Sulfur K-edge x-ray absorption spectroscopy: A spectroscopic tool to examine the redox state of S-containing metabolites in vivo

The sulfur K-edge x-ray absorption spectra for the amino acids cysteine and methionine and their corresponding oxidized forms cystine and methionine sulfoxide are presented. Distinct differences in the shape of the edge and the inflection point energy for cysteine and cystine are observed. For methionine sulfoxide the inflection point energy is 2.8 eV higher compared with methionine. Glutathione, the most abundant thiol in animal cells, also has been investigated. The x-ray absorption near-edge structure spectrum of reduced glutathione resembles that of cysteine, whereas the spectrum of oxidized glutathione resembles that of cystine. The characteristic differences between the thiol and disulfide spectra enable one to determine the redox status (thiol to disulfide ratio) in intact biological systems, such as unbroken cells, where glutathione and cyst(e)ine are the two major sulfur-containing components. The sulfur K-edge spectra for whole human blood, plasma, and erythrocytes are shown. The erythrocyte sulfur K-edge spectrum is similar to that of fully reduced glutathione. Simulation of the plasma spectrum indicated 32% thiol and 68% disulfide sulfur. The whole blood spectrum can be simulated by a combination of 46% disulfide and 54% thiol sulfur.

Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

Red Parkes quasars: Evidence for soft X-ray absorption

The Parkes Half-Jansky Flat-Spectrum Sample contains a large number of sources with unusually red optical-to-near-infrared (NIR) continua. If this is to be interpreted as extinction by dust in the line of sight, then associated material might also give rise to absorption in the soft X-ray regime. This hypothesis is tested using broadband (0.1-2.4 keV) data from the ROSAT All-Sky Survey. Significant (>3 sigma confidence level) correlations between the optical (and NIR)-to-soft X-ray continuum slope and optical extinction are found in the data, consistent with absorption by material with metallicity and a range in the gas-to-dust ratio as observed in the local ISM. Under this simple model, the soft X-rays are absorbed at a level consistent with the range of extinctions (0 < A(V) < 6 mag) implied by the observed optical reddening. Excess X-ray absorption by warm (ionized) gas, (i.e., a warm absorber) is not required by the data.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Structural Characterization of Nanocrystalline Sb-Doped SnO2 Xerogels by Multiedge X-ray Absorption Spectroscopy

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structural investigations of tungsten silver phosphate glasses by solid state NMR, vibrational and X-ray absorption near edge spectroscopies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Electronic structure of Pb1-xLaxTiO3 ferroelectric materials from Ti 2p and O 1s soft x-ray absorption spectroscopy

The electronic structure of Pb1-xLaxTiO3 (PLT) compounds for x ranging from 0 to 30 at. % of La is investigated by means of soft x-ray absorption near edge structure (XANES) at the Ti L-3,L-2 and O K edges. The greatest modification in the structure of the Ti 2p XANES spectra of the PLT compounds is observed in the region of the high energy peak of the L-3 edge (e(g) states), which exhibits a splitting in the undoped sample. As the amount of lanthanum increases, this splitting becomes less pronounced. This modification is interpreted as a decrease in the degree of disorder of titanium atoms, which is correlated to the substitution of Pb by La atoms. The structural changes observed at the low energy peaks of the O K-edge XANES spectra of the PLT compounds may be interpreted in terms of hybridization between O 2p, Ti 3d, and Pb 6p orbitals. A decrease in the degree of hybridization observed as Pb atoms are replaced by La atoms may be related to the differences in the ferroelectric properties observed between x=0.0 and x=0.30 compounds. (c) 2006 American Institute of Physics.

Fe K-edge X-ray absorption spectroscopy study of Pb(Fe2/3W 1/3)O3-PbTiO3 multiferroic ceramics

The present paper is a comprehensive study concerning Fe K-edge X-ray absorption spectroscopy (XAS) measurements, which were performed to characterize the local structure of (1 - x)Pb(Fe2/3W1/3)O 3-xPbTiO3 samples as a function of temperature and PbTiO3 content. Results obtained by the fits of extended X-ray absorption fine structure consist with rhombohedral symmetry for Pb(Fe 2/3W1/3)O3 composition at temperatures lower than room temperature. This result is in apparent disagreement with X-ray and neutron diffraction characterization which have been reported. This apparent disagreement is related to the fact that XAS probes the short-range order, whereas X-ray diffraction provides structural information about the average structure. Moreover, as the PbTiO3 content increases, a disorder has been detected at local structure of the FeO6 octahedron. Analysis of X-ray absorption near edge structure spectra did not show modifications in intensity nor energy of transitions. © 2013 American Institute of Physics.

Local order of Pb1-xLaxZr0.40Ti 0.60O3 ferroelectric ceramic materials probed by X-ray absorption and Raman spectroscopies

This paper reports on the structural characterization of Pb 1-xLaxZr0.40Ti0.60O3 (PLZT) ferroelectric ceramic compositions prepared by the conventional solid state reaction method. X-ray absorption spectroscopy (XAS) and Raman spectroscopy were used to probe the local structure of PLZT samples that exhibits a normal and relaxor ferroelectric behavior. From the Zr K-edge and Pb LIII-edge EXAFS spectra, a considerable dissymmetry of Zr and Pb sites was observed in all samples, including those showing a long-range order cubic symmetry and a relaxor behavior. The Raman spectroscopy results confirmed the existence of a local disorder in all PLZT samples through the observation of Raman active vibrational modes. The variation in the intensity of the E(TO 3) mode in the PLZT relaxor samples indicates that the process of correlation between nanodomains stabilizes at temperatures lower than T m. © 2013 Elsevier B.V. All rights reserved.

Interionic Interactions in Imidazolic Ionic Liquids Probed by Soft X-ray Absorption Spectroscopy

This work investigates pure ionic liquids (ILs) derived from an imidazolium ring with different carbonic chains and halides or bis(trifluoromethanesulfonilimide) (TFSI-) as anions, using X-ray absorption near edge spectroscopy (XANES) at different energies (N, S, O, F, and Cl edges) to probe the interionic interactions. XANES data show that the interaction with the anion is weaker when the cation is an imidazolium than when the salt is formed by smaller cations, as lithium, independently of the length of the carbonic chain attached to the imidazolium cation. The results also show that, for all studied as, it is not observed any influence of the anion on the XANES spectra of the cation, nor the opposite. 1-Methylimidazolium with Cl-, a small and strongly coordinating anion, presents in the N K XANES spectrum a splitting of the band corresponding to nitrogen in the imidazolic ring, indicating two different chemical environments. For this cation with TFSI-, on the contrary, this splitting was not observed, showing that the anion has a weaker interaction with the imidazolic ring, even without a lateral carbonic chain.

Advanced applications of X-ray Absorption Spectroscopy to the study of protein metal sites.

We present a study of the metal sites of different proteins through X-ray Absorption Fine Structure (XAFS) spectroscopy. First of all, the capabilities of XAFS analysis have been improved by ab initio simulation of the near-edge region of the spectra, and an original analysis method has been proposed. The method subsequently served ad a tool to treat diverse biophysical problems, like the inhibition of proton-translocating proteins by metal ions and the matrix effect exerted on photosynthetic proteins (the bacterial Reaction Center, RC) by strongly dehydrate sugar matrices. A time-resolved study of Fe site of RC with μs resolution has been as well attempted. Finally, a further step aimed to improve the reliability of XAFS analysis has been performed by calculating the dynamical parameters of the metal binding cluster by means of DFT methods, and the theoretical result obtained for MbCO has been successfully compared with experimental data.

Ex situ X-­Ray absorption study of Li-­rich layered cathode material Li[Li0.2Mn0.56Ni0.16Co0.08]O2

The Li-rich layered transition metal oxides (LLOs) Li2MnO3-LiMO2 (M=Mn, Co, Ni, etc.) have drawn considerable attention as cathode materials for rechargeable lithium batteries. They generate large reversible capacities but the fundamental reaction mechanism and structural perturbations during cycling remain controversial. In the present thesis, ex situ X-ray absorption spectroscopy (XAS) measurements were performed on Li[Li0.2Mn0.56Ni0.16Co0.08]O2 at different stage of charge during electrochemical oxidation/reduction. K-edge spectra of Co, Mn and Ni were recorded through a voltage range of 3.7-4.8V vs. Li/Li+, which consist of X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). Oxidation states during initial charge were discussed based on values from literature as well as XANES analysis. Information about bond distance, coordination number as well as corresponding Debye-Waller factor were extracted from Gnxas analysis of raw data in the EXAFS region. The possibility of oxygen participation in the initial charge was discussed. Co and Ni prove to take part in the oxidation/reduction process while Mn remain in the tetravalent state. The cathode material appears to retain good structural short-range order during charge-discharge. A resemblance of the pristine sample and sample 4 was discovered which was firstly reported for similar compounds.

Pre-edge analysis of X-rays absorption spectra in TiO2 modified films

The thesis is mainly focused on the pre-edge analysis of XAS spectra of Ti HCF sample hexacyanocobaltate and hexacyanoferrate samples doped on a Indium Tin Oxide (ITO) thin film. The work is aimed at the determination of Ti oxidation state, as well as indication of various coordination number in the studied samples. The experiment have been conducted using XAFS (X-ray absorption fine structure)beamline at Elettra synchrotron, Trieste (Italy) under supervision of Professor Marco Giorgetti, Department of Industrial Chemistry, University of Bologna. The Master thesis accreditation to fullfill the ASC Master of Advanced Spectroscopy in Chemistry Degree requirement.

Developments in the Theory of X-ray Absorption and Compton Scattering.

Thesis (Ph.D.)--University of Washington, 2016-06

Synchrotron X-ray powder diffraction and extended X-ray absorption fine structure spectroscopy studies on nanocrystalline ZrO(2)-CaO solid solutions

The crystal structure and the local atomic order of a series of nanocrystalline ZrO(2)-CaO solid solutions with varying CaO content were studied by synchrotron radiation X-ray powder diffraction and extended X-ray absorption fine structure (EXAFS) spectroscopy. These samples were synthesized by a pH-controlled nitrate-glycine gel-combustion process. For CaO contents up to 8 mol%, the t' form of the tetragonal phase (c/a > 1) was identified, whereas for 10 and 12 mol% CaO, the t '' form (c/a=1; oxygen anions displaced from their ideal positions in the cubic phase) was detected. Finally, the cubic phase was observed for solid solutions with CaO content of 14 mol% CaO or higher. The t'/t '' and t ''/cubic compositional boundaries were determined to be at 9 (1) and 13 (1) mol% CaO, respectively. The EXAFS study demonstrated that this transition is related to a tetragonal-to-cubic symmetry change of the first oxygen coordination shell around the Zr atoms.