1-12; 3.125/(46)/-201; 2.526/(42)/022; 4.694/(38)/-102. The infrared absorption spectrum reveals H2O (OH-stretching mode at 3,489 cm-1, HOH bending mode at 1,607 cm-1) and indicates the presence of distinctly non-equivalent CO3-groups by double and quadruple peaks of their ν1, ν2, ν3 and ν4 modes. The crystal structure of galgenbergite-(Ce) was refined with X-ray single crystal data to R1 = 0.019 for 2,448 unique reflections ( I > 2 σ( I)) and 193 parameters. The three cation sites of the structure Ca(1), Ce(2) and Ce(3) have a modest mixed site occupation by Ca and small amount of REE (Ce, La, Pr, Nd) and vice versa. The structure is based on double layers parallel to (001), which are composed of Ca(1)Ce(2)(CO3)2 single layers with an ordered chessboard like arrangement of Ca and Ce, and with a roof tile

Crystallization and preliminary X-ray diffraction study of the protealysin precursor belonging to the peptidase family M4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gromova, T. Yu., E-mail: duk@img.ras.ru; Demidyuk, I. V.; Kostrov, S. V.

2008-09-15

A protealysin precursor (the enzyme of the peptidase family M4) was crystallized for the first time. The crystal-growth conditions were found, and single crystals of the protein with dimensions of 0.3-0.5 mm were grown. The preliminary X-ray diffraction study of the enzyme was performed. The protealysin precursor was shown to crystallize in two crystal modifications suitable for the X-ray diffraction study of the three-dimensional structure of the protein molecule at atomic resolution.

Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

NASA Astrophysics Data System (ADS)

Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

2010-08-01

In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources.

PubMed

Tang, M X; Zhang, Y Y; E, J C; Luo, S N

2018-05-01

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic-plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

Crystallization and preliminary X-ray analysis of gene product 44 from bacteriophage Mu

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kondou, Youhei; Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama; Kitazawa, Daisuke

2005-01-01

Bacteriophage Mu baseplate protein gene product 44 was crystallized. The crystal belongs to space group R3, with unit-cell parameters a = b = 126.6, c = 64.2 Å. Bacteriophage Mu baseplate protein gene product 44 (gp44) is an essential protein required for the assembly of viable phages. To investigate the roles of gp44 in baseplate assembly and infection, gp44 was crystallized at pH 6.0 in the presence of 20% 2-methyl-2,4-pentanediol. The crystals belong to space group R3, with unit-cell parameters a = b = 127.47, c = 63.97 Å. The crystals diffract X-rays to at least 2.1 Å resolution andmore » are stable in the X-ray beam and are therefore appropriate for structure determination. Native data have been collected to 2.1 Å resolution using a DIP6040 image-plate system at beamline BL44XU at the SPring-8 facility in Japan.« less

Suppression of magnetic order in CaCo 1.86 As 2 with Fe substitution: Magnetization, neutron diffraction, and x-ray diffraction studies of Ca ( Co 1 – x Fe x ) y As 2

DOE PAGES

Jayasekara, W. T.; Pandey, Abhishek; Kreyssig, A.; ...

2017-02-23

Magnetization, neutron diffraction, and high-energy x-ray diffraction results for Sn-flux grown single-crystal samples of Ca(Co 1–xFe x) yAs 2, 0 ≤ x ≤ 1, 1.86 ≤ y ≤ 2, are presented and reveal that A-type antiferromagnetic order, with ordered moments lying along the c axis, persists for x ≲ 0.12(1). The antiferromagnetic order is smoothly suppressed with increasing x, with both the ordered moment and Néel temperature linearly decreasing. Stripe-type antiferromagnetic order does not occur for x ≤ 0.25, nor does ferromagnetic order for x up to at least x = 0.104, and a smooth crossover from the collapsed-tetragonal (cT)more » phase of CaCo 1.86As 2 to the tetragonal (T) phase of CaFe 2As 2 occurs. Furthermore, these results suggest that hole doping CaCo 1.86As 2 has a less dramatic effect on the magnetism and structure than steric effects due to substituting Sr for Ca.« less

Suppression of magnetic order in CaCo 1.86 As 2 with Fe substitution: Magnetization, neutron diffraction, and x-ray diffraction studies of Ca ( Co 1 – x Fe x ) y As 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jayasekara, W. T.; Pandey, Abhishek; Kreyssig, A.

Magnetization, neutron diffraction, and high-energy x-ray diffraction results for Sn-flux grown single-crystal samples of Ca(Co 1–xFe x) yAs 2, 0 ≤ x ≤ 1, 1.86 ≤ y ≤ 2, are presented and reveal that A-type antiferromagnetic order, with ordered moments lying along the c axis, persists for x ≲ 0.12(1). The antiferromagnetic order is smoothly suppressed with increasing x, with both the ordered moment and Néel temperature linearly decreasing. Stripe-type antiferromagnetic order does not occur for x ≤ 0.25, nor does ferromagnetic order for x up to at least x = 0.104, and a smooth crossover from the collapsed-tetragonal (cT)more » phase of CaCo 1.86As 2 to the tetragonal (T) phase of CaFe 2As 2 occurs. Furthermore, these results suggest that hole doping CaCo 1.86As 2 has a less dramatic effect on the magnetism and structure than steric effects due to substituting Sr for Ca.« less

Spatially resolved single crystal x-ray spectropolarimetry of wire array z-pinch plasmas

NASA Astrophysics Data System (ADS)

Wallace, M. S.; Haque, S.; Neill, P.; Pereira, N. R.; Presura, R.

2018-01-01

A recently developed single-crystal x-ray spectropolarimeter has been used to record paired sets of polarization-dependent and axially resolved x-ray spectra emitted by wire array z-pinches. In this measurement, two internal planes inside a suitable crystal diffract the x-rays into two perpendicular directions that are normal to each other, thereby separating incident x-rays into their linearly polarized components. This paper gives considerations for fielding the instrument on extended sources. Results from extended sources are difficult to interpret because generally the incident x-rays are not separated properly by the crystal. This difficulty is mitigated by using a series of collimating slits to select incident x-rays that propagate in a plane of symmetry between the polarization-splitting planes. The resulting instrument and some of the spatially resolved polarized x-ray spectra recorded for a 1-MA aluminum wire array z-pinch at the Nevada Terawatt Facility at the University of Nevada, Reno will be presented.

Spatially resolved single crystal x-ray spectropolarimetry of wire array z-pinch plasmas.

PubMed

Wallace, M S; Haque, S; Neill, P; Pereira, N R; Presura, R

2018-01-01

A recently developed single-crystal x-ray spectropolarimeter has been used to record paired sets of polarization-dependent and axially resolved x-ray spectra emitted by wire array z-pinches. In this measurement, two internal planes inside a suitable crystal diffract the x-rays into two perpendicular directions that are normal to each other, thereby separating incident x-rays into their linearly polarized components. This paper gives considerations for fielding the instrument on extended sources. Results from extended sources are difficult to interpret because generally the incident x-rays are not separated properly by the crystal. This difficulty is mitigated by using a series of collimating slits to select incident x-rays that propagate in a plane of symmetry between the polarization-splitting planes. The resulting instrument and some of the spatially resolved polarized x-ray spectra recorded for a 1-MA aluminum wire array z-pinch at the Nevada Terawatt Facility at the University of Nevada, Reno will be presented.

The crystal structure of the new ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2)

NASA Astrophysics Data System (ADS)

Fedyna, L. O.; Bodak, O. I.; Fedorchuk, A. O.; Tokaychuk, Ya. O.

2005-06-01

New ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2) was synthesized and its crystal structure was determined by direct methods from X-ray powder diffraction data (diffractometer DRON-3M, Cu Kα-radiation, R=6.99%,R=12.27%,R=11.55%). The compound crystallizes with the own cubic structure type: space group F 4¯ 3m, Pearson code cF272, a=16.6150(2) Å,Z=8. The structure of the Dy 3Cu 20Sb 11-x ( x≈2) can be obtained from the structure type BaHg 11 by doubling of the lattice parameter and subtraction of 16 atoms. The studied structure was compared with the structures of known compounds, which crystallize in the same space group with similar cell parameters.

Crystallization and preliminary X-ray analysis of gene product 44 from bacteriophage Mu

PubMed Central

Kondou, Youhei; Kitazawa, Daisuke; Takeda, Shigeki; Yamashita, Eiki; Mizuguchi, Mineyuki; Kawano, Keiichi; Tsukihara, Tomitake

2005-01-01

Bacteriophage Mu baseplate protein gene product 44 (gp44) is an essential protein required for the assembly of viable phages. To investigate the roles of gp44 in baseplate assembly and infection, gp44 was crystallized at pH 6.0 in the presence of 20% 2-methyl-2,4-pentanediol. The crystals belong to space group R3, with unit-cell parameters a = b = 127.47, c = 63.97 Å. The crystals diffract X-­rays to at least 2.1 Å resolution and are stable in the X-ray beam and are therefore appropriate for structure determination. Native data have been collected to 2.1 Å resolution using a DIP6040 image-plate system at beamline BL44XU at the SPring-8 facility in Japan. PMID:16508104

Bulk vertical micromachining of single-crystal sapphire using inductively coupled plasma etching for x-ray resonant cavities

NASA Astrophysics Data System (ADS)

Chen, P.-C.; Lin, P.-T.; Mikolas, D. G.; Tsai, Y.-W.; Wang, Y.-L.; Fu, C.-C.; Chang, S.-L.

2015-01-01

To provide coherent x-ray sources for probing the dynamic structures of solid or liquid biological substances on the picosecond timescale, a high-aspect-ratio x-ray resonator cavity etched from a single crystal substrate with a nearly vertical sidewall structure is required. Although high-aspect-ratio resonator cavities have been produced in silicon, they suffer from unwanted multiple beam effects. However, this problem can be avoided by using the reduced symmetry of single-crystal sapphire in which x-ray cavities may produce a highly monochromatic transmitted x-ray beam. In this study, we performed nominal 100 µm deep etching and vertical sidewall profiles in single crystal sapphire using inductively coupled plasma (ICP) etching. The large depth is required to intercept a useful fraction of a stopped-down x-ray beam, as well as for beam clearance. An electroplated Ni hard mask was patterned using KMPR 1050 photoresist and contact lithography. The quality and performance of the x-ray cavity depended upon the uniformity of the cavity gap and therefore verticality of the fabricated vertical sidewall. To our knowledge, this is the first report of such deep, vertical etching of single-crystal sapphire. A gas mixture of Cl2/BCl3/Ar was used to etch the sapphire with process variables including BCl3 flow ratio and bias power. By etching for 540 min under optimal conditions, we obtained an x-ray resonant cavity with a depth of 95 µm, width of ~30 µm, gap of ~115 µm and sidewall profile internal angle of 89.5°. The results show that the etching parameters affected the quality of the vertical sidewall, which is essential for good x-ray resonant cavities.

Development of X-ray spectroscopic polarimetry with bent Si crystals and CFRP substrate

NASA Astrophysics Data System (ADS)

Iizuka, Ryo; Izumiya, Takanori; Tsuboi, Yohko

2016-07-01

The light from celestial objects includes four important quantities; images, time variation, energy spectrum, and polarization. In the field of X-ray astronomy, the capabilities of the former three have remarkably developed. On the other hand, the progress for the polarimetry is considerably delayed because of technical difficulties. In order to make a breakthrough in the field of X-ray polarimetry, we have developed a new type of optics for X-ray polarimetry. The system is collecting Bragg crystal with large area and very high sensitivity for the polarization dedicated to Fe-K lines. We adopt the 400 re ection of Si(100) crystals with high sensitivity for the polarization around Fe-K lines (6 7 keV), and bent the crystals with the wide X-ray band and high S/N ratio. Furthermore, to install small area of CCD to non-focal plane, it also has the spectroscopic capability with the better resolution than that of general X-ray CCD. Our previous development was to bent Si crystals to the cylindrical shape of circle and parabola with the DLC deposition. However, for the better optics for the X-ray polarimetry, the shape should be the paraboloid of revolution to collect X-rays with high S/N ratio. We searched for the method to bent the Si crystals to the shape of the paraboloid of revolution. We devised the method to mold the crystal and the CFRP substrate simultaneously pushed to the sophisticated foundation with the paraboloid of revolution. We developed the prototype of about 8 inch in radius of one-quater size. The crystals was also bent in the circumferential direction. Therefore, the image capability examined with optical parallel beam is 0.6 degree. In this thesis, we discussed the new design for X-ray spectroscopic polarimetry, the evaluation of image capability.

Structure of Profiled Crystals Based on Solid Solutions of Bi2Te3 and Their X-Ray Diagnostics

NASA Astrophysics Data System (ADS)

Voronin, A. I.; Bublik, V. T.; Tabachkova, N. Yu.; Belov, Yu. M.

2011-05-01

In this work, we used x-ray structural diagnostic data to reveal the formation of structural regularities in profiled polycrystalline ingots based on Bi and Sb chalcogenide solid solutions. In Bi2Te3 lattice crystals, the solid phase grows such that the cleavage surfaces are perpendicular to the crystallization front. The crystallization singularity determines the nature of the growth texture. Because texture is an important factor determining the anisotropy of properties, which in turn determines the suitability of an ingot for production of modules and the possibility of figure of merit improvement, its diagnostics is an important issue for technology testing. Examples of texture analysis using the method of straight pole figure (SPF) construction for profiled crystals are provided. The structure of the surface layers in the profiled ingots was studied after electroerosion cutting. In addition, the method of estimation of the disturbed layer depth based on the nature of texture changes was used.

Solid-state NMR studies of theophylline co-crystals with dicarboxylic acids.

PubMed

Pindelska, Edyta; Sokal, Agnieszka; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Kolodziejski, Waclaw

2014-11-01

In this work, three polycrystalline materials containing co-crystals of theophylline with malonic, maleic, and glutaric acids were studied using (13)C, (15)N and (1)H solid-state NMR and FT-IR spectroscopy. The NMR assignments were supported by gauge including projector augmented waves (GIPAW) calculations of chemical shielding, performed using X-ray determined geometry. The experimental (13)C cross polarization/magic angle spinning (CP/MAS) NMR results and the calculated isotropic chemical shifts were in excellent agreement. A rapid and convenient method for theophylline co-crystals crystal structure analysis has been proposed for co-crystals, which are potentially new APIs. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing

2005-09-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in themore » mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.« less

Synthesis, crystal structures and luminescence properties of new multi-component co-crystals of isostructural Co(II) and Zn(II) complexes

NASA Astrophysics Data System (ADS)

Tella, Adedibu C.; Owalude, Samson O.; Omotoso, Mary F.; Olatunji, Sunday J.; Ogunlaja, Adeniyi S.; Alimi, Lukman O.; Popoola, Olugbenga K.; Bourne, Susan A.

2018-04-01

Two novel isostructural compounds containing multi-component co-crystals [M(C6H4NO2)2(H2O)2](C9H6O6)2 (M = Co (1), Zn (2), C6H4NO2 = Picolinic acid, C9H6O6 = Trimesic acid) have been synthesized. The compounds were characterized by elemental analysis, FT-IR, UV-Visible and 1H NMR spectroscopies as well as thermal and single crystal X-ray diffraction analyses. Single crystal X-ray diffraction analysis reveals that 1 and 2 are isostructural. Compound 1 crystallizes in triclinic space group (P-1, with a = 5.154 (10) Å, b = 11.125 (2) Å, c = 14.113 (3) Å, α = 91.01 (3)°, β = 100.54 (3)°, and γ = 102.71 (3)°). In a similar fashion, compound 2 crystallizes in triclinic space group (P-1, with a = 5.1735 (3) Å, b = 11.0930 (10) Å, c = 14.1554 (8) Å, α = 91.70 (3)°, β = 100.26 (3)°, γ = 102.90 (3)°). The metal (II) cation presents distorted MN2O4 octahedral geometry with H2O molecules coordinated to the metal in equatorial position while the picolinic acid molecules are axially coordinated through the pyridine N atom. The two trimesic acid molecules are not part of the first coordination sphere. Compounds 1 and 2 constitute an example of a class of coordination compound of multicomponent crystals having trimesic acid outside the coordination sphere where it is neither protonated or deprotonated. The two compounds were investigated for luminiscence properties.

The X-ray Crystal Structure of Glutathionylcobalamin Revealed

PubMed Central

Hannibal, Luciana; Smith, Clyde A.

2010-01-01

The first evidence of a complex between glutathione and cobalamin, glutathionylcobalamin (GSCbl), was presented by Wagner and Bernhauer more than 40 years ago (Ann N Y Acad Sci, 1964, 112, 580). More recently, NMR and EXAFS solution studies by Brown et al (Biochemistry, 1993, 32, 8421) and Scheuring et al. (Biochemistry, 1994, 33, 6310), respectively, provided evidence that the glutathionyl moiety in GSCbl is bound to the cobalt center via a Co-S bond. Despite continued efforts, the structural analysis of glutathionylcobalamin in the solid state has remained elusive. Here we report the first atomic resolution crystal structure of GSCbl, refined to a crystallographic R-factor of 0.0683. The glutathione moiety is bound to the cobalt center through the sulfur atom as expected, with a Co-S bond distance of 2.295(1) A. This distance agrees with the distance obtained from the EXAFS analysis of GSCbl (2.280(5) Å). However, the bond to the axial α-5,6-dimethylbenzimidazole base (DMB), 2.074(3) Å, is significantly shorter than that determined from the EXAFS measurements (Co-N3B = 2.15(3) Å). The corrin fold angle is 24.7°, the highest ever reported for a cobalamin structure, and points in the direction of the β-face of the corrin, towards the glutathione (GS−). The GS− ligand has been modeled in two conformations, each featuring distinct hydrogen bonding interactions. In both conformations, the α-carboxylate group of the GS− ligand interacts with the generally rigid side chain a of the cobalamin molecule, resulting in two distinct conformations. A comparison with the structure of other thiolatocobalamins revealed high similarity in the positions of the atoms in the cysteinyl moiety, the fold of the corrin rings, and the Co-S bond distances. PMID:20863098

The X-ray crystal structure of glutathionylcobalamin revealed.

PubMed

Hannibal, Luciana; Smith, Clyde A; Jacobsen, Donald W

2010-11-01

The first evidence of a complex between glutathione and cobalamin, glutathionylcobalamin (GSCbl), was presented by Wagner and Bernhauer more than 40 years ago (Ann. N.Y. Acad. Sci. 1964, 112, 580). More recently, NMR and EXAFS solution studies by Brown et al. (Biochemistry 1993, 32, 8421) and Scheuring et al. (Biochemistry 1994, 33, 6310), respectively, provided evidence that the glutathionyl moiety in GSCbl is bound to the cobalt center via a Co-S bond. Despite continued efforts, the structural analysis of glutathionylcobalamin in the solid state has remained elusive. Here, we report the first atomic resolution crystal structure of GSCbl, refined to a crystallographic R factor of 0.0683. The glutathione moiety is bound to the cobalt center through the sulfur atom as expected, with a Co-S bond distance of 2.295(1) Å. This distance agrees with the distance obtained from the EXAFS analysis of GSCbl (2.280(5) Å). However, the bond to the axial α-5,6-dimethylbenzimidazole base (DMB), 2.074(3) Å, is significantly shorter than that determined from the EXAFS measurements (Co-N3B = 2.15(3) Å). The corrin fold angle is 24.7°, the highest ever reported for a cobalamin structure, and points in the direction of the β face of the corrin, toward the glutathione (GS(-)). The GS(-) ligand has been modeled in two conformations, each featuring distinct hydrogen bonding interactions. In both conformations, the α-carboxylate group of the GS(-) ligand interacts with the generally rigid side chain a of the cobalamin molecule, resulting in two distinct conformations. A comparison with the structure of other thiolatocobalamins revealed high similarity in the positions of the atoms in the cysteinyl moiety, the fold of the corrin rings, and the Co-S bond distances.

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Improving the dissolution and bioavailability of 6-mercaptopurine via co-crystallization with isonicotinamide.

PubMed

Wang, Jian-Rong; Yu, Xueping; Zhou, Chun; Lin, Yunfei; Chen, Chen; Pan, Guoyu; Mei, Xuefeng

2015-03-01

6-Mercaptopurine (6-MP) is a clinically important antitumor drug. The commercially available form was provided as monohydrate and belongs to BCS class II category. Co-crystallization screening by reaction crystallization method (RCM) and monitored by powder X-ray diffraction led to the discovery of a new co-crystal formed between 6-MP and isonicotinamide (co-crystal 1). Co-crystal 1 was thoroughly characterized by X-ray diffraction, FT-IR and Raman spectroscopy, and thermal analysis. Noticeably, the in vitro and in vivo studies revealed that co-crystal 1 possesses improved dissolution rate and superior bioavailability on animal model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sagittal focusing of synchrotron radiation X-rays using a winged crystal

PubMed Central

Nisawa, A.; Yoneda, Y.; Ueno, G.; Murakami, H.; Okajima, Y.; Yamamoto, K.; Senba, Y.; Uesugi, K.; Tanaka, Y.; Yamamoto, M.; Goto, S.; Ishikawa, T.

2013-01-01

A Si(111) winged crystal has been designed to minimize anticlastic bending and improve sagittal focusing efficiency. The crystal was thin with wide stiffening wings. The length-to-width ratio of the crystal was optimized by finite element analysis, and the optimal value was larger than the ‘golden value’. The analysis showed that the slope error owing to anticlastic bending is less than the Darwin width. The X-rays were focused two-dimensionally using the crystal and a tangentially bent mirror. The observed profiles of the focal spot agreed well with the results of a ray-tracing calculation in the energy range from 8 to 17.5 keV. X-ray diffraction measurements with a high signal-to-noise ratio using this focusing system were demonstrated for a small protein crystal. PMID:23412477

Suppression of magnetic order in CaCo1.86As2 with Fe substitution: Magnetization, neutron diffraction, and x-ray diffraction studies of Ca (Co1-xFex) yAs2

NASA Astrophysics Data System (ADS)

Jayasekara, W. T.; Pandey, Abhishek; Kreyssig, A.; Sangeetha, N. S.; Sapkota, A.; Kothapalli, K.; Anand, V. K.; Tian, W.; Vaknin, D.; Johnston, D. C.; McQueeney, R. J.; Goldman, A. I.; Ueland, B. G.

2017-02-01

Magnetization, neutron diffraction, and high-energy x-ray diffraction results for Sn-flux grown single-crystal samples of Ca (Co1-xFex) yAs2 , 0 ≤x ≤1 , 1.86 ≤y ≤2 , are presented and reveal that A-type antiferromagnetic order, with ordered moments lying along the c axis, persists for x ≲0.12 (1 ) . The antiferromagnetic order is smoothly suppressed with increasing x , with both the ordered moment and Néel temperature linearly decreasing. Stripe-type antiferromagnetic order does not occur for x ≤0.25 , nor does ferromagnetic order for x up to at least x =0.104 , and a smooth crossover from the collapsed-tetragonal (cT) phase of CaCo1.86As2 to the tetragonal (T) phase of CaFe2As2 occurs. These results suggest that hole doping CaCo1.86As2 has a less dramatic effect on the magnetism and structure than steric effects due to substituting Sr for Ca.

A von Hamos x-ray spectrometer based on a segmented-type diffraction crystal for single-shot x-ray emission spectroscopy and time-resolved resonant inelastic x-ray scattering studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szlachetko, J.; Institute of Physics, Jan Kochanowski University, 25-406 Kielce; Nachtegaal, M.

2012-10-15

We report on the design and performance of a wavelength-dispersive type spectrometer based on the von Hamos geometry. The spectrometer is equipped with a segmented-type crystal for x-ray diffraction and provides an energy resolution in the order of 0.25 eV and 1 eV over an energy range of 8000 eV-9600 eV. The use of a segmented crystal results in a simple and straightforward crystal preparation that allows to preserve the spectrometer resolution and spectrometer efficiency. Application of the spectrometer for time-resolved resonant inelastic x-ray scattering and single-shot x-ray emission spectroscopy is demonstrated.

Development of an X-ray fluorescence holographic measurement system for protein crystals

NASA Astrophysics Data System (ADS)

Sato-Tomita, Ayana; Shibayama, Naoya; Happo, Naohisa; Kimura, Koji; Okabe, Takahiro; Matsushita, Tomohiro; Park, Sam-Yong; Sasaki, Yuji C.; Hayashi, Kouichi

2016-06-01

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2β2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm3) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

A soft x-ray octadecyl hydrogen maleate crystal spectrograph

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, P.Z.; Fill, E.E.; Tietang, G.

1996-03-01

A crystal spectrograph is described which can be used to investigate laser-produced plasmas in the region of soft x rays at wavelengths of up to 60 A. The spectrograph uses an octadecyl hydrogen maleate crystal with a 2{ital d} of 63.5 A, combined with a very thin carbon filter (3000 A thick). As examples of its application, soft x-ray spectra in the range of 43{endash}51 A from laser plasmas of Si and Cu are presented. A spectral resolution of {lambda}/{Delta}{lambda}=1100 is deduced from the spectra. {copyright} {ital 1996 American Institute of Physics.}

Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Xu, Minghua; Wu, Nan

2006-12-01

The FadA adhesin from F. nucleatum, which is involved in bacterial attachment and invasion of human oral epithelial cells, has been crystallized in space group P6{sub 1} or P6{sub 5}, and X-ray data have been collected to 1.9 Å resolution. Fusobacterium nucleatum is a Gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: themore » intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 59.3, c = 125.7 Å and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 Å. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum.« less

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, M. X.; Zhang, Y. Y.; E, J. C.

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of themore » diffraction patterns is discussed.« less

Femtosecond X-ray protein nanocrystallography

PubMed Central

Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C. H.

2012-01-01

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage. PMID:21293373

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.

PubMed

Gicquel, Yannig; Schubert, Robin; Kapis, Svetlana; Bourenkov, Gleb; Schneider, Thomas; Perbandt, Markus; Betzel, Christian; Chapman, Henry N; Heymann, Michael

2018-04-24

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography

Mg(1 + x)Ir(1 - x) (x = 0, 0.037 and 0.054), a binary intermetallic compound with a new orthorhombic structure type determined from powder and single-crystal X-ray diffraction.

PubMed

Cerný, Radovan; Renaudin, Guillaume; Favre-Nicolin, Vincent; Hlukhyy, Viktor; Pöttgen, Rainer

2004-06-01

The new binary compound Mg(1 + x)Ir(1 - x) (x = 0-0.054) was prepared by melting the elements in the Mg:Ir ratio 2:3 in a sealed tantalum tube under an argon atmosphere in an induction furnace (single crystals) or by annealing cold-pressed pellets of the starting composition Mg:Ir 1:1 in an autoclave under an argon atmosphere (powder sample). The structure was independently solved from high-resolution synchrotron powder and single-crystal X-ray data: Pearson symbol oC304, space group Cmca, lattice parameters from synchrotron powder data a = 18.46948 (6), b = 16.17450 (5), c = 16.82131 (5) A. Mg(1 + x)Ir(1 - x) is a topologically close-packed phase, containing 13 Ir and 12 Mg atoms in the asymmetric unit, and has a narrow homogeneity range. Nearly all the atoms have Frank-Kasper-related coordination polyhedra, with the exception of two Ir atoms, and this compound contains the shortest Ir-Ir distances ever observed. The solution of a rather complex crystal structure from powder diffraction, which was fully confirmed by the single-crystal method, shows the power of powder diffraction in combination with the high-resolution data and the global optimization method.

Perovskite-Type Oxides. I. Structural, Magnetic, and Morphological Properties of LaMn 1- xCu xO 3 and LaCo 1- xCu xO 3 Solid Solutions with Large Surface Area

NASA Astrophysics Data System (ADS)

Porta, Piero; De Rossi, Sergio; Faticanti, Marco; Minelli, Giuliano; Pettiti, Ida; Lisi, Luciana; Turco, Maria

1999-09-01

Perovskite-type compounds of general formula LaMn1-xCuxO3 and LaCo1-xCuxO3 (x=0.0, 0.2, 0.4, 0.6, 0.8, 1.0) were prepared by calcining the citrate gel precursors at 823, 923, and 1073 K. The decomposition of the precursors was followed by thermal analysis and the oxides were investigated by means of elemental analysis (atomic absorption and redox titration), X-ray powder diffraction, BET surface area, X-ray absorption (EXAFS and XANES), electron microscopy (SEM and TEM), and magnetic susceptibility. LaMn1-xCuxO3 samples are perovskite-like single phases up to x=0.6. At x=0.8 CuO and La2CuO4 phases are present in addition to perovskite. For x=1.0 the material is formed by CuO and La2CuO4. Mn(IV) was found by redox titration in all Mn-based perovskite samples, its fraction increasing with the increase in copper content. EXAFS and XANES analyses confirmed the presence of Mn(IV). Cation vacancies in equal amounts in the 12-coordinated A and octahedral B sites are suggested in the samples with x=0.0 and x=0.2, while for x=0.6 anionic vacancies are present. Materials with sufficiently high surface area (22-36 m2 g-1 for samples fired at 923 K and 14-22 m2 g-1 for those fired at 1073 K) were obtained. Crystallite sizes in the ranges 390-500 and 590-940 Å for samples calcined at 923 and 1073 K, respectively, were determined from the FWHM of the (102) X-ray diffraction peak. TEM patterns of LaMnO3 showed almost regular hexagonal prismatic crystals with sizes of the same order of magnitude (800 Å) of those drawn from X-ray diffraction, while no evidence of defect clustering was drawn out from TEM and electron diffraction images. For the sample with x=0.6, TEM and electron diffraction patterns revealed perturbation of the structure. Magnetic susceptibility studies show a ferromagnetic behavior that decreases with increase in x. LaCo1-xCuxO3 samples are perovskite-like single phases up to x=0.2. For x=0.4 a small amount of La2CuO4, in addition to perovskite, is detected. For

Synthesis, structure and luminescence of novel co-crystals based on bispyridyl-substituted α,β-unsaturated ketones with coformers

NASA Astrophysics Data System (ADS)

Li, Hong-Juan; Wang, Lei; Zhao, Juan-Juan; Sun, Ju-Feng; Sun, Ji-Liang; Wang, Chun-Hua; Hou, Gui-Ge

2015-01-01

Based on 2,6-bis((pyridin-4-yl)methylene)cyclohexanone (A) and N-methyl-3,5-bis((pyridin-4-yl)methylene)-4-piperidone (B) with coformers, three novel macrocyclic co-crystals, (A)ṡ(resorcinol) (1), (A)ṡ(1,3,5-benzenetriol) (2), (B)2ṡ(1,3,5-benzenetriol)2 (3) and three chain co-crystals, (A)ṡ(hydroquinone) (4), (A)ṡ(isophthalic acid) (5), (B)ṡ(isophthalic acid) (6) have been synthesized and structurally characterized by IR, 1H NMR and X-ray crystal structure analysis. Structural analysis indicates that four-component macrocycles in 1-3 are generated from "clip-like" resorcinol templates and building blocks, while 4-6 show infinite H-bonding chains. In addition, the luminescent properties of A, B and 1-6 are investigated primarily in the solid state. Compared with free building blocks, 1-6 are blue-shifted 55-60 nm with decreasing emission intensities in spite of the enhancement in 6. The change of luminescent properties might be caused mainly by incorporation of coformers into co-crystals, including H-bonds, molecular conformations, arranging dispositions and π-π characteristics. It might have potential applications for crystal engineering to construct patentable crystals with interesting luminescent properties.

X-ray Diffraction from Membrane Protein Nanocrystals

PubMed Central

Hunter, M.S.; DePonte, D.P.; Shapiro, D.A.; Kirian, R.A.; Wang, X.; Starodub, D.; Marchesini, S.; Weierstall, U.; Doak, R.B.; Spence, J.C.H.; Fromme, P.

2011-01-01

Membrane proteins constitute >30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is <300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain <100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain <200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells. PMID:21190672

Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.

PubMed

Hughes, Ronny C; Coates, Leighton; Blakeley, Matthew P; Tomanicek, Steve J; Langan, Paul; Kovalevsky, Andrey Y; García-Ruiz, Juan M; Ng, Joseph D

2012-12-01

Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott, Stacy A.; Holloway, Gavan; Coulson, Barbara S.

2005-06-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by themore » virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement.« less

Insights from soft X-rays: the chlorine and sulfur sub-structures of a CK2alpha/DRB complex.

PubMed

Raaf, Jennifer; Issinger, Olaf-Georg; Niefind, Karsten

2008-09-01

The diffraction pattern of a protein crystal is normally a product of the interference of electromagnetic waves scattered by electrons of the crystalline sample. The diffraction pattern undergoes systematic changes in case additionally X-ray absorption occurs, meaning if the wavelength of the primary X-ray beam is relatively close to the absorption edge of selected elements of the sample. The resulting effects are summarized as "anomalous dispersion" and can be always observed with "soft" X-rays (wavelength around 2 A) since they match the absorption edges of sulfur and chlorine. A particularly useful application of this phenomenon is the experimental detection of the sub-structures of the anomalous scatterers in protein crystals. We demonstrate this here with a crystal of a C-terminally truncated variant of human CK2alpha to which two molecules of the inhibitor 5,6-dichloro-1-beta-D-ribo-furanosyl-benzimidazole (DRB) are bound. The structure of this co-crystal has been solved recently. For this study we measured an additional diffraction data set at a wavelength of 2 A which showed strong anomalous dispersion effects. On the basis of these effects we detected all sulfur atoms of the protein, the two liganded DRB molecules and a total of 16 additional chloride ions some of them emerging at positions filled with water molecules in previous structure determinations. A number of chloride ions are bound to structural and functional important locations fitting to the constitutive activity and the acidophilic substrate specificity of the enzyme.

Phenylacetic acid co-crystals with acridine, caffeine, isonicotinamide and nicotinamide: Crystal structures, thermal analysis, FTIR spectroscopy and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Amombo Noa, Francoise M.; Jacobs, Ayesha

2017-07-01

Co-crystals of phenylacetic acid (PAA) with acridine (ACR), caffeine (CAF), isonicotinamide (INM) and nicotinamide (NAM) have been successfully prepared and characterised by single crystal X-ray diffraction, FTIR spectroscopy, thermal analysis and Hirshfeld surface analysis. The ACR, INM and NAM co-crystals with PAA exhibit the carboxylic acid-pyridine heterosynthon. Furthermore the amide-amide supramolecular homosynthon is observed in the PAA co-crystals with INM and NAM as well as Nsbnd H⋯O interactions between the acid and the respective base. The CAF co-crystal exhibits hydrogen bonding between the imidazole nitrogen and the COOH group of the PAA. The compounds demonstrate different stoichiometries; for PAA·ACR and PAA·INM a 1:1 ratio is displayed, a 2:1 in 2PAA·CAF and a 2:2 in the case of 2PAA·2NAM.

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soares, Alexei S.; Caspar, Donald L. D.

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

DOE PAGES

Soares, Alexei S.; Caspar, Donald L. D.

2017-08-31

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality.

PubMed

Boggon, T J; Helliwell, J R; Judge, R A; Olczak, A; Siddons, D P; Snell, E H; Stojanoff, V

2000-07-01

A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.

Synthesis and crystal structures of nitratocobaltates Na2[Co(NO3)4], K2[Co(NO3)4], and Ag[Co(NO3)3] and potassium nitratonickelate K2[Ni(NO3)4

NASA Astrophysics Data System (ADS)

Morozov, I. V.; Fedorova, A. A.; Albov, D. V.; Kuznetsova, N. R.; Romanov, I. A.; Rybakov, V. B.; Troyanov, S. I.

2008-03-01

The cobalt(II) and nickel(II) nitrate complexes with an island structure (Na2[Co(NO3)4] ( I) and K2[Co(NO3)4] ( II)] and a chain structure [Ag[Co(NO3)3] ( III) and K2[Ni(NO3)4] ( IV)] are synthesized and investigated using X-ray diffraction. In the anionic complex [Co(NO3)4]2- of the crystal structure of compound I, the Co coordination polyhedron is a twisted tetragonal prism formed by the O atoms of four asymmetric bidentate nitrate groups. In the anion [Co(NO3)4]2- of the crystal structure of compound II, one of the four NO3 groups is monodentate and the other NO3 groups are bidentate (the coordination number of the cobalt atom is equal to seven, and the cobalt coordination polyhedron is a monocapped trigonal prism). The crystal structures of compounds III and IV contain infinite chains of the compositions [Co(NO3)2(NO3)2/2]- and [Ni(NO3)3(NO3)2/2]2-, respectively. In the crystal structure of compound III, seven oxygen atoms of one monodentate and three bidentate nitrate groups form a dodecahedron with an unoccupied vertex of the A type around the Co atom. In the crystal structure of compound IV, the octahedral polyhedron of the Ni atom is formed by five nitrate groups, one of which is terminal bidentate. The data on the structure of Co(II) coordination polyhedra in the known nitratocobaltates are generalized.

Radiation of X-Rays Using Uniaxially Polarized LiNbO3 Single Crystal

NASA Astrophysics Data System (ADS)

Fukao, Shinji; Nakanishi, Yoshikazu; Mizoguchi, Tadahiro; Ito, Yoshiaki; Nakamura, Toru; Yoshikado, Shinzo

2009-03-01

X-rays are radiated due to the bremsstrahlung caused by the collision of electrons with a metal target placed opposite the negative electric surface of a crystal by changing the temperature of a LiNbO3 single crystal uniaxially polarized in the c-axis direction. It is suggested that both electric field intensity and electron density determine the intensity of X-ray radiation. Electrons are supplied by the ionization of residual gas in space, field emission from a case inside which a crystal is located, considered to be due to the high electric-field intensity formed by the surface charges on the crystal, and an external electron source, such as a thermionic source. In a high vacuum, it was found that the electrons supplied by electric-field emission mainly contribute to the radiation of X-rays. It was found that the integrated intensity of X-rays can be maximized by supplying electrons both external and by electric-field emission. Furthermore, the integrated intensity of the X-rays is stable for many repeated temperature changes.

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS

PubMed Central

Stoner-Ma, Deborah; Skinner, John M.; Schneider, Dieter K.; Cowan, Matt; Sweet, Robert M.; Orville, Allen M.

2011-01-01

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of ‘mystery density’, i.e. ambiguous or unknown features within the electron density maps, especially at ∼2 Å resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data. PMID:21169688

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

NASA Astrophysics Data System (ADS)

Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

2016-11-01

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P1211 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

NASA Astrophysics Data System (ADS)

Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

2015-07-01

Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

X-ray absorption spectroscopy: EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alp, E.E.; Mini, S.M.; Ramanathan, M.

1990-04-01

The x-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. It has also played an important role in the discovery and systematization of rare-earth elements. The discovery of synchrotron radiation in 1952, and later the availability of broadly tunable synchrotron based x-ray sources have revitalized this technique since the 1970's. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge by Sayers et. al. has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-raymore » Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. An excellent description of the principles and data analysis techniques of EXAFS is given by Teo. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, we will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and samples limitations.« less

Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

NASA Astrophysics Data System (ADS)

Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

2016-05-01

The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobility-lifetime product of 1.2 × 10-2 cm2 V-1 and an extremely small surface charge recombination velocity of 64 cm s-1 are realized by reducing the bulk defects and passivating surface traps. Single-crystal devices with a thickness of 2-3 mm show 16.4% detection efficiency at near zero bias under irradiation with continuum X-ray energy up to 50 keV. The lowest detectable X-ray dose rate is 0.5 μGyair s-1 with a sensitivity of 80 μC Gy-1air cm-2, which is four times higher than the sensitivity achieved with α-Se X-ray detectors. This allows the radiation dose applied to a human body to be reduced for many medical and security check applications.

Structure of Co-Doped Alq3 thin films investigated by grazing incidence X-ray absorption fine structure and Fourier transform infrared spectroscopy.

PubMed

Lin, Liang; Pang, Zhiyong; Fang, Shaojie; Wang, Fenggong; Song, Shumei; Huang, Yuying; Wei, Xiangjun; Yu, Haisheng; Han, Shenghao

2011-02-10

The structural properties of Co-doped tris(8-hydroxyquinoline)aluminum (Alq(3)) have been studied by grazing incidence X-ray absorption fine structure (GIXAFS) and Fourier transform infrared spectroscopy (FTIR). GIXAFS analysis suggests that there are multivalent Co-Alq(3) complexes and the doped Co atoms tend to locate at the attraction center with respect to N and O atoms and bond with them. The FTIR spectra indicate that the Co atoms interact with the meridional (mer) isomer of Alq(3) rather than forming inorganic compounds.

Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

PubMed

Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

2014-11-11

Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method. Copyright © 2014 Elsevier B.V. All rights reserved.

Resolution of the discrepancy between the variation of the physical properties of Ce 1-xYb xCoIn 5 single crystals and thin films with Yb composition

DOE PAGES

Jang, S.; White, B. D.; Lum, I. K.; ...

2014-11-18

The extraordinary electronic phenomena including an Yb valence transition, a change in Fermi surface topology, and suppression of the heavy fermion quantum critical field at a nominal concentration x≈0.2 have been found in the Ce 1-xYb xCoIn 5 system. These phenomena have no discernable effect on the unconventional superconductivity and normal-state non-Fermi liquid behaviour that occur over a broad range of x up to ~0.8. However, the variation of the coherence temperature T* and the superconducting critical temperature T c with nominal Yb concentration x for bulk single crystals is much weaker than that of thin films. To determine whethermore » differences in the actual Yb concentration of bulk single crystals and thin film samples might be responsible for these discrepancies, we employed Vegard’s law and the spectroscopically determined values of the valences of Ce and Yb as a function of x to determine the actual composition x act of bulk single crystals. This analysis is supported by energy-dispersive X-ray spectroscopy, wavelength-dispersive X-ray spectroscopy, and transmission X-ray absorption edge spectroscopy measurements. The actual composition x act is found to be about one-third of the nominal concentration x up to x~0.5, and resolves the discrepancy between the variation of the physical properties of Ce 1-xYb xCoIn 5 single crystals and thin films with Yb concentration.« less

Performance of the x-ray free-electron laser oscillator with crystal cavity

NASA Astrophysics Data System (ADS)

Lindberg, R. R.; Kim, K.-J.; Shvyd'Ko, Yu.; Fawley, W. M.

2011-01-01

Simulations of the x-ray free-electron laser (FEL) oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ˜109 photons in a nearly Fourier-limited, ps pulse. Compressing the electron beam to 100 A and 100 fs results in comparable x-ray characteristics for relaxed beam emittance, energy spread, and/or undulator parameters, albeit in a larger radiation bandwidth. Finally, preliminary simulation results indicate that the four-crystal FEL cavity can be tuned in energy over a range of a few percent.

Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

NASA Technical Reports Server (NTRS)

Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

2000-01-01

A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

Dynamical effects in Bragg coherent x-ray diffraction imaging of finite crystals

NASA Astrophysics Data System (ADS)

Shabalin, A. G.; Yefanov, O. M.; Nosik, V. L.; Bushuev, V. A.; Vartanyants, I. A.

2017-08-01

We present simulations of Bragg coherent x-ray diffractive imaging (CXDI) data from finite crystals in the frame of the dynamical theory of x-ray diffraction. The developed approach is based on a numerical solution of modified Takagi-Taupin equations and can be applied for modeling of a broad range of x-ray diffraction experiments with finite three-dimensional crystals of arbitrary shape also in the presence of strain. We performed simulations for nanocrystals of a cubic and hemispherical shape of different sizes and provided a detailed analysis of artifacts in the Bragg CXDI reconstructions introduced by the dynamical diffraction. Based on our theoretical analysis we developed an analytical procedure to treat effects of refraction and absorption in the reconstruction. Our results elucidate limitations for the kinematical approach in the Bragg CXDI and suggest a natural criterion to distinguish between kinematical and dynamical cases in coherent x-ray diffraction on a finite crystal.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of phosphopantetheine adenylyltransferase from Enterococcus faecalis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Ji Yong; Lee, Hyung Ho; Yoon, Hye Jin

2006-11-01

Phosphopantetheine adenylyltransferase from En. faecalis was crystallized and X-ray diffraction data were collected to 2.70 Å resolution. Phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme A biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from ATP to 4′-phosphopantetheine, yielding 3′-dephospho-CoA and pyrophosphate. Enterococcus faecalis PPAT has been overexpressed in Escherichia coli as a fusion with a C-terminal purification tag and crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium HEPES pH 7.5, 0.8 M sodium dihydrogen phosphate and 0.8 M potassium dihydrogen phosphate. X-ray diffraction data were collected to 2.70 Å at 100 K.more » The crystals belong to the primitive tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 160.81, c = 225.68 Å. Four copies of the hexameric molecule are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.08 Å{sup 3} Da{sup −1} and a solvent content of 60.1%.« less

Electronic structure of cobalt doped CdSe quantum dots using soft X-ray spectroscopy

DOE PAGES

Wright, Joshua T.; Su, Dong; van Buuren, Tony; ...

2014-08-21

Here, the electronic structure and magnetic properties of cobalt doped CdSe quantum dots (QDs) are studied using electron microscopy, soft X-ray spectroscopy, and magnetometry. Magnetometry measurements suggest these QDs are superparamagnetic, contrary to a spin-glass state observed in the bulk analogue. Electron microscopy shows well formed QDs, but with cobalt existing as doped into the QD and as unreacted species not contained in the QD. X-ray absorption measurements at the Co L3-edge suggest that changes in spectra features as a function of particle size can be described considering combination of a cobalt ion in a tetrahedral crystal field and anmore » octahedrally coordinated (impurity) phase. With decreasing particle sizes, the impurity phase increases, suggesting that small QDs can be difficult to dope.« less

Crystallization and preliminary X-ray analysis of a low density lipoprotein from human plasma.

PubMed

Prassl, R; Chapman, J M; Nigon, F; Sara, M; Eschenburg, S; Betzel, C; Saxena, A; Laggner, P

1996-11-15

Single crystals of human plasma low density lipoprotein (LDL), the major transport vehicle for cholesterol in blood, have been produced with a view to analysis of the three-dimensional structure by x-ray crystallography. Crystals with dimensions of approximately 200 x 100 x 50 microm have been reproducibly obtained from highly homogeneous LDL particle subspecies, isolated in the density ranges d = 1.0271-1. 0297 g/ml and d = 1.0297-1.0327 g/ml. Electron microscopic imaging of ultrathin-sectioned preparations of the crystals confirmed the existence of a regular, quasihexagonal arrangement of spherical particles of approximately 18 nm in diameter, thereby resembling the dimensions characteristic of LDL after dehydration and fixation. X-ray diffraction with synchrotron radiation under cryogenic conditions revealed the presence of well resolved diffraction spots, to a resolution of about 29 A. The diffraction patterns are indexed in terms of a triclinic lattice with unit cell dimensions of a = 16. 1 nm, b = 39.0 nm, c = 43.9 nm; alpha = 96.2 degrees, beta = 92.1 degrees, gamma = 102 degrees, and with space group P1.

X-ray absorption fine structure and X-ray excited optical luminescence studies of II-VI semiconducting nanostructures

NASA Astrophysics Data System (ADS)

Murphy, Michael Wayne

2010-06-01

Various II-VI semiconducting nanomaterials such as ZnO-ZnS nanoribbons (NRs), CdSxSe1-x nanostructures, ZnS:Mn NRs, ZnS:Mn,Eu nanoprsims (NPs), ZnO:Mn nanopowders, and ZnO:Co nanopowders were synthesized for study. These materials were characterized by techniques such as scanning electron microscopy, transmission electron microscopy, element dispersive X-ray spectroscopy, selected area electron diffraction, and X-ray diffraction. The electronic and optical properties of these nanomaterials were studied by X-ray absorption fine structure (XAFS) spectroscopy and X-ray excited optical luminescence (XEOL) techniques, using tuneable soft X-rays from a synchrotron light source. The complementary nature ofthe XAFS and XEOL techniques give site, element and chemical specific measurements which allow a better understanding of the interplay and role of each element in the system. Chemical vapour deposition (CVD) of ZnS powder in a limited oxygen environment resulted in side-by-side biaxial ZnO-ZnS NR heterostructures. The resulting NRs contained distinct wurtzite ZnS and wurtzite ZnO components with widths of 10--100 nm and 20 --500 nm, respectively and a uniform interface region of 5-15 nm. XAFS and XEOL measurements revealed the luminescence of ZnO-ZnS NRs is from the ZnO component. The luminescence of CdSxSe1-x nanostructures is shown to be dependent on the S to Se ratio, with the band-gap emission being tunable between that of pure CdS and CdSe. Excitation of the CdSxSe 1-x nanostructures by X-ray in XEOL has revealed new de-excitation channels which show a defect emission band not seen by laser excitation. CVD of Mn2+ doped ZnS results in nanostructures with luminescence dominated by the yellow Mn2+ emission due to energy transfer from the ZnS host to the Mn dopant sites. The addition of EuCl3 to the reactants in the CVD process results in a change in morphology from NR to NP. Zn1-xMnxO and Zn1-xCOxO nanopowders were prepared by sol-gel methods at dopant concentrations

Average and local crystal structures of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles

DOE PAGES

Feygenson, Mikhail; Neuefeind, Joerg C.; Tyson, Trevor A.; ...

2015-11-06

We report the comprehensive study of the crystal structure of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles by means of neutron and synchrotron x-ray scattering. In our study we used four different types of (Ga 1–xZn x)(N 1–xO x) nanoparticles, with diameters of 10–27 nm and x = 0.075–0.51, which show the narrow energy-band gaps from 2.21 to 2.61 eV. The Rietveld analysis of the neutron diffraction data revealed that the average crystal structure is the hexagonal wurtzite (space group P6 3mc), in agreement with previous reports on similar bulk materials. The pair-distribution function (PDF) analysis of the samemore » data found that the local structure is more disordered than the average one. It is best described by the model with a lower symmetry space group P1, where atoms are quasirandomly distorted from their nominal positions in the hexagonal wurtzite lattice.« less

X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

NASA Technical Reports Server (NTRS)

Hu, Zheng-Wei; Chu, Y. S.; Lai, B.; Cai, Z.; Thomas, B. R.; Chernov, A. A.

2003-01-01

Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haugh, M. J., E-mail: haughmj@nv.doe.gov; Jacoby, K. D.; Wu, M.

2014-11-15

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals thatmore » we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.« less

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Thomas, B. R.; Chernov, A. A.

2001-01-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection.

PubMed

Hu, Z W; Thomas, B R; Chernov, A A

2001-06-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

Asymmetrically cut crystal pair as x-ray magnifier for imaging at high intensity laser facilitiesa)

NASA Astrophysics Data System (ADS)

Szabo, C. I.; Feldman, U.; Seely, J. F.; Curry, J. J.; Hudson, L. T.; Henins, A.

2010-10-01

The potential of an x-ray magnifier prepared from a pair of asymmetrically cut crystals is studied to explore high energy x-ray imaging capabilities at high intensity laser facilities. OMEGA-EP and NIF when irradiating mid and high Z targets can be a source of high-energy x-rays whose production mechanisms and use as backlighters are a subject of active research. This paper studies the properties and potential of existing asymmetric cut crystal pairs from the National Institute of Standards and Technology (NIST) built in a new enclosure for imaging x-ray sources. The technique of the x-ray magnifier has been described previously. This new approach is aimed to find a design that could be used at laser facilities by magnifying the x-ray source into a screen far away from the target chamber center, with fixed magnification defined by the crystals' lattice spacing and the asymmetry angles. The magnified image is monochromatic and the imaging wavelength is set by crystal asymmetry and incidence angles. First laboratory results are presented and discussed.

A structural study of [CpM(CO)3H] (M = Cr, Mo and W) by single-crystal X-ray diffraction and DFT calculations: sterically crowded yet surprisingly flexible molecules.

PubMed

Burchell, Richard P L; Sirsch, Peter; Decken, Andreas; McGrady, G Sean

2009-08-14

The single-crystal X-ray structures of the complexes [CpCr(CO)3H] 1, [CpMo(CO)3H] 2 and [CpW(CO)3H] 3 are reported. The results indicate that 1 adopts a structure close to a distorted three-legged piano stool geometry, whereas a conventional four-legged piano stool arrangement is observed for 2 and 3. Further insight into the equilibrium geometries and potential energy surfaces of all three complexes was obtained by DFT calculations. These show that in the gas phase complex 1 also prefers a geometry close to a four-legged piano stool in line with its heavier congeners, and implying strong packing forces at work for 1 in the solid state. Comparison with their isolelectronic group 7 tricarbonyl counterparts [CpM(CO)3] (M = Mn 4 and Re 5) illustrates that 1, 2 and 3 are sterically crowded complexes. However, a surprisingly soft bending potential is evident for the M-H moiety, whose order (1 approximately = 2 < 3) correlates with the M-H bond strength rather than with the degree of congestion at the metal centre, indicating electronic rather than steric control of the potential. The calculations also reveal cooperative motions of the hydride and carbonyl ligands in the M(CO)3H unit, which allow the M-H moiety to move freely, in spite of the closeness of the four basal ligands, helping to explain the surprising flexibility of the crowded coordination sphere observed for this family of high CN complexes.

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abramchik, Yu. A.; Timofeev, V. I., E-mail: tostars@mail.ru; Muravieva, T. I.

2016-11-15

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12{sub 1}1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, βmore » = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.« less

Crystal structure of pentasodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rammohan, Alagappa; Kaduk, James A.

2017-01-27

The crystal structure of pentasodium hydrogen dicitrate, Na 5H(C 6H 5O 7) 2, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O—H...O hydrogen bonds, with O...O distances of 2.419 and 2.409 Å. Four octahedrally coordinated Na +ions share edges to form open layers parallel to theabplane. A fifth Na +ion in trigonal–bipyramidal coordination shares faces with NaO 6octahedra on both sides of these layers.

M(II)-dipyridylamide-based coordination frameworks (M=Mn, Co, Ni): Structural transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tzeng, Biing-Chiau; Selvam, TamilSelvi; Tsai, Miao-Hsin

2016-11-15

A series of 1-D double-zigzag (([M(papx){sub 2}(H{sub 2}O){sub 2}](ClO{sub 4}){sub 2}){sub n}; M=Mn, x=s (1), x=o (3); M=Co, x=s (4), x=o (5); M=Ni, x=s (6), x=o (7)) and 2-D polyrotaxane ([Mn(paps){sub 2}(ClO{sub 4}){sub 2}]{sub n} (2)) frameworks were synthesized by reactions of M(ClO{sub 4}){sub 2} (M=Mn, Co, and Ni) with papx (paps, N,N’-bis(pyridylcarbonyl)-4,4’-diaminodiphenylthioether; papo, N,N’-bis(pyridylcarbonyl)-4,4’-diaminodiphenyl ether), which have been isolated and structurally characterized by X-ray diffraction. Based on powder X-ray diffraction (PXRD) experiments, heating the double-zigzag frameworks underwent structural transformation to give the respective polyrotaxane ones. Moreover, grinding the solid samples of the respective polyrotaxanes in the presence of moisturemore » also resulted in the total conversion to the original double-zigzag frameworks. In this study, we have successfully extended studies to Mn{sup II}, Co{sup II}, and Ni{sup II} frameworks from the previous Zn{sup II}, Cd{sup II}, and Cu{sup II} ones, and interestingly such structural transformation is able to be proven experimentally by powder and single-crystal X-ray diffraction studies as well. - Graphical abstract: 1-D double-zigzag and 2-D polyrotaxane frameworks of M(II)-papx (x=s, o; M=Mn, Co, Ni) frameworks can be interconverted by heating and grinding in the presence of moiture, and such structural transformation has be proven experimentally by powder and single-crystal X-ray diffraction studies.« less

Crystal structure and magnetic properties of high-oxygen pressure annealed Sr{sub 1-x}La{sub x}Co{sub 0.5}Fe{sub 0.5}O{sub 3-{delta}} (0{<=}x{<=}0.5)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swierczek, Konrad; Materials Science Division, Argonne National Laboratory, Argonne, IL 60439; Dabrowski, Bogdan

2009-02-15

Structural and magnetic studies are presented for the perovskite type Sr{sub 1-x}La{sub x}Co{sub 0.5}Fe{sub 0.5}O{sub 3-{delta}} (0{<=}x{<=}0.5) materials annealed under moderately high-oxygen pressures of {approx}200 atm. A detailed analysis of the room temperature neutron time-of-flight diffraction data reveals that the crystal structure of the sample SrCo{sub 0.5}Fe{sub 0.5}O{sub 2.89(1)}, previously described as vacancy-disordered cubic, is similar to the formerly reported, oxygen-vacancy ordered Sr{sub 8}Fe{sub 8}O{sub 23} compound, i.e. Sr{sub 8}Co{sub 4}Fe{sub 4}O{sub 23} is tetragonal with the I4/mmm symmetry. With an increase of the La content the studied materials become nearly oxygen stoichiometric and a lowering of the crystal symmetrymore » is observed from cubic Pm3-barm (x=0.1 and 0.2) to tetragonal I4/mcm (x=0.3 and 0.4), and finally to monoclinic I12/c1 (x=0.5). Low-temperature structural and magnetic measurements show a ferromagnetic ordering with the maximum Curie temperature near 290 K at x=0.2. - Graphical Abstract: Room temperature Rietveld refinement profile using I4/mmm space group for the oxygen vacancy ordered SrCo{sub 0.5}Fe{sub 0.5}O{sub 2.89} (Sr{sub 8}Co{sub 4}Fe{sub 4}O{sub 23}). Top tick-marks denote allowed reflections in I4/mmm, bottom one emphasize the possibility of inexact indexing using Pm3-barm symmetry. Previous reports indicate that similar ordering is common for SrCo{sub 1-x}Fe{sub x}O{sub 3-{delta}} compounds possibly hindering their applications.« less

1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Bharat G.; Moates, Derek B.; Kim, Heung-Bok

The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overallmore » structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.« less

Crystal structure, Raman scattering and magnetic properties of CuCr2-xZrxSe4 and CuCr2-xSnxSe4 selenospinels

NASA Astrophysics Data System (ADS)

Pinto, C.; Galdámez, A.; Barahona, P.; Moris, S.; Peña, O.

2018-06-01

Selenospinels, CuCr2-xMxSe4 (M = Zr and Sn), were synthesized via conventional solid-state reactions. The crystal structure of CuCr1.5Sn0.5Se4, CuCr1.7Sn0.3Se4, CuCr1.5Zr0.5Se4, and CuCr1.8Zr0.2Se4 were determined using single-crystal X-ray diffraction. All the phases crystallized in a cubic spinel-type structure. The chemical compositions of the single-crystals were examined using energy-dispersive X-ray analysis (EDS). Powder X-ray diffraction patterns of CuCr1.3Sn0.7Se4 and CuCr1.7Sn0.3Se4 were consistent with phases belonging to the Fd 3 bar m Space group. An analysis of the vibrational properties on the single-crystals was performed using Raman scattering measurements. The magnetic properties showed a spin glass behavior with increasing Sn content and ferromagnetic order for CuCr1.7Sn0.3Se4.

The STAR-X X-Ray Telescope Assembly (XTA)

NASA Technical Reports Server (NTRS)

McClelland, Ryan S.; Bautz, Mark W.; Bonafede, Joseph A.; Miller, Eric D.; Saha, Timo T.; Solly, Peter M.; Zhang, William W.

2017-01-01

The Survey and Time-domain Astrophysical Research eXplorer (STAR-X) science goals are to discover what powers the most violent explosions in the Universe, understand how black holes grow across cosmic time and mass scale, and measure how structure formation heats the majority of baryons in the Universe. To achieve these goals, STAR-X requires a powerful X-ray telescope with a large field of view, large collecting area, and excellent point spread function. The STAR-X instrument, the X-Ray Telescope Assembly (XTA), meets these requirements using a powerful X-ray mirror technology based on precision-polished single crystal silicon and a mature CCD detector technology. The XTA is composed of three major subsystems: an X-ray Mirror Assembly (MA) of high resolution, lightweight mirror segments fabricated out of single crystal silicon; a Focal Plane Assembly (FPA) made of back-illuminated CCD's capable of detecting X-rays with excellent quantum efficiency; and a composite Telescope Tube that structurally links the MA and FPA. The MA consists of 5,972 silicon mirror segments mounted into five subassemblies called meta-shells. A meta-shell is constructed from an annular central structural shell covered with interlocking layers of mirror segments. This paper describes the requirements, design, and analysis of the XTA subsystems with particular focus on the MA.

The STAR-X X-Ray Telescope Assembly (XTA)

NASA Astrophysics Data System (ADS)

McClelland, Ryan S.

2017-08-01

The Survey and Time-domain Astrophysical Research eXplorer (STAR-X) science goals are to discover what powers the most violent explosions in the Universe, understand how black holes grow across cosmic time and mass scale, and measure how structure formation heats the majority of baryons in the Universe. To achieve these goals, STAR-X requires a powerful X-ray telescope with a large field of view, large collecting area, and excellent point spread function. The STAR-X instrument, the X-Ray Telescope Assembly (XTA), meets these requirements using a powerful X-ray mirror technology based on precision-polished single crystal silicon and a mature CCD detector technology. The XTA is composed of three major subsystems: an X-ray Mirror Assembly (MA) of high resolution, lightweight mirror segments fabricated out of single crystal silicon; a Focal Plane Assembly (FPA) made of back-illuminated CCDs capable of detecting X-rays with excellent quantum efficiency; and a composite Telescope Tube that structurally links the MA and FPA. The MA consists of 5,972 silicon mirror segments mounted into five subassemblies called metashells. A meta-shell is constructed from an annular central structural shell covered with interlocking layers of mirror segments. This paper describes the requirements, design, and analysis of the XTA subsystems with particular focus on the MA.

Effects of thermal expansion of the crystal lattice on x-ray crystal spectrometers used for fusion research

NASA Astrophysics Data System (ADS)

Delgado-Aparicio, L.; Bitter, M.; Podpaly, Y.; Rice, J.; Burke, W.; Sanchez del Rio, M.; Beiersdorfer, P.; Bell, R.; Feder, R.; Gao, C.; Hill, K.; Johnson, D.; Lee, S. G.; Marmar, E.; Pablant, N.; Reinke, M. L.; Scott, S.; Wilson, R.

2013-12-01

X-ray imaging crystal spectrometers with high spectral and spatial resolution are currently being used on magnetically confined fusion devices to infer the time history profiles of ion and electron temperatures as well as plasma flow velocities. The absolute measurement of flow velocities is important for optimizing various discharge scenarios and evaluating the radial electric field in tokamak and stellarator plasmas. Recent studies indicate that the crystal temperature must be kept constant to within a fraction of a degree to avoid changes of the interplanar 2d-spacing by thermal expansion that cause changes in the Bragg angle, which could be misinterpreted as Doppler shifts. For the instrumental parameters of the x-ray crystal spectrometer on Alcator C-Mod, where those thermal effects were investigated, a change of the crystal temperature by 1 °C causes a change of the lattice spacing of the order of Δd = 1 × 10-5 Å introducing a fictitious velocity drift of the order of ˜3 km s-1. This effect must be considered for x-ray imaging crystals spectrometers installed on LHD, KSTAR, EAST, J-TEXT, NSTX and, in the future, W7-X and ITER.

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c =more » 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.« less

Structural evolution of gypsum under high pressure: single-crystal X-ray experiments revisited

NASA Astrophysics Data System (ADS)

Li, Tsung-Lung; Lee, Pei-Lun

2018-05-01

The structures of gypsum at pressures up to approximately 4 GPa are studied with density functional theory (DFT) and thoroughly compared with single-crystal X-ray diffraction experiments reported in the literature [Comodi et al. in (Am Miner 93:1530-1537, 2008)]. It is found that the exchange-correlation density functional revPBE (revised Perdew-Burke-Ernzerhof) in conjunction with a nonlocal van der Waals (vdW) correction is capable of modeling the lattice constants, axial compressibility, and bulk modulus with good accuracy, suggesting that the inclusion of the vdW functional is crucially important for understanding the structure of hydrous minerals. To gain further physical insights, the geometric parameters associated with the constituting components of gypsum (water molecules, SO4 tetrahedra, and CaO8 polyhedra) are analyzed and compared with the experimental values. DFT simulations show that, under pressure, the polyhedral layers remain as nearly planar sheets of interconnecting SO4 tetrahedra and CaO8 polyhedra without further crinkling. DFT analysis on the layer compressibility along the major crystal axis reveals that, in contrast to experimental reports, the hydrous interlayer is less compressible than the polyhedral layer. Squeezed by the lateral pressure, the water molecules in the hydrous interlayer become better affixed along the major axis, making the interlayer harder to compress along this axis.

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s −1 . At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensitymore » within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s –1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution ofmore » diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ~1.5–2 compared with those observed at conventional dose rates. As a result, improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE PAGES

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.; ...

2017-10-13

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s –1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution ofmore » diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ~1.5–2 compared with those observed at conventional dose rates. As a result, improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE PAGES

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.; ...

2017-10-13

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s −1 . At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensitymore » within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

PubMed Central

Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

2013-01-01

An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659

Crystallization and X-ray diffraction of crystals formed in water-plasticized amorphous lactose.

PubMed

Jouppila, K; Kansikas, J; Roos, Y H

1998-01-01

Effects of storage time and relative humidity on crystallization and crystal forms produced from amorphous lactose were investigated. Crystallization was observed from time-dependent loss of sorbed water and increasing intensities of peaks in X-ray diffraction patterns. The rate of crystallization increased with increasing storage relative humidity. Lactose crystallized mainly as alpha-lactose monohydrate and anhydrous crystals with alpha- and beta-lactose in a molar ratio of 5:3. The results suggested that the crystal form was defined by the early nucleation process. The crystallization data are important in modeling of crystallization phenomena and prediction of stability of lactose-containing food and pharmaceutical materials.

Element-selective investigation of domain structure in CoPd and FePd alloys using small-angle soft X-ray scattering

NASA Astrophysics Data System (ADS)

Weier, C.; Adam, R.; Frömter, R.; Bach, J.; Winkler, G.; Kobs, A.; Oepen, H. P.; Grychtol, P.; Kapteyn, H. C.; Murnane, M. M.; Schneider, C. M.

2014-03-01

Recent optical pump-probe experiments on magnetic multilayers and alloys identified perpendicular spin superdiffusion as one of possible mechanisms responsible for femtosecond magnetization dynamics. On the other hand, no strong evidence for the ultrafast lateral spin transport has been reported, so far. To address this question, we studied magnetic domain structure of CoPd and FePd thin films using small-angle scattering of soft X-rays. By tuning the synchrotron-generated X-rays to the absorption edges of Fe or Co we recorded Fourier images of the magnetic domain structure corresponding to a chosen element. Applying in - situ magnetic fields resulted in pronounced rearrangement of domain structure that was clearly observed in scattering images. Our analysis of both the stand-alone, as well as magnetically coupled CoPd/FePd layers provides insight into the formation of domains under small magnetic field perturbations and pave the way to better understanding of transient changes expected in magneto-dynamic measurements.

In situ study of the growth and degradation processes in tetragonal lysozyme crystals on a silicon substrate by high-resolution X-ray diffractometry

NASA Astrophysics Data System (ADS)

Kovalchuk, M. V.; Prosekov, P. A.; Marchenkova, M. A.; Blagov, A. E.; D'yakova, Yu. A.; Tereshchenko, E. Yu.; Pisarevskii, Yu. V.; Kondratev, O. A.

2014-09-01

The results of an in situ study of the growth of tetragonal lysozyme crystals by high-resolution X-ray diffractometry are considered. The crystals are grown by the sitting-drop method on crystalline silicon substrates of different types: both on smooth substrates and substrates with artificial surface-relief structures using graphoepitaxy. The crystals are grown in a special hermetically closed crystallization cell, which enables one to obtain images with an optical microscope and perform in situ X-ray diffraction studies in the course of crystal growth. Measurements for lysozyme crystals were carried out in different stages of the crystallization process, including crystal nucleation and growth, developed crystals, the degradation of the crystal structure, and complete destruction.

Measuring the X-ray Resolving Power of Bent Potassium Acid Phthalate Diffraction Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haugh, M. J.; Wu, M.; Jacoby, K. D.

2014-11-01

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals thatmore » we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories (SNL) in Albuquerque, NM. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a dual goniometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.« less

Mechanical design of thin-film diamond crystal mounting apparatus for coherence preservation hard x-ray optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shu, Deming, E-mail: shu@aps.anl.gov; Shvyd’ko, Yuri V.; Stoupin, Stanislav

2016-07-27

A new thin-film diamond crystal mounting apparatus has been designed at the Advanced Photon Source (APS) for coherence preservation hard x-ray optics with optimized thermal contact and minimized crystal strain. This novel mechanical design can be applied to new development in the field of: x-ray optics cavities for hard x-ray free-electron laser oscillators (XFELOs), self-seeding monochromators for hard x-ray free-electron laser (XFEL) with high average thermal loading, high heat load diamond crystal monochromators and beam-sharing/beam-split-and-delay devices for XFEL facilities and future upgraded high-brightness coherent x-ray source in the MBA lattice configuration at the APS.

Effects of rare-earth co-doping on the local structure of rare-earth phosphate glasses using high and low energy X-ray diffraction.

PubMed

Cramer, Alisha J; Cole, Jacqueline M; FitzGerald, Vicky; Honkimaki, Veijo; Roberts, Mark A; Brennan, Tessa; Martin, Richard A; Saunders, George A; Newport, Robert J

2013-06-14

Rare-earth co-doping in inorganic materials has a long-held tradition of facilitating highly desirable optoelectronic properties for their application to the laser industry. This study concentrates specifically on rare-earth phosphate glasses, (R2O3)x(R'2O3)y(P2O5)(1-(x+y)), where (R, R') denotes (Ce, Er) or (La, Nd) co-doping and the total rare-earth composition corresponds to a range between metaphosphate, RP3O9, and ultraphosphate, RP5O14. Thereupon, the effects of rare-earth co-doping on the local structure are assessed at the atomic level. Pair-distribution function analysis of high-energy X-ray diffraction data (Q(max) = 28 Å(-1)) is employed to make this assessment. Results reveal a stark structural invariance to rare-earth co-doping which bears testament to the open-framework and rigid nature of these glasses. A range of desirable attributes of these glasses unfold from this finding; in particular, a structural simplicity that will enable facile molecular engineering of rare-earth phosphate glasses with 'dial-up' lasing properties. When considered together with other factors, this finding also demonstrates additional prospects for these co-doped rare-earth phosphate glasses in nuclear waste storage applications. This study also reveals, for the first time, the ability to distinguish between P-O and P[double bond, length as m-dash]O bonding in these rare-earth phosphate glasses from X-ray diffraction data in a fully quantitative manner. Complementary analysis of high-energy X-ray diffraction data on single rare-earth phosphate glasses of similar rare-earth composition to the co-doped materials is also presented in this context. In a technical sense, all high-energy X-ray diffraction data on these glasses are compared with analogous low-energy diffraction data; their salient differences reveal distinct advantages of high-energy X-ray diffraction data for the study of amorphous materials.

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoupin, Stanislav; Antipov, Sergey; Butler, James E.

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configurationmore » and data analysis using rocking-curve topography. In conclusion, the variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.« less

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics.

PubMed

Stoupin, Stanislav; Antipov, Sergey; Butler, James E; Kolyadin, Alexander V; Katrusha, Andrey

2016-09-01

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking-curve topography. The variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics

DOE PAGES

Stoupin, Stanislav; Antipov, Sergey; Butler, James E.; ...

2016-08-10

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configurationmore » and data analysis using rocking-curve topography. In conclusion, the variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.« less

Femtosecond x-ray scattering study of ultrafast photoinduced structural dynamics in solvated [ Co ( terpy ) 2 ] 2 +

DOE PAGES

Biasin, Elisa; van Driel, Tim Brandt; Kjær, Kasper S.; ...

2016-06-30

Here, we study the structural dynamics of photoexcited [Co(terpy) 2] 2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of themore » high spin state is established on a single-picosecond time scale and that this state has a lifetime of ~7 ps.« less

Monoalkylated barbiturate derivatives: X-ray crystal structure, theoretical studies, and biological activities

NASA Astrophysics Data System (ADS)

Barakat, Assem; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Islam, Mohammad Shahidul; Ghawas, Hussain Mansur; Yousuf, Sammer; Choudhary, M. Iqbal; Wadood, Abdul

2017-08-01

Barbiturate derivatives are privileged structures with a broad range of pharmaceutical applications. We prepared a series of 5-monoalkylated barbiturate derivatives (3a-l) and evaluated, in vitro, their antioxidant (DPPH assay), and α-glucosidase inhibitory activities. Compounds 3a-l were synthesized via Michael addition. The structure of compound 3k was determined using X-ray single-crystal diffraction, and geometric parameters were calculated using density functional theory at the B3LYP/6-311G(d,p) level of theory. Further, the structural analysis of 3k were also investigated. Biological studies revealed that compounds 3b (IC50 = 133.1 ± 3.2 μM), 3d (IC50 = 305 ± 7.7 μM), and 3e (IC50 = 184 ± 2.3 μM) have potent α-glucosidase enzyme inhibitors and showed greater activity than the standard drug acarbose (IC50 = 841 ± 1.73 μM). Compounds 3a-3i were found to show weak antioxidant activity against 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals (IC50 = 91 ± 0.75 to 122 ± 1.0 μM) when tested against a standard antioxidant, gallic acid (IC50 = 23 ± 0.43 μM).

TlBr and TlBr xI 1-x crystals for γ-ray detectors

NASA Astrophysics Data System (ADS)

Churilov, Alexei V.; Ciampi, Guido; Kim, Hadong; Higgins, William M.; Cirignano, Leonard J.; Olschner, Fred; Biteman, Viktor; Minchello, Mark; Shah, Kanai S.

2010-04-01

TlBr and TlBr xI 1-x are wide bandgap semiconductor materials being investigated for applications in γ-ray spectroscopy. They have a good combination of density and atomic numbers, promising to make them very efficient detectors. Their low melting points and simple cubic and orthorhombic crystal structures are favorable for bulk crystal growth. However, these semiconductors need to be extremely pure to become useful as radiation detectors. Impurities can lead to charge trapping and scattering, reducing the charge transit lengths and limiting the detector thickness to <1 mm. Additional purification steps were implemented to improve the purity and mobility-lifetime product ( μτ) of electrons. Detector-grade TlBr with the electron μτ product of up to 6×10 -3 cm 2/V has been produced, which allowed operation of detectors up to 15 mm thickness. The ternary TlBr xI 1-x was investigated at different compositions to vary the bandgap and explore the effect of added TlI on the long term stability of detectors. The material analysis and detector characterization results are included.

In Situ X-Ray Studies of Crystallization Kinetics and Ordering in Functional Organic and Hybrid Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Bin; Keum, Jong K.; Geohegan, David B.

In-Situ and time-resolved X-ray scattering and diffraction is dedicated to yielding the change of structural information as the materials are processed or grown in a controlled environment. In this chapter, we introduce the use of in situ and time-resolved X-ray techniques to understand molecular packing, crystal orientation, and phase transformation during the synthesis and processing of functional organic semiconductors, organic nanowires, and hybrid perovskite materials.

At last! The single-crystal X-ray structure of a naturally occurring sample of the ilmenite-type oxide FeCrO3.

PubMed

Pérez-Cruz, María Ana; Elizalde-González, María de la Paz; Escudero, Roberto; Bernès, Sylvain; Silva-González, Rutilo; Reyes-Ortega, Yasmi

2015-10-01

A natural single crystal of the ferrimagnetic oxide FeCrO3, which was found in an opencast mine situated in the San Luis Potosí State in Mexico, has been characterized in order to elucidate some outstanding issues about the actual structure of this material. The single-crystal X-ray analysis unambiguously shows that transition metal cations are segregated in alternating layers normal to the threefold crystallographic axis, affording a structure isomorphous to that of ilmenite (FeTiO3), in the space group R3̅. The possible occurrence of cation antisite and vacancy defects is below the limit of detection available from X-ray data. Structural and magnetic results are in agreement with the coherent slow intergrowth of magnetic phases provided by the two antiferromagnetic corundum-type parent oxides Fe2O3 (hematite) and Cr2O3 (eskolaite). Our results are consistent with the most recent density functional theory (DFT) studies carried out on digital FeCrO3 [Sadat Nabi & Pentcheva (2011). Phys. Rev. B, 83, 214424], and suggest that synthetic samples of FeCrO3 might present a cation distribution different to that of the ilmenite structural type.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

PubMed Central

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required. PMID:23793151

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

PubMed

Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-07-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

The effect of laser radiation on the diffraction of X-rays in crystals

NASA Astrophysics Data System (ADS)

Trushin, V. N.; Chuprunov, E. V.; Khokhlov, A. F.

1988-10-01

The effect of laser radiation on the intensity of the X-ray diffraction peaks of KDP, ADP, and CuSO4-5H2O crystals was studied experimentally. This intensity was found to increase as a function of the laser beam power. This result suggests that it is possible to use laser beams to control X-ray intensity in the crystals considered.

Flux growth of high-quality CoFe 2O 4 single crystals and their characterization

NASA Astrophysics Data System (ADS)

Wang, W. H.; Ren, X.

2006-04-01

We report the growth of high-quality CoFe 2O 4 single crystals using a borax flux method. The crystals were characterized by powder X-ray diffraction, electron probe microanalysis and Raman spectroscopy. We found the crystals are flux-free and highly homogeneous in composition. X-ray rocking curves of the CoFe 2O 4 single crystals showed a full-width at half-maximum of 0.15°. The saturation magnetization of the CoFe 2O 4 single crystals was measured to be 90 emu/g or equivalently 3.65 μ B/f.u. at 5 K.

X-ray free electron laser: opportunities for drug discovery.

PubMed

Cheng, Robert K Y; Abela, Rafael; Hennig, Michael

2017-11-08

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Combining piracetam and lithium salts: ionic co-crystals and co-drugs?

PubMed

Braga, Dario; Grepioni, Fabrizia; Maini, Lucia; Capucci, Davide; Nanna, Saverio; Wouters, Johan; Aerts, Luc; Quéré, Luc

2012-08-25

Mechanochemical reaction of solid piracetam with the inorganic salts LiCl and LiBr yields ionic co-crystals which are also co-drugs, characterized by markedly different thermal properties with respect to pure components, also depending on the method for preparation and/or conditions of measurements; single crystal and powder X-ray diffraction at variable temperatures, DSC, TGA, hot stage microscopy (HSM) and intrinsic dissolution rate have been used to fully characterize the solid products.

Mechanisms for Improved Hygroscopicity of L-Arginine Valproate Revealed by X-Ray Single Crystal Structure Analysis.

PubMed

Ito, Masataka; Nambu, Kaori; Sakon, Aya; Uekusa, Hidehiro; Yonemochi, Etsuo; Noguchi, Shuji; Terada, Katsuhide

2017-03-01

Valproic acid is widely used as an antiepileptic agent. Valproic acid is in liquid phase while sodium valproate is in solid phase at room temperature. Sodium valproate is hard to manufacture because of its hygroscopic and deliquescent properties. To improve these, cocrystal and salt screening for valproic acid was employed in this study. Two solid salt forms, l-arginine valproate and l-lysine valproate, were obtained and characterized. By using dynamic vapor sorption method, the critical relative humidity of sodium valproate, l-arginine valproate, and l-lysine valproate were measured. Critical relative humidity of sodium valproate was 40%, of l-lysine valproate was 60%, and of l-arginine valproate was 70%. Single-crystal X-ray structure determination of l-arginine valproate was employed. l-Lysine valproate was of low diffraction quality, and l-arginine valproate formed a 1:1 salt. Crystal l-arginine valproate has a disorder in the methylene carbon chain that creates 2 conformations. The carboxylate group of valproic acid is connected to the amino group of l-arginine. Crystalline morphologies were calculated from its crystal structure. Adsorption of water molecules to crystal facets was simulated by Material Studio. When comparing adsorption energy per site of these salts, sodium valproate is more capable of adsorption of water molecule than l-arginine valproate. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido

2014-06-09

Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystalmore » diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.« less

High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

DOEpatents

Smither, Robert K [Hinsdale, IL

2011-05-17

A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

Crystal structures of the new ternary stannides La3Mg4-xSn2+x and LaMg3-xSn2

NASA Astrophysics Data System (ADS)

Solokha, P.; De Negri, S.; Minetti, R.; Proserpio, D. M.; Saccone, A.

2016-01-01

Synthesis and structural characterization of the two new lanthanum-magnesium-stannides La3Mg4-xSn2+x (0.12≤x≤0.40) and LaMg3-xSn2 (0.33≤x≤0.78) are reported. The crystal structures of these intermetallics were determined by single crystal X-ray diffraction analysis and confirmed by Rietveld refinement of powder X-ray diffraction patterns of the corresponding samples. The La3Mg4-xSn2+x phase crystallizes in the hexagonal Zr3Cu4Si2 structure type (P6bar2m, hP9, Z=3, x=0.12(1), a=7.7974(7), c=4.8384(4) Å), which represents an ordered derivative of the hP9-ZrNiAl prototype, ubiquitous among equiatomic intermetallics. The LaMg3-xSn2 phase is the second representative of the trigonal LaMg3-xGe2 type, which is a superstructure of the LaLi3Sb2 structure type (P3bar1c, hP34-0.12, Z=6, x=0.35(1), a=8.3222(9), c=14.9546(16) Å). The scheme describing the symmetry reduction/coloring with respect to the parent type is reported here with the purpose to discuss the LaMg3-xSn2 off-stoichiometry from the geometrical point of view. Structural relationships between the La-Mg-Sn ternary phases, including the already known equiatomic LaMgSn compound (oP12-TiNiSi), are presented in the framework of the AlB2-related compounds family and discussed with the aid of group-subgroup relations in the Bärnighausen formalism.

The use of Co2+ for crystallization and structure determination, using a conventional mono­chromatic X-ray source, of flax rust avirulence protein

PubMed Central

Gunčar, Gregor; Wang, Ching-I A.; Forwood, Jade K.; Teh, Trazel; Catanzariti, Ann-Maree; Ellis, Jeffrey G.; Dodds, Peter N.; Kobe, Boštjan

2007-01-01

Metal-binding sites are ubiquitous in proteins and can be readily utilized for phasing. It is shown that a protein crystal structure can be solved using single-wavelength anomalous diffraction based on the anomalous signal of a cobalt ion measured on a conventional monochromatic X-ray source. The unique absorption edge of cobalt (1.61 Å) is compatible with the Cu Kα wavelength (1.54 Å) commonly available in macromolecular crystallography laboratories. This approach was applied to the determination of the structure of Melampsora lini avirulence protein AvrL567-A, a protein with a novel fold from the fungal pathogen flax rust that induces plant disease resistance in flax plants. This approach using cobalt ions may be applicable to all cobalt-binding proteins and may be advantageous when synchrotron radiation is not readily available. PMID:17329816

Structural, optical, mechanical and dielectric studies of pure and doped L-Prolinium trichloroacetate single crystals.

PubMed

Renuka, N; Ramesh Babu, R; Vijayan, N; Vasanthakumar, Geetha; Krishna, Anuj; Ramamurthi, K

2015-02-25

In the present work, pure and metal substituted L-Prolinium trichloroacetate (LPTCA) single crystals were grown by slow evaporation method. The grown crystals were subjected to single crystal X-ray diffraction (XRD), powder X-ray diffraction, FTIR, UV-Visible-NIR, hardness, photoluminescence and dielectric studies. The dopant concentration in the crystals was measured by inductively coupled plasma (ICP) analysis. Single crystal X-ray diffraction studies of the pure and metal substituted LPTCA revealed that the grown crystals belong to the trigonal system. Ni(2+) and Co(2+) doping slightly altered the lattice parameters of LPTCA without affecting the basic structure of the crystal. FTIR spectral analysis confirms the presence of various functional groups in the grown crystals. The mechanical behavior of pure and doped crystals was analyzed by Vickers's microhardness test. The optical transmittance, dielectric and photoluminescence properties of the pure and doped crystals were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

Diffraction imaging for in situ characterization of double-crystal X-ray monochromators

DOE PAGES

Stoupin, Stanislav; Liu, Zunping; Heald, Steve M.; ...

2015-10-30

In this paper, imaging of the Bragg-reflected X-ray beam is proposed and validated as an in situ method for characterization of the performance of double-crystal monochromators under the heat load of intense synchrotron radiation. A sequence of images is collected at different angular positions on the reflectivity curve of the second crystal and analyzed. The method provides rapid evaluation of the wavefront of the exit beam, which relates to local misorientation of the crystal planes along the beam footprint on the thermally distorted first crystal. The measured misorientation can be directly compared with the results of finite element analysis. Finally,more » the imaging method offers an additional insight into the local intrinsic crystal quality over the footprint of the incident X-ray beam.« less

Spatial resolution of a spherical x-ray crystal spectrometer at various magnifications

DOE PAGES

Gao, Lan; Hill, K. W.; Bitter, M.; ...

2016-08-23

Here, a high spatial resolution of a few μm is often required for probing small-scale high-energy-density plasmas using high resolution x-ray imaging spectroscopy. This resolution can be achieved by adjusting system magnification to overcome the inherent limitation of the detector pixel size. Laboratory experiments on investigating the relation between spatial resolution and system magnification for a spherical crystal spectrometer are presented. Tungsten Lβ 2 rays from a tungsten-target micro-focus x-ray tube were diffracted by a Ge 440 crystal, which was spherically bent to a radius of 223 mm, and imaged onto an x-ray CCD with 13-μm pixel size. The source-to-crystalmore » (p) and crystal-to-detector (q) distances were varied to produce spatial magnifications ( M = q/p) ranging from 2 to 10. The inferred instrumental spatial width reduces with increasing system magnification M. However, the experimental measurement at each M is larger than the theoretical value of pixel size divided by M. Future work will focus on investigating possible broadening mechanisms that limit the spatial resolution.« less

Role of Acentric Displacements on the Crystal Structure and Second-Harmonic Generating Properties of RbPbCO3F and CsPbCO3F

PubMed Central

2015-01-01

Two lead fluorocarbonates, RbPbCO3F and CsPbCO3F, were synthesized and characterized. The materials were synthesized through solvothermal and conventional solid-state techniques. RbPbCO3F and CsPbCO3F were structurally characterized by single-crystal X-ray diffraction and exhibit three-dimensional (3D) crystal structures consisting of corner-shared PbO6F2 polyhedra. For RbPbCO3F, infrared and ultraviolet–visible spectroscopy and thermogravimetric and differential thermal analysis measurements were performed. RbPbCO3F is a new noncentrosymmetric material and crystallizes in the achiral and nonpolar space group P6̅m2 (crystal class 6̅m2). Powder second-harmonic generation (SHG) measurements on RbPbCO3F and CsPbCO3F using 1064 nm radiation revealed an SHG efficiency of approximately 250 and 300 × α-SiO2, respectively. Charge constants d33 of approximately 72 and 94 pm/V were obtained for RbPbCO3F and CsPbCO3F, respectively, through converse piezoelectric measurements. Electronic structure calculations indicate that the nonlinear optical response originates from the distorted PbO6F2 polyhedra, because of the even–odd parity mixing of the O 2p states with the nearly spherically symmetric 6s electrons of Pb2+. The degree of inversion symmetry breaking is quantified using a mode-polarization vector analysis and is correlated with cation size mismatch, from which it is possible to deduce the acentric properties of 3D alkali-metal fluorocarbonates. PMID:24867361

Diffraction and Imaging Study of Imperfections of Protein Crystals with Coherent X-rays

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Thomas, B. R.; Chernov, A. A.; Chu, Y. S.; Lai, B.

2004-01-01

High angular-resolution x-ray diffraction and phase contrast x-ray imaging were combined to study defects and perfection of protein crystals. Imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of a uniformly grown lysozyme crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in diffraction images. X-ray imaging and diffraction characterization of the quality of apoferritin crystals will also be discussed in the presentation.

Direct detection of x-rays for protein crystallography employing a thick, large area CCD

DOEpatents

Atac, Muzaffer; McKay, Timothy

1999-01-01

An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

Expression and X-Ray Structural Determination of the Nucleoprotein of Lassa Fever Virus.

PubMed

Qi, Xiaoxuan; Wang, Wenjian; Dong, Haohao; Liang, Yuying; Dong, Changjiang; Ly, Hinh

2018-01-01

We describe methods to express the nucleoprotein (NP) of Lassa fever virus (LASV) in E. coli, to purify and crystallize it using the sitting-drop vapor diffusion method. The crystals were screened using Rigaku micro-007 X-ray generator and a dataset was collected at a resolution of 2.36 Å. The crystals belong to space group P3, with the unit cell parameters a = b = 176.35 Å, c = 56.40 Å, α = β = 90°, and γ = 120°. Using the X-ray diffraction method, we constructed a three-dimensional structure of the LASV NP that should aid in the development of novel therapeutic strategies against this virus, for which vaccine and effective treatment modalities are currently unavailable.

Enantiomeric resolution and X-ray optical activity of a tricobalt extended metal atom chain.

PubMed

Srinivasan, Anandi; Cortijo, Miguel; Bulicanu, Vladimir; Naim, Ahmad; Clérac, Rodolphe; Sainctavit, Philippe; Rogalev, Andrei; Wilhelm, Fabrice; Rosa, Patrick; Hillard, Elizabeth A

2018-02-07

A simple procedure based on anion exchange was employed for the enantiomeric resolution of the extended metal atom chain (EMAC) [Co 3 (dpa) 4 (MeCN) 2 ] 2+ . Use of the chiral salt (NBu 4 ) 2 [As 2 (tartrate) 2 ], (Λ- 1 or Δ- 1 ), resulted in the selective crystallization of the EMAC enantiomers as [Δ-Co 3 (dpa) 4 (MeCN) 2 ](NBu 4 ) 2 [Λ-As 2 (tartarte) 2 ] 2 , (Δ- 2 ) and [Λ-Co 3 (dpa) 4 (MeCN) 2 ](NBu 4 ) 2 [Δ-As 2 (tartrate) 2 ] 2 (Λ- 2 ), respectively, in the P 42 1 2 space group, whereas a racemic mixture of 1 yielded [Co 3 (dpa) 4 (MeCN) 2 ][As 2 (tartrate) 2 ]·2MeCN ( rac - 3 ), which crystallized in the C 2/ c space group. The local electronic and magnetic structure of the EMAC enantiomers was studied, exploiting a variety of dichroisms in single crystals. A strong linear dichroism at the Co K-edge was observed in the orthoaxial configuration, whereas it vanished in the axial orientation, thus spectroscopically confirming the D 4 crystal symmetry. Compounds Δ- 2 and Λ- 2 are shown to be enantiopure materials as evidenced by mirror-image natural circular dichroism spectra in the UV/vis in solution and in the X-ray range at the Co K-edge in single crystals. The surprising absence of detectable X-ray magnetic circular dichroism or X-ray magnetochiral dichroism signals at the Co K-edge, even at low temperature (3 K) and a high magnetic field (17 T), is ascribed to a strongly delocalized spin density on the tricobalt core.

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

NASA Astrophysics Data System (ADS)

Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu D.; Petukhov, A. V.; Byelov, D.; Chernyshov, D.; Okorokov, A. I.; Bouwman, W. G.; Grigoriev, S. V.

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length Ltran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length Llong is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10°.

Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

2009-01-01

Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

In vacuo X-ray data collection from graphene-wrapped protein crystals.

PubMed

Warren, Anna J; Crawshaw, Adam D; Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana; Salgado, Paula S; Evans, Gwyndaf

2015-10-01

The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torre-Fernández, Laura; Trobajo, Camino; Pedro, Imanol de

The ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O (x=0.00, 0.34, 0.59, 0.70, 1.00), and the deuterated forms, ND{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·D{sub 2}O (x=0.00, 0.38, 0.48, 0.69, 0.85), have been synthesized under mild hydrothermal conditions and characterised using X-ray and neutron diffraction, chemical and thermal analysis, and magnetic measurements. Their crystal structures, including hydrogen positions, were determined by Rietveld refinement using single-crystal X-ray and neutron powder diffraction data. The space group of these orthorhombic crystals modifies as a function of their composition. The magnetic susceptibility and magnetization measurements of these ammonium–cobalt–nickel phosphates show antiferromagnetic behaviour, and the Neel temperaturemore » evolves from 5.5 K (x=0.00) up to 13.2 K (x=1.00). - Graphical abstract: We obtained single crystals for all the members of the family. In this series, although all crystals are orthorhombic, the space group changes as a function of the composition, showing how the single-crystal diffraction data is capable to manifest structural subtleties that had not been described before for this group of materials. All the investigated materials behave antiferromagnetically with ordering temperatures from 5.5 K up to 13.2 K. Display Omitted - Highlights: • The ammonium–cobalt–nickel phosphates, NH{sub 4}[Co{sub 1−x}Ni{sub x}PO{sub 4}]·H{sub 2}O (x=0.00, 0.34, 0.59, 0.70, 1.00) and the deuterated forms ND4[Co1-xNixPO4]·D{sub 2}O (x=0.00, 0.38, 0.49, 0.68, 0.85) have synthesized by hydrothermal synthesis. • The structural studies of these compounds are introduced as a function of the composition. • The magnetic studies show an antiferromagnetically behavior with ordering temperatures from 5.5 K to 13.2 K.« less

Preparation, Structural and Dielectric Behaviors of CoxMn1-xMn2O4 (0 ≤ x ≤ 1) Nanoparticles

NASA Astrophysics Data System (ADS)

Taufiq, A.; Muzammil, M.; Fuad, A.; Hidayat, N.; Sunaryono, S.; Mufti, N.; Hidayat, A.; Diantoro, M.; Munasir, M.

2018-05-01

Cobalt-manganese oxide nanoparticles become remarkable metal oxides due to their physical characters, for example, their electrical properties. In this paper, we report the synthesis of Co x Mn1-x Mn2O4 (0 ≤ x ≤ 1) nanoparticles via a precipitation method. The structural and dielectric properties were investigated by means of X-ray diffractometer (XRD) and LCR-meter. From the data analysis, it was found that the Co x Mn1-x Mn2O4 particles structured spinel cubic with the particle size ranging from 22.7 to 28.6 nm. Increasing Co2+ ions led to declining lattice and crystal volume of the Co x Mn1-x Mn2O4 nanoparticles. Such phenomenon was originated from the substitution process of Co2+ ions that change the metal construction both at the octahedral and tetrahedral sites. Furthermore, the Co2+ ion substitution resulted in an increase in the dielectric properties of the Co x Mn1-x Mn2O4 nanoparticles regarding with dipole moment. Interestingly, the increase was also influenced by reducing the particle size and crystal volume of the Co x Mn1-x Mn2O4 nanoparticles.

Compositional homogeneity and X-ray topographic analyses of CdTe xSe 1-x grown by the vertical Bridgman technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, U. N.; Bolotnikov, A. E.; Camarda, G. S.

2015-02-01

We grew CdTe xSe 1-x crystals with nominal Se concentrations of 5%, 7%, and 10% by the vertical Bridgman technique, and evaluated their compositional homogeneity and structural quality at the NSLS’ X-ray fluorescence and white beam X-ray topography beam lines. Both X-ray fluorescence and photoluminescence mapping revealed very high compositional homogeneity of the CdTe xSe 1-x crystals. Here, we noted that those crystals with higher concentrations of Se were more prone to twinning than those with a lower content. The crystals were fairly free from strains and contained low concentrations of sub-grain boundaries and their networks.

Crystallization and preliminary X-ray analysis of pyruvate kinase from Bacillus stearothermophilus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, Kenichiro; Ito, Sohei; Shimizu-Ibuka, Akiko

2005-08-01

This report describes the crystallization and X-ray diffraction data collection of three types (wild-type, W416F/V435W and C9S/C268S) of B. stearothermophilus. Crystals of C9S/C268S belonged to space group P6{sub 2}22 and diffracted to a resolution of 2.4 Å. Pyruvate kinase (PK) from a moderate thermophile, Bacillus stearothermophilus (BstPK), is an allosteric enzyme activated by AMP and ribose 5-phosphate but not by fructose 1,6-bisphosphate (FBP). However, almost all other PKs are activated by FBP. The wild-type and W416F/V435W mutant BstPKs were crystallized by the hanging-drop vapour-diffusion method. However, they were unsuitable for structural analysis because their data sets exhibited low completeness. Amore » crystal suitable for structural analysis was obtained using C9S/C268S enzyme. The crystal belonged to space group P6{sub 2}22, with unit-cell parameters a = b = 145.97, c = 118.03 Å.« less

Improving Beamline X-ray Optics by Analyzing the Damage to Crystallographic Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zientek, John; Maj, Jozef; Navrotski, Gary

2015-01-02

The mission of the X-ray Characterization Laboratory in the X-ray Science Division (XSD) at the Advanced Photon Source (APS) is to support both the users and the Optics Fabrication Facility that produces high performance optics for synchrotron X-ray beamlines. The Topography Test Unit (TTU) in the X-ray Lab has been successfully used to characterize diffracting crystals and test monochromators by quantifying residual surface stresses. This topographic method has also been adapted for testing standard X-ray mirrors, characterizing concave crystal optics and in principle, can be used to visualize residual stresses on any optic made from single crystalline material. The TTUmore » has been instrumental in quantitatively determining crystal mounting stresses which are mechanically induced by positioning, holding, and cooling fixtures. It is this quantitative aspect that makes topography so useful since the requirements and responses for crystal optics and X-ray mirrors are quite different. In the case of monochromator crystals, even small residual or induced stresses, on the order of tens of kPa, can cause detrimental distortions to the perfect crystal rocking curves. Mirrors, on the other hand, are much less sensitive to induced stresses where stresses that are an order of magnitude greater can be tolerated. This is due to the fact that the surface rather than the lattice-spacing determines a mirror’s performance. For the highly sensitive crystal optics, it is essential to measure the in-situ rocking curves using topographs as mounting fixtures are adjusted. In this way, high heat-load monochromator crystals can be successfully mounted with minimum stress. Topographical analysis has been shown to be a highly effective method to visualize and quantify the distribution of stresses, to help identify methods that mitigate stresses, and most notably to improve diffractive crystal optic rocking curves.« less

Order-disorder-reorder process in thermally treated dolomite samples: a combined powder and single-crystal X-ray diffraction study

NASA Astrophysics Data System (ADS)

Zucchini, A.; Comodi, P.; Katerinopoulou, A.; Balic-Zunic, T.; McCammon, C.; Frondini, F.

2012-04-01

A combined powder and single-crystal X-ray diffraction analysis of dolomite [CaMg(CO3)2] heated to 1,200°C at 3 GPa was made to study the order-disorder-reorder process. The order/disorder transition is inferred to start below 1,100°C, and complete disorder is attained at approximately 1,200°C. Twinned crystals characterized by high internal order were found in samples annealed over 1,100°C, and their fraction was found to increase with temperature. Evidences of twinning domains combined with probable remaining disordered portions of the structure imply that reordering processes occur during the quench. Twin domains are hereby proposed as a witness to thermally induced intra-layer-type cation disordering.

Structure of high-resolution K β1 ,3 x-ray emission spectra for the elements from Ca to Ge

NASA Astrophysics Data System (ADS)

Ito, Y.; Tochio, T.; Yamashita, M.; Fukushima, S.; Vlaicu, A. M.; Syrocki, Ł.; Słabkowska, K.; Weder, E.; Polasik, M.; Sawicka, K.; Indelicato, P.; Marques, J. P.; Sampaio, J. M.; Guerra, M.; Santos, J. P.; Parente, F.

2018-05-01

The K β x-ray spectra of the elements from Ca to Ge have been systematically investigated using a high-resolution antiparallel double-crystal x-ray spectrometer. Each K β1 ,3 natural linewidth has been corrected using the instrumental function of this type of x-ray spectrometer, and the spin doublet energies have been obtained from the peak position values in K β1 ,3 x-ray spectra. For all studied elements the corrected K β1 x-ray lines FWHM increase linearly as a function of Z . However, for K β3 x-ray lines this dependence is generally not linear in the case of 3 d elements but increases from Sc to Co elements. It has been found that the contributions of satellite lines are considered to be [K M ] shake processes. Our theoretically predicted synthetic spectra of Ca, Mn, Cu, and Zn are in very good agreement with our high-resolution measurements, except in the case of Mn, due to the open-shell valence configuration effect (more than 7000 transitions for diagram lines and more than 100 000 transitions for satellite lines) and the influence of the complicated structure of the metallic Mn.

Single-crystal films of a combination of materials (co-crystal) involving DAST and IR-125 for electro-optic applications

NASA Astrophysics Data System (ADS)

Narayanan, A.; Titus, J.; Rajagopalan, H.; Vippa, P.; Thakur, M.

2006-03-01

Single-crystal film of DAST (4'-dimethylamino-N-methyl-4-stilbazolium tosylate) has been shown [1] to have exceptionally large electro-optic coefficients (r11 ˜ 770 pm/V at 633 nm). In this report, single crystal film of a combination of materials (co-crystal) involving DAST and a dye molecule IR-125 will be discussed. Modified shear method was used to prepare the co-crystal films. The film has been characterized using polarized optical microscopy, optical absorption spectroscopy and x-ray diffraction. The optical absorption spectrum has two major bands: one at about 350--600 nm corresponding to DAST and the other at about 600-900 nm corresponding to IR-125. The x-ray diffraction results show peaks involving the presence of DAST and IR-125 within the co-crystal film. Since the co-crystal has strong absorption at longer wavelengths it is expected to show higher electro-optic coefficients at longer wavelengths. Preliminary measurements at 1.55 μm indicate a high electro-optic coefficient of the co-crystal film. [1] Swamy, Kutty, Titus, Khatavkar, Thakur, Appl. Phys. Lett. 2004, 85, 4025; Kutty, Thakur, Appl. Phys. Lett. 2005, 87, 191111.

Laboratory-based micro-X-ray fluorescence setup using a von Hamos crystal spectrometer and a focused beam X-ray tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kayser, Y., E-mail: yves.kayser@psi.ch; Paul Scherrer Institut, 5232 Villigen-PSI; Błachucki, W.

2014-04-15

The high-resolution von Hamos bent crystal spectrometer of the University of Fribourg was upgraded with a focused X-ray beam source with the aim of performing micro-sized X-ray fluorescence (XRF) measurements in the laboratory. The focused X-ray beam source integrates a collimating optics mounted on a low-power micro-spot X-ray tube and a focusing polycapillary half-lens placed in front of the sample. The performances of the setup were probed in terms of spatial and energy resolution. In particular, the fluorescence intensity and energy resolution of the von Hamos spectrometer equipped with the novel micro-focused X-ray source and a standard high-power water-cooled X-raymore » tube were compared. The XRF analysis capability of the new setup was assessed by measuring the dopant distribution within the core of Er-doped SiO{sub 2} optical fibers.« less

Observation of divergent-beam X-ray diffraction from a crystal of diamond using synchrotron radiation.

PubMed

Glazer, A M; Collins, S P; Zekria, D; Liu, J; Golshan, M

2004-03-01

In 1947 Kathleen Lonsdale conducted a series of experiments on X-ray diffraction using a divergent beam external to a crystal sample. Unlike the Kossel technique, where divergent X-rays are excited by the presence of fluorescing atoms within the crystal, the use of an external divergent source made it possible to study non-fluorescing crystals. The resulting photographs not only illustrated the complexity of X-ray diffraction from crystals in a truly beautiful way, but also demonstrated unprecedented experimental precision. This long-forgotten work is repeated here using a synchrotron radiation source and, once again, considerable merit is found in Lonsdale's technique. The results of this experiment suggest that, through the use of modern 'third-generation' synchrotron sources, divergent-beam diffraction could soon enjoy a renaissance for high-precision lattice-parameter determination and the study of crystal perfection.

X-ray spectroscopic characterization of Co(IV) and metal–metal interactions in Co 4O 4: Electronic structure contributions to the formation of high-valent states relevant to the oxygen evolution reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadt, Ryan G.; Hayes, Dugan; Brodsky, Casey N.

2016-08-12

In this paper, the formation of high-valent states is a key factor in making highly active transition metal-based catalysts of the oxygen-evolving reaction (OER). These high oxidation states will be strongly influenced by the local geometric and electronic structures of the metal ion, which is difficult to study due to spectroscopically active and complex backgrounds, short lifetimes, and limited concentrations. Here, we use a wide range of complementary X-ray spectroscopies coupled to DFT calculations to study Co 4O 4 cubanes, which provide insight into the high-valent Co(IV) centers responsible for the activity of molecular and heterogeneous OER catalysts. The combinationmore » of X-ray absorption and 1s3p resonant inelastic X-ray scattering (Kβ RIXS) allow Co(IV) to be isolated and studied against a spectroscopically active Co(III) background. Co K- and L-edge X-ray absorption data allow for a detailed characterization of the 3d-manifold of effectively localized Co(IV) centers and provide a direct handle on the ligand field environment and covalency of the t 2g-based redox active molecular orbital. Kβ RIXS is also shown to provide a powerful probe of Co(IV), and specific spectral features are sensitive to the degree of oxo-mediated metal-metal coupling across Co 4O 4. Guided by the data, calculations show electron-hole delocalization can actually oppose Co(IV) formation. Computational extension of Co 4O 4 to CoM 3O 4 structures (M = redox-inactive metal) defines electronic structure contri-butions to Co(IV) formation. Redox activity is shown to be linearly related to covalency, and M(III) oxo inductive effects on Co(IV) oxo bonding can tune the covalency of high-valent sites over a large range and thereby tune E 0 over hundreds of mVs.« less

Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

PubMed Central

Heymann, Michael; Opthalage, Achini; Wierman, Jennifer L.; Akella, Sathish; Szebenyi, Doletha M. E.; Gruner, Sol M.; Fraden, Seth

2014-01-01

An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation. PMID:25295176

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Abramchik, Yu. A., E-mail: tostars@mail.ru; Zhukhlistova, N. E., E-mail: ugama@yandex.ru

2015-09-15

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.more » 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.« less

Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis

PubMed Central

Suganuma, Masatoshi; Teh, Aik Hong; Makino, Masatomo; Shimizu, Nobutaka; Kaneko, Tomonori; Hirata, Kunio; Yamamoto, Masaki; Kumasaka, Takashi

2009-01-01

RsbX from Bacillus subtilis is a manganese-dependent PPM phosphatase and negatively regulates the signal transduction of the general stress response by the dephosphorylation of RsbS and RsbR, which are activators of the alternative RNA polymerase σ factor SigB. In order to elucidate the structural–functional relationship of its Ser/Thr protein-phosphorylation mechanism, an X-ray crystallographic diffraction study of RsbX was performed. Recombinant RsbX was expressed in Escherichia coli, purified and crystallized. Crystals were obtained using the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 1.06 Å resolution with an R merge of 8.1%. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 33.3, b = 41.7, c = 68.6 Å, α = 98.8, β = 90.0, γ = 108.4°. PMID:19923733

Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wubben, T.; Mesecar, A.D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observedmore » in the MtPPAT-CoA complex.« less

Ethanol fixed brain imaging by phase-contrast X-ray technique

NASA Astrophysics Data System (ADS)

Takeda, Tohoru; Thet-Thet-Lwin; Kunii, Takuya; Sirai, Ryota; Ohizumi, Takahito; Maruyama, Hiroko; Hyodo, Kazuyuki; Yoneyama, Akio; Ueda, Kazuhiro

2013-03-01

The two-crystal phase-contrast X-ray imaging technique using an X-ray crystal interferometer can depict the fine structures of rat's brain such as cerebral cortex, white matter, and basal ganglia. Image quality and contrast by ethanol fixed brain showed significantly better than those by usually used formalin fixation at 35 keV X-ray energy. Image contrast of cortex by ethanol fixation was more than 3-times higher than that by formalin fixation. Thus, the technique of ethanol fixation might be better suited to image cerebral structural detail at 35 keV X-ray energy.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Single-crystal diamond refractive lens for focusing X-rays in two dimensions.

PubMed

Antipov, S; Baryshev, S V; Butler, J E; Antipova, O; Liu, Z; Stoupin, S

2016-01-01

The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

Single-crystal diamond refractive lens for focusing X-rays in two dimensions

PubMed Central

Antipov, S.; Baryshev, S. V.; Butler, J. E.; Antipova, O.; Liu, Z.; Stoupin, S.

2016-01-01

The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses. PMID:26698059

X-Ray Crystallography Reagent

NASA Technical Reports Server (NTRS)

Morrison, Dennis R. (Inventor); Mosier, Benjamin (Inventor)

2003-01-01

Microcapsules prepared by encapsulating an aqueous solution of a protein, drug or other bioactive substance inside a semi-permeable membrane by are disclosed. The microcapsules are formed by interfacial coacervation under conditions where the shear forces are limited to 0-100 dynes per square centimeter at the interface. By placing the microcapsules in a high osmotic dewatering solution. the protein solution is gradually made saturated and then supersaturated. and the controlled nucleation and crystallization of the protein is achieved. The crystal-filled microcapsules prepared by this method can be conveniently harvested and stored while keeping the encapsulated crystals in essentially pristine condition due to the rugged. protective membrane. Because the membrane components themselves are x-ray transparent, large crystal-containing microcapsules can be individually selected, mounted in x-ray capillary tubes and subjected to high energy x-ray diffraction studies to determine the 3-D smucture of the protein molecules. Certain embodiments of the microcapsules of the invention have composite polymeric outer membranes which are somewhat elastic, water insoluble, permeable only to water, salts, and low molecular weight molecules and are structurally stable in fluid shear forces typically encountered in the human vascular system.

Improvement of graphite crystal analyzer for light elements on X-ray fluorescence holography measurement

NASA Astrophysics Data System (ADS)

Happo, Naohisa; Hada, Takuma; Kubota, Atsushi; Ebisu, Yoshihiro; Hosokawa, Shinya; Kimura, Koji; Tajiri, Hiroo; Matsushita, Tomohiro; Hayashi, Kouichi

2018-05-01

Using a graphite crystal analyzer, focused monochromatic fluorescent X-rays can be obtained on an X-ray fluorescence holography (XFH) measurement. To measure the holograms of elements lighter than Ti, we improved a cylindrical-type crystal analyzer and constructed a small C-shaped analyzer. Using the constructed C-shaped analyzer, a Ca Kα hologram of a fluorite single crystal was obtained, from which we reconstructed a clear atomic image. The XFH measurements for the K, Ca, and Sc elements become possible using the presently constructed analyzer.

The high-pressure behavior of spherocobaltite (CoCO3): a single crystal Raman spectroscopy and XRD study

NASA Astrophysics Data System (ADS)

Chariton, Stella; Cerantola, Valerio; Ismailova, Leyla; Bykova, Elena; Bykov, Maxim; Kupenko, Ilya; McCammon, Catherine; Dubrovinsky, Leonid

2018-01-01

Magnesite (MgCO3), calcite (CaCO3), dolomite [(Ca, Mg)CO3], and siderite (FeCO3) are among the best-studied carbonate minerals at high pressures and temperatures. Although they all exhibit the calcite-type structure ({R}\\bar{3}{c}) at ambient conditions, they display very different behavior at mantle pressures. To broaden the knowledge of the high-pressure crystal chemistry of carbonates, we studied spherocobaltite (CoCO3), which contains Co2+ with cation radius in between those of Ca2+ and Mg2+ in calcite and magnesite, respectively. We synthesized single crystals of pure spherocobaltite and studied them using Raman spectroscopy and X-ray diffraction in diamond anvil cells at pressures to over 55 GPa. Based on single crystal diffraction data, we found that the bulk modulus of spherocobaltite is 128 (2) GPa and K' = 4.28 (17). CoCO3 is stable in the calcite-type structure up to at least 56 GPa and 1200 K. At 57 GPa and after laser heating above 2000 K, CoCO3 partially decomposes and forms CoO. In comparison to previously studied carbonates, our results suggest that at lower mantle conditions carbonates can be stable in the calcite-type structure if the radius of the incorporated cation(s) is equal or smaller than that of Co2+ (i.e., 0.745 Å).

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kusakizako, Tsukasa; Tanaka, Yoshiki; Hipolito, Christopher J.

A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-raymore » diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.« less

N-donor co-ligands driven two new Co(II)- coordination polymers with bi- and trinuclear units: Crystal structures, and magnetic properties

NASA Astrophysics Data System (ADS)

Zhou, Zhi-Hang; Han, Min-Le; Wu, Ya-Pan; Dong, Wen-Wen; Li, Dong-Sheng; Lu, Jack Y.

2016-10-01

Two new Co(II) coordination polymers(CPs), namely [Co2(bpe)2(Hbppc)]n (1) and [Co3(μ3-OH)(bppc)(bpm)(H2O)]·3H2O (2) (H5bppc=biphenyl-2,4,6,3‧,5‧-pentacarboxylic acid, bpe=1,2-bis(4-pyridyl)ethene, bpm=bis(4-pyridyl)amine), have been obtained and characterized by elemental analysis, single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), IR spectra and thermogravimetric analysis (TGA). 1 shows a binodal (4,6)-connected fsc net with a (44·610·8)(44·62) topology, while 2 shows a binodal (5,7)-connected 3D network based on trinuclear [Co3(μ3-OH)]5+ units with unusual (3.46.52.6)(32.46.57.65.7) topology. Variable-temperature magnetic susceptibility measurements reveals that complex 1 shows ferromagnetic interactions between the adjacent Co(II) ions, whereas 2 is a antiferromagnetic system.

Local Structure and Surface Properties of CoxZn1-xO Thin Films for Ozone Gas Sensing.

PubMed

Catto, Ariadne C; Silva, Luís F da; Bernardi, Maria Inês B; Bernardini, Sandrine; Aguir, Khalifa; Longo, Elson; Mastelaro, Valmor R

2016-10-05

A detailed study of the structural, surface, and gas-sensing properties of nanostructured Co x Zn 1-x O films is presented. X-ray diffraction (XRD) analysis revealed a decrease in the crystallization degree with increasing Co content. The X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopies (XPS) revealed that the Co 2+ ions preferentially occupied the Zn 2+ sites and that the oxygen vacancy concentration increased as the amount of cobalt increased. Electrical measurements showed that the Co dopants not only enhanced the sensor response at low ozone levels (ca. 42 ppb) but also led to a decrease in the operating temperature and improved selectivity. The enhancement in the gas-sensing properties was attributed to the presence of oxygen vacancies, which facilitated ozone adsorption.

A co-crystal between benzene and ethane: a potential evaporite material for Saturn’s moon Titan

PubMed Central

Maynard-Casely, Helen E.; Hodyss, Robert; Cable, Morgan L.; Vu, Tuan Hoang; Rahm, Martin

2016-01-01

Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C—H⋯π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules. The co-crystal has a 3:1 benzene:ethane stoichiometry and is described in the space group with a = 15.977 (1) Å and c = 5.581 (1) Å at 90 K, with a density of 1.067 g cm−3. The conditions under which this co-crystal forms identify it is a potential that forms from evaporation of Saturn’s moon Titan’s lakes, an evaporite material. PMID:27158505

Fluorescence X-ray absorption spectroscopy using a Ge pixel array detector: application to high-temperature superconducting thin-film single crystals.

PubMed

Oyanagi, H; Tsukada, A; Naito, M; Saini, N L; Lampert, M O; Gutknecht, D; Dressler, P; Ogawa, S; Kasai, K; Mohamed, S; Fukano, A

2006-07-01

A Ge pixel array detector with 100 segments was applied to fluorescence X-ray absorption spectroscopy, probing the local structure of high-temperature superconducting thin-film single crystals (100 nm in thickness). Independent monitoring of pixel signals allows real-time inspection of artifacts owing to substrate diffractions. By optimizing the grazing-incidence angle theta and adjusting the azimuthal angle phi, smooth extended X-ray absorption fine structure (EXAFS) oscillations were obtained for strained (La,Sr)2CuO4 thin-film single crystals grown by molecular beam epitaxy. The results of EXAFS data analysis show that the local structure (CuO6 octahedron) in (La,Sr)2CuO4 thin films grown on LaSrAlO4 and SrTiO3 substrates is uniaxially distorted changing the tetragonality by approximately 5 x 10(-3) in accordance with the crystallographic lattice mismatch. It is demonstrated that the local structure of thin-film single crystals can be probed with high accuracy at low temperature without interference from substrates.

Synthesis, characterization, X-ray crystal structure and conductometry studying of a number of new Schiff base complexes; a new example of binuclear square pyramidal geometry of Cu(II) complex bridged with an oxo group

NASA Astrophysics Data System (ADS)

Golbedaghi, Reza; Alavipour, Ehsan

2015-11-01

Three new binuclear Cu(II), Mn(II), Co(II) complexes [Cu2(L) (ClO4)](ClO4)2 (1), [Mn2(L) (ClO4)](ClO4)2 (2), and [Co2(L) (ClO4)](ClO4)2 (3), {L = 1,3-bis(2-((Z)-(2-aminopropylimino)methyl)phenoxy)propan-2-ol} have been synthesized. Single crystal X-ray structure analysis of complex 1 showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. In addition, the crystal structure studying shows, a perchlorate ion has been bridged to the Cu(II) metal centers. However, two distorted square pyramidal Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, the conductometry behaviors of all complexes were studied in acetonitrile solution.

Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides

PubMed Central

Navarro, Marcos Vicente de A. S.; Vierira, Débora F.; Nagem, Ronaldo A. P.; de Araújo, Ana Paula U.; Oliva, Maria Luiza V.; Garratt, Richard C.

2005-01-01

A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P212121, with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (V M = 2.5 Å3 Da−1). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method. PMID:16511193

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from

X-ray Binaries and the Galaxy Structure in Hard X-rays

NASA Astrophysics Data System (ADS)

Lutovinov, Alexander

The Galaxy structure in the hard X-ray energy band (¿20 keV) was studied using data of the INTEGRAL observatory. A deep and nearly uniform coverage of the galactic plane allowed to increase significantly the sensitivity of the survey and discover several dozens new galac-tic sources. The follow-up observations with XMM-Newton and CHANDRA observatories in X-rays and ground-based telescopes in optical and infrared wavebands gave us a possibility to determine optical counterparts and distances for number of new and already known faint sources. That, in turn, allowed us to build the spatial distribution of different classes of galactic X-ray binaries and obtain preliminary results of the structure of the further part of the Galaxy.

X-ray shearing interferometer

DOEpatents

Koch, Jeffrey A [Livermore, CA

2003-07-08

An x-ray interferometer for analyzing high density plasmas and optically opaque materials includes a point-like x-ray source for providing a broadband x-ray source. The x-rays are directed through a target material and then are reflected by a high-quality ellipsoidally-bent imaging crystal to a diffraction grating disposed at 1.times. magnification. A spherically-bent imaging crystal is employed when the x-rays that are incident on the crystal surface are normal to that surface. The diffraction grating produces multiple beams which interfere with one another to produce an interference pattern which contains information about the target. A detector is disposed at the position of the image of the target produced by the interfering beams.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Single-crystal diamond refractive lens for focusing X-rays in two dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antipov, S.; Baryshev, Sergey; Butler, J. E.

2016-01-01

The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources formore » secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.« less

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin.

PubMed

Jaimohan, S M; Naresh, M D; Arumugam, V; Mandal, A B

2009-10-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 A resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 A, beta = 109.35 degrees . Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

Room temperature X- and gamma-ray detectors using thallium bromide crystals

NASA Astrophysics Data System (ADS)

Hitomi, K.; Muroi, O.; Shoji, T.; Suehiro, T.; Hiratate, Y.

1999-10-01

Thallium bromide (TlBr) is a compound semiconductor with wide band gap (2.68eV) and high X- and γ-ray stopping power. The TlBr crystals were grown by the horizontal travelling molten zone (TMZ) method using purified material. Two types of room temperature X- and γ-ray detectors were fabricated from the TlBr crystals: TlBr detectors with high detection efficiency for positron annihilation γ-ray (511keV) detection and TlBr detectors with high-energy resolution for low-energy X-ray detection. The detector of the former type demonstrated energy resolution of 56keV FWHM (11%) for 511keV γ-rays. Energy resolution of 1.81keV FWHM for 5.9keV was obtained from the detector of the latter type. In order to analyze noise characteristics of the detector-preamplifier assembly, the equivalent noise charge (ENC) was measured as a function of the amplifier shaping time for the high-resolution detector. This analysis shows that parallel white noise and /1/f noise were dominant noise sources in the detector system. Current-voltage characteristics of the TlBr detector with a small Peltier cooler were also measured. Significant reduction of the detector leakage current was observed for the cooled detectors.

Crystallization and preliminary X-ray diffraction studies of θ-toxin (perfringolysin O), a pore-forming cytolysin of Clostridium perfringens

NASA Astrophysics Data System (ADS)

Sugahara, Mitsuaki; Sekino-Suzuki, Naoko; Ohno-Iwashita, Yoshiko; Miki, Kunio

1996-10-01

θ-Toxin (perfringolysin O), a cholesterol-binding, pore-forming cytolysin of Clostridium perfringens type A was crystallized by the vapor diffusion procedure using polyethyleneglycol 4000 and sodium chloride as precipitants in 2-(cyclohexylamino)ethanesulfonic acid (CHES) buffer at pH 9.5. The diffraction patterns of precession photographs indicated that the crystals belong to the orthorhombic system and the space group C222 1 with unit-cell dimensions of a = 47.7 Å, b = 182.0 Å and c = 175.8 Å. Assuming that the asymmetric unit contains one or two molecules (Mw 52 700), the Vm value is calculated as 3.6 or 1.8 Å 3/dalton, respectively. The crystals diffract X-rays to at least 3 Å resolution and are suitable for high resolution X-ray crystal structure determination.

Synthesis, characterization, single crystal X-ray and DFT analysis of disubstituted phosphorodithioates

NASA Astrophysics Data System (ADS)

Kour, Mandeep; Kumar, Sandeep; Feddag, Ahmed; Andotra, Savit; Chouaih, Abdelkader; Gupta, Vivek K.; Kant, Rajni; Pandey, Sushil K.

2018-04-01

Disubstituted phosphorodithioates of the type [{(2,5-CH3)2C6H3O}2PS2HNEt3] (1) and [{(3,5-CH3)2C6H3O)2(PS2)}2] (2) were synthesized and characterized by IR and NMR (1H,13C and 31P) spectroscopic studies and as single crystal X-ray analysis. The compound 1 crystallizes in monoclinic space group P21/c whereas compound 2 crystallizes in triclinic space group Pbar1. The X-ray analysis reveals that in compound 1 phosphorus atom is coordinated to the two S and two O atoms to form tetrahedral geometry. The structure is stabilized by cation-anion Nsbnd H⋯S hydrogen bonded interactions. In compound 2, the two phosphorus atoms have a distorted tetrahedral geometry coordinated to two (3,5-CH3)2C6H3O groups. The molecule possesses a crystallographic center of symmetry and consists of zig-zag array of Sdbnd Psbnd Ssbnd Ssbnd Pdbnd S linkages with two diphenyldithiophosphate moieties in the trans configuration. Molecular geometries, HOMO-LUMO analysis and molecular electrostatic potential of compounds 1 and 2 are investigated by theoretical calculations using B3LYP functional with the 6-311G basis combination set in the ground state and compared with the experimental values.

Systematic search for spherical crystal X-ray microscopes matching 1–25 keV spectral line sources

DOE PAGES

Schollmeier, Marius S.; Loisel, Guillaume P.

2016-12-29

Spherical-crystal microscopes are used as high-resolution imaging devices for monochromatic x-ray radiography or for imaging the source itself. Crystals and Miller indices (hkl) have to be matched such that the resulting lattice spacing d is close to half the spectral wavelength used for imaging, to fulfill the Bragg equation with a Bragg angle near 90° which reduces astigmatism. Only a few suitable crystal and spectral-line combinations have been identified for applications in the literature, suggesting that x-ray imaging using spherical crystals is constrained to a few chance matches. In this paper, after performing a systematic, automated search over more thanmore » 9 × 10 6 possible combinations for x-ray energies between 1 and 25 keV, for six crystals with arbitrary Miller-index combinations hkl between 0 and 20, we show that a matching, efficient crystal and spectral-line pair can be found for almost every He α or K α x-ray source for the elements Ne to Sn. Finally, using the data presented here it should be possible to find a suitable imaging combination using an x-ray source that is specifically selected for a particular purpose, instead of relying on the limited number of existing crystal imaging systems that have been identified to date.« less

Effect of Fe-substitution on the structure and magnetism of single crystals Mn2-xFexBO4

NASA Astrophysics Data System (ADS)

Platunov, M. S.; Kazak, N. V.; Knyazev, Yu. V.; Bezmaternykh, L. N.; Moshkina, E. M.; Trigub, A. L.; Veligzhanin, A. A.; Zubavichus, Y. V.; Solovyov, L. A.; Velikanov, D. A.; Ovchinnikov, S. G.

2017-10-01

Single crystalline Mn2-xFexBO4 with x = 0.3, 0.5, 0.7 grown by the flux method have been studied by means of X-ray diffraction and X-ray absorption spectroscopy at both Mn and Fe K edges. The compounds were found to crystallize in an orthorhombic warwickite structure (sp. gr. Pnam). The lattice parameters change linearly with x thus obeying the Vegard's law. The Fe3+ substitution for Mn3+ has been deduced from the X-ray absorption near-edge structure (XANES) spectra. Two energy positions of the absorption edges have been observed in Mn K-edge XANES spectra indicating the presence of manganese in two different oxidation states. Extended X-ray absorption fine structure (EXAFS) analysis has shown the reduction of local structural distortions upon Fe substitution. The magnetization data have revealed a spin-glass transition at TSG = 11, 14 and 18 K for x = 0.3, 0.5 and 0.7, respectively.

Solubility of carbamazepine co-crystals in ethanolic solution

NASA Astrophysics Data System (ADS)

Ramle, Noor Ashila; Rahim, Syarifah Abd; Anuar, Nornizar; El-Hadad, Omar

2017-08-01

The study aimed to determine the solubility of carbamazepine (CBZ) co-crystals formed from co-crystal formers (CCFs) of nicotinamide (NIC), saccharin (SAC), succinic acid (SUC) and fumaric acid (FUM) at various temperatures (25-50°C). High Performance Liquid Chromatography (HPLC) was used to determine the solubility and the X-Ray Powder Diffraction was used to characterize the crystals. The solubility of CBZ-NIC and CBZ-FUM co-crystals were found to be higher than the solubility of the CBZ for the range of studied temperatures. However, opposite findings was obtained for CBZ-SUC co-crystal as its solubility is lower than the solubility of CBZ. Different trend was found for CBZ-SAC co-crystal in which for temperature lower than 40°C, the solubility of CBZ crystal is higher than the CBZ-SAC co-crystal. The solubility of CBZ-SAC co-crystal is higher than the solubility of CBZ at a temperature above 40°C. CBZ co-crystals with NIC and FUM have shown to increase the solubility of CBZ by solubility ratio of 1.95 and 1.24 respectively. However, the CBZ co-crystal with SAC was found to have similar solubility value as the CBZ.

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE PAGES

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.; ...

2017-02-10

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

STRUCTURAL UNITS OF STARCH DETERMINED BY X-RAY CRYSTAL STRUCTURE METHOD.

PubMed

Sponsler, O L

1923-07-20

structure is certainly not an amorphous structure, and on the other hand it is not crystalline in the common sense of the term. Parts of the grain, it is true, act as crystals in that for certain distances the layers of units are in planes, but taken as a whole the layers are curved. As to the validity of the conclusions, those pertaining to the type of lattice and to the size of the unit may be accepted as sound in our present knowledge of x-rays and crystal structure; those, however, pertaining to the nature and the spherical arrangement of the units, while they seem convincing, need the support of further investigation into the various structures deposited by living protoplasm. In conclusion, the assumption that the units form a sort of spherical space lattice, gives a picture of the starch grain which leads us to ponder over the nature of the activity in protoplasm when it is depositing solid substances. Starch, cellulose, and pectic bodies are about the only solid deposits made directly by the living substance of plants, and all three have the same proportional formula, C(6)H(10)O(5). Investigations, as yet incomplete, indicate that cellulose also consists of a regular arrangement of C(6)H(10)O(5) groups, each acting as a unit, but the spacing (6.14 x 6.14 x 5.55) is slightly different from that of starch. Pectin has not been studied. Protoplasm may be thought of as being composed of molecules of many different sizes, polypeptides, or even proteins forming the larger, and amino-acids the smaller, if water and electrolytes are ignored. The smaller molecules, such as those of the amino-acid, leucine, are approximately equal in size to the C(6)H(10)O(5) group of starch. That being the case, what can be the state of affairs at the interface when the starch particles are being deposited? Is it probable that protoplasm is homogeneous to the extent of being able to deposit these particles at 6 A.u. intervals? From quite another view-point a clear picture of the units of

Real-time x-ray scattering study of the initial growth of organic crystals on polymer brushes

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, Sung Yup; Ahn, Kwangseok; Kim, Doris Yangsoo

2014-04-21

We studied the early-stage growth structures of pentacene organic crystals grown on polymer brushes using real-time x-ray scattering techniques. In situ x-ray reflectivity and atomic force microscopy analyses revealed that at temperatures close to the glass transition temperature of polymer brush, the pentacene overlayer on a polymer brush film showed incomplete condensation and 3D island structures from the first monolayer. A growth model based on these observations was used to quantitatively analyze the real-time anti-Bragg x-ray scattering intensities measured during pentacene growth to obtain the time-dependent layer coverage of the individual pentacene monolayers. The extracted total coverage confirmed significant desorptionmore » and incomplete condensation in the pentacene films deposited on the polymer brushes. These effects are ascribed to the change in the surface viscoelasticity of the polymer brushes around the glass transition temperature.« less

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

NASA Astrophysics Data System (ADS)

Post, J. E.; Bish, D. L.; Heaney, P. J.

2006-05-01

Sepiolite is a hydrous Mg-silicate clay mineral with fibrous morphology that typically occurs as fine-grained, poorly crystalline masses. It occurs in a wide variety of geological environments and has been mined for centuries because of its many uses, e.g. in the pharmaceutical, fertilizer, and pesticide industries. Its versatile functionality derives from the large surface area and microporosity that are characteristic of the material. In recent years, sepiolite has received considerable attention with regard to the adsorption of organics, for use as a support for catalysts, as a molecular sieve, and as an inorganic membrane for ultrafiltration. Because of its fine-grained and poorly crystalline nature, it has not been possible to study sepiolite's crystal structure using single-crystal X-ray diffraction methods, and consequently many details of the structure are still not well known. In this study, Rietveld refinements using synchrotron powder X-ray diffraction data were used to investigate the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room- temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic water site. The RT structure under vacuum retained only ~1/8 of the zeolitic water and the volume decreased 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic water is lost by ~390 K, accompanied by a decrease in the a and c unit-cell parameters. Above ~600 K the sepiolite structure folds as one-half of the crystallographically bound water is lost. Rietveld refinements of the "anhydrous" sepiolite structure reveal that, in general, unit-cell parameters a, b, â and volume steadily decrease with increasing temperature; there is an obvious change in slope at ~820 K suggesting a phase

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abramchik, Yu. A.; Timofeev, V. I., E-mail: tostars@mail.ru; Muravieva, T. I.

2017-01-15

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample,more » which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.« less

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

NASA Astrophysics Data System (ADS)

Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Sinitsyna, E. V.; Esipov, R. S.; Kuranova, I. P.

2017-01-01

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus ( T. th HB27) has high thermal stability and shows maximum activity at 75°C, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P21 and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals

PubMed Central

Pauling, Linus

1988-01-01

Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, “noise”) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals. PMID:16593948

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

PubMed Central

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S.; Zatsepin, Nadia A.; Barty, Anton; Benner, W. Henry; Boutet, Sébastien; Feld, Geoffrey K.; Hau-Riege, Stefan P.; Kirian, Richard A.; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I.; Pardini, Tommaso; Segelke, Brent; Williams, Garth J.; Spence, John C. H.; Abela, Rafael; Coleman, Matthew; Evans, James E.; Schertler, Gebhard F. X.; Frank, Matthias; Li, Xiao-Dan

2014-01-01

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution. PMID:24914166

An Excel Spreadsheet for a One-Dimensional Fourier Map in X-ray Crystallography

ERIC Educational Resources Information Center

Clegg, William

2004-01-01

The teaching of crystal structure determination with single-crystal X-ray diffraction at undergraduate level faces numerous challenges. Single-crystal X-ray diffraction is used in a vast range of chemical research projects and forms the basis for a high proportion of structural results that are presented to high-school, undergraduate, and graduate…

Combining X-ray and neutron crystallography with spectroscopy.

PubMed

Kwon, Hanna; Smith, Oliver; Raven, Emma Lloyd; Moody, Peter C E

2017-02-01

X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H + ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.

SMALL ANGLE SCATTERING OF X-RAYS BY PLASTICALLY DEFORMED SINGLE CRYSTALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, W.H.; Smoluchowski, R.

1959-05-01

The small-angle scattering of x rays from single crystals of magnesium plastically deformed by simple shear was measured in the angular range of 4' to 5 deg . The crystals were subjected to both unidirectional and cyclic shear stresses applied along the STAl 1 2-bar 0! direction. Thin slices of the deformed single crystals were prepared using strainfree cutting and polishing techniques. The thin slices had orientations such that the slip direction was either parallel or perpendicular to the incident x-ray beam in order to observe any anisotropy in the scattering that might be due to dislocations. It was foundmore » that those samples which contained deformation twins within the irradiated volume produced rather large scattered intensity. This scattered intensity is interpreted as being due to double Bragg scattering. The scattered intensity from other specimens was attributed to surface scattering. No evidence for small angle scattering by dislocations was found. (auth)« less