bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-resolution ab initio phasing: problems and advances
Authors: Lunin Vladimir Y. , Lunina Natalia L. , Petrova Tatiana E. , Skovoroda Tatiana P. , Urzhumtsev Alexandre G. , Podjarny Alberto D.
Published: July 2002

If only native amplitudes are used for structure determination, then additional `theoretical' information is necessary to determine their phases. For use in a phasing procedure, this information can be formulated as a selection criterion (figure of merit) which assigns a reliability weight to every trial phase set and distinguishes the closest ones to the true phase set. Different types of additional information may be tested as a selection criterion: electron-density histograms, connectivity properties, statistical likelihood, atomicity etc. A common feature of such criteria is that they do not unambiguously judge the phase quality at low resolution. Nevertheless, the selection of the phase sets with best criterion values increases the ratio of good phase sets in the ensemble considered. An approximate solution of the phase problem may then be found by averaging the selected phase sets. Cluster analysis of the selected phase sets and averaging within clusters allow further improvement of this solution.
Macromolecular structure determination by cryo-electron microscopy
Authors: Saibil Helen R.
Published: July 2002

Recent advances in transmission electron microscopy (EM) hardware, low-temperature methods and image-processing software have made cryo-EM an important complement to X-ray crystallography and NMR for macromolecular structure determination, particularly of large assemblies. This review provides a summary of the main advances and a survey of the capabilities of this approach.
Preliminary X-ray crystallographic analysis of Bowman–Birk trypsin inhibitor from barley seeds
Authors: Song Hyun Kyu , Suh Se Won
Published: July 2002

Bowman–Birk trypsin inhibitor from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is tetragonal, belonging to the space group P41212 (or P43212), with unit cell parameters of a = b = 62.48 and c = 94.63 Å. The asymmetric unit contains one molecule of Bowman–Birk trypsin inhibitor with corresponding crystal volume per protein mass (Vm
) of 2.89 Å3 Da−1 and the solvent content of 57% by volume. The crystals diffract to at least 1.9 Å Bragg spacing upon exposure to synchrotron X-rays. X-ray data to 1.9 Å have been collected from a native crystal.
Crystallization of the alanine dehydrogenase from Phormidium lapideum
Authors: Sedelnikova S. , Rice D. W. , Shibata H. , Sawa Y. , Baker P. J.
Published: July 2002

Amino-acid dehydrogenases catalyse the interconversion of their respective amino acids to the corresponding keto acid, with concomitant reduction of NAD or NADP. The enzymes phenylalanine, glutamate, leucine and valine dehydrogenase all share a similar three-dimensional subunit structure and a high degree of sequence similarity, indicating that they belong to an enzyme superfamily related by divergent evolution. In contrast, alanine dehydrogenase shows no sequence similarity with any of these enzymes despite catalysing a reaction with the same chemistry and thus it is predicted that it possesses a different three-dimensional structure. The alanine dehydrogenase from Phormidium lapideum has been crystallized in space group R32, cell dimensions a = b = 123.1 and c = 184.8 Å, with a monomer in the asymmetric unit. The structure determination of this enzyme will shed light on how nature has evolved two different systems to carry out the same reaction.
Crystallization and preliminary X-ray analysis of thiaminase I from Bacillus thiaminolyticus: space group change upon freezing of crystals
Authors: Campobasso Nino , Begun Jakob , Costello Colleen A. , Begley Tadhg P. , Ealick Steven E.
Published: July 2002

Thiaminase I (Mr
= 42 100) from B. thiaminolyticus, expressed in E. coli, has been crystallized by the vapor-diffusion method. Three crystal forms, two of which grew from 0.1 M sodium acetate (pH = 4.6), 0.2 M ammonium sulfate and 30%(w/v) PEG 2000, have been examined by X-ray analysis. One crystal form diffracted to 2.5 Å at room temperature, was orthorhombic, and had unit-cell edges of a = 87.7, b = 120.5 and c = 76.7 Å with space group P212121. A self-Patterson map showed a strong peak indicating noncrystallographic translational pseudosymmetry with (u, v, w) = (0.03, 0.0, 0.5). When these crystals were frozen at liquid-nitrogen temperatures, a second crystal form was observed which had unit-cell dimensions a = 85.5, b = 117.5 and c = 36.6 Å with space group P21212. A third crystal form grew from 0.1 M Tris (pH = 8.5), 0.2 M sodium acetate trihydrate and 28%(w/v) PEG 6000 to produce orthorhombic crystals of space group P212121 with cell edges of a = 114.4, b = 123.1 and c = 92.5 Å.
Crystallization and preliminary X-ray studies of a recombinant calcium-binding protein from Entamoeba histolytica
Authors: Gopal B. , Suma R. , Murthy M. R. N. , Bhattacharya A. , Bhattacharya S.
Published: July 2002

A calcium-binding protein (CaBP) of Entamoeba histolytica was purified from an E. coli recombinant clone carrying the CaBP gene in a pET-3c expression vector using anion-exchange and size-exclusion chromatography. Examination of the amino-acid sequence of the recombinant protein suggested that it has four independent EF-hand motifs. The protein dissolved in cacodylate buffer was crystallized using the hanging-drop method with 2-methylpentane-2,4-diol (MPD) as the precipitant. X-ray diffraction data have been collected on these crystals using a MAR Research imaging-plate detector system attached to a Rigaku RU200 rotating-anode X-ray generator. The crystals belong to the hexagonal space group P6122 with unit-cell dimensions of a = b = 96.21, c = 65.48 Å. Preliminary molecular-replacement computations suggest that the structure of this protein is likely to be similar to that of calmodulin (CAM).
Expression, purification and preliminary X-ray crystallographic analysis of PsaA, a putative metal-transporter protein of
Streptococcus pneumoniae
Authors: Pilling Patricia A. , Lawrence Michael C. , Berry Anne M. , Ogunniyi A. David , Lock Robert A. , Paton James C.
Published: July 2002

The putative metal-transporter protein PsaA of Streptococcus pneumoniae is of potential interest both as a vaccine and also as a drug target. The overexpression of the protein in E. coli, and its subsequent purification and crystallization are described. The crystals are rectangular rods and diffract to beyond 2.7 Å resolution. The crystal space group is P212121 with unit-cell dimensions a = 59.9, b = 66.5 and c = 69.9 Å.
Crystallization and preliminary X-ray analysis of polyamine oxidase from Zea mays L.
Authors: Binda Claudia , Coda Alessandro , Angelini Riccardo , Federico Rodolfo , Ascenzi Paolo , Mattevi Andrea
Published: July 2002

Polyamine oxidase catalyses the oxidation of the secondary amino group of spermine, spermidine and their acetyl derivatives. The enzyme plays an important role in the regulation of polyamine intracellular concentration and is a member of the family of flavin-containing amine oxidases. Crystals of maize polyamine oxidase have been grown by the hanging-drop vapour-diffusion technique. The crystals are in hexagonal space group P6122 (or P6522) with cell dimensions a = b = 184.6, c = 280.9 Å. A native data set has been collected to 2.7 Å resolution at a synchrotron radiation source.
The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus
Authors: White Stephen W. , Wilson Keith S. , Appelt Krzysztof , Tanaka Isao
Published: July 2002

Protein HU is a ubiquitous prokaryotic protein which controls the architecture of genomic DNA. It binds DNA non-specifically and promotes the bending and supercoiling of the double helical structure. HU is involved in many DNA-associated cellular processes, including replication, transcription and the packaging of DNA into chromosome-like structures. Originally determined at medium resolution, the crystal structure of HU has now been refined at 2.0 Å resolution. The high-resolution structure shows that the dimeric molecule is essentially a compact platform for two flexible and basic arms which wrap around the DNA molecule. To maximize the protein's stability, non-secondary structural regions are reduced to a minimum, there is an extensive aromatic hydrophobic core and several salt bridges and hydrogen-bonded water molecules knit together crucial regions. Based on the original medium-resolution structure of HU, several proposals were made concerning the structural basis of HU's ability to bind, bend and supercoil DNA. Each of these proposals is fully supported by the high-resolution structure. Most notably, the surfaces of the molecule which appear to mediate protein–DNA and protein–protein interactions have the ideal shapes and physicochemical properties to perform these functions.
Purification, crystallization and preliminary X-ray crystallographic analysis of a phospholipase A2 from Daboia russelli pulchella
Authors: Chandra Vikas , Nagpal Akanksha , Srinivasan A. , Singh T. P.
Published: July 2002

Phospholipases are esterolytic enzymes which hydrolyze glycerophospholipids. The pharmacological efficiency of phospholipase A2 (PLA2) enzymes is reflected by their specificity towards a tissue or organ. The Russell's viper has been classified into two classes. Class 1 contains Viper russelli russelli, Viper russelli siamensis and Viper russelli formosensis, whereas class 2 contains Daboia russelli pulchella. The sequence identity between the PLA2s from these two classes is 47%. The novel PLA2 from Daboia russelli pulchella has been crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitating agent. Crystals belong to the orthorhombic space group C2221 with unit-cell parameters a = 77.01, b = 92.29, c = 76.90 Å and two molecules in the asymmetric unit. These crystals diffract to about 2.49 Å resolution using a rotating-anode source.
Crystallization and preliminary X-ray analysis of glutamate racemase from Aquifex pyrophilus, a hyperthermophilic bacterium
Authors: Hwang Kwang Yeon , Cho Chun-Seok , Kim Sang Suk , Baek Kyuwon , Kim Sung-Hou , Yu Yeon Gyu , Cho Yunje
Published: July 2002

Glutamate racemase catalyzes the reversible reaction of L-glutamate to D-glutamate, an essential component of the bacterial cell wall. Glutamate racemase from Aquifex pyrophilus has been crystallized by the hanging-drop vapor-diffusion method using polyethylene glycol 6000 as a precipitant. The crystals belong to space group P6122 or P6522 with unit-cell parameters a = b = 72.1, c = 185.02 Å. The asymmetric unit contains one molecule, corresponding to a Vm
value of 2.35 Å3 Da−1. Complete data sets from a native and a mercury-derivative crystal have been collected at 2.0 and 2.3 Å resolution, respectively, using a synchrotron-radiation source.
An A-DNA structure with two independent duplexes in the asymmetric unit
Authors: Savitha G. , Viswamitra M. A.
Published: July 2002

The crystal and molecular structure of the self-complementary A-DNA decamer sequence d(G4CGC4) was solved at 1.9 Å resolution. The decamer crystallizes in space group P21 with two independent duplexes in the asymmetric unit. Duplex 1 has interactions which are distributed symmetrically about its length compared with duplex 2. The two end base pairs of duplex 1 have a similar NH\cdotsO hydrogen-bond pattern involving GGC segments of duplex 2 and a symmetry-related neighbour, while the end base pairs of duplex 2 interact with the GCC and GGG segments of its symmetry-related neighbours through NH\cdotsO and NH\cdotsN hydrogen bonds and a water-mediated hydrogen bond between the carboxyl groups of C40 and C8. In addition to the C4′–C5′ torsion angle γ assuming the trans conformation in certain steps, this angle also adopts the gauche
− conformation at C37 as opposed to the preferred gauche
+ conformation, with a concomitant change in phosphodiester P—O5′ (α) in the opposite sense. This facilitates stacking between adjacent bases. The study suggests that the structural alterations in the two molecules in the asymmetric unit originate from an inherent propensity of the d(G4CGC4) base sequence for varied intermolecular interactions and malleability.
Crystallization and preliminary crystallographic analysis of the snake muscle fructose 1,6-bisphosphatase
Authors: Zhu D.-W. , Xu G.-J. , Rehse P. H. , Azzi A. , Zhao F.-K. , Lin S.-X.
Published: July 2002

The snake muscle fructose 1,6-bisphosphatase, a typical allosteric enzyme which plays important roles in gluconeogenesis, was crystallized in the presence of polyethylene glycol 3350 and magnesium chloride at pH 8.5. The crystals diffract to 2.3 Å on a rotating-anode X-ray source. The space group was determined to be either P3121 or its enantiomorph P3221, with unit-cell parameters a = b = 83.7, c = 202.41 Å, α = β = 90 and γ = 120°. There are two subunits in the asymmetric unit. Preliminary molecular-replacement studies indicate that the first enantiomorph is the correct one.
Crystallization and preliminary diffraction studies of a recombinant major urinary protein
Authors: Kuser P. , Krauchenco S. , Fangel A. , Polikarpov I.
Published: July 2002

A monoclinic crystal form of a recombinant major urinary protein, (MUP) from mouse, has been obtained. MUP is a member of the lipocalin family whose biological function relates to olfaction and sexual communication. Crystals were grown by the vapour-diffusion technique against a mother liquor containing CdCl2. Crystals belong to the monoclinic space group P21 with the cell parameters a = 37.14, b = 55.79, c = 37.67 Å, and β = 93.24°. The crystals diffract to beyond 1.4 Å resolution at a synchrotron beamline.
Error estimation and bias correction in phase-improvement calculations
Authors: Cowtan Kevin
Published: July 2002

With the rise of Bayesian methods in crystallography, the error estimates attached to estimated phases are becoming as important as the phase estimates themselves. Phase improvement by density modification can cause problems in this environment because the quality of the resulting phases is usually overestimated. This problem is addressed by an extension of the γ correction [Abrahams (1997). Acta Cryst. D53, 371–376] to arbitrary density-modification techniques. The degree to which the improved phases are biased by the features of the initial map is investigated in order to determine the limits of the resulting procedure and the quality of the phase-error estimates.
Crystallization and preliminary X-ray analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tyrosine inhibitable) from Saccharomyces cerevisiae
Authors: Schneider Thomas R. , Hartmann Markus , Braus Gerhard H.
Published: July 2002

3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (E.C. 4.1.2.15) catalyzes the first step in the biosynthesis of aromatic amino acids: the condensation of phophoenolpyruvate and erythrose 4-phosphate to 3-deoxy-D-arabino-heptulosonate-7-phosphate. Diffraction-quality crystals of the tyrosine-inhibitable form of the enzyme from Saccharomyces cerevisiae have been obtained by the hanging-drop vapour-diffusion method in the presence of polyethylene glycol. The crystals belong to the triclinic space group P1, with unit-cell parameters a = 81.5, b = 94.0, c = 104.6 Å, α = 65.5, β = 85.2, γ = 75.0°, and can be flash-cooled using glycerol as a cryoprotectant. A data set to 2.3 Å has been collected at 120 K.
Purification, crystallization and preliminary X-ray analysis of catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa
Authors: Sainz G. , Vicat J. , Kahn R. , Tricot C. , Stalon V. , Dideberg O.
Published: July 2002

The catabolic ornithine carbamoyltransferase (OTCase) from Pseudomonas aeruginosa exhibits allosteric behaviour, with two conformational states of the molecule: an active R form and an inactive T form. The enzyme is a dodecamer with a molecular mass of 455700 Da. Three crystal forms have been obtained. Crystals of allosteric state T are rhombohedral, belonging to the R3 space group, with hexagonal unit-cell parameters a = b = 180.6, c = 122.0 Å. They diffract to a resolution of 4.5 Å. Two crystal forms for allosteric state R have been obtained, with hexagonal and cubic symmetries. Hexagonal crystals, which diffract to a resolution of 3.4 Å, belong to the space group P63 with unit-cell parameters a = b = 140.8, c = 145.6 Å. The cubic crystals belong to space group I23, with unit-cell parameter a = 134.32 Å and diffract to a resolution better than 2.5 Å. In all crystal forms, the dodecamer exhibits a 23 point-group symmetry.
Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 Å
Authors: Crowhurst Gina S. , Dalby Andrew R. , Isupov Michail N. , Campbell John W. , Littlechild Jennifer A.
Published: July 2002

The crystal structure of the tetrameric glycolytic enzyme phosphoglycerate mutase from the yeast Saccharomyces cerevisiae has been determined to 1.7 Å resolution in complex with the sugar substrate. The difference map indicates that 3-phosphoglycerate is bound at the base of a 12 Å cleft, positioning C2 of the substrate within 3.5 Å of the primary catalytic residue, histidine 8.
Reciprocal-space solvent flattening
Authors: Terwilliger Thomas C.
Published: July 2002

Solvent flattening is a powerful tool for improving crystallographic phases for macromolecular structures obtained at moderate resolution, but uncertainties in the optimal weighting of experimental phases and modified phases make it difficult to extract all the phase information possible. Solvent flattening is essentially an iterative method for maximizing a likelihood function which consists of (i) experimental phase information and (ii) information on the likelihood of various arrangements of electron density in a map, but the likelihood function is generally not explicitly defined. In this work, a procedure is described for reciprocal-space maximization of a likelihood function based on experimental phases and characteristics of the electron-density map. The procedure can readily be applied to phase improvement based on solvent flattening and can potentially incorporate information on a wide variety of other characteristics of the electron-density map.
Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima
Authors: Vysotski Eugene S. , Liu Zhi-Jie , Rose John , Wang B. C. , Lee John
Published: July 2002

Crystals of recombinant obelin, the Ca2+-regulated photoprotein from the marine hydroid Obelia longissima, have been grown from sodium citrate solutions. Crystals grow as hexagonal light-yellow rods (0.1 × 0.1 × 1.0 mm) which diffract to beyond 1.8 Å with synchrotron radiation of 1.0 Å wavelength. The crystals have a primitive hexagonal lattice with unit-cell parameters a = 81.55, c = 86.95 Å. The asymmetric unit contains two molecules. This represents the successful preparation of single crystals of a photoprotein obelin which have promising diffraction properties.
Capacitance XAFS method: X-ray absorption spectroscopy of low-dimensional structures
Authors: Ishii Masashi
Published: July 2002

For local structure analyses of low-dimensional structures in semiconductors, such as defects, interfaces and surfaces, a new site-selective X-ray absorption fine structure (XAFS) measurement, `capacitance XAFS method', is presented. This method measures the X-ray photon energy dependence of the capacitance involved in diode structures. Since the capacitance is changed by an X-ray induced photoemission of localized electrons in the low dimensional structures, a site-selective analysis can be made. Although macroscopic X-ray absorption can be measured by conventional XAFS analyses, low-dimensional X-ray absorption coefficients are observed by the capacitance XAFS measurements.
X-ray absorption near-edge structure (XANES) spectral changes of 2-deoxy-D-ribose by irradiation within the energy region around the oxygen K-shell absorption edge
Authors: Akamatsu Ken , Yokoya Akinari
Published: July 2002

The physicochemical characteristics of 2-deoxy-D-ribose moieties in DNA strands are important to understand biological radiation stress. So, the X-ray absorption near edge structure (XANES) of 2-deoxy-D-ribose within the energy region around the oxygen K-shell absorption edge was measured. 2-deoxy-D-ribose was exposed to 3 energies of X-rays, i.e. 526.3 eV (below O 1s→σ*), 537.8 eV (at the absorption peak of O 1s→σ*) and 552.6 eV (above O 1s→σ*) for given periods. Slight differences in spectral changes were seen in the each irradiation energy, suggesting in fact that the chemical state and following rearranged chemical structure of 2-deoxy-D-ribose may be different between the three irradiation energies.
Resonant X-ray emission spectra of K2Ni(CN)4.H2O at the Ni K-edge
Authors: Takata Y. , Iwazumi T. , Kosugi N.
Published: July 2002

Resonant X-ray emission spectra were measured at the Ni K-edge for a planar low-spin nickel complex K2Ni(CN)4.H2O. In the Ni Kβ emission spectra, a resonant X-ray Raman scattering was observed in the pre-edge region, showing linear energy dispersion of the emitted photon with the incident photon energy. No energy loss features corresponding to the ligand-to-metal charge-transfer (LMCT) was identified. The LMCT feature is characteristic of strongly correlated systems such as NiO; therefore, the LMCT effect proves to be significantly suppressed. This is consistent considering strong covalent character between low-lying π* ligand and metal 3d (occupied) orbitals in low-spin nickel complexes.
A new method for the size-selective EXAFS of neutral free clusters
Authors: Yao Makoto , Hayakawa Tetsuichiro , Nagaya Kiyonobu , Hamada Kouichi , Ohmasa Yoshinori , Nomura Masaharu
Published: July 2002

No abstract
Charge order and superconductivity in low-dimensional organic conductors
Authors: Kishigi Keita
Published: July 2002

We study the coexistent state of the spin density wave (SDW) and the charge density wave (CDW) in a one-dimensional extended Hubbard model. We find that the coexistent state of SDW and CDW is stabilized in various electron-filling cases when band parameters are for organic conductors. The ground state energies have cusp-like minima at n/4m-fillings, where n and m are integers. The maxima of the critical temperatures of the coexistent state at n/4m-fillings will be observed in X-ray scattering measurements. We discuss the suitable filling for superconductivity of which strong fluctuation in antiferromagnetic ordering may be the origin.
Study of magnetic materials using helicity-modulated X-ray magnetic circular dichroism
Authors: Maruyama H.
Published: July 2002

A new helicity-modulation technique has been applied for recording X-ray magnetic circular dichroism (XMCD) at the K-absorption edge in transition-metal magnetic materials. This technique enables the measurement of the XMCD spectrum with high precision and under extreme conditions. The refined spectrum is presented at the Fe K edge for pure Fe, Fe4N and Co-ferrite. The method is very promising for site-assignment of magnetic cations and for detailed investigation of the magnetic states in a local environment. In Mn3
MC perovskites, the dependence of the Mn K-edge XMCD spectrum on temperature and magnetic field demonstrates that the orbital moments are closely associated with the magnetic phase transition. New information obtained from the refined spectrum and novel phenomena observed in temperature and field variations is presented.
Multiple scattering approach to DAFS
Authors: Benfatto M. , Felici R. , Formoso V.
Published: July 2002

In this article we outline a general approach to the anomalous correction to the atomic scattering factor ab initio calculation based on the multiple scattering theory. This approach can be used for structural determination in any system and in particular in the surfaces where symmetry conditions make usual analysis impossible. We show as an application of the formalism calculations related to experimental data of bulk Ge.
Quantum statistical approach to Debye–Waller factor in EXAFS: application to monatomic fcc systems
Authors: Katsumata Hiroaki , Miyanaga Takafumi , Yokoyama Toshihiko , Fujikawa Takashi , Ohta Toshiaki
Published: July 2002

Temperature dependence of the Debye–Waller factors in EXAFS is studied for monatomic fcc lattice by use of the perturbation approach in terms of temperature Green's function. We apply the theory to the temperature dependence of EXAFS for Kr and Ni crystals. Furthermore we make a comparison among sc, bcc and fcc lattices for the present ab initio calculations.
Characterization of the active site structure of Pd and Pd-promoted Mo sulfide catalysts by means of XAFS
Authors: Kubota Takeshi , Okamoto Yasuaki
Published: July 2002

Recently, noble metal catalysts are noted as promising candidates for new super-deep-hydrodesulfurization (HDS) catalysts. In this study, we investigated the structure of Pd particles supported on zeolite and Al2O3 under a sulfidation or reduction condition. From EXAFS analysis, it was found for sulfided Pd catalysts that small Pd sulfide clusters are formed without sintering. It was also revealed that no extensive growth of metal Pd particles occurs in Pd/NaY sulfide catalysts even after a treatment with H2 at 673 K. The dispersion of Pd metal particles is improved by H2/H2S treatment. These results indicate that in the presence of H2S, Pd shows high resistance against particle growth. A comparison of the Mo and Pd K-edge EXAFS spectra for MoSx/Pd-NaY and Pd-NaY catalysts revealed the existence of Mo-Pd bondings by the addition of Mo sulfide, indicating a direct interaction between Mo and Pd sulfides.
XAFS spectroscopy of a single neuron from a patient with Parkinson's disease
Authors: Yoshida Sohei , Ektessabi Ali , Fujisawa Shigeyoshi
Published: July 2002

Chemical state of transition metals such as iron in a single neuron of the substantia nigra (SN) from a patient with Parkinson's disease (PD) was studied in this paper, using autopsy midbrain specimens including SN. Parkinson's disease is one of the major neurodegenerative diseases. The excessive accumulation of iron and its chemical states in SN neurons are related to the oxidative damage leading to neuronal cell death. X-ray absorption fine structure spectroscopy (XAFS) with SR micro beam (10 µm) was used to investigate the chemical state of iron in the SN neurons. X-ray absorption near-edge structure (XANES) spectroscopy results showed that the chemical state of iron in the neuromelanin granules within SN neurons changed from ferrous (Fe2+) to ferric (Fe3+) ion in the process of neuronal degeneration.
Study on local structure around Ce and Gd atoms in CeO2–Gd2O3 binary system
Authors: Nakagawa Takashi , Osuki Takahiro , Yamamoto Takao A. , Kitauji Yoshiyasu , Kano Masataka , Katsura Masahiro , Emura Shuichi
Published: July 2002

X-ray absorption spectra near Ce and Gd K-edges of binary oxide of CexGd1-xO(3+x)/2 (0 <= x <= 0.5) in C-type structure solid solution were measured by use of the beamline BL01B1 at SPring-8. Interatomic distances between rear-earth rare-earth and oxygen atoms, RGd-O and RCe-O, were evaluated with the extended x-ray absorption fine structure analysis and found to increase with x. RGd-O was larger than RCe-O by about 0.1 Å. Metal-oxygen distances estimated as their linear combinations, xRCe-O + (1-x)RGd-O, well agreed with those determined by X-ray diffraction.
XANES study in the solid state reaction of Zr–Ni system
Authors: Nakai Ikuo , Shibai Yoshifumi , Murakami Yoshiyuki
Published: July 2002

X-ray absorption near edge structure (XANES) spectra of mechanically alloyed ZrNi near Ni and Zr K edges as a function of milling time. The x-ray diffraction shows that the system is transformed into an amorphous phase by milling for about 60 h. With increasing the milling time, a small absorption near the Ni threshold rises and finally forms a peak in the amorphous phase, while an absorption near the Zr threshold shows a gradual decrease. The peak of the Ni K edge reflects 3d character strongly hybridized with 4p states, while the absorption of the Zr K edge comes from states having a 4d orbital character.
Generation of an X-ray microbeam for spectromicroscopy at SPring-8 BL39XU
Authors: Hayakawa Shinjjiro , Ikuta Natsuki , Suzuki Motohiro , Wakatsuki Masao , Hirokawa Takeshi
Published: July 2002

A pair of elliptical mirrors (KB mirror) was designed and fabricated to realize an energy tunable x-ray microbeam for spectro-microscopy at SPring-8 BL39XU. As is commonly recognized, the obtainable beam size with the aspherical total reflection mirrors is strongly affected with the slope error of the mirror. Considering that the extremely high brilliance of the undulator radiation from the SPring-8, the small mirror size and the small mirror-to-focus distance were employed to minimize effects of the slope error. Preliminary evaluation of the KB mirror was carried out using 10 keV monochromatized undulator radiation. Alignment of the mirror was assisted by the beam monitor system composed of a scintillator and a CCD, and the beam size less than 5 mm can be easily achieved even when the source was fully used. The beam size obtained with this experiment was 2 × 4 µm2 with the photon flux of 1 × 1010 photons/s. Smaller beam size may be expected with the use of intermediate slits. Characterization of trace elements with the spatial resolution will be carried out by using x-ray fluorescence (XRF) analysis and x-ray absorption fine structure (XAFS) measurements with XRF yield method.
Theoretical study of the non-local optical potential in EXAFS spectra
Authors: Hatada Keisuke , Fujikawa Takashi , Hedin Lars
Published: July 2002

We study the optical potential effects on the extended x-ray absorption fine structure (EXAFS) and x-ray photoelectron diffraction (XPD) spectra. For the valence electron optical potential we use a local density approximation because the charge density changes fairly slowly, whereas we use a non-local optical potential for the core electron part based on GW-approximation. In the Br K-edge EXAFS spectra the present optical potential gives rise to the phase difference and the amplitude reduction; the agreement with the experimental result is excellent. In the N-1s XPD spectra for N2/Ni(100), the spherical wave effects enhance the effects due to the optical potential.
XAFS study on liquid selenium under high pressure
Authors: Katayama Yoshinori
Published: July 2002

Using large-volume presses, it is now possible to measure X-ray absorption spectra under a wide range of pressure–temperature conditions. X-ray absorption fine structure (XAFS) has successfully been measured at the K edge of crystalline and liquid Se at temperatures up to 1023 K and pressures of about 5 and 8 GPa, and at temperatures up to 1173 K at about 2.5 GPa. Crystalline Se consists of infinite chain molecules. At atmospheric pressure, it is known that the chain structure of Se is largely preserved upon melting. The temperature dependence of the extended X-ray absorption fine structure (EXAFS) at 2.5 GPa indicates that twofold covalent bonds remain upon melting, as at atmospheric pressure. On the other hand, the decrease of EXAFS oscillation upon melting at 8 GPa is larger than that expected from the temperature dependence of EXAFS in the crystalline state, indicating that the covalent bonds are modified in the liquid state. The change of structure of liquid Se is discussed in relation to a proposed semiconductor–metal transition under high pressure.
Phase transitions in rare earth chlorides observed by XAFS
Authors: Matsuura Haruaki , Adya Ashok K. , Bowron Daniel T.
Published: July 2002

XAFS spectroscopy has increasingly been utilised to elucidate the nearest-neighbour structure in the condensed phases. In this paper, the XAFS spectra of NdCl3 and DyCl3 in both the solid and the liquid phases measured at the Nd and Dy LIII absorption edges on beam line BM29 of the European Synchrotron Radiation Facility (ESRF) are presented. The Fourier transformed radial structure functions, φ(r) show that the prominent peaks corresponding to M-Cl (M: Nd or Dy) first shell contribution are shifted to shorter distances in the liquid melts as compared to those found in the corresponding solids. Similar behaviour has also been observed from other diffraction techniques in typical ionic melts such as NaCl. From the temperature dependence of the radial structure functions it is clear that the change in the M-Cl distance on melting is much larger in NdCl3 than that in DyCl3.
Electronic structure effects from hydrogen bonding in the liquid phase and in chemisorption: an integrated theory and experimental effort
Authors: Pettersson Lars G. M. , Nilsson Anders , Myneni Satish , Luo Yi , Nyberg Mats , Cavalleri Matteo , Ojamäe Lars , Näslund Lars-Åke , Ogasawara Hirohito , Odelius Michael , Pelmenschikov Alexander
Published: July 2002

A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3×2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate–adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed.
Local structure analysis of Ti species stabilized in ion exchangeable layer solids by X-ray absorption spectroscopy
Authors: Han Yang-Su , Yoon Sun-Mi , Kim Dong-Kuk , Lee Eun-Jung , Choy Jin-Ho , Park Jung-Chul
Published: July 2002

Nano-sized titanium dioxides are incorporated into the interlayer spaces of ion-exchangeable layered perovskites, H1-xCa2-xLaxNb3O10 (x=0.0~0.75), by replacing the interlayer protons with positively charged TiO2 nano-sol particles or basic titanium glycolate complex (titanatrane). Powder X-ray diffraction analysis, UV-Vis absorption spectroscopy, thermogravimetric analysis, and N2 adsorption-desorption isotherm measurements show that quantum sized TiO2 particles are stabilized inbetween perovskite lattices to form micropores (SBET= 37~110 m2/g). X-ray absorption spectroscopy at the Ti K-edge was used for investigating the local environment around Ti atoms constituting the interlayer pillars. According to the XANES spectra, the 'as-pillared' Ti species have the same local environments with those of precursory species, which subsequently converted into TiO2 clusters with rutile and anatase-like local structures when TiO2 nano-sol particles and titanatrane are used as pillaring species, respectively. It is also found that the local environment of TiO2 remains almost constant irrespective of the layer charge density, while the TiO2 pillar content and the microporosity increase with the latter.
Theoretical study of Mn K-edge in La1-x
Ca
x
MnO3
Authors: Ignatov A. Yu. , Khalid S. , Sujoy R. , Ali N.
Published: July 2002

Effects of (i) local magnetic ordering, (ii) lattice distortions, and (iii) Mn 3d - O 2p hybridization on the shape of Mn K- edge XANES spectra of La1-xCaxMnO3 have been evaluated numerically and compared with available experimental data. We calculated the spin-polarized Mn K-edge spectra. An energy splitting between spin-up and spin-down XANES of 0.5-1.1 eV contributes to the broadening of the total XANES below TN(Tc). To simulate lattice polaronic distortions across a MI transition the Mn K-edge spectra were calculated twice: assuming R-3c (R=1.96 Å) and Pbnm (R1=1.91, R2=1.97, and R3=2.16 Å) symmetries. Results could qualitatively reproduce the observed energy "shift" across the transition. A pre-edge peak at E~ 6542 eV and feature B3 at ~6 eV above the main peak were found to be related to the Mn 3d - O 2p hybridization. The feature B3 should be assigned to a shake-up transition. The calculated K-edge spectrum was obtained as a convolution product of the single-electron XANES and the spectrum of many-body excitations in the Mn-O electronic states in the presence of the 1s core-hole.
X-ray Inclined Lens
Authors: Hrdý J.
Published: July 2002

As defined here, the term `inclined lens' means a longitudinal parabolic groove fabricated into a crystal monochromator. If properly designed, it should provide the horizontal (sagittal) focusing of an X-ray beam. The focusing is based on the sagittal deviation of the beam diffracted on the wall of the groove. This effect follows from the dynamical theory of inclined diffraction. The focusing efficiency is limited compared with other methods. On the other hand, the simplicity is the main advantage of this device. The exact shape of the groove is calculated and several methods of keeping the vertical dimension of the beam small are proposed.
Station 16.3: a High-Resolution Single-Crystal Diffraction Facility at the SRS, Daresbury
Authors: Collins S. P. , Cernik R. J. , Fell B. , Tang C. C. , Harris N. W. , Miller M. C. , Oszlanyi G.
Published: July 2002

SRS station 16.3 is now a fully scheduled user facility for high-resolution and high-energy single-crystal X-ray diffraction. It is based on a large three-axis diffractometer, designed and constructed at Daresbury for a wide range of physics and materials science applications. Served by wiggler 16 (a 6 T superconducting wavelength-shifter), the station has access to a broad spectrum of photon energies, extending to over 50 keV, and is designed for simple polarization-state tuning by motorized height adjustment of all optical components. This paper outlines the key design features and some of the science projects carried out during the first year of operation.
The overlap between the thin- and thick-filament reflections in the small-angle X-ray diffraction pattern from a molluscan smooth muscle
Authors: Tajima Y. , Makino K. , Hanyuu T. , Wakabayashi K. , Amemiya Y.
Published: July 2002

Small-angle X-ray diffraction studies of the living anterior byssus retractor muscle (ABRM) of Mytilus edulis have been carried out using a long (2.2 m) point-focusing camera to investigate the overlap between the thin- and thick-filament reflections. While the reflections due to the cross-bridge lattice on the thick filaments in the resting ABRM are distant in the axial direction from the thin-filament layer lines, the paramyosin cores of the thick filaments produce reflections very close to the thin-filament reflections at axial spacings of 387, 59 and 51 Å. Using such a long camera it becomes possible to separate these reflections due to an improvement in the angular resolution and increase in the difference between the widths of the thin- and thick-filament reflections, and it is shown that the intensities of the 387 and 59 Å thin-filament layer lines gradually drop to zero close to the meridian. It becomes relatively easy to observe the thin-filament-based X-ray pattern by use of the long camera, making it possible to show a partial resemblance of the small-angle X-ray pattern from the contracting ABRM with the pattern from the rigorized ABRM.
1-[4-(3,5-Dimethoxy-2-methylphenoxy)-2,6-dihydroxy-3-methylphenyl]ethanone
Authors: Karalai Chatchanok , Saewon Nisakorn , Chantrapromma Kan , Chantrapromma Suchada , Fun Hoong-Kun , Razak Ibrahim Abdul
Published: July 2002

The benzene rings of the title compound, C18H20O6, are nearly perpendicular to each other [dihedral angle 75.2 (1)°]. The two methoxy groups and the acetyl group are almost coplanar to their attached benzene rings. One hydroxyl group is involved in an intramolecular O—H...O hydrogen bond with the adjacent acetyl O atom. The crystal structure is stabilized by intermolecular O—H...O contacts.
1,1,1,2,2-Pentaiododiphosphanium tetraiodogallate(III)
Authors: Aubauer Christoph , Klapötke Thomas M. , Mayer Peter
Published: July 2002

1,1,1,2,2-Pentaiododiphosphanium tetraiodogallate(III), (P2I5)[GaI4], crystallizes in the orthorhombic space groupPbca. The structure is isotypic with (P2I5)[AlI4]. Short I...I interatomic distances indicate weak interactions between cations and anions.
3-Ethoxycarbonyl-2,2,5,5-tetramethyl-1H-2,5-dihydropyrrol-1-yloxyl
Authors: Duskova Jarmila , Labsky Jiri , Hasek Jindrich , Cisarova Ivana
Published: July 2002

The crystal and molecular structure of the title compound, C11H18NO3, has been determined from X-ray diffraction data. The compound crystallizes in the centrosymmetric space groupPnma. The main part of the molecule lies at a special position on the mirror plane.
Redetermination of 2-(naphthalen-2-yloxy)ethanoic acid
Authors: Howie R. Alan , Skakle Janet M. S. , Wardell Solange M. S. V.
Published: July 2002

The redetermination of the title compound, C12H10O3, agrees completely with the results previously reported by Pattabhi, Ragnuthan & Chacko [Acta Cryst. (1973), B34, 3118–3120], but with improved precision. In addition, now reported are intermolecular π–π, C—H...π and aryl C—H...O interactions.
Corrosion detection and control
Authors: Ford Terry
Published: July 2002

Considers briefly the history of corrosion in metallic aircraft. Summarizes the different types of corrosion which affect aircraft and the methods for monitoring and measuring this corrosion. Presents an alternative approach called “controlled search peening” where the induced surface compressive stresses stretch and yield the outer material surface and induce visible blistering and flaking at the surface, indicating the existence of exfoliation corrosion.
Marine anti‐corrosion paints based on thiouracil compounds
Authors: Tadros A.B. , Abd El Nabey B.A.
Published: July 2002

The inhibition of marine corrosion of steel by 6‐amino‐2‐thiouracil (I) and its derivatives 6‐benzylideneamino‐2‐thiouracil (II) and 6‐p‐chlorobenzylideneamino‐2‐thiouracil (III) has been tested on laboratory scale using electrochemical technique which was performed on mild steel in sea water medium and on field scale through the incorporation of the compounds individually in marine paints compositions. The paints containing the compounds were applied on unprimed steel and the coated panels were tested in Alexandria Eastern Harbour water (Egypt). The electrochemical measurements indicated that both compounds (I) and (III) acted as cathodic‐type inhibitors, but the data of compound (II) showed neither cathodic nor anodic inhibition. Two marine paint compositions were prepared using different binder materials. The three compounds were added individually in both paint compositions. The paint composition based on the soluble resin material as a sole binder and containing compound (I) showed the best corrosion protection of its steel surface till more than two months followed by the paint composition containing compound (III). The same paint containing the compounds showed antifouling property for four months.
SMEs in an environment of change: computer‐based tools to aid learning and change management
Authors: Winch Graham , McDonald John
Published: July 2002

As global competitive forces begin to impact more and more on smaller enterprises, they may find themselves more limited in the approaches available to them to prepare for fundamental change. In‐depth case studies were analysed for 11 firms in the south‐west of England, of which eight were characterised as small/medium enterprises (SMEs). Each firm had recently undergone a major change, and their managers were found to face considerable practical difficulties in developing and updating their skills in comparison with their counterparts from larger organisations. The need for innovative new approaches to SME managerial skills development is argued, and the potential benefits of a generic “computer‐aided visioning” system is highlighted as a low‐cost option for the smaller enterprise.
Dietitians and caterers: an uncertain but critical relationship
Authors: Donelan Anne
Published: July 2002

Within health care, the occupations of catering officer and dietitian stem from the same root – nursing. However, despite this common base, dietitians have recorded working tensions between these two groups. As caterers and dietitians are both responsible for ensuring the provision of nutritionally adequate and appetising food, their successful collaboration is essential to successful patient feeding. A qualitative study was undertaken to account for the values, ideals and beliefs brought to their practice. A small purposive sample of caterers and dietitians were interviewed to elucidate their views on the importance of their chosen occupation to them. The interviews were recorded and verbatim transcripts made. The content was analysed manually using a grounded theory approach, so that key issues emerged from the interviews per se. These themes – qualification, motivation, reality, constraints and perceptions – provide the basis for describing differing value systems underpinning practice, and highlighting significant interprofessional issues for caterers and dietitians.
Action learning comes of age: questioning action learning
Authors: Bourner Tom , Beaty Liz , Lawson John , O’Hara Suzanne
Published: July 2002

Questions where and for whom action learning might not work and seeks to find the limits of the method. Suggests that by better understanding the situations in which action learning works least well, its more effective use will be more fully understood.
Great expectations – CEOs’ perception of the performance gap of the HRM function in the Malaysian manufacturing sector
Authors: Othman Rozhan , Abdul‐Ghani Rohayu , Arshad Rasidah
Published: July 2002

This study examines the variations in HRM practice among Malaysian manufacturing firms. A typology of HRM practices is first identified, management expectations towards the HRM function and the performance gap of the HR departments are then examined. The findings obtained are then compared with various theoretical models. A comparison with the empirical finding of a US study is also made. Further, the implications of the findings of this study are examined. Finally, a number of suggestions are proposed to improve HRM practice.
Supporting equality: patriarchy at work in Europe
Authors: Rees Bronwen , Brewster Chris
Published: July 2002

Presents a Europe‐wide analysis of employment patterns which
reveals three major characteristics of women′s employment: occupational
segregation, part‐time working, and pay differentials. Examines how
these manifest themselves as a European‐wide phenomenon, and in more
detail looks at how they manifest themselves in France, the UK and The
Netherlands. Presents data to explore the interrelationship of these
three characteristics and their manifestation against national
backgrounds of social and employment legislation and child‐care
provision. Concludes that simple correlations do not explain women′s
position in the workforce and that neither structural nor cultural
theories are in themselves enough to understand these complex
relationships.