Extended 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.

Interpretation of unexpected behavior of infrared absorption spectra ofScF3beyond the quasiharmonic approximation

Scandium fluoride (${\mathrm{ScF}}_{3}$), having cubic ${\mathrm{ReO}}_{3}$-type structure, has attracted much scientific attention due to its rather strong negative thermal expansion (NTE) in the broad temperature range from 10 to 1100 K. Here we use the results of diffraction and extended x-ray absorption fine-structure (EXAFS) spectroscopy to interpret the influence of NTE on the temperature dependence of infrared absorption spectra of ${\mathrm{ScF}}_{3}$. Original infrared absorption and EXAFS experiments in a large temperature range are presented and interpreted using ab initio lattice dynamics simulations within and beyond quasiharmonic approximations. We demonstrate that ab initio electronic structure calculations, based on the linear combination of atomic orbitals method with hybrid functionals, are able to reproduce well the experimental values of lattice parameter ${a}_{0}$, band gap ${E}_{g}$, and lattice dynamics in ${\mathrm{ScF}}_{3}$. However, the simulations performed within quasiharmonic approximation fail to reproduce the temperature dependence of two infrared active bands due to the F--Sc--F bending (at 220 ${\mathrm{cm}}^{\ensuremath{-}1}$) and Sc--F stretching (at 520 ${\mathrm{cm}}^{\ensuremath{-}1}$) modes present in the infrared absorption spectra. To overcome this problem, an approach beyond the quasiharmonic approximation is proposed: It accounts for the negative thermal expansion of the lattice and for fluorine atom displacements due to strong F vibrational motion perpendicular to the cubic axes and allows us to explain qualitatively the temperature behavior of infrared spectra of ${\mathrm{ScF}}_{3}$.

Is the Hexacyanoferrate(II) Anion Stable in Aqueous Solution? A Combined Theoretical and Experimental Study.

A combined theoretical and experimental study was performed to elucidate the structural and dynamical properties of the isolated aqueous hexacyanoferrate(II) ion as well as in the presence of potassium counterions. It is shown that in absence of counterions, the highly negatively charged hexacyanoferrate(II) complex is not stable in aqueous solution. However, if the high negative charge is compensated by potassium counterions, a stable complex is observed, which is proven by theoretical simulations as well as by extended X-ray absorption fine structure (EXAFS) experiments. From the simulation it is found that potassium ions surrounding the complex are highly mobile and thus cannot be observed via EXAFS experiments. The structure of aqueous hexacyanoferrate(II) in the presence of potassium ions is identical to that of the solid-state structure, but the mobility of potassium ions is significantly increased in the liquid. These highly mobile potassium ions circulating the complex are the reason for the very short lifetime of hydrogen bonds between solvent water molecules and cyanide ligands being on the femtosecond scale.

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.

On ammonia binding to the oxygen-evolving complex of photosystem II: a quantum chemical study.

A recent EPR study (M. Perrez Navarro et al., Proc. Natl. Acad. Sci. 2013, 110, 15561) provided evidence that ammonia binding to the oxygen-evolving complex (OEC) of photosystem II in its S2 state takes place at a terminal-water binding position (W1) on the "dangler" manganese center MnA. This contradicted earlier interpretations of (14)N electron-spin-echo envelope modulation (ESEEM) and extended X-ray absorption fine-structure (EXAFS) data, which were taken to indicate replacement of a bridging oxo ligand by an NH2 unit. Here we have used systematic broken-symmetry density functional theory calculations on large (ca. 200 atom) model clusters of an extensive variety of substitution patterns and core geometries to examine these contradictory pieces of evidence. Computed relative energies clearly favor the terminal substitution pattern over bridging-ligand arrangements (by about 20-30 kcal mol(-1)) and support W1 as the preferred binding site. Computed (14)N EPR nuclear-quadrupole coupling tensors confirm previous assumptions that the appreciable asymmetry may be accounted for by strong, asymmetric hydrogen bonding to the bound terminal NH3 ligand (mainly by Asp61). Indeed, bridging NH2 substitution would lead to exaggerated asymmetries. Although our computed structures confirm that the reported elongation of an Mn-Mn distance by about 0.15 Å inferred from EXAFS experiments may only be reproduced by bridging NH2 substitution, it seems possible that the underlying EXAFS data were skewed by problems due to radiation damage. Overall, the present data clearly support the suggested terminal NH3 coordination at the W1 site. The finding is significant for the proposed mechanistic scenarios of OEC catalysis, as this is not a water substrate site, and effects of this ammonia binding on catalysis thus must be due to more indirect influences on the likely substrate binding site at the O5 bridging-oxygen position.

Atomistic origin of rapid crystallization of Ag-doped Ge-Sb-Te alloys: A joint experimental and theoretical study

We have applied extended X-ray absorption fine structure (EXAFS) analyses and ab initio molecular dynamics (AIMD) simulations to study the structure of Ag-doped (up to 42%) Ge1Sb2Te4 alloys. The computer models are consistent with EXAFS experiments, and reveal that the Ge environment is significantly modified by Ag doping, whereas those of Sb and Te are barely affected (except for high Ag concentrations), and suggest that Ag prefers bonding with Te. Doping with Ag promotes the conversion of Ge from tetrahedral to octahedral, and enhances the speed of crystallization of Ge–Sb–Te (GST) alloys as predicted by MD simulation. Our study sheds light on the atomistic mechanism of rapid crystallization of GST alloys, and enhancement by Ag doping. Mean-square displacements (MSDs), depicting the hopping of individual silver atoms in the silver-doped GeSbTe phase-change memory material (PCMM).

In Situ Experimental Evidence for a Nonmonotonous Structural Evolution with Composition in the Molten LiF−ZrF4 System

We propose in this paper an original approach to study the structure of the molten LiF-ZrF(4) system up to 50 mol % ZrF(4), combining high-temperature nuclear magnetic resonance (NMR) and extended X-ray absorption fine structure (EXAFS) experiments with molecular dynamics (MD) calculations. (91)Zr high-temperature NMR experiments give an average coordination of 7 for the zirconium ion on all domains of composition. MD simulations, in agreement with EXAFS experiments at the K-edge of Zr, provide evidence for the coexistence of three different Zr-based complexes, [ZrF(6)](2-), [ZrF(7)](3-), and [ZrF(8)](4-), in the melt; the evolution of the concentration of these species upon addition of ZrF(4) is quantified. Smooth variations are observed, apart from a given composition at 35 mol % ZrF(4), for which an anomalous point is observed. Concerning the anion coordination, we observe a predominance of free fluorides at low concentrations in ZrF(4), and an increase of the number of bridging fluoride ions between complexes with addition of ZrF(4).

Bond constraint theory studies of chalcogenide phase change memories

Studies of amorphous (a-) semiconductors have been driven by technological advances as well as fundamental theories. Observation of electrical switching, for example, fueled early interest in a-chalcogenides. More recently a-chalcogenide switching has been applied successfully to programmable memory devices as well as DVD technology where the quest for the discovery of better-suited materials continues. Thus, switching grants researchers today with an active arena of technological as well as fundamental study. Bond constraint theory (BCT) and rigidity theory provide a powerful framework for understanding the structure and properties of a-materials. Application of these theories to switching in a-chalcogenides holds the promise of finding the best composition suited for switching applications. Extended X-ray absorption fine structure (EXAFS) spectroscopy is an ideally suited technique to investigate the switching properties of these materials. Films of amorphous Ge2Sb2Te4, Ge2Sb2Te5, and Ge2Sb2Te7 exhibit differing bonding structures and bond statistics, which result in different electronic and optical properties. Results of new EXAFS experiments on these three critical compositions in the Ge–Sb–Te system are presented in light of BCT and rigidity theory.

Characterization of a polycapillary focusing X-ray lens for application in spatially resolved EXAFS experiments

A dispersive extended-X-ray-absorption-fine-structure (EXAFS) spectrometer based on a polycapillary focusing X-ray lens (PFXRL), a position-sensitive proportional counter and a rotating anode X-ray source is designed. When the working voltage and current of a Mo rotating anode X-ray generator are 25 kV and 100 mA, respectively, it takes 6 h to obtain the EXAFS spectrum of the Cu film. The experiments show that a dispersive EXAFS spectrometer based on a PFXRL can be applied in spatially resolved EXAFS analysis.

The anodic oxidation of silver in 1 M NaOH: electrochemistry, ex situ XPS and in situ X‐ray absorption spectroscopy

AbstractWe have investigated the electrochemical formation of oxide layers on silver in 1 M NaOH (pH 13.8) using a combination of electrochemical techniques, X‐ray photoelectron spectroscopy (XPS) and surface sensitive grazing incidence X‐ray absorption spectroscopy (XAS). While the XPS experiments were performed after the removal of the samples from the electrolyte and transfer into an ultra‐high vacuum (UHV) system under inert conditions, the XAS experiments were performed in situ and under full potential control. The application of these techniques leads to a detailed, consistent picture of the anodic oxide layer formation process on silver. All the applied techniques proved that the anodic oxidation starts at potentials lower than the corresponding Nernst potential. Extended X‐ray absorption fine structure (EXAFS) investigations suggest that the underpotential Ag+ oxide layer of some few nanometres thickness has a rather disordered structure. Time resolved XPS and EXAFS experiments have shown that the growth of these disordered layers is diffusion controlled, i.e. the thickness increases with the square root of the oxidation time. For moderately higher potentials, i.e. slightly above the Nernst equilibrium potential, the thickness of the silver(I) oxide layer increases rapidly with potential and the structure is very similar to that of crystalline Ag2O. Copyright © 2006 John Wiley & Sons, Ltd.

Why phase-change Materials work: An EXAFS Investigation of Ge-Sb-Te Alloys

AbstractStudies of amorphous (a-) semiconductors have been driven by technological advances as well as fundamental theories. Observation of electrical switching, for example, fueled early interest in a-chalcogenides. More recently a-chalcogenide switching has been applied quite successfully to DVD technology where the quest for the discovery of better-suited materials continues. Thus, switching provides researchers today with an active arena of technological as well as fundamental study. On the theoretical front, bond constraint theory and rigidity theory provide a powerful framework for understanding the structure and properties of a-materials. Applications of these theories to switching in a-chalcogenides holds the promise of finding the best composition suited for switching applications. Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is an ideally suited technique to investigate the switching properties of these materials. Results of previous EXAFS experiments will be presented and viewed through the lens of bond constraint theory and rigidity theory.

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.

P-type one-sided hexagonal spiral drift detectors

A new P-type drift detector (PDD) with one-sided hexagonal spiral shaped cathodes around the center anode has been designed, simulated, constructed and tested. The signal in PDD is generated by the transport of holes (instead of electrons as in an n-type drift detector) in the bulk of the detector and their arrival to the anode. Large arrays of drift cells are required for the extended X-ray absorption fine structure experiments (EXAFS). The large number of cells forces the design of the drift cell with a minimal number of bonds per cell. The presented design creates the drift field by the spiral-based voltage divider. Moreover, the leakage current created at the depleted part of the detector surface is also collected without an external connection to the cell. The leakage current is collected directly on the inner terminal of the divider. The lithographic processes of the wafer are done only on one side resulting in a much faster fabrication. The lithography-less side of the detector was uniformly implanted with phosphorus creating a shallow, rectifying p/sup -/n/sup +/ junction. This side is exposed to the radiation. Positive charges in the native oxide help to keep the thickness of the dead entrance layer at the minimum. Moreover, this layer is not sensitive to the radiation damage caused by very low energy X-rays that do not damage the silicon structure and produce only additional positive charge in the oxide. For the first time, the design makes an active usage of the positive charge in the oxide as a rectifying junction on p-type silicon.

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.

Fe-Si-C 합금의 합금화 과정에 따른 구조 및 자기적 특성 변화 연구

기계적 합금화 방법을 통하여 Fe-Si-C계 합금을 제조하였으며, 합금화 과정에 따른 구조 및 자기적 특성을 분석하였다 구조적 특성의 분석은 X-선 회절 실험과 EXAFS(extended X-ray absorption fine structure)실험을 통하여 수행하였고, 자기적 특성은 시료진동형자력계와 M ssbauer 분광법으로 연구하였다. 합금화 시간이 증가함에 따라 Si, C 원자들은 Fe 구조 속으로 확산되었으며, 12시간 이후로는 과포화된 bcc 고용체를 형성하였다. 합금화 시간에 따른 포화 자화값 및 초미세 자기장은 4시간까지 급격한 감소를 나타내었으며, 그 이후로는 완만한 감소를 나타내었고, 12시간 이후로는 변화가 적음을 나타내었다. 이러한 변화는 구조 특성 분석 결과와 일치하였다. Fe-Si-C alloy system has been made by mechancial alloying process. The structural and magnetic properties were analysed as a function of processing times. The structural properties were investigated by X-ray diffraction and EXAFS experiments. The magnetic properties were measured by vibrating sample magnetometer and M ssbauer spectroscopy. As processing time increases, Si and C atoms diffuse into a <TEX>${\alpha}$</TEX>-Fe structure and then bcc solid solution is formed after 12 hours of the processing time. The magnetization and the hyper fine field decreased steeply up to 4 hours and then it changed slowly. After 12 hours of the processing time, it almost saturated. These results were agreed with the structural variation.

Structure of Pt-Co/Al2O3 and Pt-Co/NaY bimetallic catalysts: characterization by in situ EXAFS, TPR, XPS and by activity in Co (carbon monoxide) hydrogenation

Temperature-programmed reduction (TPR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and in situ extended X-ray absorption fine structure (EXAFS) studies were performed to investigate Pt-Co/NaY and Pt-Co/Al2O3 bimetallic catalysts. The EXAFS experiments were carried out at the Pt LIII and Co K edges of the same sample. This particular approach allows a precise determination of the electronic and structural characteristics of the metallic part of the catalyst. For both systems in situ reduction under pure H2 results in the formation of nanometer-scale metallic clusters. For both Co and Pt, nearest neighbors are Co atoms. The complete set of parameters implies the presence of two families of nanometer-scale metallic clusters: monometallic Co nanosized particles and Pt-Co bimetallic clusters, in which only Pt-Co bonds exist (no Pt-Pt bonds). TPR and XPS results indicating a reduction of Co2+ ions in Pt-Co/NaY to a greater extent than in Pt-Co/Al2O3 give evidence of a facilitated reduction. XRD also shows the presence of nanometer-scale particles with only a very small fraction of larger bimetallic particles. In subsequent mild oxidation of the reduced systems the Co nanoparticles are still present inside the supercage of NaY zeolite in bimetallic form and the oxidation of the metallic particles is slowed down. Catalytic behavior is in good agreement with the structure of the Pt-Co bimetallic system.

Study of the Formation of the Layered Double Hydroxide [Zn−Cr−Cl

The synthesis of the layered double hydroxide (LDH) [Zn−Cr−Cl], well-known for its ability to be synthesized only with the ratio Zn:Cr = 2:1, has been followed by UV−visible and extended X-ray absorption fine structure (EXAFS) spectroscopy in order to understand the mechanisms of its formation. The UV−visible spectrum reveals first the hydrolysis of the Cr(III) monomer units, favored by the acidity conditions, followed by the formation of trimer and tetramer species. The EXAFS experiments at the Cr K-edge confirm the formation of the oligomeric species before the LDH signature. At the Zn K-edge, the results show that hexaaquozinc(II) complexes are present before the formation of the LDH phase. During LDH synthesis, oligomeric chromium(III) species and hexaaquozinc(II) complexes coexist in solution with the LDH solid. A structural pathway based on direct condensation of hexaaquozinc(II) complexes with deprotonated Cr(III) monomeric species is proposed to explain the formation of LDH solid with ratio Zn:Cr = 2. The structural pathway strongly supports the concept of cationic order in the [Zn−Cr−Cl] LDH sheets suggested by several authors but not demonstrated until now. Nevertheless we cannot exclude some faults during condensation as incorporation of a few oligomers such as dimers, trimers, and planar tetramers, but this should be very exceptional since the condensation of chromium oligomers with zinc monomers would lead to an LDH solid with a Zn:Cr ratio less than 2.

Chemical excision from amorphous MoS3; a quantitative EXAFS study

Quantitative information on the molybdenum containing species produced by the reaction of aqueous cyanide with the amorphous molybdenum sulfide MoS3 has been obtained from extended X-ray absorption fine structure (EXAFS) studies. The results of this chemical excision study, in which Mo–Mo bonded triangular clusters are extracted from the solid, suggest that 70% of the molybdenum present in MoS3 is found in Mo3 clusters. This result is consistent with earlier diffraction and EXAFS experiments, but rules out the simplistic models proposed in those studies. p