bluuebunny/crossref_metadata_2025 huggingface dataset:
Cluster configurations in modulated EuV
x
Mo8±y
O14 crystals
Authors: Leligny H. , Grebille D. , Roussel P. , Labbé Ph. , Hervieu M. , Raveau B. , Tortelier J. , Gougeon P.
Published: July 2002

Three orthorhombic crystals of chemical formula Eu
x
V
y
Mo8±z
O14 were investigated by X-ray diffraction (Mo Kα radiation, λ = 0.71073 Å). They have nearly the same lattice parameters (a ≃ 11.3, b ≃ 10.0, c ≃ 9.2 Å), display one-dimensional incommensurate modulations of wavevector q* = γc* and are characterized by the same superspace group Cmca(00γ)s00. The crystals differ both in their compositions (namely Eu0.976(6)V1.13(5)Mo7.10(5)O14, Eu0.986(4)V1.10(3)Mo7.30(1)O14 and EuMo7.96(1)O14) and in their γ components [0.195 (2), 0.245 (2) and 0.286 (3), respectively]. The average structures of these crystals appear closely related to the structures of LaMo7.7O14 (not modulated) and LaMo8O14 (modulated); however, two main differences are outlined: first, the modulation direction is c in the Eu-containing crystals but b in the modulated La-containing crystal [q* = (1/3)b*], second, the Eu-containing crystals have centrosymmetric structures while the La-containing crystals have polar structures (space group C2ca). The Mo (or Mo and V) atoms are stacked to form (001) layers of metallic clusters. The density modulation of these structures implies the existence of the new types of clusters Mo9, Mo10, Mo6V4, Mo7V3 and Mo8V2 besides the clusters M
8 (Mo8, Mo6V2 and Mo7V) and M
7 (Mo7 and Mo6V) which are already known. Mo8 units with cis and trans configurations and Mo6V2 units with a trans configuration appear as the main cluster types in these crystals. The nature of the metallic clusters changes along c, but inside one (001) layer it is likely that only one cluster type with a given configuration is present. The main structural result is the formation, in some unit cells, of strong intercluster Mo—Mo, Mo—V or V—V bonds with distances close to 2.6 Å within a layer as well as between two neighbouring layers.
On the polymorphism of a sapogenin monohydrate induced by different rotations of water molecules
Authors: Fábián László , Argay Gyula , Kálmán Alajos
Published: July 2002

The structure of 1β,3β,11α-trihydroxyspirosta-5,25(27)-diene (C27H40O5; a steroidal sapogenin) isolated from Helleborus serbicus Adam 1906 (Ranunculaceae) and crystallized from absolute ethanol as a monohydrate (melting point 519–522 K) had been characterized by two symmetry-independent binary (steroid–water) layers, cross-linked by hydrogen bonds [Kálmán et al. (1985). Acta Cryst. C41, 1645–1647]. Recently, a novel monohydrate was crystallized again from absolute ethanol (source: Helleborus multifidus subspecies serbicus) with a somewhat higher melting point of 525–526 K. X-ray analysis of these crystals [Argay et al. (1998). Acta Chim. Hung.
135, 449–456] revealed a novel polymorph (hereinafter denoted polymorph
B
), which is also built up by two binary layers of C27H40O5 and H2O, but in which the relative position of these layers differs from that found in the first modification (polymorph
A
). Comparing the two polymorphs, layers of one type are found to be similar, displaying identical hydrogen bonding, whereas layers of the second type differ with respect to the orientations adopted by the water molecules; these orientations also differ from those in the layers of the first type. Consequently, by these water rotations, hydrogen bonds, at least partly, are reversed. This leads to two different close packings: in form
A
four consecutive layers are cross-linked by two homomolecular (hydroxyl...hydroxyl and water...water) hydrogen-bond pairs, while in
B
there are only heteromolecular hydroxyl...water bonds. These hydrogen-bond dissimilarities together with the differences in the weak CH...X
etc. interactions explain the greater stability of the higher melting-point form
B
.
Conformational preferences in 2-nitrophenylthiolates: interplay between intra- and intermolecular forces; structures of (E)-1-(4-methyl-2-nitrobenzenethiolato)-2-phenylethene, S-(2-nitrophenyl)benzenecarbothiolate and 1-(2-nitrophenylthio)-2,5-pyrrolidinedione
Authors: Low John N. , Storey Emily J. , McCarron Mary , Wardell James L. , Ferguson George , Glidewell Christopher
Published: July 2002

In (E)-1-(4-methyl-2-nitrobenzenethiolato)-2-phenylethene, C15H13NO2S (1) (orthorhombic Pbca), the nitro group is almost coplanar with the adjacent aryl ring, but the dihedral angles between the nitro-aryl and styryl fragments is ∼121°. The molecules are linked by paired C—H...O hydrogen bonds in a chain of rings. In S-(2-nitrophenyl)benzenecarbothiolate, C13H9NO3S (2) (monoclinic P21/a), the nitro group is rotated by 33.0 (2)° out of the plane of the adjacent aryl ring and the thiobenzoate group is strongly twisted away from the plane of the disubstituted aryl ring. The molecules of (2) are linked into chains by C—H...O hydrogen bonds, and each chain is linked to two neighbouring chains by means of aromatic π...π stacking interactions. In 1-(2-nitrophenylthio)-2,5-pyrrolidinedione, C10H8N2O4S (3) (monoclinic P21/a), the nitro group is again almost coplanar with the adjacent aryl ring, but the pyrrolidinedione unit is almost orthogonal to the O2NC6H4SN plane. There are three types of C—H...O hydrogen bond in the structure, and these link the molecules into a two-dimensional net. The conformations of these molecules have been investigated by SCF calculations and two energy minima have been identified for each: the molecules of (1) and (3) adopt conformations in their crystals which are close to those at the overall energy minima calculated for isolated molecules, while molecules of (2) adopt a conformation in the crystal close to that calculated for the local energy minimum. Comparisons are made with the structures of some related compounds and it is concluded that, while the nature of the two conformational minima is determined by intramolecular forces, the choice between them is determined primarily by intermolecular forces.
Supramolecular chemistry of amine–phenol adducts; novel three-dimensional framework structures in adducts of bis(2-aminoethyl)amine with 4,4′-sulfonyldiphenol, 1,1,1-tris(4-hydroxyphenyl)ethane and 3,5-dihydroxybenzoic acid, and in the methanol-solvated adduct of tris(2-aminoethyl)amine with 4,4′-biphenol
Authors: Glidewell Christopher , Ferguson George , Gregson Richard M. , Campana Charles F.
Published: July 2002

Bis(2-aminoethyl)amine–4,4′-sulfonyldiphenol (1/3) (1) (orthorhombic Pccn with Z′ = 0.5) is a salt, [HN(CH2CH2NH3)2]2+.[O2S(C6H4O)2]2−.[O2S(C6H4OH)2]2, containing both dianionic and neutral bis-phenol units. The neutral and anionic bis-phenol units are linked by strong O—H...O− hydrogen bonds to form ladders built from R{_4}{^4}(48) rings: each ladder is interwoven with its two nearest neighbours to form a continuous two-dimensional sheet. The amine cations play two roles: they link each ladder to its two next-nearest neighbours by means of N—H...O hydrogen bonds and they also link each sheet to the two neighbouring sheets, again via N—H...O hydrogen bonds, thus generating a three-dimensional framework. Bis(2-aminoethyl)amine–1,1,1-tris(4-hydroxyphenyl)ethane–methanol (1/4/1) (2) (triclinic P1¯ with Z′ = 0.5) consists entirely of neutral fragments. The tris-phenol units are linked by O—H...O hydrogen bonds into molecular ladders built from R{_4}{^4}(48) rings: these ladders are linked by the amine units, firstly into sheets and thence into a three-dimensional framework. Bis(2-aminoethyl)amine–3,5-dihydroxybenzoic acid (1/2) (3) (monoclinic P21/c with Z′ = 1) is a salt [HN(CH2CH2NH3)2]2+.[{(HO)2C6H3COO}−]2. The 3,5-dihydroxybenzoate anions are linked by O—H...O hydrogen bonds into interwoven and cross-connected (001) sheets linked by further O—H...O hydrogen bonds into a three-dimensional framework. The (001) sheets are further linked by ladders formed from both cations and anions. Tris(2-aminoethyl)amine–4,4′-biphenol–methanol (1/3/1), (4) (monoclinic P21), is a salt [{(H2NCH2CH2)2N(CH2CH2NH3)}+]2.[OC6H4C6H4O]2−.[HOC6H4C6H4OH]5.[MeOH]2, with Z′ = 1. The asymmetric unit, containing ten independent molecular components, can be regarded as a supermolecule held together by a total of 13 independent hydrogen bonds, of O—H...O, O—H...N and N—H...O types. The supermolecules are linked by O—H...O and N—H...O hydrogen bonds into two-dimensional sheets, generated by translation; further N—H...O hydrogen bonds around the 21 screw axes link neighbouring sheets together into a three-dimensional framework.
Structure and thermal behavior of the new superprotonic conductor Cs2(HSO4)(H2PO4)
Authors: Chisholm Calum R. I. , Haile Sossina M.
Published: July 2002

Ongoing studies of the CsHSO4–CsH2PO4 system, aimed at developing novel proton conducting solids, resulted in the new compound Cs2(HSO4)(H2PO4) (dicesium hydrogensulfate dihydrogenphosphate). Single-crystal X-ray diffraction (performed at room temperature) revealed Cs2(HSO4)(H2PO4) to crystallize in space group P21/n with lattice parameters a = 7.856 (8), b = 7.732 (7), c = 7.827 (7) Å, and β = 99.92 (4)°. The compound has a unit-cell volume of 468.3 (8) Å3 and two formula units per cell, giving a calculated density of 3.261 Mg m−3. Six non-H atoms and two H atoms were located in the asymmetric unit, with SO4 and PO4 groups randomly arranged on the single tetrahedral anion site. Refinement using all observed reflections yielded weighted residuals of 0.0890 and 0.0399 based on F
2 and F values, respectively. Anisotropic temperature factors were employed for all six non-H atoms and fixed isotropic temperature factors for the two H atoms. The structure contains zigzag chains of hydrogen-bonded anion tetrahedra that extend in the [010] direction. Each tetrahedron is additionally linked to a tetrahedron in a neighboring chain to give a planar structure with hydrogen-bonded sheets lying parallel to (1¯01). Thermal analysis of the superprotonic transition in Cs2(HSO4)(H2PO4) showed that the transformation to the high-temperature phase occurs by a two-step process. The first is a sharp transition at 334 K and the second a gradual transition from 342 to 378 K. The heat of transformation for the entire process (∼330–382 K) is 44 ± 2 J g−1. Thermal decomposition of Cs2(HSO4)(H2PO4) takes place at much higher temperatures, with an onset of approximately 460 K.
A five-dimensional structural investigation of the misfit layer compound [Bi0.87SrO2]2[CoO2]1.82
Authors: Leligny H. , Grebille D. , Pérez O. , Masset A. C. , Hervieu M. , Raveau B.
Published: July 2002

The structure of the misfit layer compound [Bi_{0.87}SrO_2]_2[CoO_2]_{1.82}, bismuth strontium cobaltite, was determined by single-crystal X-ray diffraction using the five-dimensional superspace-group formalism. This composite crystal, of monoclinic symmetry, is composed of two subsystems exhibiting incommensurate periodicities along b, the binary axis direction. The first composite part [Bi_{0.87}SrO_2] displays an intrinsic modulation of planar monoclinic type characterized by the wavevector {\bf q}{^*} = 0.293 {\bf a}{^*}+0.915 {\bf c}{^*}. The second composite part [CoO_2] shows two different centered lattice variants. The structure of the misfit layer crystal can be described as an alternation along c of distorted rock-salt-type slabs, formed from [BiO] and [SrO] layers (first subsystem), and of [CoO_2] layers (second subsystem) displaying a distorted CdI_2-type structure. Two main structural results are obtained. First, as a consequence of the intrinsic modulation, disordered zones, characterized by Bi vacancies, are regularly distributed in the [BiO] layers. Second, strong chemical bonds are implied between the strontium atoms of the first subsystem and the oxygen atoms of the second one.
Optical transform methods 1939–1969
Authors: Harburn G. , Taylor C. A.
Published: July 2002

Sir Lawrence Bragg's flair for identifying the essential physical principles underlying the most complex phenomena is exemplified by his introduction of optical diffraction studies as a means of solving X-ray diffraction problems. This paper reviews briefly some of the many developments that have stemmed from his original idea.
Dynamic density and structure factors for rigid molecules with large librations
Authors: Scheringer C.
Published: July 2002

For rigid molecules which undergo large librations, the dynamic density and the dynamic molecular scattering factor are derived. The general case is treated where translations and librations of the molecule are coupled (no site symmetry). The dynamic molecular scattering factor is an integral which cannot generally be solved, and temperature factors generally do not appear. For the special case of statistically independent translations and librations, a temperature factor for the translations of the molecule is obtained. Moreover, temperature factors are obtained for density units which are spherically symmetric, since the motions of these density units can be described by translations only. The possible cases for which spherically symmetric density units can be assumed and, hence, temperature factors can be applied, are discussed.
Docking structures of domains into maps from cryo-electron microscopy using local correlation
Authors: Roseman Alan M.
Published: July 2002

Accurate maps of large macromolecular complexes can be calculated from cryo-electron micrographs of non-crystalline specimens to resolutions of about 10 Å. A method to dock the atomic structures of domains solved by X-ray crystallography or nuclear magnetic resonance into cryo-EM maps is presented. Domains can be docked independently into large complexes without prior definition of the boundaries. No special symmetry is assumed and the procedure is suitable for general application to almost any system where a cryo-EM map (at 15 Å resolution or better) of a complex has been obtained and the atomic structures of the components are available. This is achieved through use of a real-space density-matching procedure based on local correlation. A complete asymmetric unit search correlating a density object derived from the atomic coordinates and the density of the EM map is performed. The correlation coefficient is calculated locally in real space using only values of the search object and corresponding samples extracted from the EM map which are under the `footprint' of the positioned search object. The procedure has been demonstrated by docking the domains of GroEL from the crystal structure into a cryo-EM map Fourier filtered to 12 or 15 Å resolution. The correct positions were found without applying any additional constraints. A model of the oligomer built from the docked domains compared favourably with the known crystal structure, confirming the validity of the approach. The procedure is designed to facilitate the incorporation of additional constraints on the docking solutions, which could help to dock using lower resolution maps.
Using electron-microscopy images as a model for molecular replacement
Authors: Dodson Eleanor J.
Published: July 2002

This review addresses the technical problems encountered while using models based on electron microscopy to generate initial phases for crystallographic studies. The test cases used were the gp6 portal protein with 13-fold rotational symmetry and the human hepatitis virus HepB, a viral assembly with T = 4 icosohedral symmetry.
A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement
Authors: Vellieux F. M. D.
Published: July 2002

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst.
28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.
A flash-annealing technique to improve diffraction limits and lower mosaicity in crystals of glycerol kinase
Authors: Yeh Joanne I. , Hol Wim G. J.
Published: July 2002

A flash-annealing method has been developed that increases the diffraction limits, and simultaneously decreases the mosaicity of glycerol kinase crystals. This technique utilizes brief thawing and rapid freezing cycles of the crystal in the cold nitrogen stream. The effective resolution limits increased almost by 0.8 Å, from 3.6 to 2.8 Å, and mosaicity values halved.
Preliminary crystallographic studies of triosephosphate isomerase (TIM) from the hyperthermophilic Archaeon Pyrococcus woesei
Authors: Bell Graeme S. , Russell Rupert J. M. , Kohlhoff Michael , Hensel Reinhard , Danson Michael J. , Hough David W. , Taylor Garry L.
Published: July 2002

Recombinant triosephosphate isomerase (TIM) from a hyperthermophilic Archaeon, Pyrococcus woesei, has been crystallized. Three crystal forms have been obtained: monoclinic, orthorhombic and hexagonal. The monoclinic crystals belong to space group P21 with cell dimensions a = 79.1, b = 89.2, c = 145.4 Å and β = 92.8°, and diffract to at least 2.6 Å. The orthorhombic crystals belong to space group P21212 with a = 89.4, b = 155.9, c = 79.5 Å, and diffract to 2.9 Å. Diffraction from the hexagonal form showed extensive disorder. The monoclinic form contains two tetramers in the asymmetric unit, which are in the same orientation but related by a pseudo-centring. The orthorhombic form contains one tetramer in the asymmetric unit which is in approximately the same orientation as in the monoclinic form. Knowledge of the structure of this hyperthermostable TIM, which is tetrameric in contrast to dimeric forms previously observed, will add to the understanding of protein thermostability.
Iditis: Protein Structure Database
Authors: Gardner Stephen , Thornton Janet
Published: July 2002

The validation, enrichment and organization of the data stored in PDB files is essential for those data to be used accurately and efficiently for modelling, experimental design and the determination of molecular interactions. The Iditis protein structure database has been designed to allow the widest possible range of queries to be performed across all available protein structures. The Iditis database is the most comprehensive protein structure resource currently available, and contains over 500 fields of information describing all publicly deposited protein structures. A custom-written database engine and graphical user interface provide a natural and simple environment for the construction of searches for complex sequence- and structure-based motifs. Extensions and specialized interfaces allow the data generated by the database to used in conjunction with a wide range of applications.
Software for handling macromolecular envelopes
Authors: Kleywegt G. Jacob , Jones Thomas A.
Published: July 2002

Macromolecular phase-refinement and phase-extension calculations using real-space electron-density averaging techniques require accurate envelopes (or masks) to define the boundaries of each domain or molecule whose density is to be averaged. An extensive set of tools, implemented in four computer programs (O, MAMA, COMA and MASKIT) are described which can be used to generate such envelopes (either from an atomic model or based on local density-correlation maps), to improve them, to remove overlap owing to crystallographic or non-crystallographic symmetry, to display them and to manipulate them in a variety of manners.
Purification, crystallization and preliminary X-ray crystallographic studies of S. cerevisiae Hsp40 Sis1
Authors: Sha Bingdong , Cyr Douglas
Published: July 2002

Heat-shock protein 70 (Hsp70), one of the major molecular chaperones, has been shown to play a central role in many cellular processes. Heat-shock protein 40 (Hsp40) works as a co-chaperone for Hsp70. Hsp40, bound by unfolded polypeptide, can interact directly with Hsp70 to stimulate the ATPase activity of Hsp70. Hsp40 can also bind to unfolded polypeptides and prevent them from aggregating in vitro, thus acting as an independent molecular chaperone. The S. cerevisiae Hsp40 Sis1 C-terminal peptide-binding domain has been crystallized. The crystals diffract to 2.7 Å and belong to space group P41212 or P43212 with a = 73.63, c = 80.16 Å. The structure determination by the MAD method is under way.
Data processing
Authors: Rossmann Michael G. , van Beek Cornelis G.
Published: July 2002

X-ray diffraction data processing proceeds through indexing, pre-refinement of camera parameters and crystal orientation, intensity integration, post-refinement and scaling. The DENZO program has set new standards for autoindexing, but no publication has appeared which describes the algorithm. In the development of the new Data Processing Suite (DPS), one of the first aims has been the development of an autoindexing procedure at least as powerful as that used by DENZO. The resultant algorithm will be described. Another major problem which has arisen in recent years is scaling and post-refinement of data from different images when there are few, if any, full reflections. This occurs when the mosaic spread approaches or exceeds the angle of oscillation, as is usually the case for frozen crystals. A procedure which is able to obtain satisfactory results for such a situation will be described.
Ethylammonium nitrate: a protein crystallization reagent
Authors: Garlitz Jennifer A. , Summers Catherine A. , Flowers Robert A. , Borgstahl Gloria E. O.
Published: July 2002

Ethylammonium nitrate (EAN) is a liquid organic salt that has many potential applications in protein chemistry. Because this solvent has hydrophobic and ionic character as well as the ability to hydrogen bond, it is especially well suited for broad use in protein crystallography. For example, EAN may be used as an additive, a detergent, a precipitating agent or to deliver ligands into protein crystals. A discussion of the crystallization of lysozyme using EAN as a precipitating agent is given here.
Purification and crystallization of precursors and autoprocessed enzymes of Flavobacterium glycosylasparaginase: an N-terminal nucleophile hydrolase
Authors: Cui Tao , Liao Ping-Hsi , Guan Chudi , Guo Hwai-Chen
Published: July 2002

Glycosylasparaginase (GA) represents a novel group of proteins that are activated by self-catalyzed peptide-bond cleavage from a single-chain precursor to yield the two subunits required for hydrolase activity. The wild-type GA precursor autoproteolyzes spontaneously into α and β subunits. Strategies are reported here for purification to homogeneity of GA from Flavobacterium meningosepticum in both single-chain precursor and mature (autoprocessed) forms. The recombinant proteins crystallize in different space groups: P1 and P21 for the precursor and mature enzymes, respectively. The precursor crystals diffract to 1.9 Å resolution with laboratory X-ray radiation.
Study by X-ray absorption spectroscopy of Si3N4 films after Cu or Fe implantation and thermal treatment
Authors: Traverse A. , Delobbe A. , Zanghi D. , Girardeau T. , Flank A.-M.
Published: July 2002

Si3N4 amorphous thin layers prepared by sputtering have been implanted either with Cu or with Fe ions. X-ray absorption spectroscopy was performed at the Si K edge to characterise the electronic empty states of p character, the structural state of the initial layers and the modifications around Si induced by implantation and a post-annealing treatment. We show that the energy deposition process mainly leads to a reorganisation of the second coordination shell around Si, i.e. concerns the Si-Si bonds.
XANES study of Li-MgO and Li-La2O3-MgO catalysts for oxidative coupling of methane
Authors: Aritani Hirofumi , Yamada Hiroyuki , Yamamoto Takashi , Tanaka Tsunehiro , Imamura Seiichiro
Published: July 2002

To characterize the defect sites in the near-surface and bulk phase of Li-MgO and Li-La2O3-MgO, XANES at Mg K-edge and La L3-edge was applied. For Li-MgO, it can be suggested that Li doping at a low content (2.5 wt%) brings about the formation of defect species only in the near-surface. This is due to the localization of doped Li ions in the surface, and thus the catalytically active species containing [Li+-O-] type center exist in the surface region. After OCM reaction, the defect species are formed in the near-surface over MgO and Li-MgO. By addition of La2O3 to Li-MgO (La/(Mg+La)=0.25), the structural change during the reaction is almost suppressed in the surface. In addition, the Li-La2O3-MgO shows higher C2 selectivity than Li-MgO.
Magnetic domains in nanostructured media studied with M-TXM
Authors: Fischer P. , Eimüller T. , Schütz G. , Bayreuther G. , Tsunashima S. , Takagi N. , Denbeaux G. , Attwood D.
Published: July 2002

Combining X-ray magnetic circular dichroism (X-MCD) with a transmission X-ray microscope (TXM) allows to image element-specifically magnetic domain structures with 25 nm lateral resolution. Both in-plane and out-of-plane systems can be studied in applied magnetic fields. Thus field-dependent parameters, as individual nucleation fields in magnetic nanostructures can be deduced and related to morphology. Images of thermomagnetically written bits in magneto-optical TbFeCo media proof the reliability of the writing process and the importance of an exact thermal design of the systems. Domains observed at corresponding Co L edges proof the chemical sensitivity of M-TXM and its potential to image few monolayer systems.
XAFS investigations of tin nitrides
Authors: Lützenkirchen-Hecht Dirk , Scotti Nicole , Jacobs Herbert , Frahm Ronald
Published: July 2002

Tin nitrides (Sn3N4) prepared by the reaction of Sn-halides with KNH2 in liquid ammonia and a subsequent vacuum annealing procedure were investigated with transmission mode XAFS experiments. While the near edge data suggest the presence of a univalent Sn-compound with a valency close to +4, the analysis of the extended X-ray absorption fine structure proves the presence of two different local Sn sites in this crystal structure: While Sn(1) is surrounded by 4 nitrogen in a distance of 2.06 Å, each Sn(2) ion is coordinated with 6 nitrogen at about 2.17 Å radial distance.
Characterization of silica-supported Ni catalysts effective for methane decomposition by Ni K-edge XAFS
Authors: Takenaka Sakae , Ogihara Hitoshi , Yamanaka Ichiro , Otsuka Kiyoshi
Published: July 2002

The structural change of Ni species during the methane decomposition into hydrogen and carbon over Ni/SiO2 catalyst was investigated by Ni K-edge XANES/EXAFS. Before the contact of methane with the Ni/SiO2 catalyst, Ni species were present as Ni metal mainly. The structure of the Ni metal did not change appreciably when the Ni/SiO2 was actively decomposing methane. In contrast, the formation of nickel carbide species was observed at the deactivation stage of the catalyst.
XAFS studies of Tb or Eu cored dendrimer complexes with various properties of luminescence
Authors: Seto Takatoshi , Kawa Manabu , Sugiyama Kiyoshi , Nomura Masaharu
Published: July 2002

We studied the extended X-ray absorption fine structure (EXAFS) of Tb or Eu L3-edge of Tb(III) or Eu(III)-cored complexes of different luminescence to which different poly(benzyl ether) dendrons coordinated. The complexes were prepared via a ligand exchange reaction of dendritic carboxylic acid and acetate. Results show that (a) the Eu complex of the first generation of the 3,4- or 3,5-dibenzyloxyphenyl type had a coordination structure different from that of the 2,4-dibenzyloxyphenyl type; (b) the Eu complex of the first generation of 3,5-dinaphthylmethoxyphenyl type had a Eu-O coordination number higher than the total number of oxygen atoms in the carboxylate groups; (c) the Tb complex of the bulky fourth generation had a Tb-O coordination number higher than that of the first generation. These results show that the different poly(benzyl ether) dendrons cause the different coordination, which might differently influence the luminescence properties of the complexes.
XAFS study on gallium ions implanted in silicon carbide
Authors: Yamaguchi Hirotaka , Tanaka Yasunori
Published: July 2002

Local structure of gallium ions implanted in silicon carbide has been investigated using extended X-ray absorption fine structure on the Ga K-edge. The crystallinity of the implantation layer is compared in the samples prepared under several different conditions of implantation temperature and post-implantation annealing. It is found that significant damage is induced by the implantation at room temperature, but the crystallinity recovers by the subsequent annealing at high temperature at 1600 °C. On the other hand, the best crystallinity is obtained by the implantation at high temperature of 500 °C, but the annealing results in degrading the crystallinity. This indicates an influence of the post-implantation annealing at high temperature on the crystallinity in atomic level, which relates to the secondary defects in lattice observed by electron microscope.
Probability density of wave function of excited photoelectron: understanding XANES features
Authors: Sipr Ondrej
Published: July 2002

Interpretation of XANES spectra suffers from a poor intuitive understanding of the relation between spectral features and structural elements of a material. An attempt to alleviate this shortcoming is made by exploring a spatial distribution of probability density of wave functions of photoelectrons excited during the photoabsorption process. One has to add incoherently squares of wave functions which describe participating photoelectron diffraction (PED) processes, weighted by normalized PED cross sections. As an example, we investigate probability density of wave functions relevant to Ag L
1 and L
3 XANES of Ag2O.
Symmetry role on the pre-edge X-ray absorption fine structure at the metal K edge
Authors: Wu Ziyu , Natoli C. R. , Marcelli A. , Paris E. , Seifert F. , Zhang J. , Liu T.
Published: July 2002

The preedge features in a system with `even' symmetry, apart from quadrupolar transition contribution, are mainly dipolar in character, associated with the existence of unoccupied states made up of mixed cation-4p with higher-neighboring cation-3d orbitals, and reflect the density of states due to the medium-range order of the system. In `odd' symmetry materials these preedge features are the result of a transition from the 1s to a final density of states of p symmetry due to an unsymmetrical mixing of the ligand wave functions with the central cation 3d orbitals, similar to atetrahedral configuration. These results are validated for Fe as a photoabsorber by comparing XAS spectra of Fe2SiO4 (fayalite) to ab initio full multiple scattering calculations at the Fe K edge, but pertain to all systems containing sixfold-coordinated cations.
Theory of oxygen 1s resonant X-ray emission spectroscopy in copper-based oxides
Authors: Okada Kozo , Kotani Akio
Published: July 2002

Many-body effects on the oxygen 1s resonant X-ray emission spectrum (O 1s RXES) in copper-based oxides, such as Sr2CuO3 and La2CuO4, are discussed on the basis of cluster-model calculations. The Zhang-Rice singlet excitation, which is a typical many-body state in Cu-based oxide systems, can be detected at low temperatures where the antiferromagnetic correlation between the neighboring Cu spins is strong. Thus the present study emphasizes that the O 1s RXES can be a good tool to obtain information on the Cu 3d states. In particular the polarization-dependent RXES gives the symmetry-decomposed information.
Multielectron excitations probed by helicity-modulation XMCD at K-edge in 3d transition metal compounds
Authors: Kawamura Naomi , Yamamoto Tatsuya , Maruyama Hiroshi , Harada Isao , Suzuki Motohiro , Ishikawa Testuya
Published: July 2002

Multielectron excitations (MEE) have been investigated using X-ray magnetic circular dichroism (XMCD) at the K-edge in 3d transition metal compounds. In the range of 50-70 eV above the absorption edge, a dichroic signal that is associated with MEE was identified. This phenomenon is thought to occur due to the super Coster-Kronig transition described as the final states (1s)1(3p)5(3d)
n+2 resulting from the 3p --> 3d transitions. In order to verify this interpretation, XMCD measurements using the helicity-modulation method and calculations of the dichroic spectrum were performed based on this super Coster-Kronig transition.
XAFS analysis of triiodide ion in solutions
Authors: Sakane Hideto , Mitsui Takayuki , Tanida Hajime , Watanabe Iwao
Published: July 2002

Iodine K-edge XAFS of triiodide ions in various solvents were measured at SPring-8 BL01B1 and analyzed. Though the anion takes a linear and symmetric form, the second peak expected from enhanced multiple scatterings can be hardly observed because of its large vibrations. The bond distances and the Debye-Waller factors for the I-I couple vary when protic solvents were used. It was indicated that the larger the Mayers' acceptor number of the solvent is, the larger the Debye-Waller factor is. It was also found that among the aprotic solvents, the larger the Gutmann's donor number is, the smaller the Debye-Waller factor is.
EXAFS and thermodynamics of Fe(II) spin transition polymeric compounds
Authors: Michalowicz Alain , Moscovici Jacques , Charton Julien , Sandid Fares , Benamrane Fayçal , Garcia Yann
Published: July 2002

We have studied the temperature variations of the EXAFS spectra of three Fe(II)/triazole-based spin transition polymeric compounds compared to a monomer belonging to the same family. These compounds have various temperatures of transition and hysteresis loop widths. In the three polymers, the Fe-Fe-Fe alignment, detected by a multiple scattering signal at the double Fe-Fe distance, is preserved through the spin transition. For the four compounds, we have studied the variations versus temperature of the Debye-Waller factors for both FeN6 (first shell) and Fe-Fe-Fe (multiple scattering path, only for the polymers). We report a strong increase of σ2(FeN6) through the spin transition for the monomer and two of the polymeric species. For the polymers an increase of σ2(Fe-Fe-Fe) is also observed. These observations confirm the results available in the literature, and we confirm the interpretation as an increase of the vibrational part of the DW. For one particular polymer, we observe an unexpected behaviour: no significant increase of the Debye-Waller factor from low spin to high spin states. The EXAFS study of these non mono-crystalline species is the only way to discuss the local structure-thermodynamics properties relationships, and particularly the so-called cooperative effect in the spin transition process.
XAFS theory studied by closed-path Green's function
Authors: Fujikawa Takashi
Published: July 2002

The basic framework of X-ray absorption fine structure (XAFS) theory is formulated by use of the non-equilibrium Keldysh–Green function, which presents a unified view of XAFS spectra at zero and nonzero temperature. In particular, the relation between the scattering Green's function and the retarded Green's function G

r
is discussed, along with resonance effects in XAFS. The latter effects give rise to unexpected peaks within one-electron theory. Loss effects, both intrinsic and extrinsic, are also discussed.
XAFS study on the sulfidation mechanisms of Co–Mo catalysts supported on activated carbon and alumina: effect of complexing agent
Authors: Tsuji Koji , Umeki Takashi , Yokoyama Yasuharu , Kitada Takayuki , Iwanami Yoshimu , Nonaka Osamu , Shimada Hiromichi , Matsubayashi Nobuyuki , Nishijima Akio , Nomura Masaharu
Published: July 2002

The effect of nitrilotriacetic acid (NTA) as a complexing agent on the sulfidation mechanisms of Co-Mo catalysts supported on activated carbon and alumina was examined by the XAFS technique. The XAFS results revealed that NTA interacted with Co atoms and formed the Co-NTA interaction, while it showed almost no influence on the local structures around Mo atoms. The Co-NTA interaction suppressed the aggregation of cobalt atoms and the interaction between cobalt and alumina during sulfiding, and consequently promoted the formation of the Co-Mo-S phase.
Observation of anharmonicity for copper thin film near room temperatures
Authors: Yang Dong-Seok
Published: July 2002

The fluorescence EXAFS spectra for a copper thin film with a thickness of 3000Å measured at 300K, 350K and 400K were analyzed by the regularization method to directly obtain the radial distribution. The pair distribution was almost symmetric for 300K but asymmetric for 350K and 400K. This indicates that the atoms in copper vibrate anharmonically near room temperatures. The anharmonicity and the skewness of the asymmetric distribu-tion increases as temperature increases.
The use of the FEFF8 code to calculate the XANES and electron density of states of some sulfides
Authors: Lavrentyev A. A. , Nikiforov I. Ya. , Dubeiko V. A. , Gabrelian B. V. , Rehr J. J.
Published: July 2002

The FEFF8 was used to calculate x-ray absorption spectra (XANES) and the local partial electron density of states (LDOS) for several sulfides: InPS4 (twice defective chalcopyrite), CdIn2S4 (normal spinel) and Tl3AsS3 (space group R3m). The calculated XANES are compared with experimental spectra. The self-consistent MT-potentials found for clusters of about 35 atoms were used to calculate XANES and LDOS for clusters of 87 atoms in the approach of full multiple scattering. In all cases the agreement of the simulated XANES and experimental ones is quite good. The theoretical LDOS agree well with the experimental x-ray emission K- and L2,3-spectra.
X-ray absorption near edge studies of some binuclear copper(II) complexes
Authors: Shrivastava B. D. , Shrivastava Bhakta Darshan , Joshi S. K. , Pandey K. B. , Mishra A.
Published: July 2002

X-ray K-absorption near edge studies have been carried out onthe binuclear copper (II) dithiocarbamate (dtc) complexes having the following general structure. It has been found that the chemical shift values are higher in the chlorine adducts as compared to the values of chemical shift reported by us in an earlier work for the parent complexes, showing that the chlorine adducts are more ionic. The observed splitting of the principal absorption maximum (1s -> 4p) in the chlorine adducts has been explained in terms of the splitting of the metal 4p orbital degeneracy.
Thickness inhomogeneity and fluorescence effects in EXAFS spectroscopy for powder samples: solution of the inverse problem
Authors: Ryazhkin Anton , Babanov Yu. , Miyanaga Takafumi
Published: July 2002

For thin powder samples EXAFS spectra are often suffered from thickness inhomogeneity and for thick samples from fluorescence at energies above edge absorption. As a result EXAFS amplitude is decreased and information about the coordination numbers is distorted. For correction of x-ray absorption spectra on inhomogeneity and fluorescence effects we propose a new method of solving an inverse problem. Model calculations are carried out. This method is applied to preliminary processing EXAFS spectra for Ni-Mn alloys.
Changes in electronic structure by Li ion deintercalation in LiCoO2 from cobalt L-edge and oxygen K-edge XANES
Authors: Uchimoto Yoshiharu , Sawada Hiroshi , Yao Takeshi
Published: July 2002

Cobalt L-edge and oxygen K-edge X-ray Absorption Near Edge Structure (XANES) investigated change in electronic structure by electrochemical lithium ion de-intercalation in LiCoO2. The Co L-edge XANES of Li1−xCoO2 did not show any chemical shift even at high x value. The oxygen K-edge XANES of Li1−xCoO2 indicated that the holes compensating the lithium ion de-intercalation are located primarily in the oxygen 2p states rather than in the Co 3d states.
A Fe
x
Mn1-x
/Ir(001) multilayer probed by EXAFS and DAFS
Authors: Grenier S. , Renevier H. , Tonnerre J. M. , Fischer H.
Published: July 2002

Diffraction Anomalous Fine Structure (DAFS) and EXAFS measurements have been performed on a [Fe0.7Mn0.3/Ir(100)]40} superlattice at the K-edges of Fe and Mn. Theoretical EXAFS spectra have been refined: a slight difference in the first neighbor distance suggests a non homogeneous distribution of the Mn in the alloy. The smooth features of the DAFS spectra have been modeled to study the composition and the strain profile along the growth axis.
Sb K-edge absorption fine structure of Sb2Te3
Authors: Yiwata Noriyuki , Harigaya Makoto , Tani Katsuhiko , Hayakawa Kuniko , Fujikawa Takashi
Published: July 2002

In order to study the local structure of some antimony compounds, Sb K-edge XAFS spectra were measured for Sb2Te3 and InSb. The measurements were performed in the transmission mode at BL-01 of SPring-8. Though crystal structure of antimony telluride Sb2Te3 is known by X-ray diffraction analysis, the EXAFS analyses give controversial result on the Sb-Te distance and the coordination number of Sb2Te3. Comparing the observed XANES spectra for Sb2Te3 with FEFF8 calculation, we can explain the controversial results which are also supported by the observed X-ray powder diffraction.
Characterization of a Fresnel zone plate using higher-order diffraction
Authors: Takeuchi Akihisa , Suzuki Yoshio , Takano Hidekazu
Published: July 2002

The performance of a Fresnel zone plate has been tested by observing the focusing property of higher-order diffraction. The Fresnel zone plate was fabricated by the electron-beam lithography technique. The zone material was made from 1 µm-thick tantalum and the outermost zone width was 0.25 µm. The third-order focused spot size measured by the knife-edge scan method was 0.1 µm full width at half-maximum at an X-ray energy of 8 keV, which is exactly equal to one-third of the first-order focal spot size.
Fabrication of Silicon Crystals for a Pin-Post Water-Cooling System at SPring-8
Authors: Kuroda Masanori , Yamazaki Hiroshi , Suzuki Motohiro , Kimura Hidekazu , Kagaya Isao , Yamashita Chitoshi , Ishikawa Tetsuya
Published: July 2002

An internally cooled crystal with pin-post structure was fabricated using sand-blasting methods and Au-diffusive bonding techniques. Test operation at an undulator beamline of SPring-8 showed that the crystal possessed sufficient cooling capability for radiation from the SPring-8 standard in-vacuum undulator. The remaining problem was how to suppress the strain on the surface induced by bonding and water pressure.
Synchrotron X-ray Imaging of the Electron Density in RFeO3 (R = Y, Ho) Using an APD Detector
Authors: Streltsov Victor A. , Ishizawa Nobuo , Kishimoto Shunji
Published: July 2002

Structure factors for small hydrothermally grown yttrium and holmium orthoferrites, RFeO3 (R = Y, Ho), were measured with focused synchrotron radiation at wavelengths of 0.70 and 0.84 Å using both scintillation and high-speed avalanche photodiode (APD) detectors. Resulting APD Δρ images showed striking correlations between aspherical electron densities around Fe and rare-earth metals. Approximate high symmetry in the Δρ images indicates that cations deform the electron density far more strongly than the O atoms. The Ho—Fe magnetic interactions appear to affect the electron density distribution of the Fe atoms and the magnetic phase transitions. Space group Pnma, orthorhombic, YFeO3 (APD): M

r
= 192.76, a = 5.5931 (3), b = 7.6102 (4), c = 5.2806 (3) Å, V = 224.77 (2) Å3, Z = 4, D

x
= 5.695 Mg m−3, μ0.84 = 15.56 mm−1, F(000) = 356, T = 293 K, R = 0.045, wR = 0.073, S = 4.83 (9) for 1282 unique reflections; HoFeO3 (APD): M

r
= 268.78, a = 5.5922 (3), b = 7.6157 (5), c = 5.2798 (3) Å, V = 224.86 (2) Å3, Z = 4, D

x
= 7.939 Mg m−3, μ0.84 = 61.98 mm−1, F(000) = 356, T = 293 K, R = 0.036, wR = 0.037, S = 3.07 (6) for 1284 unique reflections.
High-Focusing Bragg-Crystal Polychromator Design for Energy-Dispersive X-ray Absorption Spectroscopy
Authors: Pellicer-Porres J. , San Miguel A. , Fontaine A.
Published: July 2002

The design of a highly focusing profiled Si(111) Bragg crystal polychromator for dispersive EXAFS (extended X-ray absorption fine structure) experiments is described. The contour of the crystal has been optimized to give the best focus over the full 4–13 keV energy range. The profile optimization has been improved taking into account all the degrees of freedom of the geometry and the results of X-ray tracing simulations. The profile of the crystal has been calculated to take full advantage of the new possibilities given by the undulator source and the optics of beamline ID24 at the European Synchrotron Radiation Facility. Full spot sizes have been measured to be between 20 and 40 µm in the 5–12 keV energy range. These values compare well with X-ray tracing simulations and are the smallest spots ever obtained with energy-dispersive EXAFS optics, keeping, however, a wide enough energy bandpass for most X-ray absorption spectroscopy experiments.
Powder X-ray diffraction under extreme conditions of pressure and temperature
Authors: Fiquet G. , Andrault D.
Published: July 2002

An important work has been carried out in the field of X-ray diffraction in obtaining accurate structural information from materials at extreme conditions of pressure and temperature. An experimental set-up combining a diamond-anvil high-pressure cell and a laser-heating technique has been installed at the high-pressure beamline ID30 at the ESRF (Grenoble) to study two major constituents of the Earth's deep interior: MgSiO3 perovskite and iron. Experiments carried out on MgSiO3 perovskite up to 86 GPa and over 2000 K yielded detailed structural information on this compound under these conditions and thus important constraints for the lower mantle mineralogical model, favouring a mixture of perovskite and magnesiowüstite. X-ray diffraction patterns recorded on imaging plates with micro-focused monochromatic radiation revealed a new high-temperature structure of iron above 40 GPa.
8-(2-Phenylethylamino)quinoline
Authors: Lynch Daniel E. , McClenaghan Ian
Published: July 2002

The structure of the title compound, C17H16N2, (I), comprises twisted molecules that contain a single intramolecular N—H...N hydrogen-bonding interaction. The dihedral angle between the two ring systems is 65.72 (4)°.
A rhombohedral polymorph of aqua(malonato)cadmium(II) hydrate
Authors: Naumov Pancě , Ristova Mirjana , Soˇptrajanov Bojan , Kim Moon-Jib , Lee Han-Jun , Ng Seik Weng
Published: July 2002

The Cd atom in the rhombohedral modification of aqua(malonato)cadmium(II) hydrate, [Cd(C3H2O4)(H2O)].H2O, shows pentagonal bipyramidal coordination. The malonate group chelates to the water-coordinated Cd atom; its two carboxyl groups also chelate adjacent Cd atoms.
7,8,9,10-Tetrahydro-11H-pyrido[2,3-a]carbazol-1-ium chloride
Authors: Lynch Daniel E. , McClenaghan Ian
Published: July 2002

The title compound, C15H15N2+·Cl−, (I), comprises the hydrochloride of an essentially planar tetracyclic molecule, which is protonated on the pyridine N atom. The Cl−anion resides in the plane of the molecule and is bound by N—H...Cl interactions from both heterocyclic NH groups.