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

Near infrared (NIR) absorption spectra correlates with subchondral bone micro-CT parameters in osteoarthritic rat models

Determining the properties and integrity of subchondral bone in the developmental stages of osteoarthritis, especially in a form that can facilitate real-time characterization for diagnostic and decision-making purposes, is still a matter for research and development. This paper presents relationships between near infrared absorption spectra and properties of subchondral bone obtained from 3 models of osteoarthritic degeneration induced in laboratory rats via: (i) menisectomy (MSX); (ii) anterior cruciate ligament transaction (ACL); and (iii) intra-articular injection of mono-ido-acetate (1 mg) (MIA), in the right knee joint, with 12 rats per model group (N = 36). After 8 weeks, the animals were sacrificed and knee joints were collected. A custom-made diffuse reflectance NIR probe of diameter 5 mm was placed on the tibial surface and spectral data were acquired from each specimen in the wavenumber range 4000–12 500 cm− 1. After spectral acquisition, micro computed tomography (micro-CT) was performed on the samples and subchondral bone parameters namely: bone volume (BV) and bone mineral density (BMD) were extracted from the micro-CT data. Statistical correlation was then conducted between these parameters and regions of the near infrared spectra using multivariate techniques including principal component analysis (PCA), discriminant analysis (DA), and partial least squares (PLS) regression. Statistically significant linear correlations were found between the near infrared absorption spectra and subchondral bone BMD (R2 = 98.84%) and BV (R2 = 97.87%). In conclusion, near infrared spectroscopic probing can be used to detect, qualify and quantify changes in the composition of the subchondral bone, and could potentially assist in distinguishing healthy from OA bone as demonstrated with our laboratory rat models.

Load-unloading response of intact and artificially degraded articular cartilage correlated with near infrared (NIR) absorption spectra

The conventional mechanical properties of articular cartilage, such as compressive stiffness, have been demonstrated to be limited in their capacity to distinguish intact (visually normal) from degraded cartilage samples. In this paper, we explore the correlation between a new mechanical parameter, namely the reswelling of articular cartilage following unloading from a given compressive load, and the near infrared (NIR) spectrum. The capacity to distinguish mechanically intact from proteoglycan-depleted tissue relative to the "reswelling" characteristic was first established, and the result was subsequently correlated with the NIR spectral data of the respective tissue samples. To achieve this, normal intact and enzymatically degraded samples were subjected to both NIR probing and mechanical compression based on a load-unload-reswelling protocol. The parameter δ(r), characteristic of the osmotic "reswelling" of the matrix after unloading to a constant small load in the order of the osmotic pressure of cartilage, was obtained for the different sample types. Multivariate statistics was employed to determine the degree of correlation between δ(r) and the NIR absorption spectrum of relevant specimens using Partial Least Squared (PLS) regression. The results show a strong relationship (R(2)=95.89%, p<0.0001) between the spectral data and δ(r). This correlation of δ(r) with NIR spectral data suggests the potential for determining the reswelling characteristics non-destructively. It was also observed that δ(r) values bear a significant relationship with the cartilage matrix integrity, indicated by its proteoglycan content, and can therefore differentiate between normal and artificially degraded proteoglycan-depleted cartilage samples. It is therefore argued that the reswelling of cartilage, which is both biochemical (osmotic) and mechanical (hydrostatic pressure) in origin, could be a strong candidate for characterizing the tissue, especially in regions surrounding focal cartilage defects in joints.

Satellites in the X-ray photoelectron spectra of transition-metal and rare-earth compounds

An attempt has been made at synthesis and in resolving some of the uncertainties related to the assignments of charge-transfer satellites in the X-ray photoelectron spectra of transition-metal and rare-earth compounds. New satellites are reported in the ligand core-hole spectra as well as in the metal core-level spectra of oxides of second- and third-row transition metals including rare earths. Satellites in the ligand levels and the metal levels tend to be mutually exclusive, a behaviour that can be understood on the basis of metal-ligand overlap. Systematics in the intensities and energy separations of satellites in the first-row transition-metal compounds have been examined in order to gain an insight into the nature of these satellites. A simple model involving the sudden approximation has been employed to explain the observed systematics in intensities of satellites appearing next to metal and ligand core levels on the basis of metal-ligand overlap.

Study of strontium compounds and minerals by X-ray absorption spectroscopy. I. K-edge shifts

The chemical shifts in the X-ray K-absorption edge of strontium in various compounds and in six minerals are measured using a single crystal X-ray spectrometer. Besides valence, the shifts are found to be governed by ionic charges on the absorbing ions, which are calculated employing Pauling's method. For the minerals the plot of chemical shift against the theoretically calculated ionic charges is used to determine the charges on the strontium ions.