X-ray Absorption Fine Structure Analysis Research Articles

Effect of fluoride mouthrinse on adhesion to bovine root dentin.

The purpose of this study was to evaluate the effect of fluoride mouthrinses on dentin bonding performance of a two-step selfetch adhesive; Clearfil SE Bond. Bovine root dentin surface was treated with either 450, 900, or 9,000 ppm F solutions for 30 s (immediate), and continually treated for one month (one month) before the bonding procedures. Microtensile bond strength (µTBS) test and scanning electron microscopic (SEM) observation of the acid-base resistance zone (ABRZ) were performed. Chemical state of fluorine on dentin surface was analyzed by X-ray absorption fine structure (XAFS). The 450 and 900 ppm F fluoride mouthrinses did not influence the µTBS to dentin, while the 9,000 ppm F fluoride solution adversely affected the µTBSs. The fluoride application to dentin significantly enhanced acid resistance at the adhesive/dentin interface including the ABRZ. The XAFS analysis indicated different concentrations of fluoride might create different chemical compounds on the dentin surface, influencing the µTBS results.

High-Resolution Extended X-ray Absorption Fine Structure Analysis Provides Evidence for a Longer Fe···Fe Distance in the Q Intermediate of Methane Monooxygenase.

Despite decades of intense research, the core structure of the methane C-H bond breaking diiron(IV) intermediate, Q, of soluble methane monooxygenase remains controversial, with conflicting reports supporting either a "diamond" diiron core structure or an open core structure. Early extended X-ray absorption fine structure (EXAFS) data assigned a short 2.46 Å Fe-Fe distance to Q (Shu et al. Science 1997, 275, 515 ) that is inconsistent with several theoretical studies and in conflict with our recent high-resolution Fe K-edge X-ray absorption spectroscopy (XAS) studies (Castillo et al. J. Am. Chem. Soc. 2017, 139, 18024 ). Herein, we revisit the EXAFS of Q using high-energy resolution fluorescence-detected extended X-ray absorption fine structure (HERFD-EXAFS) studies. The present data show no evidence for a short Fe-Fe distance, but rather a long 3.4 Å diiron distance, as observed in open core synthetic model complexes. The previously reported 2.46 Å feature plausibly arises from a background metallic iron contribution from the experimental setup, which is eliminated in HERFD-EXAFS due to the increased selectivity. Herein, we explore the origin of the short diiron feature in partial-fluorescent yield EXAFS measurements and discuss the diagnostic features of background metallic scattering contribution to the EXAFS of dilute biological samples. Lastly, differences in sample preparation and resultant sample inhomogeneity in rapid-freeze quenched samples for EXAFS analysis are discussed. The presented approaches have broad implications for EXAFS studies of all dilute iron-containing samples.

Comment on “Instability of the topological surface state in Bi2Se3 upon deposition of gold”

Polyakov et al. [Phys. Rev. B 95, 180202(R) (2017)] have presented a comparison of experimental versus calculated photoemission for gold deposited on $\mathrm{B}{\mathrm{i}}_{2}\mathrm{S}{\mathrm{e}}_{3}$, with the calculation based on a substitutional model of gold replacing bismuth, derived from an extended x-ray absorption fine-structure (EXAFS) analysis of the gold ${L}_{\mathrm{III}}$ edge. This Comment examines the coordination environment of gold in solid-state selenides in comparison to the model used, deficiencies within the EXAFS treatment presented by Polyakov et al., and provides a more thorough examination and interpretation of the x-ray absorption near-edge structure (XANES) and the EXAFS that invalidates the claims by the authors of gold being substitutional in topological insulator $\mathrm{B}{\mathrm{i}}_{2}\mathrm{S}{\mathrm{e}}_{3}$.

Role of PhaC Type I and Type II Enzymes during PHA Biosynthesis.

PHA synthases (PhaC) are grouped into four classes based on the kinetics and mechanisms of reaction. The grouping of PhaC enzymes into four classes is dependent on substrate specificity, according to the preference in forming short-chain-length (scl) or medium-chain-length (mcl) polymers: Class I, Class III and Class IV produce scl-PHAs depending on propionate, butyrate, valerate and hexanoate precursors, while Class II PhaC synthesize mcl-PHAs based on the alkane (C6 to C14) precursors. PHA synthases of Class I, in particular PhaCCs from Chromobacterium USM2 and PhaCCn/RePhaC1 from Cupriavidus necator/Ralstonia eutropha, have been analysed and the crystal structures of the C-domains have been determined. PhaCCn/RePhaC1 was also studied by X-ray absorption fine-structure (XAFS) analysis. Models have been proposed for dimerization, catalysis mechanism, substrate recognition and affinity, product formation, and product egress route. The assays based on amino acid substitution by mutagenesis have been useful to validate the hypothesis on the role of amino acids in catalysis and in accommodation of bulky substrates, and for the synthesis of PHB copolymers and medium-chain-length PHA polymers with optimized chemical properties.

Synthesis of pollucite with Cs-polluted incineration ash mixed with soil for immobilization of radioactive Cs

The Fukushima unclear leakage in Japan on March 11 t h, 2011 resulted in huge amount of Cs-polluted incineration ashes and soils produced. The conventional solidification (cement and glass solidifications etc.) methods for nuclear wastes treatment seem unsuitable because too many solidification basis materials are also required. A novel hydrothermal method therefore has been developed to directly synthesize pollucite only with Cs-polluted incineration ash and soil to immobilize Cs. The results revealed that pollucite could be synthesized with a wide range of mixing ratios between incineration ash (PA) and soil (kaolin) even at a lower temperature (≥140 °C) for a shorter time (≥3 h), and however a higher temperature or a longer time favored to form pure pollucite. Moreover, the synthesized pollucite specimens possessed a high strength (flexural strength>16 MPa), suggesting that this hydrothermal synthesis might have the potential for treatment of Cs-polluted incineration ash and soil. The Extended X-ray Absorption Fine Structure (EXAFS) analyses further revealed that the polluted Cs did be immobilized into the structure of the synthesized pollucite rather than physically adsorbed in the pores. Leaching tests also demonstrated that the amount of Cs leached from the synthesized pollucite specimens was very low, similar to that of ceramic immobilization.

A comparative study on structures and magnetic properties of SmCo4B and SmCo3.1Fe0.9B ribbons

The phase compositions, atomic structures and magnetic properties of as-spun SmCo4B and SmCo3.1Fe0.9B ribbons are comparatively studied. It was found that SmCo4B and SmCo3.1Fe0.9B ribbons consist of single SmCo4B or Sm(Co,Fe)4B phase, respectively. The SmCo4B phase displays homogeneous equiaxed grains, which contact each other directly, while Sm(Co,Fe)4B phase does not expose its clear grain profile. The Extended X-ray Absorption Fine Structure (EXAFS) analysis shows that both interatomic distance and disorder degree increase when a part of Co is substituted by Fe in SmCo4B ribbons. Such change in atomic structure increases the effect of atomic mismatch and the glass-forming ability of SmCo4B ribbons, but reduces the magnetocrystalline anisotropy. Annealing is quite helpful to improve the magnetic properties of SmCo3.1Fe0.9B ribbons.

Immobilization of a Molybdenum Complex on Bipyridine-Based Periodic Mesoporous Organosilica and Its Catalytic Activity for Epoxidation of Olefins

The dichlorodioxomolybdenum(VI) complex (MoO2Cl2) is an efficient and low-cost homogeneous catalyst for a variety of organic reactions, but its activity usually decreases after immobilization on a solid support. This report describes the synthesis of heterogeneous Mo complex catalysts using a bipyridine-periodic mesoporous organosilica (BPy-PMO) as a solid chelating ligand and MoO2Cl2 as a precursor, and their catalysis in the epoxidation of olefins with tert-butyl hydroperoxide (TBHP). The MoO2Cl(OH) complex could be immobilized on trimethylsilylated BPy-PMO (BPy-PMO-TMS), which was confirmed by Fourier-transform infrared spectroscopy, Raman spectroscopy, and X-ray absorption fine-structure analysis. The Mo complex immobilized on BPy-PMO-TMS exhibited greater catalytic activity for the epoxidation of cis-cyclooctene compared with conventional heterogeneous Mo complex catalysts using mesoporous silica, polystyrene, and naked BPy-PMO as supports. A large amount (up to 0.72 mmol g–1) of the Mo complex could...

Decontamination performance of magnetic graphene oxide towards nickel ions and its underlying mechanism investigation by XAFS

In this paper, the decontamination performance and its underlying mechanism of magnetic graphene oxide (MGO) towards nickel (Ni(II)) ions were studied by batch technique and X-ray absorption fine structure (XAFS) analysis. The conditions that affect Ni(II) uptake, such as reaction time, pH, ionic strength, coexisting ions, humic/fulvic acid (HA/FA) and temperature were investigated by control variable method. The adsorption kinetics indicated that Ni(II) uptake on MGO was corresponded with pseudo-second-order rate equation, and it can reach equilibrium after ~4.0h. The pH had ken speckle effect on Ni(II) uptake, while the ionic strength and coexisting ions had scant impact on Ni(II) uptake. The presence of HA/FA has a positive impact on Ni(II) uptake at pH<7.0, while has a negative impact on Ni(II) uptake at pH>7.0. The uptake of Ni(II) can be better described by Langmuir model than Freundlich model. The thermodynamic analysis suggests that Ni(II) uptake was an endothermic and spontaneous behavior. XAFS analysis indicate that Ni(II) was captured on the binding sites of MGO, and some Ni(II) can bind on the surfaces of the iron oxides coated on GO to form strong inner-sphere complexes with good thermodynamic stability. Results of this study indicate that MGO is a significant material for treatment of Ni(II)-bearing effluents and may also be an effective adsorbent for removing other metal ions from wastewater.

MiXAFS: a program for X-ray absorption fine-structure data analysis.

A new program called miXAFS for the analysis of X-ray absorption fine-structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X-ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R-factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.

Biosynthesis and Characterization of Copper Nanoparticles Using Shewanella oneidensis: Application for Click Chemistry.

Copper nanoparticles (Cu-NPs) have a wide range of applications as heterogeneous catalysts. In this study, a novel green biosynthesis route for producing Cu-NPs using the metal-reducing bacterium, Shewanella oneidensis is demonstrated. Thin section transmission electron microscopy shows that the Cu-NPs are predominantly intracellular and present in a typical size range of 20-40 nm. Serial block-face scanning electron microscopy demonstrates the Cu-NPs are well-dispersed across the 3D structure of the cells. X-ray absorption near-edge spectroscopy and extended X-ray absorption fine-structure spectroscopy analysis show the nanoparticles are Cu(0), however, atomic resolution images and electron energy loss spectroscopy suggest partial oxidation of the surface layer to Cu2 O upon exposure to air. The catalytic activity of the Cu-NPs is demonstrated in an archetypal "click chemistry" reaction, generating good yields during azide-alkyne cycloadditions, most likely catalyzed by the Cu(I) surface layer of the nanoparticles. Furthermore, cytochrome deletion mutants suggest a novel metal reduction system is involved in enzymatic Cu(II) reduction and Cu-NP synthesis, which is not dependent on the Mtr pathway commonly used to reduce other high oxidation state metals in this bacterium. This work demonstrates a novel, simple, green biosynthesis method for producing efficient copper nanoparticle catalysts.

Incorporation of Cadmium and Nickel into Ferrite Spinel Solid Solution: X-ray Diffraction and X-ray Absorption Fine Structure Analyses.

The feasibility of incorporating Cd and Ni in hematite was studied by investigating the interaction mechanism for the formation of CdxNi1-xFe2O4 solid solutions (CNFs) from CdO, NiO, and α-Fe2O3. X-ray diffraction results showed that the CNFs crystallized into spinel structures with increasing lattice parameters as the Cd content in the precursors was increased. Cd2+ ions were found to occupy the tetrahedral sites, as evidenced by Rietveld refinement and extended X-ray absorption fine structure analyses. The incorporation of Cd and Ni into ferrite spinel solid solution strongly relied on the processing parameters. The incorporation of Cd and Ni into the CNFs was greater at high x values (0.7 < x ≤ 1.0) than at low x values (0.0 ≤ x ≤ 0.7). A feasible treatment technique based on the investigated mechanism of CNF formation was developed, involving thermal treatment of waste sludge containing Cd and Ni. Both of these metals in the waste sludge were successfully incorporated into a ferrite spinel solid solution, and the concentrations of leached Cd and Ni from this solid solution were substantially reduced, stabilizing at low levels. This research offers a highly promising approach for treating the Cd and Ni content frequently encountered in electronic waste and its treatment residues.

Structural analysis of amorphous carbon films by BEMA theory based on spectroscopic ellipsometry measurement

The structural analysis of amorphous carbon films is imperative for the application of their unique properties into industrial fields. Density is one of the most fundamental properties of amorphous carbon films, and directly related to their structures. In the present study, thirteen amorphous carbon film samples with different sp3/(sp3+sp2) ratios and hydrogen contents were deposited by various physical and chemical vapor deposition techniques. All these films were analyzed by spectroscopic ellipsometry and simulated using Bruggeman effective medium approximation (BEMA) theory. In this simulation analysis, ten types of optical models were proposed based on the selected five kinds of standard materials (diamond, highly oriented pyrolytic graphite, glassy carbon, polyethylene, and void) with considering a feasibility of each model. The comparisons of the X-ray reflectivity density and BEMA calculated density, as well as those of the sp3/(sp3+sp2) ratios obtained from BEMA simulation and the near-edge X-ray absorption fine-structure analysis were carried out for the individual samples. Thus, using BEMA theory, it was established that the suitable optical models should be applied to make a detailed structural analysis of the individual types of amorphous carbon films.

Suppressing Isomerization of Phosphine-Protected Au9 Cluster by Bond Stiffening Induced by a Single Pd Atom Substitution.

The fluxional nature of small gold clusters has been exemplified by reversible isomerization between [Au9(PPh3)8]3+ with a crown motif (Au9(C)) and that with a butterfly motif (Au9(B)) induced by association and dissociation with compact counteranions (NO3-, Cl-). However, structural isomerization was suppressed by substitution of the central Au atom of the Au9 core in [Au9(PPh3)8]3+ with a Pd atom: [PdAu8(PPh3)8]2+ with a crown motif (PdAu8(C)) did not isomerize to that with a butterfly motif (PdAu8(B)) upon association with the counteranions. Density functional theory calculation showed that the energy difference between PdAu8(C) and PdAu8(B) is comparable to that between Au9(C) and Au9(B), indicating that the relative stabilities of the isomers are not a direct cause for the suppression of isomerization. Temperature dependence of Debye-Waller factors obtained by X-ray absorption fine-structure analysis revealed that the intracluster bonds of PdAu8(C) were stiffer than the corresponding bonds in Au9(C). Natural bond orbital analysis suggested that the radial Pd-Au and lateral Au-Au bonds in PdAu8(C) are stiffened due to the increase in the ionic nature and decrease in electrostatic repulsion between the surface Au atoms, respectively. We conclude that the formation of stiffer metal-metal bonds by Pd atom doping inhibits the isomerization from PdAu8(C) to PdAu8(B).

XAFS structural characterization of Cu vapour derived catalysts supported on poly‐4‐vinylpyridine and carbon

The use of supported metallic nanoparticles (NPs) is fundamental for the development of new catalysts with high activity and selectivity. For this reason, the choice of a suitable support, the selection of metal precursors and the preparation methods become quite important. In the present work, we show the structural effects induced on metal vapour synthesis (MVS) derived Cu NPs by different carbon‐based supports such as poly‐4‐vinylpyridine (PVPy) and carbon and how these effects can affect their catalytic activities in Huisgen azide‐alkyne cycloaddition reactions (CuAAC). The influence of the two supports on the structure of the Cu NPs was studied using high‐resolution transmission electron microscopy (HRTEM) and X‐ray absorption fine structure (XAFS) spectroscopy. As shown by XAFS analysis, Cu NPs, immobilized on PVPy, resulted in a Cu(I) oxidized phase while the ones on carbon were in a Cu(II) phase. The structural effects induced by the different supports determined a completely different catalytic behaviour of the two catalytic systems in a model CuAAC reaction: the PVPy‐supported Cu system was active and re‐usable whereas the analogous carbon‐based system was almost inactive. Copyright © 2017 John Wiley &amp; Sons, Ltd.

NiO/Nb2O5/C Hydrazine Electrooxidation Catalysts for Anion Exchange Membrane Fuel Cells

NiO/Nb2O5/C (8:1), (4:1), (2:1), NiO/C, and Ni/C catalysts for hydrazine electrooxidation were synthesized by an evaporation drying method followed by thermal annealing. Prepared catalysts were characterized by X-ray diffraction (XRD), high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), energy dispersive X-ray spectrometry (EDS), and X-ray absorption fine structure (XAFS). Catalytic activity, durability, and selectivity in the reaction of hydrazine electrooxidation were evaluated in alkaline media. The highest catalytic activity in mentioned above reaction was found for Ni/C, followed by: NiO/Nb2O5/C (8:1), NiO/Nb2O5/C (4:1). NiO/Nb2O5/C (2:1) whiles NiO/C has almost no activity for hydrazine oxidation. NiO/Nb2O5/C (8:1) and (4:1) had a highest stability during electrooxidation of hydrazine at 60°C. It was explained by oxygen defect of NiO in NiO/Nb2O5/C from XAFS analysis. The selectivity hydrazine electrooxidation as measured by ammonia production resulted in observation that metallic Ni surface facilitates N-N bond breaking of hydrazine, which was confirmed by density functional theory (DFT) calculations.

Single-Electron Transfer between CuX2 and Thiols Determined by Extended X-Ray Absorption Fine Structure Analysis: Application in Markovnikov-Type Hydrothiolation of Styrenes.

Transition-metal mediated C-S bond formation using thiol compounds has been widely used in recent years. However, there has been less focus on the interaction between the metal and thiol compounds. In this work, we have successfully evidenced the single-electron transfer between CuX2 and thiophenol utilizing EXAFS. The fitting EXAFS results reveal that two halide anions are coordinated with the CuI center, whereas no sulfur atom is observed in the first coordination sphere. This CuI ate complex serves as the key intermediate for the proton transfer in the application of Markovnikov-type hydrothiolation reactions.

A Semi-Empirical Capacity Fade Model for Li-NCA Cathode

Lithium Nickel-Cobalt-Aluminum (NCA) is a popular cathode material for Li-ion cells due to its high energy density and moderate cost. Cycling experiments confirmed that the cathode capacity fade is the dominant capacity fade mechanism [1] in such cells. Electron energy loss spectroscopy (EELS) and X-Ray Absorption Fine Structure (XAFS) analysis of the aged LiNCA particles exhibit the formation of a NiO type layer, which is inactive to Li intercalation, at the surface of the particles. Estimated amount of this inactive layer is found to match with the capacity loss of the cell. Therefore, a physics based model with one empirically determined parameter has been constructed for this reaction and it has been implemented on Li-ion battery electrochemical model [3]. The model predicts the relative capacity of a Li-NCA cell cycles at different temperatures with high accuracy (Fig.1). For constant current condition, a simple closed form solution for the capacity fade has been derived and validated. On extension this model can effectively predict the remaining useful life.

Electronic structure and room temperature ferromagnetism of C doped TiO2

Abstract C-doped TiO 2 nanoparticles were successfully synthesized using a simple hydrothermal synthesis method. After this preparation, a portion of the samples were annealed separately in air on the one hand, and in argon on the other, and another portion remained untreated. The results of X-ray diffraction show that the untreated samples primarily display anatase and rutile structures. However, after annealing, the samples displayed the rutile structure only. The Ti K -edge and L -edge Near Edge X-ray Absorption Fine Structure analyses clearly show that C atoms were successfully incorporated into the TiO 2 host lattice. All doped samples exhibit ferromagnetism at room temperature. The saturation magnetization (Ms) and coercive fields (Hc) tend to decrease after the samples are annealed in argon and in air. The maximum Ms of the untreated samples was approximately 0.038 emu/g.

In SituX-ray Absorption Fine Structure Analysis of PtCo, PtCu, and PtNi Alloy Electrocatalysts: The Correlation of Enhanced Oxygen Reduction Reaction Activity and Structure

In order to examine the relationship between the oxygen reduction reaction (ORR) activity of a fuel cell catalyst and its structure and/or electronic state, carbon-supported Pt and Pt alloys having various structures, compositions, and morphologies were studied. Regardless of the atomic ordering or morphology (core–shell or random alloy) of the catalyst, the ORR activity was primarily dependent on the Pt–Pt bond distance. Among these materials, Pt2Co, having the shortest Pt–Pt distance, exhibited the highest ORR activity. The activities of this catalyst per unit surface area and per unit mass were approximately 10 times and 6 times higher than those of a commercially available carbon supported Pt electrocatalyst (Pt/C). This work also found a monotonic increase in catalytic activity with decreasing Pt–Pt distance.

A combined in-situ XAS–DRIFTS study unraveling adsorbate induced changes on the Pt nanoparticle structure

The adsorption behavior of Platinum nanoparticles was studied for the as-received catalyst (under inert gas), under hydrogen and CO atmosphere using our newly designed in-situ cell. X-ray Absorption Spectroscopy (XAS) and Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) experiments were performed simultaneously with high data quality. Structural information and the type of adsorbate could be revealed via Extended X-ray Absorption Fine Structure (EXAFS) analysis, Δμ X-ray Absorption Near Edge Structure analysis (Δμ XANES) and in-situ DRIFTS. The as-received catalyst showed sub-surface oxygen and O(n-fold). Under CO atmosphere only CO(atop) was found. Reversible adsorbate induced changes of the Pt nanoparticle structure were derived from changes in the PtPt coordination number and the corresponding bond distance. Under reducing conditions (H2, CO) a significant increase in both values occurred. Temperature dependent desorption of CO revealed a gradual shift from PtCO to PtO. Reoxidation was clearly assigned to strong metal support interaction from the SiO2 support.