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.

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.

Small-angle X-ray scattering and X-ray absorption near-edge structure study of iron-doped siloxane-polyoxyethylene nanocomposites

The local and medium-range structures of siloxane-POE hybrids doped with Fe(III) ions and prepared by the sol-gel process were investigated by X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) and small-angle X-ray scattering (SAXS), respectively. The experimental results show that the structure of these composites depends on the doping level. EXAFS data reveal that, for low doping levels ([O]/[Fe] > 40, oxygens being of the ether-type of the POE chains), Fe(III) ions are surrounded essentially by a shell of chlorine atoms, suggesting the formation of FeCl4- anions. At high doping levels ([O]/[Fe] < 20), Fe(III) ions interacts mainly with oxygen atoms and form FeOx species. The relative proportion of FeOx species increases with iron concentration, this result being consistent with the results of SAXS measurements showing that increasing iron doping induces the formation of iron-rich nanodomains embedded in the polymer matrix.

Local order around tungsten atoms in tungstate fluorophosphate glasses by X-ray absorption spectroscopy

X-ray absorption spectroscopy was used to study the local environment of tungsten atoms in NaPO3-BaF2,-WO3 glasses and the results were compared with crystalline references Na2WO4 and WO3. XANES measurements at the W-L-1 edge allowed to determine a distorted octahedral environment of tungsten atoms in these glasses similar to the local order of tungsten in monoclinic WO3. Extended X-ray absorption fine structure (EXAFS) has been used as a local probe to monitor the effect of WO3 concentration on the tungsten environment. Based on an analysis of the EXAFS data, we proposed a three-shell model of oxygen atoms around tungsten as in monoclinic WO3. With increasing WO3 concentration, it was found that R-2 decreases from 1.96 to 1.92 angstrom whereas R-3 increases from 2.07 to 2.12 angstrom. (c) 2005 Elsevier B.V. All rights reserved.

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.

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.

In situ UV-vis and EXAFS studies of ZnO quantum-sized nanocrystals and Zn-HDS formations from sol-gel route

We have pointed Out that. zinc-based particles obtained from zinc acetate sol-gel route is a mixture of quantum-sized ZnO nanoparticles, zinc acetate, and zinc hydroxide double salt (Zn-HDS). Aiming the knowledge of the mechanisms involved in the formation of ZnO and Zn-HDS phases, the thermohydrolysis of ethanolic zinc acetate solutions induced by lithium hydroxide ([LiOH]/[Zn2+] = 0.1) or water ([H2O]/[Zn2+] = 0.05) addition was investigated at different isothermal temperatures (40, 50, 60 and 70 degrees C) by in situ measurements of turbidity, UV-vis absorption spectra and extended X-ray absorption fine structures (EXAFS). Only the growth of ZnO nanoparticles was observed in sol prepared with LiOH, while a two-step process was observed in that prepared with water addition, leading the fast growth of Zn-HDS and the formation of ZnO nanoparticles at advanced stage. A mechanism of dissolution/reprecipitation governed by the water/ethanol proportion is proposed to account for relative amount of ZnO. (c) 2007 Elsevier Ltd. All rights reserved.

EXAFS and XRD Study of the Structural Evolution during Isothermal Sintering of SnO2 Xerogels

The formation of an ordered (crystalline) phase during isothermal sintering of SnO2 monolithic xerogels, at 200, 250, 300, 400, 500, 600 and 700°C, has been analyzed by the combined use of EXAFS and XRD techniques. For the desiccated gel (110°C), EXAFS results show the formation of small microcrystallites with the incipient cassiterite structure. Between 110 and 250°C, the dehydratation reaction leads to an amorphization evidenced by a decrease of the long and short range crystallographic order. It is due to fissure formation in the xerogel network. For higher temperatures, a continuous coagulation of the crystallites occurs, leading to grain growth. Grain and pore growth obeys the same kinetic relation, so that the microstructure grows by simple enlargement while its morphology is static.

X-ray absorption fine structure as a monitor of zinc coordination sites during oogenesis of Xenopus laevis.

The x-ray absorption fine structure (XAFS) zinc K-edge steps for intact stages I,II and V,VI Xenopus laevis oocytes demonstrate that the zinc concentration is about 3 and 1 mM, respectively. However, the chi(k) function for the early stage oocytes differs markedly from that for the late one. Analysis of the XAFS data for stage I,II oocytes indicates that zinc is bound to 2.0 +/- 0.5 sulfur atoms at an average coordination distance of 2.29 +/- 0.02 angstroms and 2.0 +/- 0.5 nitrogen or oxygen (N/O) atoms at 2.02 +/- 0.02 angstroms. In marked contrast, in stage V,VI oocytes, zinc is bound to 4.1 +/- 0.4 N/O atoms at an average distance of 1.98 +/- 0.01 angstroms. Our previous studies demonstrated that 90% of the zinc in stage VI oocytes is sequestered within yolk platelets, associated with a single molecule, lipovitellin, the proteolytically processed product of vitellogenin. XAFS analysis of yolk platelets, lipovitellin, and vitellogenin demonstrates that zinc is bound to 4.0 +/- 0.5 N/O ligands at an average distance of 1.98 +/- 0.01 angstroms in each case, identical to that of stage V,VI oocytes. The higher shell contributions in the Fourier transforms indicate that two of the N/O zinc ligands are His in both stage V,VI and I,II oocytes. The results show that in stage I,II oocytes, there is a high concentration of a zinc protein whose zinc coordination site likely is composed of (His)2(Cys)2, such as, e.g., TFIIIA. As the oocytes develop, the predominant zinc species becomes one that exhibits the (His)2(N/0)2 zinc site found in lipovitellin. Hence, the ligands to the zinc atoms in intact oocytes and the changes that take place as a function of oogenesis and after their fertilization, during embryogenesis, now can be examined and explored.

Dynamical study of ZnO nanocrystal and Zn-HDS layered basic zinc acetate formation from sol-gel route

We have pointed out that zinc based particles obtained from ethanolic solution of a zinc acetate derivative (zinc oxy-acetate, Zn4O(Ac)(6)) are a mixture of nanometer sized ZnO, zinc oxy-acetate, and zinc hydroxide double salt (Zn-HDS). The knowledge of the mechanisms involved in the formation of ZnO and Zn-HDS phases, and the evolution of Zn species in reaction medium was monitored in situ during 14 h by simultaneous measurements of UV-vis absorption and extended X-ray absorption fine structures (EXAFS) spectra. This spectroscopic monitoring was initialized just after the addition of an ethanolic lithium hydroxide solution ([LiOH]/[Zn] = 0. 1) to the reaction medium kept under controlled temperature (40 degrees C). This study points out the first direct evidence of the reaction between ZnO nanoparticles and unreacted zinc oxy-acetate to form a Zn-HDS phase. The dissolution of ZnO and the reprecipitation of Zn-HDS are induced by the gradual release of water mainly produced by ethanol esterification well evidenced by gas chromatography coupled to mass spectroscopy and FT-IR measurements.

In situ and simultaneous nanostructural and spectroscopic studies of ZnO nanoparticle and Zn-HDS formations from hydrolysis of ethanolic zinc acetate solutions induced by water

The simultaneous formation of nanometer sized zinc oxide (ZnO), and acetate zinc hydroxide double salt (Zn-HDS) is described. These phases, obtained using the sol-gel synthesis route based on zinc acetate salt in alcoholic media, were identified by direct characterization of the reaction products in solution using complementary techniques: nephelometry, in situ Small-Angle X-ray Scattering (SAXS), UV-Vis spectroscopy and Extended X-ray Absorption Fine Structures (EXAFS). In particular, the hydrolytic pathway of ethanolic zinc acetate precursor solutions promoted by addition of water with the molar ratio N = [H2O]/[Zn2+] = 0.05 was investigated in this paper. The aim was to understand the formation mechanism of ZnO colloidal suspension and to reveal the factors responsible for the formation of Zn-HDS in the final precipitates. The growth mechanism of ZnO nanoparticles is based on primary particle (radius approximate to 1.5 nm) rotation inside the primary aggregate (radius < 3.5 nm) giving rise to an epitaxial attachment of particles and then subsequent coalescence. The growth of second ZnO aggregates is not associated with the Otswald ripening, and could be associated with changes in equilibrium between solute species induced by the superficial etching of Zn-HDS particles at the advanced stage of kinetic.

Short Range Order Evolution in the Preparation of SnO2 Based Materials

The evolution of Eu3+ doped SnO2 xerogels to the cassiterite structure observed during sintering was studied by means of Eu3+ spectroscopy, XRD and EXAFS at the Sn K-edge. Eu3+ ions adsorbed at the surface of colloidal particles present a broad distribution of sites, typical of oxide glasses. With sintering at 300°C, this distribution is still broadened. Crystallization is clearly observed by the three techniques with increasing sintering temperature. It is found that the addition of Eu3+ limits the crystallite growth.

Caracterização estrutural de Perovskitas Lax-1AxCoO3 (x=0 e 0,2) ,dopadas com cálcio e bario, por espectroscopia de absorção de raios X (XAS).

In this work, the structures of LaCoO3, La0,8Ba0,2CoO3 and La0,8Ca0,2CoO3 perovskites were characterized as a function of temperature (LaCoO3 structure being analyzed only at room temperature). The characterization of these materials were made by X-Ray Absorption Spectroscopy (XAS), in the cobalt K-edge, taking into account the correlated Einstein model X-ray absorption fine structure (EXAFS). The first part of the absorption spectrum corresponded the X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). These materials were prepared by the combustion method. The combustion products were calcinated at 900 0C, for 6 hours in air. Noted that the sample LaCoO3 at room temperature and samples doped with Calcium and Barium in the temperature range of 50 K to 298 K showed greater distortion to monoclinic symmetry with space group I2/a. However, the sample doped with barium at the temperatures 50 K, 220 K, and 260 K showed a slight distortion to rhombohedral symmetry with space group R-3c. The La0,8Ca0, 2CoO3 structure was few sensitive to temperature variation, showing a higher local distortion in the octahedron and a higher local thermal disorder. These interpretations were in agreement with the information electronic structural on the XANES region and geometric in the EXAFS region

New regularization method for EXAFS analysis: Application to uranium and plutonium sorption onto kaolinite

Die Röntgenabsorptionsspektroskopie (Extended X-ray absorption fine structure (EXAFS) spectroscopy) ist eine wichtige Methode zur Speziation von Schwermetallen in einem weiten Bereich von umweltrelevanten Systemen. Um Strukturparameter wie Koordinationszahl, Atomabstand und Debye-Waller Faktoren für die nächsten Nachbarn eines absorbierenden Atoms zu bestimmen, ist es für experimentelle EXAFS-Spektren üblich, unter Verwendung von Modellstrukturen einen „Least-Squares-Fit“ durchzuführen. Oft können verschiedene Modellstrukturen mit völlig unterschiedlicher chemischer Bedeutung die experimentellen EXAFS-Daten gleich gut beschreiben. Als gute Alternative zum konventionellen Kurven-Fit bietet sich das modifizierte Tikhonov-Regularisationsverfahren an. Ergänzend zur Tikhonov-Standardvariationsmethode enthält der in dieser Arbeit vorgestellte Algorithmus zwei weitere Schritte, nämlich die Anwendung des „Method of Separating Functionals“ und ein Iterationsverfahren mit Filtration im realen Raum. Um das modifizierte Tikhonov-Regularisationsverfahren zu testen und zu bestätigen wurden sowohl simulierte als auch experimentell gemessene EXAFS-Spektren einer kristallinen U(VI)-Verbindung mit bekannter Struktur, nämlich Soddyit (UO2)2SiO4 x 2H2O, untersucht. Die Leistungsfähigkeit dieser neuen Methode zur Auswertung von EXAFS-Spektren wird durch ihre Anwendung auf die Analyse von Proben mit unbekannter Struktur gezeigt, wie sie bei der Sorption von U(VI) bzw. von Pu(III)/Pu(IV) an Kaolinit auftreten. Ziel der Dissertation war es, die immer noch nicht voll ausgeschöpften Möglichkeiten des modifizierten Tikhonov-Regularisationsverfahrens für die Auswertung von EXAFS-Spektren aufzuzeigen. Die Ergebnisse lassen sich in zwei Kategorien einteilen. Die erste beinhaltet die Entwicklung des Tikhonov-Regularisationsverfahrens für die Analyse von EXAFS-Spektren von Mehrkomponentensystemen, insbesondere die Wahl bestimmter Regularisationsparameter und den Einfluss von Mehrfachstreuung, experimentell bedingtem Rauschen, etc. auf die Strukturparameter. Der zweite Teil beinhaltet die Speziation von sorbiertem U(VI) und Pu(III)/Pu(IV) an Kaolinit, basierend auf experimentellen EXAFS-Spektren, die mit Hilfe des modifizierten Tikhonov-Regularisationsverfahren ausgewertet und mit Hilfe konventioneller EXAFS-Analyse durch „Least-Squares-Fit“ bestätigt wurden.

Local atomic structure in tetragonal pure ZrO(2) nanopowders

The local atomic structures around the Zr atom of pure (undoped) ZrO(2) nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO(2) nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.