X-ray Absorption Fine Structure Experiments Research Articles

Kuramoto synchronization of quantum tunneling polarons for describing the dynamic structure in cuprate superconductors

A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by Extended X-ray Absorption Fine Structure experiments (EXAFS), anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant six-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization between coupled internal quantum tunneling polarons associated with the two-site distribution of the copper-apical-oxygen ($Cu-O_{ap}$) pair in the dynamic structure. Furthermore, we find that this first order, anti-phase synchronization transition can be fine tuned by temperature and anharmonicity of the lattice vibrations, and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide planes. Simultaneously, the internal quantum tunneling polaron extends to the copper-planar-oxygen ($Cu-O_{pl}$) pair. All these findings support an interpretation of the EXAFS data in terms of an effective, quantum mechanical triple-well-potential, which accurately represents the anti-phase synchronization of apical oxygens displacements and lattice-assisted charge transfer to the $CuO_2$ plane.

Structure of amorphous Cu2GeTe3 and the implications for its phase-change properties

The structure of amorphous ${\mathrm{Cu}}_{2}{\mathrm{GeTe}}_{3}$ is investigated by a combination of anomalous x-ray scattering and extended x-ray absorption fine-structure experiments. The experimental data are analyzed with reverse Monte Carlo modeling, and they are interpreted in terms of short-range-order parameters as well as by using ring statistics and persistent homology to study the intermediate-range order. Based on this information, the structural relationship of the amorphous phase to the corresponding crystal is discussed. It is found that the amorphous network can be rationalized by small atomic displacements of the crystal structure, directed toward the intrinsic void regions. This structural similarity establishes the possibility of a fast phase-change process. On the other hand, the atomic rearrangements also lead to the formation of new chemical bonds and to distortions on the intermediate-range-order level. These are realized by a collapse and contraction of the strict hexagonal ring arrangements of the crystal and by the formation of small, triangular rings as well as Cu cluster configurations. These structural features allow for a new understanding of the phase-change property contrast of this material, especially concerning the density change and the optical contrast.

Monitoring the Formation and Reactivity of Organometallic Alkane and Fluoroalkane Complexes with Silanes and Xe Using Time-Resolved X-ray Absorption Fine Structure Spectroscopy.

Complexes with weakly coordinating ligands are often formed in chemical reactions and can play key roles in determining the reactivity, particularly in catalytic reactions. Using time-resolved X-ray absorption fine structure (XAFS) spectroscopy in combination with time-resolved IR (TRIR) spectroscopy and tungsten hexacarbonyl, W(CO)6, we are able to structurally characterize the formation of an organometallic alkane complex, determine the W-C distances, and monitor the reactivity with silane to form an organometallic silane complex. Experiments in perfluorosolvents doped with xenon afford initially the corresponding solvated complex, which is sufficiently reactive in the presence of Xe that we can then observe the coordination of Xe to the metal center, providing a unique insight into the metal-xenon bonding. These results offer a step toward elucidating the structure, bonding, and chemical reactivity of transient species by X-ray absorption spectroscopy, which has sensitivity to small structural changes. The XAFS results indicate that the bond lengths of metal-alkane (W-H-C) bond in W(CO)5(heptane) as 3.07 (±0.06) Å, which is longer than the calculated W-C (2.86 Å) for binding of the primary C-H, but shorter than the calculated W-C (3.12 Å) for the secondary C-H. A statistical average of the calculated W-C alkane bond lengths is 3.02 Å, and comparison of this value indicates that the value derived from the XAFS measurements is averaged over coordination of all C-H bonds consistent with alkane chain walking. Photolysis of W(CO)6 in the presence of HSiBu3 allows the conversion of W(CO)5(heptane) to W(CO)5(HSiBu3) with an estimated W-Si distance of 3.20 (±0.03) Å. Time-resolved TRIR and XAFS experiments following photolysis of W(CO)6 in perfluoromethylcyclohexane (PFMCH) allows the characterization of W(CO)5(PFMCH) with a W-F distance of 2.65 (±0.06) Å, and doping PFMCH with Xe allows the characterization of W(CO)5Xe with a W-Xe bond length of 3.10 (±0.02) Å.

Upgrade of SLRI BL8 beamline for XAFS spectroscopy in a photon energy range of 1–13 keV

Beamline 8 is a bending magnet beamline at Synchrotron Light Research Institute (SLRI) in Thailand and has been opened for synchrotron users to perform X-ray absorption fine structure (XAFS) spectroscopy since 2006. The beamline was originally equipped with a double crystal monochromator (DCM) using a vertical entrance slit in order to limit divergence of a white beam, thus optimizing photon energy resolution at a cost of photon flux. In 2016 the beamline was upgraded with a vertical collimating mirror to decrease beam divergence. The maximum photon flux is consequently increased to 3 × 1011 photons s−1 (100 mA)−1 at the phosphorus K-edge (2145.5 eV). This enhances beamline utilization for phosphorus speciation and analysis of local atomic structures in diluted samples (>50 mg/kg of phosphorus). Furthermore, the highest photon energy of the beamline has been extended from 10 keV to 13 keV, enabling several heavy elements such as lead to be studied while the lowest photon energy currently covers the sodium K-edge. To demonstrate improved XAFS performance, XAFS experiments were carried out on selected samples (NaCl, Na3PO4·12H2O, PbO, PbO4, PbCO3, PbS, soil, and historical paint); quality of the experimental spectra was evaluated in terms of signal-to-noise ratio and appearance of XAFS characteristic features.

Impurity position and lattice distortion in a Mn-doped Bi2Te3 topological insulator investigated by x-ray fluorescence holography and x-ray absorption fine structure

Mn $K\ensuremath{\alpha}$ x-ray fluorescence holography (XFH) measurements were performed on a single crystal of a ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}{\mathrm{Mn}}_{0.1}$ topological insulator at 100 and 300 K to search for the impurity sites of the Mn atoms in this functional crystal. The three-dimensional atomic images were reconstructed using an ${L}_{1}$-regularized linear regression. X-ray absorption fine-structure (XAFS) experiments were also carried out at 30--300 K to obtain additional structural information. The local structural information was obtained from these data, such as the positions of the Mn impurity sites, the Mn-Te interatomic distances, the lattice distortions, and the positional fluctuations around the impurity Mn atoms. The possible Mn impurity sites are twofold, i.e., an interlayer site with an octahedral symmetry and a substitutional site of Te on the layer surface. A distinct temperature dependence is seen in the positional fluctuations of the impurity Mn atoms in the substitutional site. These findings for the impurity sites cannot be easily obtained by diffraction or XAFS experiment in the usual way, but only using a combination of the XFH and XAFS measurements.

Soller slits automatic focusing method for multi-element fluorescence detector

In X-ray absorption fine structure (XAFS) experiments, Soller slits are widely used as filter devices in order to improve the signal to noise ratio. Performing high accuracy manual focusing operations is a time-consuming process; therefore, this work introduces an automatic focusing method for Soller slits in multi-element fluorescence detectors. This method establishes a relation model between the fluorescence intensity distribution and the coordinates of the fluorescence excitation point. According to this relation model, the actual coordinates of the fluorescence excitation point can be deduced from the detected fluorescence intensity distribution and used in focusing operations. This method has proven to be feasible in an XAFS experiment at the BL14W1 beamline of the Shanghai Synchrotron Radiation Facility.

(Invited) Deprotonation of a Multi-Nuclear Copper Complex for High Oxygen Reduction Reaction Activity Investigated By in Situ X-Ray Absorption Fine Structure Spectroscopy

The oxygen reduction reaction (ORR) occurs at the cathode in polymer electrolyte fuel cells (PEFCs) and its sluggish kinetics is one of the limiting factors for widespread applications of PEFCs. Although ORR catalysts have been extensively studied, platinum-based ORR catalysts with a high overpotential (>200 mV) are used even in the present state-of-the-art PEFCs. In nature enzymatic oxygen reduction is known to occur at low overpotentials: multi-copper oxidases such as laccase catalyze ORR with an overpotential of ca. 20 mV on electrode surfaces and have been employed in enzymatic fuel cells [1-2]. These enzymes, however, are fragile and their footnotes are large, making them unsuitable for use in practical PEFCs. It is highly desirable to design and develop artificial ORR catalysts with electrocatalytic properties similar to those of the enzymes [3]. Here, we present our resent studies on in situ X-ray absorption fine structure (XAFS) spectroscopy of a dinuclear copper complex of 3,5-diamiono-1,2,4-triazole, Cu-Hdatrz [4,5], supported on a carbon black under catalytic and non-catalytic conditions to gain insights into designing highly active copper-based catalysts. It is known that the Cu-Hdatrz catalyst shows high ORR activity in basic solution [5]. Our in situ XAFS measurements in neutral and basic solutions revealed that the electron transfer from a CuI species to O2 was faster under basic conditions than that under the neutral condition and deprotonation from the triazole ligand might cause the coordination geometrical changes under a basic condition, suggesting that the deprotonated structure of the CuIactive species may be a key to understand the high ORR activity of Cu-Hdatrz or to design multinuclear copper-triazole catalysts with low overpotentials. Acknowledgements This work was supported by New Energy, Industrial Technology Development Organization (NEDO). XAFS experiments were performed under the approval of the Photon Factory Program Advisory Committee (Proposal No. 2010G200 and 2013G173) References [1] N. Mano, V. Soukharev, A. Heller, J. Phys. Chem. B, 110, 11180 (2006) [2] M.S. Thorum, C.A. Anderson, J.J. Hatch, A.S. Campbell, N.M. Marshall, S.C. Zimmerman, Y. Liu, A.A. Gewirth, J. Phys. Chem. Lett, 1, 2251 (2010) [3] C.H. Kjargaard, J. Rossmeisi, J.K. Norskov, Inorg. Chem., 49, 3567 (2010) [4] E. Aznar, S. Ferrer, J. Borras, F. Lloret, M. Liu-Gonzalez, H. Rodriguez-Prieto, S. Garcia-Granda, Eur. J. Inorg. Chem., 2006, 5115 (2006) [5] M.S. Thorum, J. Yadav, A.A. Gewirth, Ang. Chem. Int. Ed., 48, 165 (2008)

Structural and electronic properties of manganese-doped Bi2Te3 epitaxial layers

We show that in manganese-doped topological insulator bismuth telluride layers, Mn atoms are incorporated predominantly as interstitials in the van der Waals gaps between the quintuple layers and not substitutionally on Bi sites within the quintuple layers. The structural properties of epitaxial layers with Mn concentration of up to 13% are studied by high-resolution x-ray diffraction, evidencing a shrinking of both the in-plane and out-of plane lattice parameters with increasing Mn content. Ferromagnetism sets in for Mn contents around 3% and the Curie temperatures rises up to 15 K for a Mn concentration of 9%. The easy magnetization axis is along the c-axis perpendicular to the (0001) epilayer plane. Angle-resolved photoemission spectroscopy reveals that the Fermi level is situated in the conduction band and no evidence for a gap opening at the topological surface state with the Dirac cone dispersion is found within the experimental resolution at temperatures close to the Curie temperature. From the detailed analysis of the extended x-ray absorption fine-structure experiments (EXAFS) performed at the MnK-edge, we demonstrate that the Mn atoms occupy interstitial positions within the van der Waals gap and are surrounded octahedrally by Te atoms of the adjacent quintuple layers.

Oxygen Reduction Reaction at Multi-Copper Complexes Investigated by Modified Electrode and In Situ XAFS

The oxygen reduction reaction (ORR), which occurs at the cathode in polymer electrolyte fuel cells (PEFCs), requires a large overpotential (more than 200 mV) even at the highly active platinum group metal (PGM) catalysts, since this reaction contains 4-electrons and 4-protons transfer to yield two water molecules from a dioxygen molecule. However, the biocathodes which are constructed by covalently attaching multi-copper enzymes, such as laccase (Lac), at electrode surfaces show nonexsistent overpotential (ca. 20 mV) toward ORR[1-2]. Unfortunately, the pH region, where the Lacs works well as an electrocatalyst for ORR, is limited and the spatial density of reactive sites at such the biocathode seems to be insufficient as compared with the state-of-the-art PGM electrocatalysts. Thus, the extraction of reactive sites in Lac and the effective arrangement on catalyst supports have been desired[3]. Recently, Gewirth and co-workers have achieved a preparation of binuclear copper complex, Cu2(Hdatrz)2, as an electrocatalyst for ORR[4-6]. Although the catalyst shows relatively large overpotential for ORR in acidic solution, the activity in alkaline solution is quite high. The active site for ORR in the catalyst has been proved to be bi-copper centers [6-7] and the investigation of ORR mechanism at the catalyst seems to be valuable.In the present study, we have adopted in situ X-ray absorption fine structure (XAFS) spectroscopy to monitor the electronic structure of Cu centers during ORR and to determine the molecular structure of Cu2(Hdatrz)2 complexes on electrodes. In situ XANES measurement has shown that the ORR at the Cu centers requires the formation of CuI species and the rate-determining step for ORR is dependent on pH.For further development of metal complex catalysts by replacing Cu centers to other metal ions, a easy preparation of model complex electrode should be required. Chemically modified model electrodes are also constructed on gold surface to investigate ORR at multi-metal complex using electrochemistry and spectroscopic methods. This work was supported by New Energy, Industrial Technology Development Organization (NEDO). XAFS experiments were performed under the approval of the Photon Factory Program Advisory Committee (Proposal No. 2010G200 and 2013G173)[1] N. Mano, V. Soukharev, A. Heller, J. Phys. Chem. B, 110, 11180 (2006)[2] M.S. Thorum, C.A. Anderson, J.J. Hatch, A.S. Campbell, N.M. Marshall, S.C. Zimmerman, Y. Liu, A.A. Gewirth, J. Phys. Chem. Lett, 1, 2251 (2010)[3] C.H. Kjargaard, J. Rossmeisi, J.K. Norskov, Inorg. Chem., 49, 3567 (2010)[4] M.S. Thorum, J. Yadav, A.A. Gewirth, Ang. Chem. Int. Ed., 48, 165 (2008)[5] F.R. Brushett, M.S. Thorum, N.S. Lioutas, M.S. Naughton, C. Tornow, H-R. M. Jhong, A.A. Gewirth, P.A. Kenis, J. Am. Chem. Soc., 132, 12185 (2010)[6] M.S. Thorum, J.M. Hankett, A.A. Gewirth, J. Phys. Chem. Lett., 2, 295 (2011)[7] C.C.L. McCrory, A. Devadoss, X. Otterwaelder, R.D. Lowe, T.D.P. Stack, C.E.D. Chidsey, J. Am. Chem. Soc., 133, 3696 (2011)

回折法と X 線吸収分光(XAFS)法を用いた地球惑星物質の精密構造解析

Advantage of mineralogical approach in clarifying peculiar physical properties for materials is introduc in the review. Precise structure analyses of the diffraction and X?ray absorption fine structure (XAFS) spectroscopy methods provide the important information on the Earth and planetary materials. The information from both long-range-order structure by diffraction method and local structure by XAFS method is important for the understanding of the correlation between structures and physical properties of minerals. High pressure and high temperature in-situ diffraction and XAFS experiments were performed using a multi-anvil high-pressure device and synchrotron radiation. Both experiments are also useful as a probe of vibration dynamics and disordered structure. The pressure-dependent anharmonic effective potentials and characteristic values can be investigated using the diffraction and XAFS Debye-Waller factors. The ionic conduction mechanism has been proposed based on the effective one-particle potential and effective pair potential. Super ionic conduction of the mantle constituents resulting from anharmonic thermal vibration can produce the high electric and the low thermal conductivities in the Earth's lower mantle. Local structures of atoms in melt and glass of tetrahedrally coordinated materials change rapidly to higher coordinated states with pressure as if first-order phase transition. Unique structures are left in the local structures of the trace elements in minerals and tektite-impactite glass. The application of recently innovated techniques to the characterization of materials under extreme conditions contributes to the advancement of fundamental Earth-scientific knowledge.

Investigation on the stability of water-soluble ZnO quantum dots in KB cells by X-ray fluorescence and absorption methods

The structural stability of water-soluble ZnO quantum dots (QDs) in oral epidermoid carcinoma (KB) cells was studied by the External Micro Proton Induced X-ray Emission (External Micro-PIXE) technique and the X-ray absorption fine structure (XAFS) measurement. The External Micro-PIXE and XAFS experiments were respectively performed at the JAEA and the Shanghai Synchrotron Radiation Facility. The elements’ distributions were detected by the External Micro-PIXE technique. The XAFS method was applied to obtain information about zinc (Zn) K-edge spectra. The fits of the XAFS data showed that the Zn–O bond structure of water-soluble ZnO QDs was stable after being absorbed by KB cells. Its local structural parameters were almost identical with those of the standard wurtzite structure. Water-soluble ZnO QDs had good structural stability in KB cells.

A furnace to 1200 K for in situ heating x-ray diffraction, small angle x-ray scattering, and x-ray absorption fine structure experiments

A furnace with a water-cooled outside shell has been assembled to do in situ x-ray diffraction (XRD), small angle x-ray scattering (SAXS), and x-ray absorption fine structure (XAFS) experiments. The details of the furnace are described in this paper. The in situ XRD, SAXS, and XAFS experiments during the heating process demonstrate that the available temperature range of this furnace is from room temperature to 1200 K with a temperature accuracy of +/-0.1 K. By using this furnace, in situ XRD, SAXS, and XAFS experimental techniques with temperature change can be easily combined together.

Cytochemical behavior of rare earth ions in Euglena gracilis studied by XAFS

The uptake of rare earth elements (REE) by Euglena gracilis cells has been investigated in Fudan University. The remarkable ability to transport REEs to these cell’s compartments had been observed. X-ray absorption fine structure experiments (XAFS) of cerium in Euglena gracilis were performed at Beijing Synchrotron Radiation Facility (BSRF) to directly determine the cerium valence state and coordination structure in situ. Extended X-ray absorption fine structure (EXAFS) derived calculation showed that cerium was surrounded by 8 N atoms with bond length of 0.258 nm. Combining with other measurements, it may indicate that most likely REEs are mainly located in chlorophyll molecules.

Atomic and electronic structure ofMo6S9−xIx nanowires

Moybdenum-based subnanometre diameter nanowires are easy to synthesize and disperse,and they exhibit a variety of functional properties in which they are superior to otherone-dimensional materials. However, further progress in the understanding ofphysical properties and the development of new and specific applications have so farbeen impeded by the fact that their structure was not accurately known. Herewe report on a combination of systematic x-ray diffraction and extended x-rayabsorption fine structure experiments, and first-principles theoretical structurecalculations, which are used to determine the atomic skeletal structure of individualMo6S9−xIx (MoSIx) nanowires, their packing arrangement within bundles and their electronic band structure.From this work we conclude that the variations in functional properties appear to arisefrom different stoichiometry, not skeletal structure. A supplementary data file is availablefrom http://stacks.iop.org/0957-4484/16/1578

New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron-porphyrin system was needed. In this study, two models with a five-coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree-Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron-porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three-dimensional structures determined by X-ray diffraction and extended X-ray absorption fine-structure experiments. From these results, atomic charges and force-field parameters for molecular mechanics and molecular dynamics calculations were obtained.

Cu-alkali ion exchange in glass: a model for the copper diffusion based on XAFS experiments

Cu-alkali ion exchange is a suitable way to dope superficial layers of silicate glasses well beyond the Cu solubility limits, with the possibility of controlling nanocluster nucleation and growth by subsequent proper treatments. The ion exchange process gives rise to a peculiar copper distribution, with the possible presence of different oxidation states, namely, Cu + and Cu 2+. The modelization of the copper diffusion process is necessary for defining an effective preparation protocol for the copper-doped composites. In this framework, suitable techniques capable to investigate the local atomic environment of Cu atoms are crucial. With this aim, X-ray absorption fine structure (XAFS) spectroscopy in grazing incidence mode was performed using a synchrotron source on different ion-exchanged samples. Based on the experimental results, a phenomenological model is used to describe the diffusion process.

XAFS Study of the Adsorbed Ions onto the Monolayers at Air/Solution Interface

Solution surface can be studied by using X-ray Absorption Fine Structure (XAFS) method. To obtain surface sensitivity, the X-rays are introduced onto the solution surface at a very small grazing incidence angle to meet the total-reflection condition. This new spectroscopic method was successfully applied to the surfaces of aqueous solutions covered with monolayers of alkylammonium bromide, zinc stearate, and also zinc porphyrine complex. The spectra from these surfaces indicated quite interesting but not yet known facts such as, dehydration of anions adsorbed onto the alkylammonium monolayer and coordination change of zinc ions from the octahedral to tetrahedral when the metal ions come to the stearate monolayer from the bulk solution. The XAFS experiments were also performed with linearly polarized X-rays to elucidate the selective orientation of the planar Zn porphyrine complex on the solution surface.

Extended x-ray absorption fine-structure experiments with a laser-imploded target as a radiation source

The feasibility of using extended x-ray absorption fine structure (EXAFS) for characterizing metals shocked to megabar (1 bar = 0.1 MPa) pressures by a laser has been studied. High-contrast K-edge modulations for an unshocked Ti-foil absorber were obtained with a laser-imploded spherical target as a source. The high intensity and relative smoothness of the source spectrum enable us to work with thick Ti foils, which increases the relative modulation in the measured signal. Using a semiempirical model to describe the shock-compressed foil, we show that, because of the rise in Debye temperature with density, the compression extends the temperature range at which EXAFS modulations can be observed.

Differential anomalous scattering on Fe-Co-based metallic glasses

Fe-Co-based amorphous alloys were studied by x-ray diffraction and anomalous x-ray diffraction methods for a range of sample compositions and preparation methods. The main structural characteristics at short- and medium-range scales were investigated. The presence of chemical ordering with preferred Co-Co and Fe-Fe homonuclear correlations and partial Fe-rich phase separation, suggested from previous extended x-ray absorption fine-structure experiments, were clearly in evidence.

Structure of high-temperature fluid selenium

A semiempirical tight-binding energy model is developed for selenium. It includes s and p electrons as well as an empirical description of the dispersion forces that proves necessary at the liquid densities under study. The band-structure parameters are obtained by fitting ab initio calculations. The simulated liquid structures are in very good agreement with the most recent x-ray scattering and extended x-ray absorption fine-structure experiments in a broad temperature and density range. The Monte Carlo simulations performed show that the complex liquid structures observed result from the breaking and branching of the selenium chains. The total coordination number is shown to result from the balance between one-, two-, and threefold coordinated atoms. The role of these defects is discussed in relationship with the electrical conductivity of the liquid, i.e., the semiconductor-metal and metal-nonmetal transitions observed at high pressures.