Rietveld Refinement on X-Ray Diffraction Patterns of Bioapatite in Human Fetal Bones

PubMed Central

Meneghini, Carlo; Dalconi, Maria Chiara; Nuzzo, Stefania; Mobilio, Settimio; Wenk, Rudy H.

2003-01-01

Bioapatite, the main constituent of mineralized tissue in mammalian bones, is a calcium-phosphate-based mineral that is similar in structure and composition to hydroxyapatite. In this work, the crystallographic structure of bioapatite in human fetuses was investigated by synchrotron radiation x-ray diffraction (XRD) and microdiffraction (μ-XRD) techniques. Rietveld refinement analyses of XRD and μ-XRD data allow for quantitative probing of the structural modifications of bioapatite as functions of the mineralization process and gestational age. PMID:12609904

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

Preliminary X-ray crystallographic analysis of glutathione transferase zeta 1 (GSTZ1a-1a)

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

Boone, Christopher D.; Zhong, Guo; Smeltz, Marci

2014-01-21

Crystals of glutathione transferase zeta 1 were grown and shown to diffract X-rays to 3.1 Å resolution. They belonged to space group P1, with unit-cell parameters a = 42.0, b = 49.6, c = 54.6 Å, α = 82.9, β = 69.9, γ = 73.4°.

Crystallographic Characterization on Polycrystalline Ni-Mn-Ga Alloys with Strong Preferred Orientation.

PubMed

Li, Zongbin; Yang, Bo; Zou, Naifu; Zhang, Yudong; Esling, Claude; Gan, Weimin; Zhao, Xiang; Zuo, Liang

2017-04-27

Heusler type Ni-Mn-Ga ferromagnetic shape memory alloys can demonstrate excellent magnetic shape memory effect in single crystals. However, such effect in polycrystalline alloys is greatly weakened due to the random distribution of crystallographic orientation. Microstructure optimization and texture control are of great significance and challenge to improve the functional behaviors of polycrystalline alloys. In this paper, we summarize our recent progress on the microstructure control in polycrystalline Ni-Mn-Ga alloys in the form of bulk alloys, melt-spun ribbons and thin films, based on the detailed crystallographic characterizations through neutron diffraction, X-ray diffraction and electron backscatter diffraction. The presented results are expected to offer some guidelines for the microstructure modification and functional performance control of ferromagnetic shape memory alloys.

A Journey into Reciprocal Space; A crystallographer's perspective

NASA Astrophysics Data System (ADS)

Glazer, A. M.

2017-10-01

This book introduces undergraduate and graduate students to a crystallographer's view of real and reciprocal space, a concept that has been of particular use by crystallographers to understand the patterns of spots when x-rays are diffracted by crystals. It then proceeds to develop the concept in a form suitable for physics applications; such as how solid-state physicists use reciprocal space to explain various solid-state properties such as thermal and electrical phenomena.

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

NASA Technical Reports Server (NTRS)

Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

1972-01-01

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

Toward in situ x-ray diffraction imaging at the nanometer scale

NASA Astrophysics Data System (ADS)

Zatsepin, Nadia A.; Dilanian, Ruben A.; Nikulin, Andrei Y.; Gable, Brian M.; Muddle, Barry C.; Sakata, Osami

2008-08-01

We present the results of preliminary investigations determining the sensitivity and applicability of a novel x-ray diffraction based nanoscale imaging technique, including simulations and experiments. The ultimate aim of this nascent technique is non-destructive, bulk-material characterization on the nanometer scale, involving three dimensional image reconstructions of embedded nanoparticles and in situ sample characterization. The approach is insensitive to x-ray coherence, making it applicable to synchrotron and laboratory hard x-ray sources, opening the possibility of unprecedented nanometer resolution with the latter. The technique is being developed with a focus on analyzing a technologically important light metal alloy, Al-xCu (where x is 2.0-5.0 %wt). The mono- and polycrystalline samples contain crystallographically oriented, weakly diffracting Al2Cu nanoprecipitates in a sparse, spatially random dispersion within the Al matrix. By employing a triple-axis diffractometer in the non-dispersive setup we collected two-dimensional reciprocal space maps of synchrotron x-rays diffracted from the Al2Cu nanoparticles. The intensity profiles of the diffraction peaks confirmed the sensitivity of the technique to the presence and orientation of the nanoparticles. This is a fundamental step towards in situ observation of such extremely sparse, weakly diffracting nanoprecipitates embedded in light metal alloys at early stages of their growth.

Combined synchrotron X-ray tomography and X-ray powder diffraction using a fluorescing metal foil.

PubMed

Kappen, P; Arhatari, B D; Luu, M B; Balaur, E; Caradoc-Davies, T

2013-06-01

This study realizes the concept of simultaneous micro-X-ray computed tomography and X-ray powder diffraction using a synchrotron beamline. A thin zinc metal foil was placed in the primary, monochromatic synchrotron beam to generate a divergent wave to propagate through the samples of interest onto a CCD detector for tomographic imaging, thus removing the need for large beam illumination and high spatial resolution detection. Both low density materials (kapton tubing and a piece of plant) and higher density materials (Egyptian faience) were investigated, and elemental contrast was explored for the example of Cu and Ni meshes. The viability of parallel powder diffraction using the direct beam transmitted through the foil was demonstrated. The outcomes of this study enable further development of the technique towards in situ tomography∕diffraction studies combining micrometer and crystallographic length scales, and towards elemental contrast imaging and reconstruction methods using well defined fluorescence outputs from combinations of known fluorescence targets (elements).

Monochromatic X-ray sources based on a mechanism of real and virtual photon diffraction in crystals

NASA Astrophysics Data System (ADS)

Wagner, A. R.; Kuznetsov, S. I.; Potylitsyn, A. P.; Razin, S. V.; Uglov, S. R.; Zabaev, V. N.

2008-09-01

A source of monochromatic X-ray radiation is wanted in industry, science, medicine and so on. Many ways of making such a source are known. The present work describes two mechanisms for the creation of a monochromatic X-ray beam, which are parametric X-ray radiation (PXR) and bremsstrahlung diffraction (DBS). Both the experiments were carried out using an electron beam at a microtron. During the first experiment, the DBS process was investigated as a scattering of the Bremsstrahlung (BS) beam on the crystallographic surfaces of tungsten and pyrolytic graphite crystals. The second experiment consisted in the registration of the PXR and DBS yield during the passage of the electrons through the same crystals as in the first experiment. The spectral and orientation radiation characteristics and simulation results obtained for the DBS and PXR processes are presented. It is shown that the usage of mosaic crystalline targets is rather useful in order to obtain a monochromatic X-ray source based on bremsstrahlung diffraction from moderately relativistic electrons.

Nondestructive method and apparatus for imaging grains in curved surfaces of polycrystalline articles

DOEpatents

Carpenter, Donald A.

1995-01-01

A nondestructive method, and associated apparatus, are provided for determining the grain flow of the grains in a convex curved, textured polycrystalline surface. The convex, curved surface of a polycrystalline article is aligned in a horizontal x-ray diffractometer and a monochromatic, converging x-ray beam is directed onto the curved surface of the polycrystalline article so that the converging x-ray beam is diffracted by crystallographic planes of the grains in the polycrystalline article. The diffracted x-ray beam is caused to pass through a set of horizontal, parallel slits to limit the height of the beam and thereafter. The linear intensity of the diffracted x-ray is measured, using a linear position sensitive proportional counter, as a function of position in a direction orthogonal to the counter so as to generate two dimensional data. An image of the grains in the curved surface of the polycrystalline article is provided based on the two-dimensional data.

Nondestructive method and apparatus for imaging grains in curved surfaces of polycrystalline articles

DOEpatents

Carpenter, D.A.

1995-05-23

A nondestructive method, and associated apparatus, are provided for determining the grain flow of the grains in a convex curved, textured polycrystalline surface. The convex, curved surface of a polycrystalline article is aligned in a horizontal x-ray diffractometer and a monochromatic, converging x-ray beam is directed onto the curved surface of the polycrystalline article so that the converging x-ray beam is diffracted by crystallographic planes of the grains in the polycrystalline article. The diffracted x-ray beam is caused to pass through a set of horizontal, parallel slits to limit the height of the beam and thereafter. The linear intensity of the diffracted x-ray is measured, using a linear position sensitive proportional counter, as a function of position in a direction orthogonal to the counter so as to generate two dimensional data. An image of the grains in the curved surface of the polycrystalline article is provided based on the two-dimensional data. 7 Figs.

Digital lock-in detection of site-specific magnetism in magnetic materials

DOEpatents

Haskel, Daniel [Naperville, IL; Lang, Jonathan C [Naperville, IL; Srajer, George [Oak Park, IL

2008-07-22

The polarization and diffraction characteristics of x-rays incident upon a magnetic material are manipulated to provide a desired magnetic sensitivity in the material. The contrast in diffracted intensity of opposite helicities of circularly polarized x-rays is measured to permit separation of magnetic signals by element type and by atomic environment. This allows for the direct probing of magnetic signals from elements of the same species in nonequivalent atomic environments to better understand the behavior and characteristics of permanent magnetic materials. By using known crystallographic information together with manipulation of the polarization of x-rays having energies tuned near element-specific electronic excitations and by detecting and comparing the incident and diffracted photons at the same frequency, more accurate magnetic measurements can be made over shorter observation periods.

Investigation of ZrO x /ZrC-ZrN/Zr thin-film structural evolution and their degradation using X-ray diffraction and Raman spectrometry

NASA Astrophysics Data System (ADS)

Usmani, B.; Vijay, V.; Chhibber, R.; Dixit, A.

2016-11-01

The thin-film structures of DC/FR magnetron-sputtered ZrO x /ZrC-ZrN/Zr tandem solar-selective coatings are investigated using X-ray diffraction and room-temperature Raman spectroscopic measurements. These studies suggest that the major contribution is coming from h-ZrN0.28, c-ZrC, h-Zr3C2 crystallographic phases in ZrN-ZrC absorber layer, in conjunction with mixed ZrO x crystallographic phases. The change in structure for thermally annealed samples has been examined and observed that cubic and hexagonal ZrO x phase converted partially into tetragonal and monoclinic ZrO x phases, whereas hexagonal and cubic ZrN phases, from absorber layer, have not been observed for these thermally treated samples in air. These studies suggest that thermal treatment may lead to the loss of ZrN phase in absorber, degrading the thermal response for the desired wavelength range in open ambient conditions in contrast to vacuum conditions.

X-ray diffraction tomography of polycrystalline materials: present and future (Conference Presentation)

NASA Astrophysics Data System (ADS)

Stock, Stuart R.; Almer, Jonathan D.; Birkedal, Henrik

2016-10-01

Scattered x-radiation can be used for computed tomographic reconstruction of the distribution of crystallographic phases within the interior of specimens, and diffraction patterns can be measured for each volume element (voxel) within a reconstructed slice. This modality has been applied to systems as diverse as mineralized tissues and inorganic composites. Use of high energy x-rays (E < 40 keV) offers advantages including the ability to study volumes deep with specimens and to sample large ranges of reciprocal space, i.e., many reflections. The bases of diffraction tomography are reviewed, and the power of the technique is illustrated by the results obtained for specimens containing: a) different materials (SiC/Al composite), b) different polytypes (calcite/aragonite in a bivalve attachment system); c) mixtures of nanocrystalline and amorphous phases; d) a single phase, but volumes with different lattice parameters (hydroxyapatite, hAp, the mineral in bone and tooth); e) a single phase containing a spatial distribution of crystallographic texture (bone); a single phase with a spatial distribution of strains produced by in situ loading (bone). Finally, challenges and future directions are discussed.

The application of eigensymmetries of face forms to X-ray diffraction intensities of crystals twinned by `reticular merohedry'

NASA Astrophysics Data System (ADS)

Klapper, H.; Hahn, Th

2012-01-01

Crystallographic face forms {hkl} are interpreted as sets of symmetry-equivalent X-ray reflections. Extending an earlier paper on twinning by merohedry [ [Sigma] = 1, Klapper & Hahn (2010). Acta Cryst. A66, 327-346], the eigensymmetry of these forms is used to derive general relations between the diffraction intensities of overlapping twin-related reflections. The following twins by reticular merohedry are treated: [Sigma] 3 twins of rhombohedral and cubic, [Sigma] 5 twins of tetragonal and [Sigma] 7 twins of hexagonal crystals.

Crystallographic Characterization on Polycrystalline Ni-Mn-Ga Alloys with Strong Preferred Orientation

PubMed Central

Li, Zongbin; Yang, Bo; Zou, Naifu; Zhang, Yudong; Esling, Claude; Gan, Weimin; Zhao, Xiang; Zuo, Liang

2017-01-01

Heusler type Ni-Mn-Ga ferromagnetic shape memory alloys can demonstrate excellent magnetic shape memory effect in single crystals. However, such effect in polycrystalline alloys is greatly weakened due to the random distribution of crystallographic orientation. Microstructure optimization and texture control are of great significance and challenge to improve the functional behaviors of polycrystalline alloys. In this paper, we summarize our recent progress on the microstructure control in polycrystalline Ni-Mn-Ga alloys in the form of bulk alloys, melt-spun ribbons and thin films, based on the detailed crystallographic characterizations through neutron diffraction, X-ray diffraction and electron backscatter diffraction. The presented results are expected to offer some guidelines for the microstructure modification and functional performance control of ferromagnetic shape memory alloys. PMID:28772826

Measurement of strain in Al-Cu interconnect lines with x-ray microdiffraction

NASA Astrophysics Data System (ADS)

Solak, H. H.; Vladimirsky, Y.; Cerrina, F.; Lai, B.; Yun, W.; Cai, Z.; Ilinski, P.; Legnini, D.; Rodrigues, W.

1999-07-01

We report measurement of strain in patterned Al-Cu interconnect lines with x-ray microdiffraction technique with a ˜1 μm spatial resolution. Monochromatized x rays from an undulator were focused on the sample using a phase fresnel zone plate and diffracted light was collected by an area detector in a symmetric, angle dispersive x-ray diffraction geometry. Measurements were made before and after the line sample was stressed for electromigration. Results show an increase in inter- and intra-grain strain variation after the testing. Differences in strain behavior of grains with (111) and (200) crystallographic planes parallel to the substrate surface were observed. A position dependent variation of strain after the testing was measured whereas no such dependence was found before the testing.

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

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

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

A novel high-temperature furnace for combined in situ synchrotron X-ray diffraction and infrared thermal imaging to investigate the effects of thermal gradients upon the structure of ceramic materials

PubMed Central

Robinson, James B.; Brown, Leon D.; Jervis, Rhodri; Taiwo, Oluwadamilola O.; Millichamp, Jason; Mason, Thomas J.; Neville, Tobias P.; Eastwood, David S.; Reinhard, Christina; Lee, Peter D.; Brett, Daniel J. L.; Shearing, Paul R.

2014-01-01

A new technique combining in situ X-ray diffraction using synchrotron radiation and infrared thermal imaging is reported. The technique enables the application, generation and measurement of significant thermal gradients, and furthermore allows the direct spatial correlation of thermal and crystallographic measurements. The design and implementation of a novel furnace enabling the simultaneous thermal and X-ray measurements is described. The technique is expected to have wide applicability in material science and engineering; here it has been applied to the study of solid oxide fuel cells at high temperature. PMID:25178003

Advanced Organic Solid States Materials. Volume 173. Materials Research Society Symposium Proceedings

DTIC Science & Technology

1990-08-08

for their collaboration in synthetic study. We also thank Prof. N. Kasai and Dr. Y. Kai for their collaboration in X - ray crystallographic study. We...substantially with the increasing amount of doping as monitored by the powder x - ray diffraction. After doping the sample was kept for at least one day...physical properties at different oxidation states in solution and in the solid state of tEDTB complexed with TCNQF4. The X ray crystal structure of

United States Air Force Summer Research Program -- 1993 Summer Research Program Final Reports. Volume 15. Wright Laboratory

DTIC Science & Technology

1993-01-01

Two other methods were used to determine the quality of the films. One is x - ray diffraction which is used to determine the crystallographic...orientation of the films. No phases other than the YBa 2Cu3O7. x were observed in any of the films. The x - ray data for the films with high critical current...spectra cups. The first analysis was done using the Portable X - ray Fluorescence Spectrometer. The soil samples. as well as. 10 metal fragments that

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

Study of Initial Stages of Ball-Milling of Cu Powder Using X-ray Diffraction

NASA Astrophysics Data System (ADS)

Gayathri, N.; Mukherjee, Paramita

2018-04-01

The initial stage of size refinement of Cu powder is studied using detailed X-ray diffraction (XRD) analysis to understand the mechanism of formation of nanomaterials during the ball-milling process. The study was restricted to samples obtained for milling time up to 240 min to understand the deformation mechanism at the early stages of ball milling. Various model based approaches for the analysis of the XRD were used to study the evolution of the microstructural parameters such as domain size and microstrain along the different crystallographic planes. It was seen that the domain size saturates at a low value along the (311) plane whereas the size along the (220) and (200) plane is still higher. The r.m.s microstrain showed a non-monotonic change along the different crystallographic directions up to the milling time of 240 min.

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

NASA Astrophysics Data System (ADS)

Ochoa, D. A.; Levit, R.; Fancher, C. M.; Esteves, G.; Jones, J. L.; E García, J.

2017-05-01

Ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot be associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel-Fulcher-Tammann phenomenological equation. Results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.

USAF Summer Research Program - 1993 High School Apprenticeship Program Final Reports, Volume 15, Wright Laboratory

DTIC Science & Technology

1993-12-01

of the films. One is x - ray diffraction which is used to determine the crystallographic orientation of the films. No phases other than the YBa 2Cu3O 7...x were observed in any of the films. The x - ray data for the films with high critical current densities show strong peaks of reflections indicating a...Solving for x ca = (p/2 Now, if we look at a close-up of the prism face at the input ray (FIGURE 7), we want to solve for the angle between the rays

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

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

van Thor, Jasper J.; Madsen, Anders

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

DOE PAGES

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

PubMed Central

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse. PMID:26798786

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy

PubMed Central

McDonald, S. A.; Reischig, P.; Holzner, C.; Lauridsen, E. M.; Withers, P. J.; Merkle, A. P.; Feser, M.

2015-01-01

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through ‘4D’ in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance. PMID:26494523

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy

NASA Astrophysics Data System (ADS)

McDonald, S. A.; Reischig, P.; Holzner, C.; Lauridsen, E. M.; Withers, P. J.; Merkle, A. P.; Feser, M.

2015-10-01

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through ‘4D’ in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance.

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy.

PubMed

McDonald, S A; Reischig, P; Holzner, C; Lauridsen, E M; Withers, P J; Merkle, A P; Feser, M

2015-10-23

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through '4D' in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance.

Purification, crystallization and preliminary crystallographic analysis of biotin protein ligase from Staphylococcus aureus.

PubMed

Pendini, Nicole R; Polyak, Steve W; Booker, Grant W; Wallace, John C; Wilce, Matthew C J

2008-06-01

Biotin protein ligase from Staphylococcus aureus catalyses the biotinylation of acetyl-CoA carboxylase and pyruvate carboxylase. Recombinant biotin protein ligase from S. aureus has been cloned, expressed and purified. Crystals were grown using the hanging-drop vapour-diffusion method using PEG 8000 as the precipitant at 295 K. X-ray diffraction data were collected to 2.3 A resolution from crystals using synchrotron X-ray radiation at 100 K. The diffraction was consistent with the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 93.665, c = 131.95.

Synthesis and the crystal and molecular structure of the germanium(IV) complex with propylene-1,3-diaminetetraacetic acid [Ge(Pdta)

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

Sergienko, V. S., E-mail: sergienko@igic.ras.ru; Martsinko, E. E.; Seifullina, I. I.

2015-09-15

The germanium(IV) complex with propylene-1,3-diaminetetraacetic acid (H{sub 4}Pdta) is studied by elemental analysis, X-ray diffraction, thermogravimetry, and IR spectroscopy. The X-ray diffraction study reveals two crystallographically independent [Ge(Pdta)] molecules of similar structure. Both Ge atoms are octahedrally coordinated by four O atoms and two N atoms (at the cis positions) of the hexadentate pentachelate Pdta{sup 4–} ligand. An extended system of weak C—H···O hydrogen bonds connects complex molecules into a supramolecular 3D framework.

Synthesis and the crystal and molecular structure of the germanium(IV) complex with propylene-1,3-diaminetetraacetic acid [Ge( Pdta)

NASA Astrophysics Data System (ADS)

Sergienko, V. S.; Martsinko, E. E.; Seifullina, I. I.; Churakov, A. V.; Chebanenko, E. A.

2015-09-01

The germanium(IV) complex with propylene-1,3-diaminetetraacetic acid (H4 Pdta) is studied by elemental analysis, X-ray diffraction, thermogravimetry, and IR spectroscopy. The X-ray diffraction study reveals two crystallographically independent [Ge( Pdta)] molecules of similar structure. Both Ge atoms are octahedrally coordinated by four O atoms and two N atoms (at the cis positions) of the hexadentate pentachelate Pdta 4- ligand. An extended system of weak С—Н···О hydrogen bonds connects complex molecules into a supramolecular 3D framework.

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis

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

Lu, Feifei; Gao, Feng; Li, Honglin

The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv3705c from M. tuberculosis are described. The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å.

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

PubMed Central

Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

2008-01-01

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s−1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a κ-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

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.

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

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.

Phase retrieval for crystalline specimens

NASA Astrophysics Data System (ADS)

Arnal, Romain A.; Millane, Rick P.

2017-09-01

The recent availability of ultra-bright and ultra-short X-rays pulses from new sources called x-ray free-electron lasers (XFELs) has introduced a new paradigm in X-ray crystallography. Called "diffraction-before-destruction," this paradigm addresses the main problems that plague crystallography using synchrotron sources. However, the phase problem of coherent diffraction imaging remains: one has to retrieve the phase of the measured diffraction amplitude in order to reconstruct the object. Fibrous and membrane proteins that crystallize in 1D and 2D crystals can now potentially be used for data collection with free-electron lasers. The crystallographic phase problem with such crystalline specimens is eased as the Fourier amplitude can be sampled more finely than at the Bragg sampling along one or two directions. Here we characterise uniqueness of the phase problem for different types of crystalline specimen. Simulated ab initio phase retrieval using iterative projection algorithms for 2D crystals is presented.

Crystallographic texture of straight-rolled ?-uranium foils via neutron and X-ray diffraction

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

Einhorn, J. R.; Steiner, M. A.; Vogel, S. C.

The texture of recrystallized straight-rolled ?-uranium foils, a component in prospective irradiation target designs for medical isotope production, has been measured by neutron diffraction, as well as X-ray diffraction using both Cu and Mo sources. Variations in the penetration depth of neutron and X-ray radiation allow for determination of both the bulk and surface textures. The bulk ?-uranium foil texture is similar to the warm straight-rolled plate texture, with the addition of a notable splitting of the (001) poles along the transverse direction. The surface texture of the foils is similar to the bulk, with an additional (001) texture componentmore » that is oriented between the rolling and normal directions. Differences between the surface and bulk textures are expected to arise from shear forces during the rolling process and the influence that distinct strain histories have on subsequent texture evolution during recrystallization.« less

Crystallographic texture of straight-rolled ?-uranium foils via neutron and X-ray diffraction

DOE PAGES

Einhorn, J. R.; Steiner, M. A.; Vogel, S. C.; ...

2017-05-25

The texture of recrystallized straight-rolled ?-uranium foils, a component in prospective irradiation target designs for medical isotope production, has been measured by neutron diffraction, as well as X-ray diffraction using both Cu and Mo sources. Variations in the penetration depth of neutron and X-ray radiation allow for determination of both the bulk and surface textures. The bulk ?-uranium foil texture is similar to the warm straight-rolled plate texture, with the addition of a notable splitting of the (001) poles along the transverse direction. The surface texture of the foils is similar to the bulk, with an additional (001) texture componentmore » that is oriented between the rolling and normal directions. Differences between the surface and bulk textures are expected to arise from shear forces during the rolling process and the influence that distinct strain histories have on subsequent texture evolution during recrystallization.« less

Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus

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

Chon, Hyongi; Matsumura, Hiroyoshi; Koga, Yuichi

2005-03-01

A thermostable ribonuclease HIII from B. stearothermophilus (Bst RNase HIII) was crystallized and preliminary crystallographic studies were performed. Plate-like overlapping polycrystals were grown by the sitting-drop vapour-diffusion method at 283 K.

Microfocus/Polycapillary-Optic Crystallographic X-Ray System

NASA Technical Reports Server (NTRS)

Joy, Marshall; Gubarev, Mikhail; Ciszak, Ewa

2005-01-01

A system that generates an intense, nearly collimated, nearly monochromatic, small-diameter x-ray beam has been developed for use in macromolecular crystallography. A conventional x-ray system for macromolecular crystallography includes a rotating-anode x-ray source, which is massive (.500 kg), large (approximately 2 by 2 by 1 m), and power-hungry (between 2 and 18 kW). In contrast, the present system generates a beam of the required brightness from a microfocus source, which is small and light enough to be mounted on a laboratory bench, and operates at a power level of only tens of watts. The figure schematically depicts the system as configured for observing x-ray diffraction from a macromolecular crystal. In addition to the microfocus x-ray source, the system includes a polycapillary optic . a monolithic block (typically a bundle of fused glass tubes) that contains thousands of straight or gently curved capillary channels, along which x-rays propagate with multiple reflections. This particular polycapillary optic is configured to act as a collimator; the x-ray beam that emerges from its output face consists of quasi-parallel subbeams with a small angular divergence and a diameter comparable to the size of a crystal to be studied. The gap between the microfocus x-ray source and the input face of the polycapillary optic is chosen consistently with the focal length of the polycapillary optic and the need to maximize the solid angle subtended by the optic in order to maximize the collimated x-ray flux. The spectrum from the source contains a significant component of Cu K (photon energy is 8.08 keV) radiation. The beam is monochromatized (for Cu K ) by a nickel filter 10 m thick. In a test, this system was operated at a power of 40 W (current of 897 A at an accelerating potential of 45 kV), with an anode x-ray spot size of 41+/-2 microns. Also tested, in order to provide a standard for comparison, was a commercial rotating-anode x-ray crystallographic system with a pyrolytic graphite monochromator and a 250-micron pinhole collimator, operating at a power of 3.15 kW (current of 70 mA at an accelerating potential of 45 kV). The flux of collimated Cu K radiation in this system was found to be approximately 16 times that in the rotatinganode system. Data on x-ray diffraction from crystals of tetragonal form of lysozyme (protein) in this system were found to be of high quality and to be reducible by use of standard crystallographic software.

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

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

Crystallographic data processing for free-electron laser sources

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

White, Thomas A., E-mail: taw@physics.org; Barty, Anton; Stellato, Francesco

2013-07-01

A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show thatmore » the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.« less

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

Texture analysis of Napoleonic War Era copper bolts

NASA Astrophysics Data System (ADS)

Malamud, Florencia; Northover, Shirley; James, Jon; Northover, Peter; Kelleher, Joe

2016-04-01

Neutron diffraction techniques are suitable for volume texture analyses due to high penetration of thermal neutrons in most materials. We have implemented a new data analysis methodology that employed the spatial resolution achievable by a time-of-flight neutron strain scanner to non-destructively determine the crystallographic texture at selected locations within a macroscopic sample. The method is based on defining the orientation distribution function of the crystallites from several incomplete pole figures, and it has been implemented on ENGIN-X, a neutron strain scanner at the Isis Facility in the UK. Here, we demonstrate the application of this new texture analysis methodology in determining the crystallographic texture at selected locations within museum quality archaeological objects up to 1 m in length. The results were verified using samples of similar, but less valuable, objects by comparing the results of applying this method with those obtained using both electron backscatter diffraction and X-ray diffraction on their cross sections.

Crystallization and preliminary X-ray analysis of gamma-glutamyltranspeptidase from Escherichia coli K-12.

PubMed

Kumagai, H; Nohara, S; Suzuki, H; Hashimoto, W; Yamamoto, K; Sakai, H; Sakabe, K; Fukuyama, K; Sakabe, N

1993-12-20

gamma-Glutamyltranspeptidase (EC 2.3.2.2) from Escherichia coli K-12 has been purified and crystallized by means of vapor diffusion in hanging drops. Two kinds of crystals on cell dimensions were found for X-ray diffraction analysis, one from ammonium sulfate and the other from polyethylene glycol 6000 as precipitants. The crystals of the orthorhombic form grown in the presence of 15% polyethylene glycol and 20 mM sodium acetate buffer were chosen for further analysis. The crystals belonged to space group P2(1)2(1)2(1), with cell dimensions of a = 128.1, b = 129.9 and c = 79.2 A, and two molecules constitute an asymmetric unit. These crystals diffracted to 2.0 A resolution and were suitable for X-ray crystallographic studies.

X-Ray Crystallographic Studies on Acetylcholinesterase and on Its Interaction with Anticholinesterase Agents.

DTIC Science & Technology

1994-11-24

complexes with reversible ligands, including edrophonium, d-tubocurarine and huperzine A , diffracting to similar resolution. The X26c Laue beam line...The EMBL-DESY synchrotron facility at Hamburg was employed to collect a complete 2.3 A data set for a crystal of native Torpedo AChE, as well as for...at the NSLS synchrotron facility at Brookhaven National Laboratory (BNL) was used to obtain a Laue diffraction pattern for a crystal of native Torpedo

Summer Research Program (1992). High School Apprenticeship Program (HSAP) Reports. Volume 15. Wright Laboratory

DTIC Science & Technology

1992-12-28

of the sample. Two other methods were used to determine the quality of the films. One is x - ray diffraction which is used to determine the...crystallographic orientation of the films. No phases other than the YBa 2Cu307 -. were observed in any of the films. The x - ray data for the films with high...c x ( A = .42 𔃼 (𔃼 x = b = b The goal of the Gaussian elimination method Is to perform operations on A In order to obtain the values of the Identity

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.

Purification, crystallization and preliminary crystallographic analysis of biotin protein ligase from Staphylococcus aureus

PubMed Central

Pendini, Nicole R.; Polyak, Steve W.; Booker, Grant W.; Wallace, John C.; Wilce, Matthew C. J.

2008-01-01

Biotin protein ligase from Staphylococcus aureus catalyses the biotinylation of acetyl-CoA carboxylase and pyruvate carboxylase. Recombinant biotin protein ligase from S. aureus has been cloned, expressed and purified. Crystals were grown using the hanging-drop vapour-diffusion method using PEG 8000 as the precipitant at 295 K. X-ray diffraction data were collected to 2.3 Å resolution from crystals using synchrotron X-ray radiation at 100 K. The diffraction was consistent with the tetragonal space group P42212, with unit-cell parameters a = b = 93.665, c = 131.95. PMID:18540065

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

Glass transition in ferroic glass K x (ND4)1-x D2PO4: a complete x-ray diffraction line shape analysis

NASA Astrophysics Data System (ADS)

Ranjan Choudhury, Rajul; Chitra, R.; Jayakrishnan, V. B.

2016-03-01

Quenching of dynamic disorder in glassy systems is termed as the glass transition. Ferroic glasses belong to the class of paracrystalline materials having crystallographic order in-between that of a perfect crystal and amorphous material, a classic example of ferroic glass is the solid solution of ferroelectric deuterated potassium dihydrogen phosphate and antiferroelectric deuterated ammonium dihydrogen phosphate. Lowering temperature of this ferroic glass can lead to a glass transition to a quenched disordered state. The subtle atomic rearrangement that takes place at such a glass transition can be revealed by careful examination of the temperature induced changes occurring in the x-ray powder diffraction (XRD) patterns of these materials. Hence we report here results of a complete diffraction line shape analysis of the XRD patterns recorded at different temperatures from deuterated mixed crystals DK x A1-x DP with mixing concentration x ranging as 0 < x < 1. Changes observed in diffraction peak shapes have been explained on the basis of structural rearrangements induced by changing O-D-O hydrogen bond dynamics in these paracrystals.

Improved crystal orientation and physical properties from single-shot XFEL stills

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

Sauter, Nicholas K., E-mail: nksauter@lbl.gov; Hattne, Johan; Brewster, Aaron S.

X-ray free-electron laser crystallography relies on the collection of still-shot diffraction patterns. New methods are developed for optimal modeling of the crystals’ orientations and mosaic block properties. X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factorsmore » from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model the diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg’s law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographic R factors and sharpening anomalous differences that are near the level of the noise.« less

Expression, purification and preliminary crystallographic analysis of Mycobacterium tuberculosis CysQ, a phosphatase involved in sulfur metabolism

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

Erickson, Anna I.; Sarsam, Reta D.; Fisher, Andrew J., E-mail: ajfisher@ucdavis.edu

The cysQ gene from Mycobacterium tuberculosis was cloned and the expressed protein, a 3′-phosphoadenosine-5′’-phosphatase, was purified and crystallized. X-ray diffraction data were collected to 1.7 Å resolution.

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

DOE PAGES

Ochoa, D. A.; Levit, R.; Fancher, C. M.; ...

2017-04-05

We report that ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot bemore » associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel–Fulcher–Tammann phenomenological equation. Finally, results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.« less

Crystallographic features related to a van der Waals coupling in the layered chalcogenide FePS{sub 3}

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

Murayama, Chisato; Okabe, Momoko; Fukuda, Koichiro

We investigated the crystallographic structure of FePS{sub 3} with a layered structure using transmission electron microscopy and powder X-ray diffraction. We found that FePS{sub 3} forms a rotational twin structure with the common axis along the c*-axis. The high-resolution transmission electron microscopy images revealed that the twin boundaries were positioned at the van der Waals gaps between the layers. The narrow bands of dark contrast were observed in the bright-field transmission electron microscopy images below the antiferromagnetic transition temperature, T{sub N} ≈ 120 K. Low-temperature X-ray diffraction showed a lattice distortion; the a- and b-axes shortened and lengthened, respectively, as the temperature decreasedmore » below T{sub N.} We propose that the narrow bands of dark contrast observed in the bright-field transmission electron microscopy images are caused by the directional lattice distortion with respect to each micro-twin variant in the antiferromagnetic phase.« less

Dependence of Crystallographic Orientation on Pitting Corrosion Behavior of Ni-Fe-Cr Alloy 028

NASA Astrophysics Data System (ADS)

Zhang, LiNa; Szpunar, Jerzy A.; Dong, JianXin; Ojo, Olanrewaju A.; Wang, Xu

2018-06-01

The influence of crystallographic orientation on the pitting corrosion behavior of Ni-Fe-Cr alloy 028 was studied using a combination of X-ray diffraction (XRD), electron backscatter diffraction (EBSD), potentiodynamic polarization technique, and atomic force microscopy (AFM). The results show that there is anisotropy of pitting corrosion that strongly depends on crystallographic orientation of the surface plane. The distribution of pit density in a standard stereographic triangle indicates that the crystallographic planes close to {100} are more prone to pitting corrosion compared to planes {110} and {111}. The surface energy calculation of (001) and (111) shows that the plane with a high atomic packing density has a low surface energy with concomitant strong resistance to pitting corrosion. A correlation function between crystallographic orientation and pitting corrosion susceptibility suggests a method that not only predicts the pitting resistance of known textured materials, but also could help to improve corrosion resistance by controlling material texture.

Synchrotron X-ray diffraction investigations on strains in the oxide layer of an irradiated Zircaloy fuel cladding

NASA Astrophysics Data System (ADS)

Chollet, Mélanie; Valance, Stéphane; Abolhassani, Sousan; Stein, Gene; Grolimund, Daniel; Martin, Matthias; Bertsch, Johannes

2017-05-01

For the first time the microstructure of the oxide layer of a Zircaloy-2 cladding after 9 cycles of irradiation in a boiling water reactor has been analyzed with synchrotron micro-X-ray diffraction. Crystallographic strains of the monoclinic and to some extent of the tetragonal ZrO2 are depicted through the thick oxide layer. Thin layers of sub-oxide at the oxide-metal interface as found for autoclave-tested samples and described in the literature, have not been observed in this material maybe resulting from irradiation damage. Shifts of selected diffraction peaks of the monoclinic oxide show that the uniform strain produced during oxidation is orientated in the lattice and displays variations along the oxide layer. Diffraction peaks and their shifts from families of diffracting planes could be translated into a virtual tensor. This virtual tensor exhibits changes through the oxide layer passing by tensile or compressive components.

A Compact X-Ray System for Support of High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Ciszak, Ewa; Gubarev, Mikhail; Gibson, Walter M.; Joy, Marshall K.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Standard x-ray systems for crystallography rely on massive generators coupled with optics that guide X-ray beams onto the crystal sample. Optics for single-crystal diffractometry include total reflection mirrors, polycapillary optics or graded multilayer monochromators. The benefit of using polycapillary optic is that it can collect x-rays over tile greatest solid angle, and thus most efficiently, utilize the greatest portion of X-rays emitted from the Source, The x-ray generator has to have a small anode spot, and thus its size and power requirements can be substantially reduced We present the design and results from the first high flux x-ray system for crystallography that combine's a microfocus X-ray generator (40microns FWHM Spot size at a power of 45 W) and a collimating, polycapillary optic. Diffraction data collected from small test crystals with cell dimensions up to 160A (lysozyme and thaumatin) are of high quality. For example, diffraction data collected from a lysozyme crystal at RT yielded R=5.0% for data extending to 1.70A. We compare these results with measurements taken from standard crystallographic systems. Our current microfocus X-ray diffraction system is attractive for supporting crystal growth research in the standard crystallography laboratory as well as in remote, automated crystal growth laboratory. Its small volume, light-weight, and low power requirements are sufficient to have it installed in unique environments, i.e.. on-board International Space Station.

Sub-atomic dimensional metrology: developments in the control of x-ray interferometers

NASA Astrophysics Data System (ADS)

Yacoot, Andrew; Kuetgens, Ulrich

2012-07-01

Within the European Metrology Research Programme funded project NANOTRACE, the nonlinearity of the next generation of optical interferometers has been measured using x-ray interferometry. The x-ray interferometer can be regarded as a ruler or translation stage whose graduations or displacement steps are based on the lattice spacing of the crystallographic planes from which the x-rays are diffracted: in this case the graduations are every 192 pm corresponding to the spacing between the (2 2 0) planes in silicon. Precise displacement of the x-ray interferometer's monolithic translation stage in steps corresponding to discrete numbers of x-ray fringes requires servo positioning capability at the picometre level. To achieve this very fine control, a digital control system has been developed which has opened up the potential for advances in metrology using x-ray interferometry that include quadrature counting of x-ray fringes.

Microgravity

NASA Image and Video Library

2001-06-06

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.

Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase.

PubMed

Daughtry, Kelly D; Xiao, Youli; Stoner-Ma, Deborah; Cho, Eunsun; Orville, Allen M; Liu, Pinghua; Allen, Karen N

2012-02-08

Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å resolution) and in the product complex (at 2.2 Å resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.

Rietveld analysis of the cubic crystal structure of Na-stabilized zirconia

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

Fagherazzi, G.; Canton, P.; Benedetti, A.

Using x-ray Rietveld analysis the fcc (fluorite-type) structure of a Na-containing nanocrystalline zirconia powder (9.5 nm estimated of crystallite size) obtained by precipitation and subsequent calcination has been confirmed. The result shows that using conventional x-ray diffraction techniques the cubic crystallographic form of ZrO{sub 2} from the tetragonal one in nanosized powders. These conclusions are supported by the findings of independent Raman scattering experiments. {copyright} {ital 1997 Materials Research Society.}

Expression and crystallographic studies of the Arabidopsis thaliana GDP-D-mannose pyrophosphorylase VTC1.

PubMed

Zhao, Shun; Liu, Lin

2016-10-01

GDP-D-mannose pyrophosphorylase catalyzes the production of GDP-D-mannose, an intermediate product in the plant ascorbic acid (AsA) biosynthetic pathway. This enzyme is a key regulatory target in AsA biosynthesis and is encoded by VITAMIN C DEFECTIVE 1 (VTC1) in the Arabidopsis thaliana genome. Here, recombinant VTC1 was expressed, purified and crystallized. Diffraction data were obtained from VTC1 crystals grown in the absence and presence of substrate using X-rays. The ligand-free VTC1 crystal diffracted X-rays to 3.3 Å resolution and belonged to space group R32, with unit-cell parameters a = b = 183.6, c = 368.5 Å, α = β = 90, γ = 120°; the crystal of VTC1 in the presence of substrate diffracted X-rays to 1.75 Å resolution and belonged to space group P2 1 , with unit-cell parameters a = 70.8, b = 83.9, c = 74.5 Å, α = γ = 90.0, β = 114.9°.

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.

Powder X-ray diffraction laboratory, Reston, Virginia

USGS Publications Warehouse

Piatak, Nadine M.; Dulong, Frank T.; Jackson, John C.; Folger, Helen W.

2014-01-01

The powder x-ray diffraction (XRD) laboratory is managed jointly by the Eastern Mineral and Environmental Resources and Eastern Energy Resources Science Centers. Laboratory scientists collaborate on a wide variety of research problems involving other U.S. Geological Survey (USGS) science centers and government agencies, universities, and industry. Capabilities include identification and quantification of crystalline and amorphous phases, and crystallographic and atomic structure analysis for a wide variety of sample media. Customized laboratory procedures and analyses commonly are used to characterize non-routine samples including, but not limited to, organic and inorganic components in petroleum source rocks, ore and mine waste, clay minerals, and glassy phases. Procedures can be adapted to meet a variety of research objectives.

Improved crystal orientation and physical properties from single-shot XFEL stills

DOE PAGES

Sauter, Nicholas K.; Hattne, Johan; Brewster, Aaron S.; ...

2014-11-28

X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model themore » diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg's law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographic R factors and sharpening anomalous differences that are near the level of the noise.« less

Improved crystal orientation and physical properties from single-shot XFEL stills

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

Sauter, Nicholas K.; Hattne, Johan; Brewster, Aaron S.

X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model themore » diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg's law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographic R factors and sharpening anomalous differences that are near the level of the noise.« less

A simple X-ray source of two orthogonal beams for small samples imaging

NASA Astrophysics Data System (ADS)

Hrdý, J.

2018-04-01

A simple method for simultaneous imaging of small samples by two orthogonal beams is proposed. The method is based on one channel-cut crystal which is oriented such that the beam is diffracted on two crystallographic planes simultaneously. These planes are symmetrically inclined to the crystal surface. The beams are three times diffracted. After the first diffraction the beam is split. After the second diffraction the split beams become parallel. Finally, after the third diffraction the beams become convergent and may be used for imaging. The corresponding angular relations to obtain orthogonal beams are derived.

Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction

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

O'Dell, William B.; Swartz, Paul D.; Weiss, Kevin L.

Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bondsviaan oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 fromNeurospora crassa(NcPMO-2) was heterologously expressed inPichia pastoristo facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressingNcPMO-2 from a glycoengineered strain ofP. pastorisand by the use of crystal seeding methods, respectively. These improvements resulted in high-resolution (1.20 Å) X-ray diffraction data collection at 100 K and themore » production of a largeNcPMO-2 crystal suitable for room-temperature neutron diffraction data collection to 2.12 Å resolution.« less

Characterization of the carbides and the martensite phase in powder-metallurgy high-speed steel

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

Godec, Matjaz, E-mail: matjaz.godec@imt.si; Batic, Barbara Setina; Mandrino, Djordje

2010-04-15

A microstructural characterization of the powder-metallurgy high-speed-steel S390 Microclean was performed based on an elemental distribution of the carbide phase as well as crystallographic analyses. The results showed that there were two types of carbides present: vanadium-rich carbides, which were not chemically homogeneous and exhibited a tungsten-enriched or tungsten-depleted central area; and chemically homogeneous tungsten-rich M{sub 6}C-type carbides. Despite the possibility of chemical inhomogenities, the crystallographic orientation of each of the carbides was shown to be uniform. Using electron backscatter diffraction the vanadium-rich carbides were determined to be either cubic VC or hexagonal V{sub 6}C{sub 5}, while the tungsten-rich carbidesmore » were M{sub 6}C. The electron backscatter diffraction results were also verified using X-ray diffraction. Several electron backscatter diffraction pattern maps were acquired in order to define the fraction of each carbide phase as well as the amount of martensite phase. The fraction of martensite was estimated using band-contrast images, while the fraction of carbides was calculated using the crystallographic data.« less

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

Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70

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

Worrall, Liam; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk

Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I2{sub 1}2{sub 1}2{sub 1}. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry. Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I2{sub 1}2{sub 1}2{sub 1},more » with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.« less

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa

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

Kraschnefski, Mark J.; Scott, Stacy A.; Holloway, Gavan

2005-11-01

The carbohydrate-binding component (VP8*{sub 64–223}) of the human Wa rotavirus spike protein has been overexpressed in E. coli, purified and crystallized in two different crystal forms. X-ray diffraction data have been collected that have enabled determination of the Wa VP8*{sub 64–223} structure by molecular replacement. Rotaviruses exhibit host-specificity and the first crystallographic information on a rotavirus strain that infects humans is reported here. Recognition and attachment to host cells, leading to invasion and infection, is critically linked to the function of the outer capsid spike protein of the rotavirus particle. In some strains the VP8* component of the spike proteinmore » is implicated in recognition and binding of sialic-acid-containing cell-surface carbohydrates, thereby enabling infection by the virus. The cloning, expression, purification, crystallization and initial X-ray diffraction analysis of the VP8* core from human Wa rotavirus is reported. Two crystal forms (trigonal P3{sub 2}21 and monoclinic P2{sub 1}) have been obtained and X-ray diffraction data have been collected, enabling determination of the VP8*{sub 64–223} structure by molecular replacement.« less

Projection x-ray topography system at 1-BM x-ray optics test beamline at the advanced photon source

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

Stoupin, Stanislav, E-mail: sstoupin@aps.anl.gov; Liu, Zunping; Trakhtenberg, Emil

2016-07-27

Projection X-ray topography of single crystals is a classic technique for the evaluation of intrinsic crystal quality of large crystals. In this technique a crystal sample and an area detector (e.g., X-ray film) collecting intensity of a chosen crystallographic reflection are translated simultaneously across an X-ray beam collimated in the diffraction scattering plane (e.g., [1, 2]). A bending magnet beamline of a third-generation synchrotron source delivering x-ray beam with a large horizontal divergence, and therefore, a large horizontal beam size at a crystal sample position offers an opportunity to obtain X-ray topographs of large crystalline samples (e.g., 6-inch wafers) inmore » just a few exposures. Here we report projection X-ray topography system implemented recently at 1-BM beamline of the Advanced Photon Source. A selected X-ray topograph of a 6-inch wafer of 4H-SiC illustrates capabilities and limitations of the technique.« less

Beamline P02.1 at PETRA III for high-resolution and high-energy powder diffraction

PubMed Central

Dippel, Ann-Christin; Liermann, Hanns-Peter; Delitz, Jan Torben; Walter, Peter; Schulte-Schrepping, Horst; Seeck, Oliver H.; Franz, Hermann

2015-01-01

Powder X-ray diffraction techniques largely benefit from the superior beam quality provided by high-brilliance synchrotron light sources in terms of photon flux and angular resolution. The High Resolution Powder Diffraction Beamline P02.1 at the storage ring PETRA III (DESY, Hamburg, Germany) combines these strengths with the power of high-energy X-rays for materials research. The beamline is operated at a fixed photon energy of 60 keV (0.207 Å wavelength). A high-resolution monochromator generates the highly collimated X-ray beam of narrow energy bandwidth. Classic crystal structure determination in reciprocal space at standard and non-ambient conditions are an essential part of the scientific scope as well as total scattering analysis using the real space information of the pair distribution function. Both methods are complemented by in situ capabilities with time-resolution in the sub-second regime owing to the high beam intensity and the advanced detector technology for high-energy X-rays. P02.1’s efficiency in solving chemical and crystallographic problems is illustrated by presenting key experiments that were carried out within these fields during the early stage of beamline operation. PMID:25931084

Epitaxially Grown Films of Standing and Lying Pentacene Molecules on Cu(110) Surfaces

PubMed Central

2011-01-01

Here, it is shown that pentacene thin films (30 nm) with distinctively different crystallographic structures and molecular orientations can be grown under essentially identical growth conditions in UHV on clean Cu(110) surfaces. By X-ray diffraction, we show that the epitaxially oriented pentacene films crystallize either in the “thin film” phase with standing molecules or in the “single crystal” structure with molecules lying with their long axes parallel to the substrate. The morphology of the samples observed by atomic force microscopy shows an epitaxial alignment of pentacene crystallites, which corroborates the molecular orientation observed by X-ray diffraction pole figures. Low energy electron diffraction measurements reveal that these dissimilar growth behaviors are induced by subtle differences in the monolayer structures formed by slightly different preparation procedures. PMID:21479111

Crystallographic Study of Itokawa Particle, RA-QD02-0127 by Using Energy-Scanning X-Ray Diffraction Method with Synchrotron Radiation

NASA Technical Reports Server (NTRS)

Hagiya, K.; Ohsumi, K.; Komatsu, M.; Mikouchi, T.; Zolensky, M. E.; Hirata, A.; Yamaguchi, S.; Kurokawa, A.

2016-01-01

The petrographic study of Itokawa particle, RA-QD02-0127 has been performed by SEM-EDS and optical microscope observations. The purpose of this study is to understand better the metamorphic and impact shock history of asteroid Itokawa, and other S-class asteroids.

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

NASA Astrophysics Data System (ADS)

Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

Solvent and temperature effects on crambin, a hydrophobic protein

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

Llinas, M.; Lecomte, J.T.J.; De Marco, A.

1980-10-01

Crambin, a 5000-mol. wt. water-insoluble protein found in crambe abyssinica seeds is presently being studied by x-ray diffraction to 0.9 A resolution and /sup 1/H-nuclear magnetic resonance (NMR) spectroscopy. Preliminary /sup 1/H-NMR data at 250 and 600 MHz have suggested that this hydrophobic protein retains a similar globular conformation in both glacial acetic acid (AA), a Bronsted acid, and dimethylformamide (DMF), a Lewis base. These observations suggest that the globular conformation observed in these organic solvents is most likely the native structure present in the crystalline state. As suggested by the high intrinsic resolution of the crystallographic x-ray diffraction pattern,more » and demonstrated by the NMR data, crambin is a very rigid protein. Work is in progress to assign the /sup 1/H-resonances and to correlate H and /sup 13/C NMR dynamic data with the crystallographic model. It is hoped that unravelling conformational features of this hydrophobic protein will provide clues to help us understand other membrane-bound functional proteins.« less

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

PubMed Central

Kern, Jan; Hattne, Johan; Tran, Rosalie; Alonso-Mori, Roberto; Laksmono, Hartawan; Gul, Sheraz; Sierra, Raymond G.; Rehanek, Jens; Erko, Alexei; Mitzner, Rolf; Wernet, Phillip; Bergmann, Uwe; Sauter, Nicholas K.; Yachandra, Vittal; Yano, Junko

2014-01-01

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL. PMID:24914169

Direct single-shot phase retrieval from the diffraction pattern of separated objects

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

Leshem, Ben; Xu, Rui; Dallal, Yehonatan

The non-crystallographic phase problem arises in numerous scientific and technological fields. An important application is coherent diffractive imaging. Recent advances in X-ray free-electron lasers allow capturing of the diffraction pattern from a single nanoparticle before it disintegrates, in so-called ‘diffraction before destruction’ experiments. Presently, the phase is reconstructed by iterative algorithms, imposing a non-convex computational challenge, or by Fourier holography, requiring a well-characterized reference field. Here we present a convex scheme for single-shot phase retrieval for two (or more) sufficiently separated objects, demonstrated in two dimensions. In our approach, the objects serve as unknown references to one another, reducing themore » phase problem to a solvable set of linear equations. We establish our method numerically and experimentally in the optical domain and demonstrate a proof-of-principle single-shot coherent diffractive imaging using X-ray free-electron lasers pulses. Lastly, our scheme alleviates several limitations of current methods, offering a new pathway towards direct reconstruction of complex objects.« less

Direct single-shot phase retrieval from the diffraction pattern of separated objects

DOE PAGES

Leshem, Ben; Xu, Rui; Dallal, Yehonatan; ...

2016-02-22

The non-crystallographic phase problem arises in numerous scientific and technological fields. An important application is coherent diffractive imaging. Recent advances in X-ray free-electron lasers allow capturing of the diffraction pattern from a single nanoparticle before it disintegrates, in so-called ‘diffraction before destruction’ experiments. Presently, the phase is reconstructed by iterative algorithms, imposing a non-convex computational challenge, or by Fourier holography, requiring a well-characterized reference field. Here we present a convex scheme for single-shot phase retrieval for two (or more) sufficiently separated objects, demonstrated in two dimensions. In our approach, the objects serve as unknown references to one another, reducing themore » phase problem to a solvable set of linear equations. We establish our method numerically and experimentally in the optical domain and demonstrate a proof-of-principle single-shot coherent diffractive imaging using X-ray free-electron lasers pulses. Lastly, our scheme alleviates several limitations of current methods, offering a new pathway towards direct reconstruction of complex objects.« less

Applications of thermal-gradients method for the optimization of α-amylase crystallization conditions based on dynamic and static light scattering data

NASA Astrophysics Data System (ADS)

Delboni, L. F.; Iulek, J.; Burger, R.; da Silva, A. C. R.; Moreno, A.

2002-02-01

The expression, purification, crystallization, and characterization by X-ray diffraction of α-amylase are described here. Dynamic and static light scattering methods with a temperature controller was used to optimize the crystallization conditions of α-amylase from Bacillus stearothermophilus an important enzyme in many fields of industrial activity. After applying thermal gradients for growing crystals, X-ray cryo-crystallographic methods were employed for the data collection. Crystals grown by these thermal-gradients diffracted up to a maximum resolution of 3.8 Å, which allowed the determination of the unit cell constants as follows: a=61.7 Å, b=86.7 Å, c=92.2 Å and space group C222 (or C222 1).

MgO-Al2O3-ZrO2 Amorphous Ternary Composite: A Dense and Stable Optical Coating

NASA Technical Reports Server (NTRS)

Shaoo, Naba K.; Shapiro, Alan P.

1998-01-01

The process-parameter-dependent optical and structural properties of MgO-Al2O3-ZrO2 ternary mixed-composite material were investigated. Optical properties were derived from spectrophotometric measurements. The surface morphology, grain size distributions, crystallographic phases, and process- dependent material composition of films were investigated through the use of atomic force microscopy, x-ray diffraction analysis, and energy-dispersive x-ray analysis. Energy-dispersive x-ray analysis made evident the correlation between the optical constants and the process-dependent compositions in the films. It is possible to achieve environmentally stable amorphous films with high packing density under certain optimized process conditions.

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

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

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE PAGES

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

2015-01-01

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Raman scattering and X-ray powder diffraction studies of hydrate layered perovskites: dirubidium aquapentafluoromanganate(III) and dipotassium aquapentafluoroferrate(III)

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

Galicka, Karolina; Slodczyk, Aneta; Ratuszna, Alicja

2004-06-08

The structural and vibrational properties of above mentioned crystals were determined using X-ray powder diffraction and Raman scattering experiments. At room temperature hydrate layered perovskites: Rb{sub 2}MnF{sub 5}{center_dot}H{sub 2}O and K{sub 2}FeF{sub 5}{center_dot}H{sub 2}O exhibit orthorhombic--Cmcm (D{sub 2h}{sup 17}) and monoclinic--C2/c (C{sub 2h}{sup 6}) symmetry. Their structure is built up of MnF{sub 6} or FeF{sub 5}{center_dot}H{sub 2}O octahedra forming trans-linked zig-zag chains or hydrogen bonded zig-zag chains along the major crystallographic direction [0 0 1], respectively. To confirm crystal structures and to describe lattice dynamics of these compounds the vibrational normal modes (in {gamma} point of first Brillouin zone) weremore » calculated on the base of the group theory analysis and compared with the spectra obtained from Raman scattering experiments. A relatively good reliability was obtained for both X-ray powder diffraction and Raman scattering.« less

I Situ Surface X-Ray Diffraction Studies of Electrochemically Deposited Monolayers

NASA Astrophysics Data System (ADS)

Yee, Dennis

1995-01-01

In situ x-ray diffraction has been used to determine the detailed atomic structure of electrochemically deposited lead, thallium, and bismuth monolayers on the silver (111) electrode surface. A review of our previously published lead and thallium monolayer results and the first in situ surface x-ray crystallographic study of the bismuth monolayer structure is presented. The crystallographic analysis of the bismuth Bragg rod intensities and the interference between the bismuth Bragg rod and silver crystal truncation rod scattering were used to determine the detailed atomic structure of the bismuth on silver (111) system at the liquid-solid interface. Our previous in situ x-ray diffraction studies showed that the bismuth monolayer lattice is rectangular and uniaxially incommensurate with the underlying hexagonal silver surface. A crystallographic analysis of the measured structure factor magnitudes reveals that the monolayer forms chains of atoms on the silver surface, similar to the bulk Bi(110)_{rh} plane, with a near neighbor distance of 3.12 +/- 0.01 A and a bond angle of 93 +/- 1^circ, consistent with the bulk Bi(110) _{rh} plane values. The crystallographic refinement also shows that the bismuth monolayer atoms are anisotropically disordered with a rms disorder of 0.25 +/- 0.03 A in the incommensurate direction and 0.09 +/- 0.03 A rms in the commnensurate direction. The interference between the Bi(20) Bragg rod and the Ag(10L)_ {h} crystal truncation rod scattering reveals that one set of bismuth atoms is registered near the bridge sites of the silver (111) surface while another set is registered near the 3-fold hollow sites. In addition, the Bi-Ag d-spacing (3.1 +/- 0.1 A) is found to be consistent with the bulk bismuth near neighbor distance. The bismuth z-direction rms disorder (1.01 +/- 0.08 A) is found to be dominated by the roughness of the underlying silver (sigma_{Ag} = 0.9 +/- 0.1 A rms). Using the estimated bismuth-bismuth spring constant of 1.41 +/- 0.07 eV/A^2 from our measured bismuth two-dimensional compressibility, two simple models are used to try and understand the origin of the anisotropic disorder. A simple two-dimensional isotropic thermal fluctuation model shows that thermal fluctuations are not large enough to account for all of the measured excess disorder in the incommensurate direction. A simple one-dimensional Frenkel-Kontorova model shows that the substrate-induced disorder can account for the anisotropic disorder, assuming a substrate sinusoidal potential strength of 0.35 +/- 0.02 eV.

Protein crystal growth and the International Space Station

NASA Technical Reports Server (NTRS)

DeLucas, L. J.; Moore, K. M.; Long, M. M.

1999-01-01

Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

First Results from a Microfocus X-Ray System for Macromolecular Crystallography

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

1999-01-01

The design and performance of a 40 Watt laboratory crystallography system optimized for the structure determination of small protein crystals are described. This system combines a microfocus x-ray generator (40 microns FWHM spot size at a power level of 40 Watts) and a short focal length (F = 2.6 mm) polycapillary collimating optic, and produces a small diameter quasi-parallel x-ray beam. Measurements of x-ray flux, divergence and spectral purity of the resulting x-ray beam are presented. The x-ray flux in a 250 microns diameter aperture produced by the microfocus system is 14.7 times higher .than that from a 3.15 kW rotating anode generator equipped with graphite monochromator. Crystallography data taken with the microfocus system are presented, and indicate that the divergence and spectral purity of the x-ray are sufficient to refine the diffraction data using a standard crystallographic software. Significant additional improvements in flux and beam divergence are possible, and plans for achieving these coals are discussed.

X-ray transparent Microfluidics for Protein Crystallization and Biomineralization

NASA Astrophysics Data System (ADS)

Opathalage, Achini

Protein crystallization demands the fundamental understanding of nucleation and applying techniques to find the optimal conditions to achieve the kinetic pathway for a large and defect free crystal. Classical nucleation theory predicts that the nucleation occurs at high supersaturation conditions. In this dissertation we sought out to develop techniques to attain optimal supersaturation profile to a large defect free crystal and subject it to in-situ X-ray diffraction using microfluidics. We have developed an emulsion-based serial crystallographic technology in nanolitre-sized droplets of protein solution encapsulated in to nucleate 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 un-oriented crystals. As proof of concept, the structure of Glucose Isomerase was solved to 2.1 A. We have developed a suite of X-ray semi-transparent micrfluidic devices which enables; controlled evaporation as a method of increasing supersaturation and manipulating the phase space of proteins and small molecules. We exploited the inherently high water permeability of the thin X-ray semi-transparent devices as a mean of increasing the supersaturation by controlling the evaporation. We fabricated the X-ray semi-transparent version of the PhaseChip with a thin PDMS membrane by which the storage and the reservoir layers are separated, and studies the phase transition of amorphous CaCO3.

Crystallization of PTP Domains.

PubMed

Levy, Colin; Adams, James; Tabernero, Lydia

2016-01-01

Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

DOE PAGES

Welner, Ditte Hededam; Tsai, Alex Yi-Lin; DeGiovanni, Andy M.; ...

2017-03-29

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstratemore » DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.« less

Experimental determination of spin-dependent electron density by joint refinement of X-ray and polarized neutron diffraction data.

PubMed

Deutsch, Maxime; Claiser, Nicolas; Pillet, Sébastien; Chumakov, Yurii; Becker, Pierre; Gillet, Jean Michel; Gillon, Béatrice; Lecomte, Claude; Souhassou, Mohamed

2012-11-01

New crystallographic tools were developed to access a more precise description of the spin-dependent electron density of magnetic crystals. The method combines experimental information coming from high-resolution X-ray diffraction (XRD) and polarized neutron diffraction (PND) in a unified model. A new algorithm that allows for a simultaneous refinement of the charge- and spin-density parameters against XRD and PND data is described. The resulting software MOLLYNX is based on the well known Hansen-Coppens multipolar model, and makes it possible to differentiate the electron spins. This algorithm is validated and demonstrated with a molecular crystal formed by a bimetallic chain, MnCu(pba)(H(2)O)(3)·2H(2)O, for which XRD and PND data are available. The joint refinement provides a more detailed description of the spin density than the refinement from PND data alone.

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.

Graphene-based microfluidics for serial crystallography.

PubMed

Sui, Shuo; Wang, Yuxi; Kolewe, Kristopher W; Srajer, Vukica; Henning, Robert; Schiffman, Jessica D; Dimitrakopoulos, Christos; Perry, Sarah L

2016-08-02

Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.

Polymorphism of Alprazolam (Xanax): a review of its crystalline phases and identification, crystallographic characterization, and crystal structure of a new polymorph (form III).

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Van den Mooter, Guy; Blaton, Norbert

2007-05-01

A new polymorphic form of Alprazolam (Xanax), 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo-[4,3-alpha][1,4]benzodiazepine, C(17)H(13)ClN(4), has been investigated by means of X-ray powder diffraction (XRPD), single crystal X-ray diffraction, and differential scanning calorimetry (DSC). This polymorphic form (form III) was obtained during DSC experiments after the exothermic recrystallization of the melt of form I. The crystal unit cell dimensions for form III were determined from diffractometer methods. The monoclinic unit cell found for this polymorph using XRPD after indexing the powder diffractogram was confirmed by the cell parameters obtained from single crystal X-ray diffractometry on a crystal isolated from the DSC pans. The single crystal unit cell parameters are: a = 28.929(9), b = 13.844(8), c = 7.361(3) angstroms, beta = 92.82(3) degrees , V = 2944(2) angstroms(3), Z = 8, space group P2(1) (No.4), Dx = 1.393 Mg/m(3). The structure obtained from single crystal X-ray diffraction was used as initial model for Rietveld refinement on the powder diffraction data of form III. The temperature phase transformations of alprazolam were also studied using high temperature XRPD. A review of the different phases available in the Powder Diffraction File (PDF) database for this drug is described bringing some clarification and corrections. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Microstructure Analysis of Bismuth Absorbers for Transition-Edge Sensor X-ray Microcalorimeters

NASA Astrophysics Data System (ADS)

Yan, Daikang; Divan, Ralu; Gades, Lisa M.; Kenesei, Peter; Madden, Timothy J.; Miceli, Antonino; Park, Jun-Sang; Patel, Umeshkumar M.; Quaranta, Orlando; Sharma, Hemant; Bennett, Douglas A.; Doriese, William B.; Fowler, Joseph W.; Gard, Johnathon D.; Hays-Wehle, James P.; Morgan, Kelsey M.; Schmidt, Daniel R.; Swetz, Daniel S.; Ullom, Joel N.

2018-03-01

Given its large X-ray stopping power and low specific heat capacity, bismuth (Bi) is a promising absorber material for X-ray microcalorimeters and has been used with transition-edge sensors (TESs) in the past. However, distinct X-ray spectral features have been observed in TESs with Bi absorbers deposited with different techniques. Evaporated Bi absorbers are widely reported to have non-Gaussian low-energy tails, while electroplated ones do not show this feature. In this study, we fabricated Bi absorbers with these two methods and performed microstructure analysis using scanning electron microscopy and X-ray diffraction microscopy. The two types of material showed the same crystallographic structure, but the grain size of the electroplated Bi was about 40 times larger than that of the evaporated Bi. This distinction in grain size is likely to be the cause of their different spectral responses.

HRTEM Analysis of Crystallographic Defects in CdZnTe Single Crystal

NASA Astrophysics Data System (ADS)

Yasar, Bengisu; Ergunt, Yasin; Kabukcuoglu, Merve Pinar; Parlak, Mehmet; Turan, Rasit; Kalay, Yunus Eren

2018-01-01

In recent years, CdZnTe has attracted much attention due to its superior electrical and structural properties for room-temperature operable gamma and x-ray detectors. However, CdZnTe (CZT) material has often suffered from crystallographic defects encountered during the growth and post-growth processes. The identification and structural characterization of these defects is crucial to synthesize defect-free CdZnTe single crystals. In this study, Cd0.95 Zn0.05 Te single crystals were grown using a three-zone vertical Bridgman system. The single crystallinity of the material was ensured by using x-ray diffraction measurements. High-resolution electron microscopy (HRTEM) was used to characterize the nano-scale defects on the CdZnTe matrix. The linear defects oriented along the ⟨211⟩ direction were examined by transmission electron microscopy (TEM) and the corresponding HRTEM image simulations were performed by using a quantitative scanning TEM simulation package.

Macromolecular diffractive imaging using imperfect crystals

PubMed Central

Ayyer, Kartik; Yefanov, Oleksandr; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Lourdu Xavier, Paulraj; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

2016-01-01

The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7. PMID:26863980

Use of a miniature diamond-anvil cell in high-pressure single-crystal neutron Laue diffraction

PubMed Central

Binns, Jack; Kamenev, Konstantin V.; McIntyre, Garry J.; Moggach, Stephen A.; Parsons, Simon

2016-01-01

The first high-pressure neutron diffraction study in a miniature diamond-anvil cell of a single crystal of size typical for X-ray diffraction is reported. This is made possible by modern Laue diffraction using a large solid-angle image-plate detector. An unexpected finding is that even reflections whose diffracted beams pass through the cell body are reliably observed, albeit with some attenuation. The cell body does limit the range of usable incident angles, but the crystallographic completeness for a high-symmetry unit cell is only slightly less than for a data collection without the cell. Data collections for two sizes of hexamine single crystals, with and without the pressure cell, and at 300 and 150 K, show that sample size and temperature are the most important factors that influence data quality. Despite the smaller crystal size and dominant parasitic scattering from the diamond-anvil cell, the data collected allow a full anisotropic refinement of hexamine with bond lengths and angles that agree with literature data within experimental error. This technique is shown to be suitable for low-symmetry crystals, and in these cases the transmission of diffracted beams through the cell body results in much higher completeness values than are possible with X-rays. The way is now open for joint X-ray and neutron studies on the same sample under identical conditions. PMID:27158503

Distribution of Al atoms in the clathrate-I phase Ba8AlxSi46-x at x = 6.9.

PubMed

Bobnar, Matej; Böhme, Bodo; Wedel, Michael; Burkhardt, Ulrich; Ormeci, Alim; Prots, Yurii; Drathen, Christina; Liang, Ying; Nguyen, Hong Duong; Baitinger, Michael; Grin, Yuri

2015-07-28

The clathrate-I phase Ba8AlxSi46-x has been structurally characterized at the composition x = 6.9 (space group Pm3[combining macron]n, no. 223, a = 10.4645(2) Å). A crystal structure model comprising the distribution of aluminium and silicon atoms in the clathrate framework was established: 5.7 Al atoms and 0.3 Si atoms occupy the crystallographic site 6c, while 1.2 Al atoms and 22.8 Si atoms occupy site 24k. The atomic distribution was established based on a combination of (27)Al and (29)Si NMR experiments, X-ray single-crystal diffraction and wavelength-dispersive X-ray spectroscopy.

Anomalous Diffraction in Crystallographic Phase Evaluation

PubMed Central

Hendrickson, Wayne A.

2014-01-01

X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of multiwavelength anomalous diffraction (MAD) and single-wavelength anomalous diffraction (SAD) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications. PMID:24726017

In Situ XRD Studies of the Process Dynamics During Annealing in Cold-Rolled Copper

NASA Astrophysics Data System (ADS)

Dey, Santu; Gayathri, N.; Bhattacharya, M.; Mukherjee, P.

2016-12-01

The dynamics of the release of stored energy during annealing along two different crystallographic planes, i.e., {111} and {220}, in deformed copper have been investigated using in situ X-ray diffraction measurements at 458 K and 473 K (185 °C and 200 °C). The study has been carried out on 50 and 80 pct cold-rolled Cu sheets. The microstructures of the rolled samples have been characterized using optical microscopy and electron backscattered diffraction measurements. The microstructural parameters were evaluated from the X-ray diffractogram using the Scherrer equation and the modified Rietveld method. The stored energy along different planes was determined using the modified Stibitz formula from the X-ray peak broadening, and the bulk stored energy was evaluated using differential scanning calorimetry. The process dynamics of recovery and recrystallization as observed through the release of stored energy have been modeled as the second-order and first-order processes, respectively.

Synthesis and characterization of 3-acetoxy-2-methyl-N-(phenyl)benzamide and 3-acetoxy-2-methyl-N-(4- methylphenyl)benzamide

NASA Astrophysics Data System (ADS)

Kırca, Başak Koşar; Çakmak, Şükriye; Kütük, Halil; Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2018-01-01

This study treats about two successfully synthesized secondary amide compounds 3-Acetoxy-2-methyl-N-(phenyl)benzamide, I and 3-Acetoxy-2-methyl-N-(4-methylphenyl)benzamide, II. Compounds were characterized by FTIR, 1H NMR, 13C NMR and X-ray single crystal diffraction analysis techniques. Single crystal X-ray diffraction analyses show that while I crystallized in the orthorhombic system with space group Pbca, II crystallized in the triclinic system with space group P-1 and the asymmetric unit of II consists of two crystallographically independent molecules. Lattice constants are a = 7.9713 (3) Å, b = 9.5059 (3) Å, c = 37.1762 (2) Å, Z = 8 for I and a = 7.5579 (8) Å, b = 8.8601 (8) Å, c = 23.363 (3) Å, α = 97.011 (9) °, β = 96.932 (9)°, γ = 90.051 (8)°, Z = 4 for II. Crystallographic studies also show that the supramolecular structures were stabilized by intramolecular, intermolecular hydrogen bonds and Csbnd H … π interactions for both compounds. Characteristic amide bonds were observed in IR and NMR spectra.

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

Yu, Qi; Zhu, Fang-Yuan; Cheng, Li-Qian

Crystallographic structure of sol-gel-processed lead-free (K,Na)NbO{sub 3} (KNN) epitaxial films on [100]-cut SrTiO{sub 3} single-crystalline substrates was investigated for a deeper understanding of its piezoelectric response. Lattice parameter measurement by high-resolution X-ray diffraction and transmission electron microscopy revealed that the orthorhombic KNN films on SrTiO{sub 3} (100) surfaces are [010] oriented (b-axis-oriented) rather than commonly identified c-axis orientation. Based on the crystallographic orientation and corresponding ferroelectric domain structure investigated by piezoresponse force microscopy, the superior piezoelectric property along b-axis of epitaxial KNN films than other orientations can be explained.

Tomography with energy dispersive diffraction

NASA Astrophysics Data System (ADS)

Stock, S. R.; Okasinski, J. S.; Woods, R.; Baldwin, J.; Madden, T.; Quaranta, O.; Rumaiz, A.; Kuczewski, T.; Mead, J.; Krings, T.; Siddons, P.; Miceli, A.; Almer, J. D.

2017-09-01

X-ray diffraction can be used as the signal for tomographic reconstruction and provides a cross-sectional map of the crystallographic phases and related quantities. Diffraction tomography has been developed over the last decade using monochromatic x-radiation and an area detector. This paper reports tomographic reconstruction with polychromatic radiation and an energy sensitive detector array. The energy dispersive diffraction (EDD) geometry, the instrumentation and the reconstruction process are described and related to the expected resolution. Results of EDD tomography are presented for two samples containing hydroxyapatite (hAp). The first is a 3D-printed sample with an elliptical crosssection and contains synthetic hAp. The second is a human second metacarpal bone from the Roman-era cemetery at Ancaster, UK and contains bio-hAp which may have been altered by diagenesis. Reconstructions with different diffraction peaks are compared. Prospects for future EDD tomography are also discussed.

Protein crystal structure from non-oriented, single-axis sparse X-ray data

DOE PAGES

Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.; ...

2016-01-01

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases where the data are sparse.« less

Protein crystal structure from non-oriented, single-axis sparse X-ray data

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

Wierman, Jennifer L.; Lan, Ti-Yen; Tate, Mark W.

X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse. The success of SFX at XFELs has catalyzed interest in analogous experiments at synchrotron-radiation (SR) sources, where data are collected from many small crystals and the ultrashort pulses are replaced by exposure times that aremore » kept short enough to avoid significant crystal damage. The diffraction signal from each short exposure is so `sparse' in recorded photons that the process of recording the crystal intensity is itself a reconstruction problem. Using theEMCalgorithm, a successful reconstruction is demonstrated here in a sparsity regime where there are no Bragg peaks that conventionally would serve to determine the orientation of the crystal in each exposure. In this proof-of-principle experiment, a hen egg-white lysozyme (HEWL) crystal rotating about a single axis was illuminated by an X-ray beam from an X-ray generator to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of these sparse frames, typically containing only ~200 photons per frame, were recorded using a fast-framing detector. It is shown that reconstruction of three-dimensional diffraction intensity is possible using theEMCalgorithm, even with these extremely sparse frames and without knowledge of the rotation angle. Further, the reconstructed intensity can be phased and refined to solve the protein structure using traditional crystallographic software. In conclusion, this suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of theEMCalgorithm even in cases where the data are sparse.« less

Investigation of phase transition properties of ZrO2 thin films

NASA Astrophysics Data System (ADS)

Kumar, Davinder; Singh, Avtar; Kaur, Manpreet; Rana, Vikrant Singh; Kaur, Raminder

2018-05-01

This paper presents the synthesis of transparent thin films of zirconium oxide (ZrO2) deposited on glass substrates by sol-gel dip coating technique. Synthesized films were characterized for different annealing time and withdrawal speed. Change in crystallographic properties of thin films was investigated by using X-ray diffraction. Surface morphology of transparent thin films was estimated by using scanning electron microscope.

The use of analytical surface tools in the fundamental study of wear. [atomic nature of wear

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1977-01-01

Various techniques and surface tools available for the study of the atomic nature of the wear of materials are reviewed These include chemical etching, x-ray diffraction, electron diffraction, scanning electron microscopy, low-energy electron diffraction, Auger emission spectroscopy analysis, electron spectroscopy for chemical analysis, field ion microscopy, and the atom probe. Properties of the surface and wear surface regions which affect wear, such as surface energy, crystal structure, crystallographic orientation, mode of dislocation behavior, and cohesive binding, are discussed. A number of mechanisms involved in the generation of wear particles are identified with the aid of the aforementioned tools.

Hogtuvaite, a new beryllian member of the aenigmatite group from Norway, with new X-ray data on aenigmatite

USGS Publications Warehouse

Grauch, R.I.

1994-01-01

Hogtuvaite is a new beryllian member of the aenigmatite group that was discovered in Nordland County, Norway. It is a metamorphic mineral, hosted by Proterozoic granitic gneisses and mafic pegmatites of metamorphic origin. Compositional variations within and between gneiss-hosted samples of hogtuvaite are minimal; however, pegmatite-hosted samples of hogtuvaite are significantly different, containing less Al and Sn, and more Ti and Mn, than those from the gneisses. The mineralogical, optical and crystallographic properties of hogtuvaite are described. A new and uniquely indexed set of X-ray powder diffraction data for aenigmatite is presented. -from Authors

Mineralogical, crystallographic and morphological characteristics of natural kaolins from the Ivory Coast (West Africa)

NASA Astrophysics Data System (ADS)

Sei, J.; Morato, F.; Kra, G.; Staunton, S.; Quiquampoix, H.; Jumas, J. C.; Olivier-Fourcade, J.

2006-10-01

Thirteen clay samples from four deposits in the Ivory Coast (West Africa) were studied using X-ray diffraction, thermogravimetric analysis and chemical analysis. Mineralogical, crystallographic and morphological characteristics of these samples are given. Kaolinite is the principal mineral but other minerals are present in small quantities: illite, quartz, anatase and iron oxides (oxides and oxyhydroxides). The crystallographic, morphological and surface characteristics are influenced by the presence of these impurities. In particular, the presence of iron oxides was associated with reduced structural ordering and thermal stability of kaolinite and increased specific surface area. These clays could be used in the ceramics industry to make tiles and bricks, and also in agronomy as supports for chemical fertilizers or for environmental protection by immobilising potentially toxic waste products.

Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component A

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

Kim, Kyung-Jin, E-mail: kkj@postech.ac.kr; Kim, Sujin; Lee, Sujin

2006-11-01

The Corynebacterium glutamicum NTA monooxygenase component A protein, which plays the central role in NTA biodegradation, was crystallized. The initial X-ray crystallographic characterization is reported. Safety and environmental concerns have recently dictated the proper disposal of nitrilotriacetate (NTA). Biodegradation of NTA is initiated by NTA monooxygenase, which is composed of two proteins: component A and component B. The NTA monooxygenase component A protein from Corynebacterium glutamicum was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate as the precipitant. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystalmore » belongs to the monoclinic space group C2, with unit-cell parameters a = 111.04, b = 98.51, c = 171.61 Å, β = 101.94°. The asymmetric unit consists of four molecules, corresponding to a packing density of 2.3 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.« less

Nitrogen grain-boundary passivation of In-doped ZnO transparent conducting oxide

NASA Astrophysics Data System (ADS)

Ali, D.; Butt, M. Z.; Coughlan, C.; Caffrey, D.; Shvets, I. V.; Fleischer, K.

2018-04-01

We have investigated the properties and conduction limitations of spray pyrolysis grown, low-cost transparent conducting oxide ZnO thin films doped with indium. We analyze the optical, electrical, and crystallographic properties as functions of In content with a specific focus on postgrowth heat treatment of these thin films at 320 ∘C in an inert, nitrogen atmosphere, which improves the films electrical properties considerably. The effect was found to be dominated by nitrogen-induced grain-boundary passivation, identified by a combined study using i n situ resistance measurement upon annealing, x-ray photoelectron spectroscopy, photoluminescence, and x-ray diffraction studies. We also highlight the chemical mechanism of morphologic and crystallographic changes found in films with high indium content. By optimizing growth conditions according to these findings, ZnO:In with a resistivity as low as 2 ×10 -3Ω cm , high optical quality (T ≈90 % ), and sheet resistance of 32 Ω /□ has been obtained without any need for postgrowth treatments.

Crystallographic Orientation Identification in Multicrystalline Silicon Wafers Using NIR Transmission Intensity

NASA Astrophysics Data System (ADS)

Skenes, Kevin; Kumar, Arkadeep; Prasath, R. G. R.; Danyluk, Steven

2018-02-01

Near-infrared (NIR) polariscopy is a technique used for the non-destructive evaluation of the in-plane stresses in photovoltaic silicon wafers. Accurate evaluation of these stresses requires correct identification of the stress-optic coefficient, a material property which relates photoelastic parameters to physical stresses. The material stress-optic coefficient of silicon varies with crystallographic orientation. This variation poses a unique problem when measuring stresses in multicrystalline silicon (mc-Si) wafers. This paper concludes that the crystallographic orientation of silicon can be estimated by measuring the transmission of NIR light through the material. The transmission of NIR light through monocrystalline wafers of known orientation were compared with the transmission of NIR light through various grains in mc-Si wafers. X-ray diffraction was then used to verify the relationship by obtaining the crystallographic orientations of these assorted mc-Si grains. Variation of transmission intensity for different crystallographic orientations is further explained by using planar atomic density. The relationship between transmission intensity and planar atomic density appears to be linear.

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

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

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.

The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition. Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI-RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this proteinmore » are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.« less

Impurity precipitation in atomized particles evidenced by nano x-ray diffraction computed tomography

NASA Astrophysics Data System (ADS)

Bonnin, Anne; Wright, Jonathan P.; Tucoulou, Rémi; Palancher, Hervé

2014-08-01

Performances and physical properties of high technology materials are influenced or even determined by their initial microstructure and by the behavior of impurity phases. Characterizing these impurities and their relations with the surrounding matrix is therefore of primary importance but it unfortunately often requires a destructive approach, with the risk of misinterpreting the observations. The improvement we have done in high resolution X-ray diffraction computed tomography combined with the use of an X-ray nanoprobe allows non-destructive crystallographic description of materials with microscopic heterogeneous microstructure (with a grain size between 10 nm and 10 μm). In this study, the grain localization in a 2D slice of a 20 μm solidified atomized γU-Mo particle is shown and a minority U(C,O) phase (1 wt. %) with sub-micrometer sized grains was characterized inside. Evidence is presented showing that the onset of U(C,O) grain crystallization can be described by a precipitation mechanism since one single U-Mo grain has direct orientation relationship with more than one surrounding U(C,O) grains.

Crystallization and preliminary X-ray diffraction analysis of P30, the transmembrane domain of pertactin, an autotransporter from Bordetella pertussis

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

Zhu, Yanshi; Black, Isobel; Roszak, Aleksander W.

2007-07-01

P30, the transmembrane C-terminal domain of pertactin from B. pertussis has been crystallized after refolding in vitro. Preliminary X-ray crystallographic data are reported. P30, the 32 kDa transmembrane C-terminal domain of pertactin from Bordetella pertussis, is supposed to form a β-barrel inserted into the outer membrane for the translocation of the passenger domain. P30 was cloned and expressed in inclusion bodies in Escherichia coli. After refolding and purification, the protein was crystallized using the sitting-drop vapour-diffusion method at 292 K. The crystals diffract to a resolution limit of 3.5 Å using synchrotron radiation and belong to the hexagonal space groupmore » P6{sub 1}22, with unit-cell parameters a = b = 123.27, c = 134.43 Å.« less

Studies on 2-amino-5-nitropyridinium nitrate (2A5NPN): A semi-organic third order nonlinear optical single crystal

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

Sivasubramani, V.; Pandian, Muthu Senthil, E-mail: senthilpandianm@ssn.edu.in; Ramasamy, P.

2016-05-23

2-amino-5-nitropyridinium nitrate (2A5NPN) is a semi-organic nonlinear optical crystal and optically good quality 2A5NPN single crystals were successfully grown by slow evaporation solution growth technique (SEST) at ambient temperature. The crystallographic structure of the grown crystal was determined by single crystal X-Ray diffraction analysis and it belongs to Monoclinic crystal system with centro symmetric crystalline nature. The crystallinity of the grown crystal was confirmed by powder X-ray diffraction analysis. The other physical properties of grown crystals are also characterized using TG-DTA, UV-Visible NIR, chemical etching, photoconductivity and Z-scan measurements. The Z-scan method reveals that the 2A5NPN crystal possesses multi photonmore » absorption behaviour and the significantly higher third order susceptibility and it is a promising potential NLO material.« less

Native phasing of x-ray free-electron laser data for a G protein-coupled receptor.

PubMed

Batyuk, Alexander; Galli, Lorenzo; Ishchenko, Andrii; Han, Gye Won; Gati, Cornelius; Popov, Petr A; Lee, Ming-Yue; Stauch, Benjamin; White, Thomas A; Barty, Anton; Aquila, Andrew; Hunter, Mark S; Liang, Mengning; Boutet, Sébastien; Pu, Mengchen; Liu, Zhi-Jie; Nelson, Garrett; James, Daniel; Li, Chufeng; Zhao, Yun; Spence, John C H; Liu, Wei; Fromme, Petra; Katritch, Vsevolod; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim

2016-09-01

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of "diffraction-before-destruction." However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A 2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

PubMed Central

DeWalt, Emma L.; Begue, Victoria J.; Ronau, Judith A.; Sullivan, Shane Z.; Das, Chittaranjan; Simpson, Garth J.

2013-01-01

Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals. PMID:23275165

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

3D Microstructural Architectures for Metal and Alloy Components Fabricated by 3D Printing/Additive Manufacturing Technologies

NASA Astrophysics Data System (ADS)

Martinez, E.; Murr, L. E.; Amato, K. N.; Hernandez, J.; Shindo, P. W.; Gaytan, S. M.; Ramirez, D. A.; Medina, F.; Wicker, R. B.

The layer-by-layer building of monolithic, 3D metal components from selectively melted powder layers using laser or electron beams is a novel form of 3D printing or additive manufacturing. Microstructures created in these 3D products can involve novel, directional solidification structures which can include crystallographically oriented grains containing columnar arrays of precipitates characteristic of a microstructural architecture. These microstructural architectures are advantageously rendered in 3D image constructions involving light optical microscopy and scanning and transmission electron microscopy observations. Microstructural evolution can also be effectively examined through 3D image sequences which, along with x-ray diffraction (XRD) analysis in the x-y and x-z planes, can effectively characterize related crystallographic/texture variances. This paper compares 3D microstructural architectures in Co-base and Ni-base superalloys, columnar martensitic grain structures in 17-4 PH alloy, and columnar copper oxides and dislocation arrays in copper.

Ambiguities and completeness of SAS data analysis: investigations of apoferritin by SAXS/SANS EID and SEC-SAXS methods

NASA Astrophysics Data System (ADS)

Zabelskii, D. V.; Vlasov, A. V.; Ryzhykau, Yu L.; Murugova, T. N.; Brennich, M.; Soloviov, D. V.; Ivankov, O. I.; Borshchevskiy, V. I.; Mishin, A. V.; Rogachev, A. V.; Round, A.; Dencher, N. A.; Büldt, G.; Gordeliy, V. I.; Kuklin, A. I.

2018-03-01

The method of small angle scattering (SAS) is widely used in the field of biophysical research of proteins in aqueous solutions. Obtaining low-resolution structure of proteins is still a highly valuable method despite the advances in high-resolution methods such as X-ray diffraction, cryo-EM etc. SAS offers the unique possibility to obtain structural information under conditions close to those of functional assays, i.e. in solution, without different additives, in the mg/mL concentration range. SAS method has a long history, but there are still many uncertainties related to data treatment. We compared 1D SAS profiles of apoferritin obtained by X-ray diffraction (XRD) and SAS methods. It is shown that SAS curves for X-ray diffraction crystallographic structure of apoferritin differ more significantly than it might be expected due to the resolution of the SAS instrument. Extrapolation to infinite dilution (EID) method does not sufficiently exclude dimerization and oligomerization effects and therefore could not guarantee total absence of dimers account in the final SAS curve. In this study, we show that EID SAXS, EID SANS and SEC-SAXS methods give complementary results and when they are used all together, it allows obtaining the most accurate results and high confidence from SAS data analysis of proteins.

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

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

Post,J.; Bish, D.; Heaney, P.

2007-01-01

Rietveld refinements using synchrotron powder X-ray diffraction data were used to study 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 H{sub 2}O site. The RT structure under vacuum retained only {approx}1/8 of the zeolitic H{sub 2}O and the volume decreased by 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 H{sub 2}O is lost bymore » {approx}390 K, accompanied by a decrease in the a and c unit-cell parameters. Above {approx}600 K the sepiolite structure folds as one-half of the crystallographically bound H{sub 2}O is lost. Rietveld refinements of the 'anhydrous' sepiolite structure reveal that, in general, unit-cell parameters a and b and volume steadily decrease with increasing temperature; there is an obvious change in slope at {approx}820 K suggesting a phase transformation coinciding with the loss of the remaining bound H{sub 2}O molecule.« less

Microgravity

NASA Image and Video Library

2004-04-15

To the crystallographer, this may not be a diamond but it is just as priceless. A Lysozyme crystal grown in orbit looks great under a microscope, but the real test is X-ray crystallography. The colors are caused by polarizing filters. Proteins can form crystals generated by rows and columns of molecules that form up like soldiers on a parade ground. Shining X-rays through a crystal will produce a pattern of dots that can be decoded to reveal the arrangement of the atoms in the molecules making up the crystal. Like the troops in formation, uniformity and order are everything in X-ray crystallography. X-rays have much shorter wavelengths than visible light, so the best looking crystals under the microscope won't necessarily pass muster under the X-rays. In order to have crystals to use for X-ray diffraction studies, crystals need to be fairly large and well ordered. Scientists also need lots of crystals since exposure to air, the process of X-raying them, and other factors destroy them. Growing protein crystals in space has yielded striking results. Lysozyme's structure is well known and it has become a standard in many crystallization studies on Earth and in space.

Lysozyme Crystal

NASA Technical Reports Server (NTRS)

2004-01-01

To the crystallographer, this may not be a diamond but it is just as priceless. A Lysozyme crystal grown in orbit looks great under a microscope, but the real test is X-ray crystallography. The colors are caused by polarizing filters. Proteins can form crystals generated by rows and columns of molecules that form up like soldiers on a parade ground. Shining X-rays through a crystal will produce a pattern of dots that can be decoded to reveal the arrangement of the atoms in the molecules making up the crystal. Like the troops in formation, uniformity and order are everything in X-ray crystallography. X-rays have much shorter wavelengths than visible light, so the best looking crystals under the microscope won't necessarily pass muster under the X-rays. In order to have crystals to use for X-ray diffraction studies, crystals need to be fairly large and well ordered. Scientists also need lots of crystals since exposure to air, the process of X-raying them, and other factors destroy them. Growing protein crystals in space has yielded striking results. Lysozyme's structure is well known and it has become a standard in many crystallization studies on Earth and in space.

Phase-contrast x-ray imaging of microstructure and fatigue-crack propagation in single-crystal nickel-base superalloys

NASA Astrophysics Data System (ADS)

Husseini, Naji Sami

Single-crystal nickel-base superalloys are ubiquitous in demanding turbine-blade applications, and they owe their remarkable resilience to their dendritic, hierarchical microstructure and complex composition. During normal operations, they endure rapid low-stress vibrations that may initiate fatigue cracks. This failure mode in the very high-cycle regime is poorly understood, in part due to inadequate testing and diagnostic equipment. Phase-contrast imaging with coherent synchrotron x rays, however, is an emergent technique ideally suited for dynamic processes such as crack initiation and propagation. A specially designed portable ultrasonic-fatigue apparatus, coupled with x-ray radiography, allows real-time, in situ imaging while simulating service conditions. Three contrast mechanisms - absorption, diffraction, and phase contrast - span the immense breadth of microstructural features in superalloys. Absorption contrast is sensitive to composition and crack displacements, and diffraction contrast illuminates dislocation aggregates and crystallographic misorientations. Phase contrast enhances electron-density gradients and is particularly useful for fatigue-crack studies, sensitive to internal crack tips and openings less than one micrometer. Superalloy samples were imaged without external stresses to study microstructure and mosaicity. Maps of rhenium and tungsten concentrations revealed strong segregation to the center of dendrites, as manifested by absorption contrast. Though nominally single crystals, dendrites were misoriented from the bulk by a few degrees, as revealed by diffraction contrast. For dynamic studies of cyclic fatigue, superalloys were mounted in the portable ultrasonic-fatigue apparatus, subjected to a mean tensile stress of ˜50-150 MPa, and cycled in tension to initiate and propagate fatigue cracks. Radiographs were recorded every thousand cycles over the multimillion-cycle lifetime to measure micron-scale crack growth. Crack openings were very small, as determined by absorption and phase contrast, and suggested multiple fracture modes for propagation along {111} planes at room temperature, which was verified by finite element analysis. With increasing temperature, cracks became Mode I (perpendicular to the loading axis) in character and more sensitive to the microstructure. Advancing plastic zones ahead of crack tips altered the crystallographic quality, from which diffraction contrast anticipated initiation and propagation. These studies demonstrate the extreme sensitivity of x-ray radiography for detailed studies of superalloys and crack growth processes.

Magnesium-Aluminum-Zirconium Oxide Amorphous Ternary Composite: A Dense and Stable Optical Coating

NASA Technical Reports Server (NTRS)

Sahoo, N. K.; Shapiro, A. P.

1998-01-01

In the present work, the process parameter dependent optical and structural properties of MgO-Al(2)O(3)-ZrO(2) ternary mixed-composite material have been investigated. Optical properties were derived from spectrophotometric measurements. The surface morphology, grain size distributions, crystallographic phases and process dependent material composition of films have been investigated through the use of Atomic Force Microscopy (AFM), X-ray diffraction analysis and Energy Dispersive X- ray (EDX) analysis. EDX analysis made evident the correlation between the optical constants and the process dependent compositions in the films. It is possible to achieve environmentally stable amorphous films with high packing density under certain optimized process conditions.

Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum

PubMed Central

Kovalevsky, Andrey Y.; Hanson, B. Leif; Seaver, Sean; Fisher, S. Zoë; Mustyakimov, Marat; Langan, Paul

2011-01-01

Room-temperature X-ray and neutron diffraction data were measured from a family 11 endoxylanase holoenzyme (XynII) originating from the filamentous fungus Trichoderma longibrachiatum to 1.55 Å resolution using a home source and to 1.80 Å resolution using the Protein Crystallography Station at LANSCE. Crystals of XynII, which is an important enzyme for biofuel production, were grown at pH 8.5 in order to examine the effect of basic conditions on the protonation-state distribution in the active site and throughout the protein molecule and to provide insights for rational engineering of catalytically improved XynII for industrial applications. PMID:21301107

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Effect of Aluminum Addition on the Evolution of Microstructure, Crystallographic Texture and Mechanical Properties of Single Phase Hexagonal Close Packed Mg-Li Alloys

NASA Astrophysics Data System (ADS)

Bhagat Singh, P.; Sabat, R. K.; Kumaran, S.; Suwas, S.

2018-02-01

In the present investigation, an effort has been made to understand the effect of aluminum addition to α Mg-Li alloys. The corresponding composition Mg-4Li- xAl ( x = 0, 2, 4 and 6 wt.%) alloys have been prepared by stir casting route under an argon environment. Extrusion was carried out at 300 °C with the extrusion ratio of 15:1. Significant grain refinement was observed after extrusion. X-ray diffraction-based investigation of the cast and extruded alloys showed the presence of intermetallic compounds such as Mg17Al12 and AlLi in the Al-rich alloys namely, Mg-4Li- xAl ( x = 4 and 6 wt.%). These precipitates were also present in the extruded plus annealed samples, indicating the stability of the precipitates at high temperature. The bulk x-ray texture measurement revealed a crystallographic texture where the c-axis of the h.c.p crystals was perpendicular to the extrusion direction (ED) for extruded sample. A texture transition was observed on annealing. The c-axis was oriented parallel to the ED. Mechanical properties of the cast, extruded and extruded plus annealed material illustrate that the addition of Al led to enhancement in hardness, yield strength and ultimate tensile strength.

Study of the specific features of single-crystal boron microstructure

NASA Astrophysics Data System (ADS)

Blagov, A. E.; Vasil'ev, A. L.; Dmitriev, V. P.; Ivanova, A. G.; Kulikov, A. G.; Marchenkov, N. V.; Popov, P. A.; Presnyakov, M. Yu.; Prosekov, P. A.; Pisarevskii, Yu. V.; Targonskii, A. V.; Chernaya, T. S.; Chernyshov, D. Yu.

2017-09-01

A complex study of the structure of β-boron single crystal grown by the floating-zone method, with sizes significantly exceeding the analogs known in the literature, has been performed. The study includes X-ray diffraction analysis and X-ray diffractometry (measurement of pole figures and rocking curves), performed on both laboratory and synchrotron sources; atomic-resolution scanning transmission electron microscopy with spherical aberration correction; and energy-dispersive microanalysis. X-ray diffraction analysis using synchrotron radiation has been used to refine the β-boron structure and find impurity Si atoms. The relative variations in the unit-cell parameters a and c for the crystal bulk are found to be δ a/ a ≈ 0.4 and δ c/ c ≈ 0.1%. X-ray diffractometry has revealed that the single-crystal growth axis coincides with the [2\\bar 2013] crystallographic axis and makes an angle of 21.12° with the [0001] threefold axis. Electron microscopy data have confirmed that the sample under study is a β-boron crystal, which may contain 0.3-0.4 at % Si as an impurity. Planar defects (stacking faults and dislocations) are found. The results of additional measurements of the temperature dependence of the thermal conductivity of the crystal in the range of 50-300 K are indicative of its high structural quality.

Surface crystallographic structures of cellulose nanofiber films and overlayers of pentacene

NASA Astrophysics Data System (ADS)

Nakayama, Yasuo; Mori, Toshiaki; Tsuruta, Ryohei; Yamanaka, Soichiro; Yoshida, Koki; Imai, Kento; Koganezawa, Tomoyuki; Hosokai, Takuya

2018-03-01

Cellulose nanofibers or nanocellulose is a promising recently developed biomass and biodegradable material used for various applications. In order to utilize this material as a substrate in organic electronic devices, thorough understanding of the crystallographic structures of the surfaces of the nanocellulose composites and of their interfaces with organic semiconductor molecules is essential. In this work, surface crystallographic structures of nanocellulose films (NCFs) and overlayers of pentacene were investigated by two-dimensional grazing-incidence X-ray diffraction. The NCFs are found to crystallize on solid surfaces with the crystal lattice preserving the same structure of the known bulk phase, whereas distortion of interchain packing toward the surface normal direction is suggested. The pentacene overlayers on the NCFs are found to form the thin-film phase with an in-plane mean crystallite size of over 10 nm.

Structural and dielectric studies on Ag doped nano ZnSnO3

NASA Astrophysics Data System (ADS)

Deepa, K.; Angel, S. Lilly; Rajamanickam, N.; Jayakumar, K.; Ramachandran, K.

2018-04-01

Undoped and Ag-doped nano Zinc Stannate (ZSO) ternary oxide were prepared by co-precipitation method. The crystallographic, morphological and optical properties of the synthesized nanoparticles were studied using X-ray diffraction (XRD) and UV-Visible spectroscopy (UV-Vis) and Scanning electron microscopy (SEM). The electrical properties of the synthesized samples were studied by dielectric measurements. Higher concentration Ag doped ZSO nanoparticles exhibit higher dielectric constant at low frequency.

Unusual Thermal Stability of High-Entropy Alloy Amorphous Structure

DTIC Science & Technology

2012-06-20

incident angle X - ray diffractometer (GIAXRD, RIGAKU D/MAX2500) with Cu Kα radiation and at the incident angle of 1°. The surface morphology and...microanalyzer (EPMA, JEOL JAX-8800). The crystallographic structures of as-deposited and annealed metallic films were characterized utilizing a glancing ...field image and selected-area- diffraction (SAD) patterns of (a) 800 °C-, (b) 850 °C- and (c) 900 °C-annealed alloy thin films, respectively. Both

Structural Studies on Dy to 119 GPa and Applications to Lanthanide Systematics

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

Patterson, J; Akella, J

2005-05-31

The Rare Earth elements (REE) are known to undergo crystallographic as well as electronic structure changes with applied pressure. On increasing pressure, the trivalent lanthanides follow the sequence hcp {yields} Sm-type {yields} dhcp {yields} fcc {yields} dfcc. In this report we present room-temperature high-pressure x-ray diffraction data for Dy as well as our observations on the post-dfcc phases and concomitant volume changes in the heavy REE.

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

DOE PAGES

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian; ...

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements

PubMed Central

Kroon-Batenburg, Loes M. J.

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an ‘Open Science’ model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromol­ecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. A number of specific case studies are presented, including an example research thread that provides complete open access to raw data. PMID:28250944

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

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

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Effect of crystallographic orientation on the anodic formation of nanoscale pores/tubes in TiO 2 films

NASA Astrophysics Data System (ADS)

Kalantar-zadeh, K.; Sadek, A. Z.; Zheng, H.; Partridge, J. G.; McCulloch, D. G.; Li, Y. X.; Yu, X. F.; Wlodarski, W.

2009-10-01

Self-organized nanopores and nanotubes have been produced in thin films of titanium (Ti) prepared using filtered cathodic vacuum arc (FCVA), DC- and RF-sputter deposition systems. The anodization process was performed using a neutral electrolyte containing fluoride ions with an applied potential between 2 and 20 V (for clarity the results are only presented for 5 V). Scanning electron microscopy (SEM), atomic force microscopy (AFM) and X-ray diffraction (XRD) techniques were used to characterise the films. It was found that the crystallographic orientation of the Ti films played a significant role in determining whether pores or tubes were formed during the anodic etching process.

ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

PubMed Central

Hungler, Arnaud; Momin, Afaque; Diederichs, Kay; Arold, Stefan, T.

2016-01-01

Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for ‘crystallization and preliminary X-ray analysis’ publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. PMID:27980519

MUDMASTER: A Program for Calculating Crystalline Size Distributions and Strain from the Shapes of X-Ray Diffraction Peaks

USGS Publications Warehouse

Eberl, D.D.; Drits, V.A.; Środoń, Jan; Nüesch, R.

1996-01-01

Particle size may strongly influence the physical and chemical properties of a substance (e.g. its rheology, surface area, cation exchange capacity, solubility, etc.), and its measurement in rocks may yield geological information about ancient environments (sediment provenance, degree of metamorphism, degree of weathering, current directions, distance to shore, etc.). Therefore mineralogists, geologists, chemists, soil scientists, and others who deal with clay-size material would like to have a convenient method for measuring particle size distributions. Nano-size crystals generally are too fine to be measured by light microscopy. Laser scattering methods give only average particle sizes; therefore particle size can not be measured in a particular crystallographic direction. Also, the particles measured by laser techniques may be composed of several different minerals, and may be agglomerations of individual crystals. Measurement by electron and atomic force microscopy is tedious, expensive, and time consuming. It is difficult to measure more than a few hundred particles per sample by these methods. This many measurements, often taking several days of intensive effort, may yield an accurate mean size for a sample, but may be too few to determine an accurate distribution of sizes. Measurement of size distributions by X-ray diffraction (XRD) solves these shortcomings. An X-ray scan of a sample occurs automatically, taking a few minutes to a few hours. The resulting XRD peaks average diffraction effects from billions of individual nano-size crystals. The size that is measured by XRD may be related to the size of the individual crystals of the mineral in the sample, rather than to the size of particles formed from the agglomeration of these crystals. Therefore one can determine the size of a particular mineral in a mixture of minerals, and the sizes in a particular crystallographic direction of that mineral.

Biomineral shell formation under ocean acidification: a shift from order to chaos.

PubMed

Fitzer, Susan C; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S; Kamenos, Nicholas A; Phoenix, Vernon R; Cusack, Maggie

2016-02-15

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Biomineral shell formation under ocean acidification: a shift from order to chaos

PubMed Central

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-01-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments. PMID:26876022

Biomineral shell formation under ocean acidification: a shift from order to chaos

NASA Astrophysics Data System (ADS)

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-02-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.

PubMed

San Martin, Fabiana; Mechaly, Ariel E; Larrieux, Nicole; Wunder, Elsio A; Ko, Albert I; Picardeau, Mathieu; Trajtenberg, Felipe; Buschiazzo, Alejandro

2017-03-01

The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.

Non-invasive imaging of the crystalline structure within a human tooth.

PubMed

Egan, Christopher K; Jacques, Simon D M; Di Michiel, Marco; Cai, Biao; Zandbergen, Mathijs W; Lee, Peter D; Beale, Andrew M; Cernik, Robert J

2013-09-01

The internal crystalline structure of a human molar tooth has been non-destructively imaged in cross-section using X-ray diffraction computed tomography. Diffraction signals from high-energy X-rays which have large attenuation lengths for hard biomaterials have been collected in a transmission geometry. Coupling this with a computed tomography data acquisition and mathematically reconstructing their spatial origins, diffraction patterns from every voxel within the tooth can be obtained. Using this method we have observed the spatial variations of some key material parameters including nanocrystallite size, organic content, lattice parameters, crystallographic preferred orientation and degree of orientation. We have also made a link between the spatial variations of the unit cell lattice parameters and the chemical make-up of the tooth. In addition, we have determined how the onset of tooth decay occurs through clear amorphization of the hydroxyapatite crystal, and we have been able to map the extent of decay within the tooth. The described method has strong prospects for non-destructive probing of mineralized biomaterials. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Purification, partial characterization, crystallization and preliminary X-ray diffraction of a novel cardiotoxin-like basic protein from Naja naja atra (South Anhui) venom

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

Rong, Hui; Li, Yan; Lou, Xiao-hua

2007-02-01

A novel cardiotoxin-like basic protein from Naja naja atra was crystallized and diffraction data were collected to 2.35 Å resolution. A novel cardiotoxin-like basic protein was isolated from the venom of the Chinese cobra (Naja naja atra) from the south of Anhui in China. The protein inhibits the expression of vascular endothelial growth factor and basic fibroblast growth factor in human lung cancer cell line H1299 and induces the haemolysis of rabbit erythrocytes under low-lecithin conditions. After a two-step chromatographic purification, the resultant 7 kDa protein was crystallized by the hanging-drop vapour-diffusion method at room temperature. A complete data setmore » was collected to 2.35 Å resolution using an in-house X-ray diffraction system. The crystal belongs to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 43.2, c = 147.9 Å. There are two molecules in the crystallographic asymmetric unit.« less

Characterization, crystallization and preliminary X-ray diffraction analysis of an (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767: enantioselectivity for potential industrial applications.

PubMed

Kim, Seulgi; Ngo, Tri Duc; Kim, Kyeong Kyu; Kim, T Doohun

2012-11-01

The structures and reaction mechanisms of enantioselective hydrolases, which can be used in industrial applications such as biotransformations, are largely unknown. Here, the X-ray crystallographic study of a novel (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767, which can be used in the production of (S)-ketoprofen, is described. Multiple sequence alignments with other hydrolases revealed that pfEstA contains a conserved Ser67 within the S-X-X-K motif as well as a highly conserved Tyr156. Recombinant protein containing an N-terminal His tag was expressed in Escherichia coli, purified to homogeneity and characterized using SDS-PAGE, MALDI-TOF MS and enantioselective analysis. pfEstA was crystallized using a solution consisting of 1 M sodium citrate, 0.1 M CHES pH 9.5, and X-ray diffraction data were collected to a resolution of 1.9 Å with an Rmerge of 7.9%. The crystals of pfEstA belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=65.31, b=82.13, c=100.41 Å, α=β=γ=90°.

Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

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

McLean, Larry R.; Zhang, Ying; Degnen, William

2010-10-28

Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

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.

Arsenic uptake by gypsum and calcite: Modelling and probing by neutron and X-ray scattering

NASA Astrophysics Data System (ADS)

Fernández-Martínez, A.; Román-Ross, G.; Cuello, G. J.; Turrillas, X.; Charlet, L.; Johnson, M. R.; Bardelli, F.

2006-11-01

Uptaking of contaminants by solid phases is relevant to many issues in environmental science as this process can remove them from solutions and retard their transport into the hydrosphere. Here we report on two structural studies performed on As-doped gypsum (CaSO 4 2H 2O) and calcite (CaCO 3), using neutron (D20-ILL) and X-ray (ID11-ESRF) diffraction data and EXAFS (BM8-ESRF). The aim of this study is to determine whether As gets into the bulk of gypsum and calcite structures or is simply adsorbed on the surface. Different mechanisms of substitution are used as hypotheses. The combined Rietveld analysis of neutron and X-ray diffraction data shows an expansion of the unit cell volume proportional to the As concentration within the samples. DFT-based simulations confirm the increase of the unit cell volume proportional to the amount of carbonate or sulphate groups substituted. Interpolation of the experimental Rietveld data allows us to distinguish As substituted within the structure from that adsorbed on the surface of both minerals. Results obtained by EXAFS analysis from calcite samples show good agreement with the hypothesis of replacement of As into the C crystallographic site.

Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation

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

Kobayashi, Kan; RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198; Suzuki, Takehiro

2014-08-27

E. coli YfcM was expressed, purified and crystallized. Crystals of YfcM were obtained by the in situ proteolysis crystallization method. Using these crystals, an X-ray diffraction data set was collected at 1.45 Å resolution. Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallizationmore » method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (V{sub M}) of the crystal was 1.91 Å{sup 3} Da{sup −1}, indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.« less

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

Preliminary X-ray crystallographic studies of a tetrameric phospholipase A{sub 2} formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom

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

Marchi-Salvador, D. P.; Corrêa, L. C.; Salvador, G. H. M.

2007-12-01

Crotoxin B is a basic phospholipase A{sub 2} found in the venom of C. durissus terrificus and is one of the subunits that constitute crotoxin. Here, the crystallization, X-ray diffraction data collection and molecular-replacement solution of a novel tetrameric complex formed by two dimers of crotoxin B isoforms are presented. Crotoxin B is a basic phospholipase A{sub 2} found in the venom of Crotalus durissus terrificus and is one of the subunits that constitute crotoxin. This heterodimeric toxin, which is the main component of C. d. terrificus venom, is completed by an acidic, nontoxic and non-enzymatic component (crotoxin A) andmore » is involved in important envenomation effects, such as neurological disorders, myotoxicity and renal failure. Although crotoxin was first crystallized in 1938, no crystal structure is currently available for crotoxin, crotoxin A or crotoxin B. In this work, the crystallization, X-ray diffraction data collection to 2.28 Å resolution and molecular-replacement solution of a novel tetrameric complex formed by two dimers of crotoxin B isoforms (CB1 and CB2) is presented.« less

Crystal structure, spectral property, antimicrobial activity and DFT calculation of N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea

NASA Astrophysics Data System (ADS)

Zhang, Hong-Song; Zhang, Kong-Yan; Chen, Li-Chuan; Li, Yao-Xin; Chai, Lan-Qin

2017-10-01

N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea was synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis and emission spectroscopy, as well as by single-crystal X-ray diffraction. X-ray crystallographic analyses have indicated that the crystal structure consists of two dimethyl sulfoxide (DMSO) solvent molecules and the structural geometry of DMSO is a trigonal pyramid in shape. In the crystal structure, a self-assembling two-dimensional (2-D) layer supramolecular architecture is formed through intermolecular hydrogen bonds, Cdbnd O···π (thiadiazole ring) and π···π stacking interactions. The geometry of the compound has been optimized by the DFT method and the results are compared with the X-ray diffraction data. The electronic transitions and spectral features of the compound were carried out by using DFT/B3LYP method. In addition, the antimicrobial activity was also studied, and the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and HOMO-LUMO gap were also calculated.

Crystallography, chemistry and structural disorder in the new high-Tc Bi-Ca-Sr-Cu-O superconductor

NASA Technical Reports Server (NTRS)

Veblen, D. R.; Heaney, P. J.; Angel, R. J.; Finger, L. W.; Hazen, R. M.

1988-01-01

Diffraction experiments are reported which indicate that the new Bi-Ca-Sr-Cu-O layer-structure superconductor possesses a primitive orthorhombic unit cell with probable space group Pnnn. The material exhibits severe structural disorder which is primarily related to stacking within the layers. The apparent orthorhombic structure is an average resulting from orthorhombic material mixed with monoclinic domains in two twinned orientations. Two distinct types of structural disorder that are common in materials synthesized to date are also described. This disorder complicates the crystallographic analysis and suggests that X-ray and neutron diffraction methods may yield only an average structure.

Magnetic and structural characterization of ultra-thin Fe (222) films

NASA Astrophysics Data System (ADS)

Loving, Melissa G.; Brown, Emily E.; Rizzo, Nicholas D.; Ambrose, Thomas F.

2018-05-01

Varied thickness body centered cubic (BCC) ultrathin Fe films (10-50Å) have been sputter deposited onto Si (111) substrates. BCC Fe with the novel (222) texture was obtained by H- terminating the Si (111) starting substrate then immediately depositing the magnetic films. Structural results derived from grazing incidence x-ray diffraction and x-ray reflectivity confirm the crystallographic texture, film thickness, and interface roughness. Magnetic results indicate that Fe (222) exhibits soft magnetic switching (easy axis), high anisotropy (hard axis), which is maintained across the thickness range, and a positive magnetostriction (for the thicker film layers). The observed soft magnetic switching in this system makes it an ideal candidate for future magnetic memory development as well as other microelectronics applications that utilize magnetic materials.

Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin

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

Kovalevsky, A.Y.; Fisher, S.Z.; Seaver, S.

2010-08-18

Room-temperature and 100 K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7 {angstrom} resolution using a home source, to 1.6 {angstrom} resolution on NE-CAT at the Advanced Photon Source and to 2.0 {angstrom} resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from thismore » site in the low-temperature structure.« less

Crystallization, X-ray diffraction analysis and phasing of 17β-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus

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

Cassetta, Alberto, E-mail: alberto.cassetta@ic.cnr.it; Büdefeld, Tomaž; Lanišnik Rižner, Tea

2005-12-01

The expression, purification and crystallization of 17β-hydroxysteroid dehydrogenase from the filamentous fungus C. lunatus and its Y167F mutant, both in the apo form, are described. X-ray diffraction analysis and phasing by Patterson-search techniques are reported. 17β-Hydroxysteroid dehydrogenase from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is an NADP(H)-dependent enzyme that preferentially catalyses the oxidoreduction of oestrogens and androgens. The enzyme belongs to the short-chain dehydrogenase/reductase superfamily and is the only fungal hydroxysteroid dehydrogenase known to date. 17β-HSDcl has recently been characterized and cloned and has been the subject of several functional studies. Although several hypotheses on the physiological role of 17β-HSDclmore » in fungal metabolism have been formulated, its function is still unclear. An X-ray crystallographic study has been undertaken and the optimal conditions for crystallization of 17β-HSDcl (apo form) were established, resulting in well shaped crystals that diffracted to 1.7 Å resolution. The space group was identified as I4{sub 1}22, with unit-cell parameters a = b = 67.14, c = 266.77 Å. Phasing was successfully performed by Patterson search techniques. A catalytic inactive mutant Tyr167Phe was also engineered, expressed, purified and crystallized for functional and structural studies.« less

Evolution of the mössbauer spectra of ludwigite Co3 - x Fe x O2BO3 with substitution of iron for cobalt

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Ivanova, N. B.; Bayukov, O. A.; Kazak, N. V.; Bezmaternykh, L. N.; Vasiliev, A. D.

2013-06-01

A concentration series of single crystals of iron-cobalt ludwigites Co3 - x Fe x O2BO3 ( x = 0.0125, 0.025, 0.050, 0.10, 1.0) has been synthesized. The structure has been studied using X-ray diffraction and Mössbauer effect. A preferred occupation of nonequivalent crystallographic positions by iron in the ludwigite structure has been revealed. It has been found that the valence of substituting iron ions is three. It has been revealed that the structure of the γ-resonance spectrum of Co2FeO2BO3 is complicated due to a composition disorder in the system.

Catalytic Graphitization of Coal-Based Carbon Materials with Light Rare Earth Elements.

PubMed

Wang, Rongyan; Lu, Guimin; Qiao, Wenming; Yu, Jianguo

2016-08-30

The catalytic graphitization mechanism of coal-based carbon materials with light rare earth elements was investigated using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, selected-area electron diffraction, and high-resolution transmission electron microscopy. The interface between light rare earth elements and carbon materials was carefully observed, and two routes of rare earth elements catalyzing the carbon materials were found: dissolution-precipitation and carbide formation-decomposition. These two simultaneous processes certainly accelerate the catalytic graphitization of carbon materials, and light rare earth elements exert significant influence on the microstructure and thermal conductivity of graphite. Moreover, by virtue of praseodymium (Pr), it was found that a highly crystallographic orientation of graphite was induced and formed, which was reasonably attributed to the similar arrangements of the planes perpendicular to (001) in both graphite and Pr crystals. The interface between Pr and carbon was found to be an important factor for the orientation of graphite structure.

Studies on synthesis, growth, structural, thermal, linear and nonlinear optical properties of organic picolinium maleate single crystals.

PubMed

Pandi, P; Peramaiyan, G; Sudhahar, S; Chakkaravarthi, G; Mohan Kumar, R; Bhagavannarayana, G; Jayavel, R

2012-12-01

Picolinium maleate (PM), an organic material has been synthesised and single crystals were grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. PM crystal belongs to the monoclinic crystallographic system with space group P2(1)/c. The crystalline perfection of the grown crystals was analyzed by high-resolution X-ray diffraction rocking curve measurements. The presence of functional groups in PM was identified by FTIR and FT-NMR spectral analyses. Thermal behaviour and stability of picolinium maleate were studied by TGA/DTA analyses. UV-Vis spectral studies reveal that PM crystals are transparent in the wavelength region 327-1100 nm. The laser damage threshold value of PM crystal was found to be 4.3 GW/cm(2) using Nd:YAG laser. The Kurtz and Perry powder second harmonic generation technique confirms the nonlinear optical property of the grown crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparative crystallization and preliminary X-ray diffraction studies of locked nucleic acid and RNA stems of a tenascin C-binding aptamer

PubMed Central

Förster, Charlotte; Brauer, Arnd B. E.; Brode, Svenja; Schmidt, Kathrin S.; Perbandt, Markus; Meyer, Arne; Rypniewski, Wojciech; Betzel, Christian; Kurreck, Jens; Fürste, Jens P.; Erdmann, Volker A.

2006-01-01

The pharmacokinetic properties of an aptamer against the tumour-marker protein tenascin-C have recently been successfully improved by the introduction of locked nucleic acids (LNAs) into the terminal stem of the aptamer. Since it is believed that this post-SELEX optimization is likely to provide a more general route to enhance the in vitro and in vivo stability of aptamers, elucidation of the structural basis of this improvement was embarked upon. Here, the crystallographic and X-ray diffraction data of the isolated aptamer stem encompassed in a six-base-pair duplex both with and without the LNA modification are presented. The obtained all-LNA crystals belong to space group P41212 or P43212, with unit-cell parameters a = b = 52.80, c = 62.83 Å; the all-RNA crystals belong to space group R32, with unit-cell parameters a = b = 45.21, c = 186.97 Å, γ = 120.00°. PMID:16820689

Crystallization and preliminary X-ray crystallographic analysis of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

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

Ku, Min-Je; Lee, Won-Ho; Biotechnology and Genetic Engineering, Korea University, Seoul 136-701

2005-04-01

The tRNA-specific adenosine deaminase from the pathogenic bacteria S. pyogenes has been overexpressed and crystallized. The tRNA-specific adenosine deaminase from the pathogenic bacteria Streptococcus pyogenes (spTAD) has been overexpressed in Escherichia coli and crystallized in the presence of Zn{sup 2+} ion at 295 K using ammonium sulfate as a precipitant. Flash-cooled crystals of spTAD diffracted to 2.0 Å using 30%(v/v) glycerol as a cryoprotectant. X-ray diffraction data have been collected to 2.0 Å using synchrotron radiation. The crystal belongs to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 81.042, c = 81.270 Å. Themore » asymmetric unit contains one subunit of spTAD, with a corresponding crystal volume per protein weight (V{sub M}) of 3.3 Å{sup 3} Da{sup −1} and a solvent content of 62.7%.« less

Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

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

Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan

2005-11-01

The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222{sub 1}, with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V{sub M} value of 2.49 Å{sup 3} Da{sup −1}.more » The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)« less

X-ray crystallographic data for minerals

USGS Publications Warehouse

Robie, Richard A.; Bethke, Philip M.; Toulmin, M.S.; Edwards, Jerry L.

1963-01-01

X-ray crystallographic data are of particular importance to the mineralogist. Beyond the considerations of structural chemistry they provide. one of the most accurate methods for phase and/or compositional determination and for obtaining _the molar volumes and densities of minerals {Robie and Bethke, 1962).

Structural and morphological study of ZrO2 thin films

NASA Astrophysics Data System (ADS)

Kumar, Davinder; Singh, Avtar; Kaur, Manpreet; Rana, Vikrant Singh; Kaur, Raminder

2018-05-01

In this paper we discuss the fabrication of transparent thin films of Zirconium Oxide (ZrO2) deposited on glass substrates by sol-gel dip coating technique. Further these fabricated films were characterized for different annealing temperatures and withdrawal speed. X-ray diffraction is used to study the structural properties of deposited thin films and it reveals the change in crystallographic properties with the change in annealing temperature. Thickness of thin films is estimated by using scanning electron microscope.

Characterization of crust formation on a parent body of achondrites and the moon by pyroxene crystallography and chemistry

NASA Technical Reports Server (NTRS)

Takeda, H.; Miyamoto, M.; Ishii, T.; Reid, A. M.

1976-01-01

Single crystal X-ray diffraction and electron microprobe techniques were used to study lunar crustal pyroxenes in a cataclastic norite, a pyroxene-rich clast, and anorthosite lunar samples, and also in meteorites including diogenites, eucrites, and the Yamoto (1) howardite. The crystallographic and chemical characteristics of pyroxenes in these materials are compared and are discussed in terms of the lower stability limit of pigeonite. A mechanical mixing model of howardite is proposed.

Synthesis of Mn doped ZnS nanocrystals: Crystallographic and morphological study

NASA Astrophysics Data System (ADS)

Shaikh, Azharuddin Z.; Shirsath, Narendra B.; Sonawane, Prabhakar S.

2018-05-01

The influence of doping concentration on the physical properties of ZnS nanocrystals synthesized using coprecipitation method at room temperature is reported in this paper. In particular, we have studied the structural properties of Zn1-xMnxS where (x=0.01, 0.03, 0.05) by X-ray diffraction. X-ray peak broadening analysis used to calculate the crystalline sizes, lattice parameters, number of unit cell per particle and volume of unit cell. Crystalline ZnS with a cubic structure is confirmed by XRD results. The grain size of pure and Mn doped samples were found in the range of 7nm to 9nm. All the physical parameters of cubic ZnS nanocrystals were calculated are similar with standard values. The scanning electron microscope (SEM) which revealed that the synthesized nanocrystals are well-crystalline and possessing cubic phase.

Structure and mechanical properties of as-received and heat-treated stainless steel orthodontic wires.

PubMed

Khier, S E; Brantley, W A; Fournelle, R A

1988-03-01

A combination of x-ray diffraction analysis with mechanical testing in tension and bending has been used to investigate the metallurgical structures and mechanical properties for as-received and heat-treated stainless steel orthodontic wires. Two different proprietary wire types were selected, having a wide range in cross-sectional dimensions: 0.016-, 0.030-, and 0.050- or 0.051-inch diameters, and 0.017 X 0.025-inch rectangular specimens. Heat treatments were performed for 10 minutes in air at temperatures of 700 degrees, 900 degrees, and 1100 degrees F. The x-ray diffraction patterns showed that the as-received 0.016-inch diameter and 0.017 X 0.025-inch wires of both proprietary types consisted of a two-phase structure containing a martensitic phase along with the austenitic phase. This duplex structure was converted entirely to austenite with heat treatment for one wire type, but persisted after heat treatment for the other wire type. The largest diameter, 0.050- or 0.051-inch, wires of both types were single-phase austenitic structure for both the as-received and heat-treated conditions. Evidence of substantial preferred crystallographic orientation or texturing in these orthodontic wires was also found by x-ray diffraction. As in our previous studies, the modulus of elasticity in bending was significantly less than the value obtained in tension for only the smaller cross-sectional wires. The 0.05 radian flexural yield strength correlated more closely with the 0.2% offset yield strength in tension than with the yield strength for 0.05% and 0.1% permanent offsets.

Corrosion in drinking water pipes: the importance of green rusts.

PubMed

Swietlik, Joanna; Raczyk-Stanisławiak, Urszula; Piszora, Paweł; Nawrocki, Jacek

2012-01-01

Complex crystallographic composition of the corrosion products is studied by diffraction methods and results obtained after different pre-treatment of samples are compared. The green rusts are found to be much more abundant in corrosion scales than it has been assumed so far. The characteristic and crystallographic composition of corrosion scales and deposits suspended in steady waters were analyzed by X-ray diffraction (XRD). The necessity of the examination of corrosion products in the wet conditions is indicated. The drying of the samples before analysis is shown to substantially change the crystallographic phases originally present in corrosion products. On sample drying the unstable green rusts is converted into more stable phases such as goethite and lepidocrocite, while the content of magnetite and siderite decreases. Three types of green rusts in wet materials sampled from tubercles are identified. Unexpectedly, in almost all corrosion scale samples significant amounts of the least stable green rust in chloride form was detected. Analysis of corrosion products suspended in steady water, which remained between tubercles and possibly in their interiors, revealed complex crystallographic composition of the sampled material. Goethite, lepidocrocite and magnetite as well as low amounts of siderite and quartz were present in all samples. Six different forms of green rusts were identified in the deposits separated from steady waters and the most abundant was carbonate green rust GR(CO(3)(2-))(I). Copyright © 2011 Elsevier Ltd. All rights reserved.

Zr doping dependence of structural and magnetic properties of cobalt ferrite synthesized by sol-gel based Pechini method

NASA Astrophysics Data System (ADS)

Motavallian, Pourya; Abasht, Behzad; Abdollah-Pour, Hassan

2018-04-01

Nanocrystalline CoZrxFe2-xO4 (0 ≤ x ≤ 0.3 in a step of 0.05) powders were synthesized by Pechini sol-gel method. The dry gel was grinded and calcined at 700 °C in a static air atmosphere for 1 h. Some tests such as thermo gravimetric analysis (TGA) combined with differential analysis (DTA), fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM) and vibrating sample magnetometer (VSM) were carried out to investigate the thermal behaviour, structural bonds identification, crystallographic properties, morphology and magnetic properties of the obtained powders. X-ray diffraction revealed a single-phase cubic spinel structure for all samples, where the crystallite size decreases; the lattice parameter simultaneously increases with substitution of Zr. The results of FE-SEM showed that the particle size is in the 20-70 nm range. The magnetic properties such as saturation magnetization (Ms), remanent magnetization (Mr) and coercivity (Hc) were measured from the hysteresis loops. The greatest amount of saturation magnetization for CoZr0.05Fe1.95O4 sample was 67.9 emu·g-1.

A public database of macromolecular diffraction experiments.

PubMed

Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

2016-11-01

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

Magnetic topology of Co-based inverse opal-like structures

NASA Astrophysics Data System (ADS)

Grigoryeva, N. A.; Mistonov, A. A.; Napolskii, K. S.; Sapoletova, N. A.; Eliseev, A. A.; Bouwman, W.; Byelov, D. V.; Petukhov, A. V.; Chernyshov, D. Yu.; Eckerlebe, H.; Vasilieva, A. V.; Grigoriev, S. V.

2011-08-01

The magnetic and structural properties of a cobalt inverse opal-like crystal have been studied by a combination of complementary techniques ranging from polarized neutron scattering and superconducting quantum interference device (SQUID) magnetometry to x-ray diffraction. Microradian small-angle x-ray diffraction shows that the inverse opal-like structure (OLS) synthesized by the electrochemical method fully duplicates the three-dimensional net of voids of the template artificial opal. The inverse OLS has a face-centered cubic (fcc) structure with a lattice constant of 640±10 nm and with a clear tendency to a random hexagonal close-packed structure along the [111] axes. Wide-angle x-ray powder diffraction shows that the atomic cobalt structure is described by coexistence of 95% hexagonal close-packed and 5% fcc phases. The SQUID measurements demonstrate that the inverse OLS film possesses easy-plane magnetization geometry with a coercive field of 14.0 ± 0.5 mT at room temperature. The detailed picture of the transformation of the magnetic structure under an in-plane applied field was detected with the help of small-angle diffraction of polarized neutrons. In the demagnetized state the magnetic system consists of randomly oriented magnetic domains. A complex magnetic structure appears upon application of the magnetic field, with nonhomogeneous distribution of magnetization density within the unit element of the OLS. This distribution is determined by the combined effect of the easy-plane geometry of the film and the crystallographic geometry of the opal-like structure with respect to the applied field direction.

Investigation of the commensurate magnetic structure in the heavy-fermion compound CePt 2 In 7 using magnetic resonant x-ray diffraction

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

Gauthier, Nicolas; Wermeille, Didier; Casati, Nicola

In this paper, we investigated the magnetic structure of the heavy-fermion compound CePt 2In 7 below T N = 5.34 (2) K using magnetic resonant x-ray diffraction at ambient pressure. The magnetic order is characterized by a commensurate propagation vector k 1/2 = (1/2, 1/2, 1/2) with spins lying in the basal plane. Our measurements did not reveal the presence of an incommensurate order propagating along the high-symmetry directions in reciprocal space but cannot exclude other incommensurate modulations or weak scattering intensities. The observed commensurate order can be described equivalently by either a single-k structure or by a multi-k structure.more » Furthermore we explain how a commensurate-only ordering may explain the broad distribution of internal fields observed in nuclear quadrupolar resonance experiments [Sakai et al., Phys. Rev. B 83, 140408 (2011)] that was previously attributed to an incommensurate order. We also report powder x-ray diffraction showing that the crystallographic structure of CePt 2In 7 changes monotonically with pressure up to P = 7.3 GPa at room temperature. The determined bulk modulus B 0 = 81.1 (3) GPa is similar to those of the Ce-115 family. Broad diffraction peaks confirm the presence of pronounced strain in polycrystalline samples of CePt 2In 7. Lastly, we discuss how strain effects can lead to different electronic and magnetic properties between polycrystalline and single crystal samples.« less

Investigation of the commensurate magnetic structure in the heavy-fermion compound CePt 2 In 7 using magnetic resonant x-ray diffraction

DOE PAGES

Gauthier, Nicolas; Wermeille, Didier; Casati, Nicola; ...

2017-08-10

In this paper, we investigated the magnetic structure of the heavy-fermion compound CePt 2In 7 below T N = 5.34 (2) K using magnetic resonant x-ray diffraction at ambient pressure. The magnetic order is characterized by a commensurate propagation vector k 1/2 = (1/2, 1/2, 1/2) with spins lying in the basal plane. Our measurements did not reveal the presence of an incommensurate order propagating along the high-symmetry directions in reciprocal space but cannot exclude other incommensurate modulations or weak scattering intensities. The observed commensurate order can be described equivalently by either a single-k structure or by a multi-k structure.more » Furthermore we explain how a commensurate-only ordering may explain the broad distribution of internal fields observed in nuclear quadrupolar resonance experiments [Sakai et al., Phys. Rev. B 83, 140408 (2011)] that was previously attributed to an incommensurate order. We also report powder x-ray diffraction showing that the crystallographic structure of CePt 2In 7 changes monotonically with pressure up to P = 7.3 GPa at room temperature. The determined bulk modulus B 0 = 81.1 (3) GPa is similar to those of the Ce-115 family. Broad diffraction peaks confirm the presence of pronounced strain in polycrystalline samples of CePt 2In 7. Lastly, we discuss how strain effects can lead to different electronic and magnetic properties between polycrystalline and single crystal samples.« less

PREFACE: XTOP 2004 -- 7th Biennial Conference on High Resolution X-Ray Diffraction and Imaging

NASA Astrophysics Data System (ADS)

Holý, Vaclav

2005-05-01

The 7th Biennial Conference on High Resolution X-Ray Diffraction and Imaging (XTOP 2004) was held in the Prague suburb of Pruhonice, Czech Republic, during 7-10 September 2004. It was organized by the Czech and Slovak Crystallographic Association in cooperation with the Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Masaryk University, Brno, and Charles University, Prague. XTOP 2004 took place just after EPDIC IX (European Powder Diffraction Conference) organised in Prague by the same Association during 2-5 September 2004. The Organizing Committee was supported by an International Programme Committee including about 20 prominent scientists from several European and overseas countries, whose helpful suggestions for speakers are acknowledged. The conference was sponsored by the International Union of Crystallography and by several industrial sponsors; this sponsorship allowed us to support about 20 students and young scientists. In total, 147 official delegates and 8 accompanying persons from 16 countries of three continents attended our conference. The scientific programme of the conference was divided into 11 half-day sessions and 2 poster sessions. The participants presented 147 accepted contributions; of these 9 were 45-minute long invited talks, 34 were 20-minute oral presentations and 104 were posters. All posters were displayed for the whole meeting to ensure maximum exposure and interaction between delegates. We followed the very good experience from the previous conference, XTOP 2002, and also organized pre-conference tutorial lectures presented by experts in the field: `Imaging with hard synchrotron radiation' (J Härtwig, Grenoble), `High-resolution x-ray diffractometry: determination of strain and composition' (J Stangl, Linz), `X-ray grazing-incidence scattering from surfaces and nanostructures' (U Pietsch, Potsdam) and `Hard x-ray optics' (J Hrdý, Prague). According to the recommendation of the International Program Committee, the invited lectures covered a broader field than the original conference subject, namely coherent speckle diffraction (I Robinson, Urbana), scattering from soft-matter films (W de Jeu, Amsterdam), femtosecond diffraction (J Wark, Oxford), magnetic soft x-ray microscopy (P Fischer, Stuttgart), x-ray standing-wave imaging (J Zegenhagen, Grenoble), new trends in hard x-ray imaging (J Baruchel, Grenoble), anomalous x-ray scattering from nanostructures, (T Schülli, Grenoble), in-situ x-ray scattering (G Renaud, Grenoble) and x-ray waveguides (W Jark, Trieste). The topics of the oral presentations and posters can be divided into two large groups, namely x-ray imaging and x-ray diffraction. In the first group, the contributions concentrated on new developments in methods and instrumentation, including in-situ imaging, phase-contrast imaging and three-dimensional imaging. In the second group, attention was paid to anomalous scattering methods and scattering from thin films and nanostructures. The full list of all contributions together with their abstracts are available at the website http://www.xray.cz/xtop. During one session, Professor Andrew Lang, one of the pioneers of x-ray topography who gave his name to the popular topographic technique, and honorary guest of XTOP 2004, celebrated his 80th birthday. In a celebration address Professor A Authier reviewed Professor Lang's career and his invaluable contribution to the development of our field. We continue the tradition of previous XTOPs and publish a selection of original contributions from the conference in this special issue of Journal of Physics D: Applied Physics. The papers have been subject to peer review according to the normal practice of the journal. Generally, we observed that a new generation of young and very talented scientists has appeared, who are publishing very interesting and important papers. Therefore, the future prospects of x-ray imaging and high-resolution diffraction are bright and we all look forward to the next XTOP conference, organized by Tilo Baumbach and his group, which will take place in Karlsruhe, Germany, in 2006.

Calcite orientations and composition ranges within teeth across Echinoidea.

PubMed

Stock, Stuart R; Ignatiev, Konstantin; Lee, Peter L; Almer, Jonathan D

2014-08-01

Sea urchin's teeth from four families of order Echinoida and from orders Temnopleuroida, Arbacioida and Cidaroida were studied with synchrotron X-ray diffraction. The high and very high Mg calcite phases of the teeth, i.e. the first and second stage mineral constituents, respectively, have the same crystallographic orientations. The co-orientation of first and second stage mineral, which the authors attribute to epitaxy, extends across the phylogenic width of the extant regular sea urchins and demonstrates that this is a primitive character of this group. The range of compositions Δx for the two phases of Ca1-xMgxCO3 is about 0.20 or greater and is consistent with a common biomineralization process.

Crystallization and preliminary X-ray diffraction studies of Seneca Valley Virus-001, a new member of the Picornaviridae family

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

Venkataraman, Sangita; Reddy, Seshidhar P.; Loo, Jackie

2008-04-01

Seneca Valley Virus-001 of the Picornavirdae family was crystallized in the space group R3 and X-ray diffraction data was collected to a resolution of 2.3 Å. Rotation-function studies suggested the presence of two distict sets of 20 protomers that belong to two different virus particles in the crystallographic asymmetric unit. Seneca Valley Virus-001 (SVV-001) is a newly found species in the Picornaviridae family. SVV-001 is the first naturally occurring nonpathogenic picorna@@virus observed to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+)ssRNA genome of SVV-001 shares closest sequence similarity to the genomes of the members ofmore » the Cardiovirus genus. However, based on the distinct characteristics of the genome organization and other biochemical properties, it has been suggested that SVV-001 represents a new genus, namely ‘Senecavirus’, in the Picornaviridae family. In order to understand the oncolytic properties of SVV-001, the native virus was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group R3, with unit-cell parameters (in the hexagonal setting) a = b = 311.5, c = 1526.4 Å. Although the SVV crystals diffracted to better than 2.3 Å resolution, the data quality is acceptable [I/σ(I) > 2.0] to 2.6 Å resolution. The unit-cell volume and the locked rotation-function analysis suggest that six particles could be accommodated in the unit cell, with two distinct sets of one third of a particle, each containing 20 protomers, occupying the crystallographic asymmetric unit.« less

Crystallographic and magnetic properties of nanocrystalline perovskite structure SmFeO3 orthoferrite

NASA Astrophysics Data System (ADS)

Kumar, Ashwini; Shen, Jingdong; Zhao, Huihui; Zhengjian, Qi; Li, Qi

2018-05-01

In this article, we present the structural and magnetic studies of pristine SmFeO3 nanocrystalline ceramic samples as sintered at temperature 850 °C and 1000 °C. X-ray powder diffraction data confirm the existence of single-phase nature with orthorhombic (Pbnm) structure of the samples. The SEM image reveals spherical particles with a size range of 60-130 nm for SFO-850 and SFO-1000 samples. X-ray absorption spectroscopy studies on Fe L3,2 and O K-edges of SmFeO3 sample revealed the homo-valence state of Fe in these materials. From magnetization studies it has been observed the materials exhibit ferromagnetic and antiferromagnetic (canted spin structure) sub-lattices, which results strong magnetic anisotropy in the system.

Optical and structural properties of CsI thin film photocathode

NASA Astrophysics Data System (ADS)

Triloki; Rai, R.; Singh, B. K.

2015-06-01

In the present work, the performance of a cesium iodide thin film photocathode is studied in detail. The optical absorbance of cesium iodide films has been analyzed in the spectral range from 190 nm to 900 nm. The optical band gap energy of 500 nm thick cesium iodide film is calculated from the absorbance data using a Tauc plot. The refractive index is estimated from the envelope plot of transmittance data using Swanepoel's method. The absolute quantum efficiency measurement has been carried out in the wavelength range from 150 nm to 200 nm. The crystallographic nature and surface morphology are investigated by X-ray diffraction and transmission electron microscopy techniques. In addition, the elemental composition result obtained by energy dispersive X-ray analysis is also reported in the present work.

Fine Structure in Multi-Phase Zr8Ni21-Zr7Ni10-Zr2Ni7 Alloy Revealed by Transmission Electron Microscope

PubMed Central

Shen, Haoting; Bendersky, Leonid A.; Young, Kwo; Nei, Jean

2015-01-01

The microstructure of an annealed alloy with a Zr8Ni21 composition was studied by both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The presence of three phases, Zr8Ni21, Zr2Ni7, and Zr7Ni10, was confirmed by SEM/X-ray energy dispersive spectroscopy compositional mapping and TEM electron diffraction. Distribution of the phases and their morphology can be linked to a multi-phase structure formed by a sequence of reactions: (1) L → Zr2Ni7 + L’; (2) peritectic Zr2Ni7 + L’ → Zr2Ni7 + Zr8Ni21 + L”; (3) eutectic L” → Zr8Ni21 + Zr7Ni10. The effect of annealing at 960 °C, which was intended to convert a cast structure into a single-phase Zr8Ni21 structure, was only moderate and the resulting alloy was still multi-phased. TEM and crystallographic analysis of the Zr2Ni7 phase show a high density of planar (001) defects that were explained as low-energy boundaries between rotational variants and stacking faults. The crystallographic features arise from the pseudo-hexagonal structure of Zr2Ni7. This highly defective Zr2Ni7 phase was identified as the source of the broad X-ray diffraction peaks at around 38.4° and 44.6° when a Cu-K was used as the radiation source. PMID:28793460

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

Not Available

Nacre, also known as mother-of-pearl, is a biocomposite material that exhibits higher strength and fracture toughness than its component materials. It derives its strength from the brick-and-mortar layering of aragonite (CaCO{sub 3}) platelets and organic binder. It is believed that the protein binder helps redistribute the stress throughout all tablets for optimal mechanical performance. In this study, we attempt to measure the mechanical properties of aragonite within nacre and compare them to bulk aragonite and bulk nacre and understand the redistribution of stresses. Here we show that x-ray diffraction techniques are useful for isolating and measuring strain of crystallites withinmore » a composite material. Our results show that the apparent stiffness of aragonite varies with crystallographic directions and is higher than the stiffness of bulk nacre in all cases, meaning that aragonite tablets are exposed to less than the average bulk stress. The average force applied to the bulk sample is partitioned between the aragonite and the binder, so that the protein layer bears as much as 27.2% of the total applied force. Different crystallographic directions exhibit behaviors different than bulk aragonite or bulk nacre. These are related to texture of aragonite platelets (i.e. preferred orientations within nacre). By examining nacre, we can obtain a better understanding of the mechanical relationship between the ceramic and polymer in composite materials. We expect that x-ray diffraction will become the standard method for probing the mechanical properties of composite materials.« 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 transformation coinciding with the loss of the remaining bound water molecule. These temperature-resolved real-time powder X-ray diffraction studies provide the first comprehensive description of the sepiolite structure and the complex changes it undergoes as it dehydrates. Additional heating and cooling in situ powder X-ray diffraction experiments are underway in order to investigate the relative stabilities and rehydration behaviors of the partially-hydrated sepiolite phases. The results of these studies should provide a more robust model for predicting and modifying the properties and applications of this critical industrial material and environmentally important mineral.

Structure evolution of zinc oxide thin films deposited by unbalance DC magnetron sputtering

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

Aryanto, Didik, E-mail: didi027@lipi.go.id; Materials Research Group, Physics Department, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah; Marwoto, Putut

Zinc oxide (ZnO) thin films are deposited on corning glass substrates using unbalanced DC magnetron sputtering. The effect of growth temperature on surface morphology and crystallographic orientation of ZnO thin film is studied using atomic force microscopy (AFM) and X-ray diffraction (XRD) techniques. The surface morphology and crystallographic orientation of ZnO thin film are transformed against the increasing of growth temperature. The mean grain size of film and the surface roughness are inversely and directly proportional towards the growth temperature from room temperature to 300 °C, respectively. The smaller grain size and finer roughness of ZnO thin film are obtainedmore » at growth temperature of 400 °C. The result of AFM analysis is in good agreement with the result of XRD analysis. ZnO thin films deposited in a series of growth temperatures have hexagonal wurtzite polycrystalline structures and they exhibit transformations in the crystallographic orientation. The results in this study reveal that the growth temperature strongly influences the surface morphology and crystallographic orientation of ZnO thin film.« less

Crystallographic site swapping of La3+ ion in BaA'LaTeO6 (A' = Na, K, Rb) double perovskite type compounds: diffraction and photoluminescence evidence for the site swapping.

PubMed

Phatak, R; Gupta, S K; Krishnan, K; Sali, S K; Godbole, S V; Das, A

2014-02-28

Double perovskite type compounds of the formula BaA'LaTeO6 (A' = Na, K, Rb) were synthesized by solid state route and their crystal structures were determined by Rietveld analysis using powder X-ray diffraction and neutron diffraction data. Na compound crystallizes in the monoclinic system with P2₁/n space group whereas, K and Rb compounds crystallize in Fm3m space group. All the three compounds show rock salt type ordering at B site. Crystal structure analysis shows that La ion occupies A site in Na compound whereas, it occupies B site in K and Rb compounds according to the general formula of AA'BB'O6 for a double perovskite type compound. Effect of this crystallographic site swapping of the La ion was also observed in the photoluminescence study by doping Eu(3+) in La(3+) site. The large decrease in the intensity of the electric dipole ((5)D0-(7)F2) transition in the Rb compound compared to the Na compound indicates that Eu(3+) ion resides in the centrosymmetric octahedral environment in the Rb compound.

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

NASA Astrophysics Data System (ADS)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

Defect Chemistry of " BaCuO2" I. Oxygen Non -Stoichiometry, Cation Molecularity and X-ray Diffraction Determinations

NASA Astrophysics Data System (ADS)

Spinolo, G.; Anselmi-Tamburini, U.; Arimondi, M.; Ghigna, P.; Flor, G.

1995-11-01

"BaCuO2" is the key intermediate in the synthesis of the Ba2YCu3O7-δ superconductor. Its very complex crystal structure is able to accommodate a large change in oxygen content. Oxygen non-stoichiometry of "BaCuO2" materials with 1:1 and 88:90 (Ba :Cu) molecularity has been investigated by polythermal X-ray powder diffraction coupled with isobaric-isothermal gravimetry determinations under different temperature and oxygen partial pressure conditions [300≤ T≤ 820 °C, 1 ≥ P(O2) ≥ 3 • 10-3 atm]. The 1:1 composition does not give well reproducible results, thus suggesting its polyphasic nature, at least in part of the investigated range. The results for the 88:90 ≅ 0.98 (Ba :Cu) composi­ tion are well reproducible and show that the material is single phase. Ba0.98CuO1.98 + δ is oxygen over-stoichiometric in the whole investigated [T, P(O2)] range, with a maximum value δ˜0.21. A Rietveld X-ray profile fitting is in agreement with previous single-crystal data. The trend of δ vs. P(O2) is consistent with the presence of oxygen interstitial defects on (possibly different) crystallographic sites.

Crystallization and preliminary X-ray crystallographic analysis of carboxyl-terminal region 4 of SigR from Streptomyces coelicolor A3(2)

PubMed Central

Kim, Keon Young; Kim, Sunmin; Park, Jeong Kuk; Song, HyoJin; Park, SangYoun

2014-01-01

Full-length SigR from Streptomyces coelicolor A3(2) was overexpressed in Escherichia coli, purified and submitted to crystallization trials using either polyethylene glycol 3350 or 4000 as a precipitant. X-ray diffraction data were collected to 2.60 Å resolution under cryoconditions using synchrotron X-rays. The crystal packs in space group P43212, with unit-cell parameters a = b = 42.14, c = 102.02 Å. According to the Matthews coefficient, the crystal asymmetric unit cannot contain the full-length protein. Molecular replacement with the known structures of region 2 and region 4 as independent search models indicates that the crystal contains only the −35 element-binding carboxyl-terminal region 4 of full-length SigR. Mass-spectrometric analysis of the harvested crystal confirms this, suggesting a crystal volume per protein weight (V M) of 2.24 Å3 Da−1 and 45.1% solvent content. PMID:24915084

Recovery of Crystallographic Texture in Remineralized Dental Enamel

PubMed Central

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain structural integrity. PMID:25360532

Recovery of crystallographic texture in remineralized dental enamel.

PubMed

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain structural integrity.

Study of structural properties of cubic InN films on GaAs(001) substrates by molecular beam epitaxy and migration enhanced epitaxy

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

Casallas-Moreno, Y. L.; Perez-Caro, M.; Gallardo-Hernandez, S.

InN epitaxial films with cubic phase were grown by rf-plasma-assisted molecular beam epitaxy (RF-MBE) on GaAs(001) substrates employing two methods: migration-enhanced epitaxy (MEE) and conventional MBE technique. The films were synthesized at different growth temperatures ranging from 490 to 550 Degree-Sign C, and different In beam fluxes (BEP{sub In}) ranging from 5.9 Multiplication-Sign 10{sup -7} to 9.7 Multiplication-Sign 10{sup -7} Torr. We found the optimum conditions for the nucleation of the cubic phase of the InN using a buffer composed of several thin layers, according to reflection high-energy electron diffraction (RHEED) patterns. Crystallographic analysis by high resolution X-ray diffraction (HR-XRD)more » and RHEED confirmed the growth of c-InN by the two methods. We achieved with the MEE method a higher crystal quality and higher cubic phase purity. The ratio of cubic to hexagonal components in InN films was estimated from the ratio of the integrated X-ray diffraction intensities of the cubic (002) and hexagonal (1011) planes measured by X-ray reciprocal space mapping (RSM). For MEE samples, the cubic phase of InN increases employing higher In beam fluxes and higher growth temperatures. We have obtained a cubic purity phase of 96.4% for a film grown at 510 Degree-Sign C by MEE.« less

Deformation-induced crystallographic-preferred orientation of hcp-iron: An experimental study using a deformation-DIA apparatus

NASA Astrophysics Data System (ADS)

Nishihara, Yu; Ohuchi, Tomohiro; Kawazoe, Takaaki; Seto, Yusuke; Maruyama, Genta; Higo, Yuji; Funakoshi, Ken-ichi; Tange, Yoshinori; Irifune, Tetsuo

2018-05-01

Shear and uniaxial deformation experiments on hexagonal close-packed iron (hcp-Fe) was conducted using a deformation-DIA apparatus at a pressure of 13-17 GPa and a temperature of 723 K to determine its deformation-induced crystallographic-preferred orientation (CPO). Development of the CPO in the deforming sample is determined in-situ based on two-dimensional X-ray diffraction using monochromatic synchrotron X-rays. In the shear deformation geometry, the <0001> and < 11 2 bar 0 > axes gradually align to be sub-parallel to the shear plane normal and shear direction, respectively, from the initial random texture. In the uniaxial compression and tensile geometry, the <0001> and < 11 2 bar 0 > axes, respectively, gradually align along the direction of the uniaxial deformation axis. These results suggest that basal slip (0001) < 11 2 bar 0 > is the dominant slip system in hcp-Fe under the studied deformation conditions. The P-wave anisotropy for a shear deformed sample was calculated using elastic constants at the inner core condition by recent ab-initio calculations. Strength of the calculated anisotropy was comparable to or higher than axisymmetric anisotropy in Earth's inner core.

Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin.

PubMed

Matsuno, Asuka; Gai, Zuoqi; Tanaka, Miyuki; Kato, Koji; Kato, Sanae; Katoh, Tsuyoshi; Shimizu, Takeshi; Yoshioka, Takeya; Kishimura, Hideki; Tanaka, Yoshikazu; Yao, Min

2015-06-01

Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450kDa subunits, resulting in a molecular mass >3.3MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-Å resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form. Copyright © 2015 Elsevier Inc. All rights reserved.

Crystallographic Texture and Elemental Composition Mapped in Bovine Root Dentin at the 200 nm Level

PubMed Central

Deymier-Black, A. C.; Veis, A.; Cai, Z.; Stock, S. R.

2015-01-01

Summary The relationship between the mineralization of peritubular dentin (PTD) and intertubular dentin (ITD) is not well understood. Tubules are quite small, diameter ~2 μm, and this makes the near-tubule region of dentin difficult to study. Here, advanced characterization techniques are applied in a novel way to examine what organic or nanostructural signatures may indicate the end of ITD or the beginning of PTD mineralization. X-ray fluorescence intensity (Ca, P, and Zn) and X-ray diffraction patterns from carbonated apatite (cAp) were mapped around dentintubules at resolutions ten times smaller than the feature size (200 nm pixels), representing a 36% increase in resolution over earlier work. In the near tubule volumes of near-pulp, root dentin, Zn intensity was higher than in ITD remote from the tubules. This increase in Zn2+, as determined by X-ray absorption near edge structure analysis, may indicate the presence of metalloenzymes or transcription factors important to ITD or PTD mineralization. The profiles of the cAp 00.2 X-ray diffraction rings were fitted with a pseudo-Voigt function, and the spatial and azimuthal distribution of these rings’ integrated intensities indicated that the cAp platelets were arranged with their c-axes aligned tangential to the edge of the tubule lumen. This texture was continuous throughout the dentin indicating a lack of structural difference between in the Zn rich near-tubular region and the remote ITD. PMID:23630059

In situ x-ray diffraction observation of multiple texture turnovers in sputtered Cr films

NASA Astrophysics Data System (ADS)

Zhao, Z. B.; Rek, Z. U.; Yalisove, S. M.; Bilello, J. C.

2004-11-01

A series of Cr films were deposited onto native oxides of (100) Si substrates via a confocal deposition geometry in a magnetron sputter chamber. The film growth chamber was incorporated with an in situ x-ray diffraction system, which allowed the collection of x-ray diffraction data on the growing film in a quasi real time fashion without interruption of film deposition. The in situ x-ray diffraction, coupled with other ex situ characterization techniques, was used to study structural evolutions of the Cr films deposited at various Ar pressures. It was observed that the evolution of the crystallographic structures of Cr films was very sensitive to both deposition conditions and film thickness. With the confocal deposition geometry, the Cr films developed various types of out-of-plane textures. In addition to the (110) and (100) types of textures commonly reported for vapor deposited Cr films, the (111) and (112) types of textures were also observed. The film deposited at low Ar pressure (2 mTorr) developed strong (111) type texture. With the increase in either Ar pressure or film thickness, the Cr films tended to develop (112) and (100) types of texture. At high Ar pressures (>10 mTorr), several changes in texture type with increasing film thickness were observed. The sequence can be described as (110)-->(112)-->(100). The strong tendency for these films to ultimately assume the (100) type of texture could be related to significant rises in substrate temperatures during the late stages of film growth with high Ar pressures. The observation of the multiple texture type changes suggests that the evolution of Cr films is controlled by complex growth kinetics. The competitive growth of grains with different orientations can be altered not only by controllable deposition parameters such as Ar pressure, but also by the variations of in situ film attributes (e.g., residual stress and substrate temperature) occurring concurrently with film growth.

Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase

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

Angkawidjaja, Clement; You, Dong-Ju; Matsumura, Hiroyoshi

2007-03-01

A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. The crystal was grown at 277 K by the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to 1.7 Å resolution using synchrotron radiation at station BL38B1, SPring-8. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 48.79, b = 84.06,more » c = 87.04 Å. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V{sub M} was calculated to be 2.73 Å{sup 3} Da{sup −1} and the solvent content was 55%.« less

Crystallographic studies of gas sorption in metal–organic frameworks

PubMed Central

Carrington, Elliot J.; Vitórica-Yrezábal, Iñigo J.; Brammer, Lee

2014-01-01

Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors. In situ crystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathrates etc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context of in situ crystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules. PMID:24892587

Effect of wet grinding on structural properties of ball clay

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

Purohit, A., E-mail: anuradha.purohit34@gmail.com; Chander, S.; Dhaka, M. S.

2015-05-15

In this paper, the effect of wet grinding on structural properties of ball clay is undertaken. The wet grinding treatment was performed employing ball and vibro mills for different time spells of 2, 4, 8 and 16 hours. The structural properties were carried out using X-ray diffraction (XRD). The structure of ground samples is found to be simple cubic. The crystallographic parameters are calculated and slight change in lattice constant, inter planner spacing and particle size is observed with grinding treatment. The results are in agreement with the available literature.

X-Ray Diffraction Contrast Tomography in micro-CT Lab Source Systems

DTIC Science & Technology

2014-05-16

microstrucutre as determined from DCT. (e) Surface mesh representing the fracture surface, colour coded with respect to its crystallographic orientation. Grain...sake of readability, we refrain from delving too deep into the mathematics of the projection models. Instead, we refer to Appendix A where more in...S−D 2 ). From the definition of the dot product, we learn that cos θ = B ·G ‖B‖‖G‖ = B ·G f . 1.9 Given sin2 θ + cos2 θ = 1, sin θ can be also

Infrared and Raman spectroscopy and DFT calculations of DL amino acids: Valine and lysine hydrochloride

NASA Astrophysics Data System (ADS)

Paiva, F. M.; Batista, J. C.; Rêgo, F. S. C.; Lima, J. A.; Freire, P. T. C.; Melo, F. E. A.; Mendes Filho, J.; de Menezes, A. S.; Nogueira, C. E. S.

2017-01-01

Single crystals of DL-valine and DL-lysine hydrochloride were grown by slow evaporation method and the crystallographic structure were confirmed by X-ray diffraction experiment and Rietveld method. These two crystals have been studied by Raman spectroscopy in the 25-3600 cm-1 spectral range and by infrared spectroscopy through the interval 375-4000 cm-1 at room temperature. Experimental and theoretical vibrational spectra were compared and a complete analysis of the modes was done in terms of the Potential Energy Distribution (PED).

Expression, purification, crystallization and preliminary X-ray crystallographic data from TktA, a transketolase from the lactic acid bacterium Lactobacillus salivarius

PubMed Central

Horsham, Matt; Saxby, Harriet; Blake, James; Isaacs, Neil W.; Mitchell, Tim J.; Riboldi-Tunnicliffe, Alan

2010-01-01

The enzyme transketolase from the lactic acid bacterium Lactobacillus salivarius (subsp. salivarius UCC118) has been recombinantly expressed and purified using an Escherichia coli expression system. Purified transketolase from L. salivarius has been crystallized using the vapour-diffusion technique. The crystals belonged to the trigonal space group P3221, with unit-cell parameters a = b = 75.43, c = 184.11 Å, and showed diffraction to 2.3 Å resolution. PMID:20693662

Syntheses, structural characterization, and DPPH radical scavenging activity of cocrystals of caffeine with 1- and 2-naphthoxyacetic acids

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Seethalakshmi, P. G.; Sumathi, D.; Bhuvanesh, N.; Kumaresan, S.

2013-03-01

Caffeine:1-naphthoxyacetic acid [(caf)(1-naa)] and caffeine:2-naphthoxyacetic acid [(caf)(2-naa)] cocrystals have been synthesized and single crystals were grown by slow evaporation technique. The structures of the grown crystals were elucidated using single crystal X-ray diffraction analysis. Both the cocrystals belong to the monoclinic crystallographic system with space group P21/c, Z = 4, and α = γ = 90°, whereas β = 111.4244(18)° for [(caf)(1-naa)] and β = 109.281(6)° for [(caf)(2-naa)]. The crystal packing is predominantly stabilized by hydrogen bonding and π-π stacking interactions. The presence of unionized -COOH functional group in both the cocrystals was identified by FTIR spectral analysis. Thermal behavior and stability of both the cocrystals were studied by TGA/DTA analyses. Solvent-free formation of these cocrystals was confirmed by powder X-ray diffraction analyses. The theoretical energy of cocrystals showed that the formers have higher energy than cocrystals 1 and 2. DPPH radical scavenging activity of cocrystals 1 and 2 is slightly greater than the formers.

Microstructural and micromechanical characterization of IN718 theta shaped specimens built with electron beam melting

DOE PAGES

Cakmak, Ercan; Kirka, Michael M.; Watkins, Thomas R.; ...

2016-02-23

Theta-shaped specimens were additively manufactured out of Inconel 718 powders using an electron beam melting technique, as a model complex load bearing structure. We employed two different build strategies; producing two sets of specimens. Microstructural and micro-mechanical characterizations were performed using electron back-scatter, synchrotron x-ray and in-situ neutron diffraction techniques. In particular, the cross-members of the specimens were the focus of the synchrotron x-ray and in-situ neutron diffraction measurements. The build strategies employed resulted in the formation of distinct microstructures and crystallographic textures, signifying the importance of build-parameter manipulation for microstructural optimization. Large strain anisotropy of the different lattice planesmore » was observed during in-situ loading. Texture was concluded to have a distinct effect upon both the axial and transverse strain responses of the cross-members. In particular, the (200), (220) and (420) transverse lattice strains all showed unexpected overlapping trends in both builds. This was related to the strong {200} textures along the build/loading direction, providing agreement between the experimental and calculated results.« less

Strain relaxation of CdTe on Ge studied by medium energy ion scattering

NASA Astrophysics Data System (ADS)

Pillet, J. C.; Pierre, F.; Jalabert, D.

2016-10-01

We have used the medium energy ion scattering (MEIS) technique to assess the strain relaxation in molecular-beam epitaxial (MBE) grown CdTe (2 1 1)/Ge (2 1 1) system. A previous X-ray diffraction study, on 10 samples of the same heterostructure having thicknesses ranging from 25 nm to 10 μm has allowed the measurement of the strain relaxation on a large scale. However, the X-ray diffraction measurements cannot achieve a stress measurement in close proximity to the CdTe/Ge interface at the nanometer scale. Due to the huge lattice misfit between the CdTe and Ge, a high degree of disorder is expected at the interface. The MEIS in channeling mode is a good alternative in order to profile defects with a high depth resolution. For a 21 nm thick CdTe layer, we observed, at the interface, a high density of Cd and/or Te atoms moved from their expected crystallographic positions followed by a rapid recombination of defects. Strain relaxation mechanisms in the vicinity of the interface are discussed

Purification, crystallization and preliminary X-ray diffraction analysis of the IL-20-IL-20R1-IL-20R2 complex

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

Logsdon, Naomi J.; Allen, Christopher E.; Rajashankar, Kanagalaghatta R.

2012-02-08

Interleukin-20 (IL-20) is an IL-10-family cytokine that regulates innate and adaptive immunity in skin and other tissues. In addition to protecting the host from various external pathogens, dysregulated IL-20 signaling has been shown to contribute to the pathogenesis of human psoriasis. IL-20 signals through two cell-surface receptor heterodimers, IL-20R1-IL-20R2 and IL-22R1-IL-20R2. In this report, crystals of the IL-20-IL-20R1-IL-20R2 ternary complex have been grown from polyethylene glycol solutions. The crystals belonged to space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = 111, c = 135 {angstrom}, and diffracted X-rays to 3 {angstrom} resolution. The crystallographic asymmetricmore » unit contains one IL-20-IL-20R1-IL-20R2 complex, corresponding to a solvent content of approximately 54%.« less

Air and moisture stable covalently-bonded tin(ii) coordination polymers.

PubMed

de Lima, G M; Walton, R I; Clarkson, G J; Bitzer, R S; Ardisson, J D

2018-06-05

Four covalently-bonded tin(ii) coordination polymers, (1)-(4), were hydrothermally prepared in aqueous alkaline media by the reactions of SnSO4 with 1,2,4,5-benzenetetracarboxylic acid (1), 1,3,5-benzenetricarboxylic acid (2), 4-hydroxypyridine-2,6-dicarboxylic acid (3), and 1,3,5-cyclohexanetricarboxylic acid (4). All products were structurally authenticated by single-crystal X-ray diffraction, and the number of different tin centres and their oxidation states were confirmed by 119Sn Mössbauer spectroscopy. In addition, the comparison between experimental and simulated X-ray powder diffraction patterns confirmed the authenticity of the samples. Our crystallographic results for (1)-(4) show that the Sn(ii) centres are tetracoordinated and exhibit distorted disphenoidal geometries, corroborating the presence of one stereochemically active lone electron pair at each metal site. Products (1) and (2) display bi-dimensional polymeric structures, (3) exhibits a one-dimensional architecture, whereas (4) shows a remarkable three-dimensional coordination network. Hirshfeld surface and supramolecular analyses for the repeating units of (1)-(4) were also performed in order to identify structurally important non-covalent interactions.

Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

PubMed Central

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-01-01

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

Serial femtosecond crystallography: A revolution in structural biology.

PubMed

Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-07-15

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. Published by Elsevier Inc.

Preliminary crystallographic analysis of avian infectious bronchitis virus main protease

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

Li, Jun; Shen, Wei; Liao, Ming, E-mail: mliao@scau.edu.cn

The avian infectious bronchitis virus main protease has been crystallized; crystals diffract to 2.7 Å resolution. Infectious bronchitis virus (IBV) is the prototype of the genus Coronavirus. It causes a highly contagious disease which affects the respiratory, reproductive, neurological and renal systems of chickens, resulting great economic losses in the poultry industry worldwide. The coronavirus (CoV) main protease (M{sup pro}), which plays a pivotal role in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, is an attractive target for antiviral drug design. In this study, IBV M{sup pro} was overexpressed inmore » Escherichia coli. Crystals suitable for X-ray crystallography have been obtained using microseeding techniques and belong to space group P6{sub 1}22. X-ray diffraction data were collected in-house to 2.7 Å resolution from a single crystal. The unit-cell parameters were a = b = 119.1, c = 270.7 Å, α = β = 90, γ = 120°. Three molecules were predicted to be present in the asymmetric unit from a calculated self-rotation function.« 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

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.

Quantitative Analysis of Solid-State Homonuclear Correlation Spectra of Antiparallel β-Sheet Alanine Tetramers.

PubMed

Naito, Akira; Okushita, Keiko; Nishimura, Katsuyuki; Boutis, Gregory S; Aoki, Akihiro; Asakura, Tetsuo

2018-03-15

Poly-l-alanine (PLA) sequences are a key element in the structure of the crystalline domains of spider dragline silks, wild silkworm silks, antifreeze proteins, and amyloids. To date, no atomic-level structures of antiparallel (AP)-PLA longer than Ala 4 have been reported using the single-crystal X-ray diffraction analysis. In this work, dipolar-assisted rotational resonance solid-state NMR spectra were observed to determine the effective internuclear distances of 13 C uniformly labeled alanine tetramer with antiparallel (AP) β-sheet structure whose atomic coordinates are determined from the X-ray crystallographic analysis. Initial build-up rates, R j, k , were obtained from the build-up curves of the cross peaks by considering the internuclear distances arising in the master equation. Subsequently, experimentally obtained effective internuclear distances, r eff j, k (obs), were compared with the calculated r eff j, k (calc) values obtained from the X-ray crystallographic data. Fairly good correlation between r eff j, k (obs) and r eff j, k (calc) was obtained in the range of 1.0-6.0 Å, with the standard deviation of 0.244 Å, without considering the zero-quantum line-shape functions. It was further noted that the internuclear distances of intermolecular contributions provide details relating to the molecular packing in solid-state samples. Thus, the present data agree well with AP-β-sheet packing but do not agree with P-β-sheet packing.

TEM studies of plasma nitrided austenitic stainless steel.

PubMed

Stróz, D; Psoda, M

2010-03-01

Cross-sectional transmission electron microscopy and X-ray phase analysis were used to study the structure of a layer formed during nitriding the AISI 316L stainless steel at temperature 440 degrees C. It was found that the applied treatment led to the formation of 6-microm-thick layer of the S-phase. There is no evidence of CrN precipitation. The X-ray diffraction experiments proved that the occurred austenite lattice expansion - due to nitrogen atoms - depended on the crystallographic direction. The cross-sectional transmission electron microscopy studies showed that the layer consisted of a single cubic phase that contained a lot of defects such as dislocations, stacking faults, slip bands and twins. The high-resolution electron microscopy observations were applied to study the defect formation due to the nitriding process. It was shown that the presence of great number of stacking faults leads to formation of nanotwins. Weak, forbidden {100} reflections were still another characteristic feature of the S-phase. These were not detected in the X-ray spectra of the phase. Basing on the high-resolution electron microscopy studies it can be suggested that the short-range ordering of the nitrogen atoms in the octahedral sites inside the f.c.c. matrix lattice takes place and gives rise to appearance of these spots. It is suggested that the cubic lattice undergoes not only expansion but also slight rombohedral distortion that explains differences in the lattice expansion for different crystallographic directions.

Cloning, expression, purification and preliminary crystallographic characterization of a shikimate dehydrogenase from Corynebacterium glutamicum

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

Schoepe, Jan, E-mail: jschoepe@smail.uni-koeln.de; Niefind, Karsten; Chatterjee, Shivani

2006-07-01

The crystallization and preliminary X-ray characterization of a shikimate dehydrogenase from C. glutamicum is presented. The shikimate dehydrogenase from Corynebacterium glutamicum has been cloned into an Escherichia coli expression vector, overexpressed and purified. Native crystals were obtained by the vapour-diffusion technique using 2-methyl-2,4-pentanediol as a precipitant. The crystals belong to the centred monoclinic space group C2, with unit-cell parameters a = 118.77, b = 63.17, c = 35.67 Å, β = 92.26° (at 100 K), and diffract to 1.64 Å on a synchrotron X-ray source. The asymmetric unit is likely to contain one molecule, corresponding to a packing density ofmore » 2.08 Å{sup 3} Da{sup −1} and a solvent content of about 41%.« less

Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum β-lactamase conferring severe antibiotic resistance

NASA Astrophysics Data System (ADS)

Lee, J. H.; Sohn, S. G.; Jung, H. I.; An, Y. J.; Lee, S. H.

2013-07-01

OXA-17, an extended-spectrum β-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates β-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino β-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 Å resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P212121, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 Å. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

Isolation, purification, crystallization and preliminary X-ray studies of two 30 kDa proteins from silkworm haemolymph.

PubMed

Pietrzyk, Agnieszka J; Bujacz, Anna; Łochyńska, Małgorzata; Jaskólski, Mariusz; Bujacz, Grzegorz

2011-03-01

Juvenile hormone-binding protein (JHBP) and the low-molecular-mass lipoprotein PBMHP-12 belong to a group of 30 kDa proteins that comprise the major protein component of the haemolymph specific to the fifth-instar larvae stage of the mulberry silkworm Bombyx mori L. Proteins from this group are often essential for the development of the insect. In a project aimed at crystallographic characterization of B. mori JHBP (BmJHBP), it was copurified together with PBMHP-12. Eventually, the two proteins were isolated and crystallized separately. The BmJHBP crystals were orthorhombic (space group C222(1)) and the PBMHP-12 crystals were triclinic. The crystals diffracted X-rays to 2.9 Å (BmJHBP) and 1.3 Å (PBMHP-12) resolution.

Calcite orientations and composition ranges within teeth across Echinoidea

PubMed Central

Stock, Stuart R.; Ignatiev, Konstantin; Lee, Peter L.; Almer, Jonathan D.

2016-01-01

Sea urchin’s teeth from four families of order Echinoida and from orders Temnopleuroida, Arbacioida and Cidaroida were studied with synchrotron x-ray diffraction. The high and very high Mg calcite phases of the teeth, i.e. the first and second stage mineral constituents, respectively, have the same crystallographic orientations. The co-orientation of first and second stage mineral, which the authors attribute to epitaxy, extends across the phylogenic width of the extant regular sea urchins and demonstrates that this is a primitive character of this group. The range of compositions Δx for the two phases of Ca1−xMgxCO3 is about 0.20 or greater and is consistent with a common biomineralization process. PMID:25158180

Mesoscale Science with High Energy X-ray Diffraction Microscopy at the Advanced Photon Source

NASA Astrophysics Data System (ADS)

Suter, Robert

2014-03-01

Spatially resolved diffraction of monochromatic high energy (> 50 keV) x-rays is used to map microstructural quantities inside of bulk polycrystalline materials. The non-destructive nature of High Energy Diffraction Microscopy (HEDM) measurements allows tracking of responses as samples undergo thermo-mechanical or other treatments. Volumes of the order of a cubic millimeter are probed with micron scale spatial resolution. Data sets allow direct comparisons to computational models of responses that frequently involve long-ranged, multi-grain interactions; such direct comparisons have only become possible with the development of HEDM and other high energy x-ray methods. Near-field measurements map the crystallographic orientation field within and between grains using a computational reconstruction method that simulates the experimental geometry and matches orientations in micron sized volume elements to experimental data containing projected grain images in large numbers of Bragg peaks. Far-field measurements yield elastic strain tensors through indexing schemes that sort observed diffraction peaks into sets associated with individual crystals and detect small radial motions in large numbers of such peaks. Combined measurements, facilitated by a new end station hutch at Advanced Photon Source beamline 1-ID, are mutually beneficial and result in accelerated data reduction. Further, absorption tomography yields density contrast that locates secondary phases, void clusters, and cracks, and tracks sample shape during deformation. A collaboration led by the Air Force Research Laboratory and including the Advanced Photon Source, Lawrence Livermore National Laboratory, Carnegie Mellon University, Petra-III, and Cornell University and CHESS is developing software and hardware for combined measurements. Examples of these capabilities include tracking of grain boundary migrations during thermal annealing, tensile deformation of zirconium, and combined measurements of nickel superalloys and a titanium alloy under tensile forces. Work supported by NSF grant DMR-1105173

Synthesis, physical properties and self-assembly behavior of azole-fused pyrene derivatives

NASA Astrophysics Data System (ADS)

Xiao, Jinchong; Xiao, Xuyu; Zhao, Yanlei; Wu, Bo; Liu, Zhenying; Zhang, Xuemin; Wang, Sujuan; Zhao, Xiaohui; Liu, Lei; Jiang, Li

2013-05-01

A novel selenadiazole-fused pyrene derivative PySe was successfully synthesized and characterized. Its single structure is almost planar and adopts a sandwich-herringbone packing model. The self-assembly behaviors based on compound PySe and its analogue thiadiazole-fused pyrene derivative PyS were studied in detail and the as-formed nanostructures were fully characterized by means of UV-vis absorption, emission spectra, X-ray diffraction, field emission SEM and TEM. We attribute the bathochromic shift absorption and emission spectra of PyS and PySe in aqueous solution to the formation of J-type aggregation. In addition, our investigation demonstrated that the shape and size of the as-prepared nanostructures could be tuned by different chalcogen analogues and the volume ratio of water to organic solvent.A novel selenadiazole-fused pyrene derivative PySe was successfully synthesized and characterized. Its single structure is almost planar and adopts a sandwich-herringbone packing model. The self-assembly behaviors based on compound PySe and its analogue thiadiazole-fused pyrene derivative PyS were studied in detail and the as-formed nanostructures were fully characterized by means of UV-vis absorption, emission spectra, X-ray diffraction, field emission SEM and TEM. We attribute the bathochromic shift absorption and emission spectra of PyS and PySe in aqueous solution to the formation of J-type aggregation. In addition, our investigation demonstrated that the shape and size of the as-prepared nanostructures could be tuned by different chalcogen analogues and the volume ratio of water to organic solvent. Electronic supplementary information (ESI) available: TGA analysis, spectra characterization data for compound 1, 2, 3 and X-ray crystallographic data for compound PySe (2, CIF). CCDC 917821. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr00523b

Crystallographic texture and earing behavior analysis for different second cold reductions of double-reduction tinplate

NASA Astrophysics Data System (ADS)

Liao, Lu-hai; Zheng, Xiao-fei; Kang, Yong-lin; Liu, Wei; Yan, Yan; Mo, Zhi-ying

2018-06-01

Since the production of tinplate with non-earing properties is difficult, especially when it is produced via the double-reduction process, the optimal degree of second cold reduction is particularly important for achieving desirable drawing properties. The evolution of texture and the earing propensity of double-reduction tinplate with different extents of second reduction were investigated in this study. Optical microscopy and scanning electron microscopy were used to observe the changes in the microstructure at various extents of reduction. Two common testing methods, X-ray diffraction (XRD) and electron backscatter diffraction, were used to investigate the texture of the specimens, which revealed the effects of deformation percentage on the final texture development and the change in the grain boundary. The earing rate was determined via earing tests involving measurement of the height of any ear. The results obtained from both XRD analyses and earing tests revealed the same ideal value for the second cold reduction on the basis of the relationship between crystallographic texture and the degree of earing.

Influence of Sn doping in BaSnxTi1-xO3 ceramics on microstructural and dielectric properties

NASA Astrophysics Data System (ADS)

Ansari, Mohd. Azaj; Sreenivas, K.

2018-05-01

BaSnxTi1-x O3 solid solutions with varying Sn content (x = 0.00, 0.05, 0.15, 0.25) prepared by solid state reaction method have been studied for their structural and dielectric properties. X-ray diffraction and Raman spectroscopic analysis show composition induced modifications in the crystallographic structure, and with increasing Sn content the structure changes from tetragonal to cubic structure. The tetragonal distortion decreases with increasing Sn, and the structure becomes purely cubic for x =0.25. Changes in the structure are reflected in the temperature dependent dielectric properties. For increasing Sn content the peak dielectric constant is found to increase and the phase transition temperature (Tc) decreases to lower temperature. The purely cubic structure with x=0.25 shows a diffused phased transition.

The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids

NASA Astrophysics Data System (ADS)

Beckmann, Peter A.; Paty, Carol; Allocco, Elizabeth; Herd, Maria; Kuranz, Carolyn; Rheingold, Arnold L.

2004-03-01

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.

Crystallographic and magnetic structure of UCu{sub 1.5}Sn{sub 2}

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

Purwanto, A.; Robinson, R.A.; Nakotte, H.

1996-04-01

We report on the crystallographic and magnetic structures of the antiferromagnet UCu{sub 1.5}Sn{sub 2}, as determined by x-ray and neutron powder diffraction. It crystallizes in the tetragonal CaBe{sub 2}Ge{sub 2} structure type, with space group P/4nmm, and we find no site disorder between two different Sn2{ital c} sites, in contrast with a previous report. UCu{sub 1.5}Sn{sub 2} orders antiferromagnetically with a N{acute e}el temperature of about 110 K. This is unusually high among uranium intermetallics. The uranium moments align along the {ital c} axis in a collinear arrangement but alternating along the {ital c} axis. The low-temperature uranium moment ismore » 2.01{mu}{sub {ital B}}. {copyright} {ital 1996 American Institute of Physics.}« less

The Investigation of Strain-Induced Martensite Reverse Transformation in AISI 304 Austenitic Stainless Steel

NASA Astrophysics Data System (ADS)

Cios, G.; Tokarski, T.; Żywczak, A.; Dziurka, R.; Stępień, M.; Gondek, Ł.; Marciszko, M.; Pawłowski, B.; Wieczerzak, K.; Bała, P.

2017-10-01

This paper presents a comprehensive study on the strain-induced martensitic transformation and reversion transformation of the strain-induced martensite in AISI 304 stainless steel using a number of complementary techniques such as dilatometry, calorimetry, magnetometry, and in-situ X-ray diffraction, coupled with high-resolution microstructural transmission Kikuchi diffraction analysis. Tensile deformation was applied at temperatures between room temperature and 213 K (-60 °C) in order to obtain a different volume fraction of strain-induced martensite (up to 70 pct). The volume fraction of the strain-induced martensite, measured by the magnetometric method, was correlated with the total elongation, hardness, and linear thermal expansion coefficient. The thermal expansion coefficient, as well as the hardness of the strain-induced martensitic phase was evaluated. The in-situ thermal treatment experiments showed unusual changes in the kinetics of the reverse transformation (α' → γ). The X-ray diffraction analysis revealed that the reverse transformation may be stress assisted—strains inherited from the martensitic transformation may increase its kinetics at the lower annealing temperature range. More importantly, the transmission Kikuchi diffraction measurements showed that the reverse transformation of the strain-induced martensite proceeds through a displacive, diffusionless mechanism, maintaining the Kurdjumov-Sachs crystallographic relationship between the martensite and the reverted austenite. This finding is in contradiction to the results reported by other researchers for a similar alloy composition.

Radiation damage in protein crystals examined under various conditions by different methods.

PubMed

Garman, Elspeth F; Nave, Colin

2009-03-01

Investigation of radiation damage in protein crystals has progressed in several directions over the past couple of years. There have been improvements in the basic procedures such as calibration of the incident X-ray intensity and calculation of the dose likely to be deposited in a crystal of known size and composition with this intensity. There has been increased emphasis on using additional techniques such as optical, Raman or X-ray spectroscopy to complement X-ray diffraction. Apparent discrepancies between the results of different techniques can be explained by the fact that they are sensitive to different length scales or to changes in the electronic state rather than to movement of atoms. Investigations have been carried out at room temperature as well as cryo-temperatures and, in both cases, with the introduction of potential scavenger molecules. These and other studies are leading to an overall description of the changes which can occur when a protein crystal is irradiated with X-rays at both cryo- and room temperatures. Results from crystallographic and spectroscopic radiation-damage experiments can be reconciled with other studies in the field of radiation physics and chemistry.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Mineral and Geochemical Classification From Spectroscopy/Diffraction Through Neural Networks

NASA Astrophysics Data System (ADS)

Ferralis, N.; Grossman, J.; Summons, R. E.

2017-12-01

Spectroscopy and diffraction techniques are essential for understanding structural, chemical and functional properties of geological materials for Earth and Planetary Sciences. Beyond data collection, quantitative insight relies on experimentally assembled, or computationally derived spectra. Inference on the geochemical or geophysical properties (such as crystallographic order, chemical functionality, elemental composition, etc.) of a particular geological material (mineral, organic matter, etc.) is based on fitting unknown spectra and comparing the fit with consolidated databases. The complexity of fitting highly convoluted spectra, often limits the ability to infer geochemical characteristics, and limits the throughput for extensive datasets. With the emergence of heuristic approaches to pattern recognitions though machine learning, in this work we investigate the possibility and potential of using supervised neural networks trained on available public spectroscopic database to directly infer geochemical parameters from unknown spectra. Using Raman, infrared spectroscopy and powder x-ray diffraction from the publicly available RRUFF database, we train neural network models to classify mineral and organic compounds (pure or mixtures) based on crystallographic structure from diffraction, chemical functionality, elemental composition and bonding from spectroscopy. As expected, the accuracy of the inference is strongly dependent on the quality and extent of the training data. We will identify a series of requirements and guidelines for the training dataset needed to achieve consistent high accuracy inference, along with methods to compensate for limited of data.

Phase Equilibria and Crystallography of Ceramic Oxides

PubMed Central

Wong-Ng, W.; Roth, R. S.; Vanderah, T. A.; McMurdie, H. F.

2001-01-01

Research in phase equilibria and crystallography has been a tradition in the Ceramics Division at National Bureau of Standards/National Institute of Standatrds and Technology (NBS/NIST) since the early thirties. In the early years, effort was concentrated in areas of Portland cement, ceramic glazes and glasses, instrument bearings, and battery materials. In the past 40 years, a large portion of the work was related to electronic materials, including ferroelectrics, piezoelectrics, ionic conductors, dielectrics, microwave dielectrics, and high-temperature superconductors. As a result of the phase equilibria studies, many new compounds have been discovered. Some of these discoveries have had a significant impact on US industry. Structure determinations of these new phases have often been carried out as a joint effort among NBS/NIST colleagues and also with outside collaborators using both single crystal and neutron and x-ray powder diffraction techniques. All phase equilibria diagrams were included in Phase Diagrams for Ceramists, which are collaborative publications between The American Ceramic Society (ACerS) and NBS/NIST. All x-ray powder diffraction patterns have been included in the Powder Diffraction File (PDF). This article gives a brief account of the history of the development of the phase equilibria and crystallographic research on ceramic oxides in the Ceramics Division. Represented systems, particularly electronic materials, are highlighted. PMID:27500068

Diffraction leveraged modulation of X-ray pulses using MEMS-based X-ray optics

DOEpatents

Lopez, Daniel; Shenoy, Gopal; Wang, Jin; Walko, Donald A.; Jung, Il-Woong; Mukhopadhyay, Deepkishore

2016-08-09

A method and apparatus are provided for implementing Bragg-diffraction leveraged modulation of X-ray pulses using MicroElectroMechanical systems (MEMS) based diffractive optics. An oscillating crystalline MEMS device generates a controllable time-window for diffraction of the incident X-ray radiation. The Bragg-diffraction leveraged modulation of X-ray pulses includes isolating a particular pulse, spatially separating individual pulses, and spreading a single pulse from an X-ray pulse-train.

Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom

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

Xu, Gufeng; Departments of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026; Huang, Qingqiu

2005-01-01

The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. Crystals of agkicetin-C suitable for structure determination were obtained from 1.8 M ammonium sulfate, 40 mM MES pH 6.5 with 2%(v/v) PEG 400. Interestingly, low buffer concentrations of MES seem to be necessary for crystal growth. The crystals of agkicetin-C belong tomore » space group C2, with unit-cell parameters a = 177.5, b = 97.7, c = 106.8 Å, β = 118.5°, and diffract to 2.4 Å resolution. Solution of the phase problem by the molecular-replacement method shows that there are four agkicetin-C molecules in the asymmetric unit, with a V{sub M} value of 3.4 Å{sup 3} Da{sup −1}, which corresponds to a high solvent content of approximately 64%. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that may represent additional elements of non-crystallographic symmetry.« less

Preliminary X-ray crystallographic studies of BthTX-II, a myotoxic Asp49-phospholipase A{sub 2} with low catalytic activity from Bothrops jararacussu venom

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

Corrêa, L. C.; Marchi-Salvador, D. P.; Cintra, A. C. O.

2006-08-01

A myotoxic Asp49-PLA{sub 2} with low catalytic activity from B. jararacussu (BthTX-II) was crystallized in the monoclinic crystal system; a complete X-ray diffraction data set was collected and a molecular-replacement solution was obtained. The oligomeric structure of BthTX-II resembles those of the Asp49-PLA{sub 2} PrTX-III and all bothropic Lys49-PLA{sub 2}s. For the first time, a complete X-ray diffraction data set has been collected from a myotoxic Asp49-phospholipase A{sub 2} (Asp49-PLA{sub 2}) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) and a molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resemblesmore » the myotoxin Asp49-PLA{sub 2} PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA{sub 2}s. In contrast, the oligomeric structure of BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA{sub 2} from B. jararacussu). Thus, comparison between these structures should add insight into the catalytic and myotoxic activities of bothropic PLA{sub 2}s.« less

New supramolecular cocrystal of 2-amino-5-chloropyridine with 3-methylbenzoic acids: Syntheses, structural characterization, Hirshfeld surfaces and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thanigaimani, Kaliyaperumal; Khalib, Nuridayanti Che; Temel, Ersin; Arshad, Suhana; Razak, Ibrahim Abdul

2015-11-01

2-amino-5-chloropyridine: 3-methylbenzoic acid [(2A5CP) (3MBA)] (I) cocrystal was synthesized and its single crystal was grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction technique. The cocrystal belongs to the monoclinic crystallographic system with space group P21/c, Z = 4, and a = 13.3155 (5) Å, b = 5.5980 (2) Å, c = 18.3787 (7) Å, β = 110.045 (2)°. The crystal structure is stabilized by Npyridine-H•••Odbnd C, Cdbnd O-H•••Npyridine and C-H⋯O type hydrogen bonding interactions. The presence of unionized -COOH functional group in the cocrystal was identified both by spectral methods and X-ray structural analysis. The experimental studies obtained by using the methods of single crystal X-ray analysis, powder X-ray diffraction (PXRD) analysis, FTIR, 1H NMR and 13C NMR spectroscopies confirmed the predicted cocrystal. The supramolecular assembly of the cocrystal was analyzed and discussed. The molecular geometry, vibrational frequencies of the compound in the ground state were calculated by using the density functional theory (DFT) method with 6-311++G (d,p) basis set and were compared with the experimental data. Additionally, HOMO-LUMO energy gap, natural bond orbital (NBO) analysis and nonlinear optical (NLO) properties of the compound were performed at B3LYP/6-311++G (d,p) level. Hirshfeld surfaces were used to confirm the existence of inter-molecular interactions in the compound.

Crystallization and preliminary crystallographic analysis of the Clostridium perfringens enterotoxin

PubMed Central

Briggs, David C.; Smedley, James G.; McClane, Bruce A.; Basak, Ajit K.

2010-01-01

Clostridium perfringens is a Gram-positive anaerobic species of bacterium that is notable for its ability to produce a plethora of toxins, including membrane-active toxins (α-toxins), pore-forming toxins (∊-toxins) and binary toxins (ι-toxins). Here, the crystallization of the full-length wild-type C. perfringens enterotoxin is reported, which is the causative agent of the second most prevalent food-borne illness in the United States and has been implicated in many other gastrointestinal pathologies. Several crystal forms were obtained. However, only two of these optimized crystal forms (I and II) were useable for X-ray diffraction data collection. The form I crystals diffracted to d min = 2.7 Å and belonged to space group C2, while the form II crystals diffracted to d min = 4 Å and belonged to space group P213. PMID:20606275

Process-Parameter-Dependent Optical and Structural Properties of ZrO2MgO Mixed-Composite Films Evaporated from the solid Solution

NASA Technical Reports Server (NTRS)

Sahoo, N. K.; Shapiro, A. P.

1998-01-01

The process-parameter-dependent optical and structural properties of ZrO2MgO mixed-composite material have been investigated. Optical properties were derived from spectrophotometric measurements. By use of atomic force microscopy, x-ray diffraction analysis, and energy-dispersive x-ray (EDX) analysis, the surface morphology, grain size distributions, crystallographic phases, and process-dependent material composition of films have been investigated. EDX analysis made evident the correlation between the oxygen enrichment in the films prepared at a high level of oxygen pressure and the very low refractive index. Since oxygen pressure can be dynamically varied during a deposition process, coatings constructed of suitable mixed-composite thin films can benefit from continuous modulation of the index of refraction. A step modulation approach is used to develop various multilayer-equivalent thin-film devices.

Heavy doping of CdTe single crystals by Cr ion implantation

NASA Astrophysics Data System (ADS)

Popovych, Volodymyr D.; Böttger, Roman; Heller, Rene; Zhou, Shengqiang; Bester, Mariusz; Cieniek, Bogumil; Mroczka, Robert; Lopucki, Rafal; Sagan, Piotr; Kuzma, Marian

2018-03-01

Implantation of bulk CdTe single crystals with high fluences of 500 keV Cr+ ions was performed to achieve Cr concentration above the equilibrium solubility limit of this element in CdTe lattice. The structure and composition of the implanted samples were studied using secondary ion mass spectrometry (SIMS), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis, X-ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS) to characterize the incorporation of chromium into the host lattice and to investigate irradiation-induced damage build-up. It was found that out-diffusion of Cr atoms and sputtering of the targets alter the depth distribution and limit concentration of the projectile ions in the as-implanted samples. Appearance of crystallographically oriented, metallic α-Cr nanoparticles inside CdTe matrix was found after implantation, as well as a strong disorder at the depth far beyond the projected range of the implanted ions.

An ambient stable core-substituted perylene bisimide dianion: isolation and single crystal structure analysis† †Electronic supplementary information (ESI) available: Synthesis, spectroelectrochemistry, UV-vis, electrochemistry, X-ray diffraction, NMR and mass spectra. CCDC 1032959. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03671a Click here for additional data file. Click here for additional data file.

PubMed Central

Seifert, Sabine; Schmidt, David

2015-01-01

Here we report the first example of an isolable, ambient stable perylene bisimide (PBI) dianion which was synthesized by catalytic reduction of a highly electron deficient PBI derivative. The remarkable stability of this unprecedented dianion in air for months facilitated its complete characterization by different methods, including single crystal X-ray analysis. Furthermore, solvent dependent cyclic and square wave voltammetry studies revealed that the formation of PBI dianions is preferred in more polar solvents, whereas the generation of PBI radical anions should be favoured in less polar solvents. PMID:28717450

Nearest-cell: a fast and easy tool for locating crystal matches in the PDB

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

Ramraj, V., E-mail: varun@strubi.ox.ac.uk; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE; Evans, G.

2012-12-01

A fast and easy tool to locate unit-cell matches in the PDB is described. When embarking upon X-ray diffraction data collection from a potentially novel macromolecular crystal form, it can be useful to ascertain whether the measured data reflect a crystal form that is already recorded in the Protein Data Bank and, if so, whether it is part of a large family of related structures. Providing such information to crystallographers conveniently and quickly, as soon as the first images have been recorded and the unit cell characterized at an X-ray beamline, has the potential to save time and effort asmore » well as pointing to possible search models for molecular replacement. Given an input unit cell, and optionally a space group, Nearest-cell rapidly scans the Protein Data Bank and retrieves near-matches.« less

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

PubMed Central

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.; Louro, Ricardo O.; Moe, Elin

2016-01-01

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing. PMID:27599855

Preparation, crystallization and preliminary X-ray crystallographic studies of diadenosine tetraphosphate hydrolase from Shigella flexneri 2a.

PubMed

Hu, Wenxin; Wang, Qihai; Bi, Ruchang

2005-12-01

Diadenosine tetraphosphate (Ap4A) hydrolase (EC 3.6.1.41) hydrolyzes Ap4A symmetrically in prokaryotes. It plays a potential role in organisms by regulating the concentration of Ap4A in vivo. To date, no three-dimensional structures of proteins with significant sequence homology to this protein have been determined. The 31.3 kDa Ap4A hydrolase from Shigella flexneri 2a has been cloned, expressed and purified using an Escherichia coli expression system. Crystals of Ap4A hydrolase have been obtained by the hanging-drop technique at 291 K using PEG 550 MME as precipitant. Ap4A hydrolase crystals diffract X-rays to 3.26 A and belong to space group P2(1), with unit-cell parameters a = 118.9, b = 54.6, c = 128.5 A, beta = 95.7 degrees.

Crystal Structure and Theoretical Analysis of Green Gold Au 30 (S- t Bu) 18 Nanomolecules and Their Relation to Au 30 S(S- t Bu) 18

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

Dass, Amala; Jones, Tanya; Rambukwella, Milan

We report the complete X-ray crystallographic structure as determined through single crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18. While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the μ3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally shows its presence in abundance. The Au30(S-tBu)18 nanomolecule is not only distinct in its crystal structure but has unique temperature dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoreticalmore » predictions of structure, stability, and optical response.« less

Catalogue of X-Ray Texture Data for Al-Cu-Li Alloy 1460, 2090, 2096 and 2195 Near-Net-Shape Extrusions, Sheet and Plate

NASA Technical Reports Server (NTRS)

Hales, Stephen J.; Hafley, Robert A.; Alexa, Joel A.

1998-01-01

The effect of crystallographic texture on the mechanical properties of near-net-shape extrusions is of major interest ff these products are to find application in launch vehicle or aircraft structures. The objective of this research was to produce a catalogue containing quantitative texture information for extruded product, sheet and plate. The material characterized was extracted from wide, integrally stiffened panels fabricated from the Al-Cu-Li alloys 1460, 2090, 2096 and 2195. The textural characteristics of sheet and plate products of the same alloys were determined for comparison purposes. The approach involved using X-ray diffraction to generate pole figures in combination with orientation distribution function analysis. The data were compiled as a function of location in the extruded cross-sections and the variation in the major deformation- and recrystallization-related texture components was identified.

Purification, crystallization and preliminary X-ray crystallographic analysis of a cysteine-rich secretory protein (CRISP) from Naja atra venom.

PubMed

Wang, Yu-Ling; Goh, King-Xiang; Wu, Wen-guey; Chen, Chun-Jung

2004-10-01

Cysteine-rich secretory proteins (CRISPs) play an important role in the innate immune system and are transcriptionally regulated by androgens in several tissues. The proteins are mostly found in the epididymis and granules of mammals, whilst a number of snake venoms also contain CRISP-family proteins. The natrin protein from the venom of Naja atra (Taiwan cobra), which belongs to a family of CRISPs and has a cysteine-rich C-terminal amino-acid sequence, has been purified using a three-stage chromatography procedure and crystals suitable for X-ray analysis have been obtained using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.58 A resolution using synchrotron radiation; the crystals belong to space group C222(1), with unit-cell parameters a = 59.172, b = 65.038, c = 243.156 A. There are two protein molecules in the asymmetric unit and the Matthews coefficient is estimated to be 2.35 A3 Da(-1), corresponding to a solvent content of 47.60%.

Theoretical and experimental studies on vibrational and nonlinear optic properties of guanidinium 3-nitrobenzoate. Differences and similarity between guanidinium 3-nitrobenzoate and guanidinium 4-nitrobenzoate complexes

NASA Astrophysics Data System (ADS)

Drozd, Marek

2018-03-01

According to literature data two structures of guanidine with nitrobenzoic acids are known. For guanidinium 4-nitrobenzoate the detailed studies of X-ray structure, vibrational and theoretical properties were performed. This compound was classified as second harmonic generator with efficiency of 3.3 times that KDP, standard crystal. On the contrary to mentioned above results for the guanidinium 3-nitrobenzoate the basic X-ray diffraction study was performed, only. On the basis of established crystallographic results, the detailed investigation of geometry and vibrational properties were made on the basis of theoretical calculation. According to this data the equilibrium geometry of investigated molecule was established. On the basis of this calculation the detailed computational studies of vibrational properties were performed. The theoretical IR and Raman frequencies, intensities and PED analysis are presented. Additionally, the NBO charges, HOMO and LUMO shapes and NLO properties of titled crystal were calculated. On the basis of these results the crystal was classified as second order generator in NLO but with bigger efficiency that guanidinium 4-nitorobenzoate compound. The obtained data are compared with experimental crystallographic and vibrational results for real crystal of guanidinium 3-nitrobenzoate. Additionally, the theoretical vibrational spectra are compared with literature calculations of guanidinium 4-nitrobenzoate compound.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Crystallization and preliminary X-ray crystallographic analysis of strictosidine synthase from Rauvolfia: the first member of a novel enzyme family.

PubMed

Ma, Xueyan; Koepke, Juergen; Fritzsch, Günter; Diem, Ralf; Kutchan, Toni M; Michel, Hartmut; Stöckigt, Joachim

2004-10-01

Strictosidine synthase is a central enzyme involved in the biosynthesis of almost all plant monoterpenoid indole alkaloids. Strictosidine synthase from Rauvolfia serpentina was heterologously expressed in Escherichia coli. Crystals of the purified recombinant enzyme have been obtained by the hanging-drop technique at 303 K with potassium sodium tartrate tetrahydrate as precipitant. The crystals belong to the space group R3 with cell dimensions of a=b=150.3 A and c=122.4 A. Under cryoconditions (120 K), the crystals diffract to about 2.95 A.

Diamond-like phases formed from fullerene-like clusters

NASA Astrophysics Data System (ADS)

Belenkov, E. A.; Greshnyakov, V. A.

2015-11-01

The geometrically optimized structure and properties of thirteen diamond-like carbon phases formed by linking or combining fullerene-like clusters (C4, C6, C8, C12, C16, C24, or C48) have been investigated. Atoms in the structures of these phases are located in crystallographically equivalent positions. The calculations have been performed using the density functional theory in the generalized gradient approximation. The calculated values of the structural characteristics and properties (sublimation energies, bulk moduli, band gaps, X-ray diffraction patterns) of the studied diamond-like phases differ significantly from the corresponding values for cubic diamond.

The topological pressure-temperature phase diagram and crystal structures of the dimorphic system spiperone.

PubMed

Robert, B; Perrin, M-A; Coquerel, G; Céolin, R; Rietveld, I B

2016-03-01

The topological pressure-temperature phase diagram for the dimorphism of spiperone, a potent neuroleptic drug, has been constructed using literature data and improved crystal structures obtained with new crystallographic data from single-crystal X-ray diffraction at various temperatures. It is inferred that form II, which is the more dense form and exhibits the lower melting temperature, becomes the more stable phase under pressure. Under ambient conditions, form I is more stable. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

Electrooptic crystal growth and properties

NASA Astrophysics Data System (ADS)

1994-02-01

A new member in the tungsten-bronze family of ferroelectric lead potassium niobate (PKN), with general formula Pb(1-x)K(2x)Nb2O6, has been grown as bulk single crystal. Growth of PKN with charge composition x = 0.23 has been achieved using the Czochralski technique of crystal pulling. Large diameter boules were grown in platinum crucibles at temperatures between 1280 and 1300 C. Crystallographic studies were conducted using x ray diffraction techniques. The samples were characterized for ferroelectric properties between 25 and 600 C and for optical absorption. This paper presents the crystal synthesis and the results of ferroelectric and optical characterization. Bulk single crystals of potassium tantalate niobate, KTa(1-x)Nb(x)O3, ferroelectric with different values of Ta/Nb ratios have been grown by temperature gradient transport technique (TGTT). A second attached paper presents the results of the crystal growth experiments, ferroelectric characterization techniques, and properties of potassium tantalate niobate crystals.

Crystallographic and magnetic properties of the spinel-type ferrites ZnxCo1-xFe2O4 (0.0 ≤ x ≤ 0.75)

NASA Astrophysics Data System (ADS)

Azad, A. K.; Zakaria, A. K. M.; Jewel, Md. Yusuf; Khan, Abu Saeed; Yunus, S. M.; Kamal, I.; Datta, T. K.; Eriksson, S.-G.

2015-05-01

Ultrahigh frequencies (UHF) have applications in signal and power electronics to minimize product sizes, increase production quantity and lower manufacturing cost. In the UHF range of 300 MHz to 3 GHz, ferrimagnetic iron oxides (ferrites) are especially useful because they combine the properties of a magnetic material with that of an electrical insulator. Ferrites have much higher electrical resistivity than metallic ferromagnetic materials, resulting in minimization of the eddy current losses, and total penetration of the electromagnetic (EM) field. Hence ferrites are frequently applied as circuit elements, magnetic storage media like read/write heads, phase shifters and Faraday rotators. The electromagnetic properties of ferrites are affected by operating conditions such as field strength, temperature and frequency. The spinel system ZnxCo1-xFe2O4 (x=0.0, 0.25, 0.50 and 0.75) has been prepared by the standard solid state sintering method. X-ray and neutron powder diffraction measurements were performed at room temperature. Neutron diffraction data analysis confirms the cubic symmetry corresponding to the space group Fd3m. The distribution of three cations Zn2+, Co2+ and Fe3+ over the spinel lattice and other crystallographic parameters like lattice constant, oxygen position parameter, overall temperature factor and occupancies of different ions in different lattice sites for the samples have been determined from the analysis of neutron diffraction data. The lattice constant increases with increasing Zn content in the system. The magnetic structure was found to be ferrimagnetic for the samples with x≤0.50. Magnetization measurements show that with the increase of Zn content in the system the value of saturation magnetization first increases and then decreases. The variation of the magnetic moment with Zn substitution has been discussed in terms of the distribution of magnetic and non-magnetic ions over the A and B sub-lattices and their exchange coupling.

Crystallization and preliminary crystallographic analysis of human common-type acylphosphatase

PubMed Central

Yeung, Rachel C. Y.; Lam, Sonia Y.; Wong, Kam-Bo

2006-01-01

Human acylphosphatase, an 11 kDa enzyme that catalyzes the hydrolysis of carboxyl phosphate bonds, has been studied extensively as a model system for amyloid-fibril formation. However, the structure is still not known of any isoform of human acylphosphatase. Here, the crystallization and preliminary X-­ray diffraction data analysis of human common-type acylphosphatase are reported. Crystals of human common-type acylphosphatase have been grown by the sitting-drop vapour-diffusion method at 289 K using polyethylene glycol 4000 as precipitant. Diffraction data were collected to 1.45 Å resolution at 100 K. The crystals belong to space group P212121, with unit-cell parameters a = 42.58, b = 47.23, c = 57.26 Å. PMID:16511269

Electrical properties of NiAs-type MnTe films with preferred crystallographic plane of (110)

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

Yang, L.; Wang, Z. H., E-mail: zhwang@imr.ac.cn; Zhang, Z. D.

2016-01-28

NiAs-type manganese telluride (MnTe) films with preferred crystallographic plane of (110) were prepared on Si/SiO{sub 2} substrates by pulsed laser deposition. X-ray diffraction (XRD) of the films was studied at different temperatures. The XRD peak of MnTe (110) films shifts to higher angle with decreasing temperature, showing the decrease of the lattice parameter. Resistivity of the films was studied in the temperature range of 2–350 K. The bump between 150 and 250 K was observed in the films, which may be related to the special s-d and p-d overlaps induced by the compressed lattice. The magnon drag effect near its Néel temperaturemore » T{sub N} and enlarged magnetic-elastic coupling below 100 K were observed and analyzed in details.« less

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

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

Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko

2007-10-01

Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two moleculesmore » per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.« less

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

Nazareth, A.S.; Sood, D.K.; Zmood, R.B.

A focusing grid broad beam Kaufman source, using argon ions on a target of nominal composition Nd{sub 2}Fe{sub 14}B has been employed to sputter deposit magnetic thin films of thicknesses ranging from 800 {angstrom} to 1300 {angstrom} on silicon-(111) substrates at room temperature. These films were characterized for their composition depth profile by Rutherford Backscattering Spectroscopy, while x-ray diffraction was used to study the crystallographic structure. Due to a close match between (111) Si with (220) Nd{sub 2}Fe{sub 14}B lattice spacings, preferred crystallographic texturing was expected, and experimental results showed a greatly enhanced (220) texture. The degradation in magnetic propertiesmore » was attributed to the presence of oxygen in the films as indicated by concentration depth profiles. It is premised that another significant role of oxygen may be to relieve the misfit strain across the interface by its incorporation within the Nd{sub 2}Fe{sub 14}B phase.« less

Direct observation of grain rotations during coarsening of a semisolid Al–Cu alloy

PubMed Central

Dake, Jules M.; Oddershede, Jette; Sørensen, Henning O.; Werz, Thomas; Shatto, J. Cole; Uesugi, Kentaro; Schmidt, Søren; Krill, Carl E.

2016-01-01

Sintering is a key technology for processing ceramic and metallic powders into solid objects of complex geometry, particularly in the burgeoning field of energy storage materials. The modeling of sintering processes, however, has not kept pace with applications. Conventional models, which assume ideal arrangements of constituent powders while ignoring their underlying crystallinity, achieve at best a qualitative description of the rearrangement, densification, and coarsening of powder compacts during thermal processing. Treating a semisolid Al–Cu alloy as a model system for late-stage sintering—during which densification plays a subordinate role to coarsening—we have used 3D X-ray diffraction microscopy to track the changes in sample microstructure induced by annealing. The results establish the occurrence of significant particle rotations, driven in part by the dependence of boundary energy on crystallographic misorientation. Evidently, a comprehensive model for sintering must incorporate crystallographic parameters into the thermodynamic driving forces governing microstructural evolution. PMID:27671639

Synthesis, surface chemistry and pseudocapacitance mechanisms of VN nanocrystals derived by a simple two-step halide approach

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

Choi, Daiwon; Jampani, Prashanth H.; Jayakody, J. R. P.

Chloroamide precursors generated via a simple two-step ammonolysis reaction of transition metal chloride in the liquid phase at room temperature were heat treated in ammonia at moderate temperature to yield nano-sized VN crystallites. Grain growth inhibited by lowering the synthesis temperature (≈400°C) yielded agglomerated powders of spherical crystallites of cubic phase of VN with particle sizes as small as 6nm in diameter. X-ray diffraction, FTIR, mass spectroscopy (MS), and nuclear magnetic resonance (NMR) spectroscopy assessed the ammonolysis and nitridation reaction of the VCl 4-NH 3 system. X-ray Rietveld refinement, the BET technique and high-resolution transmission microscopy (HRTEM), energy dispersive x-raymore » (EDX) and thermogravimetric analysis (TGA) helped assess the crystallographic and microstructural nature of the VN nanocrystals. The surface chemistry and redox reaction leading to the gravimetric pseudo-capacitance value of (≈855 F/g) measured for the VN nanocrystals was determined and validated using FTIR, XPS and cyclic voltammetry analyses.« less

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Probing Photoinduced Structural Phase Transitions by Fast or Ultra-Fast Time-Resolved X-Ray Diffraction

NASA Astrophysics Data System (ADS)

Cailleau, Hervé Collet, Eric; Buron-Le Cointe, Marylise; Lemée-Cailleau, Marie-Hélène Koshihara, Shin-Ya

A new frontier in the field of structural science is the emergence of the fast and ultra-fast X-ray science. Recent developments in time-resolved X-ray diffraction promise direct access to the dynamics of electronic, atomic and molecular motions in condensed matter triggered by a pulsed laser irradiation, i.e. to record "molecular movies" during the transformation of matter initiated by light pulse. These laser pump and X-ray probe techniques now provide an outstanding opportunity for the direct observation of a photoinduced structural phase transition as it takes place. The use of X-ray short-pulse of about 100ps around third-generation synchrotron sources allows structural investigations of fast photoinduced processes. Other new X-ray sources, such as laser-produced plasma ones, generate ultra-short pulses down to 100 fs. This opens the way to femtosecond X-ray crystallography, but with rather low X-ray intensities and more limited experimental possibilities at present. However this new ultra-fast science rapidly progresses around these sources and new large-scale projects exist. It is the aim of this contribution to overview the state of art and the perspectives of fast and ultra-fast X-ray scattering techniques to study photoinduced phase transitions (here, the word ultra-fast is used for sub-picosecond time resolution). In particular we would like to largely present the contribution of crystallographic methods in comparison with optical methods, such as pump-probe reflectivity measurements, the reader being not necessary familiar with X-ray scattering. Thus we want to present which type of physical information can be obtained from the positions of the Bragg peaks, their intensity and their shape, as well as from the diffuse scattering beyond Bragg peaks. An important physical feature is to take into consideration the difference in nature between a photoinduced phase transition and conventional homogeneous photoinduced chemical or biochemical processes where molecules transform in an independent way each other. Actually the photoinduced phase transition with the establishment of the new electronic and structural oscopic order is preceded by precursor co-operative phenomena due to the formation of nano-scale correlated objects. These are the counterpart of pre-transitional fluctuations at thermal equilibrium which take place above the transition temperature (short range order preceding long range one). Moreover ultra-fast X-ray scattering will play a central role within the fascinating field of manipulating coherence, for instance to directly observe coherent atomic motions induced by a light pulse, such as optical phonons. In the first part of this contribution we present what experimental features are accessible by X-ray scattering to describe the physical picture for a photoinduced structural phase transition. The second part shows how a time-resolved X-ray scattering experiment can be performed with regards to the different pulsed X-ray sources. The first time-resolved X-ray diffraction experiments on photoinduced phase transitions are described and discussed in the third part. Finally some challenges for future are briefly indicated in the conclusion.

High-efficiency thermoelectric Ba8Cu14Ge6P26: bridging the gap between tetrel-based and tetrel-free clathrates† †Electronic supplementary information (ESI) available: Calculated and experimental powder XRD patterns; tables with crystallographic information; SEM and EDS results; additional DSC, thermal conductivities, and ZT figures. CCDC 1568106. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc03482b

PubMed Central

Wang, Jian; Lebedev, Oleg I.; Lee, Kathleen; Dolyniuk, Juli-Anna; Klavins, Peter; Bux, Sabah

2017-01-01

A new type-I clathrate, Ba8Cu14Ge6P26, was synthesized by solid-state methods as a polycrystalline powder and grown as a cm-sized single crystal via the vertical Bridgman method. Single-crystal and powder X-ray diffraction show that Ba8Cu14Ge6P26 crystallizes in the cubic space group Pm3n (no. 223). Ba8Cu14Ge6P26 is the first representative of anionic clathrates whose framework is composed of three atom types of very different chemical natures: a transition metal, tetrel element, and pnicogen. Uniform distribution of the Cu, Ge, and P atoms over the framework sites and the absence of any superstructural or local ordering in Ba8Cu14Ge6P26 were confirmed by synchrotron X-ray diffraction, electron diffraction and high-angle annular dark field scanning transmission electron microscopy, and neutron and X-ray pair distribution function analyses. Characterization of the transport properties demonstrate that Ba8Cu14Ge6P26 is a p-type semiconductor with an intrinsically low thermal conductivity of 0.72 W m–1 K–1 at 812 K. The thermoelectric figure of merit, ZT, for a slice of the Bridgman-grown crystal of Ba8Cu14Ge6P26 approaches 0.63 at 812 K due to a high power factor of 5.62 μW cm–1 K–2. The thermoelectric efficiency of Ba8Cu14Ge6P26 is on par with the best optimized p-type Ge-based clathrates and outperforms the majority of clathrates in the 700–850 K temperature region, including all tetrel-free clathrates. Ba8Cu14Ge6P26 expands clathrate chemistry by bridging conventional tetrel-based and tetrel-free clathrates. Advanced transport properties, in combination with earth-abundant framework elements and congruent melting make Ba8Cu14Ge6P26 a strong candidate as a novel and efficient thermoelectric material. PMID:29568451

Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

PubMed

Akter, Mahfuza; Inoue, Chika; Komori, Hirofumi; Matsuda, Nana; Sakurai, Takeshi; Kataoka, Kunishige; Higuchi, Yoshiki; Shibata, Naoki

2016-10-01

Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed. Tiny crystals were obtained from the deuterated CueO initially prepared from the original construct. The X-ray crystal structure of the deuterated CueO showed that the protein contained an incompletely truncated signal sequence at the N-terminus, which resulted in the heterogeneity of the protein sample for crystallization. Here, a new CueO expression system that had an HRV3C cleavage site just after the signal sequence was constructed. Deuterated CueO from the new construct was expressed in cells cultured in deuterated algae-extract medium and the signal sequence was completely eliminated by HRV3C protease. The deuteration level of the purified protein was estimated by MALDI-TOF mass spectrometry to be at least 83.2% compared with nondeuterated protein. Nondeuterated CueO crystallized in space group P2 1 , with unit-cell parameters a = 49.51, b = 88.79, c = 53.95 Å, β = 94.24°, and deuterated CueO crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.91, b = 106.92, c = 262.89 Å. The crystallographic parameters for the crystals of the new construct were different from those previously reported for nondeuterated crystals. The nondeuterated and deuterated CueO from the new construct had similar UV-Vis spectra, enzymatic activities and overall structure and geometry of the ligands of the Cu atoms in the active site to those of previously reported CueO structures. These results indicate that the CueO protein prepared using the new construct is suitable for further neutron diffraction studies.

Twin density of aragonite in molluscan shells characterized using X-ray diffraction and transmission electron microscopy

NASA Astrophysics Data System (ADS)

Kogure, Toshihiro; Suzuki, Michio; Kim, Hyejin; Mukai, Hiroki; Checa, Antonio G.; Sasaki, Takenori; Nagasawa, Hiromichi

2014-07-01

{110} twin density in aragonites constituting various microstructures of molluscan shells has been characterized using X-ray diffraction (XRD) and transmission electron microscopy (TEM), to find the factors that determine the density in the shells. Several aragonite crystals of geological origin were also investigated for comparison. The twin density is strongly dependent on the microstructures and species of the shells. The nacreous structure has a very low twin density regardless of the shell classes. On the other hand, the twin density in the crossed-lamellar (CL) structure has large variation among classes or subclasses, which is mainly related to the crystallographic direction of the constituting aragonite fibers. TEM observation suggests two types of twin structures in aragonite crystals with dense {110} twins: rather regulated polysynthetic twins with parallel twin planes, and unregulated polycyclic ones with two or three directions for the twin planes. The former is probably characteristic in the CL structures of specific subclasses of Gastropoda. The latter type is probably related to the crystal boundaries dominated by (hk0) interfaces in the microstructures with preferred orientation of the c-axis, and the twin density is mainly correlated to the crystal size in the microstructures.

In vivo synthesis of selenium nanoparticles by Halococcus salifodinae BK18 and their anti-proliferative properties against HeLa cell line.

PubMed

Srivastava, Pallavee; Braganca, Judith M; Kowshik, Meenal

2014-01-01

Nanoparticles synthesis by bacteria and yeasts has been widely reported, however, synthesis using halophilic archaea is still in a nascent stage. This study aimed at the intracellular synthesis of selenium nanoparticles (SeNPs) by the haloarchaeon Halococcus salifodinae BK18 when grown in the presence of sodium selenite. Crystallographic characterization of SeNPs by X-ray diffraction, Selected area electron diffraction, and transmission electron microscopy exhibited rod shaped nanoparticles with hexagonal crystal lattice, a crystallite domain size of 28 nm and an aspect ratio (length:diameter) of 13:1. Energy disruptive analysis of X-ray analysis confirmed the presence of selenium in the nano-preparation. The nitrate reductase enzyme assay and the inhibitor studies indicated the involvement of NADH-dependent nitrate reductase in SeNPs synthesis and metal tolerance. The SeNPs exhibited good anti-proliferative properties against HeLa cell lines while being non-cytotoxic to normal cell line model HaCat, suggesting the use of these SeNPs as cancer chemotherapeutic agent. This is the first study on selenium nanoparticles synthesis by haloarchaea. © 2014 American Institute of Chemical Engineers.

Relationships between pathology and crystal structure in breast calcifications: an in situ X-ray diffraction study in histological sections

PubMed Central

Scott, Robert; Stone, Nicholas; Kendall, Catherine; Geraki, Kalotina; Rogers, Keith

2016-01-01

Calcifications are not only one of the most important early diagnostic markers of breast cancer, but are also increasingly believed to aggravate the proliferation of cancer cells and invasion of surrounding tissue. Moreover, this influence appears to vary with calcification composition. Despite this, remarkably little is known about the composition and crystal structure of the most common type of breast calcifications, and how this differs between benign and malignant lesions. We sought to determine how the phase composition and crystallographic parameters within calcifications varies with pathology, using synchrotron X-ray diffraction. This is the first time crystallite size and lattice parameters have been measured in breast calcifications, and we found that these both parallel closely the changes in these parameters with age observed in fetal bone. We also discovered that these calcifications contain a small proportion of magnesium whitlockite, and that this proportion increases from benign to in situ to invasive cancer. When combined with other recent evidence on the effect of magnesium on hydroxyapatite precipitation, this suggests a mechanism explaining observations that carbonate levels within breast calcifications are lower in malignant specimens. PMID:28721386

Adsorption and photocatalytic properties of transition metal Zinc(II) complex based on 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid

NASA Astrophysics Data System (ADS)

Qiao, Yu; Ren, Shan-Shan; Liu, Li-Hui; Guan, Wei-Sheng; Li, Zhi-Min; Che, Guang-Bo; Liu, Chun-Bo; Wang, Yan-Yan; Wang, Qing-Wei; Li, Xiu-Ying; Zhu, En-Wei

2018-06-01

A new coordination polymeric zinc(II) complex, namely, [Zn2(L)(H2O)3]n·nNO3(1), (H3L = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid) has been synthesized under solvothermal conditions and structurally characterized by elemental analysis, IR spectroscopy, single-crystal X-ray diffraction analysis and powder X-ray diffraction. Complex 1 exhibits a three-dimensional structure with a Schläfli symbol of 44•69•82 topologies, constructed from two crystallographically independent five and six coordinated mode with metal center and connected H3L ligands. The complex has good thermal stability and excellent photoluminescent property. Furthermore, by comparing the photoluminescent and photocatalytic mutation results induced by interconversion of metal ions, we confirm that the properties mutation induced by metal ions is much controllable and obvious. In addition, the complex exhibits significantly enhanced photocatalytic activity for methylene blue (MB) under UV light irradiation (λ < 400 nm), and the degradation rate could reach 75% in 80 min. Meanwhile trapping experiments indicated that the •O2- and h+ are the main activated species.

Synthesis and characterization of magnesium aluminate (MgAl2O4) spinel (MAS) thin films

NASA Astrophysics Data System (ADS)

Ahmad, Syed Muhammad; Hussain, Tousif; Ahmad, Riaz; Siddiqui, Jamil; Ali, Dilawar

2018-01-01

In a quest to identify more economic routes for synthesis of magnesium aluminate (MgAl2O4) spinel (MAS) thin films, dense plasma focus device was used with multiple plasma focus shots. Structural, bonding between composite films, surface morphological, compositional and hardness properties of MAS thin films were investigated by using x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy dispersive x-rays (EDX) analysis and Vickers micro hardness test respectively. In XRD graph, the presence of MgAl2O4 diffraction peaks in crystallographic orientations (222), (400) and (622) pointed out the successful formation of polycrystalline thin films of MgAl2O4 with face centered cubic structure. The FTIR spectrums showed a major common transmittance band at 697.95 cm-1 which belongs to MgAl2O4. SEM micrographs illustrated a mesh type, granular and multi layers microstructures with significant melting effects. EDX spectrum confirmed the existence of magnesium, oxygen and aluminum in MAS films. A common increasing behavior in micro-hardness of composite MgAl2O4 films by increasing number of plasma focus shots was found.

Residual stress determination in oxide layers at different length scales combining Raman spectroscopy and X-ray diffraction: Application to chromia-forming metallic alloys

DOE PAGES

Guerain, Mathieu; Grosseau-Poussard, Jean-Luc; Geandier, Guillaume; ...

2017-11-21

In oxidizing environments, the protection of metals and alloys against further oxidation at high temperature is provided by the oxide film itself. This protection is efficient only if the formed film adheres well to the metal (substrate), i.e., without microcracks and spalls induced by thermomechanical stresses. In this study, the residual stresses at both macroscopic and microscopic scales in the oxide film adhering to the substrate and over the damaged areas have been rigorously determined on the same samples for both techniques. Ni-30Cr and Fe-47Cr alloys have been oxidized together at 900 and 1000 °C, respectively, to create films withmore » a thickness of a few microns. A multi-scale approach was adopted: macroscopic stress was determined by conventional X-ray diffraction and Raman spectroscopy, while microscopic residual stress mappings were performed over different types of bucklings using Raman micro-spectroscopy and synchrotron micro-diffraction. A very good agreement is found at macro- and microscales between the residual stress values obtained with both techniques, giving confidence on the reliability of the measurements. In addition, relevant structural information at the interface between the metallic substrate and the oxide layer was collected by micro-diffraction, a non-destructive technique that allows mapping through the oxide layer, and both the grain size and the crystallographic orientation of the supporting polycrystalline metal located either under a buckling or not were measured.« less

Residual stress determination in oxide layers at different length scales combining Raman spectroscopy and X-ray diffraction: Application to chromia-forming metallic alloys

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

Guerain, Mathieu; Grosseau-Poussard, Jean-Luc; Geandier, Guillaume

In oxidizing environments, the protection of metals and alloys against further oxidation at high temperature is provided by the oxide film itself. This protection is efficient only if the formed film adheres well to the metal (substrate), i.e., without microcracks and spalls induced by thermomechanical stresses. In this study, the residual stresses at both macroscopic and microscopic scales in the oxide film adhering to the substrate and over the damaged areas have been rigorously determined on the same samples for both techniques. Ni-30Cr and Fe-47Cr alloys have been oxidized together at 900 and 1000 °C, respectively, to create films withmore » a thickness of a few microns. A multi-scale approach was adopted: macroscopic stress was determined by conventional X-ray diffraction and Raman spectroscopy, while microscopic residual stress mappings were performed over different types of bucklings using Raman micro-spectroscopy and synchrotron micro-diffraction. A very good agreement is found at macro- and microscales between the residual stress values obtained with both techniques, giving confidence on the reliability of the measurements. In addition, relevant structural information at the interface between the metallic substrate and the oxide layer was collected by micro-diffraction, a non-destructive technique that allows mapping through the oxide layer, and both the grain size and the crystallographic orientation of the supporting polycrystalline metal located either under a buckling or not were measured.« less

Residual stress determination in oxide layers at different length scales combining Raman spectroscopy and X-ray diffraction: Application to chromia-forming metallic alloys

NASA Astrophysics Data System (ADS)

Guerain, Mathieu; Grosseau-Poussard, Jean-Luc; Geandier, Guillaume; Panicaud, Benoit; Tamura, Nobumichi; Kunz, Martin; Dejoie, Catherine; Micha, Jean-Sebastien; Thiaudière, Dominique; Goudeau, Philippe

2017-11-01

In oxidizing environments, the protection of metals and alloys against further oxidation at high temperature is provided by the oxide film itself. This protection is efficient only if the formed film adheres well to the metal (substrate), i.e., without microcracks and spalls induced by thermomechanical stresses. In this study, the residual stresses at both macroscopic and microscopic scales in the oxide film adhering to the substrate and over the damaged areas have been rigorously determined on the same samples for both techniques. Ni-30Cr and Fe-47Cr alloys have been oxidized together at 900 and 1000 °C, respectively, to create films with a thickness of a few microns. A multi-scale approach was adopted: macroscopic stress was determined by conventional X-ray diffraction and Raman spectroscopy, while microscopic residual stress mappings were performed over different types of bucklings using Raman micro-spectroscopy and synchrotron micro-diffraction. A very good agreement is found at macro- and microscales between the residual stress values obtained with both techniques, giving confidence on the reliability of the measurements. In addition, relevant structural information at the interface between the metallic substrate and the oxide layer was collected by micro-diffraction, a non-destructive technique that allows mapping through the oxide layer, and both the grain size and the crystallographic orientation of the supporting polycrystalline metal located either under a buckling or not were measured.

Structural characterization of framework-gas interactions in the metal-organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction.

PubMed

Gonzalez, Miguel I; Mason, Jarad A; Bloch, Eric D; Teat, Simon J; Gagnon, Kevin J; Morrison, Gregory Y; Queen, Wendy L; Long, Jeffrey R

2017-06-01

The crystallographic characterization of framework-guest interactions in metal-organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co 2 (dobdc) (dobdc 4- = 2,5-dioxido-1,4-benzenedicarboxylate), a metal-organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal-organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co-CH 4 and Co-Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal-CH 4 interaction and the first crystallographically characterized metal-Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as -17(1) kJ mol -1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.

Structural investigation of α-LaZr2F11 by coupling X-ray powder diffraction, 19F solid state NMR and DFT calculations

NASA Astrophysics Data System (ADS)

Martineau, Charlotte; Legein, Christophe; Body, Monique; Péron, Olivier; Boulard, Brigitte; Fayon, Franck

2013-03-01

α-LaZr2F11 has been synthesized by solid state reaction. Its crystal structure has been refined from X-ray powder diffraction data (space group no. 72 Ibam, a=7.785(1) Å, b=10.086(1) Å and c=11.102(1) Å). α-LaZr2F11 contains one La, one Zr and four F inequivalent crystallographic sites. F3 and F4 are shared between one ZrF73- polyhedron and one LaF85- polyhedron, while F1 and F2 bridge two ZrF73- polyhedra. 19F 1D MAS NMR spectra of α-LaZr2F11 are in agreement with the proposed structural model. Assignment of the 19F resonances to the corresponding crystallographic sites has been performed on the basis of both their relative intensities and their correlation patterns in a 19F 2D dipolar-based double-quantum recoupling MAS NMR spectrum. DFT calculations of the 19F chemical shielding tensors have been performed using the GIPAW method implemented in the NMR-CASTEP code, for the experimental structure and two PBE-DFT geometry optimized structures of α-LaZr2F11 (atomic position optimization and full geometry optimization with rescaling of the unit cell volume to the experimental value). Computations were done with and without using a modified La pseudopotential allowing the treatment of the 4f localized empty orbitals of La3+. A relatively nice agreement between the experimental 19F isotropic and anisotropic chemical shifts and the values calculated for the proposed structural model is obtained.

N-benzoylimido complexes of palladium. Synthesis, structural characterisation and structure-reactivity relationship.

PubMed

Besenyei, Gábor; Párkányi, László; Szalontai, Gábor; Holly, Sándor; Pápai, Imre; Keresztury, Gábor; Nagy, Andrea

2004-07-07

Benzoyl azides, ArC(O)N3, 2, (Ar = phenyl or substituted phenyl), react with [Pd2Cl2(dppm)2], 1, [dppm = bis(diphenylphosphino)methane] with the formation of novel [Pd2Cl2(mu-NC(O)Ar)(dppm)2], 3, benzoylnitrene complexes that were structurally characterised by multinuclear magnetic resonance and IR spectroscopy and, in several instances, by single crystal X-ray diffraction. As shown by crystallographic studies, the C2P4Pd2 rings adopt extended twist-boat conformations with methylene groups bending towards the bridging benzoylimido moieties. X-ray diffraction studies have revealed the chiral nature of the imido complexes, the chiral element being the propeller-like C2P4Pd2 ring. Structural data accumulated on complexes 3 such as short C-N distances (1.32 A), elongated C=O bonds (1.30 A) as well as the outstandingly high barrier to internal rotation around the N-C(O) linkage (88.3 kJ mol(-1)) are in line with extensive ppi-ppi interaction between the bridging nitrogen and the carbonyl carbon atoms. Theoretical calculations indicate an electron shift from the dimer towards the apical nitrogen atom, which, in turn, facilitates the donation of electrons towards the carbonyl moiety. To elucidate the structure-reactivity relationship of benzoyl azides towards 1, crystallographic and solution IR spectroscopic studies were carried out on a series of para-substituted benzoyl azides. The reaction obeys the Hammett equation. The large positive value of the reaction constant indicates that the azides act as electrophiles in the reaction studied. The enhanced reactivity of 2-nitrobenzoyl azide has been attributed to a decreased conjugation of the phenyl and carbonyl moieties in this reagent.

Micro X-ray diffraction analysis of thin films using grazing-exit conditions.

PubMed

Noma, T; Iida, A

1998-05-01

An X-ray diffraction technique using a hard X-ray microbeam for thin-film analysis has been developed. To optimize the spatial resolution and the surface sensitivity, the X-ray microbeam strikes the sample surface at a large glancing angle while the diffracted X-ray signal is detected with a small (grazing) exit angle. Kirkpatrick-Baez optics developed at the Photon Factory were used, in combination with a multilayer monochromator, for focusing X-rays. The focused beam size was about 10 x 10 micro m. X-ray diffraction patterns of Pd, Pt and their layered structure were measured. Using a small exit angle, the signal-to-background ratio was improved due to a shallow escape depth. Under the grazing-exit condition, the refraction effect of diffracted X-rays was observed, indicating the possibility of surface sensitivity.

Expression, crystallization and preliminary X-ray crystallographic analyses of two N-terminal acetyltransferase-related proteins from Thermoplasma acidophilum

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

Han, Sang Hee; Ha, Jun Yong; Kim, Kyoung Hoon

2006-11-01

An N-terminal acetyltransferase ARD1 subunit-related protein (Ta0058) and an N-terminal acetyltransferase-related protein (Ta1140) from T. acidophilum were crystallized. X-ray diffraction data were collected to 2.17 and 2.40 Å, respectively. N-terminal acetylation is one of the most common protein modifications in eukaryotes, occurring in approximately 80–90% of cytosolic mammalian proteins and about 50% of yeast proteins. ARD1 (arrest-defective protein 1), together with NAT1 (N-acetyltransferase protein 1) and possibly NAT5, is responsible for the NatA activity in Saccharomyces cerevisiae. In mammals, ARD1 is involved in cell proliferation, neuronal development and cancer. Interestingly, it has been reported that mouse ARD1 (mARD1{sup 225}) mediatesmore » ∊-acetylation of hypoxia-inducible factor 1α (HIF-1α) and thereby enhances HIF-1α ubiquitination and degradation. Here, the preliminary X-ray crystallographic analyses of two N-terminal acetyltransferase-related proteins encoded by the Ta0058 and Ta1140 genes of Thermoplasma acidophilum are reported. The Ta0058 protein is related to an N-terminal acetyltransferase complex ARD1 subunit, while Ta1140 is a putative N-terminal acetyltransferase-related protein. Ta0058 shows 26% amino-acid sequence identity to both mARD1{sup 225} and human ARD1{sup 235}.The sequence identity between Ta0058 and Ta1140 is 28%. Ta0058 and Ta1140 were overexpressed in Escherichia coli fused with an N-terminal purification tag. Ta0058 was crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium acetate pH 4.6, 8%(w/v) polyethylene glycol 4000 and 35%(v/v) glycerol. X-ray diffraction data were collected to 2.17 Å. The Ta0058 crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 49.334, c = 70.384 Å, α = β = γ = 90°. The asymmetric unit contains a monomer, giving a calculated crystal volume per protein weight (V{sub M}) of 2.13 Å{sup 3} Da{sup −1} and a solvent content of 42.1%. Ta1140 was also crystallized at 297 K using a reservoir solution consisting of 0.1 M trisodium citrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000 and 0.2 M sodium chloride. X-ray diffraction data were collected to 2.40 Å. The Ta1140 crystals belong to space group R3, with hexagonal unit-cell parameters a = b = 75.174, c = 179.607 Å, α = β = 90, γ = 120°. Two monomers are likely to be present in the asymmetric unit, with a V{sub M} of 2.51 Å{sup 3} Da{sup −1} and a solvent content of 51.0%.« less

Structural and magnetic properties of morphotropic phase boundary involved Tb 1-xGd xFe 2 compounds

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

Murtaza, Adil; Yang, Sen; Zhou, Chao

2016-09-01

In the present paper, structural, magnetic and magnetostrictive properties of Tb 1-xGd xFe 2 (0 <= x <= 1.0) were studied. Synchrotron x-ray diffraction (XRD) results show the non-cubic symmetry of Tb 1-xGd xFe 2 at room temperature and composition-induced crystallographic phase transition from rhombohedral phase to tetragonal phase. The Gd concentration dependent lattice parameters, lattice distortion and change of easy magnetic direction were detected by synchrotron XRD. With the Gd concentration increases, Curie temperature Tc increases while room temperature magnetization and magnetostriction coefficient lambda(111) and the anisotropy of TbFe 2 decrease. The decrease in spontaneous magnetostriction coefficient lambda(111) withmore » increasing Gd substitution can be understood on the basis of the single-ion model; the corresponding decrease of magnetostriction for Tb 1-xGd xFe 2, and the large magnetostriction value occurs on the Tb-rich side, are ascribed to decrease of lambda(111)« less

High-resolution X-ray diffraction with no sample preparation

PubMed Central

Turner, S. M. R.; Degryse, P.; Shortland, A. J.

2017-01-01

It is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions. PMID:28660862

Crystallographic orientation mapping with an electron backscattered diffraction technique in (Bi, Pb)2Sr2Ca2Cu3O10 superconductor tapes

NASA Astrophysics Data System (ADS)

Tan, T. T.; Li, S.; Oh, J. T.; Gao, W.; Liu, H. K.; Dou, S. X.

2001-02-01

It is believed that grain boundaries act as weak links in limiting the critical current density (Jc) of bulk high-Tc superconductors. The weak-link problem can be greatly reduced by elimination or minimization of large-angle grain boundaries. It has been reported that the distribution of the Jc in (Bi, Pb)2Sr2Ca2Cu3O10+x (Bi2223) superconductor tapes presents a parabolic relationship in the transverse cross section of the tapes, with the lowest currents occurring at the centre of the tapes. It was proposed that the Jc distribution is strongly dependent on the local crystallographic orientation distribution of the Bi2223 oxides. However, the local three-dimensional crystallographic orientation distribution of Bi2223 crystals in (Bi, Pb)2Sr2Ca2Cu3O10+x superconductor tapes has not yet been experimentally determined. In this work, the electron backscattered diffraction technique was employed to map the crystallographic orientation distribution, determine the misorientation of grain boundaries and also map the misorientation distribution in Bi2223 superconductor tapes. Through crystallographic orientation mapping, the relationship between the crystallographic orientation distribution, the boundary misorientation distribution and the fabrication parameters may be understood. This can be used to optimize the fabrication processes thus increasing the critical current density in Bi2223 superconductor tapes.

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

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

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

DOE PAGES

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.; ...

2016-11-11

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

Macromolecular Topography Leaps into the Digital Age

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

A low-cost, real-time digital topography system is under development which will replace x-ray film and nuclear emulsion plates. The imaging system is based on an inexpensive surveillance camera that offers a 1000x1000 array of 8 im square pixels, anti-blooming circuitry, and very quick read out. Currently, the system directly converts x-rays to an image with no phosphor. The system is small and light and can be easily adapted to work with other crystallographic equipment. Preliminary images have been acquired of cubic insulin at the NSLS x26c beam line. NSLS x26c was configured for unfocused monochromatic radiation. Six reflections were collected with stills spaced from 0.002 to 0.001 degrees apart across the entire oscillation range that the reflections were in diffracting condition. All of the reflections were rotated to the vertical to reduce Lorentz and beam related effects. This particular CCD is designed for short exposure applications (much less than 1 sec) and so has a relatively high dark current leading to noisy raw images. The images are processed to remove background and other system noise with a multi-step approach including the use of wavelets, histogram, and mean window filtering. After processing, animations were constructed with the corresponding reflection profile to show the diffraction of the crystal volume vs. the oscillation angle as well as composite images showing the parts of the crystal with the strongest diffraction for each reflection. The final goal is to correlate features seen in reflection profiles captured with fine phi slicing to those seen in the topography images. With this development macromolecular topography finally comes into the digital age.

Operando X-ray Investigation of Electrode/Electrolyte Interfaces in Model Solid Oxide Fuel Cells

PubMed Central

2016-01-01

We employed operando anomalous surface X-ray diffraction to investigate the buried interface between the cathode and the electrolyte of a model solid oxide fuel cell with atomic resolution. The cell was studied under different oxygen pressures at elevated temperatures and polarizations by external potential control. Making use of anomalous X-ray diffraction effects at the Y and Zr K-edges allowed us to resolve the interfacial structure and chemical composition of a (100)-oriented, 9.5 mol % yttria-stabilized zirconia (YSZ) single crystal electrolyte below a La0.6Sr0.4CoO3−δ (LSC) electrode. We observe yttrium segregation toward the YSZ/LSC electrolyte/electrode interface under reducing conditions. Under oxidizing conditions, the interface becomes Y depleted. The yttrium segregation is corroborated by an enhanced outward relaxation of the YSZ interfacial metal ion layer. At the same time, an increase in point defect concentration in the electrolyte at the interface was observed, as evidenced by reduced YSZ crystallographic site occupancies for the cations as well as the oxygen ions. Such changes in composition are expected to strongly influence the oxygen ion transport through this interface which plays an important role for the performance of solid oxide fuel cells. The structure of the interface is compared to the bare YSZ(100) surface structure near the microelectrode under identical conditions and to the structure of the YSZ(100) surface prepared under ultrahigh vacuum conditions. PMID:27346923

On effective and optical resolutions of diffraction data sets.

PubMed

Urzhumtseva, Ludmila; Klaholz, Bruno; Urzhumtsev, Alexandre

2013-10-01

In macromolecular X-ray crystallography, diffraction data sets are traditionally characterized by the highest resolution dhigh of the reflections that they contain. This measure is sensitive to individual reflections and does not refer to the eventual data incompleteness and anisotropy; it therefore does not describe the data well. A physically relevant and robust measure that provides a universal way to define the `actual' effective resolution deff of a data set is introduced. This measure is based on the accurate calculation of the minimum distance between two immobile point scatterers resolved as separate peaks in the Fourier map calculated with a given set of reflections. This measure is applicable to any data set, whether complete or incomplete. It also allows characterizion of the anisotropy of diffraction data sets in which deff strongly depends on the direction. Describing mathematical objects, the effective resolution deff characterizes the `geometry' of the set of measured reflections and is irrelevant to the diffraction intensities. At the same time, the diffraction intensities reflect the composition of the structure from physical entities: the atoms. The minimum distance for the atoms typical of a given structure is a measure that is different from and complementary to deff; it is also a characteristic that is complementary to conventional measures of the data-set quality. Following the previously introduced terms, this value is called the optical resolution, dopt. The optical resolution as defined here describes the separation of the atomic images in the `ideal' crystallographic Fourier map that would be calculated if the exact phases were known. The effective and optical resolution, as formally introduced in this work, are of general interest, giving a common `ruler' for all kinds of crystallographic diffraction data sets.

Epitaxial titanium diboride films grown by pulsed-laser deposition

NASA Astrophysics Data System (ADS)

Zhai, H. Y.; Christen, H. M.; Cantoni, C.; Goyal, A.; Lowndes, D. H.

2002-03-01

Epitaxial, smooth, and low-resistivity titanium diboride (TiB2) films have been grown on SiC substrates using pulsed-laser deposition. Combined studies from ex situ x-ray diffraction and in situ reflection high-energy electron diffraction indicate the crystallographic alignment between TiB2 and SiC both parallel and normal to the substrate. Atomic force microscopy and scanning electron microscopy studies show that these epitaxial films have a smooth surface, and the resistivity of these films is comparable to that of single-crystal TiB2. Growth of these films is motivated by this material's structural and chemical similarity and lattice match to the newly discovered superconductor MgB2, both to gain further insight into the physical mechanisms of diborides in general and, more specifically, as a component of MgB2-based thin-film heterostructures.

On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7

PubMed Central

Boer, D. Roeland; Müller, Axel; Fetzner, Susanne; Lowe, David J.; Romão, Maria João

2005-01-01

Isoquinoline 1-oxidoreductase (IOR) from Brevundimonas diminuta is a mononuclear molybdoenzyme of the xanthine-dehydrogenase family of proteins and catalyzes the conversion of isoquinoline to isoquinoline-1-one. Its primary sequence and behaviour, specifically in its substrate specificity and lipophilicity, differ from other members of the family. A crystal structure of the enzyme is expected to provide an explanation for these differences. This paper describes the crystallization and preliminary X-ray diffraction experiments as well as an optimized purification protocol for IOR. Crystallization of IOR was achieved using two different crystallization buffers. Streak-seeding and cross-linking were essential to obtain well diffracting crystals. Suitable cryo-conditions were found and a structure solution was obtained by molecular replacement. However, phases need to be improved in order to obtain a more interpretable electron-density map. PMID:16508115

Native SAD is maturing.

PubMed

Rose, John P; Wang, Bi-Cheng; Weiss, Manfred S

2015-07-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow 'highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a 'first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

X-ray diffraction from shock-loaded polycrystals.

PubMed

Swift, Damian C

2008-01-01

X-ray diffraction was demonstrated from shock-compressed polycrystalline metals on nanosecond time scales. Laser ablation was used to induce shock waves in polycrystalline foils of Be, 25-125 microm thick. A second laser pulse was used to generate a plasma x-ray source by irradiation of a Ti foil. The x-ray source was collimated to produce a beam of controllable diameter, which was directed at the Be sample. X-rays were diffracted from the sample, and detected using films and x-ray streak cameras. The diffraction angle was observed to change with shock pressure. The diffraction angles were consistent with the uniaxial (elastic) and isotropic (plastic) compressions expected for the loading conditions used. Polycrystalline diffraction will be used to measure the response of the crystal lattice to high shock pressures and through phase changes.

Magnetic and microstructural characterisation of FeNi: Insight into the formation and impact history of the IAB parent body

NASA Astrophysics Data System (ADS)

Nichols, C. I. O.; Krakow, R.; Herrero-Albillos, J.; Kronast, F.; Northwood-Smith, G.; Harrison, R. J.

2017-12-01

The IABs represent one of only two groups of iron meteorites that did not form by fractional crystallization of liquid Fe-Ni in the core of a differentiated planetesimal. Instead, they are believed to originate from a partially differentiated body that was severely disrupted by one or more impacts during its early history. Paleomagnetic signals from two IABs, Toluca and Odessa, were investigated using X-ray magnetic circular dichroism (XMCD) and X-ray photoemission electron microscopy (X-PEEM) to image the magnetisation of the cloudy zone. The IABs do not appear to have experienced a magnetic field, consistent with the lack of a metallic core on the parent body. We also present a detailed microstructural and magnetic study of the observed FeNi microstructures, characterising their properties using XMCD and X-PEEM. The crystallographic architecture of the microstructures was analysed using electron backscatter diffraction (EBSD). Odessa and Toluca both exhibit a complex series of microstructures, requiring an unusual evolution during slow cooling. A conventional Widmanstätten sequence of kamacite, tetrataenite rim and cloudy zone developed via slow cooling to temperatures below 400 ºC. Subsequent modification of the microstructures resulted in the formation of pearlitic plessite and spheroidized plessite. Compositional and crystallographic analysis suggests that pearlitic and spheroidized plessite formed by impact modification of the cloudy zone and martensite, respectively. This study highlights the importance of characterising microstructures in order to corroborate paleomagnetic observations, as well as improving our understanding of the processes effecting planetary formation and evolution.

Single-pulse x-ray diffraction using polycapillary optics for in situ dynamic diffraction

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

Maddox, B. R., E-mail: maddox3@llnl.gov; Akin, M. C., E-mail: akin1@llnl.gov; Teruya, A.

2016-08-15

Diagnostic use of single-pulse x-ray diffraction (XRD) at pulsed power facilities can be challenging due to factors such as the high flux and brightness requirements for diffraction and the geometric constraints of experimental platforms. By necessity, the x-ray source is usually positioned very close, within a few inches of the sample. On dynamic compression platforms, this puts the x-ray source in the debris field. We coupled x-ray polycapillary optics to a single-shot needle-and-washer x-ray diode source using a laser-based alignment scheme to obtain high-quality x-ray diffraction using a single 16 ns x-ray pulse with the source >1 m from themore » sample. The system was tested on a Mo sample in reflection geometry using 17 keV x-rays from a Mo anode. We also identified an anode conditioning effect that increased the x-ray intensity by 180%. Quantitative measurements of the x-ray focal spot produced by the polycapillary yielded a total x-ray flux on the sample of 3.3 ± 0.5 × 10{sup 7} molybdenum Kα photons.« less

Spin reorientation and magnetoelastic coupling in Tb 6Fe 1-xCo xBi 2 (x = 0, 0.125, 0.25, 0.375) alloy system

DOE PAGES

Koehler, Michael R.; Garlea, Vasile O.; McGuire, Michael A.; ...

2014-07-05

Tb 6FeBi 2 adopts a noncentrosymmetric crystal structure and orders ferromagnetically at T C1 = 250 K with an additional magnetic transition at T C2 = 60 K. The low temperature magnetoelastic response in this material is strong, and is enhanced by cobalt substitution. In this paper, the temperature dependence of the atomic and magnetic structure of Tb 6Fe 1-xCo xBi 2 (x = 0, 0.125, 0.25, and 0.375) is reported from powder X-ray diffraction (XRD) and powder neutron diffraction (PND) measurements. Below the Néel temperature a ferrimagnetic ordering between the terbium and iron moments exists in all compounds studied.more » Related to the enhanced magnetostructural response, the Co-doped compounds undergo a crystallographic phase transition below about 60 K. This transition also involves a canting of the magnetic moments away from the c-axis. The structural transition is sluggish and not fully completed in the parent Tb 6FeBi 2 compound, where a mixture of monoclinic and hexagonal phases is identified below 60 K. Lastly, the spin reorientation transition is discussed in terms of competing exchange interactions and magnetocrystalline anisotropies of the two Tb sites and Fe/Co sublattices.« less

Crystallization and preliminary crystallographic analysis of an aminoglycoside kinase from Legionella pneumophila

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

Lemke, Christopher T.; Hwang, Jiyoung; Xiong, Bing

2005-06-01

Two crystal forms of the antibiotic resistance enzyme APH(9)-Ia from L. pneumophila are reported. 9-Aminoglycoside phosphotransferase type Ia [APH(9)-Ia] is a resistance factor in Legionella pneuemophila, the causative agent of legionnaires’ disease. It is responsible for providing intrinsic resistance to the antibiotic spectinomycin. APH(9)-Ia phosphorylates one of the hydroxyl moieties of spectinomycin in an ATP-dependent manner, abolishing the antibiotic properties of this drug. Here, the crystallization and preliminary X-ray studies of this enzyme in two crystal forms is reported. One of the these crystal forms provides diffraction data to a resolution of 1.7 Å.

Purification, Crystallization, and Preliminary Crystallographic Analysis of Deoxyuridine Triphosphate Nucleotidohydrolase from Arabidopsis Thaliana

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

Bajaj,M.; Moriyama, H.

2007-01-01

The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Angstroms resolution using Cu K{alpha} radiation. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 69.90, b = 70.86 Angstroms, c = 75.55 Angstroms . Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a VM of 1.8 Angstroms 3 Da-1.

Ion density evolution in a high-power sputtering discharge with bipolar pulsing

NASA Astrophysics Data System (ADS)

Britun, N.; Michiels, M.; Godfroid, T.; Snyders, R.

2018-06-01

Time evolution of sputtered metal ions in high power impulse magnetron sputtering (HiPIMS) discharge with a positive voltage pulse applied after a negative one (regime called "bipolar pulse HiPIMS"—BPH) is studied using 2-D density mapping. It is demonstrated that the ion propagation dynamics is mainly affected by the amplitude and duration of the positive pulse. Such effects as ion repulsion from the cathode and the ionization zone shrinkage due to electron drift towards the cathode are clearly observed during the positive pulse. The BPH mode also alters the film crystallographic structure, as observed from X-ray diffraction analysis.

Effect of platinum substitution on the structural and magnetic properties of Ni2MnGa ferromagnetic shape memory alloy

NASA Astrophysics Data System (ADS)

Singh, Sanjay; D'Souza, S. W.; Nayak, J.; Caron, L.; Suard, E.; Chadov, S.; Felser, C.

2016-04-01

Ni2MnGa exhibits ideal ferromagnetic shape memory properties, however, brittleness and a low-temperature martensite transition hinder its technological applications motivating the search for novel materials showing better mechanical properties as well as higher transition temperatures. In this work, the crystal structure, phase transitions, and the magnetic properties of quaternary Ni2 -xPtxMnGa (0 ≤x ≤1 ) shape memory alloys were studied experimentally by x-ray diffraction, magnetization measurements, and neutron diffraction and compared to ab initio calculations. Compositions within 0 ≤x ≤0.25 exhibit the cubic austenite phase at room temperature. The x ≈0.3 composition exhibits a seven-layer modulated monoclinic martensite structure. Within 0.4 ≤x ≤1 , the system stabilizes in the nonmodulated tetragonal structure. The martensite transition has very narrow thermal hysteresis 0 ≤x ≤0.3 , which is a typical characteristic of a shape memory alloy. By increasing x , the temperature of the martensite transition increases, while that of the magnetic transition decreases. The x =1 composition (NiPtMnGa) in the martensite phase undergoes a para-to-ferrimagnetic transition. The saturation magnetization exhibits a nontrivial behavior with increasing up to x ≈0.25 , above which, it suddenly decreases. Powder neutron diffraction reveals the presence of antisite disorder, with about 17% of the original Ga sites being occupied by Mn. Computations suggest that the antisite disorder triggers an antiferromagnetic coupling between two Mn atoms in different crystallographic positions, resulting into a sudden drop of the saturation magnetization for higher x .

Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP{sup +}

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

Wan, Qun, E-mail: wqun@yzu.edu.cn; Kovalevsky, Andrey Y.; Wilson, Mark A.

2014-05-25

A 2.0 Å resolution neutron data set and a 1.6 Å resolution X-ray data set were collected for joint X-ray/neutron refinement of the ecDHFR–folate–NADP{sup +} complex in order to study the reaction mechanism of dihydrofolate reductase.

Computational Insights into the O2-evolving complex of photosystem II

PubMed Central

Sproviero, Eduardo M.; McEvoy, James P.; Gascón, José A.; Brudvig, Gary W.; Batista, Victor S.

2009-01-01

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based but comprises important modifications due to structural refinement, hydration and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies. PMID:18483777

XRD and FTIR structural investigation of gadolinium-zinc-borate glass ceramics

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

Borodi, G.; Pascuta, P.; Dan, V.

2013-11-13

X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy measurements have been employed to investigate the (Gd{sub 2}O{sub 3}){sub x}⋅(B{sub 2}O{sub 3}){sub (60−x)}⋅(ZnO){sub 40} glass ceramics system, with 0 ≤ x ≤ 15 mol%. After heat treatment applied at 860 °C for 2 h, some structural changes were observed and new crystalline phases appeared in the structure of the samples. In these glass ceramics four crystalline phases were identified using powder diffraction files (PDF 2), namely ZnB{sub 4}O{sub 7}, Zn{sub 4}O(B{sub 6}O{sub 12}), Zn{sub 3}(BO{sub 3}){sub 2} and GdBO{sub 3}. From the XRD data, the average unit-cell parameter and themore » quantitative ratio of the crystallographic phases in the studied samples were evaluated. FTIR data revealed that the BO{sub 3}, BO{sub 4} and ZnO{sub 4} are the main structural units of these glass ceramics network. The compositional dependence of the different structural units which appear in the studied samples was followed.« less

X-Ray Diffraction Apparatus

NASA Technical Reports Server (NTRS)

Blake, David F. (Inventor); Bryson, Charles (Inventor); Freund, Friedmann (Inventor)

1996-01-01

An x-ray diffraction apparatus for use in analyzing the x-ray diffraction pattern of a sample is introduced. The apparatus includes a beam source for generating a collimated x-ray beam having one or more discrete x-ray energies, a holder for holding the sample to be analyzed in the path of the beam, and a charge-coupled device having an array of pixels for detecting, in one or more selected photon energy ranges, x-ray diffraction photons produced by irradiating such a sample with said beam. The CCD is coupled to an output unit which receives input information relating to the energies of photons striking each pixel in the CCD, and constructs the diffraction pattern of photons within a selected energy range striking the CCD.

Quantum crystallographic charge density of urea

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

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Self-Assembled Pyridine-Dipyrrolate Cages.

PubMed

Zhang, Huacheng; Lee, Juhoon; Lammer, Aaron D; Chi, Xiaodong; Brewster, James T; Lynch, Vincent M; Li, Hao; Zhang, Zhan; Sessler, Jonathan L

2016-04-06

An inherently nonlinear pyridine dipyrrolate ligand, namely 2,6-bis(3,4-diethyl-5-carboxy-1H-pyrrol-2yl)pyridine (compound 1), is able to distinguish between different zinc(II) cation sources, namely Zn(acac)2 and Zn(OAc)2, respectively. This differentiation is manifest both in terms of the observed fluorescent behavior in mixed organic media and the reaction chemistry. Treatment of 1 with Zn(acac)2 gives rise to a cage dimer, cage-1, wherein two molecules of compound 1 act as double bridging units to connect two individual cage subunits. As inferred from X-ray crystallographic studies, this cage system consists of discrete zinc dimers with hydroxide bridges that, with the assistance of bound DMF solvent molecules, serve to fix the geometry and orientation of the pyridine dipyrrolate building blocks. When a different zinc source, Zn(OAc)2, is used to carry out an ostensibly similar complexation reaction with compound 1, an acetate-bridged 1D abacus-like cage polymer is obtained as inferred from X-ray diffraction analysis. This extended solid state structure, cage-2, contains individual zinc dimer cage submits and appears stabilized by solvent molecules (DMF) and the counteranion (acetate). Rod-like assemblies are also observed by DLS and SEM. This construct, in contrast to cage-1, proved fluorescent in mixed organic media. The structure of the ligand itself (i.e., in the absence of Zn(II)) was confirmed by X-ray crystallographic analysis and was found to assemble into a supramolecular polymer. Conversion to a dimer form was seen upon the addition of TBAOAc. On the basis of the metric parameters, the structures seen in the solid state are stabilized via hydrogen bonding interactions involving solvent molecules.

Extended x-ray absorption fine structure study of phase transitions in the piezoelectric perovskite K0.5Na0.5NbO3

NASA Astrophysics Data System (ADS)

Kodre, A.; Tellier, J.; Arčon, I.; Malič, B.; Kosec, M.

2009-06-01

Following an x-ray diffraction study of phase transitions of the piezoelectric perovskite K0.5Na0.5NbO3 the structural changes of the material are studied using extended x-ray absorption fine structure analysis, whereby the neighborhood of Nb atom is determined in the temperature range of monoclinic, tetragonal, and cubic phases. Within the entire range Nb atom is displaced from the center of the octahedron of its immediate oxygen neighbors, as witnessed by the splitting of Nb-O distance. The model shows high prevalence of the displacement in the (111) crystallographic direction of the simple perovskite cell. The corresponding splitting of the Nb-Nb distance is negligible. There is no observable disalignment of the linear Nb-O-Nb bonds from the ideal cubic arrangement, judging from the intensity of the focusing of the photoelectron wave on the Nb-Nb scattering path by the interposed oxygen atom. As a general result, the phase transitions are found as an effect of the long-range order, while the placement of the atoms in the immediate vicinity remains largely unaffected.

Deposition of ultra thin CuInS₂ absorber layers by ALD for thin film solar cells at low temperature (down to 150 °C).

PubMed

Schneider, Nathanaelle; Bouttemy, Muriel; Genevée, Pascal; Lincot, Daniel; Donsanti, Frédérique

2015-02-06

Two new processes for the atomic layer deposition of copper indium sulfide (CuInS₂) based on the use of two different sets of precursors are reported. Metal chloride precursors (CuCl, InCl₃) in combination with H2S imply relatively high deposition temperature (Tdep = 380 °C), and due to exchange reactions, CuInS₂ stoechiometry was only achieved by depositing In₂S3 layers on a CuxS film. However, the use of acac- metal precursors (Cu(acac)₂, In(acac)₃) allows the direct deposition of CuInS₂ at temperature as low as 150 °C, involving in situ copper-reduction, exchange reaction and diffusion processes. The morphology, crystallographic structure, chemical composition and optical band gap of thin films were investigated using scanning electronic microscope, x-ray diffraction under grazing incidence conditions, x-ray fluorescence, energy dispersive spectrometry, secondary ion mass spectrometry, x-ray photoelectron spectroscopy and UV-vis spectroscopy. Films were implemented as ultra-thin absorbers in a typical CIS-solar cell architecture and allowed conversion efficiencies up to 2.8%.

Probing Nucleation and Growth Behavior of Twisted Kebabs from Shish Scaffold in Sheared Polyethylene Melts by in situ X-ray Studies

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

Keum,J.; Burger, C.; Zuo, F.

2007-01-01

By utilizing synchrotron rheo-WAXD (wide-angle X-ray diffraction) and rheo-SAXS (small-angle X-ray scattering) techniques, the nucleation and growth behavior of twisted kebabs from the shear-induced shish scaffold in entangled high-density polyethylene (HDPE) melts were investigated. The evolution of the (110) reflection intensity in WAXD at the early stages of crystallization could be described by a simplified Avrami equation, while the corresponding long period of kebabs determined by SAXS was found to decrease with time. The combined SAXS and WAXD results indicate that the kebab growth in sheared HDPE melts consists of two-dimensional geometry with thermal (sporadic) nucleation. The WAXD data clearlymore » exhibited the transformations of (110) reflection from equatorial 2-arc to off-axis 4-arc and of (200) reflection from off-axis 4-arc to meridional 2-arc, which can be explained by the rotation of crystallographic a-axis around the b-axis during twisted kebab growth. This observation is also consistent with the orientation mode changes from 'Keller/Machin II' to 'intermediate' and then to 'Keller/Machin I'.« less

Real-time X-ray Diffraction: Applications to Materials Characterization

NASA Technical Reports Server (NTRS)

Rosemeier, R. G.

1984-01-01

With the high speed growth of materials it becomes necessary to develop measuring systems which also have the capabilities of characterizing these materials at high speeds. One of the conventional techniques of characterizing materials was X-ray diffraction. Film, which is the oldest method of recording the X-ray diffraction phenomenon, is not quite adequate in most circumstances to record fast changing events. Even though conventional proportional counters and scintillation counters can provide the speed necessary to record these changing events, they lack the ability to provide image information which may be important in some types of experiment or production arrangements. A selected number of novel applications of using X-ray diffraction to characterize materials in real-time are discussed. Also, device characteristics of some X-ray intensifiers useful in instantaneous X-ray diffraction applications briefly presented. Real-time X-ray diffraction experiments with the incorporation of image X-ray intensification add a new dimension in the characterization of materials. The uses of real-time image intensification in laboratory and production arrangements are quite unlimited and their application depends more upon the ingenuity of the scientist or engineer.

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour.

PubMed

Zhang, Y; Paris, O; Terrill, N J; Gupta, H S

2016-05-23

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales.

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour

NASA Astrophysics Data System (ADS)

Zhang, Y.; Paris, O.; Terrill, N. J.; Gupta, H. S.

2016-05-01

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales.

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour

PubMed Central

Zhang, Y.; Paris, O.; Terrill, N. J.; Gupta, H. S.

2016-01-01

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales. PMID:27211574

Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase from Zymomonas mobilis

PubMed Central

Zhang, Aili; Guo, Erhong; Qian, Lanfang; Tang, Nga-Yeung; Watt, Rory M.; Bartlam, Mark

2016-01-01

Exopolyphosphatase (PPX) enzymes degrade inorganic polyphosphate (poly-P), which is essential for the survival of microbial cells in response to external stresses. In this study, a putative exopolyphosphatase from Zymomonas mobilis (ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 122.0, b = 47.1, c = 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule was identified per asymmetric unit. Analytical ultracentrifugation confirmed that ZmPPX forms a dimer in solution. It was confirmed that ZmPPX possesses exopolyphosphatase activity against a synthetic poly-P substrate. PMID:26919520

Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase from Zymomonas mobilis.

PubMed

Zhang, Aili; Guo, Erhong; Qian, Lanfang; Tang, Nga-Yeung; Watt, Rory M; Bartlam, Mark

2016-03-01

Exopolyphosphatase (PPX) enzymes degrade inorganic polyphosphate (poly-P), which is essential for the survival of microbial cells in response to external stresses. In this study, a putative exopolyphosphatase from Zymomonas mobilis (ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 122.0, b = 47.1, c = 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule was identified per asymmetric unit. Analytical ultracentrifugation confirmed that ZmPPX forms a dimer in solution. It was confirmed that ZmPPX possesses exopolyphosphatase activity against a synthetic poly-P substrate.

Radiation damage free ghost diffraction with atomic resolution

DOE PAGES

Li, Zheng; Medvedev, Nikita; Chapman, Henry N.; ...

2017-12-21

The x-ray free electron lasers can enable diffractive structural determination of protein nanocrystals and single molecules that are too small and radiation-sensitive for conventional x-ray diffraction. However the electronic form factor may be modified during the ultrashort x-ray pulse due to photoionization and electron cascade caused by the intense x-ray pulse. For general x-ray imaging techniques, the minimization of the effects of radiation damage is of major concern to ensure reliable reconstruction of molecular structure. Here in this paper, we show that radiation damage free diffraction can be achieved with atomic spatial resolution by using x-ray parametric down-conversion and ghostmore » diffraction with entangled photons of x-ray and optical frequencies. We show that the formation of the diffraction patterns satisfies a condition analogous to the Bragg equation, with a resolution that can be as fine as the crystal lattice length scale of several Ångstrom. Since the samples are illuminated by low energy optical photons, they can be free of radiation damage.« less

Radiation damage free ghost diffraction with atomic resolution

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

Li, Zheng; Medvedev, Nikita; Chapman, Henry N.

The x-ray free electron lasers can enable diffractive structural determination of protein nanocrystals and single molecules that are too small and radiation-sensitive for conventional x-ray diffraction. However the electronic form factor may be modified during the ultrashort x-ray pulse due to photoionization and electron cascade caused by the intense x-ray pulse. For general x-ray imaging techniques, the minimization of the effects of radiation damage is of major concern to ensure reliable reconstruction of molecular structure. Here in this paper, we show that radiation damage free diffraction can be achieved with atomic spatial resolution by using x-ray parametric down-conversion and ghostmore » diffraction with entangled photons of x-ray and optical frequencies. We show that the formation of the diffraction patterns satisfies a condition analogous to the Bragg equation, with a resolution that can be as fine as the crystal lattice length scale of several Ångstrom. Since the samples are illuminated by low energy optical photons, they can be free of radiation damage.« less

Synchrotron Radiation X-ray Diffraction Techniques Applied to Insect Flight Muscle.

PubMed

Iwamoto, Hiroyuki

2018-06-13

X-ray fiber diffraction is a powerful tool used for investigating the molecular structure of muscle and its dynamics during contraction. This technique has been successfully applied not only to skeletal and cardiac muscles of vertebrates but also to insect flight muscle. Generally, insect flight muscle has a highly ordered structure and is often capable of high-frequency oscillations. The X-ray diffraction studies on muscle have been accelerated by the advent of 3rd-generation synchrotron radiation facilities, which can generate brilliant and highly oriented X-ray beams. This review focuses on some of the novel experiments done on insect flight muscle by using synchrotron radiation X-rays. These include diffraction recordings from single myofibrils within a flight muscle fiber by using X-ray microbeams and high-speed diffraction recordings from the flight muscle during the wing-beat of live insects. These experiments have provided information about the molecular structure and dynamic function of flight muscle in unprecedented detail. Future directions of X-ray diffraction studies on muscle are also discussed.

Structural, spectroscopic, and magnetic properties of Eu3+-doped GdVO4 nanocrystals synthesized by a hydrothermal method.

PubMed

Szczeszak, Agata; Grzyb, Tomasz; Śniadecki, Zbigniew; Andrzejewska, Nina; Lis, Stefan; Matczak, Michał; Nowaczyk, Grzegorz; Jurga, Stefan; Idzikowski, Bogdan

2014-12-01

New interesting aspects of the spectroscopic properties, magnetism, and method of synthesis of gadolinium orthovanadates doped with Eu(3+) ions are discussed. Gd(1-x)Eu(x)VO4 (x = 0, 0.05, 0.2) bifunctional luminescent materials with complex magnetic properties were synthesized by a microwave-assisted hydrothermal method. Products were formed in situ without previous precipitation. The crystal structures and morphologies of the obtained nanomaterials were analyzed by X-ray diffraction and transmission and scanning electron microscopy. Crystallographic data were analyzed using Rietveld refinement. The products obtained were nanocrystalline with average grain sizes of 70-80 nm. The qualitative and quantitative elemental composition as well as mapping of the nanocrystals was proved using energy-dispersive X-ray spectroscopy. The spectroscopic properties of red-emitting nanophosphors were characterized by their excitation and emission spectra and luminescence decays. Magnetic measurements were performed by means of vibrating sample magnetometry. GdVO4 and Gd0.8Eu0.2VO4 exhibited paramagnetic behavior with a weak influence of antiferromagnetic couplings between rare-earth ions. In the substituted sample, an additional magnetic contribution connected with the population of low-lying excited states of europium was observed.

Combining experiment and optical simulation in coherent X-ray nanobeam characterization of Si/SiGe semiconductor heterostructures

DOE PAGES

Tilka, J. A.; Park, J.; Ahn, Y.; ...

2016-07-06

Here, the highly coherent and tightly focused x-ray beams produced by hard x-ray light sources enable the nanoscale characterization of the structure of electronic materials but are accompanied by significant challenges in the interpretation of diffraction and scattering patterns. X-ray nanobeams exhibit optical coherence combined with a large angular divergence introduced by the x-ray focusing optics. The scattering of nanofocused x-ray beams from intricate semiconductor heterostructures produces a complex distribution of scattered intensity. We report here an extension of coherent xray optical simulations of convergent x-ray beam diffraction patterns to arbitrary x-ray incident angles to allow the nanobeam diffraction patternsmore » of complex heterostructures to be simulated faithfully. These methods are used to extract the misorientation of lattice planes and the strain of individual layers from synchrotron x-ray nanobeam diffraction patterns of Si/SiGe heterostructures relevant to applications in quantum electronic devices. The systematic interpretation of nanobeam diffraction patterns from semiconductor heterostructures presents a new opportunity in characterizing and ultimately designing electronic materials.« less

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

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

Gupta, Vibha; Gupta, Rakesh K.; Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021

2008-05-01

The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein productmore » was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4{sub 2}, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å.« less

Thin films of a ferroelectric phenazine/chloranilic acid organic cocrystal

NASA Astrophysics Data System (ADS)

Thompson, Nicholas J.; Jandl, Adam C.; Spalenka, Josef W.; Evans, Paul G.

2011-07-01

Phenazine-chloranilic acid cocrystal thin films can be formed by vacuum evaporation of the component molecules onto cooled substrates. Fluxes of phenazine and chloranilic acid were provided from separate sublimation sources, from which the cocrystalline phase can be formed under a wide range of impingement rates of the component molecules. Substrates consisted of Au or Ni thin films on Si wafers, cooled to 100-140 K during deposition. X-ray diffraction and scanning electron microscopy show that this process yields polycrystalline thin films of the cocrystal with voids between crystalline grains. The relative intensities of X-ray reflections differ from reported intensities of polycrystalline powders, suggesting that the films have an anisotropic distribution of crystallographic orientations. The cocrystalline thin films have an effective dielectric constant of 13 at room temperature, increasing at lower temperatures and exhibiting a broad maximum near 200 K. The means to grow thin films of organic ferroelectric materials will allow the integration of new functionalities into organic electronic device structures, including capacitors and field-effect transistors.

Expression, crystallization and preliminary crystallographic analysis of the extracellular IgV-like domain of the human natural killer cell inhibitory receptor p75/AIRM1.

PubMed

Dimasi, Nazzareno; Moretta, Lorenzo; Biassoni, Roberto; Mariuzza, Roy A

2003-10-01

p75/AIRM1 (Siglec-7) is a sialic acid-binding Ig-like lectin recently identified as an inhibitory receptor on natural killer cells. The expression, in vitro folding, circular-dichroism spectroscopy, crystallization and preliminary X-ray characterization of the Ig-V like domain of p75/AIRM1 are reported. X-ray data were collected from a single crystal at 100 K, with a maximum useful diffraction pattern extending to 1.45 A resolution on a synchrotron source. The crystal belongs to a primitive monoclinic space group, with unit-cell parameters a = 32.65, b = 49.72, c = 39.79 A, alpha = gamma = 90, beta = 113 degrees. The systematic absences indicate that the space group is P2(1). Assuming one molecule per asymmetric unit, V(M) (the Matthews coefficient) was calculated to be 1.879 A(3) Da(-1) and the solvent content was estimated to be 32.01%.

Effect of substrate temperature and gas flow ratio on the nanocomposite TiAlBN coating

NASA Astrophysics Data System (ADS)

Rosli, Z. M.; Kwan, W. L.; Juoi, J. M.

2016-07-01

Nanocomposite TiAlBN (nc-TiAlBN) coatings were successfully deposited via RF magnetron sputtering by varying the nitrogen-to-total gas flow ratio (RN), and substrate temperature (TS). All coatings were deposited on AISI 316 substrates using single Ti-Al-BN hot-pressed disc as a target. The grain size, phases, and chemical composition of the coatings were evaluated using glancing angle X-ray diffraction analysis (GAXRD) and X-ray photoelectron spectroscopy (XPS). Results showed that the grains size of the deposited nc-TiAlBN coatings were in the range of 3.5 to 5.7 nm and reached a nitride saturation state as early as 15 % RN. As the nitrogen concentration decreases, boron concentration increased from 9 at.% to 16.17 at.%. and thus, increase the TiB2 phase within the coatings. The TS, however, showed no significant effect either on the crystallographic structure, grain size, or in the chemical composition of the deposited nc-TiAlBN coating.

Effect of Zn and Te beam intensity upon the film quality of ZnTe layers on severely lattice mismatched sapphire substrates by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Nakasu, Taizo; Sun, W.; Kobayashi, M.; Asahi, T.

2017-06-01

Zinc telluride layers were grown on highly-lattice-mismatched sapphire substrates by molecular beam epitaxy, and their crystallographic properties were studied by means of X-ray diffraction pole figures. The crystal quality of the ZnTe thin film was further studied by scanning electron microscopy, X-ray rocking curves and low-temperature photoluminescence measurements. These methods show that high-crystallinity (111)-oriented single domain ZnTe layers with the flat surface and good optical properties are realized when the beam intensity ratio of Zn and Te beams is adjusted. The migration of Zn and Te was inhibited by excess surface material and cracks were appeared. In particular, excess Te inhibited the formation of a high-crystallinity ZnTe film. The optical properties of the ZnTe layer revealed that the exciton-related features were dominant, and therefore the film quality was reasonably high even though the lattice constants and the crystal structures were severely mismatched.

Crystallization and preliminary X-ray crystallographic analysis of BxlA, an intracellular beta-D-xylosidase from Streptomyces thermoviolaceus OPC-520.

PubMed

Morioka, Hideaki; Miki, Yasuhiro; Saito, Kei; Tomoo, Koji; Ishida, Toshimasa; Hasegawa, Tomokazu; Yamano, Akihito; Takada, Chiaki; Miyamoto, Katsushiro; Tsujibo, Hiroshi

2010-07-01

BxlA from Streptomyces thermoviolaceus OPC-520, together with the extracellular BxlE and the integral membrane proteins BxlF and BxlG, constitutes a xylanolytic system that participates in the intracellular transport of xylan-degradation products and the production of xylose. To elucidate the mechanism of the hydrolytic degradation of xylooligosaccharides to xylose at the atomic level, X-ray structural analysis of BxlA was attempted. The recombinant BxlA protein (molecular weight 82 kDa) was crystallized by the hanging-drop vapour-diffusion method at 289 K. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 142.2, b = 129.5, c = 101.4 A, beta = 119.8 degrees , and contained two molecules per asymmetric unit (V(M) = 2.47 A(3) Da(-1)). Diffraction data were collected to a resolution to 2.50 A and provided a data set with an overall R(merge) of 8.3%.

Thermodynamic, crystallographic, and dielectric study of the nature of glass transitions in cyclo-octanol

NASA Astrophysics Data System (ADS)

Puertas, Ricardo; Rute, Maria A.; Salud, Josep; López, David O.; Diez, Sergio; van Miltenburg, J. Kees; Pardo, Luis C.; Tamarit, Josep Ll.; Barrio, Maria; Pérez-Jubindo, Miguel A.; de La Fuente, Maria R.

2004-06-01

The stable solid polymorphism of cyclooctanol (C8H16O, for short C8 OH) is revealed to be a complex problem and only two stable solid phases, denoted on cooling from the liquid as phases I and II, are found using static (thermodynamic and x-ray diffraction) as well as dynamic (dielectric spectroscopy) experimental techniques. Both solid phases are known to exhibit glass transitions if they are cooled down fast enough to prevent transition to ordered crystalline states. Although glass transitions corresponding to both phases had been well documented by means of specific heat measurements, x-ray measurements constitute, as far as we know, the first evidence from the structural point of view. In addition, a great amount of dielectric works devoted to phase I and its glass transition, were published in the past but next to nothing relating to the dielectric properties of phase II and its glass transition. The nature of the disorder of phase II will be discussed.

Crystallization and preliminary X-ray crystallographic analysis of a highly specific serpin from the beetle Tenebrio molitor

PubMed Central

Park, Sun Hee; Piao, Shunfu; Kwon, Hyun-Mi; Kim, Eun-Hye; Lee, Bok Luel; Ha, Nam-Chul

2010-01-01

The Toll signalling pathway, which is crucial for innate immunity, is transduced in insect haemolymph via a proteolytic cascade consisting of three serine proteases. The proteolytic cascade is downregulated by a specific serine protease inhibitor (serpin). Recently, the serpin SPN48 was found to show an unusual specific reactivity towards the terminal serine protease, Spätzle-processing enzyme, in the beetle Tenebrio molitor. In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpho­lino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 Å resolution and were suitable for structure determination. The crystals belonged to space group P21. The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease. PMID:20124722

Coupling of Crystal Structure and Magnetism in the Layered, Ferromagnetic Insulator CrI 3

DOE PAGES

McGuire, Michael A.; Dixit, Hemant; Cooper, Valentino R.; ...

2014-12-23

Here, we examine the crystallographic and magnetic properties of single crystals of CrI 3, an easily cleavable, layered and insulating ferromagnet with a Curie temperature of 61 K. Our X-ray diffraction studies reveal a first-order crystallographic phase transition occurring near 210–220 K upon warming, with significant thermal hysteresis. The low-temperature structure is rhombohedral (Rmore » $$\\bar{3}$$, BiI 3-type) and the high-temperature structure is monoclinic (C2/m, AlCl 3-type). Evidence for coupling between the crystallographic and magnetic degrees of freedom in CrI 3 was found; we observed an anomaly in the interlayer spacing at the Curie temperature and an anomaly in the magnetic susceptibility at the structural transition. First-principles calculations reveal the importance of proper treatment of the long-ranged interlayer forces, and van der Waals density functional theory does an excellent job of predicting the crystal structures and their relative stability. Our calculations suggest that the ferromagnetic order found in the bulk material may persist into monolayer form, suggesting that CrI 3 and other chromium trihalides may be promising materials for spintronic and magnetoelectronic research.« less

Fabrication and testing of a newly designed slit system for depth-resolved X-ray diffraction measurements

DOE PAGES

Sinsheimer, John; Bouet, Nathalie; Ghose, Sanjit; ...

2016-10-06

A new system of slits called `spiderweb slits' have been developed for depth-resolved powder or polycrystalline X-ray diffraction measurements. The slits act on diffracted X-rays to select a particular gauge volume of sample, while absorbing diffracted X-rays from outside of this volume. Although the slit geometry is to some extent similar to that of previously developed conical slits or spiral slits, this new design has advantages over the previous ones in use for complex heterogeneous materials and in situ and operando diffraction measurements. For example, the slits can measure a majority of any diffraction cone for any polycrystalline material, overmore » a continuous range of diffraction angles, and work for X-ray energies of tens to hundreds of kiloelectronvolts. In addition, the design is generated and optimized using ray-tracing simulations, and fabricated through laser micromachining. The first prototype was successfully tested at the X17A beamline at the National Synchrotron Light Source, and shows similar performance to simulations, demonstrating gauge volume selection for standard powders, for all diffraction peaks over angles of 2–10°. A similar, but improved, design will be implemented at the X-ray Powder Diffraction beamline at the National Synchrotron Light Source II.« less

Optically induced lattice deformations, electronic structure changes, and enhanced superconductivity in YBa 2Cu 3O 6.48

DOE PAGES

Mankowsky, R.; Fechner, M.; Forst, M.; ...

2017-02-28

Resonant optical excitation of apical oxygen vibrational modes in the normal state of underdoped YBa 2Cu 3O 6+x induces a transient state with optical properties similar to those of the equilibrium superconducting state. Amongst these, a divergent imaginary conductivity and a plasma edge are transiently observed in the photo-stimulated state. Femtosecond hard x-ray diffraction experiments have been used in the past to identify the transient crystal structure in this non-equilibrium state. Here, we start from these crystallographic features and theoretically predict the corresponding electronic rearrangements that accompany these structural deformations. Using density functional theory, we predict enhanced hole-doping of themore » CuO 2 planes. The empty chain Cu dy2-z2 orbital is calculated to strongly reduce in energy, which would increase c-axis transport and potentially enhance the interlayer Josephson coupling as observed in the THz-frequency response. From these results, we calculate changes in the soft x-ray absorption spectra at the Cu L-edge. As a result, femtosecond x-ray pulses from a free electron laser are used to probe changes in absorption at two photon energies along this spectrum and provide data consistent with these predictions.« less

In situ X-ray and neutron diffraction of the Ruddlesden–Popper compounds (RE 2–xSr x)₀.₉₈(Fe₀.₈Co₀.₂) 1–yMg yO 4–δ (RE=La, Pr): Structure and CO₂ stability

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

Chatzichristodoulou, C., E-mail: ccha@dtu.dk; Hauback, B.C.; Hendriksen, P.V.

2013-05-01

The crystal structure of the Ruddlesden–Popper compounds (La₁.₀Sr₁.₀)₀.₈Fe₁.₀Co₀.₂O 4–δ and (La₁.₂Sr₀.₈)₀.₉₈(Fe₀.₈Co₀.₂)₀.₈Mg₀.₂O 4–δ was investigated at 1000 °C in N₂ (a O₂=1×10₋₄ by in-situ powder neutron diffraction. In-situ powder X-ray diffraction (PXD) was also employed to investigate the temperature dependence of the lattice parameters of the compounds in air and the oxygen activity dependence of the lattice parameters at 800 °C and 1000 °C. The thermal and chemical expansion coefficients, determined along the two crystallographic directions of the tetragonal unit cell, are highly anisotropic. The equivalent pseudo-cubic thermal and chemical expansion coefficients are in agreement with values determined by dilatometry. Themore » chemical stability in CO₂ containing environments of various Ruddlesden–Popper compounds with chemical formula (RE 2-xSr x)₀.₉₈(Fe₀.₈Co₀.₂) 1-yMg yO 4–δ (RE=La, Pr), as well as their stability limit in H₂/H₂O=4.5 were also determined by in-situ PXD for x=0.9, 1.0 and y=0, 0.2. - Graphical abstract: Influence of electronic configuration on bond length, lattice parameters and anisotropic thermal and chemical expansion. Highlights: • The thermal and chemical expansion coefficients are largely anisotropic. • The expansion of the perovskite layers is constrained along the a direction. • The studied compositions show remarkable thermodynamic stability upon reduction. • The thermal and chemical expansion coefficients are lower than related perovskites. • The investigated materials decompose in CO₂ containing atmospheres.« less

Dynamical scattering in coherent hard x-ray nanobeam Bragg diffraction

NASA Astrophysics Data System (ADS)

Pateras, A.; Park, J.; Ahn, Y.; Tilka, J. A.; Holt, M. V.; Kim, H.; Mawst, L. J.; Evans, P. G.

2018-06-01

Unique intensity features arising from dynamical diffraction arise in coherent x-ray nanobeam diffraction patterns of crystals having thicknesses larger than the x-ray extinction depth or exhibiting combinations of nanoscale and mesoscale features. We demonstrate that dynamical scattering effects can be accurately predicted using an optical model combined with the Darwin theory of dynamical x-ray diffraction. The model includes the highly divergent coherent x-ray nanobeams produced by Fresnel zone plate focusing optics and accounts for primary extinction, multiple scattering, and absorption. The simulation accurately reproduces the dynamical scattering features of experimental diffraction patterns acquired from a GaAs/AlGaAs epitaxial heterostructure on a GaAs (001) substrate.

Measurement of UO2 surface oxidation using grazing-incidence x-ray diffraction: Implications for nuclear forensics

NASA Astrophysics Data System (ADS)

Tracy, Cameron L.; Chen, Chien-Hung; Park, Sulgiye; Davisson, M. Lee; Ewing, Rodney C.

2018-04-01

Nuclear forensics involves determination of the origin and history of interdicted nuclear materials based on the detection of signatures associated with their production and trafficking. The surface oxidation undergone by UO2 when exposed to air is a potential signature of its atmospheric exposure during handling and transport. To assess the sensitivity of this oxidation to atmospheric parameters, surface sensitive grazing-incidence x-ray diffraction (GIXRD) measurements were performed on UO2 samples exposed to air of varying relative humidity (34%, 56%, and 95% RH) and temperature (room temperature, 50 °C, and 100 °C). Near-surface unit cell contraction was observed following exposure, indicating oxidation of the surface and accompanying reduction of the uranium cation ionic radii. The extent of unit cell contraction provides a measure of the extent of oxidation, allowing for comparison of the effects of various exposure conditions. No clear influence of relative humidity on the extent of oxidation was observed, with samples exhibiting similar degrees of unit cell contraction at all relative humidities investigated. In contrast, the thickness of the oxidized layers increased substantially with increasing temperature, such that differences on the order of 10 °C yielded readily observable crystallographic signatures of the exposure conditions.

Expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from Corynebacterium glutamicum

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

Kwon, Soo-Young; Kang, Beom Sik; Kim, Ghyung-Hwa

2007-11-01

PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH{sub 2}PO{sub 4} and K{sub 2}HPO{sub 4} as precipitants. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. p-Hydroxybenzoate hydroxylase (PHBH) is an FAD-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pOHB) to 3,4-dihydroxybenzoate in an NADPH-dependent reaction and plays an important role in the biodegradation of aromatic compounds. PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH{sub 2}PO{sub 4} and K{sub 2}HPO{sub 4} as precipitants. X-ray diffraction data were collectedmore » to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystal belongs to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 94.72, c = 359.68 Å, γ = 120°. The asymmetric unit contains two molecules, corresponding to a packing density of 2.65 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.« less

Crystallization and preliminary X-ray crystallographic studies of Drep-3, a DFF-related protein from Drosophila melanogaster

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

Park, Hyun Ho; Tookes, Hansel Emory; Wu, Hao, E-mail: haowu@med.cornell.edu

2006-06-01

The D. melanogaster Drep-3 protein has been crystallized. Crystals were obtained at 293 K that diffracted to 2.8 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}. During apoptosis, DNA fragmentation is mainly mediated by the caspase-activated DFF40 nuclease. DFF40 exists as a heterodimeric complex with its inhibitor DFF45. Upon apoptosis induction, DFF45 is cleaved by caspases to allow DFF40 activation. Drep-3 is a recently identified regulator of the DFF40 system in Drosophila melanogaster. Here, Drep-3 was expressed with a C-terminal His tag in Escherichia coli and the protein was purified to homogeneity. Multi-angle light-scattering analysis showed thatmore » Drep-3 is a homotetramer in solution. Native and selenomethionine-substituted Drep-3 proteins were crystallized at 293 K and X-ray diffraction data were collected to 2.8 and 3.0 Å resolution, respectively. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 56.9, b = 125.4, c = 168.7 Å. The asymmetric unit is estimated to contain one homotetramer.« less

Operation of the Australian Store.Synchrotron for macromolecular crystallography

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

Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Severalmore » real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.« less

Crystallization and preliminary X-ray analysis of human MTH1 with a homogeneous N-terminus

PubMed Central

Koga, Yukari; Inazato, Miyuki; Nakamura, Teruya; Hashikawa, Chie; Chirifu, Mami; Michi, Asuka; Yamashita, Taku; Toma, Sachiko; Kuniyasu, Akihiko; Ikemizu, Shinji; Nakabeppu, Yusaku; Yamagata, Yuriko

2013-01-01

Human MTH1 (hMTH1) is an enzyme that hydrolyses several oxidized purine nucleoside triphosphates to their corresponding nucleoside monophosphates. Crystallographic studies have shown that the accurate mode of interaction between 8-oxoguanine and hMTH1 cannot be understood without determining the positions of the H atoms, as can be observed in neutron and/or ultrahigh-resolution X-ray diffraction studies. The hMTH1 protein prepared in the original expression system from Escherichia coli did not appear to be suitable for obtaining high-quality crystals because the hMTH1 protein had heterogeneous N-termini of Met1 and Gly2 that resulted from N-terminal Met excision by methionine aminopeptidase from the E. coli host. To obtain homogeneous hMTH1, the Gly at the second position was replaced by Lys. As a result, mutant hMTH1 protein [hMTH1(G2K)] with a homogeneous N-terminus could be prepared and high-quality crystals which diffracted to near 1.1 Å resolution using synchrotron radiation were produced. The new crystals belonged to space group P212121, with unit-cell parameters a = 46.36, b = 47.58, c = 123.89 Å. PMID:23295485

Crystallization and preliminary X-ray analysis of human MTH1 with a homogeneous N-terminus.

PubMed

Koga, Yukari; Inazato, Miyuki; Nakamura, Teruya; Hashikawa, Chie; Chirifu, Mami; Michi, Asuka; Yamashita, Taku; Toma, Sachiko; Kuniyasu, Akihiko; Ikemizu, Shinji; Nakabeppu, Yusaku; Yamagata, Yuriko

2013-01-01

Human MTH1 (hMTH1) is an enzyme that hydrolyses several oxidized purine nucleoside triphosphates to their corresponding nucleoside monophosphates. Crystallographic studies have shown that the accurate mode of interaction between 8-oxoguanine and hMTH1 cannot be understood without determining the positions of the H atoms, as can be observed in neutron and/or ultrahigh-resolution X-ray diffraction studies. The hMTH1 protein prepared in the original expression system from Escherichia coli did not appear to be suitable for obtaining high-quality crystals because the hMTH1 protein had heterogeneous N-termini of Met1 and Gly2 that resulted from N-terminal Met excision by methionine aminopeptidase from the E. coli host. To obtain homogeneous hMTH1, the Gly at the second position was replaced by Lys. As a result, mutant hMTH1 protein [hMTH1(G2K)] with a homogeneous N-terminus could be prepared and high-quality crystals which diffracted to near 1.1 Å resolution using synchrotron radiation were produced. The new crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 46.36, b = 47.58, c = 123.89 Å.

Coherent x-ray diffraction imaging with nanofocused illumination.

PubMed

Schroer, C G; Boye, P; Feldkamp, J M; Patommel, J; Schropp, A; Schwab, A; Stephan, S; Burghammer, M; Schöder, S; Riekel, C

2008-08-29

Coherent x-ray diffraction imaging is an x-ray microscopy technique with the potential of reaching spatial resolutions well beyond the diffraction limits of x-ray microscopes based on optics. However, the available coherent dose at modern x-ray sources is limited, setting practical bounds on the spatial resolution of the technique. By focusing the available coherent flux onto the sample, the spatial resolution can be improved for radiation-hard specimens. A small gold particle (size <100 nm) was illuminated with a hard x-ray nanobeam (E=15.25 keV, beam dimensions approximately 100 x 100 nm2) and is reconstructed from its coherent diffraction pattern. A resolution of about 5 nm is achieved in 600 s exposure time.

DynAMITe: a prototype large area CMOS APS for breast cancer diagnosis using x-ray diffraction measurements

NASA Astrophysics Data System (ADS)

Konstantinidis, A.; Anaxagoras, T.; Esposito, M.; Allinson, N.; Speller, R.

2012-03-01

X-ray diffraction studies are used to identify specific materials. Several laboratory-based x-ray diffraction studies were made for breast cancer diagnosis. Ideally a large area, low noise, linear and wide dynamic range digital x-ray detector is required to perform x-ray diffraction measurements. Recently, digital detectors based on Complementary Metal-Oxide- Semiconductor (CMOS) Active Pixel Sensor (APS) technology have been used in x-ray diffraction studies. Two APS detectors, namely Vanilla and Large Area Sensor (LAS), were developed by the Multidimensional Integrated Intelligent Imaging (MI-3) consortium to cover a range of scientific applications including x-ray diffraction. The MI-3 Plus consortium developed a novel large area APS, named as Dynamically Adjustable Medical Imaging Technology (DynAMITe), to combine the key characteristics of Vanilla and LAS with a number of extra features. The active area (12.8 × 13.1 cm2) of DynaMITe offers the ability of angle dispersive x-ray diffraction (ADXRD). The current study demonstrates the feasibility of using DynaMITe for breast cancer diagnosis by identifying six breast-equivalent plastics. Further work will be done to optimize the system in order to perform ADXRD for identification of suspicious areas of breast tissue following a conventional mammogram taken with the same sensor.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a resuscitation-promoting factor from Mycobacterium tuberculosis

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

Ruggiero, Alessia; Tizzano, Barbara; Geerlof, Arie

2007-10-01

The first crystallization of a resuscitation-promoting factor has been performed. Multiwavelength anomalous dispersion experiments have been carried out to obtain experimental phases using data at 2.9 Å resolution from a selenomethionine derivative. The resuscitation-promoting factor RpfB, the most complex of the five resuscitation-promoting factors produced by M. tuberculosis, is devoted to bacterial reactivation from the dormant state. RpfB consists of 362 residues predicted to form five domains. An RpfB fragment containing the protein catalytic domain and a G5 domain has been successfully crystallized using vapour-diffusion methods. This is the first crystallographic study of a resuscitation-promoting factor. Crystals of this proteinmore » belong to space group I422, with unit-cell parameters a = 97.63, b = 97.63, c = 114.87 Å. Diffraction data have also been collected from a selenomethionine derivative at 2.9 Å resolution. Model building using the phases derived from the multiwavelength anomalous dispersion experiment is in progress.« less

Y-TZP zirconia regeneration firing: Microstructural and crystallographic changes after grinding.

PubMed

Ryan, Daniel Patrick Obelenis; Fais, Laiza Maria Grassi; Antonio, Selma Gutierrez; Hatanaka, Gabriel Rodrigues; Candido, Lucas Miguel; Pinelli, Ligia Antunes Pereira

2017-07-26

This study evaluated microstructural and crystallographic phase changes after grinding (G) and regeneration firing/anneling (R) of Y-TZP ceramics. Thirty five bars (Lava TM and Ice Zirkon) were divided: Y-TZP pre-sintered, control (C), regeneration firing (R), dry grinding (DG), dry grinding+regeneration firing (DGR), wet grinding (WG) and wet grinding+regeneration firing (WGR). Grinding was conducted using a diamond bur and annealing at 1,000°C. The microstructure was analyzed by SEM and the crystalline phases by X-ray diffraction (XRD). XRD showed that pre-sintered specimens contained tetragonal and monoclinic phases, while groups C and R showed tetragonal, cubic and monoclinic phases. After grinding, the cubic phase was eliminated in all groups. Annealing (DGR and WGR) resulted in only tetragonal phase. SEM showed semi-circular cracks after grinding and homogenization of particles after annealing. After grinding, surfaces show tetragonal and monoclinic phases and R can be assumed to be necessary prior to porcelain layering when grinding is performed.

High-level Expression Purification Crystallization and Preliminary X-ray Crystallographic Studies of the Receptor Binding Domain of botulinum neurotoxin Serotype D

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

Y Zhang; X Gao; G Buchko

2011-12-31

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

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

Zhang, Y.; Robinson, H.; Gao, X.

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

PubMed Central

Ryan, Rebecca A.; Williams, Sophie; Martin, Andrew V.; Dilanian, Ruben A.; Darmanin, Connie; Putkunz, Corey T.; Wood, David; Streltsov, Victor A.; Jones, Michael W.M.; Gaffney, Naylyn; Hofmann, Felix; Williams, Garth J.; Boutet, Sebastien; Messerschmidt, Marc; Seibert, M. Marvin; Curwood, Evan K.; Balaur, Eugeniu; Peele, Andrew G.; Nugent, Keith A.; Quiney, Harry M.; Abbey, Brian

2017-01-01

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data. PMID:28872125

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

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

Ryan, Rebecca A.; Williams, Sophie; Martin, Andrew V.

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treatedmore » as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C 60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C 60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. Our paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.« less

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

DOE PAGES

Ryan, Rebecca A.; Williams, Sophie; Martin, Andrew V.; ...

2017-08-22

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treatedmore » as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C 60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C 60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. Our paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.« less

Effect of cooling rate on achieving thermodynamic equilibrium in uranium-plutonium mixed oxides

NASA Astrophysics Data System (ADS)

Vauchy, Romain; Belin, Renaud C.; Robisson, Anne-Charlotte; Hodaj, Fiqiri

2016-02-01

In situ X-ray diffraction was used to study the structural changes occurring in uranium-plutonium mixed oxides U1-yPuyO2-x with y = 0.15; 0.28 and 0.45 during cooling from 1773 K to room-temperature under He + 5% H2 atmosphere. We compare the fastest and slowest cooling rates allowed by our apparatus i.e. 2 K s-1 and 0.005 K s-1, respectively. The promptly cooled samples evidenced a phase separation whereas samples cooled slowly did not due to their complete oxidation in contact with the atmosphere during cooling. Besides the composition of the annealing gas mixture, the cooling rate plays a major role on the control of the Oxygen/Metal ratio (O/M) and then on the crystallographic properties of the U1-yPuyO2-x uranium-plutonium mixed oxides.

Synthesis And Characterization Of Reduced Size Ferrite Reinforced Polymer Composites

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

Borah, Subasit; Bhattacharyya, Nidhi S.

2008-04-24

Small sized Co{sub 1-x}Ni{sub x}Fe{sub 2}O{sub 4} ferrite particles are synthesized by chemical route. The precursor materials are annealed at 400, 600 and 800 C. The crystallographic structure and phases of the samples are characterized by X-ray diffraction (XRD). The annealed ferrite samples crystallized into cubic spinel structure. Transmission Electron Microscopy (TEM) micrographs show that the average particle size of the samples are <20 nm. Particulate magneto-polymer composite materials are fabricated by reinforcing low density polyethylene (LDPE) matrix with the ferrite samples. The B-H loop study conducted at 10 kHz on the toroid shaped composite samples shows reduction in magneticmore » losses with decrease in size of the filler sample. Magnetic losses are detrimental for applications of ferrite at high powers. The reduction in magnetic loss shows a possible application of Co-Ni ferrites at high microwave power levels.« less

Resolution enhancement in coherent x-ray diffraction imaging by overcoming instrumental noise.

PubMed

Kim, Chan; Kim, Yoonhee; Song, Changyong; Kim, Sang Soo; Kim, Sunam; Kang, Hyon Chol; Hwu, Yeukuang; Tsuei, Ku-Ding; Liang, Keng San; Noh, Do Young

2014-11-17

We report that reference objects, strong scatterers neighboring weak phase objects, enhance the phase retrieval and spatial resolution in coherent x-ray diffraction imaging (CDI). A CDI experiment with Au nano-particles exhibited that the reference objects amplified the signal-to-noise ratio in the diffraction intensity at large diffraction angles, which significantly enhanced the image resolution. The interference between the diffracted x-ray from reference objects and a specimen also improved the retrieval of the phase of the diffraction signal. The enhancement was applied to image NiO nano-particles and a mitochondrion and confirmed in a simulation with a bacteria phantom. We expect that the proposed method will be of great help in imaging weakly scattering soft matters using coherent x-ray sources including x-ray free electron lasers.

Protein preparation and preliminary X-ray crystallographic analysis of a putative glucosamine 6-phosphate deaminase from Streptococcus mutants

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

Hu, Guan-Jing; Li, Lan-Fen; Li, Dan

2007-09-01

A glucosamine 6-phosphate deaminase homologue from S. mutans was expressed, purified and crystallized. Diffraction data have been collected to 2.4 Å resolution. The SMU.636 protein from Streptococcus mutans is a putative glucosamine 6-phosphate deaminase with 233 residues. The smu.636 gene was PCR-amplified from S. mutans genomic DNA and cloned into the expression vector pET-28a(+). The resultant His-tagged fusion protein was expressed in Escherichia coli and purified to homogeneity in two steps. Crystals of the fusion protein were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.4 Å resolution and belong to space group P2{sub 1}2{sub 1}2{sub 1}, withmore » unit-cell parameters a = 53.83, b = 82.13, c = 134.70 Å.« less

Preliminary X-ray crystallographic analysis of SMU.573, a putative sugar kinase from Streptococcus mutans

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

Zhou, Yan-Feng; Li, Lan-Fen; Yang, Cheng

2008-01-01

SMU.573 from S. mutans was expressed in E. coli and crystallized. The crystals belong to space group I4 and 2.5 Å resolution diffraction data were collected at an in-house chromium radiation source. SMU.573 from Streptococcus mutans is a structurally and functionally uncharacterized protein that was selected for structural biology studies. Native and SeMet-labelled proteins were expressed with an N-His tag in Escherichia coli BL21 (DE3) and purified by Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals of the SeMet-labelled protein were obtained by the hanging-drop vapour-diffusion method and a 2.5 Å resolution diffraction data set was collected using an in-house chromium radiationmore » source. The crystals belong to space group I4, with unit-cell parameters a = b = 96.53, c = 56.26 Å, α = β = γ = 90°.« less

Purification, crystallization and preliminary crystallographic analysis of Est25: a ketoprofen-specific hormone-sensitive lipase

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

Kim, SeungBum; Joo, Sangbum; Yoon, Hyun C.

2007-07-01

Est25, a ketoprofen-specific hormone-sensitive lipase from a metagenomic library, was crystallized and diffraction data were collected to 1.49 Å resolution. Ketoprofen, a nonsteroidal anti-inflammatory drug, inhibits the synthesis of prostaglandin. A novel hydrolase (Est25) with high ketoprofen specificity has previously been identified using a metagenomic library from environmental samples. Recombinant Est25 protein with a histidine tag at the N-terminus was expressed in Escherichia coli and purified in a homogenous form. Est25 was crystallized from 2.4 M sodium malonate pH 7.0 and X-ray diffraction data were collected to 1.49 Å using synchrotron radiation. The crystals belong to the monoclinic space groupmore » C2, with unit-cell parameters a = 197.8, b = 95.2, c = 99.4 Å, β = 97.1°.« less

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of MCAT from Synechocystis sp. PCC 6803.

PubMed

Liu, Yinghui; Zhang, Yanming; Cao, Xupeng; Xue, Song

2013-11-01

Malonyl-coenzymeA:acyl-carrier protein transacylase (MCAT), which catalyzes the transfer of the malonyl group from malonyl-CoA to acyl-carrier protein (ACP), is an essential enzyme in type II fatty-acid synthesis. The enzyme MCAT from Synechocystis sp. PCC 6803 (spMCAT), the first MCAT counterpart from a cyanobacterium, was cloned, purified and crystallized in order to determine its three-dimensional crystal structure. A higher-quality crystal with better diffraction was obtained by crystallization optimization. The crystal diffracted to 1.8 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 43.22, b = 149.21, c = 40.59 Å. Matthews coefficient calculations indicated that the crystal contained one spMCAT molecule in the asymmetric unit with a Matthews coefficient of 2.18 Å(3) Da(-1) and a solvent content of 43.65%.

Electrochemical Liquid Phase Epitaxy (ec-LPE): A New Methodology for the Synthesis of Crystalline Group IV Semiconductor Epifilms.

PubMed

Demuth, Joshua; Fahrenkrug, Eli; Ma, Luyao; Shodiya, Titilayo; Deitz, Julia I; Grassman, Tyler J; Maldonado, Stephen

2017-05-24

Deposition of epitaxial germanium (Ge) thin films on silicon (Si) wafers has been achieved over large areas with aqueous feedstock solutions using electrochemical liquid phase epitaxy (ec-LPE) at low temperatures (T ≤ 90 °C). The ec-LPE method uniquely blends the simplicity and control of traditional electrodeposition with the material quality of melt growth. A new electrochemical cell design based on the compression of a liquid metal electrode into a thin cavity that enables ec-LPE is described. The epitaxial nature, low strain character, and crystallographic defect content of the resultant solid Ge films were analyzed by electron backscatter diffraction, scanning transmission electron microscopy, high resolution X-ray diffraction, and electron channeling contrast imaging. The results here show the first step toward a manufacturing infrastructure for traditional crystalline inorganic semiconductor epifilms that does not require high temperature, gaseous precursors, or complex apparatus.

Native SAD is maturing

PubMed Central

Rose, John P.; Wang, Bi-Cheng; Weiss, Manfred S.

2015-01-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow ‘highly accurate data’ to be routinely collected. Today, native SAD sits on the verge of becoming a ‘first-choice’ method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development. PMID:26175902

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

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

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

High-resolution x-ray diffraction study of the heavy-fermion compound YbBiPt

DOE PAGES

Ueland, B. G.; Saunders, S. M.; Bud'ko, S. L.; ...

2015-11-30

In this study, YbBiPt is a heavy-fermion compound possessing significant short-range antiferromagnetic correlations below a temperature of T*=0.7K, fragile antiferromagnetic order below T N = 0.4K, a Kondo temperature of T K ≈ 1K, and crystalline-electric-field splitting on the order of E/k B = 1 – 10K. Whereas the compound has a face-centered-cubic lattice at ambient temperature, certain experimental data, particularly those from studies aimed at determining its crystalline-electric-field scheme, suggest that the lattice distorts at lower temperature. Here, we present results from high-resolution, high-energy x-ray diffraction experiments which show that, within our experimental resolution of ≈ 6 – 10more » × 10 –5 Å, no structural phase transition occurs between T = 1.5 and 50 K. In combination with results from dilatometry measurements, we further show that the compound's thermal expansion has a minimum at ≈ 18 K and a region of negative thermal expansion for 9 ≲ T ≲ 18 K. Despite diffraction patterns taken at 1.6 K which indicate that the lattice is face-centered cubic and that the Yb resides on a crystallographic site with cubic point symmetry, we demonstrate that the linear thermal expansion may be modeled using crystalline-electric-field level schemes appropriate for Yb 3+ residing on a site with either cubic or less than cubic point symmetry.« less

Microstructure and phase composition of hypoeutectic Te-Bi alloy as evaporation source for photoelectric cathode

NASA Astrophysics Data System (ADS)

Wang, Bao-guang; Yang, Wen-hui; Gao, Hong-ye; Tian, Wen-huai

2018-05-01

A hypoeutectic 60Te-40Bi alloy in mass percent was designed as a tellurium atom evaporation source instead of pure tellurium for an ultraviolet detection photocathode. The alloy was prepared by slow solidification at about 10-2 K·s-1. The microstructure, crystal structure, chemical composition, and crystallographic orientation of each phase in the as-prepared alloy were investigated by optical microscopy, scanning electron microscopy, X-ray diffraction, electron backscatter diffraction, and transmission electron microscopy. The experimental results suggest that the as-prepared 60Te-40Bi alloy consists of primary Bi2Te3 and eutectic Bi2Te3/Te phases. The primary Bi2Te3 phase has the characteristics of faceted growth. The eutectic Bi2Te3 phase is encased by the eutectic Te phase in the eutectic structure. The purity of the eutectic Te phase reaches 100wt% owing to the slow solidification. In the eutectic phases, the crystallographic orientation relationship between Bi2Te3 and Te is confirmed as {[0001]_{B{i_2}T{e_3}}}//{[1\\bar 21\\bar 3]_{Te}} and the direction of Te phase parallel to {[11\\bar 20]_{B{i_2}T{e_3}}} is deviated by 18° from Te N{(2\\bar 1\\bar 11)_{Te}}.

Structure-energy relationship in barbituric acid: a calorimetric, computational, and crystallographic study.

PubMed

Roux, María Victoria; Temprado, Manuel; Notario, Rafael; Foces-Foces, Concepción; Emel'yanenko, Vladimir N; Verevkin, Sergey P

2008-08-14

This paper reports the value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K for barbituric acid. The enthalpies of combustion and sublimation were measured by static bomb combustion calorimetry and transference (transpiration) method in a saturated N2 stream and a gas-phase enthalpy of formation value of -(534.3 +/- 1.7) kJ x mol(-1) was determined at T = 298.15 K. G3-calculated enthalpies of formation are in very good agreement with the experimental value. The behavior of the sample as a function of the temperature was studied by differential scanning calorimetry, and a new polymorph of barbituric acid at high temperature was found. In the solid state, two anhydrous forms are known displaying two out of the six hydrogen-bonding patterns observed in the alkyl/alkenyl derivatives retrieved from the Cambridge Crystallographic Database. The stability of these motifs has been analyzed by theoretical calculations. X-ray powder diffraction technique was used to establish to which polymorphic form corresponds to the commercial sample used in this study and to characterize the new form at high temperature.

Fabrication and testing of a newly designed slit system for depth-resolved X-ray diffraction measurements

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

Sinsheimer, John; Bouet, Nathalie; Ghose, Sanjit

2016-10-06

A new system of slits called `spiderweb slits' have been developed for depth-resolved powder or polycrystalline X-ray diffraction measurements. The slits act on diffracted X-rays to select a particular gauge volume of sample, while absorbing diffracted X-rays from outside of this volume. Although the slit geometry is to some extent similar to that of previously developed conical slits or spiral slits, this new design has advantages over the previous ones in use for complex heterogeneous materials andin situandoperandodiffraction measurements. For example, the slits can measure a majority of any diffraction cone for any polycrystalline material, over a continuous range ofmore » diffraction angles, and work for X-ray energies of tens to hundreds of kiloelectronvolts. The design is generated and optimized using ray-tracing simulations, and fabricated through laser micromachining. The first prototype was successfully tested at the X17A beamline at the National Synchrotron Light Source, and shows similar performance to simulations, demonstrating gauge volume selection for standard powders, for all diffraction peaks over angles of 2–10°. A similar, but improved, design will be implemented at the X-ray Powder Diffraction beamline at the National Synchrotron Light Source II.« less

Local terahertz field enhancement for time-resolved x-ray diffraction

DOE PAGES

Kozina, M.; Pancaldi, M.; Bernhard, C.; ...

2017-02-20

We report local field strength enhancement of single-cycle terahertz (THz) pulses in an ultrafast time-resolved x-ray diffraction experiment. We show that patterning the sample with gold microstructures increases the THz field without changing the THz pulse shape or drastically affecting the quality of the x-ray diffraction pattern. Lastly, we find a five-fold increase in THz-induced x-ray diffraction intensity change in the presence of microstructures on a SrTiO 3 thin-film sample.

Local terahertz field enhancement for time-resolved x-ray diffraction

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

Kozina, M.; Pancaldi, M.; Bernhard, C.

We report local field strength enhancement of single-cycle terahertz (THz) pulses in an ultrafast time-resolved x-ray diffraction experiment. We show that patterning the sample with gold microstructures increases the THz field without changing the THz pulse shape or drastically affecting the quality of the x-ray diffraction pattern. Lastly, we find a five-fold increase in THz-induced x-ray diffraction intensity change in the presence of microstructures on a SrTiO 3 thin-film sample.

Thermal x-ray diffraction and near-field phase contrast imaging

NASA Astrophysics Data System (ADS)

Li, Zheng; Classen, Anton; Peng, Tao; Medvedev, Nikita; Wang, Fenglin; Chapman, Henry N.; Shih, Yanhua

2017-10-01

Using higher-order coherence of thermal light sources, the resolution power of standard x-ray imaging techniques can be enhanced. In this work, we applied the higher-order measurement to far-field x-ray diffraction and near-field phase contrast imaging (PCI), in order to achieve superresolution in x-ray diffraction and obtain enhanced intensity contrast in PCI. The cost of implementing such schemes is minimal compared to the methods that achieve similar effects by using entangled x-ray photon pairs.

Thermal x-ray diffraction and near-field phase contrast imaging

DOE PAGES

Li, Zheng; Classen, Anton; Peng, Tao; ...

2017-12-27

Using higher-order coherence of thermal light sources, the resolution power of standard x-ray imaging techniques can be enhanced. Here in this work, we applied the higher-order measurement to far-field x-ray diffraction and near-field phase contrast imaging (PCI), in order to achieve superresolution in x-ray diffraction and obtain enhanced intensity contrast in PCI. The cost of implementing such schemes is minimal compared to the methods that achieve similar effects by using entangled x-ray photon pairs.

An image focusing means by using an opaque object to diffract x-rays

DOEpatents

Sommargren, Gary E.; Weaver, H. Joseph

1991-01-01

The invention provides a method and apparatus for focusing and imaging x-rays. An opaque sphere is used as a diffractive imaging element to diffract x-rays from an object so that the divergent x-ray wavefronts are transformed into convergent wavefronts and are brought to focus to form an image of the object with a large depth of field.

Soft X-Ray Diffraction Microscopy of a Frozen Hydrated Yeast Cell

DOE PAGES

Huang, Xiaojing; Nelson, Johanna; Kirz, Janos; ...

2009-11-01

We report the first image of an intact, frozen hydrated eukaryotic cell using x-ray diffraction microscopy, or coherent x-ray diffraction imaging. By plunge freezing the specimen in liquid ethane and maintaining it below -170 °C, artifacts due to dehydration, ice crystallization, and radiation damage are greatly reduced. In this example, coherent diffraction data using 520 eV x rays were recorded and reconstructed to reveal a budding yeast cell at a resolution better than 25 nm. This demonstration represents an important step towards high resolution imaging of cells in their natural, hydrated state, without limitations imposed by x-ray optics.

Does the thermal evolution of molecular structures critically affect the magnetic anisotropy?† †Electronic supplementary information (ESI) available. CCDC 1045631–1045633. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01245g

PubMed Central

Qian, Kang; Baldoví, José J.; Zhang, Yi-Quan; Overgaard, Jacob; Wang, Bing-Wu

2015-01-01

A dysprosium based single-ion magnet is synthesized and characterized by the angular dependence of the single-crystal magnetic susceptibility. Ab initio and effective electrostatic analyses are performed using the molecular structures determined from single crystal X-ray diffraction at 20 K, 100 K and 300 K. Contrary to the common assumption, the results reveal that the structural thermal effects that may affect the energy level scheme and magnetic anisotropy below 100 K are negligible. PMID:29568416

Uncovering a reconstructive solid-solid phase transition in a metal-organic framework.

PubMed

Longley, L; Li, N; Wei, F; Bennett, T D

2017-11-01

A nanoporous three-dimensional metal-organic framework (MOF), ZnPurBr undergoes a transition to a previously unreported high-temperature phase, ZnPurBr-ht. The transition, which proceeds without mass loss, is uncovered through the use of differential scanning calorimetry (DSC). The new crystal structure was solved using single-crystal X-ray diffraction, and the mechanical properties of both phases investigated by nanoindentation and density functional theory. The anisotropy of the calculated Young's moduli showed good agreement with the crystallographic alignment of the stiff purinate organic linker. The results provide a prototypical example of the importance of the use of DSC in the MOF field, where its use is not currently standard in characterization.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed

Armen, R S; Uitto, O D; Feller, S E

1998-08-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed Central

Armen, R S; Uitto, O D; Feller, S E

1998-01-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments. PMID:9675175

Shocked quartz in the cretaceous-tertiary boundary clays: Evidence for a global distribution

USGS Publications Warehouse

Bohor, B.F.; Modreski, P.J.; Foord, E.E.

1987-01-01

Shocked quartz grains displaying planar features were isolated from Cretaceous-Tertiary boundary days at five sites in Europe, a core from the north-central Pacific Ocean, and a site in New Zealand. At all of these sites, the planar features in the shocked quartz can be indexed to rational crystallographic planes of the quartz lattice. The grains display streaking indicative of shock in x-ray diffraction photographs and also show reduced refractive indices. These characteristic features of shocked quartz at several sites worldwide confirm that an impact event at the Cretaceous-Tertiary boundary distributed ejecta products in an earth-girdling dust cloud, as postulated by the Alvarez impact hypothesis.

Crystallographic studies of bovine beta2-microglobulin.

PubMed Central

Becker, J W; Ziffer, J A; Edelman, G M; Cunningham, B A

1977-01-01

Crystals of the bovine milk protein lactollin yield x-ray diffraction data extending to a resolution of 2.8 A. Lactollin is a bovine analogue of beta2-microglobulin, a protein that is homologous in amino acid sequence to the constant domains of immunoglobulins and is the light chain of the human and murine major histocompatability antigens. The protein crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 77.4, b = 47.9, and c = 34.3 A. The unit cell parameters and physical chemical solution studies indicate that the molecule exists in the crystal and in solution as a single polypeptide chain of 12,000 daltons. Images PMID:71731

Expression, purification and preliminary crystallographic analysis of sucrose phosphate synthase (SPS) from Halothermothrix orenii

PubMed Central

Huynh, Frederick; Tan, Tien-Chye; Swaminathan, Kunchithapadam; Patel, Bharat K. C.

2005-01-01

This is the first report of the crystallization of a sucrose phosphate synthase (SPS; EC 2.4.1.14). It also constitutes the first study of a sucrose phosphate synthase from a non-photosynthetic thermohalophilic anaerobic bacterium, Halothermothrix orenii. The purified recombinant spsA protein has been crystallized in the monoclinic space group C2, with unit-cell parameters a = 154.2, b = 47.9, c = 72.3 Å, β = 103.16°, using the hanging-drop vapour-diffusion method. The crystal diffracts X-rays to a resolution limit of 3.01 Å. Heavy-metal and halide-soaking trials are currently in progress to solve the structure. PMID:16508108

Crystallography: past and present

NASA Astrophysics Data System (ADS)

Hodeau, J.-L.; Guinebretiere, R.

2007-12-01

In the 19th century, crystallography referred to the study of crystal shapes. Such studies by Haüy and Bravais allowed the establishment of important hypotheses such as (i) “les molécules intégrantes qui sont censées être les plus petits solides que l’on puisse extraire d’un minéral” [1], (ii) the definition of the crystal lattice and (iii) “le cristal est clivable parallèlement à deux ou trois formes cristallines” [2]. This morphological crystallography defined a crystal like “a chemically homogeneous solid, wholly or partly bounded by natural planes that intersect at predetermined angles” [3]. It described the main symmetry elements and operations, nomenclatures of different crystal forms and also the theory of twinning. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as “any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that “diffracts” an incident X-ray beam” [3]. Mathematical tools like the Patterson methods, the direct methods, were developed. The way for solving crystalline structure was opened first for simple compounds and at that time crystallography was associated mainly with perfect crystals. In the fifties, crystallographers already had most apparatus and fundamental methods at their disposal; however, we had to wait for the development of computers to see the full use of these tools. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. Nowadays, one of the new frontiers for crystallographers is to relate the crystal structure to its physical-chemical-biological properties, this means that an accurate structural determination is needed to focus on a selective part of the structure (chemical order, anisotropy, charge transfer, magnetic order) versus an external parameter like temperature, pressure, magnetic or electric field. Modern crystallography is also extended to the study of very small crystals, powders, ill-ordered or non-crystallized materials. Thus presently, crystallography is concerned with any solid that “scatters” an incident beam. Nevertheless, as quoted by A. Guinier, “the problems facing crystallographers have only changed, ... new ones have appeared which require reflection and imagination, ... and which in turn may still bring much joy to all those who like crystallography” [4]. Such developments open up crystallography to modern materials like artificial ones and nanostructures with low- and/or multi-scaled-periodicities and/or extremely small “crystal size” and to materials of the “real world”, with mixtures of phases and/or amorphous contribution and/or defects, a common characteristic of ancient materials analysed in patrimonial research. In our contribution we will show by selected examples that these improvements were allowed (i) by the use of powerful sources, apparatus and detectors which allow micro-diffraction, in-situ diffraction, spectroscopy, resonant scattering, inelastic scattering, coherent scattering, (ii) by the development of methods like diffraction anomalous fine structure (DAFS), pair distribution function (PDF), simulated annealing, single object reconstruction, (iii) by combination of scattering and spectroscopy and by combination of scattering and microscopy. Such combination of different approaches is very efficient and, as said by H. Curien at the IUCr Bordeaux Congress in 1990, “in crystallography, there is a constant alternation between the crystal space and its associated reciprocal space, ... the alternation between experiment and model building is another feature of crystallography activity ..., the crystallographer relies both on his computer and on his diffractometer ..., all these dualistic complementarities are responsible for the fact that crystallographers tend to waver between the description of atomic structures and the explanation of macroscopic properties of solid matter” [5].

Simultaneous X-ray and neutron diffraction Rietveld refinements of nanophase iron substituted hydroxyapatite

NASA Astrophysics Data System (ADS)

Kyriacou, Andreas

The effect of Fe substitution on the crystal structure of hydroxyapatite (HAp) is studied by applying simultaneous Rietveld refinements of powder x-ray and neutron diffraction patterns. Fe is one of the trace elements replacing Ca in HAp, which is the major mineral phase in bones and teeth. The morphology and magnetic properties of the Fe-HAp system are also studied by transmission electron microscopy and magnetization measurements. Samples of Ca(5-x)Fex(PO4)3OH with 0 ≤ x ≤ 0.3 were prepared. Single phase HAp was identified in x-ray diffraction patterns (XRD) of samples with x < 0.1 inferring that the solubility limits are less than 0.1. Hematite (alpha-Fe2O3) is identified as a secondary phase for higher Fe content. The refined parameters show that Fe is incorporated in the HAp structure by replacing Ca in the two crystallographic sites with a preference at the Ca2 site. This preference explains the small effect of the Fe substitution on the lattice constants of HAp. The overall decrease of the lattice constants is explained by the ionic size difference of Ca and Fe. The increasing trend of the a-lattice constant with x in the Fe substituted samples is attributed to a lattice relaxation caused by the substitution of the 4- and 6-fold Fe at the 7- and 9-fold Ca1 and Ca2 sites. This Ca local geometry reduction is indicated by a slight increase of the Ca1-O3 and Ca2-O1 bond lengths. Above the solubility limit x = 0.05, the Fe is partitioned in and out of the HAp structure with increasing nominal Fe content x. The excess Fe is oxidized to hematite. The TEM analysis and magnetic measurements support the results of the simultaneous Rietveld refinements. The TEM images show no significant effect on the morphology and size of the HAp particles upon Fe incorporation. The particles are either spheres or short rods of dimensions 20--60 nm. Hematite particles are imaged in the samples with x exceeding the solubility limit. These particles are spheres, about 15 nm in diameter and are more resistant to electron beam damage. Magnetic measurements reveal a transition of the diamagnetic pure HAp to paramagnetic Fe substituted HAp.

Application of focused-beam flat-sample method to synchrotron powder X-ray diffraction with anomalous scattering effect

NASA Astrophysics Data System (ADS)

Tanaka, M.; Katsuya, Y.; Matsushita, Y.

2013-03-01

The focused-beam flat-sample method (FFM), which is a method for high-resolution and rapid synchrotron X-ray powder diffraction measurements by combination of beam focusing optics, a flat shape sample and an area detector, was applied for diffraction experiments with anomalous scattering effect. The advantages of FFM for anomalous diffraction were absorption correction without approximation, rapid data collection by an area detector and good signal-to-noise ratio data by focusing optics. In the X-ray diffraction experiments of CoFe2O4 and Fe3O4 (By FFM) using X-rays near the Fe K absorption edge, the anomalous scattering effect between Fe/Co or Fe2+/Fe3+ can be clearly detected, due to the change of diffraction intensity. The change of observed diffraction intensity as the incident X-ray energy was consistent with the calculation. The FFM is expected to be a method for anomalous powder diffraction.

Rietveld analysis using powder diffraction data with anomalous scattering effect obtained by focused beam flat sample method

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

Tanaka, Masahiko, E-mail: masahiko@spring8.or.jp; Katsuya, Yoshio, E-mail: katsuya@spring8.or.jp; Sakata, Osami, E-mail: SAKATA.Osami@nims.go.jp

2016-07-27

Focused-beam flat-sample method (FFM) is a new trial for synchrotron powder diffraction method, which is a combination of beam focusing optics, flat shape powder sample and area detectors. The method has advantages for X-ray diffraction experiments applying anomalous scattering effect (anomalous diffraction), because of 1. Absorption correction without approximation, 2. High intensity X-rays of focused incident beams and high signal noise ratio of diffracted X-rays 3. Rapid data collection with area detectors. We applied the FFM to anomalous diffraction experiments and collected synchrotron X-ray powder diffraction data of CoFe{sub 2}O{sub 4} (inverse spinel structure) using X-rays near Fe K absorptionmore » edge, which can distinguish Co and Fe by anomalous scattering effect. We conducted Rietveld analyses with the obtained powder diffraction data and successfully determined the distribution of Co and Fe ions in CoFe{sub 2}O{sub 4} crystal structure.« less

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

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

Wikman, Linnea E. K.; Krasotkina, Julya; Kuchumova, Anastasia

2005-04-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2{sub 1}, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity atmore » physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2{sub 1} space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment.« less

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.

Protein Crystallography from the Perspective of Technology Developments

PubMed Central

Su, Xiao-Dong; Zhang, Heng; Terwilliger, Thomas C.; Liljas, Anders; Xiao, Junyu; Dong, Yuhui

2015-01-01

Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future. PMID:25983389

Effect of ion irradiation on the surface, structural and mechanical properties of brass

NASA Astrophysics Data System (ADS)

Ahmad, Shahbaz; Bashir, Shazia; Ali, Nisar; Umm-i-Kalsoom; Yousaf, Daniel; Faizan-ul-Haq; Naeem, Athar; Ahmad, Riaz; Khlaeeq-ur-Rahman, M.

2014-04-01

Modifications to the surface, structural and mechanical properties of brass after ion irradiation have been investigated. Brass targets were bombarded by carbon ions of 2 MeV energy from a Pelletron linear accelerator for various fluences ranging from 56 × 1012 to 26 × 1013 ions/cm2. A scanning electron microscope and X-ray diffractometer were utilized to analyze the surface morphology and crystallographic structure respectively. To explore the mechanical properties e.g., yield stress, ultimate tensile strength and microhardness of irradiated brass, an universal tensile testing machine and Vickers microhardness tester were used. Scanning electron microscopy results revealed an irregular and randomly distributed sputter morphology for a lower ion fluence. With increasing ion fluence, the incoherently shaped structures were transformed into dendritic structures. Nano/micro sized craters and voids, along with the appearance of pits, were observed at the maximum ion fluence. From X-ray diffraction results, no new phases were observed to be formed in the brass upon irradiation. However, a change in the peak intensity and higher and lower angle shifting were observed, which represents the generation of ion-induced defects and stresses. Analyses confirmed modifications in the mechanical properties of irradiated brass. The yield stress, ultimate tensile strength and hardness initially decreased and then increased with increasing ion fluence. The changes in the mechanical properties of irradiated brass are well correlated with surface and crystallographic modifications and are attributed to the generation, augmentation, recombination and annihilation of the ion-induced defects.

Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

NASA Technical Reports Server (NTRS)

Gendreau, Keith (Inventor); Martins, Jose Vanderlei (Inventor); Arzoumanian, Zaven (Inventor)

2010-01-01

An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.

Philip A. Parilla | NREL

Science.gov Websites

atomic layer deposition for applications. He also manages the majority of X-ray characterization equipment at NREL, specifically X-ray diffraction and X-ray fluorescence instrumentation. Additionally, he for EERE's Hydrogen Storage program. He is also an expert in X-ray diffraction and X-ray fluorescence

Coherent X-ray diffraction imaging of nanoengineered polymeric capsules

NASA Astrophysics Data System (ADS)

Erokhina, S.; Pastorino, L.; Di Lisa, D.; Kiiamov, A. G.; Faizullina, A. R.; Tayurskii, D. A.; Iannotta, S.; Erokhin, V.

2017-10-01

For the first time, nanoengineered polymeric capsules and their architecture have been studied with coherent X-ray diffraction imaging technique. The use of coherent X-ray diffraction imaging technique allowed us to analyze the samples immersed in a liquid. We report about the significant difference between polymeric capsule architectures under dry and liquid conditions.

X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

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

Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou

Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction datamore » were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC222 1, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.« less

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

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

Murray, Thomas D.; Johns Hopkins University School of Medicine, Baltimore, MD 21205; Lyubimov, Artem Y.

A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-ray diffraction data collection using microfocus beamlines and XFELs. Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming themore » challenges intrinsic to microcrystal analysis is to pair so-called ‘fixed-target’ sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.« less

Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography.

PubMed

Ishchenko, Andrii; Cherezov, Vadim; Liu, Wei

2016-09-20

Membrane proteins (MPs) are essential components of cellular membranes and primary drug targets. Rational drug design relies on precise structural information, typically obtained by crystallography; however MPs are difficult to crystallize. Recent progress in MP structural determination has benefited greatly from the development of lipidic cubic phase (LCP) crystallization methods, which typically yield well-diffracting, but often small crystals that suffer from radiation damage during traditional crystallographic data collection at synchrotron sources. The development of new-generation X-ray free-electron laser (XFEL) sources that produce extremely bright femtosecond pulses has enabled room temperature data collection from microcrystals with no or negligible radiation damage. Our recent efforts in combining LCP technology with serial femtosecond crystallography (LCP-SFX) have resulted in high-resolution structures of several human G protein-coupled receptors, which represent a notoriously difficult target for structure determination. In the LCP-SFX technique, LCP is recruited as a matrix for both growth and delivery of MP microcrystals to the intersection of the injector stream with an XFEL beam for crystallographic data collection. It has been demonstrated that LCP-SFX can substantially improve the diffraction resolution when only sub-10 µm crystals are available, or when the use of smaller crystals at room temperature can overcome various problems associated with larger cryocooled crystals, such as accumulation of defects, high mosaicity and cryocooling artifacts. Future advancements in X-ray sources and detector technologies should make serial crystallography highly attractive and practicable for implementation not only at XFELs, but also at more accessible synchrotron beamlines. Here we present detailed visual protocols for the preparation, characterization and delivery of microcrystals in LCP for serial crystallography experiments. These protocols include methods for conducting crystallization experiments in syringes, detecting and characterizing the crystal samples, optimizing crystal density, loading microcrystal laden LCP into the injector device and delivering the sample to the beam for data collection.

Structural characterization of framework–gas interactions in the metal–organic framework Co 2 (dobdc) by in situ single-crystal X-ray diffraction

DOE PAGES

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; ...

2017-04-19

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4, N 2, O 2, Ar, and P 4 adsorption in Co2(dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(II) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(II) sites in the framework that no analogous molecular structures exist,more » demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH 4 and Co–Ar interactions observed in Co 2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH 4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(II) sites in Co 2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol –1 (for Ar). Moreover, the structures of Co 2(dobdc)·3.8N 2, Co 2(dobdc)·5.9O 2, and Co 2(dobdc)·2.0Ar reveal the location of secondary (N 2, O 2, and Ar) and tertiary (O 2) binding sites in Co 2(dobdc), while high-pressure CO 2, CO, CH 4, N 2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.« less

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

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

Langkilde, Annette E., E-mail: annette.langkilde@sund.ku.dk; Morris, Kyle L.; Serpell, Louise C.

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-raymore » crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.« less

Stress-dependent crystal structure of lanthanum strontium cobalt ferrite by in situ synchrotron X-ray diffraction

NASA Astrophysics Data System (ADS)

Geiger, Philipp T.; Khansur, Neamul H.; Riess, Kevin; Martin, Alexander; Hinterstein, Manuel; Webber, Kyle G.

2018-02-01

Lanthanum strontium cobalt ferrite La1-xSrxCo1-yFeyO3-δ (LSCF) is one of the most studied mixed ionic-electronic conductor materials due to electrical and transport properties, which are attractive for intermediate temperature solid oxide fuel cells (SOFCs), oxygen permeation membranes, and catalysis. The integration of such materials, however, depends on the thermal as well as mechanical behavior. LSCF exhibits nonlinear hysteresis during compressive stress-strain measurements, marked by a remanent strain and coercive stress, i.e., ferroelasticity. However, the origin of ferroelastic behavior has not been investigated under high compressive stress. This study, therefore, investigates the microscopic origin of stress-induced mechanical behavior in polycrystalline (La0.6Sr0.4)0.95Co0.2Fe0.8O3-δ using in situ synchrotron x-ray diffraction. The data presented here reveals that the strain response originates from the intrinsic lattice strain as well as the extrinsic domain switching strain without any apparent change in crystallographic symmetry. A comparison of the calculated microscopic strain contribution with that of a macroscopic measurement indicates a significant change in the relative contributions of intrinsic and extrinsic strain depending on the applied stress state, i.e., under maximum stress and after unloading. Direct evidence of the microscopic origin of stress-strain response outlined in this paper may assist in guiding materials design with the improved mechanical reliability of SOFCs.

Influence of Ce Doping on Structural and Transport Properties of Ca1- x Ce x MnO3 ( x=0.2) Manganite

NASA Astrophysics Data System (ADS)

Varshney, Dinesh; Mansuri, Irfan

2011-01-01

We have investigated structural, electric, magnetic and thermal transport properties of electron doped Ca1- x Ce x MnO3 ( x=0.2) manganites. The Cerium substitution for Ca2+causes electron doping into insulating CaMnO3 without e g electron. At room temperature the polycrystalline Ca0.8Ce0.2MnO3 is in the crystallographic orthorhombic structure, with Pnma space group symmetry from the refinement of x-ray powder diffraction patterns. The electrical resistivity data infers that Ca0.8Ce0.2MnO3 manganite is in the semiconducting phase. A smooth linear behavior of log plot values is obtained and is well fitted with adiabatic small polaron conduction model. Nearest-neighbor hopping of a small polaron leads to a mobility with a thermally activated form. The negative values of thermopower infer electron as carriers in Ca0.8Ce0.2MnO3. From susceptibility measurements the Ce doped CaMnO3 shows a transition from antiferromagnetic (AFM) to paramagnetic (PM) phase.

Unexpected ferromagnetic interaction in a new tetranuclear copper(II) complex: synthesis, crystal structure, magnetic properties, and theoretical studies.

PubMed

Fondo, Matilde; García-Deibe, Ana M; Corbella, Monstserrat; Ruiz, Eliseo; Tercero, Javier; Sanmartín, Jesús; Bermejo, Manuel R

2005-07-11

The new tetranuclear carbonate complex [Cu2L)2(CO3)] x 8H2O (1 x 8H2O) (H3L = (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) has been obtained by two different synthetic routes and fully characterized. Recrystallization of 1 x 8H2O in methanol yields single crystals of {[(Cu2L)2(CO3)]}2 x 12H2O (1 x 6H2O), suitable for X-ray diffraction studies. The crystal structure of 1 x 6H2O shows two crystallographically different tetranuclear molecules in the asymmetric unit, 1a and 1b. Both molecules can be understood as self-assembled from two dinuclear [Cu2L]+ cations, joined by a mu4-eta(2):eta(1):eta(1) carbonate ligand. The copper atoms of each crystallographically different [(Cu2L)2(CO3)] molecule present miscellaneous coordination polyhedra: in both 1a and 1b, two metal centers are in square pyramidal environments, one displays a square planar chromophore and the other one has a geometry that can be considered as an intermediate between square pyramid and trigonal bipyramid. Magnetic studies reveal net intramolecular ferromagnetic coupling between the metal atoms. Density functional calculations allow the assignment of the different magnetic coupling constants and explain the unexpected ferromagnetic behavior, because of the presence of an unusual NCN bridging moiety and countercomplementarity of the phenoxo (or carbonate) and NCN bridges.

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

Anti-contamination device for cryogenic soft X-ray diffraction microscopy

DOE PAGES

Huang, Xiaojing; Miao, Huijie; Nelson, Johanna; ...

2011-05-01

Cryogenic microscopy allows one to view frozen hydrated biological and soft matter specimens with good structural preservation and a high degree of stability against radiation damage. We describe a liquid nitrogen-cooled anti-contamination device for cryogenic X-ray diffraction microscopy. The anti-contaminator greatly reduces the buildup of ice layers on the specimen due to condensation of residual water vapor in the experimental vacuum chamber. We show by coherent X-ray diffraction measurements that this leads to fivefold reduction of background scattering, which is important for far-field X-ray diffraction microscopy of biological specimens.

X-Ray Diffraction for In-Situ Mineralogical Analysis of Planetesimals.

NASA Astrophysics Data System (ADS)

Sarrazin, P.; Blake, D. F.; Dera, P.; Downs, R. T.; Taylor, J.

2017-12-01

X-ray diffraction (XRD) is a general purpose technique for definitive, quantitative mineralogical analysis. When combined with XRF data for sample chemistry, XRD analyses yield as complete a characterization as is possible by any spacecraft-capable techniques. The MSL CheMin instrument, the first XRD instrument flown in space, has been used to establish the quantitative mineralogy of the Mars global soil, to discover the first habitable environment on another planet, and to provide the first in-situ evidence of silicic volcanism on Mars. CheMin is now used to characterize the depositional and diagenetic environments associated with the mudstone sediments of lower strata of Mt. Sharp. Conventional powder XRD requires samples comprised of small grains presented in random orientations. In CheMin, sample cells are vibrated to cause loose powder to flow within the cell, driven by granular convection, which relaxes the requirement for fine grained samples. Nevertheless, CheMin still requires mechanisms to collect, crush, sieve and deliver samples before analysis. XTRA (Extraterrestrial Regolith Analyzer) is an evolution of CheMin intended to analyze fines in as-delivered surface regolith, without sample preparation. Fine-grained regolith coats the surfaces of most airless bodies in the solar system, and because this fraction is typically comminuted from the rocky regolith, it can often be used as a proxy for the surface as a whole. HXRD (Hybrid-XRD) is concept under development to analyze rocks or soils without sample preparation. Like in CheMin, the diffracted signal is collected with direct illumination CCD's. If the material is sufficiently fine-grained, a powder XRD pattern of the characteristic X-ray tube emission is obtained, similar to CheMin or XTRA. With coarse grained crystals, the white bremsstrahlung radiation of the tube is diffracted into Laue patterns. Unlike typical Laue applications, HXRD uses the CCD's capability to distinguish energy and analyze the "colors" of each Laue spot, which enable phase identification. The concept was demonstrated with prototypes and dedicated crystallographic software was developed for identification the minerals responsible for the Laue patterns. High TRL subsystems are under development for future deployment opportunities of these new XRD instruments.

Observation of electromigration in a Cu thin line by in situ coherent x-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Takahashi, Yukio; Nishino, Yoshinori; Furukawa, Hayato; Kubo, Hideto; Yamauchi, Kazuto; Ishikawa, Tetsuya; Matsubara, Eiichiro

2009-06-01

Electromigration (EM) in a 1-μm-thick Cu thin line was investigated by in situ coherent x-ray diffraction microscopy (CXDM). Characteristic x-ray speckle patterns due to both EM-induced voids and thermal deformation in the thin line were observed in the coherent x-ray diffraction patterns. Both parts of the voids and the deformation were successfully visualized in the images reconstructed from the diffraction patterns. This result not only represents the first demonstration of the visualization of structural changes in metallic materials by in situ CXDM but is also an important step toward studying the structural dynamics of nanomaterials using x-ray free-electron lasers in the near future.

Note: application of a pixel-array area detector to simultaneous single crystal X-ray diffraction and X-ray absorption spectroscopy measurements.

PubMed

Sun, Cheng-Jun; Zhang, Bangmin; Brewe, Dale L; Chen, Jing-Sheng; Chow, G M; Venkatesan, T; Heald, Steve M

2014-04-01

X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are two main x-ray techniques in synchrotron radiation facilities. In this Note, we present an experimental setup capable of performing simultaneous XRD and XAS measurements by the application of a pixel-array area detector. For XRD, the momentum transfer in specular diffraction was measured by scanning the X-ray energy with fixed incoming and outgoing x-ray angles. By selecting a small fixed region of the detector to collect the XRD signal, the rest of the area was available for collecting the x-ray fluorescence for XAS measurements. The simultaneous measurement of XRD and X-ray absorption near edge structure for Pr0.67Sr0.33MnO3 film was demonstrated as a proof of principle for future time-resolved pump-probe measurements. A static sample makes it easy to maintain an accurate overlap of the X-ray spot and laser pump beam.

The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm.

PubMed

Liu, Haiguang; Spence, John C H

2014-11-01

Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these 'stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.

Synchrotron x-ray scattering study of charge-density-wave order in HgBa2CuO4 +δ

NASA Astrophysics Data System (ADS)

Tabis, W.; Yu, B.; Bialo, I.; Bluschke, M.; Kolodziej, T.; Kozlowski, A.; Blackburn, E.; Sen, K.; Forgan, E. M.; Zimmermann, M. v.; Tang, Y.; Weschke, E.; Vignolle, B.; Hepting, M.; Gretarsson, H.; Sutarto, R.; He, F.; Le Tacon, M.; Barišić, N.; Yu, G.; Greven, M.

2017-10-01

We present a detailed synchrotron x-ray scattering study of the charge-density-wave (CDW) order in simple tetragonal HgBa2CuO4 +δ (Hg1201). Resonant soft x-ray scattering measurements reveal that short-range order appears at a temperature that is distinctly lower than the pseudogap temperature and in excellent agreement with a prior transient reflectivity result. Despite considerable structural differences between Hg1201 and YBa2Cu3O6 +δ , the CDW correlations exhibit similar doping dependencies, and we demonstrate a universal relationship between the CDW wave vector and the size of the reconstructed Fermi pocket observed in quantum oscillation experiments. The CDW correlations in Hg1201 vanish already below optimal doping, once the correlation length is comparable to the CDW modulation period, and they appear to be limited by the disorder potential from unit cells hosting two interstitial oxygen atoms. A complementary hard x-ray diffraction measurement, performed on an underdoped Hg1201 sample in magnetic fields along the crystallographic c axis of up to 16 T, provides information on the form factor of the CDW order. As expected from the single-CuO2-layer structure of Hg1201, the CDW correlations vanish at half-integer values of L and appear to be peaked at integer L . We conclude that the atomic displacements associated with the short-range CDW order are mainly planar, within the CuO2 layers.

Investigation of the structure of human dental tissue at multiple length scales using high energy synchrotron X-ray SAXS/WAXS

NASA Astrophysics Data System (ADS)

Sui, Tan; Landini, Gabriel; Korsunsky, Alexander M.

2011-10-01

High energy (>50keV) synchrotron X-ray scattering experiments were carried out on beamline I12 JEEP at the Diamond Light Source (DLS, Oxford, UK). Although a complete human tooth could be studied, in the present study attention was focused on coupons from the region of the Dentin-Enamel Junction (DEJ). Simultaneous high energy SAXS/WAXS measurements were carried out. Quantitative analysis of the results allows multiple length scale characterization of the nano-crystalline structure of dental tissues. SAXS patterns analysis provide insight into the mean thickness and orientation of hydroxyapatite particles, while WAXS (XRD) patterns allow the determination of the crystallographic unit cell parameters of the hydroxyapatite phase. It was found that the average particle thickness determined from SAXS interpretation varies as a function of position in the vicinity of the DEJ. Most mineral particles are randomly orientated within dentin, although preferred orientation emerges and becomes stronger on approach to the enamel. Within the enamel, texture is stronger than anywhere in the dentin, and the determination of lattice parameters can be accomplished by Pawley refinement of the multiple peak diffraction pattern. The results demonstrate the feasibility of using high energy synchrotron X-ray beams for the characterization of human dental tissues. This opens up the opportunity of studying thick samples (e.g., complete teeth) in complex sample environments (e.g., under saline solution). This opens new avenues for the application of high energy synchrotron X-ray scattering to dental research.

X-Ray Diffraction Wafer Mapping Method for Rhombohedral Super-Hetero-Epitaxy

NASA Technical Reports Server (NTRS)

Park, Yoonjoon; Choi, Sang Hyouk; King, Glen C.; Elliott, James R.; Dimarcantonio, Albert L.

2010-01-01

A new X-ray diffraction (XRD) method is provided to acquire XY mapping of the distribution of single crystals, poly-crystals, and twin defects across an entire wafer of rhombohedral super-hetero-epitaxial semiconductor material. In one embodiment, the method is performed with a point or line X-ray source with an X-ray incidence angle approximating a normal angle close to 90 deg, and in which the beam mask is preferably replaced with a crossed slit. While the wafer moves in the X and Y direction, a narrowly defined X-ray source illuminates the sample and the diffracted X-ray beam is monitored by the detector at a predefined angle. Preferably, the untilted, asymmetric scans are of {440} peaks, for twin defect characterization.

Diffraction based method to reconstruct the spectrum of the Thomson scattering x-ray source

NASA Astrophysics Data System (ADS)

Chi, Zhijun; Yan, Lixin; Zhang, Zhen; Zhou, Zheng; Zheng, Lianmin; Wang, Dong; Tian, Qili; Wang, Wei; Nie, Zan; Zhang, Jie; Du, Yingchao; Hua, Jianfei; Shi, Jiaru; Pai, Chihao; Lu, Wei; Huang, Wenhui; Chen, Huaibi; Tang, Chuanxiang

2017-04-01

As Thomson scattering x-ray sources based on the collision of intense laser and relativistic electrons have drawn much attention in various scientific fields, there is an increasing demand for the effective methods to reconstruct the spectrum information of the ultra-short and high-intensity x-ray pulses. In this paper, a precise spectrum measurement method for the Thomson scattering x-ray sources was proposed with the diffraction of a Highly Oriented Pyrolytic Graphite (HOPG) crystal and was demonstrated at the Tsinghua Thomson scattering X-ray source. The x-ray pulse is diffracted by a 15 mm (L) ×15 mm (H)× 1 mm (D) HOPG crystal with 1° mosaic spread. By analyzing the diffraction pattern, both x-ray peak energies and energy spectral bandwidths at different polar angles can be reconstructed, which agree well with the theoretical value and simulation. The higher integral reflectivity of the HOPG crystal makes this method possible for single-shot measurement.

Diffraction based method to reconstruct the spectrum of the Thomson scattering x-ray source.

PubMed

Chi, Zhijun; Yan, Lixin; Zhang, Zhen; Zhou, Zheng; Zheng, Lianmin; Wang, Dong; Tian, Qili; Wang, Wei; Nie, Zan; Zhang, Jie; Du, Yingchao; Hua, Jianfei; Shi, Jiaru; Pai, Chihao; Lu, Wei; Huang, Wenhui; Chen, Huaibi; Tang, Chuanxiang

2017-04-01

As Thomson scattering x-ray sources based on the collision of intense laser and relativistic electrons have drawn much attention in various scientific fields, there is an increasing demand for the effective methods to reconstruct the spectrum information of the ultra-short and high-intensity x-ray pulses. In this paper, a precise spectrum measurement method for the Thomson scattering x-ray sources was proposed with the diffraction of a Highly Oriented Pyrolytic Graphite (HOPG) crystal and was demonstrated at the Tsinghua Thomson scattering X-ray source. The x-ray pulse is diffracted by a 15 mm (L) ×15 mm (H)× 1 mm (D) HOPG crystal with 1° mosaic spread. By analyzing the diffraction pattern, both x-ray peak energies and energy spectral bandwidths at different polar angles can be reconstructed, which agree well with the theoretical value and simulation. The higher integral reflectivity of the HOPG crystal makes this method possible for single-shot measurement.

Gas gun shock experiments with single-pulse x-ray phase contrast imaging and diffraction at the Advanced Photon Source

NASA Astrophysics Data System (ADS)

Luo, S. N.; Jensen, B. J.; Hooks, D. E.; Fezzaa, K.; Ramos, K. J.; Yeager, J. D.; Kwiatkowski, K.; Shimada, T.

2012-07-01

The highly transient nature of shock loading and pronounced microstructure effects on dynamic materials response call for in situ, temporally and spatially resolved, x-ray-based diagnostics. Third-generation synchrotron x-ray sources are advantageous for x-ray phase contrast imaging (PCI) and diffraction under dynamic loading, due to their high photon fluxes, high coherency, and high pulse repetition rates. The feasibility of bulk-scale gas gun shock experiments with dynamic x-ray PCI and diffraction measurements was investigated at the beamline 32ID-B of the Advanced Photon Source. The x-ray beam characteristics, experimental setup, x-ray diagnostics, and static and dynamic test results are described. We demonstrate ultrafast, multiframe, single-pulse PCI measurements with unprecedented temporal (<100 ps) and spatial (˜2 μm) resolutions for bulk-scale shock experiments, as well as single-pulse dynamic Laue diffraction. The results not only substantiate the potential of synchrotron-based experiments for addressing a variety of shock physics problems, but also allow us to identify the technical challenges related to image detection, x-ray source, and dynamic loading.

Effect of structural in-depth heterogeneities on electrical properties of Pb(Zr0.52Ti0.48) O3 thin films as revealed by nano-beam X-ray diffraction

NASA Astrophysics Data System (ADS)

Vaxelaire, N.; Kovacova, V.; Bernasconi, A.; Le Rhun, G.; Alvarez-Murga, M.; Vaughan, G. B. M.; Defay, E.; Gergaud, P.

2016-09-01

A direct quantification of a structural in-depth composition in the lead zirconate titanate Pb(Zr,Ti)O3 thin films of morphotropic composition has been conducted using the newly available X-ray nano-pencil beam (i.e., beam size of 100 nm × 1 μm) diffraction approach. We tested two samples with different Zr/Ti chemical gradients. Here, we demonstrate the presence of a significant microstructural gradient between the rhombohedral and tetragonal phases through PbZrxTi1-xO3 (PZT) films with a 100 nm in-depth resolution. The phase gradient extends over around 350 nm, and it is repeated through the PZT film three times, which corresponds to the number of thermal annealings. Moreover, this microstructural gradient is in agreement with the Zr/Ti chemical gradient observed by the secondary ion mass spectroscopy (SIMS). Indeed, the quantity of tetragonal phases rises in the Ti-rich zones as revealed by SIMS, and the quantity of rhombohedral phases rises in the Zr-rich zones. We also demonstrated a huge difference in the in-depth phase variation between the two tested samples. The gradient free sample still contains 4.7% of phase variation through the film and the amplified gradient contains 9.6% of phase variation through the film. Knowing that the gradient free sample shows better electric and piezoelectric coefficients, one can draw a correlation between the chemical composition, crystallographic homogeneity, and electro-mechanical properties of the film. The more close the film is to the morphotropic composition and the more it is crystallographically homogeneous, the higher the piezoelectric coefficients of the PZT are. Finally, the adequate knowledge of phase variation and its relation to the fabrication technique are crucial for the enhancement of the PZT electro-mechanical properties. Our methodology and findings open up new perspectives in establishing a relevant quantitative feedback to reach an ultimate electro-mechanical coupling in the sol-gel PZT thin films.

Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

PubMed Central

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

2017-01-01

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

Energetic Materials for Bio-Agent Destruction

DTIC Science & Technology

2017-03-01

Delocalization of electrons in 4 The structure of 5 was obtained by X-ray single crystal crystallography . The crystallographic data are summarized in...4 22.2 49.6 - - 8.36 5 18.8 41.7 - - 5.07 The structure of 5 was obtained by X-ray single crystal crystallography . The

X-ray and neutron diffraction studies of crystallinity in hydroxyapatite coatings.

PubMed

Girardin, E; Millet, P; Lodini, A

2000-02-01

To standardize industrial implant production and make comparisons between different experimental results, we have to be able to quantify the crystallinity of hydroxyapatite. Methods of measuring crystallinity ratio were developed for various HA samples before and after plasma spraying. The first series of methods uses X-ray diffraction. The advantage of these methods is that X-ray diffraction equipment is used widely in science and industry. In the second series, a neutron diffraction method is developed and the results recorded are similar to those obtained by the modified X-ray diffraction methods. The advantage of neutron diffraction is the ability to obtain measurements deep inside a component. It is a nondestructive method, owing to the very low absorption of neutrons in most materials. Copyright 2000 John Wiley & Sons, Inc.

X-ray Diffraction Gratings for Astrophysics

NASA Astrophysics Data System (ADS)

Paerels, Frits

2010-12-01

Over the past year, we have celebrated the tenth anniversary of the Chandra and XMM-Newton X-ray observatories. Both carry powerful, novel diffraction grating spectrometers, which have opened true X-ray spectroscopy for astrophysics. I will describe the design and operation of these instruments, as the background to some of the beautiful results they have produced. But these designs do not exhaust the versatility and essential simplicity of diffraction grating spectrometers, and I will discuss applications for the International X-ray Observatory IXO.

Amorphous boron gasket in diamond anvil cell research

NASA Astrophysics Data System (ADS)

Lin, Jung-Fu; Shu, Jinfu; Mao, Ho-kwang; Hemley, Russell J.; Shen, Guoyin

2003-11-01

Recent advances in high-pressure diamond anvil cell experiments include high-energy synchrotron x-ray techniques as well as new cell designs and gasketing procedures. The success of high-pressure experiments usually depends on a well-prepared sample, in which the gasket plays an important role. Various gasket materials such as diamond, beryllium, rhenium, and stainless steel have been used. Here we introduce amorphous boron as another gasket material in high-pressure diamond anvil cell experiments. We have applied the boron gasket for laser-heating x-ray diffraction, radial x-ray diffraction, nuclear resonant inelastic x-ray scattering, and inelastic x-ray scattering. The high shear strength of the amorphous boron maximizes the thickness of the sample chamber and increases the pressure homogeneity, improving the quality of high-pressure data. Use of amorphous boron avoids unwanted x-ray diffraction peaks and reduces the absorption of incident and x rays exiting the gasket material. The high quality of the diffraction patterns makes it possible to refine the cell parameters with powder x-ray diffraction data under high pressure and high temperature. The reactivity of boron prevents its use at high temperatures, however. When heated, boron may also react with the specimen to produce unwanted phases. The relatively porous boron starting material at ambient conditions also poses some challenges for sample preparation.

X-Ray Sum Frequency Diffraction for Direct Imaging of Ultrafast Electron Dynamics

NASA Astrophysics Data System (ADS)

Rouxel, Jérémy R.; Kowalewski, Markus; Bennett, Kochise; Mukamel, Shaul

2018-06-01

X-ray diffraction from molecules in the ground state produces an image of their charge density, and time-resolved x-ray diffraction can thus monitor the motion of the nuclei. However, the density change of excited valence electrons upon optical excitation can barely be monitored with regular diffraction techniques due to the overwhelming background contribution of the core electrons. We present a nonlinear x-ray technique made possible by novel free electron laser sources, which provides a spatial electron density image of valence electron excitations. The technique, sum frequency generation carried out with a visible pump and a broadband x-ray diffraction pulse, yields snapshots of the transition charge densities, which represent the electron density variations upon optical excitation. The technique is illustrated by ab initio simulations of transition charge density imaging for the optically induced electronic dynamics in a donor or acceptor substituted stilbene.

Effect of Citric Acid Surface Modification on Solubility of Hydroxyapatite Nanoparticles.

PubMed

Samavini, Ranuri; Sandaruwan, Chanaka; De Silva, Madhavi; Priyadarshana, Gayan; Kottegoda, Nilwala; Karunaratne, Veranja

2018-04-04

Worldwide, there is an amplified interest in nanotechnology-based approaches to develop efficient nitrogen, phosphorus, and potassium fertilizers to address major challenges pertaining to food security. However, there are significant challenges associated with fertilizer manufacture and supply as well as cost in both economic and environmental terms. The main issues relating to nitrogen fertilizer surround the use of fossil fuels in its production and the emission of greenhouse gases resulting from its use in agriculture; phosphorus being a mineral source makes it nonrenewable and casts a shadow on its sustainable use in agriculture. This study focuses on development of an efficient P nutrient system that could overcome the inherent problems arising from current P fertilizers. Attempts are made to synthesize citric acid surface-modified hydroxyapatite nanoparticles using wet chemical precipitation. The resulting nanohybrids were characterized using powder X-ray diffraction to extract the crystallographic data, while functional group analysis was done by Fourier transform infrared spectroscopy. Morphology and particle size were studied using scanning electron microscopy along with elemental analysis using energy-dispersive X-ray diffraction spectroscopy. Its effectiveness as a source of P was investigated using water release studies and bioavailability studies using Zea mays as the model crop. Both tests demonstrated the increased availability of P from nanohybrids in the presence of an organic acid compared with pure hydroxyapatite nanoparticles and rock phosphate.

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

Huang, J. Y.; E, J. C.; Huang, J. W.

Impact fracture of single-crystal Si is critical to long-term reliability of electronic devices and solar cells for its wide use as components or substrates in semiconductor industry. Single-crystal Si is loaded along two different crystallographic directions with a split Hopkinson pressure bar integrated with an in situ x-ray imaging and diffraction system. Bulk stress histories are measured, simultaneously with x-ray phase contrast imaging (XPCI) and Laue diffraction. Damage evolution is quantified with grayscale maps from XPCI. Single-crystal Si exhibits pronounced anisotropy in fracture modes, and thus fracture strengths and damage evolution. For loading along [11¯ 0] and viewing along [001],more » (1¯1¯0)[11¯ 0] cleavage is activated and induces horizontal primary cracks followed by perpendicular wing cracks. However, for loading along [011¯] and viewing along [111], random nucleation and growth of shear and tensile-splitting crack networks lead to catastrophic failure of materials with no cleavage. The primary-wing crack mode leads to a lower characteristic fracture strength due to predamage, but a more concentrated strength distribution, i.e., a higher Weibull modulus, compared to the second loading case. Furthermore, the sequential primary cracking, wing cracking and wing-crack coalescence processes result in a gradual increase of damage with time, deviating from theoretical predictions. Particle size and aspect ratios of fragments are discussed with postmortem fragment analysis, which verifies fracture modes observed in XPCI.« less

Quantitative determination of occupation sites of trace Co substituted for multiple Fe sites in M-type hexagonal ferrite using statistical beam-rocking TEM-EDXS analysis.

PubMed

Ohtsuka, Masahiro; Muto, Shunsuke; Tatsumi, Kazuyoshi; Kobayashi, Yoshinori; Kawata, Tsunehiro

2016-04-01

The occupation sites and the occupancies of trace dopants in La/Co co-doped Sr-M-type ferrite, SrFe12O19, were quantitatively and precisely determined by beam-rocking energy-dispersive X-ray spectroscopy (EDXS) on the basis of electron-channeling effects. Because the Co atoms, in particular, should be partially substituted for the five crystallographically inequivalent sites, which could be key parameters in improving the magneto-crystalline anisotropy, it is difficult yet intriguing to discover their occupation sites and occupancies without using the methods of large-scale facilities, such as neutron diffraction and synchrotron radiation. In the present study, we tackled this problem by applying an extended statistical atom location by channeling enhanced microanalysis method, using conventional transmission electron microscopy, EDXS and dynamical electron elastic/inelastic scattering theories. The results show that the key occupation sites of Co were the 2a, 4f1 and 12k sites. The quantified occupancies of Co were consistent with those of the previous study, which involved a combination of neutron diffraction and extended X-ray absorption fine structure analysis, as well as energetics considerations based on by first-principles calculations. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-l-homocysteine hydrolase (Lupinus luteus)

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

Brzezinski, Krzysztof; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan; Bujacz, Grzegorz

2008-07-01

Single crystals of recombinant S-adenosyl-l-homocysteine hydrolase from L. luteus in complex with adenosine diffract X-rays to 1.17 Å resolution at 100 K. The crystals are tetragonal, space group P4{sub 3}2{sub 1}2, and contain one copy of the dimeric enzyme in the asymmetric unit. By degrading S-adenosyl-l-homocysteine, which is a byproduct of S-adenosyl-l-methionine-dependent methylation reactions, S-adenosyl-l-homocysteine hydrolase (SAHase) acts as a regulator of cellular methylation processes. S-Adenosyl-l-homocysteine hydrolase from the leguminose plant yellow lupin (Lupinus luteus), LlSAHase, which is composed of 485 amino acids and has a molecular weight of 55 kDa, has been cloned, expressed in Escherichia coli and purified.more » Crystals of LlSAHase in complex with adenosine were obtained by the hanging-drop vapour-diffusion method using 20%(w/v) PEG 4000 and 10%(v/v) 2-propanol as precipitants in 0.1 M Tris–HCl buffer pH 8.0. The crystals were tetragonal, space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = 122.4, c = 126.5 Å and contained two protein molecules in the asymmetric unit, corresponding to the functional dimeric form of the enzyme. Atomic resolution (1.17 Å) X-ray diffraction data have been collected using synchrotron radiation.« less

The influence of sequence of precursor films on CZTSe thin films prepared by ion-beam sputtering deposition

NASA Astrophysics Data System (ADS)

Zhao, Jun; Liang, Guangxing; Zeng, Yang; Fan, Ping; Hu, Juguang; Luo, Jingting; Zhang, Dongping

2017-02-01

The CuZnSn (CZT) precursor thin films are grown by ion-beam sputtering Cu, Zn, Sn targets with different orders and then sputtering Se target to fabricate Cu2ZnSnSe4 (CZTSe) absorber thin films on molybdenum substrates. They are annealed in the same vacuum chamber at 400 °C. The characterization methods of CZTSe thin films include X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and X-ray photoelectron spectra (XPS) in order to study the crystallographic properties, composition, surface morphology, electrical properties and so on. The results display that the CZTSe thin films got the strongest diffraction peak intensity and were with good crystalline quality and its morphology appeared smooth and compact with a sequence of Cu/Zn/Sn/Se, which reveals that the expected states for CZTSe are Cu1+, Zn2+, Sn4+, Se2+. With the good crystalline quality and close to ideal stoichiometric ratio the resistivity of the CZTSe film with the sequence of Cu/Zn/Sn/Se is lower, whose optical band gap is about 1.50 eV. Project supported by the National Natural Science Foundation of China (No. 61404086), the Basical Research Program of Shenzhen (Nos. JCYJ20150324140036866, JCYJ20150324141711581), and the Natural Science Foundation of SZU (No. 2014017).

Effect of crystallographic orientation on structural and mechanical behaviors of Ni-Ti thin films irradiated by Ag7+ ions

NASA Astrophysics Data System (ADS)

Kumar, Veeresh; Singhal, Rahul

2018-04-01

In the present study, thin films of Ni-Ti shape memory alloy have been grown on Si substrate by dc magnetron co-sputtering technique using separate sputter targets Ni and Ti. The prepared thin films have been irradiated by 100 MeV Ag7+ ions at three different fluences, which are 1 × 1012, 5 × 1012, and 1 × 1013 ions/cm2. The elemental composition and depth profile of pristine film have been investigated by Rutherford backscattering spectrometry. The changes in crystal orientation, surface morphology, and mechanical properties of Ni-Ti thin films before and after irradiation have been studied by X-ray diffraction, atomic force microscopy, field-emission scanning electron microscopy, and nanoindentation techniques, respectively. X-ray diffraction measurement has revealed the existence of both austenite and martensite phases in pristine film and the formation of precipitate on the surface of the film after irradiation at an optimized fluence of 1 × 1013 ions/cm2. Nanoindentation measurement has revealed improvement in mechanical properties of Ni-Ti thin films after ion irradiation via increasing hardness and Young modulus due to the formation of precipitate and ductile phase. The improvement in mechanical behavior could be explained in terms of precipitation hardening and structural change of Ni-Ti thin film after irradiation by Swift heavy ion irradiation.

In situ high temperature X-Ray diffraction study of the phase equilibria in the UO2-PuO2-Pu2O3 system

NASA Astrophysics Data System (ADS)

Belin, Renaud C.; Strach, Michal; Truphémus, Thibaut; Guéneau, Christine; Richaud, Jean-Christophe; Rogez, Jacques

2015-10-01

The region of the U-Pu-O phase diagram delimited by the compounds UO2-PuO2-Pu2O3 is known to exhibit a miscibility gap at low temperature. Consequently, MOX fuels with a composition entering this region could decompose into two fluorite phases and thus exhibit chemical heterogeneities. The experimental data on this domain found in the literature are scarce and usually provided using DTA that is not suitable for the investigation of such decomposition phenomena. In the present work, new experimental data, i.e. crystallographic phases, lattice parameters, phase fractions and temperature of phase separation, were measured in the composition range 0.14 < Pu/(U + Pu) < 0.62 and 1.85 < O/(U + Pu) < 2 from 298 to 1750 K using a novel in situ high temperature X-ray diffraction apparatus. A very good agreement is found between the temperature of phase separation determined from our results and using the thermodynamic model of the U-Pu-O system based on the CALPHAD method. Also, the combined use of thermodynamic calculations and XRD results refinement proved helpful in the determination of the O/M ratio of the samples during cooling. The methodology used in the current work might be useful to investigate other oxides systems exhibiting a miscibility gap.

Niclosamide methanol solvate and niclosamide hydrate: structure, solvent inclusion mode and implications for properties.

PubMed

Harriss, Bethany I; Wilson, Claire; Radosavljevic Evans, Ivana

2014-08-01

Structural studies have been carried out of two solid forms of niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide, NCL], a widely used anthelmintic drug, namely niclosamide methanol monosolvate, C13H8Cl2N2O4·CH3OH or NCL·MeOH, and niclosamide monohydrate, denoted HA. The structure of the methanol solvate obtained from single-crystal X-ray diffraction is reported for the first time, elucidating the key host-guest hydrogen-bonding interactions which lead to solvate formation. The essentially planar NCL host molecules interact via π-stacking and pack in a herringbone-type arrangement, giving rise to channels along the crystallographic a axis in which the methanol guest molecules are located. The methanol and NCL molecules interact via short O-H...O hydrogen bonds. Laboratory powder X-ray diffraction (PXRD) measurements reveal that the initially phase-pure NCL·MeOH solvate readily transforms into NCL monohydrate within hours under ambient conditions. PXRD further suggests that the NCL monohydrate, HA, is isostructural with the NCL·MeOH solvate. This is consistent with the facile transformation of the methanol solvate into the hydrate when stored in air. The crystal packing and the topology of guest-molecule inclusion are compared with those of other NCL solvates for which the crystal structures are known, giving a consistent picture which correlates well with known experimentally observed desolvation properties.

In situ synchrotron high-energy X-ray diffraction study of microscopic deformation behavior of a hard-soft dual phase composite containing phase transforming matrix

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

Zhang, Junsong; Hao, Shijie; Jiang, Daqiang

This study explored a novel intermetallic composite design concept based on the principle of lattice strain matching enabled by the collective atomic load transfer. It investigated the hard-soft microscopic deformation behavior of a Ti3Sn/TiNi eutectic hard-soft dual phase composite by means of in situ synchrotron high-energy X-ray diffraction (HE-XRD) during compression. The composite provides a unique micromechanical system with distinctive deformation behaviors and mechanisms from the two components, with the soft TiNi matrix deforming in full compliance via martensite variant reorientation and the hard Ti3Sn lamellae deforming predominantly by rigid body rotation, producing a crystallographic texture for the TiNi matrixmore » and a preferred alignment for the Ti3Sn lamellae. HE-XRD reveals continued martensite variant reorientation during plastic deformation well beyond the stress plateau of TiNi. The hard and brittle Ti3Sn is also found to produce an exceptionally large elastic strain of 1.95% in the composite. This is attributed to the effect of lattice strain matching between the transformation lattice distortion of the TiNi matrix and the elastic strain of Ti3Sn lamellae. With such unique micromechanic characteristics, the composite exhibits high strength and large ductility.« less

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.

Crystallization and preliminary crystallographic analysis of a family 43 β-d-xylosidase from Geobacillus stearothermophilus T-6

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

Brüx, Christian; Niefind, Karsten; Ben-David, Alon

2005-12-01

The crystallization and preliminary X-ray analysis of a β-d-xylosidase from G. stearothermophilus T-6, a family 43 glycoside hydrolase, is described. Native and catalytic inactive mutants of the enzymes were crystallized in two different space groups, orthorhombic P2{sub 1}2{sub 1}2 and tetragonal P4{sub 1}2{sub 1}2 (or the enantiomorphic space group P4{sub 3}2{sub 1}2), using a sensitive cryoprotocol. The latter crystal form diffracted X-rays to a resolution of 2.2 Å. β-d-Xylosidases (EC 3.2.1.37) are hemicellulases that cleave single xylose units from the nonreducing end of xylooligomers. In this study, the crystallization and preliminary X-ray analysis of a β-d-xylosidase from Geobacillus stearothermophilus T-6more » (XynB3), a family 43 glycoside hydrolase, is described. XynB3 is a 535-amino-acid protein with a calculated molecular weight of 61 891 Da. Purified recombinant native and catalytic inactive mutant proteins were crystallized and cocrystallized with xylobiose in two different space groups, P2{sub 1}2{sub 1}2 (unit-cell parameters a = 98.32, b = 99.36, c = 258.64 Å) and P4{sub 1}2{sub 1}2 (or the enantiomorphic space group P4{sub 3}2{sub 1}2; unit-cell parameters a = b = 140.15, c = 233.11 Å), depending on the detergent. Transferring crystals to cryoconditions required a very careful protocol. Orthorhombic crystals diffract to 2.5 Å and tetragonal crystals to 2.2 Å.« less

Growth and characterization of single phase Cu{sub 2}O by thermal oxidation of thin copper films

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

Choudhary, Sumita; Sarma, J. V. N.; Gangopadhyay, Subhashis, E-mail: subhagan@yahoo.com

2016-04-13

We report a simple and efficient technique to form high quality single phase cuprous oxide films on glass substrate using thermal evaporation of thin copper films followed by controlled thermal oxidation in air ambient. Crystallographic analysis and oxide phase determination, as well as grain size distribution have been studied using X-ray diffraction (XRD) method, while scanning electron microscopy (SEM) has been utilized to investigate the surface morphology of the as grown oxide films. The formation of various copper oxide phases is found to be highly sensitive to the oxidation temperature and a crystalline, single phase cuprous oxide film can bemore » achieved for oxidation temperatures between 250°C to 320°C. Cu{sub 2}O film surface appeared in a faceted morphology in SEM imaging and a direct band gap of about 2.1 eV has been observed in UV-visible spectroscopy. X-ray photoelectron spectroscopy (XPS) confirmed a single oxide phase formation. Finally, a growth mechanism of the oxide film has also been discussed.« less

Microwave-assisted hydrothermal synthesis of marigold-like ZnIn2S4 microspheres and their visible light photocatalytic activity

NASA Astrophysics Data System (ADS)

Chen, Zhixin; Li, Danzhen; Xiao, Guangcan; He, Yunhui; Xu, Yi-Jun

2012-02-01

Marigold-like ZnIn2S4 microspheres were synthesized by a microwave-assisted hydrothermal method with the temperature ranging from 80 to 195 °C. X-ray diffraction, X-ray photoelectron spectroscopy, nitrogen sorption analysis, UV-visible spectroscopy, scanning electron microscopy and transmission electron microscopy were used to characterize the products. It was found that the crystallographic structure and optical property of the products synthesized at different temperatures were almost the same. The degradation of methyl orange (MO) under the visible light irradiation has been used as a probe reaction to investigate the photocatalytic activity of as-prepared ZnIn2S4, which shows that the ZnIn2S4 sample synthesized at 195 °C shows the best photocatalytic activity for MO degradation. In addition, the photocatalytic activities of all the samples prepared by the microwave-assisted hydrothermal method are better than those prepared by a normal hydrothermal method, which could be attributed to the formation of more defect sites during the microwave-assisted hydrothermal treatment.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of erythronate-4-phosphate dehydrogenase from Pseudomonas aeruginosa.

PubMed

Ha, Jun Yong; Lee, Ji Hyun; Kim, Kyoung Hoon; Kim, Do Jin; Lee, Hyung Ho; Kim, Hye-Kyung; Yoon, Hye-Jin; Suh, Se Won

2006-02-01

The enzyme erythronate-4-phosphate dehydrogenase catalyses the conversion of erythronate-4-phosphate to 3-hydroxy-4-phospho-hydroxy-alpha-ketobutyrate. It belongs to the D-isomer-specific 2-hydroxyacid dehydrogenase family. It is essential for de novo biosynthesis of vitamin B6 (pyridoxine). Erythronate-4-phosphate dehydrogenase from Pseudomonas aeruginosa, a homodimeric enzyme consisting of two identical 380-residue subunits, has been overexpressed in Escherichia coli with a C-terminal purification tag and crystallized at 297 K using 0.7 M ammonium dihydrogen phosphate, 0.4 M ammonium tartrate, 0.1 M sodium citrate pH 5.6 and 10 mM cupric chloride. X-ray diffraction data were collected to 2.20 A from a crystal grown in the presence of NADH. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 84.77, b = 101.28, c = 142.58 A. A dimeric molecule is present in the asymmetric unit, giving a crystal volume per protein weight (VM) of 3.64 A3 Da(-1) and a solvent content of 66%.

Giant magnetostriction effect near onset of spin reorientation in MnBi

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

Choi, Y.; Ryan, P. J.; McGuire, Michael A.

In materials undergoing spontaneous symmetry breaking transitions, the emergence of multiple competing order parameters is pervasive. Employing in-field x-ray diffraction, we investigate the temperature and magnetic field dependence of the crystallographic structure of MnBi, elucidating the microscopic interplay between lattices and spin. The hexagonal phase of MnBi undergoes a spin reorientation transition (TSR), whereby the easy axis direction changes from the c axis to the basal plane. Across TSR, an abrupt symmetry change is accompanied by a clear sign change in the magnetostrictive coefficient, revealing that this transition corresponds to the onset of the spin reorientation. In the vicinity ofmore » TSR, a significantly larger in-plane magnetostrictive effect is observed, presenting the emergence of an intermediate phase that is highly susceptible to an applied magnetic field. X-ray linear dichroism shows that asymmetric Bi and Mn p orbitals do not play a role in the spin reorientation. Furthermore, this work suggests that the spin reorientation is caused by structural modification rather than changes in the local electronic configuration, providing a strategy for manipulating the magnetic anisotropy by external strain.« less

Giant magnetostriction effect near onset of spin reorientation in MnBi

DOE PAGES

Choi, Y.; Ryan, P. J.; McGuire, Michael A.; ...

2018-05-11

In materials undergoing spontaneous symmetry breaking transitions, the emergence of multiple competing order parameters is pervasive. Employing in-field x-ray diffraction, we investigate the temperature and magnetic field dependence of the crystallographic structure of MnBi, elucidating the microscopic interplay between lattices and spin. The hexagonal phase of MnBi undergoes a spin reorientation transition (TSR), whereby the easy axis direction changes from the c axis to the basal plane. Across TSR, an abrupt symmetry change is accompanied by a clear sign change in the magnetostrictive coefficient, revealing that this transition corresponds to the onset of the spin reorientation. In the vicinity ofmore » TSR, a significantly larger in-plane magnetostrictive effect is observed, presenting the emergence of an intermediate phase that is highly susceptible to an applied magnetic field. X-ray linear dichroism shows that asymmetric Bi and Mn p orbitals do not play a role in the spin reorientation. Furthermore, this work suggests that the spin reorientation is caused by structural modification rather than changes in the local electronic configuration, providing a strategy for manipulating the magnetic anisotropy by external strain.« less

The effect of cerium oxide argon-annealed coatings on the high temperature oxidation of a FeCrAl alloy

NASA Astrophysics Data System (ADS)

Nguyen, C. T.; Buscail, H.; Cueff, R.; Issartel, C.; Riffard, F.; Perrier, S.; Poble, O.

2009-09-01

Ceria coatings were applied in order to improve the adherence of alumina scales developed on a model Fe-20Cr-5Al alloy during oxidation at high temperature. These coatings were performed by argon annealing of a ceria sol-gel coating at temperatures ranging between 600 and 1000 °C. The influence of these coatings on the alloy oxidation behaviour was studied at 1100 °C. In situ X-ray diffraction (XRD) was performed to characterize the coating crystallographic nature after annealing and during the oxidation process. The alumina scale morphologies were studied by means of scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDS). The present work shows that the alumina scale morphology observed on cerium sol-gel coated alloy was very convoluted. On the cerium sol-gel coated alloy, argon annealing results in an increase of the oxidation rate in air, at 1100 °C. The 600 °C argon annealing temperature results in a good alumina scale adherence under thermal cycling conditions at 1100 °C.

Crystallographic X-ray analyses of Yb@C(2v)(3)-C80 reveal a feasible rule that governs the location of a rare earth metal inside a medium-sized fullerene.

PubMed

Lu, Xing; Lian, Yongfu; Beavers, Christine M; Mizorogi, Naomi; Slanina, Zdenek; Nagase, Shigeru; Akasaka, Takeshi

2011-07-20

Single crystal X-ray diffraction studies of Yb@C(2v)(3)-C(80)·Ni(II)(OEP)·CS(2)·1.5C(6)H(6) (OEP = octaethylporphinate) reveal that a relatively flat region of the fullerene interacts with the Ni(II)(OEP) molecule, featuring shape-matching interactions. Surprisingly, it is found that the internal metal is located under a hexagonal carbon ring apart from the 2-fold axis of the C(2v)(3)-C(80) cage, presenting the first example of metallofullerenes with an asymmetrically positioned metal. Such an anomalous location of Yb(2+) is associated with its strong ability to pursue a large coordination number and the lack of hexagon along the C(2) axis of C(2v)(3)-C(80). It is accordingly assumed that a suitable cage hexagon is most likely to be preferred by the single rare earth metal to stay behind inside a medium-sized fullerene, such as C(80) and C(82).

Syntheses, characterisation and crystal structures of ferrocenyl β-diketones and their Schiff base Nsbnd Nsbnd O ligand derivatives with 2-picolylamine

NASA Astrophysics Data System (ADS)

Artigas, Vania; González, Deborah; Fuentealba, Mauricio

2017-02-01

Ferrocenyl β-diketones compounds β3-4 were synthesised by Claisen condensation reaction between acetylferrocene and ethyl benzoate or 4-bromoethyl benzoate. We also synthesised four new Schiff base ligands L1-4 by condensation reaction between β1-4 and 2-picolylamine. Identities of all these compounds were confirmed by satisfactory elemental analysis, 1H nuclear magnetic resonance (NMR) correlation and infrared (IR) spectroscopy. In addition, all these compounds were authenticated by a single-crystal X-ray diffraction analysis. In solution, 1H NMR spectra of β3 and β4 exhibit a mixture of keto:enol tautomer ratios of 12:88 and 8:92, respectively, calculated by the integration of the free cyclopentadienyl ring. In contrast, the proton NMR spectra of L1-4 showed only the keto-enamine tautomer displacements. In addition, decoupled 13C NMR spectrum clearly confirmed the existence of these tautomers. These results are in accordance with X-ray crystallographic studies, in which the enol and keto-enamine forms were elucidated for β-diketones and Schiff base ligands, respectively.

Giant magnetostriction effect near onset of spin reorientation in MnBi

NASA Astrophysics Data System (ADS)

Choi, Y.; Ryan, P. J.; McGuire, M. A.; Sales, B. C.; Kim, J.-W.

2018-05-01

In materials undergoing spontaneous symmetry breaking transitions, the emergence of multiple competing order parameters is pervasive. Employing in-field x-ray diffraction, we investigate the temperature and magnetic field dependence of the crystallographic structure of MnBi, elucidating the microscopic interplay between lattices and spin. The hexagonal phase of MnBi undergoes a spin reorientation transition (TSR), whereby the easy axis direction changes from the c axis to the basal plane. Across TSR, an abrupt symmetry change is accompanied by a clear sign change in the magnetostrictive coefficient, revealing that this transition corresponds to the onset of the spin reorientation. In the vicinity of TSR, a significantly larger in-plane magnetostrictive effect is observed, presenting the emergence of an intermediate phase that is highly susceptible to an applied magnetic field. X-ray linear dichroism shows that asymmetric Bi and Mn p orbitals do not play a role in the spin reorientation. This work suggests that the spin reorientation is caused by structural modification rather than changes in the local electronic configuration, providing a strategy for manipulating the magnetic anisotropy by external strain.

Th(As(III)4As(V)4O18): a mixed-valent oxoarsenic(III)/arsenic(V) actinide compound obtained under extreme conditions.

PubMed

Yu, Na; Klepov, Vladislav V; Kegler, Philip; Bosbach, Dirk; Albrecht-Schmitt, Thomas E; Alekseev, Evgeny V

2014-08-18

A high-temperature/high-pressure method was employed to investigate phase formation in the Th(NO3)4·5H2O-As2O3-CsNO3 system. It was observed that an excess of arsenic(III) in starting system leads to the formation of Th(As(III)4As(V)4O18), which is representative of a rare class of mixed-valent arsenic(III)/arsenic(V) compounds. This compound was studied with X-ray diffraction, energy-dispersive X-ray, and Raman spectroscopy methods. Crystallographic data show that Th(As(III)4As(V)4O18) is built from (As(III)4As(V)4O18)(4-) layers connected through Th atoms. The arsenic layers are found to be isoreticular to those in previously reported As2O3 and As3O5(OH), and the geometric differences between them are discussed. Bands in the Raman spectrum are assigned with respect to the presence of AsO3 and AsO4 groups.

Study on Iron Distribution and Electrical Activities at Grain Boundaries in Polycrystalline Silicon Substrate for Solar Cells

NASA Astrophysics Data System (ADS)

Arafune, Koji; Ohishi, Eichiro; Sai, Hitoshi; Terada, Yasuko; Ohshita, Yoshio; Yamaguchi, Masafumi

2006-08-01

To clarify the role of grain boundaries in iron sinks and carrier recombination centers, iron distributions and their chemical states were studied before and after gettering. They were measured by the X-ray microprobe fluorescence and the X-ray absorption in the near-edge structure using the beamline 37XU at the SPring-8 third-generation synchrotron facility. To determine the crystallographic orientation of the grain boundaries, electron backscatter diffraction measurements were performed. The distribution of electric active defects was characterized by electron-beam-induced current measurements. Before gettering, the iron was distributed in the small grain and its chemical state was similar to that of iron oxide. After gettering, the iron was redistributed along the small angle grain boundary, and its chemical state was similar to the iron silicide complexed with the iron oxide. Regarding the electrical activity, high carrier recombination was observed along the small-angle grain boundary. On the contrary, Σ 3 grain boundaries were relatively weak impurity sinks and showed low recombination activity.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

PubMed

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Crystallization and crystallographic studies of kallistatin

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

Lin, Fang; Zhou, Aiwu; Wei, Zhenquan, E-mail: weizhq@gmail.com

2015-08-25

The crystallization of human kallistatin in the relaxed conformation is reported. Kallistatin is a serine protease inhibitor (serpin) which specifically inhibits human tissue kallikrein; however, its inhibitory activity is inhibited by heparin. In order to elucidate the underlying mechanism, recombinant human kallistatin was prepared in Escherichia coli and the protein was crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.9 Å resolution. The crystals were found to belong to space group P6{sub 1}, with unit-cell parameters a = 113.51, b = 113.51, c = 76.17 Å. Initial analysis indicated that the crystallized kallistatin was in amore » relaxed conformation, with its reactive-centre loop inserted in the central β-sheet.« less

Nanostructured Tungsten Oxide Composite for High-Performance Gas Sensors

PubMed Central

Feng-Chen, Siyuan; Aldalbahi, Ali; Feng, Peter Xianping

2015-01-01

We report the results of composite tungsten oxide nanowires-based gas sensors. The morphologic surface, crystallographic structures, and chemical compositions of the obtained nanowires have been investigated using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Raman scattering, respectively. The experimental measurements reveal that each wire consists of crystalline nanoparticles with an average diameter of less than 250 nm. By using the synthesized nanowires, highly sensitive prototypic gas sensors have been designed and fabricated. The dependence of the sensitivity of tungsten oxide nanowires to the methane and hydrogen gases as a function of time has been obtained. Various sensing parameters such as sensitivity, response time, stability, and repeatability were investigated in order to reveal the sensing ability. PMID:26512670

Crystallographic and magnetic structure of HAVAR under high-pressure using diamond anvil cell (DAC)

NASA Astrophysics Data System (ADS)

Halevy, Itzhak; Haroush, Shlomo; Eisen, Yosef; Silberman, Ido; Moreno, Dany; Hen, Amir; Winterrose, Mike L.; Ghose, Sanjit; Chen, Zhiqiang

2010-04-01

Annealed (H1) and cold-rolled (H2) HAVAR has been studied using high-pressure synchrotron X-ray diffraction. A structural phase transformation was discovered at ˜13 GPa at ambient temperature, transforming from m - 3 m (S.G. 225) to P 63/m m c (S.G. 194) symmetry. The transition was not reversible on pressure release. The low-pressure cubic phase was found to be more compressible than the high-pressure hexagonal phase. Conventional Mössbauer and NFS shows that the HAVAR is not magnetic at room temperature and no splitting is observed. The SQUID indicates a huge difference in the temperature dependence of the magnetic susceptibility between the cold Rolled HAVAR compared to the annealed HAVAR.

Overexpression, crystallization and preliminary X-­ray crystallographic analysis of the RNA polymerase domain of primase from Streptococcus mutans strain UA159

PubMed Central

Im, Dong-Won; Kim, Tae-O; Jung, Ha Yun; Oh, Ji Eun; Lee, Se Jin; Heo, Yong-Seok

2012-01-01

Primase is the enzyme that synthesizes RNA primers on single-stranded DNA during normal DNA replication. In this study, the catalytic core domain of primase from Streptococcus mutans UA159 was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 1.60 Å resolution using a synchrotron-radiation source. The crystal belonged to space group P41 or P43, with unit-cell parameters a = b = 52.63, c = 110.31 Å. The asymmetric unit is likely to contain one molecule, with a corresponding V M of 1.77 Å3 Da−1 and a solvent content of 30.7%. PMID:22232183

Crystallization and preliminary crystallographic analysis of an Enterococcus faecalis repressor protein, CylR2, involved in regulating cytolysin production through quorum-sensing

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

Ni, Shuisong; McAteer, Kathleen; Bussiere, Dirksen E.

2004-06-01

CylR2 is one of the two regulatory proteins associated with the quorum-sensing-dependent synthesis of cytolysin for the common pathogen Enterococcus faecalis. The protein was expressed with a C-terminal 6-histidine tag and purified to homogeneity with a cobalt affinity column followed by another size exclusion column. Both native and SeMet proteins were crystallized. A complete X-ray diffraction data set from the native crystal was collected to 2.3 resolution. The crystal was tetragonal, belonging to space group P41/43, with unit-cell dimensions a=b=66.2 , c=40.9 and a=b=g=90. The asymmetric unit contained two molecules of CylR2.

Study on electrochemically deposited Mg metal

NASA Astrophysics Data System (ADS)

Matsui, Masaki

An electrodeposition process of magnesium metal from Grignard reagent based electrolyte was studied by comparing with lithium. The electrodeposition of magnesium was performed at various current densities. The obtained magnesium deposits did not show dendritic morphologies while all the lithium deposits showed dendritic products. Two different crystal growth modes in the electrodeposition process of magnesium metal were confirmed by an observation using scanning electron micro scope (SEM) and a crystallographic analysis using X-ray diffraction (XRD). An electrochemical study of the deposition/dissolution process of the magnesium showed a remarkable dependency of the overpotential of magnesium deposition on the electrolyte concentration compared with lithium. This result suggests that the dependency of the overpotential on the electrolyte concentration prevent the locally concentrated current resulting to form very uniform deposits.

Crystallographic texture in pulsed laser deposited hydroxyapatite bioceramic coatings

PubMed Central

Kim, Hyunbin; Camata, Renato P.; Lee, Sukbin; Rohrer, Gregory S.; Rollett, Anthony D.; Vohra, Yogesh K.

2008-01-01

The orientation texture of pulsed laser deposited hydroxyapatite coatings was studied by X-ray diffraction techniques. Increasing the laser energy density of the KrF excimer laser used in the deposition process from 5 to 7 J/cm2 increases the tendency for the c-axes of the hydroxyapatite grains to be aligned perpendicular to the substrate. This preferred orientation is most pronounced when the incidence direction of the plume is normal to the substrate. Orientation texture of the hydroxyapatite grains in the coatings is associated with the highly directional and energetic nature of the ablation plume. Anisotropic stresses, transport of hydroxyl groups and dehydroxylation effects during deposition all seem to play important roles in the texture development. PMID:18563207

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus

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

Kanaujia, Shankar Prasad; Ranjani, Chellamuthu Vasuki; Jeyakanthan, Jeyaraman

2007-02-01

DHNA synthetase from G. kaustophilus has been cloned, expressed, purified and crystallized. The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays a vital role in the biosynthesis of menaquinone (vitamin K{sub 2}) in this bacterium. DHNA synthetase from Geobacillus kaustophilus was crystallized in the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 77.01, b = 130.66, c = 131.69 Å. The crystal diffracted to a resolution of 2.2 Å. Preliminary studies and molecular-replacement calculations reveal the presence of three monomers in the asymmetricmore » unit.« less

Magnetic anisotropy and spin-flop transition of NiWO4 single crystals

NASA Astrophysics Data System (ADS)

Liu, C. B.; He, Z. Z.; Liu, Y. J.; Chen, R.; Shi, M. M.; Zhu, H. P.; Dong, C.; Wang, J. F.

2017-12-01

NiWO4 exhibits a spin chain structure built by magnetic Ni2+ ions, which may be considered as a one dimensional S = 1 system. In this work, large-sized single crystals of NiWO4 were successfully synthesized by a flux method and the crystal quality was confirmed by X-ray diffraction. Magnetic properties of obtained single crystals were studied by means of magnetic susceptibility and high field magnetization along crystallographic axes. The results demonstrate that NiWO4 is highly magnetic anisotropic and possesses a three-dimensional long range ordering below 60 K, where a spin flop transition can be observed at 17.5 T in applied magnetic fields along the magnetic easy axis (c-axis).

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

Schafer, Marion; Bobev, Svilen

This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K 8Cd 3.77(7)Ge 42.23, Rb 8Cd 3.65(7)Ge 42.35, and Cs 7.80(1)Cd 3.65(6)Ge 42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d 10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. Furthermore, this and several other details of the crystal chemistrymore » are elaborated.« less

Highly mobile type II twin boundary in Ni-Mn-Ga five-layered martensite

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

Sozinov, A.; Lanska, N.; Soroka, A.

2011-09-19

Twin relationships and stress-induced reorientation were studied in Ni{sub 2}Mn{sub 1.14}Ga{sub 0.86} single crystal with five-layered modulated martensite crystal structure. Very low twinning stress of about 0.1 MPa was found for twin boundaries which deviated a few degrees from the (011) crystallographic plane. However, twin boundaries oriented exactly parallel to the (011) plane exhibited considerably higher level of twinning stress, above 1 MPa. X-ray diffraction experiments and calculations based on approximation of the martensite crystal lattice as a tetragonal lattice with a slight monoclinic distortion identified the two different kinds of twin interfaces as type II and type I twinmore » boundaries.« less

Control system for the 2nd generation Berkeley AutoMounters (BAM2) at GM/CA CAT macromolecular crystallography beamlines

PubMed Central

Makarov, O.; Hilgart, M.; Ogata, C.; Pothineni, S.; Cork, C.

2011-01-01

GM/CA CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second generation Berkeley automounter is being integrated into the beamline control system at the 23-BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design. PMID:21822343

Correlating sampling and intensity statistics in nanoparticle diffraction experiments

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

Öztürk, Hande; Yan, Hanfei; Hill, John P.

2015-07-28

It is shown in a previous article [Öztürk, Yan, Hill & Noyan (2014).J. Appl. Cryst.47, 1016–1025] that the sampling statistics of diffracting particle populations within a polycrystalline ensemble depended on the size of the constituent crystallites: broad X-ray peak breadths enabled some nano-sized particles to contribute more than one diffraction spot to Debye–Scherrer rings. Here it is shown that the equations proposed by Alexander, Klug & Kummer [J. Appl. Phys.(1948),19, 742–753] (AKK) to link diffracting particle and diffracted intensity statistics are not applicable if the constituent crystallites of the powder are below 10 nm. In this size range, (i) themore » one-to-one correspondence between diffracting particles and Laue spots assumed in the AKK analysis is not satisfied, and (ii) the crystallographic correlation between Laue spots originating from the same grain invalidates the assumption that all diffracting plane normals are randomly oriented and uncorrelated. Such correlation produces unexpected results in the selection of diffracting grains. For example, three or more Laue spots from a given grain for a particular reflection can only be observed at certain wavelengths. In addition, correcting the diffracted intensity values by the traditional Lorentz term, 1/cos θ, to compensate for the variation of particles sampled within a reflection band does not maintain fidelity to the number of poles contributing to the diffracted signal. A new term, cos θ B/cos θ, corrects this problem.« less

Correlating Sampling and Intensity Statistics in Nanoparticle Diffraction Experiments

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

Ozturk, Hande; Yan, Hanfei; Hill, John P.

2015-08-01

In this article, [Öztürk, Yan, Hill & Noyan (2014). J. Appl. Cryst. 47, 1016-1025] it was shown that the sampling statistics of diffracting particle populations within a polycrystalline ensemble depended on the size of the constituent crystallites: broad X-ray peak breadths enabled some nano-sized particles to contribute more than one diffraction spot to Debye-Scherrer rings. Here it is shown that the equations proposed by Alexander, Klug & Kummer [J. Appl. Phys. (1948), 19, 742-753] (AKK) to link diffracting particle and diffracted intensity statistics are not applicable if the constituent crystallites of the powder are below 10 nm. In this sizemore » range, (i) the one-to-one correspondence between diffracting particles and Laue spots assumed in the AKK analysis is not satisfied, and (ii) the crystallographic correlation between Laue spots originating from the same grain invalidates the assumption that all diffracting plane normals are randomly oriented and uncorrelated. Such correlation produces unexpected results in the selection of diffracting grains. Three or more Laue spots from a given grain for a particular reflection can only be observed at certain wavelengths. In addition, correcting the diffracted intensity values by the traditional Lorentz term, 1/cos [theta], to compensate for the variation of particles sampled within a reflection band does not maintain fidelity to the number of poles contributing to the diffracted signal. A new term, cos [theta]B/cos [theta], corrects this problem.« less

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10(-2) Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens

NASA Astrophysics Data System (ADS)

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10-2 Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Thin Film Research. Volume 1

DTIC Science & Technology

1985-05-30

Order (FECO) ......... 23 3. X -Ray Diffraction ............................... 26 4. Transmission Electron Microscopy (TEM) ............... 26 5...remained amorphous after bombardment, as evidenced by X - ray diffraction, and showed no other changes. 0 (2) For Sb203, the crystallite size was reduced...main effect on MgF2 was the reduction in crystallite size. The films were too thir. for meaningful x - ray diffraction analysis. Durability and

X-Ray Diffraction and the Discovery of the Structure of DNA

ERIC Educational Resources Information Center

Crouse, David T.

2007-01-01

A method is described for teaching the analysis of X-ray diffraction of DNA through a series of steps utilizing the original methods used by James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. The X-ray diffraction pattern led to the conclusion of the basic helical structure of DNA and its dimensions while basic chemical principles…

High Resolution X-Ray Diffraction of Macromolecules with Synchrotron Radiation

NASA Technical Reports Server (NTRS)

Stojanoff, Vivian; Boggon, Titus; Helliwell, John R.; Judge, Russell; Olczak, Alex; Snell, Edward H.; Siddons, D. Peter; Rose, M. Franklin (Technical Monitor)

2000-01-01

We recently combined synchrotron-based monochromatic X-ray diffraction topography methods with triple axis diffractometry and rocking curve measurements: high resolution X-ray diffraction imaging techniques, to better understand the quality of protein crystals. We discuss these methods in the light of results obtained on crystals grown under different conditions. These non destructive techniques are powerful tools in the characterization of the protein crystals and ultimately will allow to improve, develop, and understand protein crystal growth. High resolution X-ray diffraction imaging methods will be discussed in detail in light of recent results obtained on Hen Egg White Lysozyme crystals and other proteins.

Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

DOE PAGES

Logan, Jonathan; Harder, Ross; Li, Luxi; ...

2016-01-01

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. Here, the performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd 5Si 2Ge 2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. Thesemore » tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd 5Si 2Ge 2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.« less

Combined near- and far-field high-energy diffraction microscopy dataset for Ti-7Al tensile specimen elastically loaded in situ

DOE PAGES

Turner, Todd J.; Shade, Paul A.; Bernier, Joel V.; ...

2016-03-18

High-energy diffraction microscopy (HEDM) constitutes a suite of combined X-ray characterization methods, which hold the unique advantage of illuminating the microstructure and micromechanical state of a material during concurrent in situ mechanical deformation. The data generated from HEDM experiments provides a heretofore unrealized opportunity to validate meso-scale modeling techniques, such as crystal plasticity finite element modeling (CPFEM), by explicitly testing the accuracy of these models at the length scales where the models predict their response. Combining HEDM methods with in situ loading under known and controlled boundary conditions represents a significant challenge, inspiring the recent development of a new high-precisionmore » rotation and axial motion system for simultaneously rotating and axially loading a sample. In this paper, we describe the initial HEDM dataset collected using this hardware on an alpha-titanium alloy (Ti-7Al) under in situ tensile deformation at the Advanced Photon Source, Argonne National Laboratory. We present both near-field HEDM data that maps out the grain morphology and intragranular crystallographic orientations and far-field HEDM data that provides the grain centroid, grain average crystallographic orientation, and grain average elastic strain tensor for each grain. Finally, we provide a finite element mesh that can be utilized to simulate deformation in the volume of this Ti-7Al specimen.« less

Microstructure and Crystallographic Texture Evolution During the Friction-Stir Processing of a Precipitation-Hardenable Aluminum Alloy

NASA Astrophysics Data System (ADS)

Nadammal, Naresh; Kailas, Satish V.; Szpunar, Jerzy; Suwas, Satyam

2015-05-01

Friction-stir processing (FSP) has been proven as a successful method for the grain refinement of high-strength aluminum alloys. The most important attributes of this process are the fine-grain microstructure and characteristic texture, which impart suitable properties in the as-processed material. In the current work, FSP of the precipitation-hardenable aluminum alloy 2219 has been carried out and the consequent evolution of microstructure and texture has been studied. The as-processed materials were characterized using electron back-scattered diffraction, x-ray diffraction, and electron probe microanalysis. Onion-ring formation was observed in the nugget zone, which has been found to be related to the precipitation response and crystallographic texture of the alloy. Texture development in the alloy has been attributed to the combined effect of shear deformation and dynamic recrystallization. The texture was found heterogeneous even within the nugget zone. A microtexture analysis revealed the dominance of shear texture components, with C component at the top of nugget zone and the B and A2* components in the middle and bottom. The bulk texture measurement in the nugget zone revealed a dominant C component. The development of a weaker texture along with the presence of some large particles in the nugget zone indicates particle-stimulated nucleation as the dominant nucleation mechanism during FSP. Grain growth follows the Burke and Turnbull mechanism and geometrical coalescence.

Quantitative Phase Composition of TiO 2-Coated Nanoporous-Au Monoliths by X-ray Absorption Spectroscopy and Correlations to Catalytic

DOE PAGES

Bagge-Hansen, Michael; Wichmann, Andre; Wittstock, Arne; ...

2014-02-03

Porous titania/metal composite materials have many potential applications in the fields of green catalysis, energy harvesting, and storage in which both the overall morphology of the nanoporous host material and the crystallographic phase of the titania (TiO 2) guest determine the material’s performance. New insights into the structure–function relationships of these materials were obtained by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy that, for example, provides quantitative crystallographic phase composition from ultrathin, nanostructured titania films, including sensitivity to amorphous components. We demonstrate that crystallographic phase, morphology, and catalytic activity of TiO 2-functionalized nanoporous gold (np-Au) can be controlled by amore » simple annealing procedure (T < 1300 K). The material was prepared by atomic layer deposition of ~2 nm thick TiO 2 on millimeter-sized samples of np-Au (40–50 nm mean ligament size) and catalytically investigated with respect to aerobic CO oxidation. Moreover, the annealing-induced changes in catalytic activity are correlated with concurrent morphology and phase changes as provided by cross-sectional scanning electron microscopy, transmission electron microscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy.« less

Three Dimensional Variable-Wavelength X-Ray Bragg Coherent Diffraction Imaging

DOE PAGES

Cha, W.; Ulvestad, A.; Allain, M.; ...

2016-11-23

Here, we present and demonstrate a formalism by which three-dimensional (3D) Bragg x-ray coherent diffraction imaging (BCDI) can be implemented without moving the sample by scanning the energy of the incident x-ray beam. This capability is made possible by introducing a 3D Fourier transform that accounts for x-ray wavelength variability. We also demonstrate the approach by inverting coherent Bragg diffraction patterns from a gold nanocrystal measured with an x-ray energy scan. Furthermore, variable-wavelength BCDI will expand the breadth of feasible in situ 3D strain imaging experiments towards more diverse materials environments, especially where sample manipulation is difficult.

Synchrotron X-Ray Diffraction Analysis of Meteorites in Thin Section: Preliminary Results

NASA Technical Reports Server (NTRS)

Treiman, A. H.; Lanzirotti, A.; Xirouchakis, D.

2004-01-01

X-ray diffraction is the pre-eminent technique for mineral identification and structure determination, but is difficult to apply to grains in thin section, the standard meteorite preparation. Bright focused X-ray beams from synchrotrons have been used extensively in mineralogy and have been applied to extraterrestrial particles. The intensity and small spot size achievable in synchrotron X-ray beams makes them useful for study of materials in thin sections. Here, we describe Synchrotron X-ray Diffraction (SXRD) in thin section as done at the National Synchrotron Light Source, and cite examples of its value for studies of meteorites in thin section.

Three Dimensional Variable-Wavelength X-Ray Bragg Coherent Diffraction Imaging

NASA Astrophysics Data System (ADS)

Cha, W.; Ulvestad, A.; Allain, M.; Chamard, V.; Harder, R.; Leake, S. J.; Maser, J.; Fuoss, P. H.; Hruszkewycz, S. O.

2016-11-01

We present and demonstrate a formalism by which three-dimensional (3D) Bragg x-ray coherent diffraction imaging (BCDI) can be implemented without moving the sample by scanning the energy of the incident x-ray beam. This capability is made possible by introducing a 3D Fourier transform that accounts for x-ray wavelength variability. We demonstrate the approach by inverting coherent Bragg diffraction patterns from a gold nanocrystal measured with an x-ray energy scan. Variable-wavelength BCDI will expand the breadth of feasible in situ 3D strain imaging experiments towards more diverse materials environments, especially where sample manipulation is difficult.

Three Dimensional Variable-Wavelength X-Ray Bragg Coherent Diffraction Imaging.

PubMed

Cha, W; Ulvestad, A; Allain, M; Chamard, V; Harder, R; Leake, S J; Maser, J; Fuoss, P H; Hruszkewycz, S O

2016-11-25

We present and demonstrate a formalism by which three-dimensional (3D) Bragg x-ray coherent diffraction imaging (BCDI) can be implemented without moving the sample by scanning the energy of the incident x-ray beam. This capability is made possible by introducing a 3D Fourier transform that accounts for x-ray wavelength variability. We demonstrate the approach by inverting coherent Bragg diffraction patterns from a gold nanocrystal measured with an x-ray energy scan. Variable-wavelength BCDI will expand the breadth of feasible in situ 3D strain imaging experiments towards more diverse materials environments, especially where sample manipulation is difficult.

Deciphering the Possible Role of Strain Path on the Evolution of Microstructure, Texture, and Magnetic Properties in a Fe-Cr-Ni Alloy

NASA Astrophysics Data System (ADS)

Kumar, Amit; Khatirkar, Rajesh Kisni; Gupta, Aman; Shekhawat, Satish K.; Suwas, Satyam

2018-06-01

In the present work, the influence of strain path on the evolution of microstructure, crystallographic texture, and magnetic properties of a two-phase Fe-Cr-Ni alloy was investigated. The Fe-Cr-Ni alloy had nearly equal proportion of austenite and ferrite and was cold rolled up to a true strain of 1.6 (thickness reduction) using two different strain paths—unidirectional rolling and multi-step cross rolling. The microstructures were characterized by scanning electron microscopy (SEM) and electron backscattered diffraction (EBSD), while crystallographic textures were determined using X-ray diffraction. For magnetic characterization, B-H loops and M-H curves were measured and magnetic force microscopy was performed. After unidirectional rolling, ferrite showed the presence of strong α-fiber (rolling direction, RD//<110>) and austenite showed strong brass type texture (consisting of Brass (Bs) ({110}<112>), Goss ({110}<001>), and S ({123}<634>)). After multi-step cross rolling, strong rotated cube ({100}<110>) was developed in ferrite, while austenite showed ND (normal direction) rotated brass ( 10 deg) texture. The strain-induced martensite (SIM) was found to be higher in unidirectionally rolled samples than multi-step cross-rolled samples. The coherently diffracting domain size, micro-strain, coercivity, and core loss also showed a strong correlation with strain and strain path. More strain was partitioned into austenite than ferrite during deformation (unidirectional as well as cross rolling). Further, the strain partitioning (in both austenite and ferrite) was found to be higher in unidirectionally rolled samples.

In-situ X-ray diffraction system using sources and detectors at fixed angular positions

DOEpatents

Gibson, David M [Voorheesville, NY; Gibson, Walter M [Voorheesville, NY; Huang, Huapeng [Latham, NY

2007-06-26

An x-ray diffraction technique for measuring a known characteristic of a sample of a material in an in-situ state. The technique includes using an x-ray source for emitting substantially divergent x-ray radiation--with a collimating optic disposed with respect to the fixed source for producing a substantially parallel beam of x-ray radiation by receiving and redirecting the divergent paths of the divergent x-ray radiation. A first x-ray detector collects radiation diffracted from the sample; wherein the source and detector are fixed, during operation thereof, in position relative to each other and in at least one dimension relative to the sample according to a-priori knowledge about the known characteristic of the sample. A second x-ray detector may be fixed relative to the first x-ray detector according to the a-priori knowledge about the known characteristic of the sample, especially in a phase monitoring embodiment of the present invention.

The effect of exit beam phase aberrations on parallel beam coherent x-ray reconstructions

NASA Astrophysics Data System (ADS)

Hruszkewycz, S. O.; Harder, R.; Xiao, X.; Fuoss, P. H.

2010-12-01

Diffraction artifacts from imperfect x-ray windows near the sample are an important consideration in the design of coherent x-ray diffraction measurements. In this study, we used simulated and experimental diffraction patterns in two and three dimensions to explore the effect of phase imperfections in a beryllium window (such as a void or inclusion) on the convergence behavior of phasing algorithms and on the ultimate reconstruction. A predictive relationship between beam wavelength, sample size, and window position was derived to explain the dependence of reconstruction quality on beryllium defect size. Defects corresponding to this prediction cause the most damage to the sample exit wave and induce signature error oscillations during phasing that can be used as a fingerprint of experimental x-ray window artifacts. The relationship between x-ray window imperfection size and coherent x-ray diffractive imaging reconstruction quality explored in this work can play an important role in designing high-resolution in situ coherent imaging instrumentation and will help interpret the phasing behavior of coherent diffraction measured in these in situ environments.

The effect of exit beam phase aberrations on parallel beam coherent x-ray reconstructions.

PubMed

Hruszkewycz, S O; Harder, R; Xiao, X; Fuoss, P H

2010-12-01

Diffraction artifacts from imperfect x-ray windows near the sample are an important consideration in the design of coherent x-ray diffraction measurements. In this study, we used simulated and experimental diffraction patterns in two and three dimensions to explore the effect of phase imperfections in a beryllium window (such as a void or inclusion) on the convergence behavior of phasing algorithms and on the ultimate reconstruction. A predictive relationship between beam wavelength, sample size, and window position was derived to explain the dependence of reconstruction quality on beryllium defect size. Defects corresponding to this prediction cause the most damage to the sample exit wave and induce signature error oscillations during phasing that can be used as a fingerprint of experimental x-ray window artifacts. The relationship between x-ray window imperfection size and coherent x-ray diffractive imaging reconstruction quality explored in this work can play an important role in designing high-resolution in situ coherent imaging instrumentation and will help interpret the phasing behavior of coherent diffraction measured in these in situ environments.

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

Motorized Beam Alignment of a Commercial X-ray Diffractometer

NASA Technical Reports Server (NTRS)

Van Zandt, Noah R.; Myers, James F.; Rogers, Richard B

2013-01-01

X-ray diffraction (XRD) is a powerful analysis method that allows researchers to noninvasively probe the crystalline structure of a material. This includes the ability to determine the crystalline phases present, quantify surface residual stresses, and measure the distribution of crystallographic orientations. The Structures and Materials Division at the NASA Glenn Research Center (GRC) heavily uses the on-site XRD lab to characterize advanced metal alloys, ceramics, and polymers. One of the x-ray diffractometers in the XRD lab (Bruker D8 Discover) uses three different x-ray tubes (Cu, Cr, and Mn) for optimal performance over numerous material types and various experimental techniques. This requires that the tubes be switched out and aligned between experiments. This alignment maximizes the x-ray tube s output through an iterative process involving four set screws. However, the output of the x-ray tube cannot be monitored during the adjustment process due to standard radiation safety engineering controls that prevent exposure to the x-ray beam when the diffractometer doors are open. Therefore, the adjustment process is a very tedious series of blind adjustments, each followed by measurement of the output beam using a PIN diode after the enclosure doors are shut. This process can take up to 4 hr to perform. This technical memorandum documents an in-house project to motorize this alignment process. Unlike a human, motors are not harmed by x-ray radiation of the energy range used in this instrument. Therefore, using motors to adjust the set screws will allow the researcher to monitor the x-ray tube s output while making interactive adjustments from outside the diffractometer. The motorized alignment system consists of four motors, a motor controller, and a hand-held user interface module. Our goal was to reduce the alignment time to less than 30 min. The time available was the 10-week span of the Lewis' Educational and Research Collaborative Internship Project (LERCIP) summer internship program and the budget goal was $1200. In this report, we will describe our motorization design and discuss the results of its implementation.

On the formation and functions of high and very high magnesium calcites in the continuously growing teeth of the echinoderm Lytechinus variegatus: development of crystallinity and protein involvement.

PubMed

Veis, Arthur; Stock, Stuart R; Alvares, Keith; Lux, Elizabeth

2011-01-01

Sea urchin teeth grow continuously and develop a complex mineralized structure consisting of spatially separate but crystallographically aligned first stage calcitic elements of high Mg content (5-15 mol% mineral). These become cemented together by epitaxially oriented second stage very high Mg calcite (30-40 mol% mineral). In the tooth plumula, ingressing preodontoblasts create layered cellular syncytia. Mineral deposits develop within membrane-bound compartments between cellular syncytial layers. We seek to understand how this complex tooth architecture is developed, how individual crystalline calcitic elements become crystallographically aligned, and how their Mg composition is regulated. Synchrotron microbeam X-ray scattering was performed on live, freshly dissected teeth. We observed that the initial diffracting crystals lie within independent syncytial spaces in the plumula. These diffraction patterns match those of mature tooth calcite. Thus, the spatially separate crystallites grow with the same crystallographic orientation seen in the mature tooth. Mineral-related proteins from regions with differing Mg contents were isolated, sequenced, and characterized. A tooth cDNA library was constructed, and selected matrix-related proteins were cloned. Antibodies were prepared and used for immunolocaliztion. Matrix-related proteins are acidic, phosphorylated, and associated with the syncytial membranes. Time-of-flight secondary ion mass spectroscopy of various crystal elements shows unique amino acid, Mg, and Ca ion distributions. High and very high Mg calcites differ in Asp content. Matrix-related proteins are phosphorylated. Very high Mg calcite is associated with Asp-rich protein, and it is restricted to the second stage mineral. Thus, the composition at each part of the tooth is related to architecture and function. Copyright © 2011 S. Karger AG, Basel.

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

Marana, S. R.; Cançado, F. C.; Valério, A. A.

The digestive lysozymes 1 and 2 from M. domestica were crystallized by vapour diffusion. The crystallographic data were processed to a maximum resolution of 1.9 Å in both cases. Lysozymes are mostly known for their defensive role against bacteria, but in several animals lysozymes have a digestive function. Here, the initial crystallographic characterization of two digestive lysozymes from Musca domestica are presented. The proteins were crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate or PEG/2-propanol as the precipitant. X-ray diffraction data were collected to a maximum resolution of 1.9 Å using synchrotron radiation. The lysozyme 1more » and 2 crystals belong to the monoclinic space group P2{sub 1} (unit-cell parameters a = 36.52, b = 79.44, c = 45.20 Å, β = 102.97°) and the orthorhombic space group P2{sub 1}2{sub 1}2 (unit-cell parameters a = 73.90, b = 96.40, c = 33.27 Å), respectively. The crystal structures were solved by molecular replacement and structure refinement is in progress.« less

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D

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

Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level withmore » high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.« less

Versatile control of the submolecular motion of di(acylamino)pyridine-based [2]rotaxanes† †Electronic supplementary information (ESI) available: Experimental procedures, spectroscopic and mass spectrometry data for all new compounds, electrochemical studies, and full crystallographic details of 1c and 2b. CCDC 1051908 and 1051909. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc00790a Click here for additional data file. Click here for additional data file.

PubMed Central

Martinez-Cuezva, Alberto; Pastor, Aurelia; Cioncoloni, Giacomo; Orenes, Raul-Angel; Alajarin, Mateo; Symes, Mark D.

2015-01-01

A cyclic network of chemical reactions has been conceived for exchanging the dynamic behaviour of di(acylamino)pyridine-based rotaxanes and surrogates. X-ray diffraction studies revealed the intercomponent interactions in these interlocked compounds and were consistent with those found in solution by dynamic NMR experiments. This particular binding site was incorporated into a molecular shuttle enabled for accessing two states with an outstanding positional discrimination through chemical manipulation. Furthermore, the ability of the di(acylamino)pyridine domain to associate with external binders with a complementary array of HB donor and acceptor sites was exploited for the advance of an unprecedented electrochemical switch operating through a reversible anion radical recognition process. PMID:28706682

Influence of gamma ray irradiation on stoichiometry of hydrothermally synthesized bismuth telluride nanoparticles

NASA Astrophysics Data System (ADS)

Abishek, N. S.; Naik, K. Gopalakrishna

2018-05-01

Bismuth telluride (Bi2Te3) nanoparticles were synthesized by the hydrothermal method at 200 °C for 24 h. The synthesized Bi2Te3 nanoparticles were irradiated with gamma rays at doses of 50 kGy and 100 kGy. The structural characterization of the pre-irradiated and post-irradiated samples was carried out by X-ray diffraction technique and was found to have rhombohedral phase having R3 ¯m (166) space group. The X-ray diffraction peaks were found to shift towards lower diffraction angle with gamma ray irradiation. The morphologies and compositions of the grown Bi2Te3 nanoparticles were studied using Field Emission Scanning Electron Microscope and X-ray energy dispersive analysis, respectively. The possible cause for the shift in the X-ray diffraction peaks with gamma ray irradiation has been discussed in the present work.

High Power Optical Coatings by Atomic Layer Deposition and Signatures of Laser-Induced Damage

DTIC Science & Technology

2012-08-28

diffraction angle 0 into crystal lattice spacing d by the Bragg condition, mX = 2d sin 0. Here X is the x - ray wavelength... angle x - ray diffraction (GAXRD) measurements, which were made at a fixed shallow incidence angle of 0.5°. Detector scans were done to measure the...was finished with 200 hafnia cycles m the fmal half period rather than 400. Crystallinity was measured by x - ray diffraction (XRD) with

Materials identification using a small-scale pixellated x-ray diffraction system

NASA Astrophysics Data System (ADS)

O'Flynn, D.; Crews, C.; Drakos, I.; Christodoulou, C.; Wilson, M. D.; Veale, M. C.; Seller, P.; Speller, R. D.

2016-05-01

A transmission x-ray diffraction system has been developed using a pixellated, energy-resolving detector (HEXITEC) and a small-scale, mains operated x-ray source (Amptek Mini-X). HEXITEC enables diffraction to be measured without the requirement of incident spectrum filtration, or collimation of the scatter from the sample, preserving a large proportion of the useful signal compared with other diffraction techniques. Due to this efficiency, sufficient molecular information for material identification can be obtained within 5 s despite the relatively low x-ray source power. Diffraction data are presented from caffeine, hexamine, paracetamol, plastic explosives and narcotics. The capability to determine molecular information from aspirin tablets inside their packaging is demonstrated. Material selectivity and the potential for a sample classification model is shown with principal component analysis, through which each different material can be clearly resolved.