A XANES study of the K-absorption edge of copper in some of its compounds and use of the same in the determination of bond length

XANES in the K-edge of copper in the systems CuO, Cu(OH)2, La2CuO4, Cu3AsO4 and CuOHF have been investigated and transitions have been assigned to the observed structures. The measurements have been used for calculating the first coordination bond distance in the above systems. It is observed that the values so determined agree fairly well with crystallographic values.

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

Nonpolarizing and polarizing filter design

We describe a nonpolarizing filter design at oblique incidence and a polarizing filter design at normal incidence that use a uniaxially anisotropic layer. The phase thicknesses and the optical admittances of 14 the layers are compensated for by the birefringent properties of a thin film at oblique incidence. This concept can be applied to the design of nonpolarizing bandpass and edge filters at oblique incidence and of polarizing beam splitters at normal incidence. Besides, the dependence of narrow-bandpass filters on normal incidence is discussed. (c) 2005 Optical Society of America.

Electron energy-loss near-edge shape as a probe to investigate the stabilization of yttria-stabilized zirconia

The electron energy-loss near-edge structure (ELNES) at the O K edge has been studied in yttria-stabilized zirconia (YSZ). The electronic structure of YSZ for compositions between 3 and 15 mol % Y2O3 has been computed using a pseudopotential-based technique to calculate the local relaxations near the O vacancies. The results showed phase transition from the tetragonal to cubic YSZ at 10 mol % of Y2O3, reproducing experimental observations. Using the relaxed defect geometry, calculation of the ELNES was carried out using the full-potential linear muffin-tin orbital method. The results show very good agreement with the experimental O K-edge signal, demonstrating the power of using ELNES to probe the stabilization mechanism in doped metal oxides.

The near-edge structure in energy-loss spectroscopy: many-electron and magnetic effects in transition metal nitrides and carbides

We investigate the ability of the local density approximation (LDA) in density functional theory to predict the near-edge structure in electron energy-loss spectroscopy in the dipole approximation. We include screening of the core hole within the LDA using Slater's transition state theory. We find that anion K-edge threshold energies are systematically overestimated by 4.22 +/- 0.44 eV in twelve transition metal carbides and nitrides in the rock-salt (B1) structure. When we apply this 'universal' many-electron correction to energy-loss spectra calculated within the transition state approximation to LDA, we find quantitative agreement with experiment to within one or two eV for TiC, TiN and VN. We compare our calculations to a simpler approach using a projected Mulliken density which honours the dipole selection rule, in place of the dipole matrix element itself. We find remarkably close agreement between these two approaches. Finally, we show an anomaly in the near-edge structure in CrN to be due to magnetic structure. In particular, we find that the N K edge in fact probes the magnetic moments and alignments of ther sublattice.

Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

Intralamellar structural modifications related to the proton exchanging in K(4)Nb(6)O(17) layered phase

Basic structural aspects about the layered hexaniobate of K(4)Nb(6)O(17) composition and its proton-exchanged form were investigated mainly by spectroscopic techniques. Raman spectra of hydrous K(4)Nb(6)O(17) and H(2)K(2)Nb(6)O(17)center dot H(2)O show significant modifications in the 950-800 cm(-1) region (Nb-O stretching mode of highly distorted NbO(6) octahedra). The band at 900 cm(-1) shifts to 940 cm(-1) after the replacement of K(+) ion by proton. Raman spectra of the original materials and the related deuterated samples are similar suggesting that no isotopic effect occurs. Major modifications were observed when H(2)K(2)Nb(6)O(17) was dehydrated: the relative intensity of the band at 940 cm(-1) decreases and new bands seems to be present at about 860-890 cm(-1). The H(+) ions should be shielded by the hydration sphere what preclude the interaction with the layers. Removing the water molecules, H(+) ions can establish a strong interaction with oxygen atoms, decreasing the bond order of Nb-O linkage. X-ray absorption near edge structure studies performed at Nb K-edge indicate that the niobium coordination number and oxidation state remain identical after the replacement of potassium by proton. From the refinement of the fine structure, it appears that the Nb-Nb coordination shell is divided into two main contributions of about 0.33 and 0.39 nm, and interestingly the population, i.e., the number of backscattering atoms is inversed between the two hexaniobate materials. 2009 Elsevier Ltd. All rights reserved.

Remarkable Capacity Retention of Nanostructured Manganese Oxide upon Cycling as an Electrode Material for Supercapacitor

Electrochemical capacity retention of nearly X-ray amorphous nanostructured manganese oxide (nanoMnO2) synthesized by mixing directly KMnO4 with ethylene glycol under ambient conditions for supercapacitor studies is enhanced significantly. Although X-ray diffraction (XRD) pattern of nanoMnO2 shows poor crystallinity, it is found that by Mn K-edge X-ray absorption near edge structure (XANES) measurement that the nanoMnO2 obtained is locally arranged in a δ-MnO2-type layered structure composed of edge-shared network of MnO6 octahedra. Field emission scanning electron microscopy and XANES measurements show that nanoMnO2 contains nearly spherical shaped morphology with δ-MnO2 structure, and 1D nanorods of α-MnO2 type structure (powder XRD) in the annealed (600 °C) sample. Volumetric nitrogen adsorption−desorption isotherms, inductively coupled plasma analysis, and thermal analysis are carried out to obtain physicochemical properties such as surface area (230 m2 g−1), porosity of nanoMnO2 (secondary mesopores of diameter 14.5 nm), water content, composition, etc., which lead to the promising electrochemical properties as an electrode for supercapacitor. The nanoMnO2 shows a very high stability even after 1200 cycles with capacity retention of about 250 F g−1.

Analysis of EXAFS data of multiphasic heterogeneous catalysts

Cu K-edge EXAFS spectra of Cu-Ni/Al2O3 and Cu-ZnO catalysts, both of which contain more than one Cu species, have been analysed making use of an additive relation for the EXAFS function. The analysis, which also makes use of residual spectra for identifying the species, shows good agreement between experimental and calculated spectra.

Molecular details of phage phi6 RNA-dependent RNA synthesis

For most RNA viruses RNA-dependent RNA polymerases (RdRPs) encoded by the virus are responsible for the entire RNA metabolism. Thus, RdRPs are critical components in the viral life cycle. However, it is not fully understood how these important enzymes function during viral replication. Double-stranded RNA (dsRNA) viruses perform the synthesis of their RNA genome within a proteinacous viral particle containing an RdRP as a minor constituent. The phi6 bacteriophage is the best-studied dsRNA virus, providing an excellent background for studies of its RNA synthesis. The purified recombinant phi6 RdRP is highly active in vitro and it possesses both RNA replication and transcription activities. The crystal structure of the phi6 polymerase, solved in complex with a number of ligands, provides a working model for detailed in vitro studies of RNA-dependent RNA polymerization. In this thesis, the primer-independent initiation of the phi6 RdRP was studied in vitro using biochemical and structural methods. A C-terminal, four-amino-acid-long loop protruding into the central cavity of the phi6 RdRP has been suggested to stabilize the incoming nucleotides of the initiation complex formation through stacking interactions. A similar structural element has been found from several other viral RdRPs. In this thesis, this so-called initiation platform loop was subjected to site-directed mutagenesis to address its role in the initiation. It was found that the initiation mode of the mutants is primer-dependent, requiring either an oligonucleotide primer or a back-priming initiation mechanism for the RNA synthesis. The crystal structure of a mutant RdRP with altered initiation platform revealed a set of contacts important for primer-independent initiation. Since phi6 RdRP is structurally and functionally homologous to several viral RdRPs, among them the hepatitis C virus RdRP, these results provide further general insight to understand primer-independent initiation. In this study it is demonstrated that manganese phasing could be used as a practical tool for solving structures of large proteins with a bound manganese ion. The phi6 RdRP was used as a case study to obtain phases for crystallographic analysis. Manganese ions are naturally bound to the phi6 RdRP at the palm domain of the enzyme. In a crystallographic experiment, X-ray diffraction data from a phi6 RdRP crystal were collected at a wavelength of 1.89 Å, which is the K edge of manganese. With this data an automatically built model of the core region of the protein could be obtained. Finally, in this work terminal nucleotidyl transferase (TNTase) activity of the phi6 RdRP was documented in the isolated polymerase as well as in the viral particle. This is the first time that such an activity has been reported in a polymerase of a dsRNA virus. The phi6 RdRP used uridine triphosphates as the sole substrate in a TNTase reaction but could accept several heterologous templates. The RdRP was able to add one or a few non-templated nucleotides to the 3' end of the single- or double-stranded RNA substrate. Based on the results on particle-mediated TNTase activity and previous structural information of the polymerase, a model for termination of the RNA-dependent RNA synthesis is suggested in this thesis.

Lung structure and function studied by synchrotron radiation

A novel method for functional lung imaging was introduced by adapting the K-edge subtraction method (KES) to in vivo studies of small animals. In this method two synchrotron radiation energies, which bracket the K-edge of the contrast agent, are used for simultaneous recording of absorption-contrast images. Stable xenon gas is used as the contrast agent, and imaging is performed in projection or computed tomography (CT) mode. Subtraction of the two images yields the distribution of xenon, while removing practically all features due to other structures, and the xenon density can be calculated quantitatively. Because the images are recorded simultaneously, there are no movement artifacts in the subtraction image. Time resolution for a series of CT images is one image/s, which allows functional studies. Voxel size is 0.1mm3, which is an order better than in traditional lung imaging methods. KES imaging technique was used in studies of ventilation distribution and the effects of histamine-induced airway narrowing in healthy, mechanically ventilated, and anaesthetized rabbits. First, the effect of tidal volume on ventilation was studied, and the results show that an increase in tidal volume without an increase in minute ventilation results a proportional increase in regional ventilation. Second, spiral CT was used to quantify the airspace volumes in lungs in normal conditions and after histamine aerosol inhalation, and the results showed large patchy filling defects in peripheral lungs following histamine provocation. Third, the kinetics of proximal and distal airway response to histamine aerosol were examined, and the findings show that the distal airways react immediately to histamine and start to recover, while the reaction and the recovery in proximal airways is slower. Fourth, the fractal dimensions of lungs was studied, and it was found that the fractal dimension is higher at the apical part of the lungs compared to the basal part, indicating structural differences between apical and basal lung level. These results provide new insights to lung function and the effects of drug challenge studies. Nowadays the technique is available at synchrotron radiation facilities, but the compact synchrotron radiation sources are being developed, and in relatively near future the method may be used at hospitals.

Nature of copper in the new cuprate superconductors Pb2Sr2Ca1-xLxCu3O8+δ

Based on Cu K-edge absorption spectroscopy as well as Cu(2p3/2) and Cu(LVV) Auger spectroscopies it is shown that the recently discovered Pb2Sr2Ca1-xLxCu3O8+δ (L=Y or Lu) superconductors contain well-defined Cu1+ species in admixture with Cu2+. The proportion of Cu1+ is small in the nonsuperconducting samples with x=1, a feature which is uniquely different from that in YBa2Cu3O7-δ.

Tetrahydrofuran Clathrate Hydrate Formation

We report on the formation of tetrahydrofuran clathrate hydrate studied by x-ray Raman scattering measurements at the oxygen K edge. A comparison of x-ray Raman spectra measured from water-tetrahydrofuran mixtures and tetrahydrofuran hydrate at different temperatures supports stochastic hydrate formation models rather than models assuming hydrate precursors. This is confirmed by molecular dynamics simulations and density functional theory calculations of x-ray Raman spectra. In addition, changes in the spectra of tetrahydrofuran hydrate with temperatures close to the hydrate's dissociation temperature were observed and may be connected to changes in hydrate's local structure due to the formation of hydrogen bonds between guest and water molecules.

Spectroscopic evidence for the removal of mobile holes on Fe doping in YBa2Cu3-xFexO7-δ

X-ray absorption spectra at the oxygen K edge using the total yield technique are reported for YBa2Cu3O6.9 and YBa2Cu2.7Fe0.3O6.9. A comparison of the two spectra reveals that the mobile holes in YBa2Cu3O7-δ are removed and localized on Fe doping. Fe thus enters the lattice primarily in the formally trivalent oxidation state.

Electronic Structure of and the Metal-Insulator Transition in La1-xSrxCoO3-δ: A Soft-X-Ray Absorption Study

We report the soft-X-ray absorption spectra at the oxygen K-edge of La1-xSrxCoO3-δ (x = 0.0, 0.1, 0.2, 0.3 and 0.4) series with experimentally determined δ values. We show that the doping of holes by replacing La3+ with Sr2+ induces states within the band gap of the insulating undoped compound for small x and these doped states have a very substantial oxygen 2p character. This indicates that the insulating compounds belong to the charge transfer insulator regime. With increasing Sr content, the doped states broaden into a band overlapping the top of the primarily oxygen p-derived band, leading to an insulator-metal transition at x ≥ 0.2.