WorldWideScience

Sample records for synthesis x-ray structure

  1. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    DOI 10.1007/s12039-015-0978-8. Synthesis, characterization, X-ray crystal structure, electrochemical evaluation and anti-cancer studies of a mixed ligand Cu(II) complex of (E)-N -((2-hydroxynaphthalen-1-yl)methylene)acetohydrazide. IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,.

  2. Synthesis, characterization, X-ray structure, optical properties and ...

    Indian Academy of Sciences (India)

    ESMA LAMERA

    Also, the values of dipole moment μ, the average polarizability ¯α, and the first static hyperpolarizability (β0) were computed. The theoretical and experimental results confirm the NLO behavior of both compounds. Keywords. Condensed phthalazine; DFT calculations; spectroscopic analysis; X-ray structure; NLO. 1.

  3. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  4. Synthesis, X-ray structure and N–H…O interactions in 1,3-diphenyl ...

    Indian Academy of Sciences (India)

    The synthesis, X-ray structure and role of intermolecular interactions have been studied in case of 1,3-diphenyl-urea, owing to its medicinal importance. The compound crystallizes in orthorhombic crystal system (space group, 21) with unit cell parameters, = 9.118(3), = 10.558(2), = 11.780(3) Å and = 4.

  5. Synthesis, characterization, x-ray structure and antimicrobial activity ...

    African Journals Online (AJOL)

    Purpose: To synthesize thiosemicarbazide and determine its antimicrobial properties. Methods: Pyridine-based thiosemicarbazide was synthesized, characterized and evaluated for antimicrobial activity. The structure of the synthesized compound was established by spectral analysis, namely, Fourier transform infrared ...

  6. Synthesis, characterization, x-ray structure and antimicrobial activity ...

    African Journals Online (AJOL)

    intermolecular N3—H1N1•••O1 hydrogen bonds. (Table 2), resulting in the formation of zigzag layers lying parallel to (100) (Fig. 2b). The existence of π•••π interactions involving the centroid of the N4/C9-C13 pyridine ring (π•••π distance = 3.5108(18) Å) further stabilize the molecular packing. The structure of compound 2.

  7. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2013-10-01

    Full Text Available Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and reducing power abilities. The results indicate the tested compounds show a varied range of inhibition values against all the tested microbial strains. Compound 3c with a p-fluoro substituent on the phenyl ring exhibits elevated antimicrobial activity, whereas the compounds 3e and 3f displayed the least antimicrobial activities. The compounds 3d, 3e, 3f and 3i showed good ferric and cupric reducing abilities, and the compounds 3b and 3c showed the weakest reducing power in the series.

  8. Synthesis of hydroxyapatite and structural refinement by X-ray diffraction

    International Nuclear Information System (INIS)

    Araujo, Jorge Correa de

    2007-01-01

    A sample of hydroxyapatite was synthesized and its crystalline structure was analyzed by X-ray diffraction by means of the Rietveld method. Two functions were used to fit the peak profiles, modified Voigt (TCHZ) and Pearson VII. The occupational factors and lattice parameters obtained by both models show that the sample does not contain relevant cationic substitutions. The interatomic distances from Ca1 to oxygens O1, O2 and O3 were adequate for a pure hydroxyapatite without defect at site Ca1. Besides, the use of multiple lines in planes (300) and (002) associated with the model Pearson VII resulted in good agreement with the TCHZ model with respect to the size-strain effects with an ellipsoidal shape of crystallites. In conclusion, the procedures adopted in the synthesis of hydroxyapatite produced a pure and crystalline material. The experimental results of transmission electron microscopy confirmed the predicted shape of crystals. (author)

  9. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    International Nuclear Information System (INIS)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N.; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G.

    2010-01-01

    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  10. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

    2010-07-01

    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  11. A pyrrolo-tetrathiafulvalene cage: Synthesis and X-ray crystal structure

    DEFF Research Database (Denmark)

    Nielsen, Kent A.; Jeppesen, Jan O.; Levillain, Eric

    2002-01-01

    A novel type of tetrathiafulvalene-cage 4 containing three monopyrrolo-tetrathiafulvalene units has been prepared employing a general and efficient synthetic approach. X-ray crystal structure analysis revealed that the cage is able to accommodate solvent molecules within a cavity in the solid state....

  12. Tin( ii ) ketoacidoximates: synthesis, X-ray structures and processing to tin( ii ) oxide

    KAUST Repository

    Khanderi, Jayaprakash

    2015-10-21

    Tin(ii) ketoacidoximates of the type [HONCRCOO]Sn (R = Me 1, CHPh 2) and (MeONCMeCOO)Sn] NH·2HO 3 were synthesized by reacting pyruvate- and hydroxyl- or methoxylamine RONH (R = H, Me) with tin(ii) chloride dihydrate SnCl·2HO. The single crystal X-ray structure reveals that the geometry at the Sn atom is trigonal bipyramidal in 1, 2 and trigonal pyramidal in 3. Inter- or intramolecular hydrogen bonding is observed in 1-3. Thermogravimetric (TG) analysis shows that the decomposition of 1-3 to SnO occurs at ca. 160 °C. The evolved gas analysis during TG indicates complete loss of the oximato ligand in one step for 1 whereas a small organic residue is additionally removed at temperatures >400 °C for 2. Above 140 °C, [HONC(Me)COO]Sn (1) decomposes in air to spherical SnO particles of size 10-500 nm. Spin coating of 1 on Si or a glass substrate followed by heating at 200 °C results in a uniform film of SnO. The band gap of the produced SnO film and nanomaterial was determined by diffuse reflectance spectroscopy to be in the range of 3.0-3.3 eV. X-ray photoelectron spectroscopy indicates surface oxidation of the SnO film to SnO in ambient atmosphere.

  13. Uranium Hydridoborates: Synthesis, Magnetism, and X-ray/Neutron Diffraction Structures.

    Science.gov (United States)

    Braunschweig, H; Gackstatter, A; Kupfer, T; Radacki, K; Franke, S; Meyer, K; Fucke, K; Lemée-Cailleau, M-H

    2015-08-17

    While uranium hydridoborate complexes containing the [BH4](-) moiety have been well-known in the literature for many years, species with functionalized borate centers remained considerably rare. We were now able to prepare several uranium hydridoborates (1-4) with amino-substituted borate moieties with high selectivity by smooth reaction of [Cp*2UMe2] (Cp* = C5Me5) and [Cp'2UMe2] (Cp' = 1,2,4-tBu3C5H2) with the aminoborane H2BN(SiMe3)2. A combination of nuclear magnetic resonance spectroscopy, deuteration experiments, magnetic SQUID measurements, and X-ray/neutron diffraction studies was used to verify the anticipated molecular structures and oxidation states of 1-4 and helped to establish a linear tridentate coordination mode of the borate anions.

  14. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    BPAH)₂(NO₃)(H₂O)₂] 2NO₃.H₂O (where, BPAH = 2-benzoylpyridine acetyl hydrazone), were synthesized and characterized by elemental analysis, molar conductance, IR spectroscopy and single crystal X-ray diffraction and Hirschfeld ...

  15. Synthesis, X-ray structure determination and germination studies on some smoke-derived karrikins

    Czech Academy of Sciences Publication Activity Database

    Nair, J. J.; Pošta, Martin; Papenfus, H. B.; Munro, O. Q.; Beier, Petr; van Staden, J.

    2014-01-01

    Roč. 91, Mar (2014), s. 53-57 ISSN 0254-6299 Institutional support: RVO:61388963 Keywords : germination * karrikin * plant growth regulator * smoke * X-ray Subject RIV: CC - Organic Chemistry Impact factor: 0.978, year: 2014

  16. Synthesis, X-ray Structure, Spectroscopic Properties and DFT Studies of a Novel Schiff Base

    Directory of Open Access Journals (Sweden)

    Kew-Yu Chen

    2014-10-01

    Full Text Available A series of Schiff bases, salicylideneaniline derivatives 1–4, was synthesized under mild conditions and characterized by 1H NMR, HRMS, UV-Vis and fluorescence spectra, and single-crystal X-ray diffraction. In solid and aprotic solvents 1–4 exist mainly as E conformers that possess an intramolecular six-membered-ring hydrogen bond. A weak intramolecular C–H×××F hydrogen bond is also observed in fluoro-functionalized Schiff base 4, which generates another S(6 ring motif. The C–H×××F hydrogen bond further stabilizes its structure and leads it to form a planar configuration. Compounds 1–3 exhibit solely a long-wavelength proton-transfer tautomer emission, while dipole-functionalized Schiff base 4 shows remarkable dual emission originated from the excited-state intramolecular charge transfer (ESICT and excited-state intramolecular proton transfer (ESIPT states. Furthermore, the geometric structures, frontier molecular orbitals (MOs and the potential energy curves for 1–4 in the ground and the first singlet excited state were fully rationalized by density functional theory (DFT and time-dependent DFT calculations.

  17. Synthesis, X-ray structure, spectroscopic properties and DFT studies of a novel Schiff base.

    Science.gov (United States)

    Chen, Kew-Yu; Tsai, Hsing-Yang

    2014-10-17

    A series of Schiff bases, salicylideneaniline derivatives 1-4, was synthesized under mild conditions and characterized by 1H NMR, HRMS, UV-Vis and fluorescence spectra, and single-crystal X-ray diffraction. In solid and aprotic solvents 1-4 exist mainly as E conformers that possess an intramolecular six-membered-ring hydrogen bond. A weak intramolecular C-H···F hydrogen bond is also observed in fluoro-functionalized Schiff base 4, which generates another S(6) ring motif. The C-H···F hydrogen bond further stabilizes its structure and leads it to form a planar configuration. Compounds 1-3 exhibit solely a long-wavelength proton-transfer tautomer emission, while dipole-functionalized Schiff base 4 shows remarkable dual emission originated from the excited-state intramolecular charge transfer (ESICT) and excited-state intramolecular proton transfer (ESIPT) states. Furthermore, the geometric structures, frontier molecular orbitals (MOs) and the potential energy curves for 1-4 in the ground and the first singlet excited state were fully rationalized by density functional theory (DFT) and time-dependent DFT calculations.

  18. Synthesis, X-ray Structure, Optical, and Electrochemical Properties of a White-Light-Emitting Molecule

    Directory of Open Access Journals (Sweden)

    Jiun-Wei Hu

    2016-01-01

    Full Text Available A new white-light-emitting molecule (1 was synthesized and characterized by NMR spectroscopy, high resolution mass spectrometry, and single-crystal X-ray diffraction. Compound 1 crystallizes in the orthorhombic space group Pnma, with a = 12.6814(6, b = 7.0824(4, c = 17.4628(9 Å, α = 90°, β = 90°, γ = 90°. In the crystal, molecules are linked by weak intermolecular C-H···O hydrogen bonds, forming an infinite chain along [100], generating a C(10 motif. Compound 1 possesses an intramolecular six-membered-ring hydrogen bond, from which excited-state intramolecular proton transfer (ESIPT takes place from the phenolic proton to the carbonyl oxygen, resulting in a tautomer that is in equilibrium with the normal species, exhibiting a dual emission that covers almost all of the visible spectrum and consequently generates white light. It exhibits one irreversible one-electron oxidation and two irreversible one-electron reductions in dichloromethane at modest potentials. Furthermore, the geometric structures, frontier molecular orbitals (MOs, and the potential energy curves (PECs for 1 in the ground and the first singlet excited state were fully rationalized by density functional theory (DFT and time-dependent DFT calculations. The results demonstrate that the forward and backward ESIPT may happen on a similar timescale, enabling the excited-state equilibrium to be established.

  19. Synthesis, X-ray Structure, Optical, and Electrochemical Properties of a White-Light-Emitting Molecule.

    Science.gov (United States)

    Hu, Jiun-Wei; Wu, Ying-Hsuan; Tsai, Hsing-Yang; Chen, Kew-Yu

    2016-01-14

    A new white-light-emitting molecule ( 1 ) was synthesized and characterized by NMR spectroscopy, high resolution mass spectrometry, and single-crystal X-ray diffraction. Compound 1 crystallizes in the orthorhombic space group Pnma , with a = 12.6814(6), b = 7.0824(4), c = 17.4628(9) Å, α = 90°, β = 90°, γ = 90°. In the crystal, molecules are linked by weak intermolecular C-H···O hydrogen bonds, forming an infinite chain along [100], generating a C (10) motif. Compound 1 possesses an intramolecular six-membered-ring hydrogen bond, from which excited-state intramolecular proton transfer (ESIPT) takes place from the phenolic proton to the carbonyl oxygen, resulting in a tautomer that is in equilibrium with the normal species, exhibiting a dual emission that covers almost all of the visible spectrum and consequently generates white light. It exhibits one irreversible one-electron oxidation and two irreversible one-electron reductions in dichloromethane at modest potentials. Furthermore, the geometric structures, frontier molecular orbitals (MOs), and the potential energy curves (PECs) for 1 in the ground and the first singlet excited state were fully rationalized by density functional theory (DFT) and time-dependent DFT calculations. The results demonstrate that the forward and backward ESIPT may happen on a similar timescale, enabling the excited-state equilibrium to be established.

  20. Synthesis, X-ray structure and N–H…O interactions in 1,3-diphenyl ...

    Indian Academy of Sciences (India)

    Unknown

    the synthesis and structural investigations of 1,3-diphenyl- urea have been undertaken. The title compound has been expected to be an excellent potential tyrosine phosphatase inhibitor and sickle-cell anemia treatment drug. 2. Experimental. A mixture of phenylisocyanate, 1⋅07 g (0⋅01 mole), aniline,. 0⋅94 g (0⋅01 mole) ...

  1. Proof of the Structure of the Stemodia chilensis Tetracyclic Diterpenoid (+)-19-Acetoxystemodan-12-ol by Synthesis from (+)-Podocarpic Acid: X-ray Structure Determination of a Key Intermediate.

    Science.gov (United States)

    Leonelli, Francesca; Mostarda, Azzurra; De Angelis, Luca; Lamba, Doriano; Demitri, Nicola; La Bella, Angela; Ceccacci, Francesca; Migneco, Luisa M; Marini Bettolo, Rinaldo

    2016-04-22

    The first synthesis of (+)-19-acetoxystemodan-12-ol (1), a stemodane diterpenoid isolated from Stemodia chilensis, is described. The structure was supported by an X-ray crystallographic analysis of intermediate (+)-9a, which confirmed the proposed structure and excluded the structure of (-)-19-hydroxystemod-12-ene as a possible candidate for the Chilean Calceolaria diterpenoid to which the (-)-19-hydroxystemar-13-ene structure (9b) had been erroneously assigned.

  2. X-ray metrology for ULSI structures

    International Nuclear Information System (INIS)

    Bowen, D. K.; Matney, K. M.; Wormington, M.

    1998-01-01

    Non-destructive X-ray metrological methods are discussed for application to both process development and process control of ULSI structures. X-ray methods can (a) detect the unacceptable levels of internal defects generated by RTA processes in large wafers, (b) accurately measure the thickness and roughness of layers between 1 and 1000 nm thick and (c) can monitor parameters such as crystallographic texture and the roughness of buried interfaces. In this paper we review transmission X-ray topography, thin film texture measurement, grazing-incidence X-ray reflectivity and high-resolution X-ray diffraction. We discuss in particular their suitability as on-line sensors for process control

  3. Crystal structure resolution by X-rays

    International Nuclear Information System (INIS)

    Jeannin, Y.

    1998-01-01

    This paper deals with the crystal structure analysis by X-rays. It details the different steps of the crystal structure resolution, the measured parameters and the possible errors with appropriate corrections. The presentation includes the x-rays intensity measurement, the structure factor calculus, the Patterson method, the direct methods, the structure analysis, the parameters refinement by least square fit, the temperature factors, disorder and twinning, the primary and secondary extinctions and a absolute configuration determination. (A.L.B.)

  4. Synthesis, X-ray structure and theoretical investigation of 2-(2 ...

    Indian Academy of Sciences (India)

    {Co(DMF)(BQ)Cl₂} and {Mn(DMF)(BQ)Cl₂} crystallized in triclinic space group P-1. The metal(II) environment exhibits trigonal bipyramidal coordination. These complexes show presence of N–H. . .Cl, C–H...Cl hydrogen bonds and strong intramolecular C–H...O interactions. The structure parameters were calculated and ...

  5. Synthesis and Single Crystal X-Ray Structure Determination of 3,3',5 ...

    African Journals Online (AJOL)

    Single crystal structure determination at 100 K revealed needle-like crystals in an orthorhombic crystal system. The asymmetric unit of the cell consists of an isolated chloride ion, one half of a tetrahedral [MnCl4]2- anion, a [H2Me4bpz]2+ dication and one half of a molecule of water. Keywords: Crystal Engineering, Hydrogen ...

  6. Synthesis and X-Ray Crystal Structures of Mononuclear Complexes of 1,3-Bis(8-quinolyloxy)propane

    International Nuclear Information System (INIS)

    Al-Mandhary, M.R.; Steel, P.

    2002-01-01

    The preparations and X-ray crystal structures of the first transition metal complexes of 1,3-bis(8-quinolyloxy)propane are described. The ligand acts as a trans-chelating N,N'-bidentate ligand in the three-coordinate silver nitrate complex and four-coordinate copper chloride complex, but as an N,O,O',N'-tetradentate ligand in the octahedral nickel chloride complex. Copyright (2002) CSIRO Australia

  7. Synthesis of 1 nm Pd Nanoparticles in a Microfluidic Reactor: Insights from in Situ X ray Absorption Fine Structure Spectroscopy and Small-Angle X ray Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Karim, Ayman M.; Al Hasan, Naila M.; Ivanov, Sergei A.; Siefert, Soenke; Kelly, Ryan T.; Hallfors, Nicholas G.; Benavidez, Angelica D.; Kovarik, Libor; Jenkins, Aaron; Winans, R. E.; Datye, Abhaya K.

    2015-06-11

    In this paper we show that the temporal separation of nucleation and growth is not a necessary condition for the colloidal synthesis of monodisperse nanoparticles. The synthesis mechanism of Pd nanoparticles was determined by in situ XAFS and SAXS in a microfluidic reactor capable of millisecond up to an hour time resolution. The SAXS results showed two autocatalytic growth phases, a fast growth phase followed by a very slow growth phase. The steady increase in the number of particles throughout the two growth phases indicates the synthesis is limited by slow continuous nucleation. The transition from fast to slow growth was caused by rapid increase in bonding with the capping agent as shown by XAFS. Based on this fundamental understanding of the synthesis mechanism, we show that 1 nm monodisperse Pd nanoparticles can be synthesized at low temperature using a strong binding capping agent such as trioctylphosphine (TOP).

  8. Structure-based design of potent HIV-1 protease inhibitors with modified P1-biphenyl ligands: synthesis, biological evaluation, and enzyme-inhibitor X-ray structural studies.

    Science.gov (United States)

    Ghosh, Arun K; Yu, Xufen; Osswald, Heather L; Agniswamy, Johnson; Wang, Yuan-Fang; Amano, Masayuki; Weber, Irene T; Mitsuya, Hiroaki

    2015-07-09

    We report the design, synthesis, X-ray structural studies, and biological evaluation of a novel series of HIV-1 protease inhibitors. We designed a variety of functionalized biphenyl derivatives to make enhanced van der Waals interactions in the S1 subsite of HIV-1 protease. These biphenyl derivatives were conveniently synthesized using a Suzuki-Miyaura cross-coupling reaction as the key step. We examined the potential of these functionalized biphenyl-derived P1 ligands in combination with 3-(S)-tetrahydrofuranyl urethane and bis-tetrahydrofuranyl urethane as the P2 ligands. Inhibitor 21e, with a 2-methoxy-1,1'-biphenyl derivative as P1 ligand and bis-THF as the P2 ligand, displayed the most potent enzyme inhibitory and antiviral activity. This inhibitor also exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray crystal structure of related Boc-derivative 17a-bound HIV-1 protease provided important molecular insight into the ligand-binding site interactions of the biphenyl core in the S1 subsite of HIV-1 protease.

  9. Synthesis, Characterization, and X-Ray Structure of Bis(O-butyldithiocarbonatobis(3-ethyl pyridinenickel(II

    Directory of Open Access Journals (Sweden)

    Inderjeet Kaur

    2014-01-01

    Full Text Available A new series of additional complexes of bis(O-butyldithiocarbonatonickel(II with ethylpyridines have been prepared and characterized by physicochemical techniques like elemental analysis, molar conductance measurements, TGA-DTA and UV-visible electronic spectroscopy, and IR-spectral data. The structure of [Ni(S2COC4H92(C7H9N2] has been established by X-ray crystallography. The complex crystallizes in the monoclinic space group P1/n with unit cell parameters a=14.0721(6, b=7.0078(2, and c=15.3604(7 Å and α=90.00, β=108.065(5, and γ=90.00°. The Ni atom in the title complex is octahedrally coordinated within a trans-N2S4 donor set, with the Ni atom located on a centre of inversion. Crystal structure was solved by direct methods and refined by full matrix least squares procedures to a final R-value of 0.0545 for 1984 observed reflections. The butyl chain is disordered over two sets of sites, with occupancy ratio of 0.572 : 0.427.

  10. Synthesis, X-ray crystal structure and optical properties research of novel diphenyl sulfone-based bis-pyrazoline derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Gong Zhongliang; Zheng Liangwen [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Zhao Baoxiang, E-mail: bxzhao@sdu.edu.cn [Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2012-02-15

    A series of novel bis-pyrazoline derivatives were synthesized by the reaction of chalcone and (sulfonylbis(3,1-phenylene))bis(hydrazine) in 20-34% yields. The structures of the compounds were determined by IR, {sup 1}H NMR, HRMS spectra, and a representative compound 3b was confirmed based on the X-ray crystallographic analysis. Absorption and fluorescence spectra of these compounds in dichloromethane solution were investigated. The results showed that the emission maxima varied from 415 to 444 nm mainly depending on C3 substituents of pyrazoline moiety. The compounds had higher quantum yields, when C3 substituent was an electron-withdrawing p-chlorophenyl group. Moreover, absorption spectra and emission spectra exhibited a blue-shift and a red-shift with increasing the polarity of solvents, respectively. Fluorescent molecules happened to collide with each other and resulted in quench of the fluorescence when the concentration increased over to 10{sup -5} M. - Highlights: Black-Right-Pointing-Pointer A series of novel diphenyl sulfone-based bis-pyrazoline derivatives were designed and synthesized. Black-Right-Pointing-Pointer Their UV-vis absorption and fluorescence emission spectra were investigated. Black-Right-Pointing-Pointer The relationship of substituents and the optical properties were discussed. Black-Right-Pointing-Pointer With increasing the solvent polarity, fluorescence emission displayed a red-shift and fluorescence quantum yields decreased. Black-Right-Pointing-Pointer Fluorescence was quenched when the concentration increased over to 10{sup -5} M.

  11. Synthesis, X-ray crystal structure and optical properties research of novel diphenyl sulfone-based bis-pyrazoline derivatives

    International Nuclear Information System (INIS)

    Gong Zhongliang; Zheng Liangwen; Zhao Baoxiang

    2012-01-01

    A series of novel bis-pyrazoline derivatives were synthesized by the reaction of chalcone and (sulfonylbis(3,1-phenylene))bis(hydrazine) in 20–34% yields. The structures of the compounds were determined by IR, 1 H NMR, HRMS spectra, and a representative compound 3b was confirmed based on the X-ray crystallographic analysis. Absorption and fluorescence spectra of these compounds in dichloromethane solution were investigated. The results showed that the emission maxima varied from 415 to 444 nm mainly depending on C3 substituents of pyrazoline moiety. The compounds had higher quantum yields, when C3 substituent was an electron-withdrawing p-chlorophenyl group. Moreover, absorption spectra and emission spectra exhibited a blue-shift and a red-shift with increasing the polarity of solvents, respectively. Fluorescent molecules happened to collide with each other and resulted in quench of the fluorescence when the concentration increased over to 10 −5 M. - Highlights: ► A series of novel diphenyl sulfone-based bis-pyrazoline derivatives were designed and synthesized. ► Their UV–vis absorption and fluorescence emission spectra were investigated. ► The relationship of substituents and the optical properties were discussed. ► With increasing the solvent polarity, fluorescence emission displayed a red-shift and fluorescence quantum yields decreased. ► Fluorescence was quenched when the concentration increased over to 10 −5 M.

  12. Synthesis, X-ray structure, spectroscopic properties and DFT studies of some dithiocarbazate complexes of nickel(II)

    Science.gov (United States)

    Takjoo, Reza; Centore, Roberto

    2013-01-01

    Two nickel(II) complexes with formulae NiL2 (1) and NiL'Im (2) (HL = allyl 2-benzylidene-hydrazinecarbodithioate, H2L' = allyl 2-(2-hydroxybenzylidene)hydrazinecarbodithioate, Im = Imidazole) have been synthesized and characterized by elemental analysis, molar conductivities, FT-IR, 1H NMR and UV/Vis spectroscopy. The crystal structure of the complexes has been determined by single crystal X-ray diffractometry. Both L and L' ligands are coordinated to the metal in the thiolate form. In 1, the square planar coordination of the metal is achieved by coordination of two bidentate ligand units acting through azomethine nitrogen and the thiolato sulfur donor atoms. The complex 2 has a square-planar geometry with the tridentate ligand coordinated to the metal through salicylate oxygen, azomethine nitrogen and the thiolato sulfur atoms, while the fourth coordination position is occupied by one N atom of imidazole. Also natural bond orbitals (NBOs), frontier molecular orbitals (FMOs) and Mulliken charge computational studies on complexes carried out in the ground state with the DFT and theory at B3LYP/6-31G(d,p) level of theory.

  13. Synthesis, characterization, X-ray crystal structures of heterocyclic Schiff base compounds and in vitro cholinesterase inhibition and anticancer activity

    Science.gov (United States)

    Arafath, Md. Azharul; Adam, Farook; Al-Suede, Fouad Saleih R.; Razali, Mohd R.; Ahamed, Mohamed B. Khadeer; Abdul Majid, Amin Malik Shah; Hassan, Mohd Zaheen; Osman, Hasnah; Abubakar, Saifullah

    2017-12-01

    Four heterocyclic embedded Schiff base derivatives (1-4) were synthesized and characterized by melting point, elemental analysis, FTIR, 1H, 13C NMR, UV-Visible spectral data. The structures of compounds 1, 2 and 4 were successfully established through single crystal X-ray diffraction analysis. In vitro cholinesterase inhibition assays showed that the cyclized derivative 1 displayed higher BuChE enzyme inhibitory activity with IC50 value of 1.45 ± 0.09 μM. The anti-proliferative efficacies of the compounds were also evaluated using human colorectal HCT 116 and breast MCF-7 adenocarcinoma cell lines. In addition, a human normal endothelial cell line (Ea.hy926) was also tested to assess the safety and selectivity of the compounds towards normal and cancer cells, respectively. Among the compounds tested, compound 2 displayed potent cytotoxic effect (IC50 = 34 μM) against HCT 116 cells with highest selectivity index of 3.1 with respect to the normal endothelial cells. Whereas, compound 4 exhibited significant anti-proliferative effect (IC50 = 21.1 μM) against MCF-7 cells with highest selectivity index of 3.3 with respect to the normal endothelial cells. The docking result of these compounds against hAChE showed potent activities with different binding modes. These compounds could be a promising pharmacological agent to treat cancer and Alzheimer's disease.

  14. Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Novel Protease Inhibitors: Design, Synthesis, Protein-Ligand X-ray Structure and Biological Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Takayama, Jun; Rao, Kalapala Venkateswar; Ratia, Kiira; Chaudhuri, Rima; Mulhearn, Debbie C.; Lee, Hyun; Nichols, Daniel B.; Baliji, Surendranath; Baker, Susan C.; Johnson, Michael E.; Mesecar, Andrew D. (Purdue); (UC); (UIC)

    2012-02-21

    The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15h (enzyme IC{sub 50} = 0.56 {mu}M; antiviral EC{sub 50} = 9.1 {mu}M) and the corresponding (R)-Me 15g (IC{sub 50} = 0.32 {mu}M; antiviral EC{sub 50} = 9.1 {mu}M) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15g-bound SARS-CoV PLpro and a corresponding model of 15h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.

  15. Synthesis, X-Ray Crystal Structures, Biological Evaluation, and Molecular Docking Studies of a Series of Barbiturate Derivatives

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2016-01-01

    Full Text Available A series of barbiturates derivatives synthesized and screened for different set of bioassays are described. The molecular structures of compounds 5a, 5d, and 5f were solved by single-crystal X-ray diffraction techniques. The results of bioassay show that compounds 4a, 4b, 4c, 4d, 4e, 4f, and 4g are potent antioxidants in comparison to the tested standards, butylated hydroxytoluene (BHT, and N-acetylcysteine. Compounds 4a–4e (IC50=101.8±0.8–124.4±4.4 μM and 4g (IC50=104.1±1.9 μM were more potent antioxidants than the standard (BHT, IC50=128.8±2.1 μM. The enzyme inhibition potential of these compounds was also evaluated, in vitro, against thymidine phosphorylase, α-glucosidase, and β-glucuronidase enzymes. Compounds 4c, 4h, 4o, 4p, 4q, 5f, and 5m were found to be potent α-glucosidase inhibitors and showed more activity than the standard drug acarbose, whereas compounds 4v, and 5h were found to be potent thymidine phosphorylase inhibitors, more active than the standard drug, 7-deazaxanthine. All barbiturates derivatives (4a–4x, 4z, and 5a–5m were found to be noncytotoxic against human prostate (PC-3, Henrietta Lacks cervical (HeLa and Michigan Cancer Foundation-7 breast (MCF-7 cancer cell lines, and 3T3 normal fibroblast cell line, except 4y which was cytotoxic against all the cell lines.

  16. In situ powder X-ray diffraction, synthesis, and magnetic properties of the defect zircon structure ScVO(4-x).

    Science.gov (United States)

    Shafi, Shahid P; Kotyk, Matthew W; Cranswick, Lachlan M D; Michaelis, Vladimir K; Kroeker, Scott; Bieringer, Mario

    2009-11-16

    We report the formation pathway of ScVO(4) zircon from ScVO(3) bixbyite with emphasis on the synthesis and stability of the novel intermediate defect zircon phase ScVO(4-x) (0.0 situ powder X-ray diffraction. The oxidation of ScVO(3) to ScVO(4) involves two intermediates of composition ScVO(3.5+y) (0.00 diffraction, neutron diffraction, and bulk magnetic susceptibility data as well as (45)Sc and (51)V solid state NMR spectroscopy. ScVO(4-x) can only be obtained by oxidation of ScVO(3) or ScVO(3.5+y) while the reduction of ScVO(4) does not yield the novel defect structure. Mechanistic insights into the oxidative formation of ScVO(4) via the defect structure are presented.

  17. Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands.

    Science.gov (United States)

    Ghosh, Arun K; Takayama, Jun; Kassekert, Luke A; Ella-Menye, Jean-Rene; Yashchuk, Sofiya; Agniswamy, Johnson; Wang, Yuan-Fang; Aoki, Manabu; Amano, Masayuki; Weber, Irene T; Mitsuya, Hiroaki

    2015-11-01

    We describe the design, synthesis and biological evaluation of a series of novel HIV-1 protease inhibitors bearing isophthalamide derivatives as the P2-P3 ligands. We have investigated a range of acyclic and heterocyclic amides as the extended P2-P3 ligands. These inhibitors displayed good to excellent HIV-1 protease inhibitory activity. Also, a number of inhibitors showed very good antiviral activity in MT cells. Compound 5n has shown an enzyme Ki of 0.17 nM and antiviral IC50 of 14 nM. An X-ray crystal structure of inhibitor 5o-bound to HIV-1 protease was determined at 1.11Å resolution. This structure revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Synthesis, structural, X-ray photoelectron spectroscopy (XPS) studies and IR induced anisotropy of Tl{sub 4}HgI{sub 6} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Parasyuk, O.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine); Khyzhun, O.Y. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Piasecki, M. [Institute of Physics, J. Dlugosz University Częstochowa, Armii Krajowej 13/15, Częstochowa (Poland); Kityk, I.V., E-mail: iwank74@gmail.com [Electrical Engineering Department, Czestochowa University Technology, Armii Krajowej 17, PL-42-217, Czestochowa (Poland); Lakshminarayana, G. [Wireless and Photonic Networks Research Centre, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor (Malaysia); Luzhnyi, I. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Fochuk, P.M. [Yuriy Fed’kovych Chernivtsi National University, 2 Kotziubynskoho Str., 58012, Chernivtsi (Ukraine); Fedorchuk, A.O. [Department of Inorganic and Organic Chemistry, Lviv National University of Veterinary Medicine and Biotechnologies, Pekarska Street 50, 79010, Lviv (Ukraine); Levkovets, S.I.; Yurchenko, O.M.; Piskach, L.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine)

    2017-02-01

    In the present work, we report on the synthesis and structural properties including X-ray protoelectron spectroscopy (XPS) analysis of Tl{sub 4}HgI{sub 6} crystals that were grown by Bridgman-Stockbarger method up to 80 mm in length and 18 mm in diameter. The existence of the ternary compound Tl{sub 4}HgI{sub 6} that melts incongruently at 641 K was confirmed. Phase equilibria and structural properties for the TlI–HgI{sub 2} system were investigated by differential thermal analysis (DTA) and X-ray diffraction (XRD) methods. X-ray photoelectron spectra were measured for both pristine and Ar{sup +} ion-bombarded Tl{sub 4}HgI{sub 6} single crystal surfaces. The data reveal that the Tl{sub 4}HgI{sub 6} single crystal is sensitive with respect to Ar{sup +} ion-bombardment as 3.0 keV Ar{sup +} irradiation over 5 min at an ion current density 14 μA/cm{sup 2} induces changes to the elemental stoichiometry of the Tl{sub 4}HgI{sub 6} surface, leading to a decrease of the mercury content in the topmost surface layers. X-ray photoelectron spectroscopy (XPS) measurements indicate very low hygroscopic nature of the Tl{sub 4}HgI{sub 6} single crystal surface. The IR coherent bicolor laser treatment at wavelengths 10.6/5.3 μm has shown an occurrence of anisotropy at wavelengths 1540 nm of Er:glass laser. This may open the applications of Tl{sub 4}HgI{sub 6} as a material for IR laser triggering. - Highlights: • Phase diagram of the HgI{sub 2}–TlI system was built. • Tl{sub 4}HgI{sub 6} single crystals were grown by Bridgman Stockbarger method. • XRD, XPS analysis was done. • Ir induced anisotropy was established. • The compounds may be proposed as Ir laser operated polarizers.

  19. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1995-01-01

    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  20. Synthesis of hydroxyapatite and structural refinement by X-ray diffraction; Sintese da hidroxiapatita e refinamento estrutural por difracao de raios-X

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Jorge Correa de [Universidade do Estado do Rio de Janeiro (UERJ), Sao Goncalo, RJ (Brazil). Faculdade de Formacao de Professores; Sena, Lidia [Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial (INMETRO), Duque de Caxias, RJ (Brazil). Div. de Metrologia de Materiais; Bastos, Ivan Napoleao [Universidade do Estado do Rio de Janeiro (UERJ), Nova Friburgo, RJ (Brazil). Inst. Politecnico]. E-mail: jcaraujo@iprj.uerj.br; Soares, Gloria Dulce de Almeida [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil)

    2007-07-01

    A sample of hydroxyapatite was synthesized and its crystalline structure was analyzed by X-ray diffraction by means of the Rietveld method. Two functions were used to fit the peak profiles, modified Voigt (TCHZ) and Pearson VII. The occupational factors and lattice parameters obtained by both models show that the sample does not contain relevant cationic substitutions. The interatomic distances from Ca1 to oxygens O1, O2 and O3 were adequate for a pure hydroxyapatite without defect at site Ca1. Besides, the use of multiple lines in planes (300) and (002) associated with the model Pearson VII resulted in good agreement with the TCHZ model with respect to the size-strain effects with an ellipsoidal shape of crystallites. In conclusion, the procedures adopted in the synthesis of hydroxyapatite produced a pure and crystalline material. The experimental results of transmission electron microscopy confirmed the predicted shape of crystals. (author)

  1. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  2. An efficient synthesis, X-ray and spectral characterization of ...

    Indian Academy of Sciences (India)

    An efficient synthesis, X-ray and spectral characterization of biphenyl derivatives. Ravindra R Kamble Dharesh B Biradar Gangadhar Y Meti Tasneem Taj Tegginamath Gireesh Imthiyaz Ahmed M Khazi Sundar T Vaidyanathan Raju Mohandoss Balasubramanian Sridhar Viraraghav Parthasarathi. Volume 123 Issue 4 July ...

  3. Synthesis, quantum chemical computations and x-ray ...

    African Journals Online (AJOL)

    Benyza N

    2017-05-01

    May 1, 2017 ... Journal of Fundamental and Applied Sciences is licensed under a Creative Commons Attribution-NonCommercial 4.0. International License. Libraries Resource Directory. We are listed under Research Associations category. SYNTHESIS, QUANTUM CHEMICAL COMPUTATIONS AND X-RAY.

  4. A glimpse of structural biology through X-ray crystallography.

    Science.gov (United States)

    Shi, Yigong

    2014-11-20

    Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

  5. Synthesis and X-ray crystal structure of the first tetrathiafulvalene-based acceptor-donor-acceptor sandwich

    DEFF Research Database (Denmark)

    Simonsen, Klaus B.; Thorup, Niels; Cava, Michael P.

    1998-01-01

    The synthesis and characterization of a bis-macrocyclic A-D-A sandwich produced in a simple one-pot reaction is reported. Only one acceptor unit participates in charge-transfer interactions with the TTF unit in the solid state....

  6. Native Chemical Ligation at Asx-Cys, Glx-Cys: Chemical Synthesis and High Resolution X-ray Structure of ShK Toxin by Racemic Protein Crystallography

    Science.gov (United States)

    Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B. H.

    2013-01-01

    We have re-examined the utility of native chemical ligation at −Gln/Glu-Cys− [Glx-Cys] and −Asn/Asp-Cys− [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at −Gln-Cys− and Asn-Cys− sites without side reactions. After optimization, ligation at a −Glu-Cys− could also be used as a ligation site, with minimal levels of byproduct formation. However, −Asp-Cys− is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at −Gln-Cys− enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule. PMID:23919482

  7. X-ray diffraction of modulated structures

    International Nuclear Information System (INIS)

    Tsujimoto, T.; Hashimoto, K.; Saito, K.

    1977-01-01

    Modulated structures are regarded as a macrolattice, in which each lattice point is a ''unit region of concentration variation'' (abbreviated to ''unit region'') and an average lattice parameter is Qa 0 . The X-ray intensity diffracted from modulated structures, I/sub m(s) is given by I/sub m(s). I/sub d/(s). I/sub u/(s) is the scattering intensity from the ''unit region'' and I/sub u/(s) is that from the imaginary macrolattice in which each lattice point is the unit scattering factor. A region containing one zone-complex has been chosen as the ''unit region'' and the effects of the lattice spacing of the macrolattice and its disturbance on diffraction patterns have been discussed. When zone-complexes are small, I/sub m(s) is dominated by I/sub d/(s) and peaks of I/sub d/(s) are observed as side-bands or additional diffraction lines. The number of additional diffraction lines increases with an increase in Qa 0 and typical side-bands appear at a stage of this process. When the periodicity of the macrolattice is distrubed deeply or Qa 0 is large, I/sub u/(s) is observed directly as diffraction effects. The present theory explains reasonably the asymmetry of side-bands in position, the movement of main diffraction line with aging and the change of side-bands into diffraction lines of metastable phases during aging

  8. Zinc(II) complexes with potent cyclin-dependent kinase inhibitors derived from 6-benzylaminopurine: synthesis, characterization, X-ray structures and biological activity

    Czech Academy of Sciences Publication Activity Database

    Trávníček, Zdeněk; Kryštof, Vladimír; Šipl, M.

    2006-01-01

    Roč. 100, č. 2 (2006), s. 214-225 ISSN 0162-0134 R&D Projects: GA ČR GA203/04/1168 Institutional research plan: CEZ:AV0Z50380511 Keywords : Zinc(II) complexes * 6-Benzylaminopurine derivatives * Bohemine * Olomoucine * X-ray structures Subject RIV: CA - Inorganic Chemistry Impact factor: 2.654, year: 2006

  9. Spectroscopic studies, theoretical models and structural characterization. II. Synthesis and X-ray powder diffraction of the elpasolites Cs2NaSmCl6

    International Nuclear Information System (INIS)

    Poblete, V.; Acevedo, R.

    1998-01-01

    In this research work, we report the synthesis and structural characterization of the stoichiometric elpasolite Cs 2 NaSmCl 6 . The synthesis was performed under a solid state reaction in nitrogen atmosphere from the chemicals CsCl, NaCl and SmCl 3 weighted stoichiometrically. The best possible crystallization temperature was obtained using thermal studies of the type DTA/TGA (the thermal treatment was allowed to proceed for 2.5 hours at 755 Centigrade, showing a temperature gradient of 10 Centigrade/minute). The structural characterization by powder X-ray diffraction (XDR) indicates that this elpasolite belongs to the Fm 3m (O h 5 ) space group and the optimized structural parameters are as follows: a 0 = 10.8342 Armstrong, V 1271.72 Armstrong 3 , Z=4, M=651.88, D x =3.406 y D exp=3.41 ± 0.01. The profile refinement, using the Rietveld method, allowed us to fit the experimental and the calculated intensities of a total of 32 lines. The above result indicates that the condition R exp 2+ + 3Cl -1 and the counter ions filling the octahedral holes, in full agreement with anti fluorite type crystal. According to the above description, these elpasolite adopt the form (M 1/3 □ 2/3 ) 4 X 2 , where M labels the central metal, X stand for the chlorine ions and □ represent the vacancies, which may accommodate a significant amount of defects without collapsing. This experimental study provides the necessary input to test theoretical models against experimental data. (Author)

  10. Model for Astrophysical X-Ray Absorption Fine Structure

    International Nuclear Information System (INIS)

    Forrey, R.C.; Woo, J.W.; Cho, K.

    1998-01-01

    We present a theoretical model and database designed to provide analysis of astrophysical X-ray absorption fine structure (XAFS). The model includes spherical wave corrections and multiple-scattering contributions to the modification of the X-ray absorption coefficient. The model and database provide the basis for the astrophysical XAFS analysis (AXA) tool, which may be used to analyze properties of interstellar grains and molecules from high-resolution X-ray spectra expected to be observed by future satellite missions (e.g., the Advanced X-ray Astrophysics Facility). copyright copyright 1998. The American Astronomical Society

  11. X-ray absorption near-edge structure (XANES) spectroscopy

    NARCIS (Netherlands)

    Henderson, Grant S.; De Groot, Frank M F|info:eu-repo/dai/nl/08747610X; Moulton, Benjamin J A

    2014-01-01

    The previous Reviews in Mineralogy volume on spectroscopic methods (Vol. 18 Spectroscopic Methods in Mineralogy and Geology, Frank C. Hawthorne, ed. 1988), contained a single chapter on X-ray absorption spectroscopy which reviewed aspects of both EXAFS (Extended X-ray Absorption Fine Structure) and

  12. Synthesis and single crystal X-ray analysis of two griseofulvin metabolites

    DEFF Research Database (Denmark)

    Rønnest, Mads Holger; Harris, Pernille; Gotfredsen, Charlotte Held

    2010-01-01

    The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis.......The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis....

  13. Synthesis, characterization and x-ray crystal structure of a dimethyltin (IV) dichloride complex of 2-acetylpyridine benzophenone azine

    International Nuclear Information System (INIS)

    Mustaffa Shamsuddin; Md Abu Affan; Ramli Atan

    1998-01-01

    Dimethyltin dichloride react with 2-ac ethylpyridine benzophenone azine (apba) in refluxing dry hexane to give (SnMe 2 Cl 2 (apba)) where the azine ligand acts as a bidentate N-N chelating ligand. The complex has been characterized by IR spectroscopy, 1 H and 13 C NMR spectroscopic data and elemental analyses. The crystal structure of the dimethyltin(IV) derivative has also been determined. Crystals are monoclinic with space group P2(1)/n with cell dimensions: a = 10.1819(3) Armstrong, b = 18.3113(5) Armstrong, c = 12.6451(4) Armstrong

  14. Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Kalyaneswar; Uppalapati, Maruti; Ault-Riché, Dana; Kenney, John; Lowitz, Joshua; Sidhu, Sachdev S.; Kent, Stephen B.H. (Antibody Solutions); (Toronto); (Reflexion); (UC)

    2012-10-23

    Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF{sub 165} to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {l_brace}D-protein antagonist + L-protein form of VEGF-A{r_brace}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 {angstrom}. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 {angstrom}{sup 2} in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2.

  15. X-ray absorption spectroscopy: EXAFS [Extended X-ray Absorption Fine Structure] and XANES [X-ray Absorption Near Edge Structure

    International Nuclear Information System (INIS)

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

    1990-04-01

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

  16. Synthesis of a 2,2'-bipyridyl functionalized oligovinylene-phenylene using Heck and Horner-Wadsworth-Emmons reactions and X-ray crystal structure of E-(4-(4-bromostyryl)phenyl)(methyl)sulfane.

    Science.gov (United States)

    Karácsony, Orsolya; Deschamps, Jeffrey R; Trammell, Scott A; Nita, Rafaela; Knight, D Andrew

    2012-05-14

    The synthesis of a new 2,2'-bipyridyl functionalized oligovinylenephenylene (OVP-5) containing a methyl protected thiol using Heck coupling and the Horner-Wadsworth-Emmons reaction and is described. A key step involving a diisopropylcarbodiimide promoted dehydration of a stable β-hydroxyphosphonate intermediate was identified. The structure of precursor E-(4-(4-bromostyryl)phenyl)(methyl)sulfane was determined using X-ray crystallography.

  17. Synthesis of a 2,2'-Bipyridyl Functionalized Oligovinylene-Phenylene Using Heck and Horner-Wadsworth-Emmons Reactions and X-ray Crystal Structure of E-(4-(4-Bromostyrylphenyl(methylsulfane

    Directory of Open Access Journals (Sweden)

    Orsolya Karácsony

    2012-05-01

    Full Text Available The synthesis of a new 2,2'-bipyridyl functionalized oligovinylenephenylene (OVP-5 containing a methyl protected thiol using Heck coupling and the Horner-Wadsworth-Emmons reaction and is described. A key step involving a diisopropylcarbodiimide promoted dehydration of a stable b-hydroxyphosphonate intermediate was identified. The structure of precursor E-(4-(4-bromostyrylphenyl(methylsulfane (1 was determined using X-ray crystallography.

  18. Some ecological aspects during X-ray structure analysis

    International Nuclear Information System (INIS)

    Mammadov, S.C.; Gurbanov, M.M.; Bayramov, C.C.; Zeynalov, H.I.

    2004-01-01

    Full text : At present solid-state and crystals substances take special place in most fields of our life. Radiography, electron and neutron diffraction analysis are usually held for clarification of the structure of above-mentioned matters. But X-ray analysis got the largest expansion due to its technical possibilities and accuracy of the received results. The basis of this analysis forms the diffraction of X-ray beams through the crystal during which arises air ionization that can render negative influence on associates. Further in clause some stages, directions and also methods of protection during carrying out of X-ray analysis are most in detail described [az

  19. A laboratory-based hard x-ray monochromator for high-resolution x-ray emission spectroscopy and x-ray absorption near edge structure measurements.

    Science.gov (United States)

    Seidler, G T; Mortensen, D R; Remesnik, A J; Pacold, J I; Ball, N A; Barry, N; Styczinski, M; Hoidn, O R

    2014-11-01

    We report the development of a laboratory-based Rowland-circle monochromator that incorporates a low power x-ray (bremsstrahlung) tube source, a spherically bent crystal analyzer, and an energy-resolving solid-state detector. This relatively inexpensive, introductory level instrument achieves 1-eV energy resolution for photon energies of ∼5 keV to ∼10 keV while also demonstrating a net efficiency previously seen only in laboratory monochromators having much coarser energy resolution. Despite the use of only a compact, air-cooled 10 W x-ray tube, we find count rates for nonresonant x-ray emission spectroscopy comparable to those achieved at monochromatized spectroscopy beamlines at synchrotron light sources. For x-ray absorption near edge structure, the monochromatized flux is small (due to the use of a low-powered x-ray generator) but still useful for routine transmission-mode studies of concentrated samples. These results indicate that upgrading to a standard commercial high-power line-focused x-ray tube or rotating anode x-ray generator would result in monochromatized fluxes of order 10(6)-10(7) photons/s with no loss in energy resolution. This work establishes core technical capabilities for a rejuvenation of laboratory-based hard x-ray spectroscopies that could have special relevance for contemporary research on catalytic or electrical energy storage systems using transition-metal, lanthanide, or noble-metal active species.

  20. X-ray structural analysis of some Indian coals

    International Nuclear Information System (INIS)

    Binoy K Saikia, B.K.

    2009-01-01

    Coal is one of the most abundant energy resources and has the capability to meet future energy needs with high reliability. The use of coal as an energy source and as a source of organic chemicals feedstock may become more important in the future. It is physically and chemically a heterogeneous and carbonaceous rock which consists of organic and inorganic materials. Assam coal has been, and continuous to be, a valuable energy source, especially for the various industry in India and for liquefactions of coal. The basic chemical structure of coal that has been widely accepted today was built up from the synthesis of results obtained from X-ray diffraction data. The present paper reports a comparative investigation of coals from different collieries/areas of Makum coal field, Assam viz. Ledo, Tikak, Baragolai, Tipong and Tirap collieries Makum coal field, Assam with the help of X-ray diffraction (XRD). The X-ray diffraction patterns indicate that the coals are amorphous in nature. The present XRD method includes the evaluation of Function of Radial Distribution of Atoms (FRDA) and structural interpretations of the coals from their Radial Distribution Function (RDF) plots after proper corrections for air scatter, absorption by sample and polarization. The curve intensity profiles in FRDA clearly show quite regular molecular packets for these coals. The first maxima in the FRDA curves was obtained at r= 0.4 Amstrong for Ledo, Baragolai and Tipong coals whereas for Tikak coal it was observed at r= 0.5 Amstrong. The first maximum in the pair distribution function plots, G (r) of Ledo, Tikak, and Tipong coals was obtained at r=0.15 nm whereas for Baragolai and Tirap coals it was observed at r=0.14 nm and r=0.12 nm respectively, which relates to the C=C (aliphatic/aromatic) bonds in coal matrix. The Assam coal samples from Ledo, Tikak, Baragolai, Tipong and Tirap collieries of Makum coalfield have almost the same RDF inter-atomic distances except slight differences. This

  1. New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

    Science.gov (United States)

    Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

    2018-03-01

    The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

  2. Design, Synthesis, and X-ray Crystal Structures of 2,4-Diaminofuro[2,3-d]pyrimidines as Multireceptor Tyrosine Kinase and Dihydrofolate Reductase Inhibitors

    Science.gov (United States)

    Gangjee, Aleem; Li, Wei; Lin, Lu; Zeng, Yibin; Ihnat, Michael; Warnke, Linda A.; Green, Dixy W.; Cody, Vivian; Pace, Jim; Queener, Sherry F.

    2009-01-01

    To optimize dual receptor tyrosine kinase (RTK) and dihydrofolate reductase (DHFR) inhibition, the E- and Z-isomers of 5-[2-(2-methoxyphenyl)prop-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamines (1a and 1b) were separated by HPLC and the X-ray crystal structures (2.0 Å and 1.4 Å respectively) with mouse DHFR and NADPH as well as 1b with human DHFR (1.5 Å) were determined. The E- and Z-isomers adopt different binding modes when bound to mouse DHFR. A series of 2,4-diaminofuro[2,3-d]pyrimidines 2–13 were designed and synthesized using the X-ray crystal structures of 1a and 1b with DHFR to increase their DHFR inhibitory activity. Wittig reactions of appropriate 2-methoxyphenyl ketones with 2,4-diamino-6-chloromethyl furo[2,3-d]pyrimidine afforded the C8–C9 unsaturated compounds 2–7 and catalytic reduction gave the saturated 8–13. Homologation of the C9-methyl analog maintains DHFR inhibitory activity. In addition, inhibition of EGFR and PDGFR-β were discovered for saturated C9-homologated analogs 9 and 10 that were absent in the saturated C9-methyl analogs. PMID:19748785

  3. X-ray structure based evaluation of analogs of citalopram

    DEFF Research Database (Denmark)

    Topiol, Sid; Bang-Andersen, Benny; Sanchez, Connie

    2017-01-01

    The recent publication of X-ray structures of SERT includes structures with the potent antidepressant S-Citalopram (S-Cit). Earlier predictions of ligand binding at both a primary (S1) and an allosteric modulator site (S2), were confirmed. We provide herein examples of a series of Citalopram anal...

  4. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Unknown

    Powder data is especially useful to deduce accurate cell parameters. Rietveld's refinement procedure1,2 has revolutionized the application of powder X-ray diffraction by resulting in a large number of structures being refined in the last decade. If a suitable starting model is available, it has become routine to refine structures ...

  5. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    Science.gov (United States)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  6. Second-sphere coordination complex via hydrogen bonding: Synthesis, characterization, X-ray crystal structure determination and packing of hexaamminecobalt(III) chloride di( para-nitrobenzoate)

    Science.gov (United States)

    Sharma, Raj Pal; Bala, Ritu; Sharma, Rajni; Perez, Julio; Miguel, Daniel

    2006-09-01

    A reddish orange coloured crystalline solid of hexaamminecobalt(III) chloride di( para-nitrobenzoate) was obtained when hexaamminecobalt(III) chloride was reacted with the sodium salt of para-nitrobenzoic acid (1:3 molar ratio) in hot aqueous medium. This cobalt(III) complex salt has been characterized by elemental analyses and spectroscopic techniques (e.g. UV/visible, IR and NMR). Single-crystal X-ray structure determination of the title complex salt revealed that it contains the cationic cobaltammine ([Co(NH 3) 6] 3+) and mixed anions (Cl -, NO 2C 6H 4COO -), which are held together by electrostatic forces attractions through second-sphere coordination, i.e. N-H⋯O (carboxylate and nitro) and N-H⋯Cl hydrogen bonds, resulting in a three-dimensional network.

  7. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  8. Astrophysical extended X-ray absorption fine-structure analysis

    International Nuclear Information System (INIS)

    Woo, J.W.; Forrey, R.C.; Cho, K.; Department of Physics and Division of Applied Sciences, Harvard University)

    1997-01-01

    We present an astrophysical extended X-ray absorption fine-structure (EXAFS) analysis (AEA) tool. The AEA tool is designed to generate a numerical model of the modification to the X-ray absorption coefficient due to the EXAFS phenomenon. We have constructed a complete database (elements up to the atomic number 92) of EXAFS parameters: central atom phase shift (2δ 1 ), backscattering phase shift (φ b ), and backscattering amplitude (F). Using the EXAFS parameter data base, the AEA tool can generate a numerical model of any compound when the atomic numbers of neighboring atoms and their distances to the central X-ray-absorbing atom are given. copyright 1997 The American Astronomical Society

  9. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  10. Nano structured materials studied by coherent X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Gulden, Johannes

    2013-03-15

    Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

  11. Nano structured materials studied by coherent X-ray diffraction

    International Nuclear Information System (INIS)

    Gulden, Johannes

    2013-03-01

    Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

  12. Functional coordination polymers and MOFs from reactions of the lanthanides and barium with azole ligands. Synthesis and characterization with a focus on structure determination from X-ray powder diffraction data

    International Nuclear Information System (INIS)

    Rybak, Jens-Christoph

    2012-01-01

    This thesis deals with the synthesis and characterization of coordination polymers and MOFs of the lanthanides and barium with different azolic N-heterocycles. A total of 18 new organic-inorganic hybrid materials, as well as a series of co-doped compounds is presented. Besides the structural characterization of these materials from X-ray diffraction powder data, the focus of the investigations is on the thermal and photoluminescence spectroscopic properties. The lanthanides La - Lu, except Eu and Pm, can be reacted with 1H-1,2,3-triazole to give the series of the isotypic dense 3D-MOFs 3 ∞ [Ln(Tz * ) 3 ]. Investigation of the photoluminescence properties of these compounds reveals a broad range of different luminescence phenomena, including the first observation of an intrinsic inner-filter effect of the Ln 3+ -ions. The structure of this isotypic series of compounds was solved and refined from X-ray powder diffraction data. A 2D-polymorph of these compounds 2 ∞ [Ln(Tz * ) 3 ], is observed for Ln = Sm, Tb and was characterized by single crystal data. The reaction of Eu with 1H-benzotriazole yields the 1D-coordination polymer 1 ∞ [Eu(Btz) 2 (BtzH) 2 ], which is the first example of a divalent rare earth benzotriazolate. Analysis of the thermal properties reveals the transformation to the 3D-MOF 3 ∞ [Eu(Btz) 2 ] at higher temperatures. The structure of this material was also solved from X-ray powder diffraction data. Investigation of the photoluminescence properties of the co-doped compounds 3 ∞ [Ba 1-x Eu x (Im) 2 ], which were obtained from reaction of the salt-like hydrides BaH 2 and EuH 2 with imidazole, show that the synthesis of luminescent MOF materials by co-doping of non-luminescent networks with luminescence centers is possible. The structure of these materials was solved from X-ray powder diffraction data of the undoped compound 3 ∞ [BaEu(Im) 2 ]. Structural characterization of materials from X-ray powder diffraction data is an important aspect

  13. Structural Investigations of Nanowires Using X-Ray Diffraction

    DEFF Research Database (Denmark)

    Stankevic, Tomas

    Advancements in growth of the nanowire-based devices opened another dimension of possible structures and material combinations, which nd their applications in a wide variety of elds, including everyday life. Characterization of such devices brings its own challenges and here we show that X-rays oer...

  14. Synthesis, characterization, electrochemical studies and X-ray structures of mixed-ligand polypyridyl copper(II complexes with the acetate

    Directory of Open Access Journals (Sweden)

    Adekunle Oluwafunmilayo F.

    2016-01-01

    Full Text Available [Cu(phen2(CH3COO](ClO4.2H2O (1 and [Cu(bipy2(CH3COO]-(ClO4.H2O (2 {phen = 1,10-phenanthroline, bipy = 2,2’-bipyridine}were synthesized and characterized. The complexes were characterized by employying elemental analyses, infrared and UV-Visible spectroscopy, room temperature magnetic measurements and the crystal structures elucidated using X-ray diffraction experiment. The redox properties of the complexes were also investigated. Both structures have a square pyramidal CuN4O chromophore which exhibit significant distortions due to long Cu-O [2.217(3 Å for (1 and 2.179 (1 for (2] and Cu-N [2.631(2 Å for (1 and 2.714(1 Å for (2] bonds. This distortion if further shown by the O-Cu-N bond angles [147.71(8 o for (1 and 153.40(5 o for (2]. The elemental analyses further support the structural details unveiled by the single crystal X-ray diffraction analysis. The infrared spectra shows the acetate vibrational frequencies at 1587 cm-1,1428 cm-1, 1314 cm-1 for (1 and 1571 cm-1, 1441 cm-1, 1319c m-1 for (2 and the perchlo-rate bands at 1059 cm-1, 720 cm-1 (1 and 1080 cm-1,768 cm-1 (2. The broad d-d bands for the copper ion at 14,514 cm-1(1 and 14,535 cm-1(2 support the adoption of square pyramid geometries. The magnetic moments for the two complexes are 1.83 B.M for (1 and 1.72 B.M for (2. The peak to peak values of the two complexes show that the electrode reactions are quasi-reversibile with ΔEp = 0.023V (1 and 0.025V for (2. In both structures, there are π-π intermolecular interactions in addition to hydrogen bonding between the units.

  15. X-ray Structures of Precursors of Styrylpyridine-Derivatives Used to Obtain 4-((E-2-(Pyridin-2-ylvinylbenzamido-TEMPO: Synthesis and Characterization

    Directory of Open Access Journals (Sweden)

    Guillermo Soriano-Moro

    2015-04-01

    Full Text Available The synthesis and characterization of the precursor isomers trans-4-(2-(pyridin-2-ylvinylbenzaldehyde (I, trans-4-(2-(pyridin-4-ylvinylbenzaldehyde (II, trans-4-(2-(pyridin-2-ylvinylbenzoic acid (III and (E-4-(2-(pydridin-4-ylvinylbenzoic acid (IV are reported. These compounds were prepared in order to obtain trans-4-((E-2-(pyridin-2-ylvinylbenzamide-TEMPO (V. Compounds I and II were obtained by using a Knoevenagel reaction in the absence of a condensing agent and solvent. Oxidation of the aldehyde group using the Jones reagent afforded the corresponding acid forms III and IV. A condensation reaction with 4-amino-TEMPO using oxalyl chloride/DMF/CH2Cl2 provided the 4-((E-2-(pyridin-2-ylvinylbenzamide-TEMPO. Single crystals of compounds I, II and III were obtained and characterized by X-ray diffraction. Compound I belongs to space group P21/c, a = 12.6674(19 Å, b = 7.2173(11 Å, c = 11.5877(14 Å, b = 97.203(13° and the asymmetric unit was Z = 4, whereas compound II was in the space group P21, with a = 3.85728(9 Å, b = 10.62375(19 Å, c = 12.8625(2 Å, b = 91.722 (2° and the asymmetric unit was Z = 2. Compound III crystallized as single colorless needle crystals, belonging to the monoclinic system with space group P21, with Z = 2, with a = 3.89359(7 Å, b = 17.7014(3 Å, c = 8.04530(12 Å, b = 94.4030 (16°. All compounds were completely characterized by IR, 1H-NMR, EI-MS and UV-Vis.

  16. The development of structural x-ray crystallography

    Science.gov (United States)

    Woolfson, M. M.

    2018-03-01

    From its birth in 1912, when only the simplest structures could be solved, x-ray structural crystallography is now able to solve macromolecular structures containing many thousands of independent non-hydrogen atoms. This progress has depended on, and been driven by, great technical advances in the development of powerful synchrotron x-ray sources, advanced automated equipment for the collection and storage of large data sets and powerful computers to deal with everything from data processing to running programmes employing complex algorithms for the automatic solution of structures. The sheer number of developments in the subject over the past century makes it impossible for this review to be exhaustive, but it will describe some major developments that will enable the reader to understand how the subject has grown from its humble beginnings to what it is today.

  17. Synthesis and X-ray Crystal Structure of a Stable cis-1,2-bis(diphenylphosphinoethene Monodentate Thiolate Platinum Complex and TGA Studies of its Precursors

    Directory of Open Access Journals (Sweden)

    Vaz Rodrigo H.

    2002-01-01

    Full Text Available The stable Pt(II complex [Pt(SPh2(dppen (4, (dppen, Ph2PCH=CHPPh2 was obtained from [PtCl(SPh2(SnPh3cod] (1 (cod = 1,5-cyclooctadiene by reductive elimination reaction of SnClPh3 and substitution of the cod ligand by the diphosphine, albeit in low yields. Yields of 80% were obtained when [Pt(SPh2cod] (3 was used as the starting material instead. The viability of these reactions was suggested by a TG study, performed on the starting materials. Complex 4 was characterized by multinuclear NMR (195Pt, 31P, ¹H and 13C and IR spectroscopies and elemental analysis. The molecular structure, solved by an X-ray diffraction study, exhibted a slightly distorted square-planar geometry and short C=C and Pt-P bond distances which were interpreted in terms of a p interaction between the double bond and the metal-ligand bond, as observed for other diphosphine compounds described previously.

  18. Synthesis, Characterization, and X-Ray Crystal Structure of Bis(O-amyl dithiocarbonato-κ2S,S′bis(4-cyanopyridine-κNnickel(II

    Directory of Open Access Journals (Sweden)

    Kuldeep Singh

    2014-01-01

    Full Text Available The [Ni(S2CO-n-C5H112(C6H4N22] adduct of 4-cyanopyridine with [Ni(S2CO-n-C5H112] was synthesized and characterized by elemental analysis, magnetic susceptibility measurement, IR, electronic spectral data, and X-ray diffraction analysis. The Ni atom in the title complex is octahedrally coordinated within a trans-N2S4 donor set, with the Ni atom located on a centre of inversion. The title compound exhibits magnetic moment value (3.20 B.M which is in agreement with magnetic moment values observed for paramagnetic octahedral complexes of nickel(II. The title complex crystallizes in the orthorhombic space group Pbca with unit cell parameters a = 11.455(5, b = 9.602(4, and c = 26.374(1 Å. Crystal structure was solved by direct methods and refined by full matrix least-squares procedures to a final R value of 0.0499 for 2004 observed reflections. The amyl chain is disordered over two sets of sites, with occupancy ratios of 0.595 : 0.405. Infinite long chains of molecules are formed with the help of C–H⋯N hydrogen bond.

  19. Diffraction anomalous fine structure using X-ray anomalous dispersion

    International Nuclear Information System (INIS)

    Soejima, Yuji; Kuwajima, Shuichiro

    1998-01-01

    A use of X-ray anomalous dispersion effects for structure investigation has recently been developed by using synchrotron radiation. One of the interesting method is the observation of anomalous fine structure which arise on diffraction intensity in energy region of incident X-ray at and higher than absorption edge. The phenomenon is so called Diffraction Anomalous Fine Structure (DAFS). DAFS originates in the same physical process an that of EXAFS: namely photoelectric effect at the corresponding atom and the interaction of photoelectron waves between the atom and neighboring atoms. In contrast with EXAFS, the method is available for only the crystalline materials, but shows effective advantages of the structure investigations by a use of diffraction: one is the site selectivity and the other is space selectivity. In the present study, demonstrations of a use of X-ray anomalous dispersion effect for the superstructure determination will be given for the case of PbZrO 3 , then recent trial investigations of DAFS in particular on the superlattice reflections will be introduced. In addition, we discuss about Forbidden Reflection near Edge Diffraction (FRED) which is more recently investigated as a new method of the structure analysis. (author)

  20. Synthesis of 2-deoxy-2,2-difluoro-α-maltosyl fluoride and its X-ray structure in complex with Streptomyces coelicolor GlgEI-V279S

    Energy Technology Data Exchange (ETDEWEB)

    Thanna, Sandeep; Lindenberger, Jared J.; Gaitonde, Vishwanath V.; Ronning, Donald R.; Sucheck, Steven J. (Toledo)

    2015-06-05

    Streptomyces coelicolor (Sco) GlgEI is a glycoside hydrolase involved in α-glucan biosynthesis and can be used as a model enzyme for structure-based inhibitor design targeting Mycobacterium tuberculosis (Mtb) GlgE. The latter is a genetically validated drug target for the development of anti-Tuberculosis (TB) treatments. Inhibition of Mtb GlgE results in a lethal buildup of the GlgE substrate maltose-1-phosphate (M1P). However, Mtb GlgE is difficult to crystallize and affords lower resolution X-ray structures. Sco GlgEI-V279S on the other hand crystallizes readily, produces high resolution X-ray data, and has active site topology identical to Mtb GlgE. We report the X-ray structure of Sco GlgEI-V279S in complex with 2-deoxy-2,2-difluoro-α-maltosyl fluoride (α-MTF, 5) at 2.3 Å resolution. α-MTF was designed as a non-hydrolysable mimic of M1P to probe the active site of GlgE1 prior to covalent bond formation without disruption of catalytic residues. The α-MTF complex revealed hydrogen bonding between Glu423 and the C1F which provides evidence that Glu423 functions as proton donor during catalysis. Further, hydrogen bonding between Arg392 and the axial C2 difluoromethylene moiety of α-MTF was observed suggesting that the C2 position tolerates substitution with hydrogen bond acceptors. The key step in the synthesis of α-MDF was transformation of peracetylated 2-fluoro-maltal 1 into peracetylated 2,2-difluoro-α-maltosyl fluoride 2 in a single step via the use of Selectfluor®

  1. Colliding Stellar Winds Structure and X-ray Emission

    Science.gov (United States)

    Pittard, J. M.; Dawson, B.

    2018-04-01

    We investigate the structure and X-ray emission from the colliding stellar winds in massive star binaries. We find that the opening angle of the contact discontinuity (CD) is overestimated by several formulae in the literature at very small values of the wind momentum ratio, η. We find also that the shocks in the primary (dominant) and secondary winds flare by ≈20° compared to the CD, and that the entire secondary wind is shocked when η ≲ 0.02. Analytical expressions for the opening angles of the shocks, and the fraction of each wind that is shocked, are provided. We find that the X-ray luminosity Lx∝η, and that the spectrum softens slightly as η decreases.

  2. A zinc(II) quinolinone complex (Et3NH)[Zn(qui)Cl2]: Synthesis, X-ray structure, spectral properties and in vitro cytotoxicity

    Science.gov (United States)

    Buchtík, Roman; Nemec, Ivan; Trávníček, Zdeněk

    2014-02-01

    A new zinc(II) complex with 2-phenyl-3-hydroxy-4(1H)-quinolinone (Hqui) of the composition (Et3NH)[Zn(qui)Cl2] was prepared and characterized by elemental analysis, FT IR, 1D and 2D NMR, and fluorescence spectroscopy, mass spectrometry and single crystal X-ray analysis. The molecular structure is composed of the triethylammonium (Et3NH+) cations and tetrahedral [ZnII(qui)Cl2]- complex anions, in which the Zn(II) atoms are bidentate coordinated by one qui ligand through keto (OK) and phenolate (OP) oxygen atoms and by two chlorido ligands, thus forming the {O2Cl2} donor set, with Zn-OK = 1.9860(14) Å, Zn-OP 1.9961(14) Å and Zn-Cl = 2.2509(6) Å and 2.2266(6) Å. The complex cations are aligned into 1D supramolecular chains through the NH⋯Cl hydrogen bonding between the amine group of the quinolinone ligand and the chlorido ligand of the adjacent complex anion. The amine group from the Et3NH+ cations provides the NH⋯OP hydrogen bond with the phenolate oxygen atoms from the complex anion. Screening of in vitro cytotoxicity of the compound was studied on human osteosarcoma (HOS) and human breast adenocarcinoma (MCF7) cell lines, with IC50 > 50 μM. The fluorescence study showed that the complex exhibits a relatively high integral intensity (29%) as compared to the standard quinine sulfate, and 1.6-fold enhancement of emission with respect to free Hqui.

  3. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DEFF Research Database (Denmark)

    Yennawar, Hemant; Møller, Magda; Gillilan, Richard

    2011-01-01

    The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...... the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray...

  4. Soft x-ray-excited luminescence and optical x-ray absorption fine structures of tris (8-hydroxyquinoline) aluminum

    Science.gov (United States)

    Naftel, S. J.; Zhang, P.; Kim, P.-S.; Sham, T. K.; Coulthard, I.; Antel, W. J.; Freeland, J. W.; Frigo, S. P.; Fung, M.-K.; Lee, S. T.; Hu, Y. F.; Yates, B. W.

    2001-03-01

    Photoluminescence from tris (8-hydroxyquinoline) aluminum (Alq3) films has been observed using tunable soft x rays as an excitation source. The photons were tuned to energies above and below the K absorption edges of C, N, O, and Al. The luminescence was in turn used to monitor the absorption. It was found that the luminescence induced by soft x ray exhibits additional emission bands at shorter wavelengths compared to ultraviolet excitation. While all K edges exhibit optical x-ray absorption fine structures (XAFS) similar to those of total electron and fluorescence yield, the optical XAFS at the C K-edge resonance are enhanced for the C1s to π* transitions, indicating site specificity. These observations are attributed to the energetics of the process and the local electronic structure.

  5. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns

    Science.gov (United States)

    Starodub, D.; Aquila, A.; Bajt, S.; Barthelmess, M.; Barty, A.; Bostedt, C.; Bozek, J. D.; Coppola, N.; Doak, R. B.; Epp, S. W.; Erk, B.; Foucar, L.; Gumprecht, L.; Hampton, C. Y.; Hartmann, A.; Hartmann, R.; Holl, P.; Kassemeyer, S.; Kimmel, N.; Laksmono, H.; Liang, M.; Loh, N. D.; Lomb, L.; Martin, A. V.; Nass, K.; Reich, C.; Rolles, D.; Rudek, B.; Rudenko, A.; Schulz, J.; Shoeman, R. L.; Sierra, R. G.; Soltau, H.; Steinbrener, J.; Stellato, F.; Stern, S.; Weidenspointner, G.; Frank, M.; Ullrich, J.; Strüder, L.; Schlichting, I.; Chapman, H. N.; Spence, J. C. H.; Bogan, M. J.

    2012-12-01

    Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.

  6. Automatic protein structure solution from weak X-ray data

    Science.gov (United States)

    Skubák, Pavol; Pannu, Navraj S.

    2013-11-01

    Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

  7. Neutron and X-ray diffraction from modulated structures

    International Nuclear Information System (INIS)

    Harris, P.

    1994-07-01

    This thesis describes X-ray and neutron scattering experiments performed on two examples of modulated structures. After an introduction to the subject of modulated structures, the thesis is divided in three parts. A single crystal elastic neutron scattering experiment between 4.2 and 115 Κ has been performed and four-circle X-ray data have been collected at 8 Κ for the monoclinic low-temperature phase of the layered perovskite PAMC. The results from the neutron scattering experiment indicate that magnetoelastic effects influence the ordering of the crystal. The X-ray experiments have made it possible to determine the crystal structure in the low-temperature phase. The superspace group is P2 1 /b(β-30)Os, with β = 1/3. A small-angle neutron scattering experiment has been performed on the magnetic structure of manganese silicide. When a magnetic field is applied, the modulation vectors turn towards the field direction, showing domain growth and diverging peak widths as they approach the field direction. Phase 'A' is established to have the modulation vectors directed perpendicular to the field direction. Cooling in zero field shows increasing peak widths at low temperatures, indicating a lock-in transition below the lowest reached temperature. To be able to analyse the data of the magnetic order in MnSi, and analytical calculation of the three dimensional resolution function for a small-angle neutron scattering spectrometer has been performed. The calculation is done by application of a combination of phase space analysis and Gaussian approximations for the neutron distribution as well as for the transmission functions of the different apertures. A finite mosaic spread of the crystal and finite correlation widths of the Bragg reflections have been included in the cross section. (au) (3 tabs., 48 ills., 100 refs.)

  8. Acemetacin cocrystal structures by powder X-ray diffraction

    Directory of Open Access Journals (Sweden)

    Geetha Bolla

    2017-05-01

    Full Text Available Cocrystals of acemetacin drug (ACM with nicotinamide (NAM, p-aminobenzoic acid (PABA, valerolactam (VLM and 2-pyridone (2HP were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R32(9R22(8R32(9 with three different syn amides (VLM, 2HP and caprolactam. The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I or syn (type II. ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O...H, N...H, Cl...H and C...H interactions. The physicochemical properties of these cocrystals are under study.

  9. Status and limitations of multilayer X-ray interference structures

    International Nuclear Information System (INIS)

    Kortright, J.B.

    1996-01-01

    Trends in the performance of x-ray multilayer interference structures with periods ranging from 9 to 130 (angstrom) are reviewed. Analysis of near-normal incidence reflectance data vs photon energy reveals that the effective interface with σ in a static Debye-Waller model, describing interdiffusion and roughness, decreases as the multilayer period decreases, and reaches a lower limit of roughly 2 (angstrom). Specular reflectance and diffuse scattering from uncoated and multilayer-coated substrates having different roughness suggest that this lower limit results largely from substrate roughness. The increase in interface width with period thus results from increasing roughness of interdiffusion as the layer thickness increases

  10. An efficient synthesis, X-ray and spectral characterization of ...

    Indian Academy of Sciences (India)

    -thiazolidin-2,4-dione derivatives containing biphenyl ring system derivatised with the tetrazole (9), 1,2,4-triazoles (16), and 1,3,4- oxadiazole 17, 18. The single crystal X-ray analysis of one of the compounds 9 is also described as part of the.

  11. X-ray structure determination and deuteration of nattokinase

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki, E-mail: chatake@rri.kyoto-u.ac.jp [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

    2013-11-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  12. Note: A simple-structured anode exchangeable X-ray tube.

    Science.gov (United States)

    Nguyen, Thanh-hai; Lee, Chang Jun; Park, Rae-jun; Jin, Gye-Hwan; Kim, Sung Youb; Jeon, Insu

    2013-05-01

    An anode exchangeable X-ray tube of very simple structure was developed. Aluminum, chromium, and copper anode targets were prepared and used to investigate X-ray spectra. X-ray images of a thin wood plate were taken using those targets. The measured energies of the characteristic X-rays of each target agreed well with the presented results. The difference of resolution and brightness of each image was found based on MTF values and intensities. The developed X-ray tube can give high durability, and higher quality X-ray images of an arbitrary object by exchanging anode targets.

  13. In situ X-ray powder diffraction, synthesis, and magnetic properties of InVO3

    International Nuclear Information System (INIS)

    Lundgren, Rylan J.; Cranswick, Lachlan M.D.; Bieringer, Mario

    2006-01-01

    We report the first synthesis and high-temperature in situ X-ray diffraction study of InVO 3 . Polycrystalline InVO 3 has been prepared via reduction of InVO 4 using a carbon monoxide/carbon dioxide buffer gas. InVO 3 crystallizes in the bixbyite structure in space group Ia-3 (206) with a=9.80636(31) A with In 3+ /V 3+ disorder on the (8b) and (24d) cation sites. In situ powder X-ray diffraction experiments and thermal gravimetric analysis in a CO/CO 2 buffer gas revealed the existence of the metastable phase InVO 3 . Bulk samples with 98.5(2)% purity were prepared using low-temperature reduction methods. The preparative methods limited the crystallinity of this new phase to approximately 225(50) A. Magnetic susceptibility and neutron diffraction experiments suggest a spin-glass ground state for InVO 3 . - Graphical abstract: In situ powder X-ray diffractograms for the reduction of InVO 4 in CO/CO 2 . The three temperature regions show the conversion of InVO 4 to InVO 3 and final decomposition into In 2 O 3 and V 2 O 3

  14. Synthesis and X-Ray Crystal Structure of the First Pure and Air-Stable Salt of Peroxymonosulphuric Acid: (Ph4PHSO5

    Directory of Open Access Journals (Sweden)

    Marco Crisma

    2000-06-01

    Full Text Available In this paper we describe the synthesis of tetraphenylphosphonium peroxymonosulphate, its crystal structure and packing mode. The asymmetric unit accomodates two independent molecules of the monopersulphate anion, which are held together by hydrogen bonds. In the packing mode, rows of such dimers are surrounded by four rows of tetraphenyl cations. The consequence is that the highly water sensitive HSO5¯ anions are segregated inside hydrophobic channels composed by the lipophilic cations. This circumstance presumably accounts for the exceptional stability of the title compound.

  15. Titanium Dioxide Nanoparticles: Synthesis, X-Ray Line Analysis and Chemical Composition Study

    OpenAIRE

    Chenari,Hossein Mahmoudi; Seibel,Christoph; Hauschild,Dirk; Reinert,Friedrich; Abdollahian,Hossein

    2016-01-01

    TiO$_{2}$ nanoparticleshave been synthesized by the sol-gel method using titanium alkoxide and isopropanolas a precursor. The structural properties and chemical composition of the TiO$_{2}$ nanoparticles were studied usingX-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy.The X-ray powder diffraction pattern confirms that the particles are mainly composed of the anatase phase with the preferential orientation along [101] direction.The physical parameters suc...

  16. Sonochemical synthesis of nano-scale mixed-ligands lead(II) coordination polymers as precursors for preparation of PbO and PbBr(OH) nano-structures; thermal, structural and X-ray powder diffraction studies.

    Science.gov (United States)

    Sadeghzadeh, Homa; Morsali, Ali; Yilmaz, Veysel T; Büyükgüngör, Orhan

    2010-03-01

    Nano-structures of two new lead(II) two-dimensional coordination polymers, [Pb(2)(2-pyc)(2)(I)(2)](n) (1) and [Pb(2)(2-pyc)(2)(Br)(2)](n) (2), {2-Hpyc=2-pyridinecarboxilic acid } were synthesized by a sonochemical method that produce the coordination polymers at nano-size. The new nano-structures were characterized by scanning electron microscopy, X-ray powder diffraction, IR spectroscopy and elemental analyses. Compounds 1 and 2 were structurally characterized by single crystal X-ray diffraction and consist of two-dimensional polymeric units. The thermal stability of compounds 1 and 2 were studied by thermal gravimetric and differential thermal analyses. PbO and PbBr(OH) nano-structures were obtained by calcination of the nano-structures of compounds 1 and 2 at 400 degrees C, respectively. Copyright 2009 Elsevier B.V. All rights reserved.

  17. Novel organophosphorus compounds; synthesis, spectroscopy and X-ray crystallography

    Czech Academy of Sciences Publication Activity Database

    Shariatinia, Z.; Sohrabi, M.; Yousefi, M.; Kovaľ, Tomáš; Dušek, Michal

    2012-01-01

    Roč. 11, č. 2 (2012), s. 125-133 ISSN 1024-1221 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : organophosphorus compounds * NMR * X-ray crystallography * hydrogen bond Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.686, year: 2012

  18. Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Brindisi, Margherita; Nyalapatla, Prasanth R.; Takayama, Jun; Ella-Menye, Jean-Rene; Yashchuk, Sofiya; Agniswamy, Johnson; Wang, Yuan-Fang; Aoki, Manabu; Amano, Masayuki; Weber, Irene T.; Mitsuya, Hiroaki

    2017-10-01

    Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands for specific interactions in the S2-S3 extended site. Compound 4b has shown an enzyme Ki of 0.025 nM and antiviral IC50 of 69 nM. An X-ray crystal structure of inhibitor 4b-HIV-1 protease complex was determined at 1.33 Å resolution. We have also determined X-ray structure of 3b-bound HIV-1 protease at 1.27 Å resolution. These structures revealed important molecular insight into the inhibitor–HIV-1 protease interactions in the active site.

  19. Electronic structure of nanoscale Cu/Pt alloys: A combined X-ray diffraction and X-ray absorption investigations

    International Nuclear Information System (INIS)

    Chen Xing; Chu Wangsheng; Cai Quan; Xia Dingguo; Wu Zhonghua; Wu Ziyu

    2006-01-01

    PVP-protected Cu/Pt clusters were prepared by glycol/water reduction method and characterized with transmission electron microscopy (TEM), X-ray diffraction (XRD) and absorption spectra. TEM and XRD analysis show that the Cu/Pt clusters with different molar ratio have fcc structure with particle size of about 4 nm, while the lattice parameters in these clusters reduce with increasing Cu concentration. From the X-ray absorption near edge structure (XANES) at Cu-K edge and Pt-L 2,3 edge, we demonstrate that the d-electronic states of Cu and Pt are affected by the local environment as a function of Cu/Pt molar ratio. With increasing Cu concentration, Pt loses a fraction of 5d electrons and the hybridization between p- and d-states at Cu sites is enhanced

  20. Electronic structure of nanoscale Cu/Pt alloys: A combined X-ray diffraction and X-ray absorption investigations

    Energy Technology Data Exchange (ETDEWEB)

    Chen Xing [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graduate School of the Chinese Academy of Sciences, 100864 Beijing (China); Chu Wangsheng [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); University of Science and Technology of China, Hefei, 230036 (China); Cai Quan [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graduate School of the Chinese Academy of Sciences, 100864 Beijing (China); Xia Dingguo [College of Environmental and Energy Engineering, Beijing University of Technology, 100022 Beijing (China); Wu Zhonghua [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Wu Ziyu [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China) and National Center for Nanoscience and Technology (China)]. E-mail: wuzy@ihep.ac.cn

    2006-11-15

    PVP-protected Cu/Pt clusters were prepared by glycol/water reduction method and characterized with transmission electron microscopy (TEM), X-ray diffraction (XRD) and absorption spectra. TEM and XRD analysis show that the Cu/Pt clusters with different molar ratio have fcc structure with particle size of about 4 nm, while the lattice parameters in these clusters reduce with increasing Cu concentration. From the X-ray absorption near edge structure (XANES) at Cu-K edge and Pt-L{sub 2,3} edge, we demonstrate that the d-electronic states of Cu and Pt are affected by the local environment as a function of Cu/Pt molar ratio. With increasing Cu concentration, Pt loses a fraction of 5d electrons and the hybridization between p- and d-states at Cu sites is enhanced.

  1. Structural studies using X-ray absorption and scattering techniques

    International Nuclear Information System (INIS)

    Ericson, Agneta.

    1989-01-01

    The thesis presents extended X-ray absorption fine structure, EXAFS, and large angle X-ray scattering, LAXS, techniques; instrumentation, data collection and reduction, and applications. These techniques have been used to determine the structures of magnesium halides and organomagnesium halides in diethyl ether and tetrahydrofuran solution. The iodides were used for the LAXS measurements and Br K edge EXAFS data were collected for the corresponding bromides. Two different complexes are present in the diethyl ether solution of magnesium iodide; a polymeric chain-type structure where magnesium is tetrahedrally coordinated, as well as dimeric complex with octahedrally coordinated magnesium. Solvated MgI + is the dominating species in tetrahydrofuran solution. The organomagnesium halides are present in diethyl ether solution as both solvated monomeric and dimeric complexes. Magnesium coordinates a halide ion, an alkyl or aryl group and four solvent molecules octahedrally in the monomeric complex. In the dimeric complex magnesium is octahedrally coordinated by two bridging halide ions, an alkyl or aryl group and three solvent molecules. The distribution of monomeric and dimeric complexes in various solutions are given by a dimerisation constant, K dl . The results indicate that the Schlenk equilibrium is present in these solutions, however, in an extended form. In diethyl ether solution, where MgX 2 does not dissociate, no MgX 2 complex and thereby no Schlenk equilibrium has been observed. In tetrahydrofuran solution MgI 2 has dissociated into mainly MgI + and I - . This indicates that the concentration of MgI 2 is low and that the Schlenk equilibrium should be expanded even further to include the dissociation equilibrium of the magnesium halide. In the thesis Fe K edge EXAFS data collected for the semireduced form of protein A of methane monooxygenase from Methylococcus capsulatus, are also presented. (139 refs.)

  2. Synthesis, NMR characterization, X-ray crystal structure of Co(II) Ni(II) and Cu(II) complexes of a pyridine containing self-assembling

    International Nuclear Information System (INIS)

    Ranjbar, M.; Taghavipour, M.; Moghimi, A.; Aghabozorg, H.

    2002-01-01

    In the recent years, the self-assembling systems have been attracted chemists. The intermolecular bond in such systems mainly consists of ion pairing and hydrogen bonding [1,2]. The reaction between self-assembling system liquid LH 2 (py dc=2,6-pyridinedicarboxylic acid and py da=2,6- pyridine diamin) with cobalt (II) nitrate, nickel (II) chloride, and copper (II) acetate in water leads to the formation of self- assemble coordination complexes, [py da.H] 2 [M(py dc) 2 ]. H 2 O, M=Co(II),Ni(II), and Cu(II). The characterization was performed using elemental analysis, ESI mass spectroscopy, 1 H and 13 C NMR and X-ray crystallography. The crystal systems are monoclinic with space group P2 1 /n and four molecules per unit cell. These complexes shows 13 C NMR resonances of cationic counter ion [(py dc,H)] + in DMSO- d 6 but no signal corresponding to the two coordinated ligands [py dc] 2- The metal atoms are six-coordinated with a distorted octahedral geometry. The two [py de] 2- units are almost perpendicular to each other

  3. Study of complex waveguide structure using soft X-ray reflectivity technique

    Science.gov (United States)

    Singh, Amol; Modi, Mohammed H.; Dhawan, R.; Jonnard, P.; Le Guen, K.; André, J.-M.

    2017-05-01

    Grazing incidence x-ray reflectivity (GIXRR) technique is commonly used for structural investigation of layered structures. In case of complex x-ray waveguide structure it is difficult to obtain structural parameters using GIXRR technique owing to narrowly spaced Kiessig fringes. We used GIXRR and soft x-ray reflectivity (SXR) technique to study the x-ray waveguide structure composed of 4 layers Al/ZrC/Al/W on a Si substrate. Structural parameters of the stacks, density, thickness and roughness of the layers, are determined through fitting of SXR data. Advantages of SXR over GIXRR for such layered structure are shown.

  4. Directional fine structure in absorption of white x rays: A tomographic interpretation

    International Nuclear Information System (INIS)

    Korecki, P.; Szymonski, M.; Tolkiehn, M.; Novikov, D. V.; Materlik, G.

    2006-01-01

    We discuss directional fine structure in absorption of white x rays for tomographic imaging of crystal structure at the atomic level. The interference between a direct x-ray beam and the secondary waves coherently scattered inside a specimen modifies the total wave field at the position of the absorbing atoms. For a white x-ray beam, the wave field variations cancel out by energy integration for all directions, except for the near forward scattering components, coinciding with the incident beam. Therefore, two-dimensional patterns of the angular-dependent fine structure in absorption of white x rays can be interpreted as real-space projections of atomic structure. In this work, we present a theory describing the directional fine structure in white x-ray absorption and a tomographic approach for crystal structure retrieval developed on its basis. The tomographic algorithm is applied to the experimental x-ray absorption data recorded for GaP crystals

  5. X-ray Structure of the Mature Ectodomain of Phogrin

    Energy Technology Data Exchange (ETDEWEB)

    Noguera, M. E. [National Univ. of Quilmes, Buenos Aires (Argentina); Primo, M. [Univ. of Buenos Aires (Argentina); Jakoncic, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Poskus, E. [Univ. of Buenos Aires (Argentina); Solimena, M. [Dresden Univ. of Technology and Max Planck Inst. of Molecular Cell Biology and Genetics (Germany); Ermacora, M. R. [National Univ. of Quilmes and Multidisciplinary Inst. of Cellular Biology, Buenos Aires (Argentina)

    2014-11-26

    Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretion, ensuring proper granulogenesis, and β-cell proliferation. The role of their cytoplasmic tail has been partially unveiled, while that of their luminal region remains unclear. To advance the understanding of its structure–function relationship, the X-ray structure of the mature ectodomain of phogrin (ME phogrin) at pH 7.4 and 4.6 has been solved at 1.95- and 2.01-Å resolution, respectively. Likewise to the ME of ICA512, ME phogrin adopts a ferredoxin-like fold: a sheet of four antiparallel β-strands packed against two α-helices. Furthermore, sequence conservation among vertebrates, plants and insects suggests that the structural similarity extends to all the receptor family. Crystallized ME phogrin is monomeric, in agreement with solution studies but in striking contrast with the behavior of homodimeric ME ICA512. The structural details that may cause the quaternary structure differences are analyzed. The results provide a basis for building models of the overall orientation and oligomerization state of the receptor in biological membranes.

  6. Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

    Science.gov (United States)

    Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

    2013-08-14

    We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

  7. Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1 gp120.

    Science.gov (United States)

    Curreli, Francesca; Kwon, Young Do; Belov, Dmitry S; Ramesh, Ranjith R; Kurkin, Alexander V; Altieri, Andrea; Kwong, Peter D; Debnath, Asim K

    2017-04-13

    In our attempt to optimize the lead HIV-1 entry antagonist, NBD-11021, we present in this study the rational design and synthesis of 60 new analogues and determination of their antiviral activity in a single-cycle and a multicycle infection assay to derive a comprehensive structure-activity relationship (SAR). Two of these compounds, NBD-14088 and NBD-14107, showed significant improvement in antiviral activity compared to the lead entry antagonist in a single-cycle assay against a large panel of Env-pseudotyped viruses. The X-ray structure of a similar compound, NBD-14010, confirmed the binding mode of the newly designed compounds. The in vitro ADMET profiles of these compounds are comparable to that of the most potent attachment inhibitor BMS-626529, a prodrug of which is currently undergoing phase III clinical trials. The systematic study presented here is expected to pave the way for improving the potency, toxicity, and ADMET profile of this series of compounds with the potential to be moved to the early preclinical development.

  8. X-ray photoemission spectroscopy (XPS) and extended x-ray absorption fine structure (EXAFS) studies of silicate based glasses

    International Nuclear Information System (INIS)

    Karim, D.; Lam, D.J.

    1979-01-01

    The application of the x-ray photoemission spectroscopy (XPS) technique to study the electronic structure and bonding of heavy metal oxides in alkali- and alkali-earth-silicate glasses had been demonstrated. The bonding characteristics of the iron oxide and uranium oxide in sodium silicate glasses were deduced from the changes in the oxygen 1s levels and the heavy metal core levels. It is reasonable to expect that the effect of leaching on the heavy metal ions can be monitored using the appropriate core levels of these ions. To study the effect of leaching on the glass forming network, the valence band structure of the bridging and nonbridging oxygens in sodium silicate glasses were investigated. The measurement of extended x-ray absorption fine-structure (EXAFS) is a relatively new analytical technique for obtaining short range (<5 A) structural information around atoms of a selected species in both solid and fluid systems. Experiments have recently begun to establish the feasibility of using EXAFS to study the bonding of actinides in silicate glasses. Because of the ability of EXAFS to yield specific structural data even in complex multicomponent systems, it could prove to be an invaluable tool in understanding glass structure

  9. Synthesis and X-ray crystal structure of cationic polynuclear hydroxide acetylacetonate lanthanide(III) clusters with homodinuclear or heterodinuclear decacarbonyl hydrides: [HMo2(CO)1]- and [HCrW(CO)1]-

    International Nuclear Information System (INIS)

    Volpe, M.; Bombieri, G.; Marchini, N.

    2006-01-01

    The synthesis and characterization of new polynuclear lanthanide(III) ionic clusters of general formula [Ln 9 (acac) 16 (OH) 1 ] + [Mo 2 (CO) 1 (μ-H)] - (Ln = Sm, Eu, Gd, Dy, Yb) and [Sm 9 (acac) 16 (OH) 1 ] + [CrW(CO) 1 (μ-H)] - is reported. The polynuclear complexes, prepared under pure nitrogen atmosphere by interaction of the hydridic metal carbonyls with the β-dichetonate Ln(acac) 3 .3H 2 O (Ln = Sm, Eu, Gd, Dy, Yb). The new clusters were characterized by elemental analysis, complexometric titration for Ln, atomic absorption for Cr, W and Mo, gas-volumetric analysis for CO, FTIR spectroscopy and single crystal X-ray structure determination of [Sm 9 (acac) 16 (OH) 1 ][Mo 2 (CO) 1 (μ-H)]. The Eu and Yb complexes are isostructural to the Sm one for which, similarly to their homonuclear chromium and tungsten derivative analogues, a square antiprismatic arrangement of eight Sm ions with the ninth at the center of the antiprism has been found

  10. Structured scintillators for X-ray imaging with micrometre resolution

    DEFF Research Database (Denmark)

    Olsen, Ulrik Lund; Schmidt, Søren; Poulsen, Henning Friis

    2009-01-01

    is shown to be negligible. The concept of such a 3D detector enables ray tracing and super resolution algorithms to be applied. Realized pore geometries have a lower aspect ratio than used in simulations and the roughness of the pore walls gives a 13% decrease in waveguide efficiency. Compared to currently......A 3D X-ray detector for imaging of 30–200 keV photons is described. It comprises a stack of semitransparent structured scintillators, where each scintillator is a regular array of waveguides in silicon, and with pores filled with CsI. The performance of the detector is described theoretically...... and explored in detail through simulations. The resolution of a single screen is shown to be determined only by the pitch, at least up to 100 keV. In comparison to conventional homogenous screens an improvement in efficiency by a factor 5–15 is obtainable. The cross-talk between screens in the 3D detector...

  11. A community resource of experimental data for NMR / X-ray crystal structure pairs.

    Science.gov (United States)

    Everett, John K; Tejero, Roberto; Murthy, Sarath B K; Acton, Thomas B; Aramini, James M; Baran, Michael C; Benach, Jordi; Cort, John R; Eletsky, Alexander; Forouhar, Farhad; Guan, Rongjin; Kuzin, Alexandre P; Lee, Hsiau-Wei; Liu, Gaohua; Mani, Rajeswari; Mao, Binchen; Mills, Jeffrey L; Montelione, Alexander F; Pederson, Kari; Powers, Robert; Ramelot, Theresa; Rossi, Paolo; Seetharaman, Jayaraman; Snyder, David; Swapna, G V T; Vorobiev, Sergey M; Wu, Yibing; Xiao, Rong; Yang, Yunhuang; Arrowsmith, Cheryl H; Hunt, John F; Kennedy, Michael A; Prestegard, James H; Szyperski, Thomas; Tong, Liang; Montelione, Gaetano T

    2016-01-01

    We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development. © 2015 The Protein Society.

  12. The structure of liquid semiconductors, superionic conductors and glasses by neutron scattering, X-ray diffraction and extended X-ray absorption fine structure

    International Nuclear Information System (INIS)

    Buchanan, P.

    2001-09-01

    A study of the applicability of modern X-ray and neutron scattering techniques to the study of the structure of liquid semiconductors and glasses has been made. The results demonstrate how neutron scattering with isotopic substitution (NDIS), anomalous X-ray scattering and Extended X-ray Absorption Fine Structure (EXAFS) can be successfully used to elucidate the structure of materials that cannot be studied by NDIS alone. The local coordination structure of Ag 2 Se in its room temperature, superionic and liquid phases has been determined using the EXAFS technique. This EXAFS data have been combined with previously available neutron diffraction data to provide a refinement of the structure obtained through neutron diffraction alone. The structure of GeO 2 has been determined to the full partial structure factor level using a combination of anomalous X-ray scattering and neutron diffraction measurements. The data are in good agreement with previously obtained results. The partial structure factors of P 40 Se 60 and P 50 Se 50 have been determined to the first order difference level using the anomalous X-ray diffraction technique. The structure of liquid Ga 2 Te 3 has been determined to the partial structure factor level using combined neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction. The structure of liquid FeSe 2 has been determined to the first order difference level using the NDIS technique alone. The structure of liquid FeTe 2 was determined at the total structure factor level using neutron diffraction in order to estimate the effect of chalcogenide ion size on the structure. The results demonstrate the feasibility of the additional structural determination techniques for disordered materials made possible through the development of third generation X-ray synchrotron sources. (author)

  13. Synthesis and X-ray crystal structure of a novel organometallic (µ(3)-oxido)(µ(3)-imido) trinuclear iridium complex

    DEFF Research Database (Denmark)

    Schau-Magnussen, Magnus; Malcho, Phillip; Herbst, Konrad

    2011-01-01

    Reaction of the organometallic aqua ion [Cp*Ir(H(2)O)(3)](2+) with tert-butyl(trimethylsilyl)amine in acetone yielded a novel trinuclear (µ(3)-oxido)(µ(3)-imido)pentamethylcyclopentadienyliridium(iii) complex, [(Cp*Ir)(3)(O)(N(t)Bu)](2+). Single crystal structure analyses show the complex can be ...

  14. Synthesis of new nano Schiff base complexes: X-ray crystallography ...

    African Journals Online (AJOL)

    This study presents synthesis and characterization of new nano uranyl Schiff base complexes. Electrochemistry of these complexes showed a quasireversible redox reaction without any successive reactions. Furthermore, X-ray crystallography exhibited that beside the coordination of tetradentate Schiff base, one solvent ...

  15. Synthesis, X-ray structure, and characterization of a complex containing the hexakis(urea)cobalt(II) cation and lattice urea molecules.

    Science.gov (United States)

    Drakopoulou, Labrini; Papatriantafyllopoulou, Constantina; Terzis, Aris; Perlepes, Spyros P; Manessi-Zoupa, Evy; Papaefstathiou, Giannis S

    2007-01-01

    The 12: 1 reaction of urea (U) with CoI(2) in EtOH yielded the "clathrate-coordination" compound [CoU(6)]I2.4U (1). The complex crystallizes in the monoclinic space group P2(1)/c. The lattice constants are a = 9.844(4), b = 7.268(3), c = 24.12(1) A, and beta=98.12(1) degrees composite function. The crystal structure determination demonstrates the existence of octahedral [CoU6](2+) cations, I(-) counterions, and two different types (two U(1) and two U(2)) of hydrogen-bonded, lattice urea molecules. The [CoU(6)](2+) cations and the U(1) lattice molecules form two-dimensional hydrogen-bonded layers which are parallel to the ab plane. The I(-) anions are placed above and below each layer, and are hydrogen bonded both to U(1) molecules and [CoU(6)](2+) cations. Each U(2) molecule is connected to a [CoU(6)](2+) cation through an N-Hcdots, three dots, centeredO hydrogen bond resulting in a three-dimensional network. Room temperature magnetic susceptibility and spectroscopic (solid-state UV/Vis, IR, Raman) data of 1 are discussed in terms of the nature of bonding and the known structure.

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

    Energy Technology Data Exchange (ETDEWEB)

    McLean, Larry R.; Zhang, Ying; Degnen, William; Peppard, Jane; Cabel, Dasha; Zou, Chao; Tsay, Joseph T.; Subramaniam, Arun; Vaz, Roy J.; Li, Yi (Sanofi)

    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.

  17. Structural study of polymers under stretch using a new X-ray TV detector

    International Nuclear Information System (INIS)

    Ohishi, Yasuo; Uemura, Akio; Amemiya, Yoshiyuki.

    1994-01-01

    Time-resolved synchrotron radiation small angle X-ray scattering experiment to investigate the structural change of polyethylene during stretching have been made by utilizing a new X-ray TV detector installed at the Photon Factory. This X-ray TV detector specially developed for real-time measurements of diffraction patterns employs an X-ray image intensifier with a Be-window of a 150 mm diameter. The TV detector has a sensitivity and a time resolution of 30 frames per second. This capability allows us to observe weak SAXS patterns in a time-resolved mode. (author)

  18. Structure and dynamics in liquid water from x-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Wernet, Philippe

    2009-01-01

    Oxygen K-edge x-ray absorption spectra of water are discussed. The spectra of gas-phase water, liquid water and ice illustrate the sensitivity of oxygen K-edge x-ray absorption spectroscopy to hydrogen bonding in water. Transmission mode spectra of amorphous and crystalline ice are compared to x-ray Raman spectra of ice. The good agreement consolidates the experimental spectrum of crystalline ice and represents an incentive for theoretical calculations of the oxygen K-edge absorption spectrum of crystalline ice. Time-resolved infrared-pump and x-ray absorption probe results are finally discussed in the light of this structural interpretation.

  19. Ruthenium(II) bipyridine complexes bearing quinoline-azoimine (NN'N″) tridentate ligands: synthesis, spectral characterization, electrochemical properties and single-crystal X-ray structure analysis.

    Science.gov (United States)

    Al-Noaimi, Mousa; Abdel-Rahman, Obadah S; Fasfous, Ismail I; El-khateeb, Mohammad; Awwadi, Firas F; Warad, Ismail

    2014-05-05

    Four octahedral ruthenium(II) azoimine-quinoline complexes having the general molecular formula [Ru(II)(L-Y)(bpy)Cl](PF6) {L-Y=YC6H4N=NC(COCH3)=NC9H6N, Y=H (1), CH3 (2), Br (3), NO2 (4) and bpy=2,2'-bipyrdine} were synthesized. The azoimine-quinoline based ligands behave as NN'N″ tridentate donors and coordinated to ruthenium via azo-N', imine-N' and quinolone-N″ nitrogen atoms. The composition of the complexes has been established by elemental analysis, spectral methods (FT-IR, electronic, (1)H NMR, UV/Vis and electrochemical (cyclic voltammetry) techniques. The crystal structure of complex 1 is reported. The Ru(II) oxidation state is greatly stabilized by the novel tridentate ligands, showing Ru(III/II) couples ranging from 0.93-1.27 V vs. Cp2Fe/Cp2Fe(+). The absorption spectrum of 1 in dichloromethane was modeled by time-dependent density functional theory (TD-DFT). Copyright © 2014 Elsevier B.V. All rights reserved.

  20. [μ-1,1'-Bis(diphenylphosphine)ferrocene]bis(chlorogold): Synthesis, iron-57 and gold-197 Moessbauer spectroscopy, x-ray crystal structure, and antitumor activity

    International Nuclear Information System (INIS)

    Hill, D.T.; Girard, G.R.; McCabe, F.L.; Johnson, R.K.; Eggleston, D.S.; Stupik, P.D.; Zhang, J.H.; Reiff, W.M.

    1989-01-01

    The title compound 2, Fdpp(AuCl) 2 , synthesized via the addition of Fdpp (1) to an aqueous solution of [(HOCH 2 CH 2 ) 2 S]AuCl generated in situ by the thiodiglycol reduction of HAuCl 4 showed a 31 P[ 1 H] NMR chemical shift at δ 27.39, which was downfield from that of 1 at δ -17.34 relative to (CH 3 O)PO. The 57 Fe Moessbauer spectrum of 2 is a doublet with parameters (IS = 0.50 mm/s relative to Fe, QS = 2.33 mm/s) similar to those of ferrocene. The 197 Au Moessbauer spectrum of 2 is an asymmetric doublet (QS = 6.93 mm/s) with an IS of 3.81 mm/s relative to Au metal. Fdpp(AuCl) 2 crystallized in space group P bar 1 with lattice constants a = 16.192 (4) angstrom, b = 16.921 (4) angstrom, and c = 10.878 (5) angstrom with Z = 3. Two crystallographically independent molecules, A and B, were observed in the structure of 2 with a chloroform solvate molecule per 1.5 formula units of the gold complex. For A, the P atoms are 180 degree opposed and the rings exactly staggered, while in B the P atoms are 150 degree apart and the rings are partially staggered. The P-Au-Cl linkage is nearly linear, and the bond distances fall within normal ranges. Evaluation in an ip P388 leukemia mouse model showed 1 and 2 to have only marginal activity with an increased life span (ILS) relative to untreated controls of 30% at a maximally tolerated dose (MTD) of 231 μmol/kg and 40% ILS at 4 μmol/kg, respectively. 27 refs., 4 figs., 3 tabs

  1. Hard X-ray irradiation of cosmic silicate analogs: structural evolution and astrophysical implications

    Science.gov (United States)

    Gavilan, L.; Jäger, C.; Simionovici, A.; Lemaire, J. L.; Sabri, T.; Foy, E.; Yagoubi, S.; Henning, T.; Salomon, D.; Martinez-Criado, G.

    2016-03-01

    Context. Protoplanetary disks, interstellar clouds, and active galactic nuclei contain X-ray-dominated regions. X-rays interact with the dust and gas present in such environments. While a few laboratory X-ray irradiation experiments have been performed on ices, X-ray irradiation experiments on bare cosmic dust analogs have been scarce up to now. Aims: Our goal is to study the effects of hard X-rays on cosmic dust analogs via in situ X-ray diffraction. By using a hard X-ray synchrotron nanobeam, we seek to simulate cumulative X-ray exposure on dust grains during their lifetime in these astrophysical environments and provide an upper limit on the effect of hard X-rays on dust grain structure. Methods: We prepared enstatite (MgSiO3) nanograins, which are analogs to cosmic silicates, via the melting-quenching technique. These amorphous grains were then annealed to obtain polycrystalline grains. These were characterized via scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM) before irradiation. Powder samples were prepared in X-ray transparent substrates and were irradiated with hard X-rays nanobeams (29.4 keV) provided by beamline ID16B of the European Synchrotron Radiation Facility (Grenoble). X-ray diffraction images were recorded in transmission mode, and the ensuing diffractograms were analyzed as a function of the total X-ray exposure time. Results: We detected the amorphization of polycrystalline silicates embedded in an organic matrix after an accumulated X-ray exposure of 6.4 × 1027 eV cm-2. Pure crystalline silicate grains (without resin) do not exhibit amorphization. None of the amorphous silicate samples (pure and embedded in resin) underwent crystallization. We analyze the evolution of the polycrystalline sample embedded in an organic matrix as a function of X-ray exposure. Conclusions: Loss of diffraction peak intensity, peak broadening, and the disappearance of discrete spots and arcs reveal the amorphization

  2. X-Ray Diffraction and the Discovery of the Structure of DNA

    Science.gov (United States)

    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…

  3. Deficiency in plasma protein synthesis caused by x-ray-induced lethal albino alleles in mouse

    International Nuclear Information System (INIS)

    Garland, R.C.; Satrustegui, J.; Gluecksohn-Waelsch, S.; Cori, C.F.

    1976-01-01

    Plasma protein synthesis was studied in mice bearing x-ray induced lethal mutations at the albino locus. Newborn albino mutants showed a decrease in each of the three principal plasma proteins, albumin, α-fetoprotein, and transferrin, when compared with colored littermate controls. Incorporation of [ 14 C] leucine into plasma proteins of the newborn albinos 30 min after injection was only 1 / 5 that of the controls, but incorporation into total liver protein was only slightly diminished. Incorporation of [ 14 C] leucine into an albumin fraction obtained by immunoprecipitation from livers incubated in vitro in an amino acid mixture was also strongly diminished. Thus, the liver of 18-day-old albino fetuses incorporated into this fraction 1 / 3 and that of newborn albinos 1 / 8 as much as the controls, but in both cases the incorporation into total liver protein was only 25 percent less than in the respective controls. These results indicate that the rather severe structural abnormalities observed in the mutants in the endoplasmic reticulum and the Golgi apparatus are not associated with a general deficiency of hepatic protein synthesis. Instead the data from this and previous work show that the progressive deficiency from fetal life to birth involves certain specific proteins represented by several perinatally developing enzymes and by plasma proteins. It is suggested that the mutational effects observed in these mice are due to deletions involving regulatory rather than structural genes at or near the albino locus

  4. Application of x-ray diffraction for analysis in the synthesis of ferrites

    International Nuclear Information System (INIS)

    Casanova Gomez, Abdel; Alfonso Olmo, Esteban; Alonso Perez, Jose Antonio; Rodriguez, Joelis; Bercoff, Paula G.; Arana, Mercedes; Correa Reina, Jose Raul

    2016-01-01

    As a fundamental part of the work to obtain ferrites, from waste materials (Tailings) of the nickel industry, it is the analytical control and monitoring products as well as the conditions of synthesis. Through this work the study of magnetic products is carried out using magnetometry and X-ray diffraction characterization of their properties, and the qualitative and quantitative analysis. First, the ideal temperature calcination was determined for which an average crystallite size of magnetic spinel as large as possible and with high magnetic response is obtained. Subsequently the magnetic and phase analysis of final products, following five different formulations synthesis, was performed. This analysis showed, that in general the method results in solids, even with varying amounts of hematite as impurity in four formulations, having a high magnetic saturation after calcination. XRD analysis made to the products featured determining the average crystallite size as indicative aspect of border interference. Furthermore, the structural refinement (profile matching variant) for the quantitative analysis of phases was carried on, fact that arguments the differences of magnetism for the five formulations. Rietveld method for detailed determination of the structure of the ferrite F-59 and its nonstoichiometric formula was also applied. (Author)

  5. Effects of proton irradiation on structure of NdFeB permanent magnets studied by X-ray diffraction and X-ray absorption fine structure

    International Nuclear Information System (INIS)

    Yang, L.; Zhen, L.; Xu, C.Y.; Sun, X.Y.; Shao, W.Z.

    2011-01-01

    The effects of proton irradiation on the structure of NdFeB permanent magnet were investigated by X-ray diffraction and X-ray absorption fine structure (XAFS). The results reveal that proton irradiation has no effect on the long-range structure, but significantly affects the atomic local structure of the NdFeB magnet. The alignment degree of the magnet decreases and the internal stress of the lattice increases after proton irradiation. XAFS results show that the coordination number of Fe-Nd in the first neighboring coordination shell of the Fe atoms decreases and the disorder degree increases.

  6. Effects of proton irradiation on structure of NdFeB permanent magnets studied by X-ray diffraction and X-ray absorption fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Yang, L. [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Zhen, L., E-mail: lzhen@hit.edu.c [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China); Xu, C.Y.; Sun, X.Y.; Shao, W.Z. [School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001 (China)

    2011-01-15

    The effects of proton irradiation on the structure of NdFeB permanent magnet were investigated by X-ray diffraction and X-ray absorption fine structure (XAFS). The results reveal that proton irradiation has no effect on the long-range structure, but significantly affects the atomic local structure of the NdFeB magnet. The alignment degree of the magnet decreases and the internal stress of the lattice increases after proton irradiation. XAFS results show that the coordination number of Fe-Nd in the first neighboring coordination shell of the Fe atoms decreases and the disorder degree increases.

  7. Imaging nanoscale magnetic structures with polarized soft x-ray photons

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, P.; Im, M.-Y.

    2010-01-18

    Imaging nanoscale magnetic structures and their fast dynamics is scientifically interesting and technologically of highest relevance. The combination of circularly polarized soft X-ray photons which provide a strong X-ray magnetic circular dichroism effect at characteristic X-ray absorption edges, with a high resolution soft X-ray microscope utilizing Fresnel zone plate optics allows to study in a unique way the stochastical behavior in the magnetization reversal process of thin films and the ultrafast dynamics of magnetic vortices and domain walls in confined ferromagnetic structures. Future sources of fsec short and high intense soft X-ray photon pulses hold the promise of magnetic imaging down to fundamental magnetic length and time scales.

  8. A structural study of ceramic oxides by X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Akhtar, M.J.

    1995-01-01

    A detailed structural study of ceramic oxides is presented by employing X-ray Absorption Spectroscopy (XAS). In the present work X-ray Absorption Near Edge Structure (XANES) is used for the investigation of valence state of metal cations; whereas, Extended X-ray Absorption Fine Structure EXAFS) is employed for the determination for bond lengths, coordination numbers and nature of the elements present in the near neighbour shells surrounding the absorbing atom. These results show that local environment of dopant and host cations are different; and this variation in local structure depends on the nature and concentration of the dopant ions. (author)

  9. X ray measurement of residual stresses on metallic structures

    International Nuclear Information System (INIS)

    Barbarin, P.; Convert, M.; Miege

    1983-01-01

    The principle of measuring residual stresses by X ray diffraction (the famous Bragg'law is used) may be applied at an industrial level. CETIM has perfected an outfit adjusted to measurements on the spot, which can be used on metallic parts of a large size. This paper describes this equipment, giving its advantages towards previous devices, and assessing measurements errors. Some actual cases for results obtained are given. This paper starts with a brief historical account and theoretical backgrounds of the method [fr

  10. Comparison of the decameric structure of peroxiredoxin-II by transmission electron microscopy and X-ray crystallography

    DEFF Research Database (Denmark)

    Harris, J. Robin; Schröder, Ewald; Isupov, Michail N.

    2001-01-01

    Peroxiredoxin; Transmission electron microscopy; X-ray structure; Negative staining; angular reconstitution; Molecular fitting......Peroxiredoxin; Transmission electron microscopy; X-ray structure; Negative staining; angular reconstitution; Molecular fitting...

  11. Synthesis of nanoparticles through x-ray radiolysis using synchrotron radiation

    Science.gov (United States)

    Yamaguchi, A.; Okada, I.; Fukuoka, T.; Ishihara, M.; Sakurai, I.; Utsumi, Y.

    2016-09-01

    The synthesis and deposition of nanoparticles consisting of Cu and Au in a CuSO4 solution with some kinds of alcohol and electroplating solution containing gold (I) trisodium disulphite under synchrotron X-ray radiation was investigated. The functional group of alcohol plays an important in nucleation, growth and aggregation process of copper and cupric oxide particles. We found that the laboratory X-ray source also enables us to synthesize the NPs from the metallic solution. As increasing X-ray exposure time, the full length at half width of particle size distribution is broader and higher-order nanostructure containing NPs clusters is formed. The surface-enhanced Raman scattering (SERS) of 4, 4'-bipyridine (4bpy) in aqueous solution was measured using higher-order nanostructure immobilized on silicon substrates under systematically-varied X-ray exposure. This demonstration provide a clue to develop a three-dimensional printing and sensor for environmental analyses and molecular detection through simple SERS measurements.

  12. X-ray diffraction, neutron diffraction and analysis of molecular structures

    International Nuclear Information System (INIS)

    Fontecilla-Camps, J.C.

    1997-01-01

    The only method that is capable to show the atomic structure of most of macromolecules is the X ray diffraction; neutron diffraction is mostly used for the localization of hydrogen atoms, too light to be detected by X ray diffraction. With the growing number of known structures, the molecular crystallographic study may combine the molecular replacement technique and the co-crystallization method, or use the new Laue method, and leads to the functional and topological analysis of biological molecular structures

  13. Size-selective extended X-ray absorption fine structure spectroscopy of free selenium clusters

    International Nuclear Information System (INIS)

    Nagaya, K.; Yao, M.; Hayakawa, T.; Ohmasa, Y.; Kajihara, Y.; Ishii, M.; Katayama, Y.

    2002-01-01

    In a recent paper [M. Yao et al., J. Synchrotron Radiat. 8, 542 (2001)], we proposed a new method for the size-selective EXAFS (extended x-ray absorption fine structure) of neutral-free clusters, in which not only the x-ray absorption process but also the deexcitation processes are utilized as the structural information. In order to verify this method experimentally, we have developed the synchronous measurements of EXAFS and photoelectron photoion coincidence and carried them out for a Se cluster beam by utilizing the third-generation intense x-ray source. The EXAFS spectra for Se small clusters have been obtained and compared critically with theoretical predictions

  14. Investigating the Defect Structures in Transparent Conducting Oxides Using X-ray and Neutron Scattering Techniques.

    Science.gov (United States)

    González, Gabriela B

    2012-05-11

    Transparent conducting oxide (TCO) materials are implemented into a wide variety of commercial devices because they possess a unique combination of high optical transparency and high electrical conductivity. Created during the processing of the TCOs, defects within the atomic-scale structure are responsible for their desirable optical and electrical properties. Therefore, studying the defect structure is essential to a better understanding of the behavior of transparent conductors. X-ray and neutron scattering techniques are powerful tools to investigate the atomic lattice structural defects in these materials. This review paper presents some of the current developments in the study of structural defects in n-type TCOs using x-ray diffraction (XRD), neutron diffraction, extended x-ray absorption fine structure (EXAFS), pair distribution functions (PDFs), and x-ray fluorescence (XRF).

  15. Investigating the Defect Structures in Transparent Conducting Oxides Using X-ray and Neutron Scattering Techniques

    Directory of Open Access Journals (Sweden)

    Gabriela B. González

    2012-05-01

    Full Text Available Transparent conducting oxide (TCO materials are implemented into a wide variety of commercial devices because they possess a unique combination of high optical transparency and high electrical conductivity. Created during the processing of the TCOs, defects within the atomic-scale structure are responsible for their desirable optical and electrical properties. Therefore, studying the defect structure is essential to a better understanding of the behavior of transparent conductors. X-ray and neutron scattering techniques are powerful tools to investigate the atomic lattice structural defects in these materials. This review paper presents some of the current developments in the study of structural defects in n-type TCOs using x-ray diffraction (XRD, neutron diffraction, extended x-ray absorption fine structure (EXAFS, pair distribution functions (PDFs, and x-ray fluorescence (XRF.

  16. Ultrafast conversions between hydrogen bonded structures in liquid water observed by femtosecond x-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Haidan; Huse, Nils; Schoenlein, Robert W.; Lindenberg, Aaron M.

    2010-05-01

    We present the first femtosecond soft x-ray spectroscopy in liquids, enabling the observation of changes in hydrogen bond structures in water via core-hole excitation. The oxygen K-edge of vibrationally excited water is probed with femtosecond soft x-ray pulses, exploiting the relation between different water structures and distinct x-ray spectral features. After excitation of the intramolecular OH stretching vibration, characteristic x-ray absorption changes monitor the conversion of strongly hydrogen-bonded water structures to more disordered structures with weaker hydrogen-bonding described by a single subpicosecond time constant. The latter describes the thermalization time of vibrational excitations and defines the characteristic maximum rate with which nonequilibrium populations of more strongly hydrogen-bonded water structures convert to less-bonded ones. On short time scales, the relaxation of vibrational excitations leads to a transient high-pressure state and a transient absorption spectrum different from that of statically heated water.

  17. Synthesis of Novel Amphiphilic Azobenzenes and X-ray Scattering Studies of Their Langmuir Monolayers

    DEFF Research Database (Denmark)

    Sørensen, Thomas Just; Kjær, Kristian; Breiby, Dag Werner

    2008-01-01

    . At the air-water interface, the amphiphilic azobenzenes form noncrystalline but stable Langmuir films that display an unusual reversible monolayer collapse close to 35 mN/m. The structures and phase transitions were studied by X-ray reflectivity (XR) and grazing-incidence X-ray diffraction, both utilizing...... synchrotron radiation. Compression beyond the collapse point does not change the XR data, showing that the film is unchanged at the molecular level, even at areas less than half of that of the collapse. This leads to the conclusion that few macroscopic collapse sites are responsible for reversibly removing...

  18. Grazing Incidence X-Ray Fluorescence of periodic structures – a comparison between X-ray Standing Waves and Geometrical Optics calculations.

    OpenAIRE

    Reinhardt Falk; Nowak Stanislaw H.; Beckhoff Burkhard; Dousse Jean-Claude; Schoengen Max

    2014-01-01

    Grazing incidence X-ray fluorescence spectra of nano-scaled periodic line structures were recorded at the four crystal monochromator beamline in the laboratory of the Physikalisch-Technische Bundesanstalt at the synchrotron radiation facility BESSY II. For different tilt angles between the lines and the plane of incidence of the monochromatic synchrotron radiation, spectral features are observed which can be understood and explained with calculations of the emerging X-ray standing wave (XSW) ...

  19. Synthesis of the new boron hydride nido-undecaborane(15), B11H15, and the x-ray structure of its conjugate base tetradecahydroundecaborate(1-), [B11H14]-

    International Nuclear Information System (INIS)

    Getman, T.D.; Krause, J.A.; Shore, S.G.

    1988-01-01

    The preparation of nido-undecaborane, B 11 H 15 , from the protonation of K[B 11 H 14 ] and the subsequent deprotonation of B 11 H 15 by P(CH 3 ) 3 to give [P(CH 3 ) 3 H][B 11 H 14 ] is described. The structure of [P(CH 3 ) 3 H][B 11 H 14 ] has been determined from single-crystal x-ray data. The spectral data indicate that the boron framework of B 11 H 15 is similar to that of [B 11 H 14 ] - . 11 references, 1 figure

  20. EXAFS (Extended X-Ray Absorption Fine Structure): theory and applications

    International Nuclear Information System (INIS)

    Lagarde, P.; Raoux, D.

    1984-01-01

    EXAFS (Extended X-Ray Absorption Fine Structure) is introduced in a general way and the qualities of such a techique are shown. Some examples of applications of EXAFS in several branches of science are presented. (L.C.) [pt

  1. Synthesis, X-ray crystallography, and DFT calculations of a novel phosphoramide

    Czech Academy of Sciences Publication Activity Database

    Shariatinia, Z.; Dušek, Michal; Eigner, Václav

    2014-01-01

    Roč. 640, č. 14 (2014), 2945-2955 ISSN 0044-2313 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : phosphoramide * x-ray structure * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.160, year: 2014

  2. Structural characterization of thin-film cadmium stearate by X-ray diffraction technique

    International Nuclear Information System (INIS)

    Mohamad Deraman; Mohd Ali Sufi; Kok Kuan Ying; Muhamad Mat Salleh; Chew Tat Tian

    1990-01-01

    X-ray diffraction measurement were carried out on thin films of cadmium stearate using an X-ray diffractometer at Unit Tenaga Nuklear. Structure characteristic obtained from the measured diffraction pattern are compared with that of thin films of manganese stearate reported earlier by Pomerantz et. al. Some of the structural similarities (such as inter-planar spacing) and differences (such as the absence of subsidiary peak between Bragg peaks) are found and discussed

  3. Study of magnetic metal periodic structures by X-Ray and electron microscopy methods

    Science.gov (United States)

    Prutskov, G. V.; Chesnokov, Yu. M.; Vasilliev, A. L.; Likhachev, I. A.; Pashaev, E. M.; Subbotin, I. A.

    2017-11-01

    Complex studies of magnetic periodic metallic systems based on Dy/Gd layers have been carried out by X-ray diffraction, resonance X-ray reflectometry, transmission electronic microscopy, and energydispersve microanalysis. The application of these methods and joint analysis of their results provide an effective approach to study of the structure and determination of the parameters of individual layers and interfaces and their structural quality with a high degree of reliability.

  4. Ultrafast X-ray determination of transient structures in solids and liquids

    Energy Technology Data Exchange (ETDEWEB)

    Tomov, I.V.; Rentzepis, P.M

    2004-04-19

    Transient structures in solids and liquids have been studied by means of time-resolved X-ray diffraction and absorption with nanosecond and picosecond resolution. These experimental studies utilized two table top laser-driven X-ray sources: a picosecond laser-driven X-ray diode and a femtosecond laser produced plasma. Kinetics of single crystals lattice deformation induced by laser pulse heating has been recorded with 10 ps resolution. The development and utilization of picosecond and subpicosecond EXAFS experimental system is described.

  5. Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods.

    Science.gov (United States)

    Chergui, Majed; Collet, Eric

    2017-08-23

    We review the tremendous advances in ultrafast X-ray science, over the past 15 years, making the best use of new ultrashort X-ray sources including table-top or large-scale facilities. Different complementary X-ray-based techniques, including spectroscopy, scattering, and diffraction, are presented. The broad and expanding spectrum of these techniques in the ultrafast time domain is delivering new insight into the dynamics of molecular systems, of solutions, of solids, and of biosystems. Probing the time evolution of the electronic and structural degrees of freedom of these systems on the time scales of femtosecond to picoseconds delivers new insight into our understanding of dynamical matter.

  6. Photovoltaic X-ray detectors based on epitaxial GaAs structures

    Energy Technology Data Exchange (ETDEWEB)

    Achmadullin, R.A. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Artemov, V.V. [Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninski pr., Moscow B-333, 117333 (Russian Federation); Dvoryankin, V.F. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation)]. E-mail: vfd217@ire216.msk.su; Dvoryankina, G.G. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Dikaev, Yu.M. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Ermakov, M.G. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Ermakova, O.N. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Chmil, V.B. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation); Holodenko, A.G. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation); Kudryashov, A.A.; Krikunov, A.I.; Petrov, A.G.; Telegin, A.A. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Vorobiev, A.P. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation)

    2005-12-01

    A new type of the photovoltaic X-ray detector based on epitaxial p{sup +}-n-n'-n{sup +} GaAs structures which provides a high efficiency of charge collection in the non-bias operation mode at room temperature is proposed. The GaAs epitaxial structures were grown by vapor-phase epitaxy on heavily doped n{sup +}-GaAs(1 0 0) substrates. The absorption efficiency of GaAs X-ray detector is discussed. I-V and C-V characteristics of the photovoltaic X-ray detectors are analyzed. The built-in electric field profiles in the depletion region of epitaxial structures are measured by the EBIC method. Charge collection efficiency to {alpha}-particles and {gamma}-radiation are measured. The application of X-ray detectors is discussed.

  7. Hard X-ray Microscopy with Elemental, Chemical and Structural Contrast

    International Nuclear Information System (INIS)

    Schroer, C.G.; Boye, P.; Feldkamp, J.P.

    2010-01-01

    We review hard X-ray microscopy techniques with a focus on scanning microscopy with synchrotron radiation. Its strength compared to other microscopies is the large penetration depth of hard x rays in matter that allows one to investigate the interior of an object without destructive sample preparation. In combination with tomography, local information from inside of a specimen can be obtained, even from inside special non-ambient sample environments. Different X-ray analytical techniques can be used to produce contrast, such as X-ray absorption, fluorescence, and diffraction, to yield chemical, elemental, and structural information about the sample, respectively. This makes X-ray microscopy attractive to many fields of science, ranging from physics and chemistry to materials, geo-, and environmental science, biomedicine, and nanotechnology. Our scanning microscope based on nanofocusing refractive X-ray lenses has a routine spatial resolution of about 100 nm and supports the contrast mechanisms mentioned above. In combination with coherent X-ray diffraction imaging, the spatial resolution can be improved to the 10 nm range. The current state-of-the-art of this technique is illustrated by several examples, and future prospects of the technique are given. (author)

  8. X-rays in protoplanetary disks : Their impact on the thermal and chemical structure, a grid of models

    NARCIS (Netherlands)

    Aresu, G.; Kamp, I.; Meijerink, R.; Woitke, P.; Thi, W. F.; Spaans, M.C.

    X-rays impact protoplanetary disks hydrostatic, thermal and chemical structure. The range of efficiency of X-rays is explored using a grid modelling approach: different parameters affects the structure of the disk, this determines different contribution of the X-ray radiation to the chemistry and

  9. Noninvasive 3D Structural Analysis of Arthropod by Synchrotron X-Ray Phase Contrast Tomography

    Directory of Open Access Journals (Sweden)

    Shengkun Yao

    2015-01-01

    Full Text Available X-ray imaging techniques significantly advanced our understanding of materials and biology, among which phase contrast X-ray microscopy has obvious advantages in imaging biological specimens which have low contrast by conventional absorption contrast microscopy. In this paper, three-dimensional microstructure of arthropod with high contrast has been demonstrated by synchrotron X-ray in-line phase contrast tomography. The external morphology and internal structures of an earthworm were analyzed based upon tomographic reconstructions with and without phase retrieval. We also identified and characterized various fine structural details such as the musculature system, the digestive system, the nervous system, and the circulatory system. This work exhibited the high efficiency, high precision, and wide potential applications of synchrotron X-ray phase contrast tomography in nondestructive investigation of low-density materials and biology.

  10. Noninvasive 3D Structural Analysis of Arthropod by Synchrotron X-Ray Phase Contrast Tomography

    International Nuclear Information System (INIS)

    Yao, S.; Zong, Y.; Fan, J.; Sun, Z.; Jiang, H.

    2015-01-01

    X-ray imaging techniques significantly advanced our understanding of materials and biology, among which phase contrast X-ray microscopy has obvious advantages in imaging biological specimens which have low contrast by conventional absorption contrast microscopy. In this paper, three-dimensional microstructure of arthropod with high contrast has been demonstrated by synchrotron X-ray in-line phase contrast tomography. The external morphology and internal structures of an earthworm were analyzed based upon tomographic reconstructions with and without phase retrieval. We also identified and characterized various fine structural details such as the musculature system, the digestive system, the nervous system, and the circulatory system. This work exhibited the high efficiency, high precision, and wide potential applications of synchrotron X-ray phase contrast tomography in nondestructive investigation of low-density materials and biology.

  11. Ultrafast Structural Dynamics in InSb Probed by Time-Resolved X-Ray Diffraction

    International Nuclear Information System (INIS)

    Chin, A.H.; Shank, C.V.; Chin, A.H.; Schoenlein, R.W.; Shank, C.V.; Glover, T.E.; Leemans, W.P.; Balling, P.

    1999-01-01

    Ultrafast structural dynamics in laser-perturbed InSb are studied using time-resolved x-ray diffraction with a novel femtosecond x-ray source. We report the first observation of a delay in the onset of lattice expansion, which we attribute to energy relaxation processes and lattice strain propagation. In addition, we observe direct indications of ultrafast disordering on a subpicosecond time scale. copyright 1999 The American Physical Society

  12. Titanium dioxide nanoparticles: synthesis, X-Ray line analysis and chemical composition study

    Energy Technology Data Exchange (ETDEWEB)

    Chenari, Hossein Mahmoudi, E-mail: mahmoudi_hossein@guilan.ac.ir, E-mail: h.mahmoudiph@gmail.com [University of Guilan, Rasht (Iran, Islamic Republic of); Seibel, Christoph; Hauschild, Dirk; Reinert, Friedrich [Karlsruhe Institute of Technology - KIT, Gemeinschaftslabor für Nanoanalytik, Karlsruhe (Germany); Abdollahian, Hossein [Nanotechnology Research Center of Urmia University, Urmia, (Iran, Islamic Republic of)

    2016-11-15

    TiO{sub 2} nanoparticles have been synthesized by the sol-gel method using titanium alkoxide and isopropanol as a precursor. The structural properties and chemical composition of the TiO{sub 2} nanoparticles were studied using X-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy.The X-ray powder diffraction pattern confirms that the particles are mainly composed of the anatase phase with the preferential orientation along [101] direction. The physical parameters such as strain, stress and energy density were investigated from the Williamson- Hall (W-H) plot assuming a uniform deformation model (UDM), and uniform deformation energy density model (UDEDM). The W-H analysis shows an anisotropic nature of the strain in nano powders. The scanning electron microscopy image shows clear TiO{sub 2} nanoparticles with particle sizes varying from 60 to 80nm. The results of mean particle size of TiO{sub 2} nanoparticles show an inter correlation with the W-H analysis and SEM results. Our X-ray photoelectron spectroscopy spectra show that nearly a complete amount of titanium has reacted to TiO{sub 2}. (author)

  13. Small-angle X-ray scattering (SAXS) studies of the structure of mesoporous silicas

    Science.gov (United States)

    Zienkiewicz-Strzałka, M.; Skibińska, M.; Pikus, S.

    2017-11-01

    Mesoporous ordered silica nanostructures show strong interaction with X-ray radiation in the range of small-angles. Small-angle X-ray scattering (SAXS) measurements based on the elastically scattered X-rays are important in analysis of condensed matter. In the case of mesoporous silica materials SAXS technique provides information on the distribution of electron density in the mesoporous material, in particular describing their structure and size of the unit cell as well as type of ordered structure and finally their parameters. The characterization of nanopowder materials, nanocomposites and porous materials by Small-Angle X-ray Scattering seems to be valuable and useful. In presented work, the SAXS investigation of structures from the group of mesoporous ordered silicates was performed. This work has an objective to prepare functional materials modified by noble metal ions and nanoparticles and using the small-angle X-ray scattering to illustrate their properties. We report the new procedure for describing mesoporous materials belonging to SBA-15 and MCM-41 family modified by platinum, palladium and silver nanoparticles, based on detailed analysis of characteristic peaks in the small-angle range of X-ray scattering. This procedure allows to obtained the most useful parameters for mesoporous materials characterization and their successfully compare with experimental measurements reducing the time and material consumption with good precision for particles and pores with a size below 10 nm.

  14. Microbeam high-resolution diffraction and x-ray standing wave methods applied to semiconductor structures

    International Nuclear Information System (INIS)

    Kazimirov, A; Bilderback, D H; Huang, R; Sirenko, A; Ougazzaden, A

    2004-01-01

    A new approach to conditioning x-ray microbeams for high angular resolution x-ray diffraction and scattering techniques is introduced. We combined focusing optics (one-bounce imaging capillary) and post-focusing collimating optics (miniature Si(004) channel-cut crystal) to generate an x-ray microbeam with a size of 10 μm and ultimate angular resolution of 14 μrad. The microbeam was used to analyse the strain in sub-micron thick InGaAsP epitaxial layers grown on an InP(100) substrate by the selective area growth technique in narrow openings between the oxide stripes. For the structures for which the diffraction peaks from the substrate and the film overlap, the x-ray standing wave technique was applied for precise measurements of the strain with a Δd/d resolution of better than 10 -4 . (rapid communication)

  15. X-ray irradiation-induced structural modifications in PM-355 polymeric nuclear track detector film

    Science.gov (United States)

    Nouh, S. A.; Bahareth, Radiyah A.; Abutalib, M. M.

    2014-06-01

    Samples from sheets of the polymeric material PM-355 have been exposed to X-rays from a 50 kV X-ray tube in the dose range of 10-300 kGy. The resultant effect of X-ray irradiation on the structural properties of PM-355 has been investigated using different techniques such as X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, Vickers hardness and refractive index measurements. The results indicate that the X-ray irradiation of PM-355 in the dose range of 10-20 kGy causes initially chain scission. Above 20 and up to 100 kGy, the active free radicals produced from scission contribute to chemical reactions that lead to the crosslinking. Thus, the X-ray irradiation in the dose range of 20-100 kGy leads to a more compact structure of the PM-355 polymer, resulting in an enhancement of its Vickers hardness and refractive index. Moreover, the irradiation in the dose range of 100-300 kGy leads to the predominance of the degradation. This degradation is reported by FTIR spectroscopy and enhances the degree of ordering in the degraded samples as revealed by XRD technique. Additionally, it decreases both the Vickers hardness and refractive index of the PM-355 samples.

  16. Synthesis and single crystal X-ray structure of the tetragonal tungsten bronze Pb{sub 0.91}K{sub 1.72}Li{sub 1.46}Nb{sub 5}O{sub 15}

    Energy Technology Data Exchange (ETDEWEB)

    Capitelli, F. [Institute of Crystallography - CNR, Via Salaria Km 29.300, 00016 Monterotondo Rome (Italy); Rossi, M. [Earth Sciences Department, Federico II University, Via Mezzocannone 8, 80134 Naples (Italy); Elaatmani, M.; Zegzouti, A. [Laboratoire de Chimie du Solide Mineral, Faculte des Sciences Semlalia, Universite Cadi Ayyad, Marrakech (Morocco)

    2010-11-15

    Crystals of Pb{sub 0.91}K{sub 1.72}Li{sub 1.46}Nb{sub 5}O{sub 15}, belonging to tetragonal tungsten bronze materials, were grown by the slow cooling technique, and characterized by means of single crystal X-ray diffraction: the structure was solved in the P4bm tetragonal space group, with the following unit cell parameters: a = 12.548(5), c = 4.042(5)A, V = 636.4(9)A{sup 3}. The three-dimensional framework can be described as a layered structure down crystallographic axis c, with arrays of NbO{sub 6} octahedra, whose corner sharing makes up the formation of tunnels filled up by Li, Pb and K displaying complex cation-oxygen coordinations. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  17. Synthesis and X-ray structure analysis of a new binuclear Schiff base Co(II) complex with the ligand N,N'-bis(3-methoxysalicylidene)-1,4-butanediamine

    Energy Technology Data Exchange (ETDEWEB)

    Nasr-Esfahani, M., E-mail: m-nasresfahani@iaun.ac.ir [Islamic Azad University, Najafabad Branch, Department of Materials Science and Engineering (Iran, Islamic Republic of)

    2009-12-15

    The title binuclear complex, tris[N,N-bis(3-methoxysalicylidene)-1,4-diaminobutane] dicobalt(II), C{sub 60}H{sub 70}Co{sub 2}N{sub 6}O{sub 15}, was prepared by the reaction of the tetradentate Schiff base ligand bis(3-methoxysalicylidene)-1,4-diaminobutane and Co(CH{sub 3}COO){sub 2} . 4H{sub 2}O in a ethanol solution and structurally characterized by single-crystal X-ray diffraction. This complex has a dinuclear structure where two Co(II) ions are bridged by one N{sup 0},N'-bis(3-methoxysalicylidene)-1,4-diaminobutane. The two Co(II) ions, have two distorted octahedral coordination involving two O and two N atoms.

  18. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

    Science.gov (United States)

    Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; Berntsen, Peter; Bielecki, Johan; Daurer, Benedikt J.; DeMirci, Hasan; Fromme, Petra; Hantke, Max Felix; Maia, Filipe R. N. C.; Munke, Anna; Nettelblad, Carl; Pande, Kanupriya; Reddy, Hemanth K. N.; Sellberg, Jonas A.; Sierra, Raymond G.; Svenda, Martin; van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu; Aquila, Andrew; Zwart, Peter H.; Mancuso, Adrian P.

    2017-10-01

    We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

  19. X-ray absorption fine structure (XAFS) studies of cobalt silicide thin films

    International Nuclear Information System (INIS)

    Naftel, S.J.; Coulthard, I.; Hu, Y.; Sham, T.K.; Zinke-Allmang, M.

    1998-01-01

    Cobalt silicide thin films, prepared on Si(100) wafers, have been studied by X-ray absorption near edge structures (XANES) at the Si K-, L 2,3 - and Co K-edges utilizing both total electron (TEY) and fluorescence yield (FLY) detection as well as extended X-ray absorption fine structure (EXAFS) at the Co K-edge. Samples made using DC sputter deposition on clean Si surfaces and MBE were studied along with a bulk CoSi 2 sample. XANES and EXAFS provide information about the electronic structure and morphology of the films. It was found that the films studied have essentially the same structure as bulk CoSi 2 . Both the spectroscopy and materials characterization aspects of XAFS (X-ray absorption fine structures) are discussed

  20. Effects of x rays on DNA synthesis in synchronized Chinese hamster ovary cells

    International Nuclear Information System (INIS)

    Laughlin, T.J.; Taylor, J.H.

    1980-01-01

    Chinese hamster ovary cells were synchronized at the beginning of S phase with 5-fluorodeoxyuridine and irradiated with moderte levels ( 3 H]thymidine at various times after irradiation. The cells were lysed immediately after termination of the pulse, and the rate of DNA synthesis, size of the nascent strands, and number of active replicons were determined. The level of DNA synthesis in cells pulse-labeled immediately after x irradiation with 1000 rad was suppressed 20 to 25% but returned to control levels within 4 h after irradiation. Our data demonstrate that this x-ray-induced suppression of DNA synthesis was due entirely to a reduction in the number of active replicons, with no appreciable change in the rate of chain growth

  1. Annealing induced atomic rearrangements on (Ga,In) (N,As) probed by hard X-ray photoelectron spectroscopy and X-ray absorption fine structure.

    Science.gov (United States)

    Ishikawa, Fumitaro; Higashi, Kotaro; Fuyuno, Satoshi; Morifuji, Masato; Kondow, Masahiko; Trampert, Achim

    2018-04-13

    We study the effects of annealing on (Ga 0.64 ,In 0.36 ) (N 0.045 ,As 0.955 ) using hard X-ray photoelectron spectroscopy and X-ray absorption fine structure measurements. We observed surface oxidation and termination of the N-As bond defects caused by the annealing process. Specifically, we observed a characteristic chemical shift towards lower binding energies in the photoelectron spectra related to In. This phenomenon appears to be caused by the atomic arrangement, which produces increased In-N bond configurations within the matrix, as indicated by the X-ray absorption fine structure measurements. The reduction in the binding energies of group-III In, which occurs concomitantly with the atomic rearrangements of the matrix, causes the differences in the electronic properties of the system before and after annealing.

  2. Intact Imaging of Human Heart Structure Using X-ray Phase-Contrast Tomography.

    Science.gov (United States)

    Kaneko, Yukihiro; Shinohara, Gen; Hoshino, Masato; Morishita, Hiroyuki; Morita, Kiyozo; Oshima, Yoshihiro; Takahashi, Masashi; Yagi, Naoto; Okita, Yutaka; Tsukube, Takuro

    2017-02-01

    Structural examination of human heart specimens at the microscopic level is a prerequisite for understanding congenital heart diseases. It is desirable not to destroy or alter the properties of such specimens because of their scarcity. However, many of the currently available imaging techniques either destroy the specimen through sectioning or alter the chemical and mechanical properties of the specimen through staining and contrast agent injection. As a result, subsequent studies may not be possible. X-ray phase-contrast tomography is an imaging modality for biological soft tissues that does not destroy or alter the properties of the specimen. The feasibility of X-ray phase-contrast tomography for the structural examination of heart specimens was tested using infantile and fetal heart specimens without congenital diseases. X-ray phase-contrast tomography was carried out at the SPring-8 synchrotron radiation facility using the Talbot grating interferometer at the bending magnet beamline BL20B2 to visualize the structure of five non-pretreated whole heart specimens obtained by autopsy. High-resolution, three-dimensional images were obtained for all specimens. The images clearly showed the myocardial structure, coronary vessels, and conduction bundle. X-ray phase-contrast tomography allows high-resolution, three-dimensional imaging of human heart specimens. Intact imaging using X-ray phase-contrast tomography can contribute to further structural investigation of heart specimens with congenital heart diseases.

  3. X-ray and photoelectron spectroscopy of the structure, reactivity, and electronic structure of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Hamad, Kimberly Sue [Univ. of California, Berkeley, CA (United States)

    2000-01-01

    Semiconductor nanocrystals are a system which has been the focus of interest due to their size dependent properties and their possible use in technological applications. Many chemical and physical properties vary systematically with the size of the nanocrystal and thus their study enables the investigation of scaling laws. Due to the increasing surface to volume ratio as size is decreased, the surfaces of nanocrystals are expected to have a large influence on their electronic, thermodynamic, and chemical behavior. In spite of their importance, nanocrystal surfaces are still relatively uncharacterized in terms of their structure, electronic properties, bonding, and reactivity. Investigation of nanocrystal surfaces is currently limited by what techniques to use, and which methods are suitable for nanocrystals is still being determined. This work presents experiments using x-ray and electronic spectroscopies to explore the structure, reactivity, and electronic properties of semiconductor (CdSe, InAs) nanocrystals and how they vary with size. Specifically, x-ray absorption near edge spectroscopy (XANES) in conjunction with multiple scattering simulations affords information about the structural disorder present at the surface of the nanocrystal. X-ray photoelectron spectroscopy (XPS) and ultra-violet photoelectron spectroscopy (UPS) probe the electronic structure in terms of hole screening, and also give information about band lineups when the nanocrystal is placed in electric contact with a substrate. XPS of the core levels of the nanocrystal as a function of photo-oxidation time yields kinetic data on the oxidation reaction occurring at the surface of the nanocrystal.

  4. Modeling Radiation Effects of Ultrasoft X Rays on the Basis of Amorphous Track Structure.

    Science.gov (United States)

    Buch, Tamara; Scifoni, Emanuele; Krämer, Michael; Durante, Marco; Scholz, Michael; Friedrich, Thomas

    2018-01-01

    There is experimental evidence that ultrasoft X rays (0.1-5 keV) show a higher biological effectiveness than high-energy photons. Similar to high-LET radiation, this is attributed to a rather localized dose distribution associated with a considerably smaller range of secondary electrons, which results in an increasing yield of double-strand breaks (DSBs) and potentially more complex lesions. We previously reported on the application of the Giant LOop Binary LEsion (GLOBLE) model to ultrasoft X rays, in which experimental values of the relative biological effectiveness (RBE) for DSB induction were used to show that this increasing DSB yield was sufficient to explain the enhanced effectiveness in the cell inactivation potential of ultrasoft X rays. Complementary to GLOBLE, we report here on a modeling approach to predict the increased DSB yield of ultrasoft X rays on the basis of amorphous track structure formed by secondary electrons, which was derived from Monte Carlo track structure simulations. This procedure is associated with increased production of single-strand break (SSB) clusters, which are caused by the highly localized energy deposition pattern induced by low-energy photons. From this, the RBE of ultrasoft X rays can be determined and compared to experimental data, showing that the inhomogeneity of the energy deposition pattern represents the key variable to describe the increased biological effectiveness of ultrasoft X rays. Thus, this work demonstrates an extended applicability of the amorphous track structure concept and tests its limits with respect to its predictive power. The employed model mechanism offers a possible explanation for how the cellular response to ultrasoft X rays is directly linked to the energy deposition properties on the nanometric scale.

  5. Fabrication of high-aspect-ratio nano structures using a nano x-ray shadow mask

    International Nuclear Information System (INIS)

    Kim, Yong Chul; Lee, Seung S

    2008-01-01

    This paper describes a novel method for the fabrication of high-aspect-ratio nano structures (HAR-nano structures) using a nano x-ray shadow mask and deep x-ray lithography (DXRL). The nano x-ray shadow mask is fabricated by depositing an x-ray absorber layer (Au, 3 µm) onto the back side of a nano shadow mask. The nano shadow mask is produced with nano-sized apertures whose dimensions are reduced to several tens of nanometers by the accumulation of low-stress silicon nitride (Si x N y ) using the LPCVD process on the shadow mask. A shadow mask containing apertures with a size of 1 µm is fabricated on a bulk micromachined Si x N y membrane. The thickness of an absorber layer must be in the range of several tens of micrometers in order to obtain a contrast of more than 100 for the conventional DXRL process at the Pohang Light Source (PLS). However, a 3 µm thick absorber layer can provide a sufficient contrast if the modified DXRL of the central beam-stop method is used, which blocks high-energy x-rays. A nano shadow mask with 30 nm sized apertures is fabricated and a nano x-ray shadow mask with 250 nm sized apertures is fabricated by depositing a 3 µm thick absorber layer on a nano shadow mask with 500 nm sized apertures. HAR-nano structures (circles with a diameter of 420 nm and lines with a width of 274 nm) with aspect ratios of over 10:1 on a 3.2 µm SU-8 are successfully fabricated by using the nano x-ray shadow mask and the central beam-stop method

  6. One pot synthesis, X-ray crystal structure of 2-(2‧-hydroxyphenyl)oxazolo[4,5-b]pyridine derivatives and studies of their optical properties

    Science.gov (United States)

    Briseño-Ortega, Horacio; Juárez-Guerra, Lizbeth; Rojas-Lima, Susana; Mendoza-Huizar, Luis Humberto; Vázquez-García, Rosa A.; Farfán, Norberto; Arcos-Ramos, Rafael; Santillan, Rosa; López-Ruiz, Heralio

    2018-04-01

    A series of five 2-(2-hydroxyphenyl)oxazolo [4,5-b]pyridines (HPOP) (3a-e), where four are novel, were synthesized by a mild, one pot, phenylboronic acid-NaCN catalyzed reaction. Spectroscopic characterization and photophysical properties of these compounds are reported. Absorption and excitation spectra of the compounds were dependent on the substituents in the phenyl ring. Fluorescence quantum yields (0.009-0.538) were associated with the donor strength and the position of the substituents. Also, DFT analysis allowed us to determine the contribution of diethylamino and methoxy moieties to the π-system, which is in agreement with the experimental data analyzed in solution and by cyclic voltammetry. The results obtained in the solid state by single-crystal X-ray diffraction experiments indicate that, the quasi-planarity envisioned for the explored compounds is present, supporting the hypothesis that both the H-bonding of a hydroxyl group to the Cdbnd N moiety and a donor groups such as diethylamino and methoxy moieties favor an electronic communication. Due to the facile synthesis and their photophysical properties, the novel HPOP 3a-e have potential application as organic semiconductors.

  7. Functional coordination polymers and MOFs from reactions of the lanthanides and barium with azole ligands. Synthesis and characterization with a focus on structure determination from X-ray powder diffraction data; Funktionale Koordinationspolymere und MOFs aus Reaktionen der Lanthanide und des Bariums mit Azol-Liganden. Synthese und Charakterisierung mit dem Fokus der Strukturbestimmung anhand von Roentgenpulverbeugungsdaten

    Energy Technology Data Exchange (ETDEWEB)

    Rybak, Jens-Christoph

    2012-07-01

    This thesis deals with the synthesis and characterization of coordination polymers and MOFs of the lanthanides and barium with different azolic N-heterocycles. A total of 18 new organic-inorganic hybrid materials, as well as a series of co-doped compounds is presented. Besides the structural characterization of these materials from X-ray diffraction powder data, the focus of the investigations is on the thermal and photoluminescence spectroscopic properties. The lanthanides La - Lu, except Eu and Pm, can be reacted with 1H-1,2,3-triazole to give the series of the isotypic dense 3D-MOFs {sup 3}{sub ∞}[Ln(Tz{sup *}){sub 3}]. Investigation of the photoluminescence properties of these compounds reveals a broad range of different luminescence phenomena, including the first observation of an intrinsic inner-filter effect of the Ln{sup 3+}-ions. The structure of this isotypic series of compounds was solved and refined from X-ray powder diffraction data. A 2D-polymorph of these compounds {sup 2}{sub ∞}[Ln(Tz{sup *}){sub 3}], is observed for Ln = Sm, Tb and was characterized by single crystal data. The reaction of Eu with 1H-benzotriazole yields the 1D-coordination polymer {sup 1}{sub ∞}[Eu(Btz){sub 2}(BtzH){sub 2}], which is the first example of a divalent rare earth benzotriazolate. Analysis of the thermal properties reveals the transformation to the 3D-MOF {sup 3}{sub ∞}[Eu(Btz){sub 2}] at higher temperatures. The structure of this material was also solved from X-ray powder diffraction data. Investigation of the photoluminescence properties of the co-doped compounds {sup 3}{sub ∞}[Ba{sub 1-x}Eu{sub x}(Im){sub 2}], which were obtained from reaction of the salt-like hydrides BaH{sub 2} and EuH{sub 2} with imidazole, show that the synthesis of luminescent MOF materials by co-doping of non-luminescent networks with luminescence centers is possible. The structure of these materials was solved from X-ray powder diffraction data of the undoped compound {sup 3}{sub

  8. X-Ray and Neutron Scattering Study of the Magnetic Structure of Neodymium Metal

    DEFF Research Database (Denmark)

    Lebech, Bente; Als-Nielsen, Jens Aage; McEwen, K. A.

    1979-01-01

    A combined x-ray and neutron diffraction study has shown that the so-called "triple-q⃗" structure is not the correct model of the magnetic structure of neodymium. The x-ray data showed only the Bragg reflections originating from the double-hcp lattice. Hence, all additional reflections observed...... below TN by neutrons are of magnetic origin. Additional neutron-diffraction data have shown that the magnetic structure must be described by modulation wave vectors with components both parallel and perpendicular to the 〈100〉 axes....

  9. Near-edge x-ray absorption fine structure spectroscopy at atmospheric pressure with a table-top laser-induced soft x-ray source

    Energy Technology Data Exchange (ETDEWEB)

    Kühl, Frank-Christian, E-mail: Frank-christian.kuehl@mail.de; Müller, Matthias, E-mail: matthias.mueller@llg-ev.de; Schellhorn, Meike; Mann, Klaus [Laser-Laboratorium Göttingen e.V., Hans-Adolf-Krebs-Weg 1, D-37077 Göttingen (Germany); Wieneke, Stefan [Hochschule für angewandte Wissenschaft und Kunst, Von-Ossietzky-Str 99, D-37085 Göttingen (Germany); Eusterhues, Karin [Friedrich-Schiller-Universität Jena, Fürstengraben 1, D-07743 Jena (Germany)

    2016-07-15

    The authors present a table-top soft x-ray absorption spectrometer, accomplishing investigations of the near-edge x-ray absorption fine structure (NEXAFS) in a laboratory environment. The system is based on a low debris plasma ignited by a picosecond laser in a pulsed krypton gas jet, emitting soft x-ray radiation in the range from 1 to 5 nm. For absorption spectroscopy in and around the “water window” (2.3–4.4 nm), a compact helium purged sample compartment for experiments at atmospheric pressure has been constructed and tested. NEXAFS measurements on CaCl{sub 2} and KMnO{sub 4} samples were conducted at the calcium and manganese L-edges, as well as at the oxygen K-edge in air, atmospheric helium, and under vacuum, respectively. The results indicate the importance of atmospheric conditions for an investigation of sample hydration processes.

  10. High-Resolution Structure of the Photosynthetic Mn4Ca Catalyst from X-ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yachandra, Vittal; Yano, Junko; Kern, Jan; Pushkar, Yulia; Sauer, Kenneth; Glatzel, Pieter; Bergmann, Uwe; Messinger, Johannes; Zouni, Athina; Yachandra, Vittal K.

    2007-08-01

    The application of high-resolution X-ray spectroscopy methods to study the photosynthetic water oxidizing complex, which contains a unique hetero-nuclear catalytic Mn4Ca cluster, are described. Issues of X-ray damage especially at the metal sites in the Mn4Ca cluster are discussed. The structure of the Mn4Ca catalyst at high-resolution which has so far eluded attempts of determination by X-ray diffraction, EXAFS and other spectroscopic techniques has been addressed using polarized EXAFS techniques applied to oriented PS II membrane preparations and PS II single crystals. A review of how the resolution of traditional EXAFS techniques can be improved, using methods such as range-extended EXAFS is presented, and the changes that occur in the structure of the cluster as it advances through the catalytic cycle are described. X-ray absorption and emission techniques (XANES and K? emission) have been used earlier to determine the oxidation states of the Mn4Ca cluster, and in this report we review the use of X-ray resonant Raman spectroscopy to understand the electronic structure of the Mn4Ca cluster as it cycles through the intermediate S-states.

  11. Effect of anode shape on pinch structure and X-ray emission of plasma focus device

    Science.gov (United States)

    Talukdar, N.; Neog, N. K.; Borthkur, T. K.

    The effect of anode shapes on pinch structure and X-ray emission of plasma focus device operated with cylindrical, diverging, oval and converging anode tips is reported. The pinch structure in the radial compression phase has been investigated by employing a triple pinhole camera. It has been observed that pinch structure as well as the X-ray emission of PF device strongly depends upon anode tip designs. For the first time the studies were carried out in two new shapes of anode tips that is the oval and the divergent one. It has been observed that the oval and diverging anode tips are more conducive for the formation of instabilities and hotspot generation. The studies of X-ray emission were also carried out by employing three channels of a p-i-n diode X-ray spectrometer in entire anode designs to corroborate the results of a triple pinhole camera. Additionally, the effective hard X-ray photon energy was also estimated by the radiography method for all the anode tip designs, which indirectly provide a qualitative idea of the generation of induced accelerating field in the pinched column during compression.

  12. New structural studies of liquid crystal by reflectivity and resonant X-ray diffraction

    International Nuclear Information System (INIS)

    Fernandes, P.

    2007-04-01

    This memory presents three structural studies of smectic Liquid Crystals by reflectivity and resonant diffraction of X-rays. It is divided in five chapters. In the first a short introduction to Liquid Crystals is given. In particular, the smectic phases that are the object of this study are presented. The second chapter is consecrated to the X-ray experimental techniques that were used in this work. The three last chapters present the works on which this thesis can be divided. Chapter three demonstrates on free-standing films of MHPOBC (historic liquid crystal that possesses the antiferroelectric sub-phases) the possibility to extend the technique of resonant X-ray diffraction to liquid crystals without resonant element. In the fourth chapter the structure of the B 2 liquid crystal phase of bent-core molecules (or banana molecules) is elucidated by using resonant X-ray diffraction combined with polarization analysis of the diffracted beam. A model of the polarization of the resonant beam diffracted by four different structures proposed for the B 2 phase is developed in this chapter. In the fifth chapter a smectic binary mixture presenting a very original critical point of phase separation is studied by X-ray reflectivity and optical microscopy. A concentration gradient in the direction perpendicular to the plane of the film seems to be induced by the free-standing film geometry. The results of a simplified model of the system are compatible with this interpretation

  13. X-Ray structure and biophysical properties of rabbit fibroblast growth factor 1

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jihun; Blaber, Sachiko I.; Irsigler, Andre; Aspinwall, Eric; Blaber, Michael; (FSU)

    2010-01-14

    The rabbit is an important and de facto animal model in the study of ischemic disease and angiogenic therapy. Additionally, fibroblast growth factor 1 (FGF-1) is emerging as one of the most important growth factors for novel pro-angiogenic and pro-arteriogenic therapy. However, despite its significance, the fundamental biophysical properties of rabbit FGF-1, including its X-ray structure, have never been reported. Here, the cloning, crystallization, X-ray structure and determination of the biophysical properties of rabbit FGF-1 are described. The X-ray structure shows that the amino-acid differences between human and rabbit FGF-1 are solvent-exposed and therefore potentially immunogenic, while the biophysical studies identify differences in thermostability and receptor-binding affinity that distinguish rabbit FGF-1 from human FGF-1.

  14. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse

    Directory of Open Access Journals (Sweden)

    J. Szlachetko

    2014-03-01

    Full Text Available Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10−18 s to femtoseconds (10−15 s and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS, we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.

  15. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...

  16. Photovoltaic x-ray detectors based on the GaAs epitaxial structures

    CERN Document Server

    Akhmadullin, R A; Dvoryankina, G G; Dikaev, Y M; Ermakov, M G; Ermakova, O N; Krikunov, A I; Kudryashov, A A; Petrov, A G; Telegin, A A

    2002-01-01

    The new photovoltaic detector of the X-ray radiation is proposed on the basis of the GaAs epitaxial structures, which operates with high efficiency of the charge carriers collection without shift voltage and at the room temperature. The structures are grown by the method of the gas-phase epitaxy on the n sup + -type highly-alloyed substrates. The range of sensitivity to the X-ray radiation is within the range of effective energies from 8 up to 120 keV. The detector maximum response in the current short circuit mode is determined

  17. Purification, crystallization and preliminary X-ray structure analysis of the laccase from Ganoderma lucidum

    International Nuclear Information System (INIS)

    Lyashenko, Andrey V.; Belova, Oksana; Gabdulkhakov, Azat G.; Lashkov, Alexander A.; Lisov, Alexandr V.; Leontievsky, Alexey A.; Mikhailov, Al’bert M.

    2011-01-01

    The purification, crystallization and preliminary X-ray structure analysis of the laccase from G. lucidum are reported. The ligninolytic enzymes of the basidiomycetes play a key role in the global carbon cycle. A characteristic property of these enzymes is their broad substrate specificity, which has led to their use in various biotechnologies, thus stimulating research into the three-dimensional structures of ligninolytic enzymes. This paper presents the purification, crystallization and preliminary X-ray analysis of the laccase from the ligninolytic basidiomycete Ganoderma lucidum

  18. X-ray absorption in GaGdN: A study of local structure

    Science.gov (United States)

    Martínez-Criado, G.; Sancho-Juan, O.; Garro, N.; Sans, J. A.; Cantarero, A.; Susini, J.; Roever, M.; Mai, D.-D.; Bedoya-Pinto, A.; Malindretos, J.; Rizzi, A.

    2008-07-01

    In this study, we report on the incorporation of dilute Gd amounts into GaN films grown by molecular beam epitaxy. A combination of x-ray fluorescence with x-ray absorption spectroscopic techniques enabled us to examine not only the distribution of rare earth atoms in the GaN matrix but also the short-range structural order. Our results show Gd atoms in a trivalent state with tetrahedral coordination, thus substituting Ga in the wurtzite GaN structure.

  19. X-ray absorption in GaGdN: A study of local structure

    International Nuclear Information System (INIS)

    Martinez-Criado, G.; Sans, J. A.; Susini, J.; Sancho-Juan, O.; Cantarero, A.; Garro, N.; Roever, M.; Mai, D.-D.; Bedoya-Pinto, A.; Malindretos, J.; Rizzi, A.

    2008-01-01

    In this study, we report on the incorporation of dilute Gd amounts into GaN films grown by molecular beam epitaxy. A combination of x-ray fluorescence with x-ray absorption spectroscopic techniques enabled us to examine not only the distribution of rare earth atoms in the GaN matrix but also the short-range structural order. Our results show Gd atoms in a trivalent state with tetrahedral coordination, thus substituting Ga in the wurtzite GaN structure

  20. Solution spectroelectrochemical cell for in situ X-ray absorption fine structure

    International Nuclear Information System (INIS)

    Antonio, M.R.; Soderholm, L.

    1995-01-01

    A purpose-built spectroelectrochemical cell for in situ fluorescence XAFS (X-ray Absorption Fine Structure) measurements of bulk solution species during constant-potential electrolysis is described. The cell performance was demonstrated by the collection of europium L 3 -edge XANES (X-ray Absorption Near Edge Structure) throughout the course of electrolysis of an aqueous solution of EuCl 3 ·6H 2 O in 1 M H 2 SO 4 . The europium L 3 -edge resonances reported here for the Eu III and Eu II ions demonstrate that their 2p 3/2 → 5d electronic transition probabilities are not the same

  1. Resonant inelastic soft x-ray scattering and electronic structure of LiBC

    International Nuclear Information System (INIS)

    Karimov, P F; Skorikov, N A; Kurmaev, E Z; Finkelstein, L D; Leitch, S; MacNaughton, J; Moewes, A; Mori, T

    2004-01-01

    The electronic structure of LiBC has been studied using soft x-ray fluorescence measurements. Resonant inelastic x-ray scattering (RIXS) spectra were measured with the excitation energy tuned to the boron and carbon K-edges. RIXS spectra show dispersive features, which were assigned to the calculated energy bands using the site-selective quantitative band mapping method based on the concept of k-momentum conservation. It is concluded that while the electronic structure calculations are in general agreement with experimental spectra, carbon and boron K-emission bands show some deviation due to an incomplete hybridization of the C 2p-B 2p states

  2. Dark-field X-ray microscopy for multiscale structural characterization

    DEFF Research Database (Denmark)

    Simons, Hugh; King, A.; Ludwig, W.

    2015-01-01

    Many physical and mechanical properties of crystalline materials depend strongly on their internal structure, which is typically organized into grains and domains on several length scales. Here we present dark-field X-ray microscopy; a non-destructive microscopy technique for the three...... of the interactions between crystalline elements is a key step towards the formulation and validation of multiscale models that account for the entire heterogeneity of a material. Furthermore, dark-field X-ray microscopy is well suited to applied topics, where the structural evolution of internal nanoscale elements...

  3. X-Ray Absorption Fine Structure Study for Fe60Ni40 Alloy

    International Nuclear Information System (INIS)

    Yang, Dong-Seok; Oh, Kyuseung; Na, Wonkyung; Kim, Nayoung; Yoo, Yong-Goo; Min, Seung-Gi; Yu, Seong-Cho

    2007-01-01

    Fe60Ni40 alloys were fabricated by the mechanical alloying process with process periods of 1, 2, 4, 6, 12 and 24 hours, respectively. The formation of alloy and the structural evolution of the alloy were examined by X-ray diffraction and extended X-ray absorption fine structure methods. With increase of alloying time the BCC phase of iron was changed significantly during the mechanical alloying process. The alloying was activated in about 6 hours and completed in about 24 hours

  4. X-ray diffraction study of the structure of detonation nanodiamonds

    International Nuclear Information System (INIS)

    Ozerin, A. N.; Kurkin, T. S.; Ozerina, L. A.; Dolmatov, V. Yu.

    2008-01-01

    The spatial structure of aggregates formed by detonation nanodiamonds is investigated using the wide-angle and small-angle X-ray scattering techniques. The effective sizes of crystallites and the crystallite size distribution function are determined. The shape of scattering aggregates is restored from the small-angle X-ray scattering data. An analysis of the results obtained allowed the conclusion that the nanodiamond aggregates have an extended spatial structure composed of nine to ten clusters, each involving four to five crystallites with a crystal lattice of the diamond type

  5. Covering complete proteomes with X-ray structures: a current snapshot

    Energy Technology Data Exchange (ETDEWEB)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-10-23

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

  6. X-ray crystal structure of divalent metal-activated ß-xyloisdase, RS223BX

    Science.gov (United States)

    We report the first X-ray structure of a glycoside hydrolase family 43 ß-xylosidase, RS223BX, which is strongly activated by the addition of divalent metal cations. The 2.69 Å structure reveals that the Ca2+ cation is located at the back of the active site pocket. The Ca2+ coordinates to H274 to sta...

  7. Isolation, Characterization and X-ray Structure Determination of the ...

    African Journals Online (AJOL)

    NICO

    2014-12-20

    Dec 20, 2014 ... varied both sterically and electronically. On the other hand, the aminothiazole ring system is a useful structural element in medicinal chemistry.5 We have reported substituted pyrazolones with various amino thiazoles and their molecular structures were determined.6 The ligands can exist in three tautomeric.

  8. The (oxo)[(2,3,7,8,12,13,17,18-octachloro-5,10,15,20-tetrakis(4-tolylporphyrinato)]vanadium(IV): Synthesis, UV-visible, Cyclic voltammetry and X-ray crystal structure

    Science.gov (United States)

    Mchiri, Chadlia; Amiri, Nesrine; Jabli, Souhir; Roisnel, Thierry; Nasri, Habib

    2018-02-01

    The present work is concerned with the oxo vanadium(IV) complex of 2,3,7,8,12,13,17,18-octachloro-5,10,15,20-tetrakis(4-tolylporphyrin) with formula [V(Cl8TTP)O] (I), which was prepared by reacting the (oxo)[5,10,15,20-tetrakis(4-tolylporphyrinato)]vanadium(IV) complex ([V(TTP)O]), under aerobic atmosphere, with a large excess of thionyl chloride (SOCl2). The title compound was characterized by UV-visible spectroscopy, cyclic voltammetry and X-ray crystal structure. The electron-withdrawing chlorine substituents at the pyrrole carbons in the vanadyl-Cl8TTP derivative produce remarkable redshifts of the Soret and Q absorption bands and an important anodic shift of the porphyrin ring oxidation and reduction potentials. This is an indication that the porphyrin core of complex (I) is severely nonplanar in solution. The molecular structure of our vanadyl derivative shows a very high saddle distortion and an important ruffled deformation of the porphyrin macrocycle. The crystal structure of (I) is made by one-dimensional chains parallel to the c axis where channels are located between these chains.

  9. Structure of drug-target proteins determined by both X-ray and neutron diffraction

    International Nuclear Information System (INIS)

    Kuroki, Ryota

    2009-01-01

    Crystallography enables us to obtain accurate atomic positions within proteins. High resolution X-ray crystallography provides information for most of the atoms comprising a protein, with the exception of hydrogens. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent of the structural determination of drug-target proteins, porcine pancreatic elastase (PPE) and human immuno-deficiency virus type-1 protease (HIV-PR) by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor (FR13080) was determined to 0.94A resolution by X-ray diffraction and 1.75 A resolution by neutron diffraction. It was found that there are two characteristic hydrogen bonding interactions in which hydrogen atoms were confirmed. One is located between a catalytic aspartate and histidine, another is involved in the inhibitor recognition site. The structure of HIV-PR with its potent inhibitor (KNI-272) was also determined to 0.93 A resolution by X-ray diffraction and 2.3 A resolution by neutron diffraction. The ionization state of the catalytic residues were clarified to show that Asp125 is protonated and Asp25 is deprotonated. The ionization state and the location of hydrogen atoms of the catalytic residue in HIV-PR were firstly determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron to identify the location of ambiguous hydrogen atoms will be shown. (author)

  10. A structural study of bone changes in knee osteoarthritis by synchrotron-based X-ray fluorescence and X-ray absorption spectroscopy techniques

    Science.gov (United States)

    Sindhupakorn, Bura; Thienpratharn, Suwittaya; Kidkhunthod, Pinit

    2017-10-01

    Osteoarthritis (OA) is characterized by degeneration of articular cartilage and thickening of subchondral bone. The present study investigated the changing of biochemical components of cartilage and bone compared between normal and OA people. Using Synchrotron-based X-ray fluorescence (SR-XRF) and X-ray absorption spectroscopy (XAS) techniquesincluding X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) were employed for the bone changes in kneeosteoarthritisstudies. The bone samples were collected from various osteoarthritis patients with both male and female in the ages range between 20 and 74 years old. SR-XRF results excited at 4240 eV for Ca elements show a majority three main groups, based on their XRF intensities, 20-36 years, 40-60 years and over 70 years, respectively. By employing XAS techniques, XANES features can be used to clearly explain in term of electronic transitions occurring in bone samples which are affected from osteoarthritis symptoms. Moreover, a structural change around Ca ions in bone samples is obviously obtained by EXAFS results indicating an increase of Ca-amorphous phase when the ages increase.

  11. Structure investigation of metal ions clustering in dehydrated gel using x-ray anomalous dispersion effect

    CERN Document Server

    Soejima, Y; Sugiyama, M; Annaka, M; Nakamura, A; Hiramatsu, N; Hara, K

    2003-01-01

    The structure of copper ion clusters in dehydrated N-isopropylacrylamide/sodium acrylate (NIPA/SA) gel has been studied by means of small angle X-ray scattering (SAXS) method. In order to distinguish the intensity scattered by Cu ions, the X-ray anomalous dispersion effect around the Cu K absorption edge has been coupled with SAXS. It is found that the dispersion effect dependent on the incident X-ray energy is remarkable only at the momentum transfer q = 0.031 A sup - sup 1 , where a SAXS peak is observed. The results indicate that copper ions form clusters in the dehydrated gel, and that the mean size of clusters is the same as that of SA clusters produced by microphase separation. It is therefore naturally presumed that copper ions are adsorbed into the SA molecules. On the basis of the presumption, a mechanism is proposed for microphase-separation and clustering of Cu ions.

  12. Single crystal X-ray structure of the artists’ pigment zinc yellow

    DEFF Research Database (Denmark)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold

    2017-01-01

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

  13. Two-dimensional imaging detectors for structural biology with X-ray lasers.

    Science.gov (United States)

    Denes, Peter

    2014-07-17

    Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors--monolithic or hybrid--are the standard for XFELs today. For structural biology, improvements are needed for today's 10-100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  14. Emerging opportunities in structural biology with X-ray free-electron lasers

    Science.gov (United States)

    Schlichting, Ilme; Miao, Jianwei

    2012-01-01

    X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs. PMID:22922042

  15. Energy-scanning X-ray diffraction of synthetic multilayer structure

    International Nuclear Information System (INIS)

    Malaurent, J.C.; Duval, H.; Fert, A.

    1987-01-01

    An energy-scanning X-ray diffraction technique is used to study a synthetic periodic multilayer structure with two amorphous components. The source was the Bremsstrahlung from the X-ray tube, and the detector was a silicon-lithium diode. Experimental results obtained for a multilayer PdSi/MgCu with large period show a deviation from the classical Bragg's law. The deviation is produced by the variation of the refractive index of the multilayer with the wavelength of the incident X-ray. The period d was determined to within 1%. A measure of the refraction index enabled an estimate to be made of the width of each layer. It was also possible to estimate the fluctuation of the period along the multilayer from the full widths of the diffracted Bragg peaks at maximum intensities. The limits of the method are discussed. (orig.)

  16. Parameter study of self-absorption effects in Total Reflection X-ray Fluorescence-X-ray Absorption Near Edge Structure analysis of arsenic

    International Nuclear Information System (INIS)

    Meirer, F.; Pepponi, G.; Streli, C.; Wobrauschek, P.; Kregsamer, P.; Zoeger, N.; Falkenberg, G.

    2008-01-01

    Total reflection X-ray Fluorescence (TXRF) analysis in combination with X-ray Absorption Near Edge Structure (XANES) analysis is a powerful method to perform chemical speciation studies at trace element levels. However, when measuring samples with higher concentrations and in particular standards, damping of the oscillations is observed. In this study the influence of self-absorption effects on TXRF-XANES measurements was investigated by comparing measurements with theoretical calculations. As(V) standard solutions were prepared at various concentrations and dried on flat substrates. The measurements showed a correlation between the damping of the oscillations and the As mass deposited. A Monte-Carlo simulation was developed using data of the samples shapes obtained from confocal white light microscopy. The results showed good agreement with the measurements; they confirmed that the key parameters are the density of the investigated atom in the dried residues and the shape of the residue, parameters that combined define the total mass crossed by a certain portion of the incident beam. The study presents a simple approach for an a priori evaluation of the self-absorption in TXRF X-ray absorption studies. The consequences for Extended X-ray Absorption Fine Structure (EXAFS) and XANES measurements under grazing incidence conditions are discussed, leading to the conclusion that the damping of the oscillations seems to make EXAFS of concentrated samples non feasible. For XANES 'fingerprint' analysis samples should be prepared with a deposited mass and sample shape leading to an acceptable absorption for the actual investigation

  17. What is proposed by current X-ray structural analysis?

    Czech Academy of Sciences Publication Activity Database

    Kratochvíl, B.; Hušák, M.; Brynda, Jiří; Sedláček, Juraj

    2008-01-01

    Roč. 102, - (2008), s. 889-901 E-ISSN 1213-7103 Institutional research plan: CEZ:AV0Z50520514 Keywords : powder diffraction data * protein crystallography * molecular replacement * crystal - structures * HIV-1 protease Subject RIV: EB - Genetics ; Molecular Biology

  18. Surface extended x-ray absorption fine structure of low-Z absorbates using fluorescence detection

    International Nuclear Information System (INIS)

    Stoehr, J.; Kollin, E.B.; Fischer, D.A.; Hastings, J.B.; Zaera, F.; Sette, F.

    1985-05-01

    Comparison of x-ray fluorescence yield (FY) and electron yield surface extended x-ray absorption fine structure spectra above the S K-edge for c(2 x 2) S on Ni(100) reveals an order of magnitude higher sensitivity of the FY technique. Using FY detection, thiophene (C 4 H 4 S) chemisorption on Ni(100) is studied with S coverages down to 0.08 monolayer. The molecule dissociates at temperatures as low as 100K by interaction with fourfold hollow Ni sites. Blocking of these sites by oxygen leaves the molecule intact

  19. Covering complete proteomes with X-ray structures: a current snapshot

    Energy Technology Data Exchange (ETDEWEB)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher [University of Alberta, Edmonton, Alberta T6G 2V4 (Canada); Joachimiak, Andrzej, E-mail: andrzejj@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States); Kurgan, Lukasz, E-mail: andrzejj@anl.gov [University of Alberta, Edmonton, Alberta T6G 2V4 (Canada)

    2014-11-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

  20. Covering complete proteomes with X-ray structures: a current snapshot

    International Nuclear Information System (INIS)

    Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz

    2014-01-01

    The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins. Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined

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

    Directory of Open Access Journals (Sweden)

    Jennifer L. Wierman

    2016-01-01

    Full Text Available 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 are 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 the EMC algorithm, 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 the EMC algorithm, 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. This suggests that synchrotron-based serial crystallography of micrometre-sized crystals can be practical with the aid of the EMC algorithm even in cases

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

    Science.gov (United States)

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

    2015-04-14

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

  3. Synthesis, X-ray crystal structure, photo luminescent property, antimicrobial activities and DFT computational study of Zn(II) coordination polymer derived from multisite N,O donor Schiff base ligand (H2L1)

    Science.gov (United States)

    Majumdar, Dhrubajyoti; Surendra Babu, M. S.; Das, Sourav; Biswas, Jayanta Kumar; Mondal, Monojit; Hazra, Suman

    2017-06-01

    A unique thiocyanato linked 1D chain of Zn(II) coordination polymer [Zn2L1(μ1,3-SCN)(η1SCN)]n (1) has been synthesized using potential multisite compartmental N,O donor Schiff base blocker ligand (L1H2) in presence of Zn(OAc)2 and KSCN. The Schiff base ligand [N, N‧-bis(3-methoxysalicylidenimino)-1,3-daminopropane] (L1H2) is 2:1 M ratio condensation product of O-vaniline and 1,3-diaminopropane in methanol medium. The characterization of Complex 1 was accomplished by means of different micro analytical techniques like elemental analyses, IR, UV-Vis, 1H NMR, emission spectroscopy and Single X-ray crystallographic study. Complex 1 crystallizes in Orthorhombic system, space group Pbca, with values a = 11.579(2), b = 18.538(3), and c = 22.160(4) Å; α = β = γ = 90.00°; V = 4756.6(14) and Z = 8. The single crystal X-ray revealed that the one dimensional chain system with the repeating unit [Zn2(μ1,3-SCN)(η1SCN)(L1)]n bridge by an end to end μ1,3 thiocyanate anion. Within each repeating unit two different types of Zn(II) ions are present. One of these is five-coordinate in a square pyramidal geometry while the other is six-coordinate in an octahedral geometry. A brief but lucid comparative approach has been demonstrated in between Schiff base (L1H2) and complex 1 with respect to their photoluminescence activities. Active luminescence behavior of complex 1 in presence of ligand (L1H2) is due to quenching of PET process which is mediated by 'chelating effect'. Complex 1 exhibits strong antimicrobial efficacy against some important Gram + ve and Gram -ve bacteria. Apart from antimicrobial potential, a combined experimental and theoretical investigation has been performed via DFT on molecular structure of complex 1 with respect to Hirshfeld surface analysis.

  4. Structural investigation of porcine stomach mucin by X-ray fiber diffraction and homology modeling

    Energy Technology Data Exchange (ETDEWEB)

    Veluraja, K., E-mail: veluraja@msuniv.ac.in [Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012 (India); Vennila, K.N. [CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamilnadu 600025 (India); Umamakeshvari, K.; Jasmine, A. [Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012 (India); Velmurugan, D. [CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamilnadu 600025 (India)

    2011-03-25

    Research highlights: {yields} Techniques to get oriented mucin fibre. {yields} X-ray fibre diffraction pattern for mucin. {yields} Molecular modeling of mucin based on X-ray fibre diffraction pattern. -- Abstract: The basic understanding of the three dimensional structure of mucin is essential to understand its physiological function. Technology has been developed to achieve orientated porcine stomach mucin molecules. X-ray fiber diffraction of partially orientated porcine stomach mucin molecules show d-spacing signals at 2.99, 4.06, 4.22, 4.7, 5.37 and 6.5 A. The high intense d-spacing signal at 4.22 A is attributed to the antiparallel {beta}-sheet structure identified in the fraction of the homology modeled mucin molecule (amino acid residues 800-980) using Nidogen-Laminin complex structure as a template. The X-ray fiber diffraction signal at 6.5 A reveals partial organization of oligosaccharides in porcine stomach mucin. This partial structure of mucin will be helpful in establishing a three dimensional structure for the whole mucin molecule.

  5. Synthesis and X-ray Powder Structure of a New Pillared Layered Cadmium Phosphonate, Giving Evidence that the Intercalation of Alkylamines into Cd(O(3)PR).H(2)O Is Topotactic.

    Science.gov (United States)

    Fredoueil, Florence; Massiot, Dominique; Janvier, Pascal; Gingl, Franz; Bujoli-Doeuff, Martine; Evain, Michel; Clearfield, Abraham; Bujoli, Bruno

    1999-04-19

    A new pillared layered phosphonate, cadmium 2-aminoethylphosphonate, Cd(O(3)PC(2)H(4)NH(2)) (1), has been synthesized, and its structure was solved ab initio from X-ray powder diffraction data and refined by Rietveld methods. Compound 1 is orthorhombic: space group Pna2(1), a = 15.4643(2) Å, b = 5.16512(7) Å, c = 6.27650(8) Å, and Z = 4. Its layer arrangement is similar to that in Cd(O(3)PR).H(2)O, except that the water molecule coordinated to cadmium in Cd(O(3)PR).H(2)O is replaced by the nitrogen atom from the amino ends of the ethyl chains borne by phosphorus of the upper and lower layers. The strong similarity of the IR, (31)P, and (113)Cd NMR data for Cd(O(3)PC(2)H(4)NH(2)) and Cd(O(3)PCH(3)).n-NH(2)C(4)H(9) clearly shows the topotactic character of the intercalation of n-alkylamines in the dehydrated form of Cd(O(3)PR).H(2)O to yield Cd(O(3)PR).n-NH(2)R'.

  6. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  7. Combined EUV reflectance and X-ray reflectivity data analysis of periodic multilayer structures

    NARCIS (Netherlands)

    Yakunin, S.N.; Makhotkin, Igor Alexandrovich; Nikolaev, K.V.; van de Kruijs, Robbert Wilhelmus Elisabeth; Chuev, M.A.; Bijkerk, Frederik

    2014-01-01

    We present a way to analyze the chemical composition of periodical multilayer structures using the simultaneous analysis of grazing incidence hard X-Ray reflectivity (GIXR) and normal incidence extreme ultraviolet reflectance (EUVR). This allows to combine the high sensitivity of GIXR data to layer

  8. The 1s x-ray absorption pre-edge structures in transition metal oxides

    NARCIS (Netherlands)

    de Groot, Frank|info:eu-repo/dai/nl/08747610X; Vanko, Gyoergy; Glatzel, Pieter

    2009-01-01

    We develop a general procedure to analyse the pre-edges in 1s x-ray absorption near edge structure (XANES) of transition metal oxides and coordination complexes. Transition metal coordination complexes can be described from a local model with one metal ion. The 1s 3d quadrupole transitions are

  9. Cation distribution in NiZn-ferrite films via extended x-ray absorption fine structure

    Science.gov (United States)

    Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.; Kirkland, J. P.

    1996-04-01

    We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films. A least-squares fitting of experimental EXAFS data with theoretical, multiple-scattering, EXAFS data allowed the quantitative determination of site distributions for all transition metal cations.

  10. Some applications of nanometer scale structures for current and future X-ray space research

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Abdali, S; Frederiksen, P K

    1994-01-01

    Nanometer scale structures such as multilayers, gratings and natural crystals are playing an increasing role in spectroscopic applications for X-ray astrophysics. A few examples are briefly described as an introduction to current and planned applications pursued at the Danish Space Research Insti...

  11. A logical explanation of structurally unfit X-ray diffraction peaks in ...

    Indian Academy of Sciences (India)

    2018-02-05

    Feb 5, 2018 ... Abstract. In the present paper we suggest the cause and solution of some unidentified X-ray diffraction (XRD) peaks in ferroelectric ... to some structurally unfit minor peaks of all three trail samples show good agreement to the values estimated from the .... This shows that the value of 2θ limits the (a + b) val-.

  12. A logical explanation of structurally unfit X-ray diffraction peaks in ...

    Indian Academy of Sciences (India)

    2018-02-05

    Feb 5, 2018 ... Abstract. In the present paper we suggest the cause and solution of some unidentified X-ray diffraction (XRD) peaks in ferroelectric nanoparticles. Indeed, a relationship between the structurally unfit XRD peaks and domains in the ferroelectric nanoparticles is suggested. BaTiO3, PbTiO3 and ...

  13. Grating-based X-ray tomography of 3D food structures

    DEFF Research Database (Denmark)

    Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur

    2016-01-01

    A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiation...

  14. THE X-RAY STRUCTURE AND THE 13 C NMR DATA OF ...

    African Journals Online (AJOL)

    The alkaloids pellitorine and chelerythrine acetonate were isolated from the stem bark of Zanthoxylum davyi together with methyl octadecyl ketone, lupeol and hesperidin. The alkaloid skimmianie was isolated from the leaves. The X-Ray structure of chelerythrine acetonate was also determined. Key Words: Zanthoxylum ...

  15. Synthesis, X-ray Diffraction Study and Antimicrobial Activity of Calcium Sulphate Nanocomposites from Plant Charcoal

    Directory of Open Access Journals (Sweden)

    Pinak P. N. Choudhury

    2009-04-01

    Full Text Available Calcium sulphate nanocomposite materials (CB have been synthesised from plant charcoal. Crushed charcoal powder was heated to red hot over a Bunsen burner flame and produced a white material which has been isolated. The surface morphology of the material has been studied by Scanning Electron Microscopy (SEM and the elements were analyzed by Energy Dispersion Spectroscopy (EDS. To explore the structural features of the materials X-Ray Diffraction (XRD patterns were recorded. The material showed pronounced inhibitory effects against Streptococcus faecaelis, Bacillus subtilis, Klebsilla pneumoni, E. coli, Proteus vulgaris and Pseudomonas aeruginosa.

  16. Synthesis, X-ray Diffraction Study and Antimicrobial Activity of Calcium Sulphate Nanocomposites from Plant Charcoal

    Science.gov (United States)

    Bhattacharjee, Chira R.; Paul, Satya B.; Nath, Abhijit; Choudhury, Pinak P. N.; Choudhury, Sudip

    2009-01-01

    Calcium sulphate nanocomposite materials (CB) have been synthesised from plant charcoal. Crushed charcoal powder was heated to red hot over a Bunsen burner flame and produced a white material which has been isolated. The surface morphology of the material has been studied by Scanning Electron Microscopy (SEM) and the elements were analyzed by Energy Dispersion Spectroscopy (EDS). To explore the structural features of the materials X-Ray Diffraction (XRD) patterns were recorded. The material showed pronounced inhibitory effects against Streptococcus faecaelis, Bacillus subtilis, Klebsilla pneumoni, E. coli, Proteus vulgaris and Pseudomonas aeruginosa.

  17. Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

    International Nuclear Information System (INIS)

    Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D.

    2013-01-01

    The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF 3 COOH/CH 2 Cl 2 yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH 3 groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

  18. Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D., E-mail: mdvargas@vm.uff.br, E-mail: walk@vm.uff.br [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Instituto de Quimica

    2013-02-15

    The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF{sub 3}COOH/CH{sub 2}Cl{sub 2} yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH{sub 3} groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

  19. Application of the X-ray diffractometer DRON to the study of long period structures

    International Nuclear Information System (INIS)

    Gordelij, V.I.; Lushchikov, V.I.; Syrykh, A.G.; Cherezon, V.G.

    1991-01-01

    It is shown that the stock-produced X-ray diffractometer DRON can be adapted for the study of long period structures up to ∼150 A. The experimental data on small-angle diffraction spectra, measured on it, from both lamellar and lateral structures of biological and lipid membranes are reported. The data show that lattice constants of these structures could be determined within the accuracy of 1 A. 15 refs.; 7 figs

  20. Synthesis of highly stable and biocompatible gold nanoparticles for use as a new X-ray contrast agent.

    Science.gov (United States)

    Iranpour, Pooya; Ajamian, Maral; Safavi, Afsaneh; Iranpoor, Nasser; Abbaspour, Abdolkarim; Javanmardi, Sanaz

    2018-04-18

    This work reports a novel reduction procedure for the synthesis of Gum Arabic (GA) capped-gold nanoparticles (AuNPs) in glucosammonium formate as a new ionic liquid. The GA coated AuNPs show good stability in physiological media. The synthesized AuNPs were characterized by UV-Vis spectroscopy, transmission electron microscopy, dynamic light scattering and X-ray diffraction analysis. These stable AuNPs are introduced as a new contrast agent for X-ray Computed Tomography (X-ray CT). These nanoparticles have higher contrasting properties than the commercial contrast agent, Visipaque. The precursors used (Gum Arabic and glucose based-ionic liquid) for synthesis of AuNPs are biocompatible and non-toxic.

  1. Reactivity and operational stability of N-tailed TAMLs through kinetic studies of the catalyzed oxidation of orange II by H2 O2 : synthesis and X-ray structure of an N-phenyl TAML.

    Science.gov (United States)

    Warner, Genoa R; Mills, Matthew R; Enslin, Clarissa; Pattanayak, Shantanu; Panda, Chakadola; Panda, Tamas Kumar; Gupta, Sayam Sen; Ryabov, Alexander D; Collins, Terrence J

    2015-04-13

    The catalytic activity of the N-tailed ("biuret") TAML (tetraamido macrocyclic ligand) activators [Fe{4-XC6 H3 -1,2-(NCOCMe2 NCO)2 NR}Cl](2-) (3; N atoms in boldface are coordinated to the central iron atom; the same nomenclature is used in for compounds 1 and 2 below), [X, R=H, Me (a); NO2 , Me (b); H, Ph (c)] in the oxidative bleaching of Orange II dye by H2 O2 in aqueous solution is mechanistically compared with the previously investigated activator [Fe{4-XC6 H3 -1,2-(NCOCMe2 NCO)2 CMe2 }OH2 ](-) (1) and the more aggressive analogue [Fe(Me2 C{CON(1,2-C6 H3 -4-X)NCO}2 )OH2 ](-) (2). Catalysis by 3 of the reaction between H2 O2 and Orange II (S) occurs according to the rate law found generally for TAML activators (v=kI kII [Fe(III) ][S][H2 O2 ]/(kI [H2 O2 ]+kII [S]) and the rate constants kI and kII at pH 7 both decrease within the series 3 b>3 a>3 c. The pH dependency of kI and kII was investigated for 3 a. As with all TAML activators studied to-date, bell-shaped profiles were found for both rate constants. For kI , the maximal activity was found at pH 10.7 marking it as having similar reactivity to 1 a. For kII , the broad bell pH profile exhibits a maximum at pH about 10.5. The condition kI ≪kII holds across the entire pH range studied. Activator 3 b exhibits pronounced activity in neutral to slightly basic aqueous solutions making it worthy of consideration on a technical performance basis for water treatment. The rate constants ki for suicidal inactivation of the active forms of complexes 3 a-c were calculated using the general formula ln([S0 ]/[S∞ ])=(kII /ki )[Fe(III) ]; here [Fe(III) ], [S0 ], and [S∞ ] are the total catalyst concentration and substrate concentration at time zero and infinity, respectively. The synthesis and X-ray characterization of 3 c are also described. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Structural investigation of porcine stomach mucin by X-ray fiber diffraction and homology modeling.

    Science.gov (United States)

    Veluraja, K; Vennila, K N; Umamakeshvari, K; Jasmine, A; Velmurugan, D

    2011-03-25

    The basic understanding of the three dimensional structure of mucin is essential to understand its physiological function. Technology has been developed to achieve orientated porcine stomach mucin molecules. X-ray fiber diffraction of partially orientated porcine stomach mucin molecules show d-spacing signals at 2.99, 4.06, 4.22, 4.7, 5.37 and 6.5 Å. The high intense d-spacing signal at 4.22 Å is attributed to the antiparallel β-sheet structure identified in the fraction of the homology modeled mucin molecule (amino acid residues 800-980) using Nidogen-Laminin complex structure as a template. The X-ray fiber diffraction signal at 6.5 Å reveals partial organization of oligosaccharides in porcine stomach mucin. This partial structure of mucin will be helpful in establishing a three dimensional structure for the whole mucin molecule. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Atomic structure of large angle grain boundaries determined by quantitative X-ray diffraction techniques

    International Nuclear Information System (INIS)

    Fitzsimmons, M.R.; Sass, S.L.

    1988-01-01

    Quantitative X-ray diffraction techniques have been used to determine the atomic structure of the Σ = 5 and 13 [001] twist boundaries in Au with a resolution of 0.09 Angstrom or better. The reciprocal lattices of these boundaries were mapped out using synchrotron radiation. The atomic structures were obtained by testing model structures against the intensity observations with a chi square analysis. The boundary structure were modeled using polyhedra, including octahedra, special configurations of tetrahedra and Archimedian anti-prisms, interwoven together by the boundary symmetry. The results of this work point to the possibility of obtaining general rules for grain boundary structure based on X-ray diffraction observations that give the atomic positions with high resolution

  4. miXAFS: a program for X-ray absorption fine-structure data analysis.

    Science.gov (United States)

    Ikemoto, H

    2018-03-01

    A new program called miXAFS for the analysis of X-ray absorption fine-structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X-ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R-factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.

  5. X-ray absorption spectroscopy by full-field X-ray microscopy of a thin graphite flake: Imaging and electronic structure via the carbon K-edge

    Directory of Open Access Journals (Sweden)

    Carla Bittencourt

    2012-04-01

    Full Text Available We demonstrate that near-edge X-ray-absorption fine-structure spectra combined with full-field transmission X-ray microscopy can be used to study the electronic structure of graphite flakes consisting of a few graphene layers. The flake was produced by exfoliation using sodium cholate and then isolated by means of density-gradient ultracentrifugation. An image sequence around the carbon K-edge, analyzed by using reference spectra for the in-plane and out-of-plane regions of the sample, is used to map and spectrally characterize the flat and folded regions of the flake. Additional spectral features in both π and σ regions are observed, which may be related to the presence of topological defects. Doping by metal impurities that were present in the original exfoliated graphite is indicated by the presence of a pre-edge signal at 284.2 eV.

  6. Spectral, DFT and X-ray diffraction studies on regioselective synthesis of thiazolo-quinazoline system

    Science.gov (United States)

    Gautam, Deepika; Gautam, Poonam; Chaudhary, R. P.

    2017-10-01

    Unsymmetrical quinazoline-3-thione 2, obtained from one pot condensation of 2-tetralone, p-chlorobenzaldehyde and thiourea in acidic medium, on reaction with α-halo acids afforded thiazolo-quinazoline derivatives 3, 7 and not their regioisomers 4 and 8 respectively. The cyclised product obtained by the reaction of thione 2 with 1,2-dibromoethane has been assigned structure 5. Condensation of thione 2 with 3-chloropropionic acid and 1,3-dibromopropane furnished thiazino-quinazoline derivatives 10 and 12 instead of their regioisomers 11 and 13 respectively. The structure of the cyclised products has been established by means of spectral data (IR, NMR and Mass). X-ray diffraction studies of a representative compound supported our claim on structural assignments. DFT studies on regioisomers further validated the claim for assigned structures. The reaction of thione 2 with 3-chloropropionc acid in presence of acetic acid yielded thiazinan-4-one 10.

  7. New platinum (II) and palladium (II) complexes of coumarin-thiazole Schiff base with a fluorescent chemosensor properties: Synthesis, spectroscopic characterization, X-ray structure determination, in vitro anticancer activity on various human carcinoma cell lines and computational studies.

    Science.gov (United States)

    Şahin, Ömer; Özdemir, Ümmühan Özmen; Seferoğlu, Nurgül; Genc, Zuhal Karagöz; Kaya, Kerem; Aydıner, Burcu; Tekin, Suat; Seferoğlu, Zeynel

    2018-01-01

    A new coumarin-thiazole based Schiff base (Ligand, L) and its Pd(II), Pt(II) complexes; ([Pd(L) 2 ] and [Pt(L) 2 ]), were synthesized and characterized using spectrophotometric techniques (NMR, IR, UV-vis, LC-MS), magnetic moment, and conductivity measurements. A single crystal X-ray analysis for only L was done. The crystals of L have monoclinic crystal system and P21/c space group. To gain insight into the structure of L and its complexes, we used density functional theory (DFT) method to optimize the molecules. The photophysical properties changes were observed after deprotonation of L with CN - via intermolecular charge transfer (ICT). Additionally, as the sensor is a colorimetric and fluorimetric cyanide probe containing active sites such as coumarin-thiazole and imine (CH=N), it showed fast color change from yellow to deep red in the visible region, and yellow fluorescence after CN - addition to the imine bond, in DMSO. The reaction mechanisms of L with CN - , F - and AcO - ions were evaluated using 1 H NMR shifts. The results showed that, the reaction of L with CN - ion was due to the deprotonation and addition mechanisms at the same time. The anti-cancer activity of L and its Pd(II) and Pt(II) complexes were evaluated in vitro using MTT assay on the human cancer lines MCF-7 (human breast adenocarcinoma), LS174T (human colon carcinoma), and LNCAP (human prostate adenocarcinoma). The anti-cancer effects of L and its complexes, on human cells, were determined by comparing the half maximal inhibitory concentration (IC 50 ) values. The activity results showed that, the Pd(II) complex of L has higher anti-tumor effect than L and its Pt(II) complex against the tested human breast adenocarcinoma (MCF-7), human prostate adenocarcinoma (LNCAP), and human colon carcinoma (LS174T) cell lines. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. X-Ray computed tomography for visualising inner structures of industrial materials

    International Nuclear Information System (INIS)

    Jaafar Abdullah; Salzali Mohd; Mohamad Rabaie Shari; Engku Mohd Fahmi Engku Chik; Hearie Hassan; Airwan Affandi Mahmood

    2010-01-01

    X-ray computed tomography (CT) is a powerful non-invasive imaging technique for viewing an objects inner structures in 2-D or 3-D cross-section images without the need to physically section it. The invention of CT techniques revolutionised the field of medical diagnostic imaging because it provided more detailed and useful information than any previous non-invasive imaging techniques. The method is increasingly being used in industry, aerospace, geosciences and archaeology. This paper describes the development of an X-ray computed tomography system for imaging and visualising of industrial materials. The theoretical aspects of CT scanner, the system configurations and the adopted algorithm for image reconstruction are discussed. The penetrating rays from a 160 kV/ 10 mA industrial X-ray machine and a bank of Linear Array Detectors (LAD) in combination with a three-axis sample table were used to construct the CT system. The movement of the sample table in vertical, linear and rotary motion is controlled by a Lab View-based software, the x-ray transmission data is collected by using a commercial image grabber package, and the image reconstruction is performed by using the classical Linear Back Projection (LBP) algorithm. Several samples from selected industrial components or products were scanned using this CT scanner. Some of the reconstructed images are presented in this paper. (author)

  9. Revealing the 3D internal structure of natural polymer microcomposites using X-ray ultra microtomography.

    Science.gov (United States)

    Pakzad, A; Parikh, N; Heiden, P A; Yassar, R S

    2011-07-01

    Properties of composite materials are directly affected by the spatial arrangement of reinforcement and matrix. In this research, partially hydrolysed cellulose microcrystals were used to fabricate polycaprolactone microcomposites. The spatial distribution of cellulose microcrystals was characterized by a newly developed technique of X-ray ultra microscopy and microtomography. The phase and absorption contrast imaging of X-ray ultra microscopy revealed two-dimensional and three-dimensional information on CMC distribution in polymer matrices. The highest contrast and flux (signal-to-noise ratio) were obtained using vanadium foil targets with the accelerating voltage of 30 keV and beam current of >200 nA. The spatial distribution of cellulose microcrystals was correlated to the mechanical properties of the microcomposites. It was observed that heterogeneous distribution and clustering of cellulose microcrystals resulted in degradation of tensile strength and elastic modulus of composites. The utilization of X-ray ultra microscopy can open up new opportunities for composite researchers to explore the internal structure of microcomposites. X-ray ultra microscopy sample preparation is relatively simple in comparison to transmission electron microscopy and the spatial information is gathered at much larger scale. © 2011 The Authors Journal of Microscopy © 2011 The Royal Microscopical Society.

  10. Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

    Science.gov (United States)

    Lengyel, Jeffrey; Hnath, Eric; Storms, Marc; Wohlfarth, Thomas

    2014-09-01

    Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Moreover, the combination of Cryo-TEM and other methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics modeling are allowing researchers to address scientific questions previously thought intractable. Future technological developments are widely believed to further enhance the method and it is not inconceivable that Cryo-TEM could become as routine as X-ray crystallography for protein structure determination.

  11. Synthesis, characterization, single crystal X-ray and DFT analysis of disubstituted phosphorodithioates

    Science.gov (United States)

    Kour, Mandeep; Kumar, Sandeep; Feddag, Ahmed; Andotra, Savit; Chouaih, Abdelkader; Gupta, Vivek K.; Kant, Rajni; Pandey, Sushil K.

    2018-04-01

    Disubstituted phosphorodithioates of the type [{(2,5-CH3)2C6H3O}2PS2HNEt3] (1) and [{(3,5-CH3)2C6H3O)2(PS2)}2] (2) were synthesized and characterized by IR and NMR (1H,13C and 31P) spectroscopic studies and as single crystal X-ray analysis. The compound 1 crystallizes in monoclinic space group P21/c whereas compound 2 crystallizes in triclinic space group Pbar1. The X-ray analysis reveals that in compound 1 phosphorus atom is coordinated to the two S and two O atoms to form tetrahedral geometry. The structure is stabilized by cation-anion Nsbnd H⋯S hydrogen bonded interactions. In compound 2, the two phosphorus atoms have a distorted tetrahedral geometry coordinated to two (3,5-CH3)2C6H3O groups. The molecule possesses a crystallographic center of symmetry and consists of zig-zag array of Sdbnd Psbnd Ssbnd Ssbnd Pdbnd S linkages with two diphenyldithiophosphate moieties in the trans configuration. Molecular geometries, HOMO-LUMO analysis and molecular electrostatic potential of compounds 1 and 2 are investigated by theoretical calculations using B3LYP functional with the 6-311G basis combination set in the ground state and compared with the experimental values.

  12. Atomic structure of machined semiconducting chips: An x-ray absorption spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Paesler, M.; Sayers, D.

    1988-12-01

    X-ray absorption spectroscopy (XAS) has been used to examine the atomic structure of chips of germanium that were produced by single point diamond machining. It is demonstrated that although the local (nearest neighbor) atomic structure is experimentally quite similar to that of single crystal specimens information from more distant atoms indicates the presence of considerable stress. An outline of the technique is given and the strength of XAS in studying the machining process is demonstrated.

  13. A setup for synchrotron-radiation-induced total reflection X-ray fluorescence and X-ray absorption near-edge structure recently commissioned at BESSY II BAMline.

    Science.gov (United States)

    Fittschen, U; Guilherme, A; Böttger, S; Rosenberg, D; Menzel, M; Jansen, W; Busker, M; Gotlib, Z P; Radtke, M; Riesemeier, H; Wobrauschek, P; Streli, C

    2016-05-01

    An automatic sample changer chamber for total reflection X-ray fluorescence (TXRF) and X-ray absorption near-edge structure (XANES) analysis in TXRF geometry was successfully set up at the BAMline at BESSY II. TXRF and TXRF-XANES are valuable tools for elemental determination and speciation, especially where sample amounts are limited (TXRF requires a well defined geometry regarding the reflecting surface of a sample carrier and the synchrotron beam. The newly installed chamber allows for reliable sample positioning, remote sample changing and evacuation of the fluorescence beam path. The chamber was successfully used showing accurate determination of elemental amounts in the certified reference material NIST water 1640. Low limits of detection of less than 100 fg absolute (10 pg ml(-1)) for Ni were found. TXRF-XANES on different Re species was applied. An unknown species of Re was found to be Re in the +7 oxidation state.

  14. Synchrotron x-ray methods in studies of thin organic film structure

    International Nuclear Information System (INIS)

    Gentle, I.

    2002-01-01

    Full text: In recent years, the study of the structures of organic films as thin as a single monolayer has been revolutionized by methods that take advantage of the characteristics of synchrotron radiation. In particular, the methods of grazing incidence X-ray diffraction (GIXD) and X-ray reflectivity have led to a number of valuable insights into structural aspects of thin films at molecular resolution. Our group has been studying films formed at the air/water interface as insoluble monolayers and subsequently transferred to solid substrates using either the vertical (Langmuir-Blodgett) or horizontal (Langmuir-Schaeffer) methods. The main aim of these experiments is to exert control over film structure in the direction parallel to the substrate surface. This is highly desirable in order to design devices that exploit the optical and electrooptical properties of functional materials, but is difficult to do. By varying the chemical structure of the film materials and controlling deposition conditions a degree of control is possible, but only using synchrotron methods can it be easily verified. We have also developed a novel method of rapidly collecting data from GIXD measurements by the application of area detection (imaging plates), which has made possible measurements of dynamic processes such as in-situ annealing. Such measurements are not possible using traditional scanning methods. One area of current interest is films composed of porphyrins as functional materials, either alone or as mixed films with fatty acids. We have been investigating ways of assembling porphyrins in such a way as to overcome the tendency to aggregate, and to produce patterning and ordered structures in the plane of the interface. Examples will be given of how film composition and deposition method affects the final structure, and of how X-ray methods can be used to elucidate both the structures and the mechanisms. Copyright (2002) Australian X-ray Analytical Association Inc

  15. The structural analysis of zinc borate glass by laboratory EXAFS and X-ray diffraction measurements

    International Nuclear Information System (INIS)

    Kajinami, Akihiko; Harada, Yasushi; Inoue, Shinsuke; Deki, Shigehito; Umesaki, Norimasa

    1999-01-01

    The structure of zinc borate glass has been investigated by laboratory EXAFS and X-ray diffraction measurement as preliminary investigations for the detailed study in SPring-8. The zinc borate glass was prepared in the range from 40 to 65 mol% of zinc oxide content. The X-ray diffraction was measured by horizontal θ-θ goniometer with 60 kV and 300 mA output of Mo target. The EXAFS of zinc borate glass was measured by laboratory EXAFS system with 20 kV, 100 mA output of Mo target for the K absorption edge of zinc atom. From the X-ray diffraction and the EXAFS measurements, it is found that the zinc ion is surrounded by four oxygen atoms and formed a tetrahedral structure whose (Zn-O) distance is about 2 A and that the structure is unchanged with the zinc oxide content. The diffraction data show that the neighboring structure of boron atom transforms from BO 4 tetrahedra to BO 3 tetragonal planar structure with increasing of the zinc oxide content. (author)

  16. Sister chromatid exchanges in X-ray irradiated blood lymphocytes from patients with hereditary diseases with radioresistant DNA synthesis

    International Nuclear Information System (INIS)

    Pleskach, N.M.; Andriadze, M.I.; Mikhel'son, V.M.; Zhestyanikov, V.D.

    1988-01-01

    X-ray irradiation induced sister chromatid exchanges (SCE) in blood lymphocytes from patient with Down's syndrome and adult progeria (in both the cases radioresistant DNA synthesis takes place). In normal lymphocytes (in which ionizing radiation inhibits the replicative synthesis of DNA) the rate of SCE rises with the rise of radiation dose. Thus, the rate of SCE in X-ray irradiated lymphocytes is in reverse dependence with radioresistance of replicative synthesis of DNA. The data obtained are explained in accordance with the replicative hypothesis of the SCE nature (Painter, 1980a): in cells of patients with Down's syndrome, xeroderma pigmentosum from 2 and progeria of adults the time of existence of partly replicated clusters of replicons is decreased due to radioresistant replicative synthesis of DNA, but the presence of partly replicated clusters of replicons in necessary for SCE formation. Therefore the rate of SCF in X-irradiated cells of these patients decreases

  17. Structural and microstructural characterization of U3Si2 nuclear fuel using X-ray diffraction

    International Nuclear Information System (INIS)

    Ichikawa, Rodrigo U.; Garcia, Rafael H.L.; Silva, Andre S.B. da; Saliba-Silva, Adonis M.; Lima, Nelson B.; Martinez, Luis G.; Turrillas, Xavier

    2017-01-01

    In this work, two uranium silicide powdered samples, containing 67% and 42 mol% of Si, were analyzed using X-ray diffraction (named as 67 Si and 42 Si). For structural characterization, Rietveld refinement was used to estimate cell parameters, volume fraction (weight percent) of crystalline phases and atomic positions. For the main phases, X-ray line profile analysis (XLPA) was used to estimate mean crystallite sizes and micro strains. The 67 Si sample presents higher content of USi 2( tetragonal) and the 42 Si sample presents higher content of U 3 Si 2 (tetragonal) as identified and calculated from the XRD profiles. Overall there are no appreciable structural changes and the parameters refined are in good accordance with the ones reported in the literature. Mean crystallite sizes determined by XLPA revealed small crystallites of the order of 10 1 nm and low micro strain for all samples. (author)

  18. Soft x-ray measurement of internal tearing mode structure in a reversed-field pinch

    International Nuclear Information System (INIS)

    Chartas, G.; Hokin, S.

    1991-01-01

    The structure of internally resonant tearing modes has been studied in the Madison Symmetric Torus reversed-field pinch with a soft x-ray detector system consisting of an imaging array at one toroidal location and several detectors at different toroidal locations. The toroidal mode numbers of m = 1 structures are in the range n = -5, -6, -7. The modes propagate with phase velocity v = 1--6 x 10 6 cm/s, larger than the diamagnetic drift velocity v d ∼ 5 x 10 5 cm/s. Phase locking between modes with different n in manifested as a beating of soft x-ray signals which is found to be strongest near the resonant surfaces of the modes (r/a = 0.1 -- 0.5). 15 refs., 5 figs

  19. Structural characterization of oxidized allotaxially grown CoSi2 layers by x-ray scattering

    International Nuclear Information System (INIS)

    Kaendler, I. D.; Seeck, O. H.; Schlomka, J.-P.; Tolan, M.; Press, W.; Stettner, J.; Kappius, L.; Dieker, C.; Mantl, S.

    2000-01-01

    A series of buried CoSi 2 layers prepared by a modified molecular beam epitaxy process (allotaxy) and a subsequent wet-oxidation process was investigated by x-ray scattering. The oxidation time which determines the depth in which the CoSi 2 layers are located within the Si substrates has been varied during the preparation. The electron density profiles and the structure of the interfaces were extracted from specular reflectivity and diffuse scattering measurements. Crystal truncation rod investigations yielded the structure on an atomic level (crystalline quality). It turns out that the roughness of the CoSi 2 layers increases drastically with increasing oxidation time, i.e., with increasing depth of the buried layers. Furthermore, the x-ray data reveal that the oxidation growth process is diffusion limited. (c) 2000 American Institute of Physics

  20. Studies on polymer thin film structure by X-ray and neutron reflectivity and grazing incidence small angle scattering

    International Nuclear Information System (INIS)

    Ogawa, Hiroki; Kanaya, Toshiji

    2011-01-01

    We have reviewed structure studies of polymer thin films using synchrotron radiation X-ray and neutron reflectivity as well as recently developed grazing incidence small-angle X-ray and neutron scattering, including studies on polymer thin films with embedded ordered nanometer cells, distribution of glass transition temperature Tg in thin polystyrene films, and dewetting process of polymer blend thin films. (author)

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

    Science.gov (United States)

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

    2017-08-01

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

  2. Deep x-ray lithography processing for batch fabrication of thick polymer-based antenna structures

    Science.gov (United States)

    Rashidian, Atabak; Klymyshyn, David M.; Boerner, Martin; Mohr, Jürgen

    2010-02-01

    Deep x-ray lithography is applied for the first time to fabricate polymer-based antenna structures with different portions of ceramic contents. To produce successful and viable antenna structures, three different methods are proposed using positive and negative tone resists. In the first method the structures are lithographically fabricated avoiding an intermediate molding step using SU-8 as a photosensitive resist filled with fine ceramic powder with particles in the submicron range. In the second and third methods a polymethylmethacrylate (PMMA) mold is first fabricated by x-ray lithography, and then SU-8/MMA mixed with the high ceramic powder content is injected into the mold. In these methods a final step of crosslinking for SU-8 and polymerization for MMA is also required. Optimized fabrication parameters allow the production of high quality antenna structures as thick as 2.3 mm. X-ray lithography capabilities in fabrication of antennas and other passive microwave components with special features reinforce the idea of fabricating integrated passive microwave circuits along with active circuits using this emerging technology.

  3. Synthesis and X-ray structure determination of highly active Pd(II), Pd(I), and Pd(0) complexes of di(tert-butyl)neopentylphosphine (DTBNpP) in the arylation of amines and ketones.

    Science.gov (United States)

    Hill, Lensey L; Crowell, Jason L; Tutwiler, Strudwick L; Massie, Nicholas L; Hines, C Corey; Griffin, Scott T; Rogers, Robin D; Shaughnessy, Kevin H; Grasa, Gabriela A; Johansson Seechurn, Carin C C; Li, Hongbo; Colacot, Thomas J; Chou, Joe; Woltermann, Christopher J

    2010-10-01

    The air-stable complex Pd(η(3)-allyl)(DTBNpP)Cl (DTBNpP = di(tert-butyl)neopentylphosphine) serves as a highly efficient precatalyst for the arylation of amines and enolates using aryl bromides and chlorides under mild conditions with yields ranging from 74% to 98%. Amination reactions of aryl bromides were carried out using 1-2 mol % Pd(η(3)-allyl)(DTBNpP)Cl at 23-50 °C without the need to exclude oxygen or moisture. The C-N coupling of the aryl chlorides occurred at relatively lower temperature (80-100 °C) and catalyst loading (1 mol %) using the Pd(η(3)-allyl)(DTBNpP)Cl precatalyst than the catalyst generated in situ from DTBNpP and Pd(2)(dba)(3) (100-140 °C, 2-5 mol % Pd). Other Pd(DTBNpP)(2)-based complexes, (Pd(DTBNpP)(2) and Pd(DTBNpP)(2)Cl(2)) were ineffective precatalysts under identical conditions for the amination reactions. Both Pd(DTBNpP)(2) and Pd(DTBNpP)(2)Cl(2) precatalysts gave nearly quantitative conversions to the product in the α-arylation of propiophenone with p-chlorotoluene and p-bromoanisole at a substrate/catalyst loading of 100/1. At lower substrate/catalyst loading (1000/1), the conversions were lower but comparable to that of Pd(t-Bu(3)P)(2). In many cases, the tri-tert-butylphosphine (TTBP) based Pd(I) dimer, [Pd(μ-Br)(TTBP)](2), stood out to be the most reactive catalyst under identical conditions for the enolate arylation. Interestingly, the air-stable Pd(I) dimer, Pd(2)(DTBNpP)(2)(μ-Cl)(μ-allyl), was less active in comparison to [Pd(μ-Br)(TTBP)](2) and Pd(η(3)-allyl)(DTBNpP)Cl. The X-ray crystal structures of Pd(η(3)-allyl)(DTBNpP)Cl, Pd(DTBNpP)(2)Cl(2), Pd(DTBNpP)(2), and Pd(2)(DTBNpP)(2)(μ-Cl)(μ-allyl) are reported in this paper along with initial studies on the catalyst activation of the Pd(η(3)-allyl)(DTBNpP)Cl precatalyst.

  4. Synthesis of a 2,2'-Bipyridyl Functionalized Oligovinylene-Phenylene Using Heck and Horner-Wadsworth-Emmons Reactions and X-ray Crystal Structure of E-(4-(4-Bromostyryl)phenyl)(methyl)sulfane

    OpenAIRE

    Karácsony, Orsolya; Deschamps, Jeffrey R.; Trammell, Scott A.; Nita, Rafaela; Knight, D. Andrew

    2012-01-01

    The synthesis of a new 2,2'-bipyridyl functionalized oligovinylenephenylene (OVP-5) containing a methyl protected thiol using Heck coupling and the Horner-Wadsworth-Emmons reaction and is described. A key step involving a diisopropylcarbodiimide promoted dehydration of a stable b-hydroxyphosphonate intermediate was identified. The structure of precursor E-(4-(4-bromostyryl)phenyl)(methyl)sulfane (1) was determ...

  5. REAL STRUCTURE AND RESIDUAL STRESSES IN ADVANCED WELDS DETERMINED BY X-RAY AND NEUTRON DIFFRACTION

    Directory of Open Access Journals (Sweden)

    Karel Trojan

    2017-07-01

    Full Text Available The paper outlines the capability of X-ray diffraction (XRD for evaluation of real structure changes and residual stresses (RS on cross-section of advanced thick welds due to the welding of ferromagnetic plates. The results of neutron diffraction describe a three-dimensional state of RS and also verify previous assumptions of RS redistribution as a result of the surface preparation for determination 2D maps measured by XRD.

  6. ANALYSING THE SOIL STRUCTURE UNDER DIFFERENT TILLAGE SYSTEMS USING X-RAY MICROTOMOGRAPHY AND PF CURVES

    OpenAIRE

    Beekkerk van Ruth, Jöran; Degre, Aurore; Aubinet, Marc; Roisin, Christian; Léonard, Angélique; Beckers, Eléonore

    2011-01-01

    Assessing soil structure is primordial when comparing tillage systems. Whilst most conventional techniques characterize global parameters, X-ray microtomography allows a characterization of the poral space at a µm-scale. These results, combined with data from pF curves, can form a solid basis in order to quantify soil physical fertility. Soil samples were taken from the organic topsoil on two Belgian experimental sites implementing both conventional tillage (CT, ploughing) and simplified ...

  7. Characterization of alkanethiol/ZnO structures by X-ray photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Ogata, K.; Hama, T.; Hama, K.; Koike, K.; Sasa, S.; Inoue, M.; Yano, M.

    2005-01-01

    1-Propanethiol (CH 3 CH 2 CH 2 SH) was connected with O-polar zinc oxide (ZnO) surfaces toward biofunctional devices. X-ray photoelectron spectroscopy (XPS) measurement revealed that the S-O bonds were formed between 1-propanethiol and ZnO layers. Although the surface coverage of the molecule is less than a few percent, 1-propanethiol/ZnO structures were stable even at thermal treatment of 400 deg. C

  8. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

    Energy Technology Data Exchange (ETDEWEB)

    Bunkóczi, Gábor; McCoy, Airlie J.; Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Holton, James M.; Read, Randy J.; Terwilliger, Thomas C.

    2014-12-22

    We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

  9. The structure of NH4F as determined by neutron and X-ray diffraction

    NARCIS (Netherlands)

    Adrian, H.W.W.; Feil, D.

    1969-01-01

    Neutron and X-ray intensities of NH4F were measured at -196°C and -155°C respectively. The wurtzite type structure and space group P63mc were confirmed. The displacement of the two h.c.p. sublattices, formed by each of the F-- and NH+4- ions, is such that all bond-distances are equivalent. The N-H

  10. single crystal growth, x-ray structure analysis, optical band gap

    African Journals Online (AJOL)

    2015-09-01

    Sep 1, 2015 ... Hg...Hgand Cl...Cl interactions are stabilizing the structures in 3D pattern. UV-vis absorption spectra illustrate the change in opticalband gap from 3.01eVto 3.42eV on replacing the metal halide group.Raman and Hyper-Raman tensors calculations were performed based on single crystal X-ray data and the ...

  11. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.

    Science.gov (United States)

    Finer-Moore, J S; Kossiakoff, A A; Hurley, J H; Earnest, T; Stroud, R M

    1992-03-01

    The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the

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

    Science.gov (United States)

    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

  13. X-ray radiation generated by a beam of relativistic electrons in composite structure

    Science.gov (United States)

    Blazhevich, S. V.; Noskov, A. V.

    2018-04-01

    The dynamic theory of coherent X-ray radiation generated by a beam of relativistic electrons in the three-layer structure consisting of an amorphous layer, a vacuum (air) layer and a single crystal has been developed. The phenomenon description is based on two main radiation mechanisms, namely, parametric X-ray radiation (PXR) and diffracted transition radiation (DTR). The possibility to increase the spectral-angular density of DTR under the condition of constructive interference of the transition radiation waves from different boundaries of such a structure has been demonstrated. It is shown that little changes in the layers thicknesses should not cause a considerable change in the interference picture, for example, the transition of constructive interference into destructive one. It means that in the considered process the conditions of constructive interference are enough stable to use them for increasing the intensity of X-ray source that can be created based on the interaction of relativistic electrons with such a structure.

  14. Structural Modification of Cobalt Catalysts: Effect of Wetting Studied by X-Ray and Infrared Techniques

    Directory of Open Access Journals (Sweden)

    Khodakov A.

    1999-07-01

    Full Text Available The effect of wetting on the structure and localisation of cobalt species on various supports (Al2O3, SiO2, TiO2, HZSM-5 zeolite was studied using X-ray diffraction, Fourier transform infrared spectroscopy with CO as a molecular probe, X-ray photoelectron spectroscopy and extended X-ray absorption fine structure analysis. Aqueous impregnation to incipient wetness of reduced and passivated cobalt catalysts results, even in the absence of any promoter, in a considerable decrease in the concentration of Co crystalline phases and modifies the surface sites. The decrease in the concentration of Co3O4 crystallites was especially pronounced on silica supported catalysts prepared via impregnation of cobalt and on a mixture of Co3O4 and HZSM-5 zeolite. Saturation with water of the passivated Co/SiO2 sample results in an amorphous solid with a local structure close to that of Co2SiO4. For Co/Al2O3 and Co/TiO2 catalysts, the effect of wetting on the concentration of Co3O4 crystalline phase was considerably smaller.

  15. Distinct local structure of nanoparticles and nanowires of V2O5 probed by x-ray absorption spectroscopy

    Science.gov (United States)

    Joseph, B.; Iadecola, A.; Maugeri, L.; Bendele, M.; Okubo, M.; Li, H.; Zhou, H.; Mizokawa, T.; Saini, N. L.

    2013-12-01

    We have used V K-edge x-ray absorption spectroscopy to study local structures of bulk, nanoparticles and nanowires of V2O5. The extended x-ray absorption fine structure measurements show different local displacements in the three morphologically different V2O5 samples. It is found that the nanowires have a significantly ordered chain structure in comparison to the V2O5 bulk. In contrast, nanoparticles have larger interlayer disorder. The x-ray absorption near-edge structure spectra show different electronic structure that appears to be related with the local atomic disorder in the three V2O5 samples.

  16. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    Science.gov (United States)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

  17. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

    Energy Technology Data Exchange (ETDEWEB)

    Van Benschoten, Andrew H. [University of California San Francisco, San Francisco, CA 94158 (United States); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C.; Wall, Michael E. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Jackson, Colin J. [Australian National University, Canberra, ACT 2601 (Australia); Sauter, Nicholas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Urzhumtsev, Alexandre [Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy (France); Fraser, James S., E-mail: james.fraser@ucsf.edu [University of California San Francisco, San Francisco, CA 94158 (United States)

    2015-07-28

    A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

  18. Transmission X-ray scattering as a probe for complex liquid-surface structures

    Energy Technology Data Exchange (ETDEWEB)

    Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; Kuzmenko, Ivan

    2016-01-28

    The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibility of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.

  19. Yes, one can obtain better quality structures from routine X-ray data collection.

    Science.gov (United States)

    Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

    2016-01-01

    Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ data collected to the lower 2θmax angles. Also the results of translation-libration-screw (TLS) analysis and vibrational entropy values are more

  20. Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compounds-synthesis, X-Ray studies and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Machura, B., E-mail: basia@ich.us.edu.pl [Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice (Poland); Switlicka, A.; Zwolinski, P. [Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice (Poland); Mrozinski, J., E-mail: jmroz@wchuwr.chem.uni.wroc.pl [Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14 St., 50-383 Wroclaw (Poland); Kalinska, B. [Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14 St., 50-383 Wroclaw (Poland); Kruszynski, R., E-mail: rafal.kruszynski@p.lodz.pl [Department of X-Ray Crystallography and Crystal Chemistry, Institute of General and Ecological Chemistry, Technical University of Lodz, 116 Zeromski St., 90-924 Lodz (Poland)

    2013-01-15

    Seven novel heterobimetallic Cu/Hg polymers based on thiocyanate bridges have been synthesised and characterised by means of IR, EPR, magnetic measurements and single crystal X-Ray. Three of them, [Cu(pzH){sub 4}Hg(SCN){sub 4}]{sub n} (1) [Cu(indH){sub 4}Hg(SCN){sub 4}]{sub n} (2) and [Cu(ampy){sub 2}Hg(SCN){sub 4}]{sub n} (3), have one-dimensional coordination structure. Two compounds [Cu(pzH){sub 2}Hg(SCN){sub 4}]{sub n} (4) and [Cu(abzimH)Hg(SCN){sub 4}]{sub n} (5) form two-dimensional nets, whereas the complexes [Cu(pyCN){sub 2}Hg(SCN){sub 4}]{sub n} (6) and [Cu(pyCH(OH)(OMe)){sub 2}Hg(SCN){sub 4}]{sub n} (7) are three-dimensional coordination polymers. The chains of 1 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the three dimensional net. In 2 the N-H Bullet Bullet Bullet S hydrogen bonds link the polymeric chains to the two dimensional layer extending along crystallographic (0 0 1) plane. The polymeric chains of compound 3 are joined by the intermolecular N-H Bullet Bullet Bullet N and N-H Bullet Bullet Bullet S hydrogen bonds to the three dimensional net. The polymeric layers of 4 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the three dimensional net. - Graphical abstract: Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compound-synthesis,X-Ray studies and magnetic properties. Highlights: Black-Right-Pointing-Pointer Novel heterobimetallic Cu/Hg coordination polymers were synthesised. Black-Right-Pointing-Pointer The multidimensional structures have been proved by single X-ray analysIs. Black-Right-Pointing-Pointer A variation in the crystalline architectures was observed depending on auxiliary ligands. Black-Right-Pointing-Pointer Magnetic measurements indicate weak exchange interaction between Cu(II) in the crystal lattices below 10 K.

  1. NXDC-neutron and x-ray diffraction code for crystal structures calculations

    International Nuclear Information System (INIS)

    Abbas, Y.; El-Sherif, A.

    1982-01-01

    A computer program NXDC for the calculations of neutron diffraction and x-ray diffraction intensities is reported. The program is very flexible and allows the intensity of a reflection with a given Miller indices to be calculated if the unit cell and its contents are specified together with the equipement used Neutrons or X-rays-and if necessary introducing temperature and absorption factors corrections. For the refinement of crystal structures provision is made for the comparison of the calculated intensities and the intergrated intensities observed from the diffraction diagrams using the least-squares analysis to obtain the reliability factor R. The program is written in FORTRAN Iv and is very suitable for minicomputers

  2. Investigation of temperature dependence of muonic X-ray spectra structure in silicon and vanadium oxides

    International Nuclear Information System (INIS)

    Andreeff, A.; Evseev, V.S.; Minkova, A.; Ortlepp, H.-G.; Roganov, V.S.; Rybakov, V.N.; Sabirov, B.M.; Fromm, W.

    1979-01-01

    To study the influence of matter macroscopic properties on the negative muon atomic capture the muonic X-ray spectra have been measured from silicon at 77 deg and 295 deg, from VO 2 at 295 deg and 355 deg, and from V 2 O 3 at 77 deg and 295 deg using a Ge(Li) spectrometer 55 cm 3 in volume and ''on-line'' technique. It is shown that neither changes of a conductivity in all targets, nor a rebuilding of both vanadium oxydes crystal structure at phase transition does not cause any alteration in muonic X-ray spectrum. The obtained results are discussed in terms of a ''time pit''

  3. Extended x-ray absorption fine structure of NaBr and Ge at high pressure

    Science.gov (United States)

    Ingalls, R.; Crozier, E. D.; Whitmore, J. E.; Seary, A. J.; Tranquada, J. M.

    1980-06-01

    The x-ray absorption spectra of Ge and of Br in NaBr have been measured to pressures of 52 and 21 kbars, respectively, in a boron carbide and diamond anvil cell in which pressure was measured via the ruby-fluorescence technique. Although Bragg peaks from the diamond anvil reduced the accuracy, atomic spacings in both materials could be determined by extended x-ray absorption fine-structure (EXAFS) analysis. Changes in the nearest-neighbor separations in NaBr, and Ge to at least 40 kbars, agreed with literature values, indicating that the EXAFS phase shifts are quite insensitive to such pressures. In addition the near-edge peak positions in the NaBr spectra appeared to readily shift with pressure, which suggests that NaBr may be quite suitable as a pressure standard in future work of this type.

  4. Single shot near edge x-ray absorption fine structure spectroscopy in the laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Mantouvalou, I., E-mail: ioanna.mantouvalou@tu-berlin.de; Witte, K.; Martyanov, W.; Jonas, A.; Grötzsch, D.; Kanngießer, B. [Institute for Optics and Atomic Physics, Technical University of Berlin, D-10623 Berlin (Germany); Streeck, C. [Physikalisch-Technische Bundesanstalt (PTB), D-10587 Berlin (Germany); Löchel, H.; Rudolph, I.; Erko, A. [Helmholtz-Zentrum Berlin, D-14109 Berlin (Germany); Stiel, H. [Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, D-12489 Berlin (Germany)

    2016-05-16

    With the help of adapted off-axis reflection zone plates, near edge X-ray absorption fine structure spectra at the C and N K-absorption edge have been recorded using a single 1.2 ns long soft X-ray pulse. The transmission experiments were performed with a laser-produced plasma source in the laboratory rendering time resolved measurements feasible independent on large scale facilities. A resolving power of E/ΔE ∼ 950 at the respective edges could be demonstrated. A comparison of single shot spectra with those collected with longer measuring time proves that all features of the used reference samples (silicon nitrate and polyimide) can be resolved in 1.2 ns. Hence, investigations of radiation sensitive biological specimen become possible due to the high efficiency of the optical elements enabling low dose experiments.

  5. X-ray scattering study of the interplay between magnetism and structure in CeSb

    CERN Document Server

    McMorrow, D F; Lebech, B; Soerensen, S A; Christensen, M J; Vogt, O

    1997-01-01

    The chemical and magnetic structures of CeSb have been investigated using high-resolution x-ray scattering techniques. Experiments performed in the non-resonant regime (x-ray energy of E = 9.4 keV) showed that when the sample was cooled below its Neel temperature of T sub N approx. 16.5 K, peaks appeared with commensurate wave vectors q. From their polarization and wave-vector dependence, the peaks are deduced to arise mainly from a periodic lattice distortion. In the resonant regime, when the x-ray energy was tuned to the L absorption edges of Ce, weak, resonantly enhanced magnetic scattering was observed at the L sub t sub t edge (E = 6.164 keV), with no scattering found at either L sub t or L sub t sub t sub t. Of the six possible zero-field commensurate magnetic structures reported in earlier neutron experiments, we found the phases with q sub m =2/3 and 4/7 only, with the domain that has moments perpendicular to the surface absent. Neutron scattering experiments on the same single crystal confirm that th...

  6. X-ray scattering study of the interplay between magnetism and structure in CeSb

    DEFF Research Database (Denmark)

    McMorrow, Desmond Francis; Lussier, J.-G.; Lebech, Bente

    1997-01-01

    The chemical and magnetic structures of CeSb have been investigated using high-resolution x-ray scattering techniques. Experiments performed in the non-resonant regime (x-ray energy of E = 9.4 keV) showed that when the sample was cooled below its Neel temperature of T-N approximate to 16.5 K, peaks...... appeared with commensurate wave vectors q. From their polarization and wave-vector dependence, the peaks are deduced to arise mainly from a periodic lattice distortion. In the resonant regime, when the x-ray energy was tuned to the L absorption edges of Ce, weak, resonantly enhanced magnetic scattering...... was observed at the L(II) edge (E = 6.164 keV), with no scattering found at either L(I) or L(III) Of the six possible zero-field commensurate magnetic structures reported in earlier neutron experiments, we found the phases with q(m) = 2/3 and 4/7 only, with the domain that has moments perpendicular...

  7. X-ray absorption near edge structure (XANES) study of some hydroxamic mixed ligand copper complexes

    International Nuclear Information System (INIS)

    Mishra, A; Parsai, N; Shrivastava, B D; Soni, N

    2012-01-01

    With the advent of modern bright synchrotron radiation sources, X-ray absorption spectra has emerged as a powerful technique for local structure determination, which can be applied to any type of material. The X-ray absorption measurements of four hydroxamic mixed ligand copper complexes have been performed at the recently developed BL-8 Dispersive EXAFS beamline at 2.5 GeV Indus-2 synchrotron at RRCAT, Indore, India. The X-ray absorption near edge structure (XANES) data obtained has been processed using data analysis program Athena. The energies of the K absorption edge, chemical shifts, edge-widths, shifts of the principal absorption maximum in the complexes have been determined. The values of the chemical shift suggest that copper is in oxidation state +2 in all of the complexes. The chemical shift data has been utilized to estimate effective nuclear charge on copper atom. The order of the chemical shifts has been correlated to the relative ionic character of the bonding in these complexes.

  8. Enhanced reflectance X-ray absorption fine structure sensitivity using a whispering-gallery waveguide

    CERN Document Server

    Chernov, V A; Kovalenko, N V; Zolotarev, K V

    2000-01-01

    A new technique of reflectance X-ray absorption fine structure (REFL-XAFS) utilizing waveguides where X-rays are reflected many times along the waveguide surface is discussed. The multiple total reflection (MTR) phenomenon highly increases X-ray interaction with the waveguide surface and hence offers higher sensitivity compared to conventional (single reflection) REFL-XAFS. On the one hand, this technique is a direct structural method for characterizing waveguides (e.g. capillaries) where the application of other methods is very difficult. On the other hand, the conventional thin wafer can be transformed to a whispering-gallery (WG) waveguide by bending to a curved mirror. Ray tracing calculations demonstrate that the WG waveguide is very suitable for REFL-XAFS measurements. This method was experimentally realized for a cylindrically bent silica wafer with the surface covered with a GeO sub 2 monolayer. The Ge K-edge REFL-XAFS measurements were performed using both MTR and conventional techniques. The MTR tec...

  9. Structure of the Si(1 1 3) surface studied by surface X-ray diffraction

    International Nuclear Information System (INIS)

    Mizuno, Yoshihito; Akimoto, Koichi; Aoyama, Tomohiro; Suzuki, Hidetoshi; Nakahara, Hitoshi; Ichimiya, Ayahiko; Sumitani, Kazushi; Takahashi, Toshio; Zhang Xiaowei; Sugiyama, Hiroshi; Kawata, Hiroshi

    2004-01-01

    We carried out a grazing incidence X-ray diffraction analysis of the Si(1 1 3) 3 x 1 surface using synchrotron radiation. We compared the experimental structure factors obtained from the integrated intensities of the fractional-order reflections with the calculated structure factors of the dimerized structure model of Ranke. By minimizing the R-factor, we determined the position and the size of the pentagon in the 3 x 1 dimerized structure model of Ranke. In addition, we found that a model with randomly distributed interstitial atoms at the center of the pentagon gives a smaller R-factor value

  10. Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Kalyaneswar; Pentelute, Brad L.; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A.; Kent, Stephen B.H.; (UC)

    2009-06-30

    We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers L-plectasin and D-plectasin were prepared by total chemical synthesis; interestingly, L-plectasin showed the expected antimicrobial activity, while D-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group P1 with one L-plectasin molecule and one D-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%-15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation.

  11. La2MnVO6 Double Perovskite: A Structural, Magnetic and X-Ray Absorption Investigation

    International Nuclear Information System (INIS)

    Mandal, T.; Croft, M.; Hadermann, J.; Van Tendeloo, G.; Stephens, P.; Greenblatt, M.

    2009-01-01

    The synthesis, electron diffraction (ED), synchrotron X-ray and neutron structure, X-ray absorption spectroscopy (XAS) and magnetic property studies of La2MnVO6 double perovskite are described. Analysis of the synchrotron powder X-ray diffraction data for La2MnVO6 indicates a disordered arrangement of Mn and V at the B-site of the perovskite structure. Absence of super-lattice reflections in the ED patterns for La2MnVO6 supports the disordered cation arrangement. Room temperature time-of-flight (TOF) neutron powder diffraction (NPD) data show no evidence of cation ordering, in corroboration with the ED and synchrotron studies (orthorhombic Pnma, a = 5.6097(3), b = 7.8837(5) and c = 5.5668(3); 295 K, NPD). A comparison of XAS analyses of La2TVO6 with T = Ni and Co shows T2+ formal oxidation state while the T = Mn material evidences a Mn3+ admixture into a dominantly Mn2+ ground state. V-K edge measurements manifest a mirror image behavior with a V4+ state for T = Ni and Co with a V3+ admixture arising in the T = Mn material. The magnetic susceptibility data for La2MnVO6 show ferromagnetic correlations; the observed effective moment, μeff (5.72 μB) is much smaller than the calculated moment (6.16 μμB) based on the spin-only formula for Mn2+ (d5, HS)/V4+ (d1), supportive of the partly oxidized Mn and reduced V scenario (Mn3+/V3+).

  12. Providing x-rays

    International Nuclear Information System (INIS)

    Mallozzi, P.J.; Epstein, H.M.

    1985-01-01

    This invention provides an apparatus for providing x-rays to an object that may be in an ordinary environment such as air at approximately atmospheric pressure. The apparatus comprises: means (typically a laser beam) for directing energy onto a target to produce x-rays of a selected spectrum and intensity at the target; a fluid-tight enclosure around the target; means for maintaining the pressure in the first enclosure substantially below atmospheric pressure; a fluid-tight second enclosure adjoining the first enclosure, the common wall portion having an opening large enough to permit x-rays to pass through but small enough to allow the pressure reducing means to evacuate gas from the first enclosure at least as fast as it enters through the opening; the second enclosure filled with a gas that is highly transparent to x-rays; the wall of the second enclosure to which the x-rays travel having a portion that is highly transparent to x-rays (usually a beryllium or plastic foil), so that the object to which the x-rays are to be provided may be located outside the second enclosure and adjacent thereto and thus receive the x-rays substantially unimpeded by air or other intervening matter. The apparatus is particularly suited to obtaining EXAFS (extended x-ray fine structure spectroscopy) data on a material

  13. Energetic electron processes fluorescence effects for structured nanoparticles X-ray analysis and nuclear medicine applications

    Energy Technology Data Exchange (ETDEWEB)

    Taborda, A.; Desbrée, A. [Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-HOM/SDI/LEDI, BP-17, 31, Avenue de la Division Leclerc, 92262 Fontenay-aux-Roses (France); Carvalho, A. [IEQUALTECS, Lda, Rua Dr. Francisco Sá Carneiro, 36, 2500-065 S. Gregório CLD (Portugal); Chaves, P.C. [C" 2TN, Campus Tecnológico e Nuclear, Instituto Superior Técnico, Universidade de Lisboa, EN10 km 139.7, 2685-066 Bobadela LRS (Portugal); Reis, M.A., E-mail: mareis@ctn.tecnico.ulisboa.pt [IEQUALTECS, Lda, Rua Dr. Francisco Sá Carneiro, 36, 2500-065 S. Gregório CLD (Portugal); C" 2TN, Campus Tecnológico e Nuclear, Instituto Superior Técnico, Universidade de Lisboa, EN10 km 139.7, 2685-066 Bobadela LRS (Portugal)

    2016-08-15

    Superparamagnetic iron oxide (SPIO) nanoparticles are widely used as contrast agents for nuclear magnetic resonance imaging (MRI), and can be modified for improved imaging or to become tissue-specific or even protein-specific. The knowledge of their detailed elemental composition characterisation and potential use in nuclear medicine applications, is, therefore, an important issue. X-ray fluorescence techniques such as particle induced X-ray emission (PIXE) or X-ray fluorescence spectrometry (XRF), can be used for elemental characterisation even in problematic situations where very little sample volume is available. Still, the fluorescence coefficient of Fe is such that, during the decay of the inner-shell ionised atomic structure, keV Auger electrons are produced in excess to X-rays. Since cross-sections for ionisation induced by keV electrons, for low atomic number atoms, are of the order of 10{sup 3} barn, care should be taken to account for possible fluorescence effects caused by Auger electrons, which may lead to the wrong quantification of elements having atomic number lower than the atomic number of Fe. Furthermore, the same electron processes will occur in iron oxide nanoparticles containing {sup 57}Co, which may be used for nuclear medicine therapy purposes. In the present work, simple approximation algorithms are proposed for the quantitative description of radiative and non-radiative processes associated with Auger electrons cascades. The effects on analytical processes and nuclear medicine applications are quantified for the case of iron oxide nanoparticles, by calculating both electron fluorescence emissions and energy deposition on cell tissues where the nanoparticles may be embedded.

  14. Energetic electron processes fluorescence effects for structured nanoparticles X-ray analysis and nuclear medicine applications

    Science.gov (United States)

    Taborda, A.; Desbrée, A.; Carvalho, A.; Chaves, P. C.; Reis, M. A.

    2016-08-01

    Superparamagnetic iron oxide (SPIO) nanoparticles are widely used as contrast agents for nuclear magnetic resonance imaging (MRI), and can be modified for improved imaging or to become tissue-specific or even protein-specific. The knowledge of their detailed elemental composition characterisation and potential use in nuclear medicine applications, is, therefore, an important issue. X-ray fluorescence techniques such as particle induced X-ray emission (PIXE) or X-ray fluorescence spectrometry (XRF), can be used for elemental characterisation even in problematic situations where very little sample volume is available. Still, the fluorescence coefficient of Fe is such that, during the decay of the inner-shell ionised atomic structure, keV Auger electrons are produced in excess to X-rays. Since cross-sections for ionisation induced by keV electrons, for low atomic number atoms, are of the order of 103 barn, care should be taken to account for possible fluorescence effects caused by Auger electrons, which may lead to the wrong quantification of elements having atomic number lower than the atomic number of Fe. Furthermore, the same electron processes will occur in iron oxide nanoparticles containing 57Co, which may be used for nuclear medicine therapy purposes. In the present work, simple approximation algorithms are proposed for the quantitative description of radiative and non-radiative processes associated with Auger electrons cascades. The effects on analytical processes and nuclear medicine applications are quantified for the case of iron oxide nanoparticles, by calculating both electron fluorescence emissions and energy deposition on cell tissues where the nanoparticles may be embedded.

  15. Structural study of the X-ray-induced enzymatic reaction of octahaem cytochrome C nitrite reductase.

    Science.gov (United States)

    Trofimov, A A; Polyakov, K M; Lazarenko, V A; Popov, A N; Tikhonova, T V; Tikhonov, A V; Popov, V O

    2015-05-01

    Octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens catalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochrome c nitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

  16. Electronic structure and optical properties of CdS{sub x}Se{sub 1−x} solid solution nanostructures from X-ray absorption near edge structure, X-ray excited optical luminescence, and density functional theory investigations

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, M. W. [DESY (Deutsches Elektronen-Synchrotron), FS-PEX, Notkestrasse 85, 22607 Hamburg (Germany); Yiu, Y. M., E-mail: yyiu@uwo.ca; Sham, T. K. [Department of Chemistry, University of Western Ontario, London, ON N6A5B7 (Canada); Ward, M. J. [Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853 (United States); Liu, L. [Institute of Functional Nano and Soft Materials (FUNSOM) and Soochow University-Western University Center for Synchrotron Radiation Research, Soochow University, Suzhou, Jiangsu, 215123 (China); Hu, Y. [Canadian Light Source, University of Saskatchewan, Saskatoon, SK S7N2V3 (Canada); Zapien, J. A. [Center Of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR (China); Liu, Yingkai [Institute of Physics and Electronic Information, Yunnan Normal University, Kunming, Yunnan, 650500 (China)

    2014-11-21

    The electronic structure and optical properties of a series of iso-electronic and iso-structural CdS{sub x}Se{sub 1−x} solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.

  17. Silicon Σ13(5 0 1) grain boundary interface structure determined by bicrystal Bragg rod X-ray scattering

    International Nuclear Information System (INIS)

    Howes, P.B.; Rhead, S.; Roy, M.; Nicklin, C.L.; Rawle, J.L.; Norris, C.A.

    2013-01-01

    The atomic structure of the silicon Σ13(5 0 1) symmetric tilt grain boundary interface has been determined using Bragg rod X-ray scattering. In contrast to conventional structural studies of grain boundary structure using transmission electron microscopy, this approach allows the non-destructive measurement of macroscopic samples. The interface was found to have a single structure that is fully fourfold coordinated. X-ray diffraction data were measured at Beamline I07 at the Diamond Light Source

  18. X-ray structure analyses of biological molecules and particles in Japan. A brief history and future prospect

    International Nuclear Information System (INIS)

    Nakasako, Masayoshi; Yamamoto, Masaki

    2015-01-01

    In Japan, X-ray structure analyses of molecules and particles from biology started in the 1970s. The structure analysis methods have been developed through the innovation of various techniques in advance, and have contributed for understanding the elementary and microscopic processes in life. Here we summarize briefly the history of X-ray structure analyses for structural biology in Japan and think about the prospect. (author)

  19. X-rays in the Cryo-Electron Microscopy Era: Structural Biology's Dynamic Future.

    Science.gov (United States)

    Shoemaker, Susannah C; Ando, Nozomi

    2018-01-23

    Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa) while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kilodaltons in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions at the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology.

  20. Structural studies coupling X-ray diffraction and high-energy X-ray scattering in the UO2(2+)-HBr(aq) system.

    Science.gov (United States)

    Wilson, Richard E; Skanthakumar, S; Cahill, C L; Soderholm, L

    2011-11-07

    The structural chemistry of uranium(VI) in concentrated aqueous hydrobromic acid solutions was investigated using both single crystal X-ray diffraction and synchrotron-based high-energy X-ray scattering (HEXS) to reveal the structure of the uranium(VI) complexes in solution prior to crystallization. The crystal structures of a series of uranyl tetrabromide salts are reported, including Cs(2)UO(2)Br(4), Rb(2)UO(2)Br(4)·2H(2)O, K(2)UO(2)Br(4)·2H(2)O, and (NH(4))(2)UO(2)Br(4)·2H(2)O, as well as a molecular dimer of uranium(VI), (UO(2))(2)(OH)(2)Br(2)(H(2)O)(4). Limited correspondence exists between the structures observed in the solid state and those in solution. Quantitative analysis of the HEXS data show an average U-Br coordination number of 1.9(2) in solution, in contrast to the U-Br coordination number of 4 in the solid salts. © 2011 American Chemical Society

  1. The microscopic structure of liquid mercury from neutron and x-ray diffraction

    International Nuclear Information System (INIS)

    Bafile, U.

    1999-01-01

    Complete text of publication follows. New neutron and X-ray diffraction investigations of the microscopic structure of liquid mercury were recently carried out. The direct comparison of the structure factors S(Q) measured with the two techniques showing a very good agreement, is reported here. It is also shown that, by exploiting the very good stability of the D20 neutron diffractometer at ILL, Grenoble, the very small density effects due to pressurization of mercury up to 2 kbar can be detected to obtain the first neutron measurement of the isothermal density derivative of S(Q), which is a very sensitive probe of the interaction law in liquid systems. (author)

  2. Structure of ordered polyelectrolyte films from atomic-force microscopy and X-ray reflectivity data

    International Nuclear Information System (INIS)

    Belyaev, V.V.; Tolstikhina, A.L.; Stepina, N.D.; Kayushina, R.L.

    1998-01-01

    The possible application of atomic-force microscopy and X-ray reflectometry methods to structural studies of polyelectrolyte films obtained due to alternating adsorption of oppositely charged polyanion [sodium polysterenesulfonate (PSS)] and polycation [poly(allylamine) hydrochloride (PAA)] layers on solid substrates has been considered. The atomic-force microscopy study has revealed the characteristic features of the surface topography of samples consisting of different numbers of polyelectrolyte layers deposited from solutions characterized by different ionic strength values. It is shown that the shape of the reflectivity curves obtained from thin polyelectrolyte films depends on their surface structure

  3. Time-resolved pump-probe X-ray absorption fine structure spectroscopy of Gaq3

    International Nuclear Information System (INIS)

    Dicke, Benjamin

    2013-01-01

    Gallium(tris-8-hydroxyquinoline) (Gaq 3 ) belongs to a class of metal organic compounds, used as electron transport layer and emissive layer in organic light emitting diodes. Many research activities have concentrated on the optical and electronic properties, especially of the homologue molecule aluminum(tris-8-hydroxyquinoline) (Alq 3 ). Knowledge of the first excited state S 1 structure of these molecules could provide deeper insight into the processes involved into the operation of electronic devices, such as OLEDs and, hence, it could further improve their efficiency and optical properties. Until now the excited state structure could not be determined experimentally. Most of the information about this structure mainly arises from theoretical calculations. X-ray absorption fine structure (XAFS) spectroscopy is a well developed technique to determine both, the electronic and the geometric properties of a sample. The connection of ultrashort pulsed X-ray sources with a pulsed laser system offers the possibility to use XAFS as a tool for studying the transient changes of a sample induced by a laser pulse. In the framework of this thesis a new setup for time-resolved pump-probe X-ray absorption spectroscopy at PETRA III beamline P11 was developed for measuring samples in liquid form. In this setup the sample is pumped into its photo-excited state by a femtosecond laser pump pulse with 343 nm wavelength and after a certain time delay probed by an X-ray probe pulse. In this way the first excited singlet state S 1 of Gaq 3 dissolved in benzyl alcohol was analyzed. A structural model for the excited state structure of the Gaq 3 molecule based on the several times reproduced results of the XAFS experiments is proposed. According to this model it was found that the Ga-N A bond length is elongated, while the Ga-O A bond length is shortened upon photoexcitation. The dynamics of the structural changes were not the focus of this thesis. Nevertheless the excited state lifetime

  4. X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction

    International Nuclear Information System (INIS)

    Blum, Marc-Michael; Tomanicek, Stephen J.; John, Harald; Hanson, B. Leif; Rüterjans, Heinz; Schoenborn, Benno P.; Langan, Paul; Chen, Julian C.-H.

    2010-01-01

    The crystal structure of perdeuterated diisopropyl fluorophosphatase is reported and compared with the hydrogenated structure. Diffraction guidelines for neutron crystallography experiments are summarized. The signal-to-noise ratio is one of the limiting factors in neutron macromolecular crystallography. Protein perdeuteration, which replaces all H atoms with deuterium, is a method of improving the signal-to-noise ratio of neutron crystallography experiments by reducing the incoherent scattering of the hydrogen isotope. Detailed analyses of perdeuterated and hydrogenated structures are necessary in order to evaluate the utility of perdeuterated crystals for neutron diffraction studies. The room-temperature X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase) is reported at 2.1 Å resolution. Comparison with an independently refined hydrogenated room-temperature structure of DFPase revealed no major systematic differences, although the crystals of perdeuterated DFPase did not diffract neutrons. The lack of diffraction is examined with respect to data-collection and crystallographic parameters. The diffraction characteristics of successful neutron structure determinations are presented as a guideline for future neutron diffraction studies of macromolecules. X-ray diffraction to beyond 2.0 Å resolution appears to be a strong predictor of successful neutron structures

  5. Electronic structure and X-ray spectroscopic properties of YbNi2P2

    International Nuclear Information System (INIS)

    Shcherba, I.D.; Bekenov, L.V.; Antonov, V.N.; Noga, H.; Uskokovic, D.; Zhak, O.; Kovalska, M.V.

    2016-01-01

    Highlights: • We present new experimental and theoretical data for YbNi 2 P 2 . • The presence of divalent and trivalent Yb ion found in YbNi 2 P 2 . • The calculation show good agreement with the experimental measurements. - Abstract: X-ray absorption spectrum at the Yb L 3 edge and X-ray emission spectra of Ni and P at the K and L 2,3 edges have been studied experimentally and theoretically in the mixed valent compound YbNi 2 P 2 with ThCr 2 Si 2 type crystal structure. The electronic structure of YbNi 2 P 2 is investigated using the fully relativistic Dirac linear muffin-tin orbital (LMTO) band-structure method. The effect of the spin–orbit (SO) interaction and Coulomb repulsion U on the electronic structure of YbNi 2 P 2 is examined in the frame of the LSDA + SO + U method. The core-hole effect in the final states as well as the effect of the electric quadrupole E 2 transitions have been investigated. A good agreement between the theory and the experiment was found. Both the trivalent and the divalent Yb ions in YbNi 2 P 2 are reflected in the experimentally measured Yb L 3 X-ray absorption spectrum simultaneously. We found that the best agreement between the experimental spectrum and sum of the theoretically calculated Yb 2+ and Yb 3+ spectra is achieved with 73% ytterbium ions in 2+ state and 27% ions in 3+ state.

  6. Synthesis, characterization and molecular modelling of a novel dipyridamole supramolecule - X-ray structure, quantum mechanics and molecular dynamics study to comprehend the hydrogen bond structure-activity relationship

    Science.gov (United States)

    Vepuri, Suresh B.; Devarajegowda, H. C.; Soliman, Mahmoud E.

    2016-02-01

    Hydrochloride salt formation for Active Pharmaceutical Ingredients (APIs) is the primary choice to impart aqueous solubility and to promote dissolution. Dipyridamole (DIP) is a cardiovascular drug which is practically insoluble in water. We discovered a new form of DIP called as dipyridamole hydrochloride trihydrate (DIPHT), which was prepared by an unusual method of reacting the DIP with hydrated hydrochloric acid (HCl) that was liberated in situ by the reaction of ferric chloride with water. The liberated HCl was consumed as reagent in situ by the scavenger (API) and was converted to a hydrochloride trihydrate. The product was characterized by FTIR, mass spectroscopy, PXRD and DSC. Supramolecular structure of this novel DIPHT was revealed by single crystal XRD. A sustained intramolecular hydrogen bond alliance was found in DIP and the DIPHT. Stability of this hydrogen bond was further evaluated by means of molecular modelling studies. We performed electron calculations using quantum mechanics (QM) on both the base and salt structures to compare their geometry and molecular orbital energy levels. Molecular Dynamics (MD) simulations were also conducted in explicit solvent models to provide more insights into the hydrogen bond strength and conformational preferences of the base and salt structure. Together with QM and MD, we were able to explain the influence of hydrogen bonds on proton uptake activity of DIP and stability of DIP and DIPHT. DIPHT which can dissolve faster than DIP in water may enhance the dissolution and bioavailability of the drug. As the current drug development research is shifting to repurpose the existing drugs in order to subside the untoward risks in new drug development, we believe that DIPHT with its intrinsic aqueous solubility could bring more application for DIP and generate interest within the pharmaceutical industry.

  7. Structure of porcine heart cytoplasmic malate dehydrogenase: combining x-ray diffraction and chemical sequence data in structural studies

    International Nuclear Information System (INIS)

    Birktoft, J.J.; Bradshaw, R.A.; Banaszak, L.J.

    1987-01-01

    The amino acid sequence of cytoplasmic malate dehydrogenase (sMDH) has been determined by a combination of X-ray crystallographic and chemical sequencing methods. The initial molecular model incorporated an X-ray amino acid sequence that derived primarily from an evaluation of a multiple isomorphous replacement phased electron density map calculated at 2.5-A resolution. Following restrained least-squares crystallographic refinement, difference electron density maps were calculated from model phases, and attempts were made to upgrade the X-ray amino acid sequence. The method used to find the positions of peptides in the X-ray structure was similar to those used for studying protein homology and was shown to be successful for large fragments. For sMDH, X-ray methods by themselves were insufficient to derive a complete amino acid sequence, even with partial chemical sequence data. However, for this relatively large molecule at medium resolution, the electron density maps were of considerable help in determining the linear position of peptide fragments. The N-acetylated polypeptide chain of sMDH has 331 amino acids and has been crystallographically refined to an R factor of 19% for 2.5-A resolution diffraction data

  8. X-ray diffraction using the time structure of the SRS

    International Nuclear Information System (INIS)

    Tanner, B.K.

    1983-01-01

    The subject is discussed under the headings: introduction (advances in the techniques of X-ray topography; comparison with transmission electron microscopy); stroboscopic X-ray topography; stroboscopic X-ray topography of travelling surface acoustic waves; possible general diffraction experiments. (U.K.)

  9. Serial data acquisition for the X-ray plasma diagnostics with selected GEM detector structures

    International Nuclear Information System (INIS)

    Czarski, T.; Chernyshova, M.; Pozniak, K.T.; Kasprowicz, G.; Zabolotny, W.; Kolasinski, P.; Krawczyk, R.; Wojenski, A.; Zienkiewicz, P.

    2015-01-01

    The measurement system based on GEM—Gas Electron Multiplier detector is developed for X-ray diagnostics of magnetic confinement tokamak plasmas. The paper is focused on the measurement subject and describes the fundamental data processing to obtain reliable characteristics (histograms) useful for physicists. The required data processing have two steps: 1—processing in the time domain, i.e. events selections for bunches of coinciding clusters, 2—processing in the planar space domain, i.e. cluster identification for the given detector structure. So, it is the software part of the project between the electronic hardware and physics applications. The whole project is original and it was developed by the paper authors. The previous version based on 1-D GEM detector was applied for the high-resolution X-ray crystal spectrometer KX1 in the JET tokamak. The current version considers 2-D detector structures for the new data acquisition system. The fast and accurate mode of data acquisition implemented in the hardware in real time can be applied for the dynamic plasma diagnostics. Several detector structures with single-pixel sensors and multi-pixel (directional) sensors are considered for two-dimensional X-ray imaging. Final data processing is presented by histograms for selected range of position, time interval and cluster charge values. Exemplary radiation source properties are measured by the basic cumulative characteristics: the cluster position distribution and cluster charge value distribution corresponding to the energy spectra. A shorter version of this contribution is due to be published in PoS at: 1 st EPS conference on Plasma Diagnostics

  10. Serial data acquisition for the X-ray plasma diagnostics with selected GEM detector structures

    Science.gov (United States)

    Czarski, T.; Chernyshova, M.; Pozniak, K. T.; Kasprowicz, G.; Zabolotny, W.; Kolasinski, P.; Krawczyk, R.; Wojenski, A.; Zienkiewicz, P.

    2015-10-01

    The measurement system based on GEM—Gas Electron Multiplier detector is developed for X-ray diagnostics of magnetic confinement tokamak plasmas. The paper is focused on the measurement subject and describes the fundamental data processing to obtain reliable characteristics (histograms) useful for physicists. The required data processing have two steps: 1—processing in the time domain, i.e. events selections for bunches of coinciding clusters, 2—processing in the planar space domain, i.e. cluster identification for the given detector structure. So, it is the software part of the project between the electronic hardware and physics applications. The whole project is original and it was developed by the paper authors. The previous version based on 1-D GEM detector was applied for the high-resolution X-ray crystal spectrometer KX1 in the JET tokamak. The current version considers 2-D detector structures for the new data acquisition system. The fast and accurate mode of data acquisition implemented in the hardware in real time can be applied for the dynamic plasma diagnostics. Several detector structures with single-pixel sensors and multi-pixel (directional) sensors are considered for two-dimensional X-ray imaging. Final data processing is presented by histograms for selected range of position, time interval and cluster charge values. Exemplary radiation source properties are measured by the basic cumulative characteristics: the cluster position distribution and cluster charge value distribution corresponding to the energy spectra. A shorter version of this contribution is due to be published in PoS at: 1st EPS conference on Plasma Diagnostics

  11. X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.

    Science.gov (United States)

    Blum, Marc Michael; Tomanicek, Stephen J; John, Harald; Hanson, B Leif; Rüterjans, Heinz; Schoenborn, Benno P; Langan, Paul; Chen, Julian C H

    2010-04-01

    The signal-to-noise ratio is one of the limiting factors in neutron macromolecular crystallography. Protein perdeuteration, which replaces all H atoms with deuterium, is a method of improving the signal-to-noise ratio of neutron crystallography experiments by reducing the incoherent scattering of the hydrogen isotope. Detailed analyses of perdeuterated and hydrogenated structures are necessary in order to evaluate the utility of perdeuterated crystals for neutron diffraction studies. The room-temperature X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase) is reported at 2.1 A resolution. Comparison with an independently refined hydrogenated room-temperature structure of DFPase revealed no major systematic differences, although the crystals of perdeuterated DFPase did not diffract neutrons. The lack of diffraction is examined with respect to data-collection and crystallographic parameters. The diffraction characteristics of successful neutron structure determinations are presented as a guideline for future neutron diffraction studies of macromolecules. X-ray diffraction to beyond 2.0 A resolution appears to be a strong predictor of successful neutron structures.

  12. X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction

    Science.gov (United States)

    Blum, Marc-Michael; Tomanicek, Stephen J.; John, Harald; Hanson, B. Leif; Rüterjans, Heinz; Schoenborn, Benno P.; Langan, Paul; Chen, Julian C.-H.

    2010-01-01

    The signal-to-noise ratio is one of the limiting factors in neutron macromolecular crystallography. Protein perdeuteration, which replaces all H atoms with deuterium, is a method of improving the signal-to-noise ratio of neutron crystallography experiments by reducing the incoherent scattering of the hydrogen isotope. Detailed analyses of perdeuterated and hydrogenated structures are necessary in order to evaluate the utility of perdeuterated crystals for neutron diffraction studies. The room-temperature X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase) is reported at 2.1 Å resolution. Comparison with an independently refined hydrogenated room-temperature structure of DFPase revealed no major systematic differences, although the crystals of perdeuterated DFPase did not diffract neutrons. The lack of diffraction is examined with respect to data-collection and crystallo­graphic parameters. The diffraction characteristics of successful neutron structure determinations are presented as a guideline for future neutron diffraction studies of macromolecules. X-ray diffraction to beyond 2.0 Å resolution appears to be a strong predictor of successful neutron structures. PMID:20383004

  13. Light-Induced Structural Flexibility of Thylakoid Membranes - Investigated using Small-Angle X-ray and Neutron Scattering

    OpenAIRE

    Aagaard, Thomas Helverskov

    2005-01-01

    Using small-angle x-ray and neutron scattering the light-induced structural changes in pea thylakoids have been investigated. It is shown that light-induced shinkage in the thylakoids is connected to photosynthetic electron transduction. Using small-angle x-ray and neutron scattering the light-induced structural changes in pea thylakoids have been investigated. It is shown that light-induced shinkage in the thylakoids is connected to photosynthetic electron transduction.

  14. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

    Energy Technology Data Exchange (ETDEWEB)

    Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

    2009-07-20

    We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

  15. Raphide crystal structure in agave tequilana determined by x-ray originating from synchrotron radiation

    International Nuclear Information System (INIS)

    Tadokoro, Makoto; Ozawa, Yoshiki; Mitsumi, Minoru; Toriumi, Kohshiro; Ogura, Tetsuya

    2005-01-01

    The first single crystal structure of small natural raphides in an agave plant is completely determined using an intense X-ray originating from a synchrotron radiation. The SEM image shows that the tip of the crystal is approximately hundreds of nanometer in width sharply grow to stick to the tissue of herbivorous vermin. Furthermore, the crystal develops cracks that propagate at an inclination of approximately 45deg towards the direction of crystal growth such that the crystal easily splits into small pieces in the tissue. (author)

  16. Determination of Ni(II) crystal structure by powder x-ray diffraction ...

    African Journals Online (AJOL)

    X-ray powder diffraction pattern was used to determine the length of the unit cell, “a”, the lattice structure type, and the number of atoms per unit cell of Ni(II) crystal. The “a” value was determined to be 23.66 ± 0.005 Å, particle size of 34.87 nm, volume 13.24 Å and Strain value ε = 9.8 x 10-3. The cell search on PXRD patterns ...

  17. X-ray reflectivity investgation of structure and kinetics of photoswitchable lipid monolayers

    DEFF Research Database (Denmark)

    Chatterjee, Kuntal; Haushahn, Björn; Shen, Chen

    The mechanical and dynamic properties of phospholipid membranes are of importance for important biological functions, such as switching of embedded proteins. In order to investigate these properties we study model systems in which amphiphilic photoswitchable molecules are integrated into Langmuir......- and cis-conformation by illumination with UV and blue light. We have followed the structural changes in this model membrane and the switching kinetics of the system with Langmuir isotherms and in situ X-ray reflectivity at the LISA diffractometer P08, PETRA III....

  18. X-ray diffraction and molecular-dynamics studies: Structural analysis of phases in diglyceride monolayers

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Larsen, Niels Bent; Bjørnholm, T.

    1998-01-01

    We report a detailed structural analysis of the phases of 1,2-sn-dipalmitoylglycerol Langmuir monolayers at room temperature. Pressure-induced transitions have been investigated by combination of molecular-dynamics simulations and grazing-incidence x-ray diffraction (XRD). The diglyceride film......; At the lowest pressure the tilt angle reaches approximate to 14 degrees in a direction close to a nearest neighbor direction. Both arrangements of the alkyl chains are confirmed by XRD. For higher order and fractional order Bragg peaks, simulations predict higher intensities than observed with XRD. This may...

  19. Malnutrition and myelin structure: an X-ray scattering study of rat sciatic and optic nerves

    International Nuclear Information System (INIS)

    Vargas, V.; Vargas, R.; Marquez, G.; Vonasek, E.; Mateu, L.; Luzzati, V.; Borges, J.

    2000-01-01

    Taking advantage of the fast and accurate X-ray scattering techniques recently developed in our laboratory, we tackled the study of the structural alterations induced in myelin by malnutrition. Our work was performed on sciatic and optic nerves dissected from rats fed with either a normal or a low-protein caloric diet, as a function of age (from birth to 60 days). By way of electrophysiological controls we also measured (on the sciatic nerves) the height and velocity of the compound action potential. Malnutrition was found to decrease the amount of myelin and to impair the packing order of the membranes in the sheaths. (orig.)

  20. Extended X-ray absorption fine structure investigation of nitrogen stabilized expanded austenite

    DEFF Research Database (Denmark)

    Oddershede, Jette; Christiansen, Thomas; Ståhl, Kenny

    2010-01-01

    As-delivered austenitic stainless steel and nitrogen stabilized expanded austenite, both fully nitrided and denitrided (in H2), were investigated with Cr, Fe and Ni extended X-ray absorption fine structure. The data shows pronounced short-range ordering of Cr and N. For the denitrided specimen...... the N atoms remaining in the solid state after H2-reduction are trapped by Cr atoms. Quantitative interpretation in terms of the local distortions around Cr atoms and their N coordination number reveals that no Cr–N clusters or CrN platelets are present....

  1. X-ray diffraction studies of the structure and orientations of thiophene and fluorenone based molecule

    International Nuclear Information System (INIS)

    Porzio, William; Pasini, Mariacecilia; Destri, Silvia; Giovanella, Umberto; Fontaine, Philippe

    2006-01-01

    The crystal structure of a conjugated molecule containing thiophene and fluorenone residues has been determined from powder X-ray diffraction (XRD). Thin films ( -5 Pa) onto oxidized silicon substrates, are oriented along with different crystallographic directions. A comparison of XRD in both Grazing Incidence and Bragg-Brentano geometries allowed to perform a quantitative analysis of the various orientations. This approach is generally applicable in the case of multi-oriented films. The results fully account for the poor performance of this molecule in p-type field effect transistor devices

  2. Local Structure Determination of Carbon/Nickel Ferrite Composite Nanofibers Probed by X-ray Absorption Spectroscopy.

    Science.gov (United States)

    Nilmoung, Sukunya; Kidkhunthod, Pinit; Maensiri, Santi

    2015-11-01

    Carbon/NiFe2O4 composite nanofibers have been successfully prepared by electrospinning method using a various concentration solution of Ni and Fe nitrates dispersed into polyacrylonitride (PAN) solution in N,N' dimethylformamide. The phase and mophology of PAN/NiFe2O4 composite samples were characterized and investigated by X-ray diffraction and scanning electron microscopy. The magnetic properties of the prepared samples were measured at ambient temperature by a vibrating sample magnetometer. It is found that all composite samples exhibit ferromagnetism. This could be local-structurally explained by the existed oxidation states of Ni2+ and Fe3+ in the samples. Moreover, local environments around Ni and Fe ions could be revealed by X-ray absorption spectroscopy (XAS) measurement including X-ray absorption near edge structure (XANES) and Extended X-ray absorption fine structure (EXAFS).

  3. Iron speciation in human cancer cells by K-edge total reflection X-ray fluorescence-X-ray absorption near edge structure analysis

    Energy Technology Data Exchange (ETDEWEB)

    Polgari, Zs. [Eoetvoes Lorand University, Institute of Chemistry, Department of Analytical Chemistry, Laboratory of Environmental Chemistry and Bioanalytics, P.O. Box 32, H-1518, Budapest (Hungary); Meirer, F. [Institute of Atomic and Subatomic Physics, Vienna University of Technology, Vienna (Austria); MiNALab, CMM-irst, Fondazione Bruno Kessler, Povo, Trento (Italy); Sasamori, S.; Ingerle, D. [Institute of Atomic and Subatomic Physics, Vienna University of Technology, Vienna (Austria); Pepponi, G. [MiNALab, CMM-irst, Fondazione Bruno Kessler, Povo, Trento (Italy); Streli, C. [Institute of Atomic and Subatomic Physics, Vienna University of Technology, Vienna (Austria); Rickers, K. [Hamburger Synchrotronstrahlungslabor at DESY, Hamburg (Germany); Reti, A.; Budai, B. [Department of Clinical Research, National Institute of Oncology, Budapest (Hungary); Szoboszlai, N. [Eoetvoes Lorand University, Institute of Chemistry, Department of Analytical Chemistry, Laboratory of Environmental Chemistry and Bioanalytics, P.O. Box 32, H-1518, Budapest (Hungary); Zaray, G., E-mail: zaray@ludens.elte.hu [Eoetvoes Lorand University, Institute of Chemistry, Department of Analytical Chemistry, Laboratory of Environmental Chemistry and Bioanalytics, P.O. Box 32, H-1518, Budapest (Hungary)

    2011-03-15

    X-ray absorption near edge structure (XANES) analysis in combination with synchrotron radiation induced total reflection X-ray fluorescence (SR-TXRF) acquisition was used to determine the oxidation state of Fe in human cancer cells and simultaneously their elemental composition by applying a simple sample preparation procedure consisting of pipetting the cell suspension onto the quartz reflectors. XANES spectra of several inorganic and organic iron compounds were recorded and compared to that of different cell lines. The XANES spectra of cells, independently from the phase of cell growth and cell type were very similar to that of ferritin, the main Fe store within the cell. The spectra obtained after CoCl{sub 2} or NiCl{sub 2} treatment, which could mimic a hypoxic state of cells, did not differ noticeably from that of the ferritin standard. After 5-fluorouracil administration, which could also induce an oxidative-stress in cells, the absorption edge position was shifted toward higher energies representing a higher oxidation state of Fe. Intense treatment with antimycin A, which inhibits electron transfer in the respiratory chain, resulted in minor changes in the spectrum, resembling rather the N-donor Fe-{alpha},{alpha}'-dipyridyl complex at the oxidation energy of Fe(III), than ferritin. The incorporation of Co and Ni in the cells was followed by SR-TXRF measurements.

  4. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

    Directory of Open Access Journals (Sweden)

    Norbert Kučerka

    2015-09-01

    Full Text Available We review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition. From model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc..

  5. Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering.

    Science.gov (United States)

    Kučerka, Norbert; Heberle, Frederick A; Pan, Jianjun; Katsaras, John

    2015-09-21

    We review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach produces robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). From model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid's different moieties (e.g., acyl chains, headgroups, backbones, etc.).

  6. Near-Edge X-ray Absorption Fine Structure Spectroscopy of Diamondoid Thiol Monolayers on Gold

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Fabbri, J; Lee, J I; Schreiner, P; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J; Carlson, B; Vance, A L; Yang, W; Terminello, L J; van Buuren, T; Melosh, N

    2007-11-27

    Diamondoids, hydrocarbon molecules with cubic-diamond-cage structures, have unique properties with potential value for nanotechnology. The availability and ability to selectively functionalize this special class of nanodiamond materials opens new possibilities for surface-modification, for high-efficiency field emitters in molecular electronics, as seed crystals for diamond growth, or as robust mechanical coatings. The properties of self-assembled monolayers (SAMs) of diamondoids are thus of fundamental interest for a variety of emerging applications. This paper presents the effects of thiol substitution position and polymantane order on diamondoid SAMs on gold using near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and X-ray photoelectron spectroscopy (XPS). A framework to determine both molecular tilt and twist through NEXAFS is presented and reveals highly ordered diamondoid SAMs, with the molecular orientation controlled by the thiol location. C 1s and S 2p binding energies are lower in adamantane thiol than alkane thiols on gold by 0.67 {+-} 0.05 eV and 0.16 {+-} 0.04 eV respectively. These binding energies vary with diamondoid monolayer structure and thiol substitution position, consistent with different amounts of steric strain and electronic interaction with the substrate. This work demonstrates control over the assembly, in particular the orientational and electronic structure, providing a flexible design of surface properties with this exciting new class of diamond clusters.

  7. Non-destructive X-ray examination of weft knitted wire structures

    Science.gov (United States)

    Obermann, M.; Ellouz, M.; Aumann, S.; Martens, Y.; Bartelt, P.; Klöcker, M.; Kordisch, T.; Ehrmann, A.; Weber, M. O.

    2016-07-01

    Conductive yarns or wires are often integrated in smart textiles to enable data or energy transmission. In woven fabrics, these conductive parts are fixed at defined positions and thus protected from external loads. Knitted fabrics, however, have relatively loose structures, resulting in higher impacts of possible mechanical forces on the individual yarns. Hence, metallic wires with smaller diameters in particular are prone to break when integrated in knitted fabrics. In a recent project, wires of various materials including copper, silver and nickel with diameters varying between 0.05 mm and 0.23 mm were knitted in combination with textile yarns. Hand flat knitting machines of appropriate gauges were used to produce different structures. On these samples, non-destructive examinations, using an industrial X-ray system Seifert x|cube (225 kV) equipped with a minifocus X-ray tube, were carried out, directly after knitting as well as after different mechanical treatments (tensile, burst, and washing tests). In this way, structural changes of the stitch geometry could be visualized before failure. In this paper, the loop geometries in the knitted fabrics are depicted depending on knitted structures, wire properties and the applied mechanical load. Consequently, it is shown which metallic wires and yarns are most suitable to be integrated into knitted smart textiles.

  8. Structure and dynamics of CdTe studied by X-ray and neutron scattering

    Science.gov (United States)

    Stone, Matthew; Niedziela, Jennifer

    2015-03-01

    We present x-ray diffraction and inelastic neutron scattering studies of the structure and lattice dynamics of commercially available cadmium telluride. We also present complementary density functional theory calculations. The x-ray data show a subtle structural transition is present near 80 K, which manifests also in the measured phonon density of states. Refinement of the structure above and below the transition temperature shows no change to the long-range ordered structure. The inelastic neutron scattering studies were performed using an isotopically un-enriched sample of CdTe, which possesses a high cross section for thermal neutron absorption. The neutron portion of the study was performed with a thin-plate geometry in the reflection condition at the ARCS instrument at the SNS, showing the high flux of the instrument makes possible lattice dynamics studies of materials with high thermal neutron absorption. Single crystal and powder inelastic neutron scattering measurements will be presented. Current interpretation of the nature of the transition and future studies will be discussed. This research at ORNL's Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

  9. X-ray crystallography

    Science.gov (United States)

    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.

  10. Characterization of the Electronic Structure of Silicon Nanoparticles Using X-ray Absorption and Emission

    Energy Technology Data Exchange (ETDEWEB)

    Vaverka, April Susan Montoya [Univ.of California, Davis, CA (United States)

    2008-01-01

    Resolving open questions regarding transport in nanostructures can have a huge impact on a broad range of future technologies such as light harvesting for energy. Silicon has potential to be used in many of these applications. Understanding how the band edges of nanostructures move as a function of size, surface termination and assembly is of fundamental importance in understanding the transport properties of these materials. In this thesis work I have investigated the change in the electronic structure of silicon nanoparticle assemblies as the surface termination is changed. Nanoparticles are synthesized using a thermal evaporation technique and sizes are determined using atomic force microscopy (AFM). By passivating the particles with molecules containing alcohol groups we are able to modify the size dependent band edge shifts. Both the valence and conduction bands are measured using synchrotron based x-ray absorption spectroscopy (XAS) and soft x-ray fluorescence (SXF) techniques. Particles synthesized via recrystallization of amorphous silicon/SiO2 multilayers of thicknesses below 10 nm are also investigated using the synchrotron techniques. These samples also show quantum confinement effects but the electronic structure is different from those synthesized via evaporation methods. The total bandgap is determined for all samples measured. The origins of these differences in the electronic structures are discussed.

  11. Particle-scale structure in frozen colloidal suspensions from small-angle x-ray scattering

    KAUST Repository

    Spannuth, Melissa

    2011-02-01

    During directional solidification of the solvent in a colloidal suspension, the colloidal particles segregate from the growing solid, forming high-particle-density regions with structure on a hierarchy of length scales ranging from that of the particle-scale packing to the large-scale spacing between these regions. Previous work has concentrated mostly on the medium- to large-length scale structure, as it is the most accessible and thought to be more technologically relevant. However, the packing of the colloids at the particle scale is an important component not only in theoretical descriptions of the segregation process, but also to the utility of freeze-cast materials for new applications. Here we present the results of experiments in which we investigated this structure across a wide range of length scales using a combination of small-angle x-ray scattering and direct optical imaging. As expected, during freezing the particles were concentrated into regions between ice dendrites forming a microscopic pattern of high- and low-particle-density regions. X-ray scattering indicates that the particles in the high-density regions were so closely packed as to be touching. However, the arrangement of the particles does not conform to that predicted by standard interparticle pair potentials, suggesting that the particle packing induced by freezing differs from that formed during equilibrium densification processes. © 2011 American Physical Society.

  12. Improving small-angle X-ray scattering data for structural analyses of the RNA world.

    Science.gov (United States)

    Rambo, Robert P; Tainer, John A

    2010-03-01

    Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA(val), and yeast tRNA(phe) that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways.

  13. Structure in defocused beams of x-ray mirrors: causes and possible solutions

    Science.gov (United States)

    Sutter, John P.; Alcock, Simon G.; Rust, Fiona; Wang, Hongchang; Sawhney, Kawal

    2014-09-01

    Grazing incidence mirrors are now a standard optic for focusing X-ray beams. Both bimorph and mechanically bendable mirrors are widely used at Diamond Light Source because they permit a wide choice of focal lengths. They can also be deliberately set out of focus to enlarge the X-ray beam, and indeed many beamline teams now wish to generate uniform beam spots of variable size. However, progress has been slowed by the appearance of fine structure in these defocused beams. Measurements showing the relationship between the medium-frequency polishing error and this structure over a variety of beam sizes will be presented. A theoretical model for the simulations of defocused beams from general mirrors will then be developed. Not only the figure error and its first derivative the slope error, but also the second derivative, the curvature error, must be considered. In conclusion, possible ways to reduce the defocused beam structure by varying the actuators' configuration and settings will be discussed.

  14. Time-Resolved Soft X-ray Diffraction Reveals Transient Structural Distortions of Ternary Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Klaus Mann

    2009-11-01

    Full Text Available Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2–5.2 nm. The investigated system was the lyotropic liquid crystal C16E7/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 μs. Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 Å resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  15. Electronic structure effects in catalysis probed by X-ray and electron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kaya, Sarp; Friebel, Daniel [SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); SIMES, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Ogasawara, Hirohito [SIMES, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Anniyev, Toyli [SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); SIMES, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Nilsson, Anders, E-mail: nilsson@slac.stanford.edu [SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); SIMES, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2013-10-15

    Highlights: •Strain, ligand and uncoordinated sites allow for fine-tuning the electronic structure of catalyst material. •XES and XAS provide means to project out the electronic structure in an atom specific way. •HERFD XAS allows for detail probing of the electronic structure of platinum catalyst during the oxygen reduction reaction. -- Abstract: Here we review some recent developments in using electron and X-ray spectroscopy measurements to elucidate the chemical bond formation on catalyst surfaces used in chemical energy transformations. The d-band model allows a simple understanding of the bond strength of oxygen atom interacting with transition metals in terms of the energy position of the d-band. It is in particular the population of the antibonding states appearing through the interaction of the d-band with the O 2p orbitals that determines the bond strength. We demonstrate how we can fine tune the d-band position and population of antibonding states for strained Pt films on Cu(1 1 1) and Ag(1 1 1) and ligand affected Pt surfaces due to either Ni, Co or Fe in the subsurface layer. We show the effect of nanostructuring in Pt monolayer model electrocatalysts on a Rh(1 1 1) single-crystal substrate on the adsorption strength of chemisorbed species using In situ high energy resolution fluorescence detection X-ray absorption spectroscopy (HERFD XAS) at the Pt L{sub 3} edge.

  16. Revisit of alpha-chitin crystal structure using high resolution X-ray diffraction data.

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

    High resolution synchrotron X-ray fiber diffraction data recorded from crab tendon chitin have been used to describe the crystal structure of alpha-chitin. Crystal structures at 100 and 300 K have been solved using restrained crystallographic refinement against diffraction intensities measured from the fiber diffraction patterns. The unit cell contains two polymer chains in a 2(1) helix conformation and in the antiparallel orientation. The best agreement between predicated and observed X-ray diffraction intensities is obtained for a model that includes two distinctive conformations of C6-O6 hydroxymethl group. Those conformations are different from what is proposed in the generally accepted alpha-chitin crystal structure (J. Mol. Biol. 1978, 120, 167-181). Based on refined positions of the O6 atoms, a network of hydrogen bonds involving O6 is proposed. This network of hydrogen bonds can explain the main features of the polarized FTIR spectra of alpha-chitin and sheds some light on the origin of splitting of the amide I band observed on alpha-chitin IR spectra.

  17. Investigation of soil structure development and properties of macropore networks with X-ray computed tomography

    Science.gov (United States)

    Pagenkemper, Sebastian; Uteau Puschmann, Daniel; Peth, Stephan; Horn, Rainer

    2014-05-01

    X-ray computed tomography provides a non-destructive method to visualize and quantify three-dimensional pore networks. Geometrical and morphological parameters of the complex pore system such as connectivity, tortuosity, porosity and pore surface area would be very useful for modeling and simulating of transport and exchange processes. Thus, quantitative data on relevant soil structural features and their modification by soil management could be provided. The scope of this study was to analyze and quantify the development of soil structure in the subsoil depending on three different precrop species (alfalfa, chicory and fescue), at three depths (45, 60 and 75 cm) and three cultivation periods (1, 2 and 3 yrs) on an experimental field trial (Germany) with a Haplic Luvisol as major soil type. Morphological (air-filled porosity, pore surface area) and geometrical (pore diameter, connectivity, continuity, tortuosity) parameters were gathered with X-ray CT and evaluated with image analysis. Furthermore, the results were linked with air-capacity data from laboratory measurements to validate the data and with tortuosity/connectivity data from diffusion-based measurements. Air-filled porosity was highest for alfalfa (3 yrs, 75 cm). Tortuosity values ranged between 1.3 and 4.38, while alfalfa (3 yrs) showed the highest value, which may indicate structural development due to crack formation by enhanced root water uptake. An increase in accessible surfaces may improve water and nutrient supply for plants, whereas the high tortuosity values may also assume that oxygen supply is limited.

  18. Local structure of Fe in Fe-doped misfit-layered calcium cobaltite: An X-ray absorption spectroscopy study

    International Nuclear Information System (INIS)

    Prasoetsopha, Natkrita; Pinitsoontorn, Supree; Bootchanont, Atipong; Kidkhunthod, Pinit; Srepusharawoot, Pornjuk; Kamwanna, Teerasak; Amornkitbamrung, Vittaya; Kurosaki, Ken; Yamanaka, Shinsuke

    2013-01-01

    Polycrystalline Ca 3 Co 4−x Fe x O 9+δ ceramics (x=0, 0.01, 0.03, 0.05) were fabricated using a simple thermal hydro-decomposition method and a spark plasma sintering technique. Thermoelectric property measurements showed that increasing Fe concentration resulted in a decrease in electrical resistivity, thermopower and thermal conductivity, leading to an improvement in the dimensionless figure-of-merit, >35% for x=0.05 at 1073 K. An X-ray absorption spectroscopy technique was used to investigate the local structure of Fe ions in the Ca 3 Co 4−x Fe x O 9+δ structure for the first time. By fitting data from the extended X-ray absorption fine structure (EXAFS) spectra and analyzing the X-ray absorption near-edge structure (XANES) spectra incorporated with first principle simulation, it was shown that Fe was substituted for Co in the the Ca 2 CoO 3 (rocksalt, RS) layer rather than in the CoO 2 layer. Variation in the thermoelectric properties as a function of Fe concentration was attributed to charge transfer between the CoO 2 and the RS layers. The origin of the preferential Fe substitution site was investigated considering the ionic radii of Co and Fe and the total energy of the system. - Graphical abstract: The Fe K-edge XANES spectra of: (a) experimental result in comparison to the simulated spectra when Fe atoms were substituted in the RS layer; (b) with magnetic moment; (c) without magnetic moment, and in the CoO 2 layer; (d) with magnetic moment and (e) without magnetic moment. Highlights: • Synthesis, structural studies, and thermoelectric properties of Ca 3 Co 4−x Fe x O 9+δ . • Direct evidence for the local structure of the Fe ions in the Ca 3 Co 4−x Fe x O 9+δ using XAS analysis. • EXAFS and XANES analysis showed that Fe was likely to be situated in the RS layer structure. • Changes in TE property with Fe content was due to charge transfer between the CoO 2 and the RS layers. • Total energy calculation showed energetically favorable Fe

  19. Effect of X-rays on protein synthesis and RNA synthesis in adenovirus-infected cells

    International Nuclear Information System (INIS)

    Gorzkowski, B.; Majle, T.; Obrepalska, B.; Semkow, R.

    1977-01-01

    Ionizing radiation exerts a deteriorating effect on the rate of protein and RNA synthesis in HeLa cells. This effect is higher in cells infected with adenovirus, thus pointing to a higher radiosensitivity of viral syntheses compared with the cellular ones. (author)

  20. Structure of sodium above 100 GPa by single-crystal x-ray diffraction.

    Science.gov (United States)

    McMahon, M I; Gregoryanz, E; Lundegaard, L F; Loa, I; Guillaume, C; Nelmes, R J; Kleppe, A K; Amboage, M; Wilhelm, H; Jephcoat, A P

    2007-10-30

    At pressures above a megabar (100 GPa), sodium crystallizes in a number of complex crystal structures with unusually low melting temperatures, reaching as low as 300 K at 118 GPa. We have utilized this unique behavior at extreme pressures to grow a single crystal of sodium at 108 GPa, and have investigated the complex crystal structure at this pressure using high-intensity x-rays from the new Diamond synchrotron source, in combination with a pressure cell with wide angular apertures. We confirm that, at 108 GPa, sodium is isostructural with the cI16 phase of lithium, and we have refined the full crystal structure of this phase. The results demonstrate the extension of single-crystal structure refinement beyond 100 GPa and raise the prospect of successfully determining the structures of yet more complex phases reported in sodium and other elements at extreme pressures.

  1. Head structures of Priacma serrata Leconte (Coleptera, Archostemata) inferred from X-ray tomography.

    Science.gov (United States)

    Hörnschemeyer, Thomas; Beutel, Rolf G; Pasop, Freek

    2002-06-01

    Internal and external features of the head of Priacma serrata were studied with X-ray microtomography and with histological methods. The comparison of both techniques shows that X-ray tomography is a promising new technique for the investigation of insect anatomy. The still somewhat coarse resolution of the X-ray data is compensated for by advantages like the nondestructive and artifact-free data acquisition. The head of P. serrata and other adults of Archostemata is characterized by many derived features. Muscular features of Priacma, especially muscles of the labium and pharynx, differ strongly from what is found in other groups of Coleoptera. Several character states are considered as autapomorphies of Archostemata: scale-like surface structures, constricted neck, strongly reduced tentorium, and the plate-like, enlarged prementum. The scales provide a protecting surface pattern and may have evolved with a more exposed lifestyle. The enlarged prementum forms a lid, which closes the mouth and covers the ligula when it is pulled back by contraction of the unusually strong submento-premental muscle. The presence of four cone-shaped protuberances on the dorsal side of the head is considered an autapomorphy of Cupedidae. The galea with a narrow stalk and a round and pubescent distal galeomere is another autapomorphy of this family. It has probably evolved as an adaptation to pollen-feeding. The shape of the mandible of Cupedidae is plesiomorphic compared to what is found in adults of Ommatidae. The vertical arrangement of apical teeth is an autapomorphy of the latter family. The lateral insertion of the antenna in Priacma is a groundplan feature of Cupedidae. The dorsal shift is a synapomorphy of all other cupedid genera. A cladistic analysis of characters of the head and additional data resulted in the following branching pattern: ((Crowsoniella + (Omma + Tetraphalerus)) + (Micromalthus + (Priacma + (Paracupes + (Cupes + Tenomerga + Prolixocupes + Rhipsideigma

  2. Introduction to the application and limits of anomalous X-ray diffraction in the determination of partial structure factors

    International Nuclear Information System (INIS)

    Bienenstock, A.

    1993-01-01

    The use of anomalous X-ray scattering to obtain the first differences and partial structure factors normally obtained with isotopic substitution neutron diffraction is described and compared with the neutron technique. Both the problems associated with the X-ray technique (low-Z problems, scattering factor problems, Compton scattering problems, fluorescence problems, storage ring stability problems) and the situations in which it is highly valuable are discussed. 12 refs

  3. Electronic structure of human hemoglobin: ultrasoft X-ray emission study

    International Nuclear Information System (INIS)

    Soldatov, A.V.; Kravtsova, A.N.; Fedorovich, E.N.; Kurmaev, E.Z.; Moewes, A.

    2004-01-01

    Full text: The iron L 2,3 and carbon, nitrogen and oxygen Kα X-ray emission spectra (XES) of human hemoglobin have been recorded at the soft X-ray spectroscopy endstation on Undulator Beam line 8.0 at Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratory. The theoretical calculations of Fe L 3 -XES have been performed using ab initio code FEFF8.2. The calculations have been carried out for the structure of hemoglobin presented in PDB (entry 3HHB) as well as for the molecule with symmetrical heme plane. It was found that the Fe L 3 emission spectrum calculated for the ideal molecule agrees slightly better with the experiment as compared with those calculated for the real molecule. Thus, one can use the structure of the ideal molecule for theoretical Fe L 3 -XES simulations. The theoretical analysis has shown that the fist peak of experimental Fe L 3 - emission spectrum is enhanced by the nearest nitrogen atoms lying in heme plane around the central iron atom. The theoretical C K- and N K-XES spectra of hemoglobin have been calculated. A good agreement between theoretical and experimental spectra has been obtained. The distribution of the partial electronic densities of states in the valence and conduction bands of hemoglobin has been determined

  4. Heterophase fluctuation of omega phase and X-ray diffuse scattering from dual phase structure

    International Nuclear Information System (INIS)

    Farjami, Susan; Kubo, Hiroshi

    2003-01-01

    Heterophase fluctuation of athermal omega embryos has been analyzed by assuming a dual phase structure of omega embryos composed of omega and bcc matrix phase. The two-dimensional modulation of dual phase was suggested from the quantitative estimation of coherent free energy of omega embryos using microscopic theory of elasticity and the Landau anharmonic theory for phase transformation. The X-ray diffraction theory was developed in connection to the formation of omega embryos having the dual phase structure. The offset of the diffuse peak position from the ideal omega point in the X-ray diffraction pattern is attributed to the dual phase (incommensurate phase) of omega embryos. It was also shown that the ellipsoidal shape of the diffuse intensity tailing toward the fundamental spot of the matrix phase is originated from the equilibrium shape of the omega embryo. The quantitative estimation of elastic energy modulus (EEM) in the disordered bcc matrix and in the ordered bcc matrix indicates a difference in the deviation amount of the minimum point k(q m ) from the ideal omega point k(q ω ) and a difference in the elliptical shape of embryos

  5. X-ray structure of a sodium salt of digeneaside isolated from red alga Ceramium botryocarpum.

    Science.gov (United States)

    Claude, Audrey; Bondu, Stéphanie; Michaud, François; Bourgougnon, Nathalie; Deslandes, Eric

    2009-03-31

    X-ray diffraction analysis has been recently used to determine the crystal structure of the floridoside (2-O-alpha-d-galactopyranosylglycerol) isolated from red alga Palmaria palmata and Dilsea carnosa, respectively [Simon-Colin, C.; Michaud, F.; Léger, J.-M.; Deslandes, E. Carbohydr. Res.2003, 338, 2413-2416; Vonthron-Senechau, C.; Sopkova-de Oliveira Santos. J.; Mussio, I.; Rusig, A. M. Carbohydr. Res. 2008, 343, 2697-2698]. In this present study, a similar analysis was performed on another compound belonging to the glycopyranosyl-glycerols family present in red algae, digeneaside. The crystal structure of a hydrated sodium salt of digeneaside (sodium 2-O-alpha-d-mannopyranosyl-d-glycerate monohydrate) was determined by single-crystal X-ray diffraction analysis at 110+/-3K. The space group is C2 with Z=4, a=17.9315(12), b=6.2693(4), c=10.7805(7)A, beta=90.746(7) degrees .

  6. Characterization of nano-structure by small-angle X-ray and neutron scattering

    International Nuclear Information System (INIS)

    Ohnuma, Masato

    2017-01-01

    This paper outlines the cases when small-angle X-ray scattering method and small-angle neutron scattering method in transmission arrangement were applied to heterogeneity with low-volume rate (10% or below), such as nano-sized deposits and trace defects. In particular, it explains not only general analysis, but also the possibility of use of the small angle scattering method as a simple inspection method in nanostructure evaluation, as well as correspondence of small-angle scattering method with powder diffraction method in crystal structure evaluation. From the small-angle scattering profiles of a series of sample groups, we can judge which sample has the smallest nanostructure, by only comparing profiles without analysis. The object to be measured is a heterogeneous structure (void, second phase, crack, etc.) having a diameter of about 1 to several hundred nm present in a material. This paper also outlines the usual small-angle scattering analysis method, as well as further analysis using the difference between X-ray and neutron on scattering length contrast. (A.O.)

  7. Local structure of semicrystalline P3HT films probed by nanofocused coherent X-rays.

    Science.gov (United States)

    Kurta, Ruslan P; Grodd, Linda; Mikayelyan, Eduard; Gorobtsov, Oleg Y; Zaluzhnyy, Ivan A; Fratoddi, Ilaria; Venditti, Iole; Russo, Maria Vittoria; Sprung, Michael; Vartanyants, Ivan A; Grigorian, Souren

    2015-03-21

    The hidden structural properties of semicrystalline polymer films are revealed by nanofocused X-ray scattering studies. X-ray cross-correlation analysis (XCCA) is employed to diffraction patterns from blends of poly(3-hexylthiophene) (P3HT) with gold nanoparticles (AuNPs). Spatially resolved maps of orientational distribution of crystalline domains allow us to distinguish sample regions of predominant face-on morphology, with a continuous transition to edge-on morphology. The average size of crystalline domains was determined to be of the order of 10 nm. As compared to pristine P3HT film, the P3HT/AuNPs blend is characterized by substantial ordering of crystalline domains, which can be induced by Au nanoparticles. The inhomogeneous structure of the polymer film is clearly visualized on the spatially resolved nanoscale 2D maps obtained using XCCA. Our results suggest that the observed changes of the polymer matrix within crystalline regions can be attributed to nanoconfinement in the presence of gold nanoparticles.

  8. In-situ X-ray structure measurements on aerodynamically levitated high temperature liquids

    International Nuclear Information System (INIS)

    Weber, Richard; Benmore, Christopher; Mei Qiang; Wilding, Martin

    2009-01-01

    High energy, high flux X-ray sources enable new measurements of liquid and amorphous materials in extreme conditions. Aerodynamic levitation in combination with laser beam heating can be used to access high purity and non-equilibrium liquids at temperatures up to 3000 K. In this work, a small aerodynamic levitator was integrated with high energy beamline 11 ID-C at the Advanced Photon Source. Scattered X-rays were detected with a Mar345 image plate. The experiments investigated a series of binary in the CaO-Al 2 O 3 , MgO-SiO 2 , SiO 2 -Al 2 O 3 metal oxide compositions and pure SiO 2 . The results show that the liquids exhibit large changes in structure when the predominant network former is diluted. Measurements on glasses with the same compositions as the liquids suggest that significant structural rearrangement consistent with a fragile-strong transition occurs in these reluctant glass forming liquids as they vitrify.

  9. Layered structure analysis of multilayers by X-ray reflectometry using the Cu-Kβ line

    International Nuclear Information System (INIS)

    Usami, Katsuhisa; Ueda, Kazuhiro; Hirano, Tatsumi; Hoshiya, Hiroyuki; Narishige, Shinji.

    1997-01-01

    The suitability of X-ray reflectometry using the Cu-K β line for layered structure analysis of NiFe/Cu/NiFe/Ta layered films was studied. Structural parameters such as film thickness, density, and interface width can be determined more accurately than by Cu-K α1 X-ray reflectometry, owing to the abnormal dispersion effect. The standard deviations in determination of film thicknesses were within ±0.3% for NiFe and Ta films and ±0.03 nm for 2 nm Cu film. Those for the densities and interface widths were within ±2% and ±0.04 nm for all films, respectively. Analysis of some layered films regarding the change in Cu film thickness showed that in all these samples the density of the films most closely reflected the density of bulk material, and the interface width between the upper NiFe and Cu films increased with increasing Cu film thickness. (author)

  10. Conceptual Design of Dielectric Accelerating Structures for Intense Neutron and Monochromatic X-ray Sources

    Science.gov (United States)

    Blanovsky, Anatoly

    2004-12-01

    Bright compact photon sources, which utilize electron beam interaction with periodic structures, may benefit a broad range of medical, industrial and scientific applications. A class of dielectric-loaded periodic structures for hard and soft X-ray production has been proposed that would provide a high accelerating gradient when excited by an external RF and/or primary electron beam. Target-distributed accelerators (TDA), in which an additional electric field compensates for lost beam energy in internal targets, have been shown to provide the necessary means to drive a high flux subcritical reactor (HFSR) for nuclear waste transmutation. The TDA may also be suitable for positron and nuclear isomer production, X-ray lithography and monochromatic computer tomography. One of the early assumptions of the theory of dielectric wake-field acceleration was that, in electrodynamics, the vector potential was proportional to the scalar potential. The analysis takes into consideration a wide range of TDA design aspects including the wave model of observed phenomena, a layered compound separated by a Van der Waals gap and a compact energy source based on fission electric cells (FEC) with a multistage collector. The FEC is a high-voltage power source that directly converts the kinetic energy of the fission fragments into electrical potential of about 2MV.

  11. Evaluation of osteoporotic bone structure through synchrotron radiation X-ray microfluorescence images

    Energy Technology Data Exchange (ETDEWEB)

    Lima, I. [Nuclear Engineering Program/COPPE/UFRJ, P.O. Box 68509, Av. Horacio Macedo 2030, Sala I-133, Cidade Universitaria, 21941-914 Rio de Janeiro, RJ (Brazil)], E-mail: inaya@lin.ufrj.br; Anjos, M.J. [Nuclear Engineering Program/COPPE/UFRJ, P.O. Box 68509, Av. Horacio Macedo 2030, Sala I-133, Cidade Universitaria, 21941-914 Rio de Janeiro, RJ (Brazil); Physics Institute, UERJ (Brazil); Farias, M.L.F. [University Hospital, UFRJ (Brazil); Pantaleao, T.U.; Correa da Costa, V.M. [Biophysics Institute, UFRJ (Brazil); Lopes, R.T. [Nuclear Engineering Program/COPPE/UFRJ, P.O. Box 68509, Av. Horacio Macedo 2030, Sala I-133, Cidade Universitaria, 21941-914 Rio de Janeiro, RJ (Brazil)

    2008-12-15

    The abnormal accumulation or deficiency of trace elements may theoretically impair the formation of bone and contribute to osteoporosis. In this context, the knowledge of major and trace elements is very important in order to clarify many issues regarding diseases of the bone, such as osteoporosis, that remain unresolved. Several kinds of imaging techniques can be useful to access morphology and the minerals present in osteoporotic bones. In this work, synchrotron radiation X-ray microfluorescence was used as an X-ray imaging technique to investigate bone structures. Therefore, this research aims to improve the knowledge about some aspects of bone quality. The measurements were carried out at the Brazilian Synchrotron Laboratory Light Laboratory, in Brazil. A white beam with an energy range of 4-23 keV, a 45 deg./45 deg. geometry and a capillary optics were used. It was demonstrated that bone quality can and must be evaluated not only by considering the architecture of bones but also by taking into account the concentration and the distribution of minerals. Our results showed that the elemental distributions in bone zones on a micron scale were very helpful to understand functions in those structures.

  12. X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vitova, Tonya

    2008-02-15

    The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

  13. Morphological and structural characterization of PHBV/organoclay nanocomposites by small angle X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Carli, Larissa N., E-mail: lncarli@ucs.br [Instituto de Quimica, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves, 9500, Porto Alegre, 91501-970, RS (Brazil); Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, Rua Francisco Getulio Vargas, 1130, Caxias do Sul, 95070-560, RS (Brazil); Bianchi, Otavio, E-mail: obianchi@ucs.br [Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, Rua Francisco Getulio Vargas, 1130, Caxias do Sul, 95070-560, RS (Brazil); Machado, Giovanna, E-mail: giovannamachado@uol.com.br [Centro de Tecnologias Estrategicas do Nordeste, Av. Prof. Luiz Freire, 01, Cidade Universitaria, Recife, 50740-540, PE (Brazil); Programa de Pos-Graduacao de Materiais, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, Recife, 50670-901, PE (Brazil); Crespo, Janaina S., E-mail: jscrespo@ucs.br [Centro de Ciencias Exatas e Tecnologia, Universidade de Caxias do Sul, Rua Francisco Getulio Vargas, 1130, Caxias do Sul, 95070-560, RS (Brazil); Mauler, Raquel S., E-mail: raquel.mauler@ufrgs.br [Instituto de Quimica, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves, 9500, Porto Alegre, 91501-970, RS (Brazil)

    2013-03-01

    In this work, the morphological and structural behaviors of poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) nanocomposites were investigated using small angle X-ray scattering (SAXS), wide angle X-ray diffraction (WAXD) and transmission electron microscopy (TEM). The nanocomposites with 1, 3 and 5 wt.% of organically modified montmorillonite Cloisite Registered-Sign 30B (OMMT) were prepared by melt processing in a twin screw extruder using two different processing conditions (low and high shear intensity). The lamellar long period of the polymer was lower for the nanocomposites, with high polydispersity values. However, the crystalline thickness increased with the clay content and was independent of the processing conditions. This behavior resulted in a high linear crystallinity of the nanocomposites with 3 and 5 wt.% OMMT. The disruption factor ({beta}) was in agreement with the WAXD and TEM findings, indicating a good dispersion of the nanoparticles in the PHBV matrix with 3 wt.% of OMMT during the high shear intensity of melt processing. Highlights: Black-Right-Pointing-Pointer SAXS was used for morphological and crystalline studies of PHBV/OMMT nanocomposites. Black-Right-Pointing-Pointer The crystalline structure was influenced by the presence of clay. Black-Right-Pointing-Pointer The degree of clay dispersion in a polymer matrix was quantified. Black-Right-Pointing-Pointer The morphology comprised exfoliated particles, nanoscale and microscale clusters. Black-Right-Pointing-Pointer The results obtained by SAXS agreed well with TEM and WAXD results.

  14. Perlite-SO3H nanoparticles as an efficient and reusable catalyst for one-pot three-component synthesis of 1,2-dihydro-1-aryl-naphtho[1,2-e][1,3]oxazine-3-one derivatives under both microwave-assisted and thermal solvent-free conditions: Single crystal X-ray structure analysis and theoretical study

    Directory of Open Access Journals (Sweden)

    Ali Ramazani

    2016-01-01

    Full Text Available A general synthetic route for the synthesis of 1,2-dihydro-1-aryl-naphtho[1,2-e][1,3]oxazine-3-one derivatives has been developed using perlite-SO3H nanoparticles as efficient catalyst under both microwave-assisted and thermal solvent-free conditions. The combination of 2-naphthol, aldehyde and urea enabled the synthesis of 1,2-dihydro-1-aryl-naphtho[1,2-e][1,3]oxazine-3-one derivatives in the presence of perlite-SO3H nanoparticles in good to excellent yields. This method provides several advantages like simple work-up, environmentally benign, and shorter reaction times along with high yields. In order to explore the recyclability of the catalyst, the perlite-SO3H nanoparticles in solvent-free conditions were used as catalyst for the same reaction repeatedly and the change in their catalytic activity was studied. It was found that perlite-SO3H nanoparticles could be reused for four cycles with negligible loss of their activity. Single crystal X-ray structure analysis and theoretical studies also were investigated for 4i product. The electronic properties of the compound have been analyzed using DFT calculations (B3LYP/6-311+G*. The FMO analysis suggests that charge transfer takes place within the molecule and the HOMO is localized mainly on naphthalene and oxazinone rings whereas the LUMO resides on the naphthalene ring.

  15. X-ray CT Scanning Reveals Long-Term Copper Pollution Effects on Functional Soil Structure

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Homstrup, Martin

    Soil structure plays the main role in the ability of the soil to fulfill essential soil functions such as the root growth, rate of water infiltration and retention, transport of gaseous and chemicals/pollutants through the soil. Soil structure is a dynamic soil property and affected by various...... factors such as soil type, land use, and soil contamination. In this study, we quantified the soil structure using X-ray CT scanning and revealed the effect of a long history of Copper (Cu) pollution on it. A fallow field at Hygum Denmark provides this opportunity as it had a long history of Copper...... columns, macroporosity showed a significant decrease along the column depth. The results suggest that Cu contamination has a strong impact on soil structure and hence on all soil physical and biological processes....

  16. Local layer structure of smectic liquid crystals by X-ray micro-diffraction

    CERN Document Server

    Takanishi, Y

    2003-01-01

    The local layer structure of smectic liquid crystal has been measured using time-resolved synchrotron X-ray micro-diffraction. Typical layer disorders observed in surface stabilized (anti-) ferroelectric liquid crystals, i.e. a stripe texture, a needed-like defect and a zigzag defect, are directly analyzed. The detailed analysis slows that the surface anchoring force due to the interaction between the liquid crystal molecule and the alignment thin film plays an important role to realize both the static and dynamic local layer structures. The layer structure of the circular domain observed in the liquid crystal of bent-shaped molecules found to depend on the applied electric field though the optical micrograph shows little difference. The frustrated, double and single layer structures of the bent-shaped molecule liquid crystal are determined depending on the terminal alkyl chain length. (author)

  17. Growth, structure, and performance of depth-graded W/Si multilayers for hard x-ray optics

    DEFF Research Database (Denmark)

    Windt, D.L.; Christensen, Finn Erland; Craig, W.W.

    2000-01-01

    We describe the development of depth-graded W/Si multilayer films prepared by magnetron sputtering for use as broad-band reflective coatings for hard x-ray optics. We have used specular and nonspecular x-ray reflectance analysis to characterize the interface imperfections in both periodic and depth......), and somewhat larger interface widths (i.e., sigma=0.35-0.4 nm) for structures grown at higher Ar pressures, higher background pressures, or with larger target-to-substrate distances. We find no variation in interface widths with magnetron power. Nonspecular x-ray reflectance analysis and TEM suggest....... X-ray reflectance analysis was also used to measure the variation in the W and Si deposition rates with bilayer thickness: we find that the W and Si layer thicknesses are nonlinear with the deposition times, and we discuss possible mechanisms responsible for this nonlinearity. Finally, hard x...

  18. Very large-scale structures in sintered silica aerogels as evidenced by atomic force microscopy and ultra-small angle X-ray scattering experiments

    CERN Document Server

    Marliere, C; Etienne, P; Woignier, T; Dieudonné, P; Phalippou, J

    2001-01-01

    During the last few years the bulk structure of silica aerogels has been extensively studied mainly by scattering techniques (neutrons, X-rays, light). It has been shown that small silica particles aggregate to constitute a fractal network. Its spatial extension and fractal dimension are strongly dependent on the synthesis conditions (e.g., pH of gelifying solutions). These typical lengths range from 1 to 10 nm. Ultra-small angle X-ray scattering (USAXS) and atomic force microscopy (AFM) experiments have been carried out on aerogels at different steps of densification. The results presented in this paper reveal the existence of a spatial arrangement of the solid part at a very large length scale. The evolution of this very large-scale structure during the densification process has been studied and reveals a contraction of this macro-structure made of aggregates of clusters. (16 refs).

  19. Three-dimensional magnetization structures revealed with X-ray vector nanotomography

    Science.gov (United States)

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Gliga, Sebastian; Holler, Mirko; Raabe, Jörg; Heyderman, Laura J.

    2017-07-01

    In soft ferromagnetic materials, the smoothly varying magnetization leads to the formation of fundamental patterns such as domains, vortices and domain walls. These have been studied extensively in thin films of thicknesses up to around 200 nanometres, in which the magnetization is accessible with current transmission imaging methods that make use of electrons or soft X-rays. In thicker samples, however, in which the magnetization structure varies throughout the thickness and is intrinsically three dimensional, determining the complex magnetic structure directly still represents a challenge. We have developed hard-X-ray vector nanotomography with which to determine the three-dimensional magnetic configuration at the nanoscale within micrometre-sized samples. We imaged the structure of the magnetization within a soft magnetic pillar of diameter 5 micrometres with a spatial resolution of 100 nanometres and, within the bulk, observed a complex magnetic configuration that consists of vortices and antivortices that form cross-tie walls and vortex walls along intersecting planes. At the intersections of these structures, magnetic singularities—Bloch points—occur. These were predicted more than fifty years ago but have so far not been directly observed. Here we image the three-dimensional magnetic structure in the vicinity of the Bloch points, which until now has been accessible only through micromagnetic simulations, and identify two possible magnetization configurations: a circulating magnetization structure and a twisted state that appears to correspond to an ‘anti-Bloch point’. Our imaging method enables the nanoscale study of topological magnetic structures in systems with sizes of the order of tens of micrometres. Knowledge of internal nanomagnetic textures is critical for understanding macroscopic magnetic properties and for designing bulk magnets for technological applications.

  20. Synthesis, spectroscopy, X-ray crystallography, and DFT computations of nanosized phosphazenes

    Czech Academy of Sciences Publication Activity Database

    Shariatinia, Z.; Moghadam, E.J.; Maghsoudi, N.; Mousavi, H.S.M.; Dušek, Michal; Eigner, Václav

    2015-01-01

    Roč. 641, č. 5 (2015), s. 967-978 ISSN 0044-2313 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : phosphazene * ultrasonic * nanoparticle * x-ray crystallography * DFT calculation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.261, year: 2015

  1. Monitoring of the YBa2Cu3O7 synthesis by X-ray powder diffraction

    International Nuclear Information System (INIS)

    Gonzalez G, J.C.; Osorio A, Ana M.; Bejar R, Manuel; Bustamante D, Angel

    2011-01-01

    We study the formation dynamics of the YBa 2 Cu 3 O 7 superconducting phase, from Y, Ba and Cu acetates prepared by the Sol-Gel method. The monitoring is done through by Rietveld refinement of the X-ray powder diffractograms at the end product resulting in three specific stages of the thermal treatment: (a) precursor, (b) calcined and (c) sinterized. (author).

  2. Synthesis and Single Crystal X-Ray Crystallographic Analysis of 2 ...

    African Journals Online (AJOL)

    dihydropyrimidin-1-ium) tetrachlorocobaltate(II) [H2pymo]2[CoCl4]. The compound was re-crystallized in diethyl ether to obtain a suitable single crystal for X-ray diffraction analysis which revealed a molecule crystallizes in the orthorhombic ...

  3. X-ray irradiation-induced structural changes on Single Wall Carbon Nanotubes

    Science.gov (United States)

    Bardi, N.; Jurewicz, I.; King, A. K.; Alkhorayef, M. A.; Bradley, D.; Dalton, A. B.

    2017-11-01

    Dosimetry devices based on Carbon Nanotubes are a promising new technology. In particular using devices based on single wall Carbon Nanotubes may offer a tissue equivalent response with the possibility for device miniaturisation, high scale manufacturing and low cost. An important precursor to device fabrication requires a quantitative study of the effects of X-ray radiation on the physical and chemical properties of the individual nanotubes. In this study, we concentrate on the effects of relatively low doses, 20 cGy and 45 cGy , respectively. We use a range of characterization techniques including scanning electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy to quantify the effects of the radiation dose on inherent properties of the nanotubes. Specifically we find that the radiation exposure results in a reduction in the sp2 nature of the nanotube bond structure. Moreover, our analysis indicates that the exposure results in nanotubes that have an increased defect density which ultimately effects the electrical properties of the nanotubes.

  4. Microscopic bosonization of band structures: x-ray processes beyond the Fermi edge

    Science.gov (United States)

    Snyman, Izak; Florens, Serge

    2017-11-01

    Bosonization provides a powerful analytical framework to deal with one-dimensional strongly interacting fermion systems, which makes it a cornerstone in quantum many-body theory. However, this success comes at the expense of using effective infrared parameters, and restricting the description to low energy states near the Fermi level. We propose a radical extension of the bosonization technique that overcomes both limitations, allowing computations with microscopic lattice Hamiltonians, from the Fermi level down to the bottom of the band. The formalism rests on the simple idea of representating the fermion kinetic term in the energy domain, after which it can be expressed in terms of free bosonic degrees of freedom. As a result, one- and two-body fermionic scattering processes generate anharmonic boson-boson interactions, even in the forward channel. We show that up to moderate interaction strengths, these non-linearities can be treated analytically at all energy scales, using the x-ray emission problem as a showcase. In the strong interaction regime, we employ a systematic variational solution of the bosonic theory, and obtain results that agree quantitatively with an exact diagonalization of the original one-particle fermionic model. This provides a proof of the fully microscopic character of bosonization, on all energy scales, for an arbitrary band structure. Besides recovering the known x-ray edge singularity at the emission threshold, we find strong signatures of correlations even at emission frequencies beyond the band bottom.

  5. X-ray detector

    International Nuclear Information System (INIS)

    Whetten, N.R.; Houston, J.M.

    1977-01-01

    An ionization chamber for use in determining the spatial distribution of x-ray photons in tomography systems comprises a plurality of substantially parallel, planar anodes separated by parallel, planar cathodes and enclosed in a gas of high atomic weight at a pressure from approximately 10 atmospheres to approximately 50 atmospheres. The cathode and anode structures comprise metals which are substantially opaque to x-ray radiation and thereby tend to reduce the resolution limiting effects of x-ray fluoresence in the gas. In another embodiment of the invention the anodes comprise parallel conductive bars disposed between two planar cathodes. Guard rings eliminate surface leakage currents between adjacent electrodes. 8 figures

  6. Extended x-ray absorption fine structure: Studies of zinc-neutralized sulfonated polystyrene ionomers

    International Nuclear Information System (INIS)

    Ding, Y.S.; Yarusso, D.J.; Pan, H.K.D.; Cooper, S.L.

    1984-01-01

    Extended x-ray absorption fine structure (EXAFS) measurements were performed on a series of zinc-neutralized sulfonated polystyrene ionomers and the local structure around the zinc atom was determined. An interference effect in the EXAFS signal between sulfur and oxygen atoms was found to be significant in these materials. A model for the local structure in the zinc-neutralized sulfonated polystyrene ionomers is proposed which suggests a highly ordered tetrahedral coordination of oxygen around the zinc atoms at a distance of 1.97 +- 0.02 A. In addition there are four sulfur atoms and four oxygen atoms at a distance of 3.15 +- 0.05 A. No zinc-zinc coordination within 5 A was detected in this study

  7. Investigation of nanoscale structures by small-angle X-ray scattering in a radiochromic dosimeter

    DEFF Research Database (Denmark)

    Skyt, Peter Sandegaard; Jensen, Grethe Vestergaard; Wahlstedt, Isak Hannes

    2014-01-01

    This study examines the nanoscale structures in a radiochromic dosimeter that was based on leuco-malachite-green dye and the surfactant sodium dodecyl sulfate (SDS) suspended in a gelatin matrix. Small-angle X-ray scattering was used to investigate the structures of a range of compositions...... of the dosimeter. When omitting gelatin, ellipsoidal micelles of SDS were formed with a core radius near 15 Å, an eccentricity of 1.6, and a head-group shell thickness near 7 Å. Gelatin significantly changed the micelles to a cylindrical shape with around three times lower core radius and four times larger shell...... thickness, which shows that the gelatin is present in the shell and the outer part of the core. Insight into the detailed structure might help to improve the dosimeter performance and increase the dose response to clinically relevant dose levels....

  8. X-ray Crystallography Facility

    Science.gov (United States)

    2000-01-01

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

  9. X-rays and magnetism

    International Nuclear Information System (INIS)

    Fischer, Peter; Ohldag, Hendrik

    2015-01-01

    Magnetism is among the most active and attractive areas in modern solid state physics because of intriguing phenomena interesting to fundamental research and a manifold of technological applications. State-of-the-art synthesis of advanced magnetic materials, e.g. in hybrid structures paves the way to new functionalities. To characterize modern magnetic materials and the associated magnetic phenomena, polarized x-rays have emerged as unique probes due to their specific interaction with magnetic materials. A large variety of spectroscopic and microscopic techniques have been developed to quantify in an element, valence and site-sensitive way properties of ferro-, ferri-, and antiferromagnetic systems, such as spin and orbital moments, and to image nanoscale spin textures and their dynamics with sub-ns time and almost 10 nm spatial resolution. The enormous intensity of x-rays and their degree of coherence at next generation x-ray facilities will open the fsec time window to magnetic studies addressing fundamental time scales in magnetism with nanometer spatial resolution. This review will give an introduction into contemporary topics of nanoscale magnetic materials and provide an overview of analytical spectroscopy and microscopy tools based on x-ray dichroism effects. Selected examples of current research will demonstrate the potential and future directions of these techniques. (report on progress)

  10. Fine surface structure of unfixed and hydrated macrophages observed by laser-plasma x-ray contact microscopy

    International Nuclear Information System (INIS)

    Yamamoto, Yoshimasa; Friedman, Herman; Yoshimura, Hideyuki; Kinjo, Yasuhito; Shioda, Seiji; Debari, Kazuhiro; Shinohara, Kunio; Rajyaguru, Jayshree; Richardson, Martin

    2000-01-01

    A compact, high-resolution, laser-plasma, x-ray contact microscope using a table-top Nd:glass laser system has been developed and utilized for the analysis of the surface structure of live macrophages. Fine fluffy surface structures of murine peritoneal macrophages, which were live, hydrolyzed and not sliced and stained, were observed by the x-ray microscope followed by analysis using an atomic force microscopy. In order to compare with other techniques, a scanning electron microscopy (SEM) was utilized to observe the surface structure of the macrophages. The SEM offered a fine whole cell image of the same macrophages, which were fixed and dehydrated, but the surfaces were ruffled and different from that of x-ray images. A standard light microscope was also utilized to observe the shape of live whole macrophages. Light microscopy showed some fluffy surface structures of the macrophages, but the resolution was too low to observe the fine structures. Thus, the findings of fine fluffy surface structures of macrophages by x-ray microscopy provide valuable information for studies of phagocytosis, cell spreading and adherence, which are dependent on the surface structure of macrophages. Furthermore, the present study also demonstrates the usefulness of x-ray microscopy for analysis of structures of living cells

  11. Structural Characterization of Doped GaSb Single Crystals by X-ray Topography

    Energy Technology Data Exchange (ETDEWEB)

    Honnicke, M.G.; Mazzaro, I.; Manica, J.; Benine, E.; M da Costa, E.; Dedavid, B. A.; Cusatis, C.; Huang, X. R.

    2009-09-13

    We characterized GaSb single crystals containing different dopants (Al, Cd and Te), grown by the Czochralski method, by x-ray topography and high angular resolution x-ray diffraction. Lang topography revealed dislocations parallel and perpendicular to the crystal's surface. Double-crystal GaSb 333 x-ray topography shows dislocations and vertical stripes than can be associated with circular growth bands. We compared our high-angular resolution x-ray diffraction measurements (rocking curves) with the findings predicted by the dynamical theory of x-ray diffraction. These measurements show that our GaSb single crystals have a relative variation in the lattice parameter ({Delta}d/d) on the order of 10{sup -5}. This means that they can be used as electronic devices (detectors, for example) and as x-ray monochromators.

  12. The Protein Structure Factory X-ray Diffraction Beamlines at BESSY - Results from structural studies of human proteins

    International Nuclear Information System (INIS)

    Mueller, U.

    2004-01-01

    The Protein Structure Factory is one of the large scale structural genomics projects in Europe. The PSF follows the integrated approach to gain insight into the three dimensional structure of human proteins by X-ray diffraction methods. Therefore, synchrotron based X-ray data collection facilities, including two tunable energy beamlines and one fixed energy beamline are set into operation at the Berlin electron storage ring BESSY. Attached to these beamlines and experimental end-stations, a dedicated infrastructure was established in order to provide optimal conditions for carrying out experiments. Within the first year operation, this new facility did increase the availability of high brilliance PX-beamtime considerably for the structure biology community within Europe. The experimental usage of anomalous dispersion techniques enabled us to analyze the three dimensional structure for a number of human proteins. (author)

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. 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

  14. The crystal structure of benzoic acid: a redetermination with X-rays at room temperature

    International Nuclear Information System (INIS)

    Feld, R.; Lehmann, M.S.; Muir, K.W.; Speakman, J.C.

    1981-01-01

    The crystal structure of benzoic acid, C 6 H 5 CO 2 H, has been redetermined by X-ray diffraction at room temperature. Extensive neutron-diffraction measurements have also been made; by single-crystal methods at room temperature and 130 K; and, at 130 K and 5 K, by powder-profile analysis on C 6 D 5 CO 2 H. The structure consists of centrosymmetric dimers, in which two molecules are linked by a pair of hydrogen bonds between their carboxyl groups. Better precision attaches to the X-ray results. Full-matrix refinement, on 1011 independent reflexions, converged at R = 3.7%. This refinement was indeed based on a model that was formally ordered, so far as concerns all atoms except the acidic hydrogen. However the structural results implied an averaged molecule, with the C - O distances 1.258, 1.268(2)Angstroem and the C - C - O angles 118.7, 117.8(1) 0 ; and the acidic hydrogen appeared as two half atoms on the hydrogen bond, 0.9 Angstroem from each oxygen atom. These findings are most simply interpreted as due to disorder; the two configurations, A and B (of Fig. 1), occur randomly and in nearly equal proportions. Owing to difficulties inherent in the crystal texture of benzoic acid, the neutron results were less satisfactory. Large single crystals were affected by twinning. Though the powder method avoids this difficulty, the structure, further confused by modulation, is rather too complicated for profile refinement. At 5 K however, the structure may be ordered, consisting wholly of dimers in the A-configuration. (orig.)

  15. Speciation and localization of Zn in the hyperaccumulator Sedum alfredii by extended X-ray absorption fine structure and micro-X-ray fluorescence.

    Science.gov (United States)

    Lu, Lingli; Liao, Xingcheng; Labavitch, John; Yang, Xiaoe; Nelson, Erik; Du, Yonghua; Brown, Patrick H; Tian, Shengke

    2014-11-01

    Differences in metal homeostasis among related plant species can give important information of metal hyperaccumulation mechanisms. Speciation and distribution of Zn were investigated in a hyperaccumulating population of Sedum alfredii by using extended X-ray absorption fine structure and micro-synchrotron X-ray fluorescence (μ-XRF), respectively. The hyperaccumulator uses complexation with oxygen donor ligands for Zn storage in leaves and stems, and variations in the Zn speciation was noted in different tissues. The dominant chemical form of Zn in leaves was most probably a complex with malate, the most prevalent organic acid in S. alfredii leaves. In stems, Zn was mainly associated with malate and cell walls, while Zn-citrate and Zn-cell wall complexes dominated in the roots. Two-dimensional μ-XRF images revealed age-dependent differences in Zn localization in S. alfredii stems and leaves. In old leaves of S. alfredii, Zn was high in the midrib, margin regions and the petiole, whereas distribution of Zn was essentially uniform in young leaves. Zinc was preferentially sequestered by cells near vascular bundles in young stems, but was highly localized to vascular bundles and the outer cortex layer of old stems. The results suggest that tissue- and age-dependent variations of Zn speciation and distribution occurred in the hyperaccumulator S. alfredii, with most of the Zn complexed with malate in the leaves, but a shift to cell wall- and citric acid-Zn complexes during transportation and storage in stems and roots. This implies that biotransformation in Zn complexation occurred during transportation and storage processes in the plants of S. alfredii. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  16. X-ray magnetic microscopy for correlations between magnetic domains and crystal structure

    International Nuclear Information System (INIS)

    Denbeaux, G.; Anderson, E.; Bates, B.; Chao, W.; Liddle, J.A.; Harteneck, B.; Pearson, A.; Salmassi, F.; Schneider, G.; Fischer, P.; Eimuller, T.; Taylor, S.; Chang, H.; Kusinski, G.J.

    2002-01-01

    Accurately determining the resolution of x-ray microscopes has been a challenge because good test patterns for x-ray microscopy have been hard to make. We report on a sputter-deposited multilayer imaged in cross section as a test pattern with small features and high aspect ratios. One application of high-resolution imaging is magnetic materials. Off-axis bend magnet radiation is known to have a component of circular polarization which can be used for x-ray magnetic circular dichroism. We calculate the integrated circular polarization collected by the illumination optics in the XM-1 full-field x-ray microscope. (authors)

  17. The structure of para-toluidine by X-ray and neutron diffraction

    International Nuclear Information System (INIS)

    Bertinotti, A.L.

    1965-12-01

    The crystal and molecular structure of para-toluidine has been solved by X-ray and neutron diffraction counter techniques. The molecules are arranged in the form of infinite chains in the crystal, each molecule being linked to two neighbours by hydrogen bonds. The presence of the H bonds makes clear the difference in the melting points between para-toluidine and benzene hydrocarbons of related symmetry and molecular weight. Their direction accounts for the (001) cleavage and the growth anisotropy of crystals from supersaturated vapour phase. A structure-seeking method by computer has been elaborated, using lattice energy calculations applied to molecules treated as rigid bodies and making use of a simplex method for function minimization without calculation of derivatives. The way the available information is handled allows to increase the range of convergence, as shown in the case of para-toluidine. (author) [fr

  18. Production of RXLR effector proteins for structural analysis by X-ray crystallography.

    Science.gov (United States)

    Hughes, Richard K; Banfield, Mark J

    2014-01-01

    Structural analysis of RXLR effector proteins from oomycete plant pathogens is an emerging area of research. These studies are aimed at understanding the molecular basis of how these proteins manipulate plant cells to promote infection and also to help define how they can lead to activation of the plant innate immune system. Here, we describe a medium-throughput procedure for cloning and expression testing oomycete RXLR proteins in Escherichia coli. We also describe methods for purification of soluble protein and crystallization, with the aim of determining three-dimensional structures by X-ray crystallography. The procedures are generally applicable to any research program where the production of soluble recombinant protein in E. coli has proven difficult, or where there is a desire to evaluate E. coli thoroughly as a host before considering alternative hosts for heterologous expression.

  19. Probing chemistry within the membrane structure of wood with soft X-ray spectral microscopy

    International Nuclear Information System (INIS)

    Cody, George D.

    2000-01-01

    Scanning Transmission Soft X-ray spectral microscopy on Carbon's 1s absorption edge reveals the distribution of structural biopolymers within cell membrane regions of modern cedar and oak. Cellulose is extremely susceptible to beam damage. Spectroscopic studies of beam damage reveals that the chemical changes resulting from secondary electron impact may be highly selective and is consistent with hydroxyl eliminations and structural rearrangement of pyranose rings in alpha-cellulose to hydroxyl substituted γ pyrones. A study of acetylated cellulose demonstrates significantly different chemistry; principally massive decarboxylation. Defocusing the beam to a 2 μm spot size allows for the acquisition of 'pristine' cellulose spectra. Spectral deconvolution is used to assess the distribution of lignin and cellulose in the different regions of the cell membrane. Using the intensity of the hydroxylated aromatic carbons 1s-π * transition, the ratio of coniferyl and syringyl based lignin within the middle lamellae and secondary cell wall of oak, an angiosperm can be determined

  20. Variability: A X-ray ruler for the AGN structure model

    Directory of Open Access Journals (Sweden)

    Guainazzi M.

    2012-12-01

    Full Text Available Validating our understanding of the innermost structure of Active Galactic Nuclei (AGN would require resolving sub-parsec scales. Lacking adequate direct imaging, X-ray astronomy can still contribute to this undertaking through the study of spectral variability on time-scales from days to years. This bears information on the location of gaseous and dusty systems in the innermost regions around the accreting supermassive black hole. In this paper I discuss the application of this concept in two specific contexts: a “fast” column density variations in heavily obscured AGN; b reverberation of optically-thick reprocessing. These results lend support to a scenario where obscuration and optically thick reprocessing are due to a variety of different systems, ranging from the Broad Line Regions to a clumpy structure extended on larger scales up to hundreds of parsecs.

  1. X-ray Tomography Characterisation of Lattice Structures Processed by Selective Electron Beam Melting

    Directory of Open Access Journals (Sweden)

    Everth Hernández-Nava

    2017-08-01

    Full Text Available Metallic lattice structures intentionally contain open porosity; however, they can also contain unwanted closed porosity within the structural members. The entrained porosity and defects within three different geometries of Ti-6Al-4V lattices, fabricated by Selective Electron Beam Melting (SEBM, is assessed from X-ray computed tomography (CT scans. The results suggest that horizontal struts that are built upon loose powder show particularly high (~20 × 10−3 vol % levels of pores, as do nodes at which many (in our case 24 struts meet. On the other hand, for struts more closely aligned (0° to 54° to the build direction, the fraction of porosity appears to be much lower (~0.17 × 10−3% arising mainly from pores contained within the original atomised powder particles.

  2. Solution x-ray scattering and structure formation in protein dynamics

    Science.gov (United States)

    Nasedkin, Alexandr; Davidsson, Jan; Niemi, Antti J.; Peng, Xubiao

    2017-12-01

    We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

  3. Electronic structure, charge distribution and X-ray emission spectra of V3Si

    International Nuclear Information System (INIS)

    Anisimov, V.I.; Gubanov, V.A.; Ivanovskii, A.L.; Kurmaev, E.Z.; Weber, J.; Lacroix, R.

    1979-01-01

    Cluster calculations of the electronic structure and charge distribution in V 3 Si have been performed using two different molecular orbital methods: a semiempirical LCAO and the MS Xα model. The results are compared with X-ray emission spectra and band structure calculations. An analysis of the calculated electronic distribution reveals a charge transfer from Si-atoms to V-atoms, the additional charge on a V-atom being 0.6e (LCAO) and 0.4e (MS Xα method). The results are in good agreement with experiment, which indicates that the cluster approach is adequate for the description of charge distributions and spectra characteristics of the A-15 compounds. (author)

  4. Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering.

    Science.gov (United States)

    Chen, Gang; Modestino, Miguel A; Poon, Billy K; Schirotzek, André; Marchesini, Stefano; Segalman, Rachel A; Hexemer, Alexander; Zwart, Peter H

    2012-09-01

    A fluctuation X-ray scattering experiment has been carried out on platinum-coated gold nanoparticles randomly oriented on a substrate. A complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles randomly oriented about a single axis is demonstrated. This algorithm operates on angular correlations among the measured intensity distributions and recovers the angular correlation functions of a single particle from measured diffraction patterns. Taking advantage of the cylindrical symmetry of the nanoparticles, a cylindrical slice model is proposed to reconstruct the structure of the nanoparticles by fitting the experimental ring angular auto-correlation and small-angle scattering data obtained from many scattering patterns. The physical meaning of the refined structure is discussed in terms of their statistical distributions of the shape and electron density profile.

  5. The Crystal Structure of the Malaria Pigment Hemozoin as Elucidated by X-ray Powder Diffraction

    DEFF Research Database (Denmark)

    Straasø, Tine

    in the eradication of malaria. This thesis is a step towards that goal. When examining red blood cells from an infected person under a microscope dark pigment is observed. This dark pigment is actually small crystals called hemozoin. Hemozoin is a by-product formed by the parasite and a necessity for parasitic......Malaria is a widespread and severe disease caused by an infection by the parasite of the genus Plasmodium, the lifecycle of which is very complex. During its lifecycle the parasite resides in both a mosquito and a human host. If this cycle can be disrupted at any point, it will result...... survival. Successful inhibition of hemozoin crystallization will lead to parasitic death and thus break the cycle. The aim of this thesis is to elucidate the structure of hemozoin by means of X-ray diffraction techniques. Knowledge of the structure will help facilitate intelligent drug design in the future...

  6. A method for measuring the time structure of synchrotron x-ray beams

    International Nuclear Information System (INIS)

    Moses, W.W.; Derenzo, S.E.

    1989-08-01

    We describe a method employing a plastic scintillator coupled to a fast photomultiplier tube to generate a timing pulse from the x-ray bursts emitted from a synchrotron radiation source. This technique is useful for performing synchrotron experiments where detailed knowledge of the timing distribution is necessary, such as time resolved spectroscopy or fluorescence lifetime experiments. By digitizing the time difference between the timing signal generated on one beam crossing with the timing signal generated on the next beam crossing, the time structure of a synchrotron beam can be analyzed. Using this technique, we have investigated the single bunch time structure at the National Synchrotron Light Source (NSLS) during pilot runs in January, 1989, and found that the majority of the beam (96%) is contained in one rf bucket, while the remainder of the beam (4%) is contained in satellite rf buckets preceeding and following the main rf bucket by 19 ns. 1 ref., 4 figs

  7. X-ray structural studies of quinone reductase 2 nanomolar range inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Pegan, Scott D.; Sturdy, Megan; Ferry, Gilles; Delagrange, Philippe; Boutin, Jean A.; Mesecar, Andrew D. (IdRS); (Purdue); (Colorado); (UIC)

    2011-09-06

    Quinone reductase 2 (QR2) is one of two members comprising the mammalian quinone reductase family of enzymes responsible for performing FAD mediated reductions of quinone substrates. In contrast to quinone reductase 1 (QR1) which uses NAD(P)H as its co-substrate, QR2 utilizes a rare group of hydride donors, N-methyl or N-ribosyl nicotinamide. Several studies have linked QR2 to the generation of quinone free radicals, several neuronal degenerative diseases, and cancer. QR2 has been also identified as the third melatonin receptor (MT3) through in cellulo and in vitro inhibition of QR2 by traditional MT3 ligands, and through recent X-ray structures of human QR2 (hQR2) in complex with melatonin and 2-iodomelatonin. Several MT3 specific ligands have been developed that exhibit both potent in cellulo inhibition of hQR2 nanomolar, affinity for MT3. The potency of these ligands suggest their use as molecular probes for hQR2. However, no definitive correlation between traditionally obtained MT3 ligand affinity and hQR2 inhibition exists limiting our understanding of how these ligands are accommodated in the hQR2 active site. To obtain a clearer relationship between the structures of developed MT3 ligands and their inhibitory properties, in cellulo and in vitro IC{sub 50} values were determined for a representative set of MT3 ligands (MCA-NAT, 2-I-MCANAT, prazosin, S26695, S32797, and S29434). Furthermore, X-ray structures for each of these ligands in complex with hQR2 were determined allowing for a structural evaluation of the binding modes of these ligands in relation to the potency of MT3 ligands.

  8. X-ray structural studies of quinone reductase 2 nanomolar range inhibitors.

    Science.gov (United States)

    Pegan, Scott D; Sturdy, Megan; Ferry, Gilles; Delagrange, Philippe; Boutin, Jean A; Mesecar, Andrew D

    2011-07-01

    Quinone reductase 2 (QR2) is one of two members comprising the mammalian quinone reductase family of enzymes responsible for performing FAD mediated reductions of quinone substrates. In contrast to quinone reductase 1 (QR1) which uses NAD(P)H as its co-substrate, QR2 utilizes a rare group of hydride donors, N-methyl or N-ribosyl nicotinamide. Several studies have linked QR2 to the generation of quinone free radicals, several neuronal degenerative diseases, and cancer. QR2 has been also identified as the third melatonin receptor (MT3) through in cellulo and in vitro inhibition of QR2 by traditional MT3 ligands, and through recent X-ray structures of human QR2 (hQR2) in complex with melatonin and 2-iodomelatonin. Several MT3 specific ligands have been developed that exhibit both potent in cellulo inhibition of hQR2 nanomolar, affinity for MT3. The potency of these ligands suggest their use as molecular probes for hQR2. However, no definitive correlation between traditionally obtained MT3 ligand affinity and hQR2 inhibition exists limiting our understanding of how these ligands are accommodated in the hQR2 active site. To obtain a clearer relationship between the structures of developed MT3 ligands and their inhibitory properties, in cellulo and in vitro IC₅₀ values were determined for a representative set of MT3 ligands (MCA-NAT, 2-I-MCANAT, prazosin, S26695, S32797, and S29434). Furthermore, X-ray structures for each of these ligands in complex with hQR2 were determined allowing for a structural evaluation of the binding modes of these ligands in relation to the potency of MT3 ligands. Copyright © 2011 The Protein Society.

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

    Science.gov (United States)

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

    2016-01-01

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

  10. Structural characterization of cellulosic materials using x-ray and neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Penttila, P.

    2013-11-01

    Cellulosic biomass can be used as a feedstock for sustainable production of biofuels and various other products. A complete utilization of the raw material requires understanding on its structural aspects and their role in the various processes. In this thesis, x-ray and neutron scattering methods were applied to study the structure of various cellulosic materials and how they are affected in different processes. The obtained results were reviewed in the context of a model for the cellulose nanostructure. The dimensions of cellulose crystallites and the crystallinity were determined with wide-angle x-ray scattering (WAXS), whereas the nanoscale fibrillar structure of cellulose was characterized with small-angle x-ray and neutron scattering (SAXS and SANS). The properties determined with the small-angle scattering methods included specific surface areas and distances characteristic of the packing of cellulose microfibrils. Also other physical characterization methods, such as x-ray microtomography, infrared spectroscopy, and solid-state NMR were utilized in this work. In the analysis of the results, a comprehensive understanding of the structural changes throughout a range of length scales was aimed at. Pretreatment of birch sawdust by pressurized hot water extraction was observed to increase the crystal width of cellulose, as determined with WAXS, even though the cellulose crystallinity was slightly decreased. A denser packing of microfibrils caused by the removal of hemicelluloses and lignin in the extraction was evidenced by SAXS. This resulted in the opening of new pores between the microfibril bundles and an increase of the specific surface area. Enzymatic hydrolysis of microcrystalline cellulose (MCC) did not lead to differences in the average crystallinity or crystal size of the hydrolysis residues, which was explained to be caused by limitations due to the large size of the enzymes as compared to the pores inside the fibril aggregates. The SAXS intensities

  11. Structural changes of green roof growing substrate layer studied by X-ray CT

    Science.gov (United States)

    Jelinkova, Vladimira; Sacha, Jan; Dohnal, Michal; Snehota, Michal

    2017-04-01

    Increasing interest in green infrastructure linked with newly implemented legislation/rules/laws worldwide opens up research potential for field of soil hydrology. A better understanding of function of engineered soils involved in green infrastructure solutions such as green roofs or rain garden is needed. A soil layer is considered as a highly significant component of the aforesaid systems. In comparison with a natural soil, the engineered soil is assumed to be the more challenging case due to rapid structure changes early stages after its build-up. The green infrastructure efficiency depends on the physical and chemical properties of the soil, which are, in the case of engineered soils, a function of its initial composition and subsequent soil formation processes. The project presented in this paper is focused on fundamental processes in the relatively thick layer of engineered soil. The initial structure development, during which the pore geometry is altered by the growth of plant roots, water influx, solid particles translocation and other soil formation processes, is investigated with the help of noninvasive imaging technique  X-ray computed tomography. The soil development has been studied on undisturbed soil samples taken periodically from green roof test system during early stages of its life cycle. Two approaches and sample sizes were employed. In the first approach, undisturbed samples (volume of about 63 cm3) were taken each time from the test site and scanned by X-ray CT. In the second approach, samples (volume of about 630 cm3) were permanently installed at the test site and has been repeatedly removed to perform X-ray CT imaging. CT-derived macroporosity profiles reveal significant temporal changes of soil structure. Clogging of pores by fine particles and fissures development are two most significant changes that would affect the green roof system efficiency. This work has been supported by the Ministry of Education, Youth and Sports within

  12. Extended x-ray absorption fine structure (EXAFS): a novel probe for local structure of glassy solids

    International Nuclear Information System (INIS)

    Wong, J.

    1979-01-01

    The extended x-ray absorption fine structure (EXAFS) is the oscillation in the absorption coefficient extending a few hundred eVs on the high energy side of an x-ray absorption edge. This mode of spectroscopy has recently been realized to be a powerful tool in probing the local atomic structure of all states of matter, particularly with the advent of intense synchrotron radiation. More importantly is the unique ability of EXAFS to probe the structure and dynamics around individual atomic species in a multi-atomic system. In this paper, the physical processes associated with the EXAFS phenomenon will be discussed. Experimental results obtained at the Stanford Synchrotron Radiation Laboratory on some oxide and metallic glasses will be presented. The local structure in these materials are elucidated using a Fourier transform technique

  13. X-ray physico-chemical imaging during activation of cobalt-based Fischer-Tropsch synthesis catalysts

    Science.gov (United States)

    Beale, Andrew M.; Jacques, Simon D. M.; Di Michiel, Marco; Mosselmans, J. Frederick W.; Price, Stephen W. T.; Senecal, Pierre; Vamvakeros, Antonios; Paterson, James

    2017-11-01

    The imaging of catalysts and other functional materials under reaction conditions has advanced significantly in recent years. The combination of the computed tomography (CT) approach with methods such as X-ray diffraction (XRD), X-ray fluorescence (XRF) and X-ray absorption near-edge spectroscopy (XANES) now enables local chemical and physical state information to be extracted from within the interiors of intact materials which are, by accident or design, inhomogeneous. In this work, we follow the phase evolution during the initial reduction step(s) to form Co metal, for Co-containing particles employed as Fischer-Tropsch synthesis (FTS) catalysts; firstly, working at small length scales (approx. micrometre spatial resolution), a combination of sample size and density allows for transmission of comparatively low energy signals enabling the recording of `multimodal' tomography, i.e. simultaneous XRF-CT, XANES-CT and XRD-CT. Subsequently, we show high-energy XRD-CT can be employed to reveal extent of reduction and uniformity of crystallite size on millimetre-sized TiO2 trilobes. In both studies, the CoO phase is seen to persist or else evolve under particular operating conditions and we speculate as to why this is observed. This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.

  14. Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster from X-ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yano, Junko; Yano, Junko; Yachandra, Vittal K.

    2007-10-24

    Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria iscatalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a setof three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-rayspectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier X-ray absorption and emission spectroscopy methods. These studies are revealing that the assignment of formaloxidation states is overly simplistic. A more accurate description should consider the charge density on the Mn atoms that includes the covalency of the bonds and delocalization of the charge over the cluster. The geometric and electronic structure of the Mn4Ca cluster in the S-states derived from X-ray spectroscopy are leading to a detailed understanding of the mechanism of the O-O bond formation during the photosynthetic water

  15. Comparison of agricultural soils' structure depending on tillage system using X-ray microtomography

    Science.gov (United States)

    Beckers, Eléonore; Degré, Aurore; Ly, Sarann; Léonard, Angélique

    2010-05-01

    This study aims at characterizing agricultural soils' structure depending on the tillage system: conventional tillage or conservational tillage. Tillage reduction is an increasing practice, but the micro-structural effects on soils and on their hydrodynamic parameters are still not well described. Recent research shows non-converging results. Our point is to highlight fundamental differences in structure through characterization of soils porosity's parameters using X-ray microtomography measurements coupled to image analysis. This attempt is in line with a more integrated experiment of which the aim is to quantify the effects of tillage intensity on lateral flow production, and finally on global water balance. Parameters' measurements consist in a combined approach, based on two different space-time scales of exploration: fundamental scale, with soil sampling campaign for microtomography analysis, and field scale, with continuous flow measurements (plots' dimensions: 18*28 m). For their part, parameters for water balance determination (precipitation, evapotranspiration…) are monitored on the field. All of these measurements have the main objective of hydrological modeling enhancement by taking into account a better lateral flow description. Discussion in this paper will focus on the first results obtained by X-ray microtomography measurements. Our experiment takes place in Gentinnes (Walloon Brabant, Belgium), on a field organized in a split-plot scheme. Since 2004, plots have been cultivated in conventional tillage or in reduced tillage. The latter consists in sowing after stubble ploughing of about 10cm. The crop rotation is sugar beet followed by winter wheat. The soil is mainly composed of silt loam. Soils samples, with a 3 cm diameter and a 5 cm height, were removed from the upper layer (Ap horizon) for both management practices. Samples are scanned by X-ray microtomography using a Skyscan-1172 high-resolution desk-top micro-CT system (Skyscan, Kontich

  16. Synthesis, characterization and in vitro cytotoxicity of Co(II) complexes with N6-substituted adenine derivatives: X-ray structures of 6-(4-chlorobenzylamino)purin-di-ium diperchlorate dihydrate and [Co6(μ-L6)4Cl8(DMSO)10] · 4DMSO

    Czech Academy of Sciences Publication Activity Database

    Klanicová, A.; Trávníček, Zdeněk; Popa, Igor; Čajan, Michal; Doležal, Karel

    2006-01-01

    Roč. 25, č. 6 (2006), s. 1421-1432 ISSN 0277-5387 R&D Projects: GA ČR GA203/04/1168 Institutional research plan: CEZ:AV0Z50380511 Keywords : Cobalt(II) complexes * X-ray structures * Cytokinins Subject RIV: CA - Inorganic Chemistry Impact factor: 1.843, year: 2006

  17. Ultrafast time-resolved transient structures of solids and liquids by means of extended X-ray absorption fine structure.

    Science.gov (United States)

    Tomov, Ivan V; Rentzepis, Peter M

    2004-01-23

    Detection of ultrafast transient structures and the evolution of ultrafast structural intermediates during the course of reactions has been a long standing goal of chemists and biologists. This article will be restricted to nanosecond, picosecond and shorter time-resolved extended X-ray absorption fine structure (EXAFS) studies, its aim being to present the progress and problems encounter in measurements and understanding the structure of transients. The recent advances in source technology has stimulated a wide variety of novel experiments using both synchrotrons and smaller laboratory size systems. With more efficient X-ray lenses and detectors many of the previously difficult experiments to perform, because of the exposure time required and weak signals, will now be easily performed. The experimental system for the detection of ultrafast, time-resolved EXAFS spectra of molecules in liquids is described and the method for the analysis of EXAFS spectra to yield transient structures is given. We believe that utilizing our table-top ultrafast X-ray source and the polycapillary optics in conjunction with dispersive spectrometer and charge coupled devices (CCD) we will be able to determine the structure of many reaction intermediates and excited states of chemical and biological molecules in solid and liquid state.

  18. Synthesis, X-ray crystallography, spectroscopy, electrochemistry, thermal and kinetic study of uranyl Schiff base complexes

    Czech Academy of Sciences Publication Activity Database

    Asadi, Z.; Golzard, F.; Eigner, Václav; Dušek, Michal

    2013-01-01

    Roč. 66, č. 20 (2013), s. 3629-3646 ISSN 0095-8972 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : X-ray crystallography * uranyl Schiff base complex * kinetics of thermal decomposition * cyclic voltammetry * kinetics and mechanism Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.224, year: 2013

  19. Grazing angle X-ray fluorescence from periodic structures on silicon and silica surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, S.H., E-mail: nowak@ifg-adlershof.de [Physics Department, University of Fribourg, CH-1700 Fribourg (Switzerland); Banaś, D. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Błchucki, W.; Cao, W.; Dousse, J.-Cl. [Physics Department, University of Fribourg, CH-1700 Fribourg (Switzerland); Hönicke, P. [Physikalisch-Technische Bundesanstalt (PTB), D-10587 Berlin (Germany); Hoszowska, J. [Physics Department, University of Fribourg, CH-1700 Fribourg (Switzerland); Jabłoński, Ł. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Kayser, Y. [Physics Department, University of Fribourg, CH-1700 Fribourg (Switzerland); Kubala-Kukuś, A.; Pajek, M. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Reinhardt, F. [Physikalisch-Technische Bundesanstalt (PTB), D-10587 Berlin (Germany); Savu, A.V. [Microsystems Laboratory (LMIS1), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Szlachetko, J. [Institute of Physics, Jan Kochanowski University, 25-406 Kielce (Poland); Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland)

    2014-08-01

    Various 3-dimensional nano-scaled periodic structures with different configurations and periods deposited on the surface of silicon and silica substrates were investigated by means of the grazing incidence and grazing emission X-ray fluorescence techniques. Apart from the characteristics which are typical for particle- and layer-like samples, the measured angular intensity profiles show additional periodicity-related features. The latter could be explained by a novel theoretical approach based on simple geometrical optics (GO) considerations. The new GO-based calculations were found to yield results in good agreement with experiment, also in cases where other theoretical approaches are not valid, e.g., periodic particle distributions with an increased surface coverage.

  20. Grazing angle X-ray fluorescence from periodic structures on silicon and silica surfaces

    International Nuclear Information System (INIS)

    Nowak, S.H.; Banaś, D.; Błchucki, W.; Cao, W.; Dousse, J.-Cl.; Hönicke, P.; Hoszowska, J.; Jabłoński, Ł.; Kayser, Y.; Kubala-Kukuś, A.; Pajek, M.; Reinhardt, F.; Savu, A.V.; Szlachetko, J.

    2014-01-01

    Various 3-dimensional nano-scaled periodic structures with different configurations and periods deposited on the surface of silicon and silica substrates were investigated by means of the grazing incidence and grazing emission X-ray fluorescence techniques. Apart from the characteristics which are typical for particle- and layer-like samples, the measured angular intensity profiles show additional periodicity-related features. The latter could be explained by a novel theoretical approach based on simple geometrical optics (GO) considerations. The new GO-based calculations were found to yield results in good agreement with experiment, also in cases where other theoretical approaches are not valid, e.g., periodic particle distributions with an increased surface coverage

  1. Isoprenoid compounds from Euphorbia portlandica. X-ray structure of lupeportlandol, a new lupane triterpene

    Energy Technology Data Exchange (ETDEWEB)

    Madureira, Ana M.; Ferreira, Maria-Jose U. [Universidade de Lisboa, Lisboa (Portugal). Faculdade de Farmacia. Centro de Estudos de Ciencias Farmaceuticas]. E-mail: mjuferreira@ff.ul.pt; Duarte, Maria Teresa; Ascenso, Jose R. [Instituto Superior Tecnico, Lisboa (Portugal). Centro de Quimica Estrutural; Piedade, Maria Fatima M. [Universidade de Lisboa, Campo Grande, Lisboa (Portugal). Faculdade de Ciencias. Dept. de Quimica e Bioquimica

    2004-10-01

    Phytochemical survey of the Me{sub 2}CO extracts of the whole dried plant Euphorbia portlandica led to the isolation of a new pentacyclic triterpene alcohol, with the lupane skeleton, named lupeportlandol. Its structure was established as 3{alpha}-hydroxy-19{alpha}H-lup-20(29)-ene. The known pentacyclic triterpene glutinol and the steroid {beta}-sitostenone were also isolated. The characterization of the new compound and its acetylated derivative was based on spectroscopic methods and an X-ray diffraction analysis. Lupeportlandol acetate was inactive in cytotoxicity assays in vitro against three human tumor cell lines: MCF-7 (breast cancer), NCI-H460 (non-small cell lung cancer) and SF-268 (CNS cancer). (author)

  2. Redetermination of the borax structure from laboratory X-ray data at 145 K.

    Science.gov (United States)

    Gainsford, Graeme J; Kemmitt, Tim; Higham, Caleb

    2008-04-23

    THE TITLE COMPOUND, SODIUM TETRABORATE DECAHYDRATE (MINERAL NAME: borax), Na(2)[B(4)O(5)(OH)(4)]·8H(2)O, has been studied previously using X-ray [Morimoto (1956). Miner. J.2, 1-18] and neutron [Levy & Lisensky (1978). Acta Cryst. B34, 3502-3510] diffraction data. The structure contains tetra-borate anions [B(4)O(5)(OH)(4)](2-) with twofold rotation symmetry, which form hydrogen-bonded chains, and [Na(H(2)O)(6)] octa-hedra that form zigzag chains [Na(H(2)O)(4/2)(H(2)O)(2/1)]. The O-H bond distances obtained from the present redetermination at 145 K are shorter than those in the neutron study by an average of 0.127 (19) Å.

  3. Redetermination of the borax structure from laboratory X-ray data at 145 K

    Directory of Open Access Journals (Sweden)

    Caleb Higham

    2008-05-01

    Full Text Available The title compound, sodium tetraborate decahydrate (mineral name: borax, Na2[B4O5(OH4]·8H2O, has been studied previously using X-ray [Morimoto (1956. Miner. J. 2, 1–18] and neutron [Levy & Lisensky (1978. Acta Cryst. B34, 3502–3510] diffraction data. The structure contains tetraborate anions [B4O5(OH4]2− with twofold rotation symmetry, which form hydrogen-bonded chains, and [Na(H2O6] octahedra that form zigzag chains [Na(H2O4/2(H2O2/1]. The O—H bond distances obtained from the present redetermination at 145 K are shorter than those in the neutron study by an average of 0.127 (19 Å.

  4. Full analysis of feldspar texture and crystal structure by combining X-ray and electron techniques

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci; Piazolo, Sandra; Katerinopoulou, Anna

    2013-01-01

    Feldspar crystals typically show a range of exsolution and polysynthetic twinning textures that can present problems for their full characterization, but at the same time give important information about their genesis. We present an integrated procedure for the micro-texture analysis, twin law......-temperature (HT) feldspars had similar global chemical compositions but underwent significantly different cooling histories, with cooling times probably differing by over an order of magnitude. Powder X-ray diffraction with Rietveld refinement was used for a preliminary identification of the mineral components...... a simultaneous calculation for structurally different components. Combined results of various methods helped improve accuracy and resolve ambiguities that arise from the application of a single technique. The approach is widely applicable to the study of mineral intergrowths and bridges an existing gap...

  5. Atomic structure of the SbCu surface alloy: A surface X-ray diffraction study

    DEFF Research Database (Denmark)

    Meunier, I.; Gay, J.M.; Lapena, L.

    1999-01-01

    The dissolution at 400 degrees C of an antimony layer deposited at room temperature on a Cu(111) substrate leads to a surface alloy with a p(root 3x root 3)R 30 degrees x 30 degrees superstructure and a Sb composition of 1/3.We present here a structural study of this Sb-Cu compound by surface X......-ray diffraction (SXRD). The best agreement is obtained for a Cu,Sb surface layer with Sb atoms substituting 1/3 of the Cu atoms, over an essentially unperturbed Cu(111) plane. The largest relaxation is undergone by the Sb atoms which rise by 0.32+0.02 Angstrom over the mean plane of its Cu neighbours....... No substantial in-plane relaxations were observed. (C) 1999 Elsevier Science B.V. All rights reserved....

  6. Antiferro-quadrupolar structures in UPd3 inferred from x-ray resonant Bragg diffraction.

    Science.gov (United States)

    Fernández-Rodríguez, Javier; Lovesey, Stephen W; Blanco, Jesús A

    2010-01-20

    A systematic analysis of resonant x-ray Bragg diffraction data for UPd(3), with signal enhancement at the U M(IV) edge, including possible structural phase transitions leads to a new determination of the space groups of the material in the phases between T(0)=7.8 K and T(+1)=6.9 K, as P 222(1), and between T(-1)=6.7 K and T(2)=4.4 K, as P2(1). In addition, the quadrupolar order parameters, {Q(ab)}, inferred from diffraction data for the phase between T(-1) and T(2), are {Q(xz)} and {Q(yz)} at the (103) Bragg reflection and {Q(xy)} at the (104) reflection. © 2010 IOP Publishing Ltd

  7. X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides

    Energy Technology Data Exchange (ETDEWEB)

    M Gleghorn; E Davydova; R Basu; L Rothman-Denes; K Murakami

    2011-12-31

    We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.

  8. Liquid structure of trihexyltetradecylphosphonium chloride at ambient temperature: an X-ray scattering and simulation study.

    Science.gov (United States)

    Gontrani, Lorenzo; Russina, Olga; Celso, Fabrizio Lo; Caminiti, Ruggero; Annat, Gary; Triolo, Alessandro

    2009-07-09

    We report on an experimental and simulation study done on a representative room temperature ionic liquid, namely tetradecyltrihexylphosphonium chloride, at ambient conditions. The study was conducted using small and wide angle X-ray scattering and molecular dynamics simulations. Both approaches converge in indicating that this material is characterized by the existence of strong P-Cl interactions (with characteristic distances between 3.5 and 5.0 A) and by the occurrence of nanoscale segregation, despite the symmetric nature of the cation and similarly to other room temperature ionic liquids. A good agreement is found between the structure factor and pair correlation functions obtained from MD simulations and the corresponding experimental observables, thus strongly validating the interaction potential used in the simulations.

  9. Simulation of x-rays in refractive structure by the Monte Carlo method using the supercomputer SKIF

    International Nuclear Information System (INIS)

    Yaskevich, Yu.R.; Kravchenko, O.I.; Soroka, I.I.; Chembrovskij, A.G.; Kolesnik, A.S.; Serikova, N.V.; Petrov, P.V.; Kol'chevskij, N.N.

    2013-01-01

    Software 'Xray-SKIF' for the simulation of the X-rays in refractive structures by the Monte-Carlo method using the supercomputer SKIF BSU are developed. The program generates a large number of rays propagated from a source to the refractive structure. The ray trajectory under assumption of geometrical optics is calculated. Absorption is calculated for each ray inside of refractive structure. Dynamic arrays are used for results of calculation rays parameters, its restore the X-ray field distributions very fast at different position of detector. It was found that increasing the number of processors leads to proportional decreasing of calculation time: simulation of 10 8 X-rays using supercomputer with the number of processors from 1 to 30 run-times equal 3 hours and 6 minutes, respectively. 10 9 X-rays are calculated by software 'Xray-SKIF' which allows to reconstruct the X-ray field after refractive structure with a special resolution of 1 micron. (authors)

  10. X-ray Emission and Absorption Studies of Silicides in Relation to their Electronic Structure

    NARCIS (Netherlands)

    Weijs, P.J.W.; Wiech, G.; Zahorowski, W.; Speier, W.; Goedkoop, J.B.; Czyzyk, Marek; Acker, J.F. van; Leuken, E. van; Groot, R.A. de; Laan, G. van der; Sarma, D.D.; Kumar, L.; Buschow, K.H.J.; Fuggle, J.C.

    1990-01-01

    The valence bands and conduction bands of about 30 transition metal silicides (of which we concentrate on 4 here) have been investigated by measurements of Si X-ray emission bandsspectra, X-ray absorption spectra near the Si K (1s) edge, photoemission spectra, and Bremsstrahlung Isochromat spectra.

  11. X-ray holographic imaging of magnetic order in meander domain structures

    Directory of Open Access Journals (Sweden)

    Jaouen Nicolas

    2013-01-01

    Full Text Available We performed x-ray holography experiments using synchrotron radiation. By analyzing the scattering of coherent circularly polarized x-rays tuned at the Co-2p resonance, we imaged perpendicular magnetic domains in a Co/Pd multilayer. We compare results obtained for continuous and laterally confined films.

  12. Higher order structure analysis of nano-materials by spectral reflectance of laser-plasma soft x-ray

    International Nuclear Information System (INIS)

    Azuma, Hirozumi; Takeichi, Akihiro; Noda, Shoji

    1995-01-01

    We have proposed a new experimental arrangement to measure spectral reflectance of nano-materials for analyzing higher order structure with laser-plasma soft x-rays. Structure modification of annealed Mo/Si multilayers and a nylon-6/clay hybrid with poor periodicity was investigated. The measurement of the spectral reflectance of soft x-rays from laser-produced plasma was found to be a useful method for the structure analysis of nano-materials, especially those of rather poor periodicity

  13. Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers.

    Science.gov (United States)

    Neutze, Richard

    2014-07-17

    X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 10(12) X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.

  14. Local structure of LiCoO2 nanoparticles studied by Co K-edge x-ray absorption spectroscopy

    Science.gov (United States)

    Maugeri, L.; Iadecola, A.; Joseph, B.; Simonelli, L.; Olivi, L.; Okubo, M.; Honma, I.; Wadati, H.; Mizokawa, T.; Saini, N. L.

    2012-08-01

    We have studied the local structure of LiCoO2 nanoparticles by Co K-edge x-ray absorption spectroscopy as a function of particle size. Extended x-ray absorption fine structure data reveal substantial changes in the near neighbor distances and the associated mean square relative displacements with decreasing particle size. X-ray absorption near edge structure spectra show clear local geometrical changes with decreasing particle size, similar to those that appear in the charging (delithiation) process. The results suggest that the LiCoO2 nanoparticles are characterized by a large atomic disorder confined to the Co-O octahedra, similar to the distortions generated during the delithiation, and this disorder should be the primary limiting factor for a reversible diffusion of Li ions when nanoparticles of LiCoO2 are used as cathode material in rechargeable Li ion batteries.

  15. Structural investigations of LiFePO4 electrodes and in situ studies by Fe X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Deb, Aniruddha; Bergmann, Uwe; Cramer, S.P.; Cairns, Elton J.

    2005-01-01

    Fe K-edge X-ray absorption near edge spectroscopy (XANES) and extended X-ray absorption fine structure (EXAFS) have been performed on electrodes containing LiFePO 4 to determine the local atomic and electronic structure and their stability with electrochemical cycling. A versatile electrochemical in situ cell has been constructed for long-term soft and hard X-ray experiments for the structural investigation on battery electrodes during the lithium-insertion/extraction processes. The device is used here for an X-ray absorption spectroscopic study of lithium insertion/extraction in a LiFePO 4 electrode, where the electrode contained about 7.7 mg of LiFePO 4 on a 20 μm thick Al-foil. Fe K-edge X-ray absorption near edge spectroscopy (XANES) and extended X-ray absorption fine structure (EXAFS) have been performed on this electrode to determine the local atomic and electronic structure and their stability with electrochemical cycling. The initial state (LiFePO 4 ) showed iron to be in the Fe 2+ state corresponding to the initial state (0.0 mAh) of the cell, whereas in the delithiated state (FePO 4 ) iron was found to be in the Fe 3+ state corresponding to the final charged state (3 mAh). XANES region of the XAS spectra revealed a high spin configuration for the two states (Fe (II), d 6 and Fe (III), d 5 ). The results confirm that the olivine structure of the LiFePO 4 and FePO 4 is retained by the electrodes in agreement with the XRD observations reported previously. These results confirm that LiFePO 4 cathode material retains good structural short-range order leading to superior cycling capability

  16. Probing Complex Structural Behaviour in Dynamically Compressed Matter Using Ultrafast X-ray Diffraction

    Science.gov (United States)

    McMahon, Malcolm

    2017-06-01

    Over the last 25 years, the static compression community has found that structural complexity is almost ubiquitous in high-density matter, even in the elemental metals. And modern structure prediction methods have reported that this complexity continues to ultra-high pressures. The prediction that aluminum will adopt an incommensurate host--guest structure at multi-TPa pressures is particularly noteworthy. As such compressions can only be achieved dynamically, two fundamental questions arise. Firstly, are such complex structural forms able to form on the nanosecond timescales of dynamic compression experiments, and, secondly, if they do, how can we determine their structures? We are currently conducting campaigns at both NIF and LCLS to address and answer these questions, using nanosecond and femtosecond x-ray diffraction to detect phase changes, including melting, and determine the detailed structural response to dynamic compression. A particular aim is to obtain structural data on a par with that long available in static compression research. An overview of recent results from these campaigns, and comparisons to previous studies, will be given. This work is supported by EPSRC under Grant No. EP/J017051/1. Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515.

  17. Structure solution from powder neutron and x-ray diffraction data: getting the best of both worlds

    International Nuclear Information System (INIS)

    Hunter, B.A.

    2000-01-01

    Full text: Powder diffraction methods have traditionally been used in three main areas: phase identification and quantification, lattice parameter determination and structure refinement. Until recently structure solution has been the almost exclusive domain of single crystal diffraction methods, predominantly using x-rays. The increasing use of synchrotron and neutron sources, and the unrelenting advances in computing hardware and software means that powder methods are challenging single crystal methods as a practical method for structure solution, especially when single crystal method can not be applied. It is known that structural refinements from a known starting structure using combined X-ray and neutron data sets are capable of providing highly accurate structures. Likewise, using combined x-ray and neutron powder diffraction data in the structure solution process should also be a powerful technique, although to date no one is pursuing this methodology. This paper present examples of solutions to the problem. Namely we are using high resolution powder X-ray and neutron methods to solve the structures of molecular materials and minerals, then refining the structures using both sets of data. In this way we exploit the advantages of both methods while minimising the disadvantages. We present our solution for a small amino acid structure, a metalorganic and a mineral structure

  18. Local structure of metallic chips examined by X-ray microdiffraction

    Energy Technology Data Exchange (ETDEWEB)

    Saksl, K., E-mail: ksaksl@imr.saske.sk [Institut of Materials Research, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice (Slovakia); Rokicki, P. [The Faculty of Mechanical Engineering and Aeronautics, Rzeszow University of Technology, Al. Powstancow Warszawy 12, 35-959 Rzeszow (Poland); Siemers, C. [Institut fuer Werkstoffe, Technische Universitaet Braunschweig, Langer Kamp 8, 38106 Braunschweig (Germany); Ostroushko, D. [Faculty of Metallurgy and Materials Engineering, VŠB – Technical University of Ostrava, 17.listopadu 15, 708 33 Ostrava (Czech Republic); Bednarčík, J.; Rütt, U. [HASYLAB at DESY, Notkestr. 85, D-22607 Hamburg (Germany)

    2013-12-25

    Highlights: •We present a detailed microstructure and phase analysis of chips produced by cutting. •3D analysis proved mixed nature of shear bands propagation to the material. •We examine phase composition of the chips by focused X-ray beam. •Crystallites in segment and shear band change their orientation up to 10°. -- Abstract: Nickel-base alloys are used in high-temperature applications whenever steels or titanium alloys cannot be applied anymore. This class of alloys is furthermore used in low-temperature applications in the oil or gas industry in case the corrosion resistance of stainless steels in related liquid media is not sufficient and titanium alloys would be too expensive. Nickel-base alloys, however, due to their high strength and toughness can be machined only at low cutting speeds as otherwise poor surface quality and enhanced tool wear is observed. From all aspects influencing the machinability, the chip formation mechanism is the key factor and only a thorough understanding of this mechanism can lead to an optimisation of the cutting process. In the current study, a detailed microstructure and phase analysis of Alloy 625 chips produced in an orthogonal cutting process at conventional cutting speeds is presented. Utilising hard monochromatic X-rays focused down to micrometre size, microstructural differences between distinct structural units of the chips, namely, the segments and shear bands, are investigated. Scanning cross sections of the chips with this small beam allowed us to determine misorientation between the segments and shear bands crystal lattices which as we found are not changing abruptly but continuously, with an absolute difference up to 10°.

  19. Interaction of femtosecond X-ray pulses with periodical multilayer structures

    Energy Technology Data Exchange (ETDEWEB)

    Ksenzov, Dmitry

    2010-07-01

    The VUV Free Electron Laser FLASH operates in soft X-ray range and produces high-intensive pulse trains with few tens femtoseconds duration. The transversely fully coherent beam will open new experiments in solid state physics which can not be studied with present radiation sources. The study of the time dependent response of the multilayer to the X-ray pulse can provide insights into the process of interaction of highly intense FEL radiation with matter. To test the influence of electron excitation on the optical properties of boron carbide, the refractive index of B{sub 4}C was measured near B K-edge by energy-resolved photon-in-photon-out method probing a Bragg reflection from periodical multilayers. The measured data clearly show that the variation of the fine structure of the Kabsorption edges due to the chemical nature of the absorber element. The knowledge obtained from experiments with continuous radiation was used to design the respective experiments with pulse from the FEL. In my thesis, it is proposed that the geometrical setup, where the incident pulse arrives from the FEL under the angle close to the 1st order ML Bragg peak, provides the most valuable information. Preliminary simulation considering form factors of neutral and ionized boron showed that due to ionization, pronounced changes in the reflectivity curve are expected. The proposed scheme can be the powerful tool to study the various processes within the electronic subsystem of the FEL pulse interaction with matter. This type of investigations gives a deep understanding of the nature of the electronic excitation and the recombination at the femtosecond scale. (orig.)

  20. Synthesis and Characterization of a Neutral Six-coordinate Tris-adduct of an Indium(III) Trihalide. X-ray Crystal Structure of InCl3(THF)3

    Science.gov (United States)

    1994-05-05

    proposed by Fairbrother et al., but no solid- state structure was obtained.4 They used colligative property measurements to postulate that the...compound identification and structure elucidation have been Infrared and Raman spectroscopy, as well as colligative property measurements. Tris-adducts of

  1. X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Tyagi, Rajiv; Kumaran, Desigan; Burley, Stephen K.; Swaminathan, Subramanyam (SGX); (BNL)

    2010-01-12

    Histidine degradation in Agrobacterium tumefaciens involves four enzymes, including histidase (EC 4.3.1.3), urocanase (EC 4.2.1.49), imidazolonepropionase (EC 3.5.2.7), and N-formylglutamate amidohydrolase (EC 3.5.3.8). The third enzyme of the pathway, imidazolone-propionase, a 45.6 kDa protein, catalyzes conversion of imidazolone-5-propanoate to N-forminio-L-glutamate. Initial studies of the role of imidazolonepropionase in histidine degradation were published in 1953. Subsequent publications have been limited to enzyme kinetics, crystallization, and a recently reported structure determination. The imidazolonepropionases are members of metallodepenent-hydrolases (or amidohydroase) superfamily, which includs ureases, adenosine deaminases, phosphotriesterases, dihydroorotases, allantoinases, hydantoinases, adenine and cytosine deaminases, imidazolonepropionases, aryldial-kylphosphatases, chlorohydrolases, and formylmethanofuran dehydroases. Proteins belonging to this large group share a common three-dimensional structural motif (an eightfold {alpha}/{beta} or TIM barrel) with similar active sites. Most superfamily members also share a conserved metal binding site, involving four histidine residues and one aspartic acid. Imidazolonepropionase is one of the targets selected for X-ray crystallpgrahpic structure determination by the New York Structural GenomiX Research Consortium (NYSGXRC) Target ID: 9252b to correlate the structure function relationship of poorly studied by important enzyme. Here they report the crystal structure of imidazolonepropionase from Agrobacterium tumefaciens determined at 1.87 {angstrom} resolution.

  2. Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

    Directory of Open Access Journals (Sweden)

    Zhen Huang

    2008-03-01

    Full Text Available Selenium derivatization (via selenomethionine of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2’-position of the ribose. All the synthesis of 2’-SeMe modified phosphoramidite building blocks (U, C, T, A, G and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

  3. Synthesis of metallic nanoparticles by sol-gel protein method and characterization by diffraction of X-ray

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Y.C.; Utuni, V.H.S.; Sasaki, J.M. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Fisica; Nogueira, N.A.S. [Universidade Federal do Ceara (UFC/UFERSA), Fortaleza, CE (Brazil). Dept. Engenharia Metalurgica e Materiais

    2012-07-01

    Full text: Nanoscience has led many scientists to revolutionize the areas of materials and fabrications. An area extensively studied is the synthesis of magnetic nanoparticles, noting the importance of these materials, this work proposes a new rote of obtaining nanoparticles of FeNi alloys from edible gelatin. Nanoparticles FeNi alloy is obtained by using the sol-gel proteic method, which consists in preparing a solution of the organic precursor and salts, after preparing it these solutions are mixed, in order to disperse the metals in the organic matrix, the mixture is dried to form a powder which will be submitted to calcination. The salts of iron nitrate (III) and nickel nitrate (II) were dispersed in gelatin solution and dried in an oven at 100 deg C, and calcined at 500 deg C at different times (4, 5, 6 and 7 hours). In order to promote the reduction of metal oxides obtained from the decomposition, the whole solution was calcined under nitrogen atmosphere. This set of samples was prepared in order to reach the lowest temperature for producing the FeNi alloy and follow the TG (thermogravimetry) and DTA (differential thermal analysis) analysis in order to minimize particle size. The samples were characterized by X-ray powder diffraction (XRPD) technique, and the structural and microstructure parameters were determined after refinement using Rietveld method. For all samples, the desired phase of FeNi were obtained. The particle size, microstrains were obtained by the Scherrer equation and Williamson-Hall plotting. Also, Moessbauer spectroscopy was used in order to analyze the site composition of iron and Ni. (author)

  4. Synthesis, Single Crystal X-ray Analysis, and Antifungal Profiling of Certain New Oximino Ethers Bearing Imidazole Nuclei

    Directory of Open Access Journals (Sweden)

    Reem I. Al-Wabli

    2017-11-01

    Full Text Available Fungal infections threaten human health, particularly in immune-compromised patients worldwide. Although there are a large number of antifungal agents available, the desired clinical attributes for the treatment of fungal infections have not yet been achieved. Azoles are the mainstay class of the clinically used antifungal agents. In the current study, the synthesis, spectroscopic characterization, and antifungal activity of certain new oximino ethers Va–n bearing imidazole nuclei are reported. The (E-configuration of the imine double bond of the synthesized compounds Va–n has been confirmed via single crystal X-ray analysis of compound Vi as a representative example of this class of compounds. The molecular structure of compound Vi was crystallized in the monoclinic, P21/c, a = 18.7879(14 Å, b = 5.8944(4 Å, c = 16.7621(12 Å, β = 93.063(3°, V = 1855.5(2 Å3, Z = 4. The in vitro antifungal activity of the synthesized compounds Va–n were evaluated using diameter of the inhibition zone (DIZ and minimum inhibitory concentration (MIC assays against different fungal strains. Compound Ve manifested anti-Candida albicans activity with an MIC value of 0.050 µmol/mL, being almost equipotent with the reference antifungal drug fluconazole (FLC,while compounds Vi and Vn are the most active congeners against Candida parapsilosis, being equipotent and about twenty-three times more potent than FLC with an MIC value of 0.002 µmol/mL. The results of the current report might support the development of new potent and safer antifungal azoles.

  5. Depth-selective structural analysis of thin films using total-external-reflection x-ray diffraction.

    Science.gov (United States)

    Kawamura, Tomoaki; Omi, Hiroo

    2010-12-01

    Total-external-reflection (TER) x-ray diffraction is the depth-sensitive technique for evaluating layered structures, including epitaxial heterostructures, ion-doped bulk crystals and several quantum-well structures. This technique can control the depth of observation by changing both incident and exit angles of x-rays from the surface. In this review, the principle of the TER technique and measurement apparatus are briefly described, and applications of layered-semiconductor samples evaluated using the TER technique are introduced.

  6. An Investigation into the Elementary Temporal Structure of Solar Flare Hard X-Ray Bursts Using BATSE

    Science.gov (United States)

    Newton, Elizabeth

    1998-01-01

    The research performed under this contract is part of an on-going investigation to explore the finest time-resolution hard X-ray data available on solar flares. Since 1991, the Burst and Transient Source Experiment (BATSE) aboard the Compton Gamma Ray Observatory has provided almost continual monitoring of the Sun in the hard X-ray and gamma-ray region of the spectrum. BATSE provides for the first time a temporal resolution in the data comparable to the timescales on which flare particle energization occurs. Under this contract, we have employed an important but under-utilized BATSE data type, the Time-To-Spill (TTS) data, to address the question of how fine a temporal structure exists in flare hard X-ray emission. By establishing the extent to which 'energy release fragments,' or characteristic (recurrent) time structures, are building blocks of flare emission, it is possible to place constraints on particle acceleration theories.

  7. X-ray Absorption Fine Structure (XAFS) Studies of Oxide Glasses—A 45-Year Overview

    Science.gov (United States)

    Zanotto, Edgar Dutra

    2018-01-01

    X-ray Absorption Fine Structure (XAFS) spectroscopy has been widely used to characterize the short-range order of glassy materials since the theoretical basis was established 45 years ago. Soon after the technique became accessible, mainly due to the existence of Synchrotron laboratories, a wide range of glassy materials was characterized. Silicate glasses have been the most studied because they are easy to prepare, they have commercial value and are similar to natural glasses, but borate, germanate, phosphate, tellurite and other less frequent oxide glasses have also been studied. In this manuscript, we review reported advances in the structural characterization of oxide-based glasses using this technique. A focus is on structural characterization of transition metal ions, especially Ti, Fe, and Ni, and their role in different properties of synthetic oxide-based glasses, as well as their important function in the formation of natural glasses and magmas, and in nucleation and crystallization. We also give some examples of XAFS applications for structural characterization of glasses submitted to high pressure, glasses used to store radioactive waste and medieval glasses. This updated, comprehensive review will likely serve as a useful guide to clarify the details of the short-range structure of oxide glasses. PMID:29382102

  8. X-ray Absorption Fine Structure (XAFS Studies of Oxide Glasses—A 45-Year Overview

    Directory of Open Access Journals (Sweden)

    Valmor Roberto Mastelaro

    2018-01-01

    Full Text Available X-ray Absorption Fine Structure (XAFS spectroscopy has been widely used to characterize the short-range order of glassy materials since the theoretical basis was established 45 years ago. Soon after the technique became accessible, mainly due to the existence of Synchrotron laboratories, a wide range of glassy materials was characterized. Silicate glasses have been the most studied because they are easy to prepare, they have commercial value and are similar to natural glasses, but borate, germanate, phosphate, tellurite and other less frequent oxide glasses have also been studied. In this manuscript, we review reported advances in the structural characterization of oxide-based glasses using this technique. A focus is on structural characterization of transition metal ions, especially Ti, Fe, and Ni, and their role in different properties of synthetic oxide-based glasses, as well as their important function in the formation of natural glasses and magmas, and in nucleation and crystallization. We also give some examples of XAFS applications for structural characterization of glasses submitted to high pressure, glasses used to store radioactive waste and medieval glasses. This updated, comprehensive review will likely serve as a useful guide to clarify the details of the short-range structure of oxide glasses.

  9. X-ray structures define human P2X3 receptor gating cycle and antagonist action

    Science.gov (United States)

    Mansoor, Steven E.; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

    2016-10-01

    P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the ‘cytoplasmic cap’, which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.

  10. X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae

    Science.gov (United States)

    Tran, Phidung Hong

    X-ray diffraction by using resonant anomalous scattering has become a popular tool for solving crystal structures in the last ten years with the expanded availability of tunable synchrotron radiation for protein crystallography. Mercury atoms were used for phasing. The crystal structure of N-6 deoxyribose nucleic acid methyltransferase from Streptoccocus pneumoniae (DpnM) was solved by using the Multiple Anomalous Diffraction technique. The crystal structure reveals the formation of mercaptide between the mercury ion and the thiol group on the cysteine amino acid in a hydrophobic environment. The crystal structure contains the bound ligand, S- adenosyl-l-methionine on the surface of the concave opening. The direction of the β-strands on the beta sheets are identical to other solved methyltransferases. The highly conserved motifs, DPPY and the FxGxG, are found to be important in ligand binding and possibly in methyl group transfer. The structure has a concave cleft with an opening on the order of 30 Å that can accommodate a DNA duplex. By molecular modelling coupled to sequence alignment, two other highly conserved residues Arg21 and Gly19 are found to be important in catalysis.

  11. X-ray television area detectors for macromolecular structural studies with synchrotron radiation sources

    International Nuclear Information System (INIS)

    Arndt, U.W.; Gilmore, D.J.

    1978-01-01

    Two-dimensional X-ray diffraction patterns may be recorded quantitatively by means of X-ray-to-electron converters which are scanned in a television-type raster scan. Detectors of this type are capable of operating over the whole range of counting rates from very low to higher than those with which other types of converters can deal. The component parts of an X-ray television detector are examined and the limits to the precision of the measurements are analysed. (Auth.)

  12. Application of X-ray phase-contrast tomography in quantative studies of heat induced structural changes in meat

    DEFF Research Database (Denmark)

    Miklos, R.; Nielsen, M. S.; Einarsdottir, Hildur

    2013-01-01

    X-ray computed tomography is increasingly used in the studies of food structure. This paper describes the perspectives of use of phase contrast computed tomography in studies of heat induced structural changes in meat. From the data it was possible to obtain reconstructed images of the sample...

  13. Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Lingling [Stanford Univ., CA (United States)

    1996-04-01

    Synchrotron small angle x-ray scattering (SAXS) has been applied to the structural study of several biological systems, including the nitrogenase complex, the heat shock cognate protein (hsc70), and lysozyme folding. The structural information revealed from the SAXS experiments is complementary to information obtained by other physical and biochemical methods, and adds to our knowledge and understanding of these systems.

  14. The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P.; Bledsoe, Randy K.; Mclay, Iain; Stewart, Eugene L.; Uings, Iain J.; Weingarten, Gordon; Williams, Shawn P. (GSKNC); (GSK)

    2009-07-23

    The amino-pyrazole 2,6-dichloro-N-ethyl benzamide 1 is a selective GR agonist with dexamethasone-like in vitro potency. Its X-ray crystal structure in the GR LBD (Glucocorticoid ligand-binding domain) is described and compared to other reported structures of steroidal GR agonists in the GR LBD (3E7C).

  15. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy : A molecular dynamics simulation study

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    2003-01-01

    The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been

  16. High-energy X-ray diffraction studies of short- and intermediate-range structure in oxide glasses

    International Nuclear Information System (INIS)

    Suzuya, Kentaro

    2002-01-01

    The feature of high-energy X-ray diffraction method is explained. The oxide glasses studies by using BL04B2, high-energy X-ray diffraction beam line of SPring-8, and the random system materials by high-energy monochromatic X-ray diffraction are introduced. An advantage of third generation synchrotron radiation is summarized. On SPring-8, the high-energy X-ray diffraction experiments of random system are carried out by BL04B2 and BL14B1 beam line. BL04B2 can select Si (111)(E=37.8 keV, λ=0.033 nm) and Si(220)(E=61.7 keV, λ=0.020 nm) as Si monochromator. The intermediate-range structure of (MgO) x (P 2 O 5 ) 1-x glass ,MgP 2 O 6 glass, B 2 O 3 glass, SiO 2 and GeO 2 are explained in detail. The future and application of high-energy X-ray diffraction are stated. (S.Y.)

  17. Crystal structure investigations on cation-substituted alums by X-ray and neutron diffraction

    International Nuclear Information System (INIS)

    Abdeen, A.M.

    1980-04-01

    The crystal structures of the three alums: NH 4 Al(SO 4 ) 2 .12H 2 O, (NH 3 CH 3 )Al(SO 4 ) 2 .12H 2 O and (NH 3 OH)Al(SO 4 ) 2 .12H 2 O have been determined from three-dimensional neutron diffraction data enhanced by X-ray diffraction when necessary. These compounds crystallize cubic in space group Pa3. The structures of the three alums exhibit partial occupancies of crystallographic sites for the NH 4 , (NH 3 CH 3 ) and (NH 3 OH) group atoms. This can be explained by a quantized rotation of the three groups around an axis perpendicular to the [111] direction. Some of the (SO 4 ) 2- groups in the NH 4 -alum are disordered with about 17% of the sulfate tetrahedra being in a reversed orientation around the sulfur atom. The disorder in (NH 3 CH 3 ) and (NH 3 OH)-alums is only 4,3% and 3.0% respectively. The atoms in the alum structures are held together by a system of hydrogen bonds between the water molecules and between the water molecules and the sulfate oxygen atoms. In these three structures there is a strong indication that shorter hydrogen bonds tend to be nearly linear. (orig.)

  18. X-ray crystal structure of a xanthine oxidase complex with the flavonoid inhibitor quercetin.

    Science.gov (United States)

    Cao, Hongnan; Pauff, James M; Hille, Russ

    2014-07-25

    Xanthine oxidase catalyzes the sequential hydroxylation of hypoxanthine to uric acid via xanthine as intermediate. Deposition of crystals of the catalytic product uric acid or its monosodium salt in human joints with accompanying joint inflammation is the major cause of gout. Natural flavonoids are attractive leads for rational design of preventive and therapeutic xanthine oxidase inhibitors due to their beneficial antioxidant, anti-inflammatory, and antiproliferative activities in addition to their micromolar inhibitory activities toward xanthine oxidase. We determined the first complex X-ray structure of mammalian xanthine oxidase with the natural flavonoid inhibitor quercetin at 2.0 Å resolution. The inhibitor adopts a single orientation with its benzopyran moiety sandwiched between Phe 914 and Phe 1009 and ring B pointing toward the solvent channel leading to the molybdenum active center. The favorable steric complementarity of the conjugated three-ring structure of quercetin with the active site and specific hydrogen-bonding interactions of exocyclic hydroxy groups with catalytically relevant residues Arg 880 and Glu 802 correlate well with a previously reported structure-activity relationship of flavonoid inhibitors of xanthine oxidase. The current complex provides a structural basis for the rational design of flavonoid-type inhibitors against xanthine oxidase useful for the treatment of hyperuricemia, gout, and inflammatory disease states.

  19. X-ray structure of the pestivirus NS3 helicase and its conformation in solution.

    Science.gov (United States)

    Tortorici, M Alejandra; Duquerroy, Stéphane; Kwok, Jane; Vonrhein, Clemens; Perez, Javier; Lamp, Benjamin; Bricogne, Gerard; Rümenapf, Till; Vachette, Patrice; Rey, Félix A

    2015-04-01

    Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the

  20. Soft x-ray lasers

    International Nuclear Information System (INIS)

    Matthews, D.L.; Rosen, M.D.

    1988-01-01

    One of the elusive dreams of laser physicists has been the development of an x-ray laser. After 25 years of waiting, the x-ray laser has at last entered the scientific scene, although those now in operation are still laboratory prototypes. They produce soft x rays down to about five nanometers. X-ray lasers retain the usual characteristics of their optical counterparts: a very tight beam, spatial and temporal coherence, and extreme brightness. Present x-ray lasers are nearly 100 times brighter that the next most powerful x-ray source in the world: the electron synchrotron. Although Lawrence Livermore National Laboratory (LLNL) is widely known for its hard-x-ray laser program which has potential applications in the Strategic Defense Initiative, the soft x-ray lasers have no direct military applications. These lasers, and the scientific tools that result from their development, may one day have a place in the design and diagnosis of both laser fusion and hard x-ray lasers. The soft x-ray lasers now in operation at the LLNL have shown great promise but are still in the primitive state. Once x-ray lasers become reliable, efficient, and economical, they will have several important applications. Chief among them might be the creation of holograms of microscopic biological structures too small to be investigated with visible light. 5 figs

  1. Solid solutions of uranium and thorium phosphates: synthesis, characterization and X-ray photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Dacheux, N.; Brandel, V.; Genet, M.; Bak, K.; Berthier, C.

    1996-01-01

    New solid solutions of uranium-thorium phosphates based on uranium-uranyl phosphate U(U O 2 )(P O 4 ) 2 and thorium phosphate-diphosphate Th 4 (P O 4 ) 4 (P 2 O 7 ) were synthesized in air or under an inert atmosphere via dry and wet chemical processes. The products were characterized by means of chemical analysis, X-ray diffraction and ultraviolet-visible and infrared absorption spectroscopies. Solid solutions of uranium-uranyl-thorium phosphates U 1-x Th x (U O 2 )(P O 4 ) 2 (with O≤ x ≤ 0.6) were obtained in air by substitution of uranium (IV) by thorium. Solid solutions of thorium-uranium phosphate-diphosphate (Th 1-y U y ) 4 (P O 4 ) 4 (P 2 O 7 ) (with Y ≤0.9) were prepared by substitution of thorium by uranium (IV) under an inert atmosphere. These new materials have been studied by XPS (X-ray photoelectron spectroscopy) in order to verify the oxidation states of uranium and to estimate the P/U, P/Th, P/O and U/Th ratios. (authors). 33 refs., 10 figs., 4 tabs

  2. Structural analysis of polymer thin films using GISAXS in the tender X-ray region: Concept and design of GISAXS experiments using the tender X-ray energy at BL-15A2 at the Photon Factory

    Energy Technology Data Exchange (ETDEWEB)

    Takagi, H., E-mail: takagih@post.kek.jp; Igarashi, N.; Mori, T.; Saijo, S.; Nagatani, Y.; Shimizu, N. [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Ohta, H. [Mitsubishi Electric System & Service Co., Ltd, Accelerator Engineering Center, 2-8- 8 Umezono, Tsukuba, Ibaraki 305-0045 (Japan); Yamamoto, K. [Graduate School of Engineering, Department of Materials Science & Technology, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan)

    2016-10-14

    If small angle X-ray scattering (SAXS) utilizing the soft X-ray region is available, advanced and unique experiments, which differ from traditional SAXS methods, can be realized. For example, grazing-incidence small angle X-ray scattering (GISAXS) using hard X-ray is a powerful tool for understanding the nanostructure in both vertical and lateral directions of thin films, while GISAXS utilizing the tender X-ray region (SX-GISAXS) enables depth-resolved analysis as well as a standard GISAXS analysis in thin films. Thus, at BL-15A2 at the Photon Factory, a dedicated diffractometer for SX-GISAXS (above 2.1 keV) was constructed. This diffractometer is composed of four vacuum chambers and can be converted into the vacuum state from the sample chamber in front of the detector surface. Diffractions are clearly observed until 12th peak when measuring collagen by SAXS with an X-ray energy of 2.40 keV and a camera length of 825 mm. Additionally, we conducted the model experiment using SX-GISAXS with an X-ray energy of 2.40 keV to confirm that a poly(methyl methacrylate)-poly(n-butyl acrylate) block copolymer thin film has a microphase-separated structure in the thin film, which is composed of lamellae aligned both parallel and perpendicular to the substrate surface. Similarly, in a polystyrene-poly(methyl methacrylate) block copolymer thin film, SX-GISAXS with 3.60 keV and 5.73 keV revealed that hexagonally packed cylinders are aligned parallel to the substrate surface. The incident angle dependence of the first order peak position of the q{sub z} direction obtained from experiments at various incident X-ray energies agrees very well with the theoretical one calculated from the distorted wave Born approximation.

  3. X-ray crystallographic structure determination of the smoke-derived karrikin KAR3

    Czech Academy of Sciences Publication Activity Database

    Nair, J. J.; Munro, O. Q.; Pošta, Martin; Papenfus, H. B.; Beier, Petr; van Staden, J.

    2013-01-01

    Roč. 88, September (2013), s. 107-109 ISSN 0254-6299 Institutional support: RVO:61388963 Keywords : germination * karrikin * plant growth regulator * smoke * X-ray Subject RIV: CC - Organic Chemistry Impact factor: 1.340, year: 2013

  4. Capturing molecular structural dynamics by 100 ps time-resolved X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Sato, Tokushi; Nozawa, Shunsuke; Ichiyanagi, Kohei; Tomita, Ayana; Chollet, Matthieu; Ichikawa, Hirohiko; Fujii, Hiroshi; Adachi, Shin-ichi; Koshihara, Shin-ya

    2009-01-01

    An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. The X-ray positional active feedback to crystals in a monochromator combined with a figure-of-merit scan of the laser beam position has been utilized as an essential tool to stabilize the spatial overlap of the X-ray and laser beams at the sample position. As a typical example, a time-resolved XAFS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented

  5. Synthesis, spectral and single crystal X-ray structural studies on bis(2,2’-bipyridinesulphidoM(II (M = Cu or Zn and diaqua 2,2’-bipyridine zinc(IIsulphate dihydrate

    Directory of Open Access Journals (Sweden)

    ARUMUGAM MANOHAR

    2010-08-01

    Full Text Available Reaction of bis(diethanoldithiocarbamatocopper(II, [Cu(deadtc2] and bis(di-n-propyldithiocarbamatozinc(II, [Zn(dnpdtc2] complexes with 2,2’-bipyridine (2,2’-bipy (1:1 ratio in ethanol was investigated. Simple mixing of the reactants in 1:1 ratio resulted in five-coordinated [Cu(2,2’--bipy2S]•CH3CH2OSO3H (1 and [Zn(2,2’-bipy2S]•CH3CH2OSO3H·2H2O (2. Refluxing the reactants and cooling the contents result in the formation of [Zn(2,2’-bipy(H2O2]SO4 (3 and [Cu(2,2’-bipy(H2O2]SO4 (4. Complexes 1 and 2 are monomeric with trigonal bipyramidal geometry. A distorted octahedral environment was observed in complexes 3 and 4. The crystal structure of 4 has already been reported in the literature. Crystal structures of 1, 2 and 3 are reported in this paper. The M–S distances in 1 and 2 are 2.318(1 Å and 2.323 Å, respectively. The N–M–S angles are larger than the N–M–N angles due to the steric requirements.

  6. Skull x-ray

    Science.gov (United States)

    X-ray - head; X-ray - skull; Skull radiography; Head x-ray ... There is low radiation exposure. X-rays are monitored and regulated to provide the minimum amount of radiation exposure needed to produce the image. Most ...

  7. Neck x-ray

    Science.gov (United States)

    X-ray - neck; Cervical spine x-ray; Lateral neck x-ray ... There is low radiation exposure. X-rays are monitored so that the lowest amount of radiation is used to produce the image. Pregnant women and ...

  8. Three-dimensional visualization of magnetic domain structure with strong uniaxial anisotropy via scanning hard X-ray microtomography

    Science.gov (United States)

    Suzuki, Motohiro; Kim, Kab-Jin; Kim, Sanghoon; Yoshikawa, Hiroki; Tono, Takayuki; Yamada, Kihiro T.; Taniguchi, Takuya; Mizuno, Hayato; Oda, Kent; Ishibashi, Mio; Hirata, Yuushou; Li, Tian; Tsukamoto, Arata; Chiba, Daichi; Ono, Teruo

    2018-03-01

    An X-ray tomographic technique was developed to investigate the internal magnetic domain structure in a micrometer-sized ferromagnetic sample. The technique is based on a scanning hard X-ray nanoprobe using X-ray magnetic circular dichroism (XMCD). From transmission XMCD images at the Gd L3 edge as a function of the sample rotation angle, the three-dimensional (3D) distribution of a single component of the magnetic vector in a GdFeCo microdisc was reconstructed with a spatial resolution of 360 nm, using a modified algebraic reconstruction algorithm. The method is applicable to practical magnetic materials and can be extended to 3D visualization of the magnetic domain formation process under external magnetic fields.

  9. Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges

    Science.gov (United States)

    Neutze, Richard; Moffat, Keith

    2012-01-01

    X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today’s synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics. PMID:23021004

  10. Time-resolved pump and probe x-ray absorption fine structure spectroscopy at beamline P11 at PETRA III

    Energy Technology Data Exchange (ETDEWEB)

    Göries, D., E-mail: dennis.goeries@desy.de; Roedig, P.; Stübe, N.; Meyer, J.; Warmer, M.; Weckert, E.; Meents, A., E-mail: alke.meents@desy.de [DESY Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg (Germany); Dicke, B.; Naumova, M.; Rübhausen, M. [Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761 Hamburg (Germany); Galler, A.; Gawelda, W.; Geßler, P.; Sotoudi Namin, H.; Beckmann, A. [European XFEL, Albert-Einstein Ring 19, 22761 Hamburg (Germany); Britz, A.; Bressler, C. [European XFEL, Albert-Einstein Ring 19, 22761 Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg (Germany); Schlie, M. [Institut für Experimentalphysik, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)

    2016-05-15

    We report about the development and implementation of a new setup for time-resolved X-ray absorption fine structure spectroscopy at beamline P11 utilizing the outstanding source properties of the low-emittance PETRA III synchrotron storage ring in Hamburg. Using a high intensity micrometer-sized X-ray beam in combination with two positional feedback systems, measurements were performed on the transition metal complex fac-Tris[2-phenylpyridinato-C2,N]iridium(III) also referred to as fac-Ir(ppy){sub 3}. This compound is a representative of the phosphorescent iridium(III) complexes, which play an important role in organic light emitting diode (OLED) technology. The experiment could directly prove the anticipated photoinduced charge transfer reaction. Our results further reveal that the temporal resolution of the experiment is limited by the PETRA III X-ray bunch length of ∼103 ps full width at half maximum (FWHM).

  11. X-ray structure of a blue complex pigment from the blue flowers of Centaurea cyanus

    International Nuclear Information System (INIS)

    Shiono, M.; Matsugaki, N.; Takeda, K.

    2005-01-01

    Full text: The blue pigment of the cornflower, named protocyanin, has long been investigated, but its precise structure has remained unclear. Our recent research demonstrated the components of protocyanin to be anthocyanin (AN), flavone glycoside (FL), Fe 3+ , Mg 2+ and Ca 2+ ions and we succeeded in the reconstruction of protocyanin. In this study, we revealed the X-ray structure of protocyanin. The crystal structure of the reconstructed protocyanin was determined at a resolution of 1.05 A. The refined molecule has pseudo threefold symmetry and four metal ions, Fe 3+ , Mg 2+ and two Ca 2+ , align along the pseudo three-fold axis. The four metals are coordinated to six AN molecules and six FL molecules. The inner Fe 3+ and Mg 2+ ions are each coordinated to three AN molecules respectively, while the outer two Ca 2+ ions are each coordinated to three FL molecules . Both AN and FL molecules are self-associated with each other as AN-AN and FL-FL in pair and this hydrophobic association also exists between AN and FL molecules. Protocyanin is a tetra-metal (Fe 3+ , Mg 2+ , 2Ca 2+ ) nuclear complex of twelve molecules of anthocyanin and flavone glycoside, a new type of supramolecular pigment. (author)

  12. Structural variations in lignite coal: a small angle X-ray scattering investigation

    Science.gov (United States)

    Sastry, P. U.; Sen, D.; Mazumder, S.; Chandrasekaran, K. S.

    2000-04-01

    The structural morphology of raw and processed lignite coal specimens from Neyveli (Tamil Nadu, India) is characterized over a length scale of 5-100 nm by small angle X-ray scattering (SAXS). The scattering profile from the unprocessed lignite specimen exhibits two distinct power laws indicating different fractal morphologies over different length scales: a pore fractal (dimension Dp˜2.7) for the pore-coal interface below 17 nm and a surface fractal (dimension Ds˜2.3) above 17 nm. As a result of industrial processing at different temperature, pressure and carbonization, significant changes in the structure are noticed as indicated by the scattering profiles. The fractal roughness of the pore-coal interface becomes smooth (average Ds˜2) for a large window of the length scale, whereas a part of the pore fractal transforms to a surface ( Ds˜2.8). The specimen treated at relatively higher temperature exhibits further variation from the fractal geometry with a tendency to form a new non-fractal micropore structure for the length scale ≤8 nm.

  13. Stable anilinyl radicals coordinated to nickel: X-ray crystal structure and characterization.

    Science.gov (United States)

    Kochem, Amélie; Gellon, Gisèle; Leconte, Nicolas; Baptiste, Benoit; Philouze, Christian; Jarjayes, Olivier; Orio, Maylis; Thomas, Fabrice

    2013-12-02

    Two anilinosalen and a mixed phenol-anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1, 2, and 3 were prepared and characterized. They could be readily one-electron oxidized (E(1/2)=-0.30, -0.26 and 0.10 V vs. Fc(+)/Fc, respectively) into anilinyl radicals species [1](+), [2](+), and [3](+), respectively. The radical complexes are extremely stable and were isolated as single crystals. X-ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [1](+) and [2](+). No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [3](+), with shortening of one C(ortho)-C(meta) bond. Radical species [1](+) and [2](+) exhibit a strong absorption band at around 6000 cm(-1) (class III mixed valence compounds). This band is significantly less intense than [3](+), consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed-valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Electron microscopy and x-ray diffraction evidence for two Z-band structural states.

    Science.gov (United States)

    Perz-Edwards, Robert J; Reedy, Michael K

    2011-08-03

    In vertebrate muscles, Z-bands connect adjacent sarcomeres, incorporate several cell signaling proteins, and may act as strain sensors. Previous electron microscopy (EM) showed Z-bands reversibly switch between a relaxed, "small-square" structure, and an active, "basketweave" structure, but the mechanism of this transition is unknown. Here, we found the ratio of small-square to basketweave in relaxed rabbit psoas muscle varied with temperature, osmotic pressure, or ionic strength, independent of activation. By EM, the A-band and both Z-band lattice spacings varied with temperature and pressure, not ionic strength; however, the basketweave spacing was consistently 10% larger than small-square. We next sought evidence for the two Z-band structures in unfixed muscles using x-ray diffraction, which indicated two Z-reflections whose intensity ratios and spacings correspond closely to the EM measurements for small-square and basketweave if the EM spacings are adjusted for 20% shrinkage due to EM processing. We conclude that the two Z-reflections arise from the small-square and basketweave forms of the Z-band as seen by EM. Regarding the mechanism of transition during activation, the effects of Ca(2+) in the presence of force inhibitors suggested that the interconversion of Z-band forms was correlated with tropomyosin movement on actin. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Determining the Structure of Biomaterials Interfaces using Synchrotron-based X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    McBride, M

    2002-01-24

    The purpose of this project is to explore the feasibility of using surface X-ray diffraction (SXRD) to determine the structure of biomineral surfaces in electrolyte solutions and of the adsorbed layer of acidic amino acids that are believed to play a central role in the control of biomineral formation and function. The work is a critical component in the development of an integrated picture of the physical and chemical basis for deposition and dissolution at solid-liquid interfaces in biological systems, and brings a new and very powerful surface-sensitive capability to LLNL. We have chosen as our model systems calcium carbonate and calcium phosphate in aspartic and glutamic acid-bearing solutions. The calcium compounds are ubiquitous among biomineral structures, both those that are beneficial such as bones and teeth, and those that are pathological such as kidney stones, while the two acidic amino acids--both as simple and poly-amino acids--are the dominant constituents of protein mixtures implicated in the control of biomineralization. The goals of the work are: (1) to determine the surface structure of pure calcium phosphate and calcium carbonate surfaces in aqueous solution using SXRD; (2) to determine how those surfaces are modified by the presence of aspartic and glutamic acid, both as the simple amino acids and as poly-aspartate and poly-glutamate and (3) to model the interactions of acidic amino acids with calcite.

  16. High-resolution x-ray imaging using a structured scintillator

    Energy Technology Data Exchange (ETDEWEB)

    Hormozan, Yashar, E-mail: hormozan@kth.se; Sychugov, Ilya; Linnros, Jan [Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, Kista, Stockholm SE-16440 (Sweden)

    2016-02-15

    Purpose: In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Methods: Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator array to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. Results: The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. Conclusions: The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.

  17. Analysis of Soil Structure Turnover with Garnet Particles and X-Ray Microtomography.

    Science.gov (United States)

    Schlüter, Steffen; Vogel, Hans-Jörg

    2016-01-01

    Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other.

  18. Synthesis and characterization of new N-(diphenylphosphino)-naphthylamine chalcogenides: X-ray structures of (1-NHC 10H 7)P(Se)Ph 2 and Ph 2P(S)OP(S)Ph 2

    KAUST Repository

    Tomah Al-Masri, Harbi

    2012-09-01

    The reaction of 1-naphthylamine with one equivalent of chlorodiphenylphosphine in the presence of triethylamine gave the (1-NHC 10H 7)PPh 2 (1) ligand. Refluxing of 1 with elemental sulfur or grey selenium in toluene (1:1 molar ratio) afforded (1-NHC 10H 7)P(S)Ph 2 (2) and (1-NHC 10H 7)P(Se)Ph 2 (3), respectively. Moreover, the byproduct {Ph 2P(S)} 2O (4) was isolated from the reaction of 1 with elemental sulfur. Compounds 1-3 were identified and characterized by multinuclear ( 1H, 13C, 31P, 77Se) NMR spectroscopy, mass spectrometry, and elemental analysis. Crystal structure determinations of 3 and 4 were carried out. Copyright © 2012 Taylor and Francis Group, LLC.

  19. A cell for extended x-ray absorption fine structure studies of oxygen sensitive products of redox reactions

    International Nuclear Information System (INIS)

    Furenlid, L.R.; Renner, M.W.; Fajer, J.

    1990-01-01

    We describe a cell suitable for extended x-ray absorption fine structure (EXAFS) studies of oxygen and/or water sensitive products of redox reactions. The cell utilizes aluminized Mylar windows that are transparent to x rays, provide low gas permeability, and allow vacuum to be maintained in the cell. The windows are attached to the glassware with an epoxy that resists attack by common organic solvents. Additional side arms allow multiple spectroscopic probes of the same sample under anaerobic and anhydrous conditions

  20. Madelung's potentials structure of X-ray emission spectra, and reactivity of alkali metal metavanadates

    Energy Technology Data Exchange (ETDEWEB)

    Kirsanov, V.V.; Fotiev, A.A.; Tskhaj, V.A.; Cherkashenko, V.M. (AN SSSR, Sverdlovsk. Inst. Khimii)

    1983-07-01

    Madelung constants of ionic sublattices, describing the dependence of Madelung potentials on ionic charges in crystallographically non-equivalent V, O and M positions, were calculated for metavanadates MVO/sub 3/ (M=Li, Na, K, Rb, Cs). Semiempirical interpretation of the fine structure and shifts of intensity maximums of X-ray VKsub(..beta..''..beta..sup(5))- and VLsub(..cap alpha..)-emission spectra and X-ray spectral assessment of the degree of chemical bond ionicity in metavanadate oxy-vanadium sublattice are given. The reactivity of these compounds during their interaction with vanadium pentoxide and the activity of different ions in this process were considered.

  1. Coupled-cluster response theory for near-edge x-ray-absorption fine structure of atoms and molecules

    DEFF Research Database (Denmark)

    Coriani, Sonia; Christiansen, Ove; Fransson, Thomas

    2012-01-01

    triple corrected excitation energies CCSDR(3). This work is a first step toward the extension of these theoretical electronic structure methods of well-established high accuracy in UV-vis absorption spectroscopies to applications concerned with x-ray radiation. From the imaginary part of the linear...... response function, the near K-edge x-ray absorption spectra of neon, water, and carbon monoxide are determined and compared with experiment. Results at the CCSD level show relative peak intensities in good agreement with experiment with discrepancies in transition energies due to incomplete treatment...

  2. Three-Dimensional Modeling of Quasicrystal Structures from X-ray Diffraction: An Icosahedral Al-Cu-Fe Alloy.

    Science.gov (United States)

    Hong, Seung-Tae

    2017-07-03

    Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al 0.63 Cu 0.25 Fe 0.12 . Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2 5 = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis. This resulted in an initial phasing model based on chemically sensible electron density maps. The following procedure was exactly the same as that used to determine ordinary crystal structures, except that fractional indices were assigned to the reciprocal vectors relative to the three orthogonal 2-fold axes in icosahedral (I h ) symmetry to which the observed diffraction data conformed. Finally, ∼30 000 atoms were located within a sphere of a ∼48 Å radius. Structural motifs or basic repeating units with a hierarchical nature can be found. Isolated icosahedral clusters are surrounded by a concentric dodecahedron, beyond which there is a concentric truncated icosahedron. These are strikingly similar to those obtained via HD crystallography, but show very clear real-space relationships between the clusters.

  3. Syntheses and crystal structure determination by X-ray powder diffraction of new compounds of Benzovesamicol

    International Nuclear Information System (INIS)

    Rukiah, M.; Assaad, Th.

    2012-06-01

    The compound 2,2,2-Trifluoro-N-(1a,2,7,7 a-tetra-hydronaphtho[2,3-b]oxiren-3-yl)- acetamide, C 1 2H 1 0F 3 NO 2 , an important precursor in the preparation of benzovesamicol analogues for the diagnosis of Alzheimers disease, was prepared by the epoxidation of 5,8-dihydronaphthalene-1-amine using 3-chloroperoxybenzoic acid. The structure was determined by X-ray powder diffraction, multinuclear NMR spectroscopy and FT-IR spectroscopy. A pair of molecules form intermolecular N- H...O hydrogen bonds, involving the amino and oxirene groups, to produce a dimer.The two racemic compounds (2RS,3RS)-5-amino-3-(4-phenylpiperazin-1-yl)-1,2,3,4 tetrahydronaphthalene-2-ol, C 2 0H 2 5N 3 O, (I) and (2RS,3RS)-5-amino-3-[4-(3- methoxyphenyl)piperazin-1-yl]-1,2,3,4-tetrahydronaphthalene-2-ol, C 2 1H 2 7N 3 O 2 , (II) important benzovesamicol analogues for the diagnosis of Alzheimer's disease, have been synthesized and characterized by FT-IR, and 1 H and 13 C NMR spectroscopic analyses. The crystal structures were analyses using powder diffraction as no suitable single crystal were obtained. The two compounds are racemic mixtures of enantiomers which crystallize in the monoclinic system in a centrosymmetric space group (P21/c). Crystallography, in particular powder X-ray diffraction, was pivotal in revealing that the enantio-resolution did not succeed. In two compounds, the piperazine ring has a chair conformation, while the cyclohexene ring assumes a half-chair conformation. In (I) the crystal packing is mediated by weak contacts, principally by complementary intermolecular N--H...O hydrogen bonds that connect successive molecules into a chain. Further stabilization is provided by weak C--H...N contacts and by a weak intermolecular C--H...π interaction. While in (II), the crystal packing is dominated by intermolecular O--H...N hydrogen bonding which links molecules along the c direction. (authors)

  4. Investigation into structure of berylliumaluminium silicate glasses and crystals by X-ray spectroscopy

    International Nuclear Information System (INIS)

    Tykachinskij, I.D.; Gorbachev, V.V.; Petrakov, V.N.; Varshal, B.G.; Bystrakov, A.S.; Dmitriev, I.D.; Zatsepin, A.F.; Blaginina, L.A.

    1983-01-01

    For the purpose of elucidating the structural state of Be 2+ and Al 3+ ions as well as the nature of Be-O bond the investigation of glasses obtained from BeO, Al 2 O 3 and SiO 2 with different component composition is undertaken by X-ray spectroscopy. In three-component beryllium alumosilicate glasses at the ratio γ=Al 2 O 3 /BeO=0.34-1.92 the main part of Al 3+ cations forms AlO 4 groups. Be 2+ cations probably occupy several non-equivalent states. At the ''crystal-glass'' transition the reorganization of near structure of beryllium alumosilicate frame with appearance in a glass in contrast to crystal analog of beryllium cations playing the role of a glass former (being a part of glass net) as well as a modifier role occurs. For compositions with γ=1 the degree of ionic character of the Be-O bond is the greatest. The increase of Be 2+ cations fraction being a part of the glass net is characteristic feature of the glasses with parameter values γ not equal to 1

  5. Visualization of the internal structure of Didymosphenia geminata frustules using nano X-ray tomography.

    Science.gov (United States)

    Zgłobicka, Izabela; Li, Qiong; Gluch, Jürgen; Płocińska, Magdalena; Noga, Teresa; Dobosz, Romuald; Szoszkiewicz, Robert; Witkowski, Andrzej; Zschech, Ehrenfried; Kurzydłowski, Krzysztof J

    2017-08-22

    For the first time, the three-dimensional (3D) internal structure of naturally produced Didymosphenia geminata frustules were nondestructively visualized at sub-100 nm resolution. The well-optimized hierarchical structures of these natural organisms provide insight that is needed to design novel, environmentally friendly functional materials. Diatoms, which are widely distributed in freshwater, seawater and wet soils, are well known for their intricate, siliceous cell walls called 'frustules'. Each type of diatom has a specific morphology with various pores, ribs, minute spines, marginal ridges and elevations. In this paper, the visualization is performed using nondestructive nano X-ray computed tomography (nano-XCT). Arbitrary cross-sections through the frustules, which can be extracted from the nano-XCT 3D data set for each direction, are validated via the destructive focused ion beam (FIB) cross-sectioning of regions of interest (ROIs) and subsequent observation by scanning electron microscopy (SEM). These 3D data are essential for understanding the functionality and potential applications of diatom cells.

  6. Crystal structure and charge density analysis of Li2NH by synchrotron X-ray diffraction

    International Nuclear Information System (INIS)

    Noritake, T.; Nozaki, H.; Aoki, M.; Towata, S.; Kitahara, G.; Nakamori, Y.; Orimo, S.

    2005-01-01

    Complex hydrides, such as lithium amide (LiNH 2 ) and lithium imide (Li 2 NH), have recently been noticed as one of the most promising materials for reversible hydrogen storage. In this paper, we reveal the bonding nature of hydrogen in Li 2 NH crystal by synchrotron powder X-ray diffraction measurement at room temperature. The crystal structure was refined by Rietveld method and the charge density distribution was analyzed by maximum entropy method (MEM). The Li 2 NH crystal is anti-fluorite type structure (space group Fm3-bar m) consisting of Li and NH. Hydrogen atom occupies randomly the 48h (Wyckoff notation) sites around N atom. The refined lattice constant is a=5.0742(2)A. The charge density distribution around NH anion in Li 2 NH is almost spherical. The number of electrons within the sphere around the Li and NH is estimated from the obtained charge density distribution. As the result, the ionic charge is expressed as [Li 0.99+ ] 2 [NH] 1.21- . Therefore, it is confirmed experimentally that Li 2 NH is ionically bonded

  7. Electronic structure of titania aerogels: Soft x-ray absorption study

    International Nuclear Information System (INIS)

    Kucheyev, S.O.; Van Buuren, T.V.; Baumann, T.F.; Satcher, J.H.; Willey, T.M.; Muelenberg, R.W.; Felter, T.E.; Poco, J.E.; Gammon, S.A.; Terminello, L.J.

    2004-01-01

    Full text: Titania aerogels - a somewhat extreme form of nanoporous TiO 2 - are open-cell solid foams derived from highly crosslinked gels by drying them under supercritical conditions. In this presentation, the unoccupied electronic states of TiO 2 aerogels are studied by soft x-ray absorption near-edge structure (XANES) spectroscopy. High-resolution O K-edge and Ti L 2,3 -edge XANES spectra of aerogels are compared with those of rutile, anatase, and unrelaxed amorphous phases of full- density TiO 2 . Results show that all the main spectroscopic features of aerogels, reflecting the element-specific partial density of empty electronic states and correlation effects, can be attributed to the absence of long-range order in stoichiometric amorphous TiO 2 . Based on these results, we discuss the effects of short- and long-range order on the electronic structure of TiO 2 . This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48

  8. The structure and function of glutamate receptors: Mg2+ block to X-ray diffraction.

    Science.gov (United States)

    Mayer, Mark L

    2017-01-01

    Experiments on the action of glutamate on mammalian and amphibian nervous systems started back in the 1950s but decades passed before it became widely accepted that glutamate was the major excitatory neurotransmitter in the CNS. The pace of research greatly accelerated in the 1980s when selective ligands that identified glutamate receptor subtypes became widely available, and voltage clamp techniques, coupled with rapid perfusion, began to resolve the unique functional properties of what cloning subsequently revealed to be a large family of receptors with numerous subtypes. More recently the power of X-ray crystallography and cryo-EM has been applied to the study of glutamate receptors, revealing their atomic structures, and the conformational changes that underlie their gating. In this review I summarize the history of this field, viewed through the lens of a career in which I spent 3 decades working on the structure and function of glutamate receptor ion channels. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'. Published by Elsevier Ltd.

  9. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... is not a packing effect, but caused by intramolecular steric hindrance....

  10. Determination of crystal structures by x-ray diffraction: applications to a lanthanide complex and a natural organic compound

    International Nuclear Information System (INIS)

    Miranda, J.M. de.

    1986-01-01

    The study fir determining crystal structures of the Ho (ReO sub(4)) sub(3) 4 TDTD 3 H sub(2) O complex and the natural organic compound C sub(14) H sub(16) O sub(6) by X-ray diffraction are presented. The experimental equipments are described in details. (M.C.K.)

  11. Far-ultraviolet and X-ray irradiated protoplanetary disks: a grid of models : I. The disk structure

    NARCIS (Netherlands)

    Meijerink, R.; Aresu, G.; Kamp, I.; Spaans, M.; Thi, W. -F; Woitke, P.

    2012-01-01

    Context. Planets are thought to eventually form from the mostly gaseous (~99% of the mass) disks around young stars. The density structure and chemical composition of protoplanetary disks are affected by the incident radiation field at optical, far-ultraviolet (FUV), and X-ray wavelengths, as well

  12. Far-ultraviolet and X-ray irradiated protoplanetary disks : a grid of models I. The disk structure

    NARCIS (Netherlands)

    Meijerink, R.; Aresu, G.; Kamp, I.; Spaans, M.; Thi, W. -F.; Woitke, P.

    2012-01-01

    Context. Planets are thought to eventually form from the mostly gaseous (similar to 99% of the mass) disks around young stars. The density structure and chemical composition of protoplanetary disks are affected by the incident radiation field at optical, far-ultraviolet (FUV), and X-ray wavelengths,

  13. Far-ultraviolet and X-ray irradiated protoplanetary disks: a grid of models. I. The disk structure

    NARCIS (Netherlands)

    Meijerink, R.; Aresu, G.; Kamp, I.; Spaans, M.; Thi, W.-F.; Woitke, P.

    2012-01-01

    Context. Planets are thought to eventually form from the mostly gaseous (~99% of the mass) disks around young stars. The density structure and chemical composition of protoplanetary disks are affected by the incident radiation field at optical, far-ultraviolet (FUV), and X-ray wavelengths, as well

  14. Complex of structural roentgenometric and optical parameters of chest X-ray picture for automated fluorograms processing

    International Nuclear Information System (INIS)

    Rodzaevskij, S.A.

    1986-01-01

    The formalized description necessary for the development of algorithms for determination of main object boundaries by the roentgenologic picture during computerized photoroentgenograms processing is drawn up on the basis of the complex of structural roentgenometric parameters of the chest X-ray picture

  15. Single crystal X-ray structural features of aromatic compounds having a pentafluorosulfuranyl (SF5) functional group

    Czech Academy of Sciences Publication Activity Database

    Du, J.; Hua, G.; Beier, Petr; Slawin, A. M. Z.; Woollins, J. D.

    2017-01-01

    Roč. 28, č. 3 (2017), s. 723-733 ISSN 1040-0400 Institutional support: RVO:61388963 Keywords : pentafluorosulfuranyl (SF5) group * aromatic compounds * single crystal X-ray structure * intramolecular interactions * intermolecular interactions Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 1.582, year: 2016

  16. The atomic surface structure of SrTiO3 (001) studied with synchrotron X-rays

    NARCIS (Netherlands)

    Vonk, V.; Konings, S.; van Hummel, G.J.; Harkema, Sybolt; Graafsma, H

    2005-01-01

    The atomic surface structure of single terminated SrTiO3(0 0 1) (1 × 1) is investigated employing surface X-ray diffraction. In order to obtain these surfaces a special treatment is needed consisting of chemical etching and annealing. Since this is done in an aqueous and subsequently oxygen

  17. Solution of Ge(111)-(4x4)-Ag structure using direct methods applied to X-ray diffraction data

    DEFF Research Database (Denmark)

    Collazo-Davila, C.; Grozea, D.; Marks, L.D.

    1998-01-01

    A structure model for the Ge(111)-(4 x 4)-Ag surface is proposed. The model was derived by applying direct methods to surface X-ray diffraction data. It is a missing top layer reconstruction with six Ag atoms placed on Ge substitutional sites in one triangular subunit of the surface unit cell. A ...

  18. Internal structure of an intact Convallaria majalis pollen grain observed with X-ray Fresnel coherent diffractive imaging

    NARCIS (Netherlands)

    Mancuso, Adrian P; Groves, Matthew R; Polozhentsev, Oleg E; Williams, Garth J; McNulty, Ian; Antony, Claude; Santarella-Mellwig, Rachel; Soldatov, Aleksander V; Lamzin, Victor; Peele, Andrew G; Nugent, Keith A; Vartanyants, Ivan A

    2012-01-01

    We have applied Fresnel Coherent Diffractive Imaging (FCDI) to image an intact pollen grain from Convallaria majalis. This approach allows us to resolve internal structures without the requirement to chemically treat or slice the sample into thin sections. Coherent X-ray diffraction data from this

  19. Synthesis, x-ray crystallography and leishmanicidal activity of benzimidazolinyl piperidine derivative

    International Nuclear Information System (INIS)

    Saify, Z.S.; Begum, N.; Yousuf, S.; Ashraf, S.

    2014-01-01

    Protozoan parasites of the Leishmania genus are the main cause of vector-borne disease leishmaniasis throughout the world. It is caused by at least 17 different species of protozoan Leishmania and transmitted by the bite of infected sand flies. Leishmaniasis could be fatal. Present drugs have limitations to cure it due to the development of drug resistance. Hence, to design an effective leishmanicidal agent would be of great interest. Benzimidazolinyl piperidine has served as potential target due to a vast range of biological activities. In the present study a new 4-(2-keto-1-benzimidazolinyl)piperidine derivative, 1-(2-(4-fluorophenyl)-2-oxoethyl)-4-(2-oxo-2,3-dihydro-1H-benzo(d)imidazol) piperidinium bromide has been synthesized and characterized by X-ray crystallography, 1D and 2D NMR spectroscopy. Evaluation by in vitro leishmanicidal assay showed good activity. (author)

  20. Soft X-ray resonant magnetic scattering of magnetic nano-structures; Diffusion magnetique resonnante des rayons X mous dans les nanostructures magnetiques

    Energy Technology Data Exchange (ETDEWEB)

    Gerrit, Van der Laana [Daresbury Lab., Warrington WA (United Kingdom)

    2008-06-15

    Soft X-ray resonant magnetic scattering offers a unique element-, site- and valence-specific probe to study magnetic structures on the nano-length scale. This new technique, which combines X-ray scattering with X-ray magnetic circular and linear dichroism, is ideally suited to investigate magnetic superlattices and magnetic domain structures. The theoretical analysis of the polarization dependence to determine the vector magnetization profile is presented. This is illustrated with examples studying the closure domains in self-organizing magnetic domain structures, the magnetic order in patterned samples, and the local configuration of magnetic nano-objects using coherent X-rays. (author)

  1. Inner Disk Structure of Dwarf Novae in the Light of X-Ray Observations

    Directory of Open Access Journals (Sweden)

    S. Balman

    2015-02-01

    Full Text Available Diversity of the X-ray observations of dwarf nova are still not fully understood. I review the X-ray spectral characteristics of dwarf novae during the quiescence in general explained by cooling flow models and the outburst spectra that show hard X-ray emission dominantly with few sources that reveal soft X-ray/EUV blackbody emission. The nature of aperiodic time variability of brightness of dwarf novae shows band limited noise, which can be adequately described in the framework of the model of propagating fluctuations. The frequency of the break (1-6 mHz indicates inner disk truncation of the optically thick disk with a range of radii (3.0-10.0×109 cm. The RXTE and optical (RTT150 data of SS Cyg in outburst and quiescence reveal that the inner disk radius moves towards the white dwarf and receeds as the outburst declines to quiescence. A preliminary analysis of SU UMa indicates a similar behaviour. In addition, I find that the outburst spectra of WZ Sge shows two component spectrum of only hard X-ray emission, one of which may be fitted with a power law suggesting thermal Comptonization occuring in the system. Cross-correlations between the simultaneous UV and X-ray light curves (XMM −Newton of five DNe in quiescence show time lags in the X-rays of 96-181 sec consistent with travel time of matter from a truncated inner disk to the white dwarf surface. All this suggests that dwarf novae and other plausible nonmagnetic systems have truncated accretion disks indicating that the disks may be partially evaporated and the accretion may occur through hot (coronal flows in the disk.

  2. Synthesis, characterization, and X-ray crystal structure of the manganese(III) complex Mn(Sal.sub.2./sub.hn)(CH.sub.3./sub.OH)(N.sub.3./sub.) [Sal.sub.2./sub.hn = N,N'-bis(Salicylidene)-1,2-Hexanediamine

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Hadadzade, H.; Fejfarová, Karla; Dušek, Michal

    2010-01-01

    Roč. 36, č. 8 (2010), s. 618-621 ISSN 1070-3284 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : crystal structure * Jana2006 * x-ray diffraction * Schiff bases Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.591, year: 2010

  3. Synthesis, characterization, X-ray structure, optical properties and ...

    Indian Academy of Sciences (India)

    ESMA LAMERA

    inflammatory,4 antioxidant activities5 and vasorelexant effect.6 In addition, these compounds are promising materials for the development of new .... ticomponent reaction under ultrasonic irradiation of phthalhydrazide (1 mmol), 1.05 mmol of ...

  4. Synthesis, characterization, X-ray structure, optical properties and ...

    Indian Academy of Sciences (India)

    Unité de Recherche de Chimie de l'Environnement et Moléculaire Structurale, Université des Frères Mentouri, Constantine 25000, Algeria; Laboratoire Énergétique Appliquée et Matériaux, Université de Jijel, 18000 Jijel, Algeria; Département des sciences de la matière, Université Oum El Bouaghi, 04000 Oum El Bouaghi, ...

  5. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,. MARYAM MOHAMADIa,b, MEHDI ABBASNEJADc, HADI AMIRI RUDBARId and. GIUSEPPE BRUNOe. aDepartment of Chemistry, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran. bDepartment of Chemistry ...

  6. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    ... Department of Chemistry, Payame Noor University (PNU), 19395-4697 Tehran, Iran; Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran; Department of Chemical Sciences, University of Messina, Via F.

  7. Synthesis, characterization, x-ray structure and antimicrobial activity ...

    African Journals Online (AJOL)

    chlorophenyl)-2-(pyridin-4- ylcarbonyl) hydrazinecarbothioamide. ... Conclusion: The title compound represents a good lead for the development of potent antibacterial agent against Gram positive bacteria and MRSA strains. Keywords: Isoniazid ...

  8. Synthesis, characterization and X-ray structure of an oxazine ...

    African Journals Online (AJOL)

    Bulletin of the Chemical Society of Ethiopia. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 24, No 2 (2010) >. Log in or Register to get access to full text downloads.

  9. Revealing Soil Structure and Functional Macroporosity along a Clay Gradient Using X-ray Computed Tomography

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Arthur, Emmanuel

    2013-01-01

    The influence of clay content in soil-pore structure development and the relative importance of macroporosity in governing convective fluid flow are two key challenges toward better understanding and quantifying soil ecosystem functions. In this study, soil physical measurements (soil......-water retention and air permeability) and x-ray computed tomography (CT) scanning were combined and used from two scales on intact soil columns (100 and 580 cm3). The columns were sampled along a natural clay gradient at six locations (L1, L2, L3, L4, L5 and L6 with 0.11, 0.16, 0.21, 0.32, 0.38 and 0.46 kg kg−1...... clay content, respectively) at a field site in Lerbjerg, Denmark. The water-holding capacity of soils markedly increased with increasing soil clay content, while significantly higher air permeability was observed for the L1 to L3 soils than for the L4 to L6 soils. Higher air permeability values...

  10. Cation distribution in NiZn-ferrite films determined using x-ray absorption fine structure

    Science.gov (United States)

    Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.

    1996-04-01

    We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films, Ni0.15ZnyFe2.85-yO4 (y=0.16, 0.23, 0.40, 0.60). The Ni, Zn, and Fe EXAFS were collected from each sample and analyzed to Fourier transforms. Samples of Ni-ferrite, Zn-ferrite, and magnetite were similarly studied as empirical standards. These standards, together with EXAFS data generated from the theoretical EXAFS FEFF codes, allowed the correlation of features in the Fourier transforms with specific lattice sites in the spinel unit cell. We find that the Ni ions reside mostly on the octahedral (B) sites whereas the Zn ions are predominantly on the tetrahedral (A) sites. The Fe ions reside on both A and B sites in a ratio determined by the ratio of Zn/Fe. The addition of Zn displaces a larger fraction of Fe cations onto the B sites serving to increase the net magnetization. The fraction of A site Ni ions is measured to increase peaking at ≊25% for y=0.6. At higher Zn concentrations (y≥0.5) the lattice experiences local distortions around the Zn sites causing a decrease in the superexchange resulting in a decrease in the net magnetization.

  11. The sequence and X-ray structure of the trypsin from Fusarium oxysporum.

    Science.gov (United States)

    Rypniewski, W R; Hastrup, S; Betzel, C; Dauter, M; Dauter, Z; Papendorf, G; Branner, S; Wilson, K S

    1993-06-01

    The trypsin from Fusarium oxysporum is equally homologous to trypsins from Streptomyces griseus, Streptomyces erythraeus and to bovine trypsin. A DFP (diisopropylfluorophosphate) inhibited form of the enzyme has been crystallized from 1.4 M Na2SO4, buffered with citrate at pH 5.0-5.5. The crystals belong to space group P2(1) with cell parameters a = 33.43 A, b = 67.65 A, c = 39.85 A and beta = 107.6 degrees. There is one protein molecule in the asymmetric unit. X-ray diffraction data to a resolution of 1.8 A were collected on film using synchrotron radiation. The structure was solved by molecular replacement using models of bovine and S. griseus trypsins and refined to an R-factor of 0.141. The overall fold is similar to other trypsins, with some insertions and deletions. There is no evidence of the divalent cation binding sites seen in other trypsins. The covalently bound inhibitor molecule is clearly visible.

  12. X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers.

    Science.gov (United States)

    Nagle, J F; Zhang, R; Tristram-Nagle, S; Sun, W; Petrache, H I; Suter, R M

    1996-03-01

    Bilayer form factors obtained from x-ray scattering data taken with high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of dipalmitoylphosphatidylcholine at 50 degrees C under varying osmotic pressure. Artifacts in the magnitudes of the form factors due to liquid crystalline fluctuations have been eliminated by using modified Caillé theory. The Caillé fluctuation parameter eta 1 increases systematically with increasing lamellar D spacing and this explains why some higher order peaks are unobservable for the larger D spacings. The corrected form factors fall on one smooth continuous transform F(q); this shows that the bilayer does not change shape as D decreases from 67.2 A (fully hydrated) to 60.9 A. The distance between headgroup peaks is obtained from Fourier reconstruction of samples with four orders of diffraction and from electron density models that use 38 independent form factors. By combining these results with previous gel phase results, area AF per lipid molecule and other structural quantities are obtained for the fluid L alpha phase. Comparison with results that we derived from previous neutron diffraction data is excellent, and we conclude from diffraction studies that AF = 62.9 +/- 1.3 A2, which is in excellent agreement with a previous estimate from NMR data.

  13. X-ray structural studies of epitaxial yttrium silicide on Si(111)

    International Nuclear Information System (INIS)

    Martinez-Miranda, L.J.; Santiago-Aviles, J.J.; Graham, W.R.; Heiney, P.A.; Siegal, M.P.

    1994-01-01

    We performed a series of glancing angle and reflection x-ray diffraction experiments to study both the in-plane and out-of-plane structure of epitaxial YSi 2-x films grown on Si(111), with thicknesses ranging from 85 A to 510 A. These measurements allowed us to characterize the mean film lattice constants, the position correlation lengths of the film, and the presence and extent of strain as a function of film thickness. We find that the strain along the basal plane increases as a function of increasing thickness to approximately 1% in the 510 A film; the corresponding out-of-plane strain is such that the film unit cell volume increases as a function of thickness. The corresponding in-plane microscopic strain varies from 0.5% for the 85 A film to 0.3% for the 510 A film. We relate our results to the mode of film growth and the presence of pinholes in the films

  14. Structural Studies of Bleached Melanin by Synchrotron Small-angle X-ray Scattering¶

    Energy Technology Data Exchange (ETDEWEB)

    Littrell, Kenneth C.; Gallas, James M.; Zajac, Gerry W.; Thiyagarajan, Pappannan

    2003-01-01

    Small-angle X-ray scattering was used to measure the effects of chemical bleaching on the size and morphology of tyrosine-derived synthetic melanin dispersed in aqueous media. The average size as measured by the radius of gyration of the melanin particles in solution, at neutral to mildly basic pH, decreases from 16.5 to 12.5 angstroms with increased bleaching. The melanin particles exhibit scattering characteristic of sheet-like structures with a thickness of approximately 11 angstroms at all but the highest levels of bleaching. The scattering data are well described by the form factor for scattering from a pancake-like circular cylinder. These data are consistent with the hypothesis that unbleached melanin, at neutral to mildly basic pH, is a planar aggregate of 6- to 10-nm-sized melanin protomolecules, hydrogen bonded through their quinone and phenolic perimeters. The observed decrease in melanin particle size with increased bleaching is interpreted as evidence for deaggregation, most probably the result of oxidative disruption of hydrogen bonds and an increase in the number of charged, carboxylic acid groups, whereby the melanin aggregates disassociate into units composed of decreasing numbers of protomolecules.

  15. Analysis of fine structure of X-ray spectra from laser-irradiated gold dot

    International Nuclear Information System (INIS)

    Yang Guohong; Zhang Jiyan; Zhang Baohan; Zhou Yuqing; Li Jun

    2000-01-01

    The X-ray emission spectra from highly stripped plasma of gold has been observed by focusing a Nd-glass frequency tripled laser beam onto the surface of the gold dot at the XINGGUANG II laser facilities. The spectra of gold ions in the range of 0.0003 nm-0.0004 nm was recorded using the plate PET (2d = 0.8742 nm) crystal spectrometer. The code of average energy of relativistic sub-arrays was built on the basis of the code MCDF (Multi-Configuration-Dirac-Fock). Using the spin-orbit-split-arrays (SOSA) formalism, mean wavelengths and full widths at half height of isolated peaks of sub-arrays of lower charged gold ions, isoelectronic with Cu, Zn, Ga and Ge, was calculated. Twenty-six lines are interpreted, they pertain mainly to transitions of 3d-nf (n = 5,6,7) of gold ions from Ni-like to As-like. These results of experiment and calculation have important application in plasma diagnostics and examination of high Z elemental atomic structure calculation

  16. Structure of Nanoporous Biocarbon for Hydrogen Storage as Determined by Small Angle X-Ray Scattering

    Science.gov (United States)

    Wood, Mikael; Burress, J.; Pobst, J.; Carter, S.; Pfeifer, P.; Wexler, C.; Shah, P.; Suppes, G.

    2008-03-01

    As a member of the Alliance for Collaborative Research in Alternative Fuel Technology (ALL-CRAFT) our research group studies the properties of nanoporous biocarbon, produced from waste corn cob, with the goal of achieving the Department of Energy's gravimetric and volumetric standards for both hydrogen and methane gas storage. Small Angle X-Ray Scattering (SAXS) is a valuable tool in our investigation of the geometry of the pore space in our carbon samples. In this talk, we will compare the experimental SAXS data with theoretical results for various pore geometries to determine which pore models are consistent with experiment. Using data from nitrogen adsorption isotherms, along with SAXS, yields significant structural information about the pore space. This analysis should allow us to fully optimize our production process and to achieve the DOE's target storage capacities. This work supported by: 1. National Science Foundation (PFI-0438469) 2. U.S. Department of Education (P200A040038) 3. U.S. Department of Energy (DE-AC02-06CH11357) 4. University of Missouri (RB-06-040) 5. U.S. Department of Defense (N00164-07-P-1306) 6. U.S. Department of Energy (DE-FG02-07ER46411)

  17. Extended x-ray absorption fine structure investigation of annealed carbon expanded austenite

    DEFF Research Database (Denmark)

    Oddershede, Jette; Christiansen, Thomas L.; Somers, Marcel A. J.

    2012-01-01

    Carbon expanded austenite synthesized through carburizing of austenitic stainless steel powder at 380°C was annealed at 470°C and investigated with extended X-ray absorption fine structure (EXAFS) and synchrotron powder diffraction (SPD). SPD showed that the samples consisted of carbon expanded...... austenite and Hägg carbide, Ξ-M5C2. EXAFS showed that the Cr atoms were mainly present in environments similar to the carbides Hägg Ξ-M5C2 and M23C6. The environments of the Fe and Ni atoms were concluded to be largely metallic austenite. Light optical micrograph of stainless steel AISI 316 gas......-carburized in a temperature regime around 470°C. The surface zone is converted into carbon expanded austenite; the high interstitial content of carbon dissolved in the surface results in highly favorable materials properties. In the present article the local atomic environment of (annealed) carbon expanded austenite...

  18. Natural and synthetic prion structure from X-ray fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Wille, Holger; Bian, Wen; McDonald, Michele; Kendall, Amy; Colby, David W.; Bloch, Lillian; Ollesch, Julian; Borovinskiy, Alexander L.; Cohen, Fred E.; Prusiner, Stanley B.; Stubbs, Gerald; (Vanderbilt); (UCSF)

    2009-10-21

    A conformational isoform of the mammalian prion protein (PrP{sup Sc}) is the sole component of the infectious pathogen that causes the prion diseases. We have obtained X-ray fiber diffraction patterns from infectious prions that show cross-{beta} diffraction: meridional intensity at 4.8 {angstrom} resolution, indicating the presence of {beta} strands running approximately at right angles to the filament axis and characteristic of amyloid structure. Some of the patterns also indicated the presence of a repeating unit along the fiber axis, corresponding to four {beta}-strands. We found that recombinant (rec) PrP amyloid differs substantially from highly infectious brain-derived prions, both in structure as demonstrated by the diffraction data, and in heterogeneity as shown by electron microscopy. In addition to the strong 4.8 {angstrom} meridional reflection, the recPrP amyloid diffraction is characterized by strong equatorial intensity at approximately 10.5 {angstrom}, absent from brain-derived prions, and indicating the presence of stacked {beta}-sheets. Synthetic prions recovered from transgenic mice inoculated with recPrP amyloid displayed structural characteristics and homogeneity similar to those of naturally occurring prions. The relationship between the structural differences and prion infectivity is uncertain, but might be explained by any of several hypotheses: only a minority of recPrP amyloid possesses a replication-competent conformation, the majority of recPrP amyloid has to undergo a conformational maturation to acquire replication competency, or inhibitory forms of recPrP amyloid interfere with replication during the initial transmission.

  19. Structural characterization of the human cerebral myelin sheath by small angle x-ray scattering

    International Nuclear Information System (INIS)

    De Felici, M; Felici, R; Ferrero, C; Tartari, A; Gambaccini, M; Finet, S

    2008-01-01

    Myelin is a multi-lamellar membrane surrounding neuronal axons and increasing their conduction velocity. When investigated by small-angle x-ray scattering (SAXS), the lamellar quasi-periodical arrangement of the myelin sheath gives rise to distinct peaks, which allow the determination of its molecular organization and the dimensions of its substructures. In this study we report on the myelin sheath structural determination carried out on a set of human brain tissue samples coming from surgical biopsies of two patients: a man around 60 and a woman nearly 90 years old. The samples were extracted either from white or grey cerebral matter and did not undergo any manipulation or chemical-physical treatment, which could possibly have altered their structure, except dipping them into a formalin solution for their conservation. Analysis of the scattered intensity from white matter of intact human cerebral tissue allowed the evaluation not only of the myelin sheath periodicity but also of its electronic charge density profile. In particular, the thicknesses of the cytoplasm and extracellular regions were established, as well as those of the hydrophilic polar heads and hydrophobic tails of the lipid bilayer. SAXS patterns were measured at several locations on each sample in order to establish the statistical variations of the structural parameters within a single sample and among different samples. This work demonstrates that a detailed structural analysis of the myelin sheath can also be carried out in randomly oriented samples of intact human white matter, which is of importance for studying the aetiology and evolution of the central nervous system pathologies inducing myelin degeneration.

  20. X-ray diffraction study on the evaluation of the damage of steel structures subjected to earthquake

    International Nuclear Information System (INIS)

    Kaneta, Kiyoshi; Nishizawa, Hidekazu; Koshika, Norihide.

    1985-01-01

    The purpose of this study is to investigate the behavior of steel structures subjected to a strong earthquake and to evaluate the damage from a microscopic point of view. For this purpose, the authors have adopted two kinds of research techniques. The first is the ''ON-LINE EARTHQUAKE RESPONSE SIMULATION SYSTEM (ON-LINE SIMULATION SYSTEM)'', which is composed of an electro-hydrauric testing machine controled by a computer and a full scale specimen. Since a term of restoring force in the equation of motion is to be substituted by the actual reaction of a specimen under test, we can obtain the non-linear response of structure without any assumption about the hysteretic characteristics. Based on this method, the dynamic behavior of simple steel structures subjected to an intense earthquakes were simulated. The second technique is the ''X-RAY DIFFRACTION METHOD''. Although this method is usually regarded an experimental technique particular to the material science, we have realized the good applicability for the study of structural engineering. Because X-ray diffraction method is advantageous in investigating the microscopic behavior of steel member such as the plastic deformation and the low cycle fatigue. From the view point stated above, we have adopted this method for the evaluation of low cycle fatigue damage of steel member subjected to an earthquake. The experiment has been performed by radiating the X-ray at several stages of the ON-LINE SIMULATION. As has been expected, the X-ray diffraction patterns have changed in a regular manner depending on the degree of fatigue damage, and the results have shown a good possibility that the X-ray diffraction approach can offer a powerful tool for the detection of the earthquake damage of steel members. (author)

  1. Flexible retrospective phase stepping in x-ray scatter correction and phase contrast imaging using structured illumination.

    Directory of Open Access Journals (Sweden)

    Han Wen

    Full Text Available The development of phase contrast methods for diagnostic x-ray imaging is inspired by the potential of seeing the internal structures of the human body without the need to deposit any harmful radiation. An efficient class of x-ray phase contrast imaging and scatter correction methods share the idea of using structured illumination in the form of a periodic fringe pattern created with gratings or grids. They measure the scatter and distortion of the x-ray wavefront through the attenuation and deformation of the fringe pattern via a phase stepping process. Phase stepping describes image acquisition at regular phase intervals by shifting a grating in uniform steps. However, in practical conditions the actual phase intervals can vary from step to step and also spatially. Particularly with the advent of electromagnetic phase stepping without physical movement of a grating, the phase intervals are dependent upon the focal plane of interest. We describe a demodulation algorithm for phase stepping at arbitrary and position-dependent (APD phase intervals without assuming a priori knowledge of the phase steps. The algorithm retrospectively determines the spatial distribution of the phase intervals by a Fourier transform method. With this ability, grating-based x-ray imaging becomes more adaptable and robust for broader applications.

  2. Structural Characterization of Perpendicularly Aligned Submicrometer-Thick Synthetic Glycolipid Polycrystalline Films Using Conventional X-ray Diffraction

    Directory of Open Access Journals (Sweden)

    Shigesaburo Ogawa

    2017-12-01

    Full Text Available The structural analysis of the synthetic glycolipid crystalline phase has been performed during the past few decades; however, it has not been sufficiently understood in terms of both static and dynamic aspects. We have recently shown that grazing incidence X-ray diffraction (GIXD affords better information than conventional powder X-ray diffraction (PXRD for the crystal structure analysis of octyl β-d-galactoside (MOβGal using sub-micrometer-thick crystalline films and a two-dimensional detector, together with a synchrotron radiation source. However, access to this technique is not universal because of the limited machine time at the required synchrotron radiation sources. Herein, we employed XRD analysis on MOβGal hemihydrate crystalline films using commercial X-ray sources instead of synchrotron radiation sources to extend the availability of the methodology. We investigated some technical aspects of the methodology, such as incident angle and radiation time, using MOβGal polycrystalline films with different thicknesses in order to obtain sufficient reciprocal data for identifying the lattice constants with conventional X-ray sources. Complementary uses of GIXD with a two-dimensional detector, with much higher incident angles than the total reflection angle using a NANO-Viewer system and out-of-plane and in-plane measurements using SmartLab, enabled us to determine the complete lattice parameters for the MOβGal hemihydrate crystalline film.

  3. X-ray Absorption Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Yano, Junko; Yachandra, Vittal K.

    2009-07-09

    This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn4Ca cluster in Photosystem II is presented.

  4. X-ray spectroscopy of electronic structure of amorphous silicon and silicyne

    International Nuclear Information System (INIS)

    Mashin, A.I.; Khokhlov, A.F.; Mashin, N.I.; Domashevskaya, Eh.P.; Terekhov, V.A.

    2001-01-01

    SiK β and SiL 23 emission spectra of crystalline silicon (c-Si), amorphous hydrogenated silicon (α-Si:H) and silicyne have been studied by X-ray and ultrasoft X-ray spectroscopy. It is observed that SiL 23 emission spectra of silicyne displays not two maximums, as it usually observed for the c-Si and α-Si:H, but three ones. The third one is seen at high energies near 95.7 eV, and has an intensity about 75%. An additional maximum in the short- wave part of SiK β emission spectrum is observed. This difference of shapes of X-ray spectra between α-Si:H and silicyne is explained by the presence in silicyne a strong π-component of chemical bonds of a silicon atoms in silicyne [ru

  5. X-ray spectroscopy of electronic structure of amorphous silicon and silicyne

    CERN Document Server

    Mashin, A I; Mashin, N I; Domashevskaya, E P; Terekhov, V A

    2001-01-01

    SiK subbeta and SiL sub 2 sub 3 emission spectra of crystalline silicon (c-Si), amorphous hydrogenated silicon (alpha-Si:H) and silicyne have been studied by X-ray and ultrasoft X-ray spectroscopy. It is observed that SiL sub 2 sub 3 emission spectra of silicyne displays not two maximums, as it usually observed for the c-Si and alpha-Si:H, but three ones. The third one is seen at high energies near 95.7 eV, and has an intensity about 75%. An additional maximum in the short- wave part of SiK subbeta emission spectrum is observed. This difference of shapes of X-ray spectra between alpha-Si:H and silicyne is explained by the presence in silicyne a strong pi-component of chemical bonds of a silicon atoms in silicyne

  6. X-ray detector

    International Nuclear Information System (INIS)

    Houston, J.M.; Whetten, N.R.

    1981-01-01

    An ionization chamber for use in determining the spatial distribution of x-ray photons in tomography systems comprises a plurality of substantially parallel, planar anodes separated by parallel, planar cathodes and enclosed in a gas of high atomic weight at a pressure from approximately 10 atmospheres to approximately 50 atmospheres. The cathode and anode structures comprise metals which are substantially opaque to x-ray radiation and thereby tend to reduce the resolution limiting effects of xray fluoresence in the gas. In another embodiment of the invention the anodes comprise parallel conductive bars disposed between two planar cathodes. Guard rings eliminate surface leakage currents between adjacent electrodes

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

    Energy Technology Data Exchange (ETDEWEB)

    Zientek, John; Maj, Jozef; Navrotski, Gary; Srajer, George; Harmata, Charles; Maj, Lech; Lazarski, Krzysztof; Mikula, Stanislaw

    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 TTU 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.

  8. Aqueous phase synthesis of upconversion nanocrystals through layer-by-layer epitaxial growth for in vivo X-ray computed tomography

    KAUST Repository

    Li, Feifei

    2013-05-21

    Lanthanide-doped core-shell upconversion nanocrystals (UCNCs) have tremendous potential for applications in many fields, especially in bio-imaging and medical therapy. As core-shell UCNCs are mostly synthesized in organic solvents, tedious organic-aqueous phase transfer processes are usually needed for their use in bio-applications. Herein, we demonstrate the first example of one-step synthesis of highly luminescent core-shell UCNCs in the "aqueous" phase under mild conditions using innocuous reagents. A microwave-assisted approach allowed for layer-by-layer epitaxial growth of a hydrophilic NaGdF4 shell on NaYF4:Yb, Er cores. During this process, surface defects of the nanocrystals could be gradually passivated by the homogeneous shell deposition, resulting in obvious enhancement in the overall upconversion emission efficiency. In addition, the up-down conversion dual-mode luminescent NaYF4:Yb, Er@NaGdF4:Ce, Ln (Eu, Tb, Sm, Dy) nanocrystals were also synthesized to further validate the successful formation of the core-shell structure. More significantly, based on their superior solubility and stability in water solution, high upconversion efficiency and Gd-doped predominant X-ray absorption, the as-prepared NaYF4:Yb, Er@NaGdF4 core-shell UCNCs exhibited high contrast in in vitro cell imaging and in vivo X-ray computed tomography (CT) imaging, demonstrating great potential as multiplexed luminescent biolabels and CT contrast agents.

  9. Thermal, structural, and fabrication aspects of diamond windows for high power synchrotron x-ray beamlines

    International Nuclear Information System (INIS)

    Khounsary, A.M.; Phillips, W.

    1992-01-01

    Recent advances in chemical vapor deposition (CVD) technology have made it possible to produce thin free-standing diamond foils that can be used as the window material in high heat load, synchrotron beamlines. Numerical simulations suggest that these windows can offer an attractive and at times the only altemative to beryllium windows for use in third generation x-ray synchrotron radiation beamlines. Utilization, design, and fabrication aspects of diamond windows for high heat load x-ray beamlines are discussed, as are the microstructure characteristics bearing on diamond's performance in this role. Analytic and numerical results are also presented to provide a basis for the design and testing of such windows

  10. X-ray inspection of composite materials for aircraft structures using detectors of Medipix type

    International Nuclear Information System (INIS)

    Jandejsek, I; Jakubek, J; Jakubek, M; Krejci, F; Soukup, P; Turecek, D; Vavrik, D; Zemlicka, J; Prucha, P

    2014-01-01

    This work presents an overview of promising X-ray imaging techniques employed for non-destructive defectoscopy inspections of composite materials intended for the Aircraft industry. The major emphasis is placed on non-tomographic imaging techniques which do not require demanding spatial and time measurement conditions. Imaging methods for defects visualisation, delamination detection and porosity measurement of various composite materials such as carbon fibre reinforced polymers and honeycomb sendwiches are proposed. We make use of the new large area WidePix X-ray imaging camera assembled from up to 100 edgeless Medipix type detectors which is highly suitable for this type of measurements

  11. Micro-fresnel structures for microscopy of laser generated bright x-ray sources

    International Nuclear Information System (INIS)

    Ceglio, N.M.; Shavers, D.C.; Flanders, D.C.; Smith, H.I.

    1979-01-01

    A brief parametric survey of the x-ray characteristics of a gold micro-disk irradiated at 3 x 10 14 watt/cm 2 by a 1 nsec Nd-glass laser pulse has been provided as an example of a laser generated bright x-ray source. It was shown that a simple phenomenological model of the laser generated x-ray source as a microscopic equilibrium plasma radiating as a blackbody for a finite time determined by its hydrodynamic disassembly and radiation losses, serves to provide an adequate approximation to the x-ray characteristics of such sources. The current state of x-ray microscopy within the LLL laser fusion program was briefly reviewed. Kirpatrick--Baez grazing incidence reflection x-ray microscopes are being used to provide 3 to 5 μm resolution, broadband images (ΔE/E approx. 0.3) over a spectral range from .6 keV to 3.5 keV. Zone Plate Coded Imaging is used to provide 5 to 10 μm resolution, broadband (ΔE/E approx. 0.5) images over a spectral range from 3 keV to 50 keV. Efficient x-ray lensing elements with anticipated submicron resolution are being developed for narrowband (ΔE/E approx. 10 -2 ) imaging applications over a spectral range .1 keV to 8 keV. The x-ray lens design is that of a transmission blazed Fresnel phase plate. Micro--Fresnel zone plates with 3200 A minimum linewidth have been fabricated and preliminary resolution tests begun. The first resolution test pattern, having minimum linewidth of 2.5 μm, was imaged in lambda = 8.34 A light with no difficulty. Newer test patterns with submicron minimum line are being prepared for the next stage of resolution testing. An off-axis Fresnel zone plate with 1600 A minimum linewidth is presently being fabricated for use as an imaging spectrometer in order to provide spatially separated, chromatically distinct images of characteristic line emissions from laser fusion targets

  12. Tillage effects on topsoil structural quality assessed using X-ray CT, soil cores and visual soil evaluation

    DEFF Research Database (Denmark)

    Garbout, Amin; Munkholm, Lars Juhl; Hansen, Søren Baarsgaard

    2013-01-01

    Soil structure plays a key role in the ability of soil to fulfil essential functions and services in relation to, e.g., root growth, gas and water transport and organic matter turnover. The objective of this paper was: (1) To quantify tillage effects on soil structural quality in the entire topsoil....... Visual soil structure evaluation was carried out in the field at the same time as sampling. CT images (0.39 × 0.39 × 0.6 mm3 voxels) were produced using a medical X-ray CT scanner. The visual assessment showed a good structural quality in the top 5–8 cm for both treatments (Sq soil...... tillage and natural consolidation, and aggravated by a poor structural stability due to a low organic matter content. The visual soil evaluation scores were negatively correlated to soil porosity and number of pore networks estimated from X-ray CT imaging and positively correlated to the macropore...

  13. Synthesis and Pharmacology of Mono-, Di-, and Trialkyl-Substituted 7-Chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides Combined with X-ray Structure Analysis to Understand the Unexpected Structure-Activity Relationship at AMPA Receptors

    DEFF Research Database (Denmark)

    Larsen, Anja Probst; Francotte, Pierre; Frydenvang, Karla

    2016-01-01

    of a series of mono-, di-, or trialkyl-substituted 7-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides, comprising in total 16 new modulators. The trisubstituted compounds 7b, 7d, and 7e revealed potent activity (EC2× = 2.7-4.3 μM; concentration of compound responsible for a 2-fold increase...... the cyclopropyl group constitutes the best choice of substituent. 7b was subjected to X-ray structural analysis in complex with the GluA2 ligand-binding domain. We propose an explanation of the unexpected structure-activity relationship of this new series of mono-, di-, and trialkyl-substituted 1......, whereas introduction of a 4-cyclopropyl group does not enhance potency of 2,3,4-alkyl-substituted BTDs. A hydrogen bond donor in the 2-position of the BTD is not necessary for modulator potency....

  14. Probing the graphite band structure with resonant soft-x-ray fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Carlisle, J.A.; Shirley, E.L.; Hudson, E.A. [Lawrence Berkeley National Lab., CA (United States)] [and others

    1997-04-01

    Soft x-ray fluorescence (SXF) spectroscopy using synchrotron radiation offers several advantages over surface sensitive spectroscopies for probing the electronic structure of complex multi-elemental materials. Due to the long mean free path of photons in solids ({approximately}1000 {angstrom}), SXF is a bulk-sensitive probe. Also, since core levels are involved in absorption and emission, SXF is both element- and angular-momentum-selective. SXF measures the local partial density of states (DOS) projected onto each constituent element of the material. The chief limitation of SXF has been the low fluorescence yield for photon emission, particularly for light elements. However, third generation light sources, such as the Advanced Light Source (ALS), offer the high brightness that makes high-resolution SXF experiments practical. In the following the authors utilize this high brightness to demonstrate the capability of SXF to probe the band structure of a polycrystalline sample. In SXF, a valence emission spectrum results from transitions from valence band states to the core hole produced by the incident photons. In the non-resonant energy regime, the excitation energy is far above the core binding energy, and the absorption and emission events are uncoupled. The fluorescence spectrum resembles emission spectra acquired using energetic electrons, and is insensitive to the incident photon`s energy. In the resonant excitation energy regime, core electrons are excited by photons to unoccupied states just above the Fermi level (EF). The absorption and emission events are coupled, and this coupling manifests itself in several ways, depending in part on the localization of the empty electronic states in the material. Here the authors report spectral measurements from highly oriented pyrolytic graphite.

  15. Texture, residual stress and structural analysis of thin films using a combined X-ray analysis

    International Nuclear Information System (INIS)

    Lutterotti, L.; Chateigner, D.; Ferrari, S.; Ricote, J.

    2004-01-01

    Advanced thin films for today's industrial and research needs require highly specialized methodologies for a successful quantitative characterization. In particular, in the case of multilayer and/or unknown phases a global approach is necessary to obtain some or all the required information. A full approach has been developed integrating novel texture and residual stress methodologies with the Rietveld method (Acta Cryst. 22 (1967) 151) (for crystal structure analysis) and it has been coupled with the reflectivity analysis. The complete analysis can be done at once and offers several benefits: the thicknesses obtained from reflectivity can be used to correct the diffraction spectra, the phase analysis help to identify the layers and to determine the electron density profile for reflectivity; quantitative texture is needed for quantitative phase and residual stress analyses; crystal structure determination benefits of the previous. To achieve this result, it was necessary to develop some new methods, especially for texture and residual stresses. So it was possible to integrate them in the Rietveld, full profile fitting of the patterns. The measurement of these spectra required a special reflectometer/diffractometer that combines a thin parallel beam (for reflectivity) and a texture/stress goniometer with a curved large position sensitive detector. This new diffraction/reflectivity X-ray machine has been used to test the combined approach. Several spectra and the reflectivity patterns have been collected at different tilting angles and processed at once by the special software incorporating the aforementioned methodologies. Some analysis examples will be given to show the possibilities offered by the method

  16. In situ analysis of cracks in structural materials using synchrotron X-ray tomography and diffraction

    International Nuclear Information System (INIS)

    Steuwer, A.; Edwards, L.; Pratihar, S.; Ganguly, S.; Peel, M.; Fitzpatrick, M.E.; Marrow, T.J.; Withers, P.J.; Sinclair, I.; Singh, K.D.; Gao, N.; Buslaps, T.; Buffiere, J.-Y.

    2006-01-01

    The structural integrity and performance of many components and structures are dominated by cracks and hence the study of cracked bodies study is of major economical and social importance. Despite nearly 30 years of study, there is still no detailed consensus regarding either the fundamental parameters that drive cracks or the precise mechanisms of their growth in most materials. Thus, virtually all crack life prediction models currently in engineering use are largely phenomenological rather than physically based. Historically, a major hindrance to our understanding of crack initiation and propagation has been the inability to measure either the crack tip stresses or the crack morphology deep within materials. The development of very high-resolution strain and tomography mapping on third generation synchrotron sources such as the ESRF has opened up the possibility of developing complementary techniques to monitor the entire plastic/process zone growth mechanisms and the accompanying crack tip field and crack wake field around growing cracks. If realized, such techniques would produce unique information that would be invaluable both in validating present finite element simulations of fatigue crack growth and in developing the future high accuracy simulations necessary for the development of physically realistic fatigue life-prediction models. Recent technique developments at the ESRF, Grenoble, opens up the possibility of imaging cracks and crack tip stress/strain fields, and the ability to study the extend of crack closure and overload effects, even under in situ loading. In this paper, first results from synchrotron X-ray diffraction and tomography experiments performed on ID11 and ID19 (respectively) at the ESRF, Grenoble, are presented and discussed in comparison with predictions from finite element modeling

  17. WHOLE CELL TOMOGRAPHY/MOLECULAR BIOLOGY/STRUCTURAL BIOLOGY: Affordable x-ray microscopy with nanoscale resolution

    Energy Technology Data Exchange (ETDEWEB)

    Evans, James E.; Blackborow, Paul; Horne, Stephen J.; Gelb, Jeff

    2013-03-01

    Biological research spans 10 orders of magnitude from angstroms to meters. While electron microscopy can reveal structural details at most of these spatial length scales, transmission electron tomography only reliably reconstructs three-dimensional (3-D) volumes of cellular material with a spatial resolution between 1-5 nm from samples less than 500 nm thick1. Most biological cells are 2-30 times thicker than this threshold, which means that a cell must be cut into consecutive slices with each slice reconstructed individually in order to approximate the contextual information of the entire cell. Fortunately, due to a larger penetration depth2, X-ray computed tomography bypasses the need to physically section a cell and enables imaging of intact cells and tissues on the micrometer or larger scale with tens to hundreds of nanometer spatial resolution. While the technique of soft x-ray microscopy has been extensively developed in synchrotron facilities, advancements in laboratory x-ray source designs now increase its accessibility by supporting commercial systems suitable for a standard laboratory. In this paper, we highlight a new commercial compact cryogenic soft x-ray microscope designed for a standard laboratory setting and explore its capabilities for mesoscopic investigations of intact prokaryotic and eukaryotic cells.

  18. Azo dicarboxylates are not conjugated: X-ray crystal structure and theoretical calculations on di-t-butylazodicarboxylate

    Science.gov (United States)

    Goh, Mean See; Rintoul, Llew; Pfrunder, Michael C.; McMurtrie, John C.; Arnold, Dennis P.

    2015-10-01

    The X-ray crystal structure of trans-di-t-butyl azodicarboxylate (DTBAD, 2) was determined and this revealed that the torsion angle between the Ndbnd N and Cdbnd O double bonds is 84.0(2)°, and that between the anti-disposed Cdbnd O vectors is 180°. This is the first report of the solid state structure of an azodicarboxylate ester. The molecule was subjected to Density Functional Theory geometry optimization at the B3LYP/6-31G(d) level in cyclohexane medium, and the global minimum structure agreed in principle with that determined in the solid state by crystallography. The N-C(O) torsion angle in the optimized structure is 107.7°, and the Cdbnd O vectors lie in an anti relationship. Similar calculations on the unknown cis-Ndbnd N isomer revealed an optimum geometry whose energy is predicted to lie only 11.9 kJ/mol higher than that of the trans isomer. M062X/6-311+G(d) model chemistry was used to determine relative electronic energies and to conduct Natural Bond Orbital (NBO) calculations. Exploration of the energetics of rotations about the N-C(O) bonds revealed a clear preference for near-orthogonality in azodicarboxylates, and suggests almost complete absence of classical conjugation between the neighbouring π bonds. Electronic transitions were simulated using the time-dependent DFT (TD-DFT) approach at the B3LYP/6-311+G(d) level, and the weak band in the near-UV for 2 in cyclohexane was reproduced in the calculations. The electronic isolation of the Ndbnd N bond may be important in the numerous applications of azodicarboxylates in organic synthesis, and the small energy difference between the trans and cis isomers implies the likely involvement of the latter in the successful photochemical diaza-Diels-Alder reaction of diethyl azodicarboxylate with 1,3-cyclohexadiene.

  19. Structural refinement of neutron and x-ray data by the Rietveld method: application to Al2O3 and BiVO4

    International Nuclear Information System (INIS)

    Cox, D.E.; Moodenbaugh, A.R.; Sleight, A.W.; Chen, H.Y.

    1979-01-01

    The application of the Rietveld refinement technique to neutron and x-ray powder data from standard samples of Al 2 O 3 is described. The results are compared with those obtained by conventional refinements of the corresponding integrated intensities, and also with x-ray single crystal data. The Rietveld technique has also been used to analyze neutron and x-ray powder data in a structural study of BiVO 4 . Since V has a very small neutron scattering amplitude, the x-ray data allow a more accurate determination of the V position to be made

  20. O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside

    Directory of Open Access Journals (Sweden)

    Roman Sommer

    2016-12-01

    Full Text Available Selenoglycosides are used as reactive glycosyl donors in the syntheses of oligosaccharides. In addition, such heavy atom analogs of natural glycosides are useful tools for structure determination of their lectin receptors using X-ray crystallography. Some lectins, e.g., members of the tectonin family, only bind to carbohydrate epitopes with O-alkylated ring hydroxy groups. In this context, we report the first synthesis of an O-methylated selenoglycoside, specifically methyl 2-O-methyl-L-selenofucopyranoside, a ligand of the lectin tectonin-2 from the mushroom Laccaria bicolor. The synthetic route required a strategic revision and further optimization due to the intrinsic lability of alkyl selenoglycosides, in particular for the labile fucose. Here, we describe a successful synthetic access to methyl 2-O-methyl-L-selenofucopyranoside in 9 linear steps and 26% overall yield starting from allyl L-fucopyranoside.