X-ray Absorption Fine Structure Study Research Articles

Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study.

The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.

Local structure study of the Fe ions in mixed-valence iron(II)-iron(III) metal formate frameworks

X-ray Absorption Spectroscopy (XAS) methods have been used to study the mixed-valence iron(II)-iron(III) metal–organic frameworks (MOFs) that undergo order–disorder phase transitions. In particular, this paper reports X-ray Absorption Fine Structure (XAFS) study of the electronic and local structure at the Fe K-edge (7 keV) for three mixed-valence iron(II)-iron(III) formate frameworks, namely dietylammonium ((C2H5)2NH2[FeIIIFeII(HCOO)6], DEtAFeFe), dimethylammonium ((CH3)2NH2[FeIIIFeII(HCOO)6], DMAFeFe) and N-etylmethylammonium (CH3NH2C2H5[FeIIIFeII(HCOO)6], EtMeAFeFe) analogues. DMAFeFe (DEtAFeFe) was studied at 140 K and 155 K (240 K and 250 K) in detail to obtain information on the structural changes during the phase transitions. The near-edge x-ray absorption fine structure (XANES) analysis confirms the octahedrally coordinated Fe in the studied samples and the electron transfer from divalent to trivalent iron ions. A slight variation was found in the Fe-O bond lengths and quantified the order in the bond length distribution measured by the Debye-Waller factor (σ2) around the phase transition temperature. The Fe2+/Fe3+ ions are homogeneously distributed in the order–disorder phase transition samples. The slight variation in the local structure defines the nature of the phase transition.

Anomalous X-Ray Scattering and Extended X-Ray Absorption Fine Structure Study of the Local Structure of CrFeCoNiMox (x = 0.11, 0.18, and 0.23) High-Entropy Alloys

Anomalous x-ray scattering (AXS) and extended x-ray absorption fine structure (EXAFS) were used to determine the local structure of Mo in CrFeCoNiMox (x = 0.11, 0.18, and 0.23), a high-entropy alloy with a face-centered cubic (FCC) lattice. No superlattice peaks were observed down to the 10–4 intensity level. This observation along with the nearly constant decrease of the FCC diffraction peaks above the Mo K absorption edge suggests that Mo atoms have no preferred site occupancy in the FCC lattice. Modeling of the EXAFS data suggests a local chemical order in CrFeCoNiMox, where in Mo-rich samples (e.g., x = 0.23), Mo atoms are preferably surrounded by lighter atoms, such as Cr.

XAFS studies of glass structure

X-ray absorption fine structure (XAFS) spectroscopy has become one of the most important techniques to characterise the local coordination of specific atomic species present in condensed matter. The possibility of investigating the structure of noncrystalline materials has made XAFS very attractive for the study of the short range structure of the glassy state. The XAFS acronym denotes the structure present above the x-ray absorption edges; such a structure is distinguished as x-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS). XANES carries information on the atomic arrangement around the absorbing species: distances and bonding angles. XANES also provides information on the electronic states in the proximity of the conduction band: different chemical environments may be identified from known features in the spectrum. EXAFS provides information on the average distance and radial distribution function of the nearest neighbours of the absorbing species. In the last decade, the enormous progress of experimental techniques and the excellent quality of experimental spectra, consequent to the development of the synchrotron radiation facilities, have stimulated the evolution of the XAFS theory and analysis procedures. This paper is a survey on the theoretical development of XAFS and on the methods for determining the short range information in disordered materials. Applications of XAFS to some vitreous systems are reported.

XAFS Study of Thermally Oxidated Sapphire Implanted with Zinc Ions

The local structure of Zn in Al2O3 is studied by the X-ray absorption fine structure (XAFS) method after the implantation of Zn ions and thermal oxidation, which results in the formation of nanoparticles in sapphire. Based on the data of X-ray absorption near edge spectra (XANES), it can be concluded that Zn atoms interact with oxygen and the Al2O3 substrate. The sapphire sample implanted with Zn ions and annealed in oxygen at 600°C contains zinc in three different states: ZnO, zinc spinel (ganite) ZnAl2O4, and metallic Zn in the form of nanoparticles. Since the fraction of zero-valent zinc is close to 50%, very small Zn metal clusters consisting of the minimum possible number of chemically bonded atoms are expected to be formed. The average number of Zn–Zn bonds for each zinc atom in them slightly exceeds unity, i.e., Zn dimers dominate in the sapphire matrix.

Studies of Buried Layers and Interfaces of Tungsten Carbide Coatings on the MWCNT Surface by XPS and NEXAFS Spectroscopy

Currently, X-ray photoelectron spectroscopy (XPS) is widely used to characterize the nanostructured material surface. The ability to determine the atom distribution and chemical state with depth without the sample destruction is important for studying the internal structure of the coating layer several nanometers thick, and makes XPS the preferable tool for the non-destructive testing of nanostructured systems. In this work, ultra-soft X-ray spectroscopy methods are used to study hidden layers and interfaces of pyrolytic tungsten carbide nanoscale coatings on the multi-walled carbon nanotube (MWCNT) surfaces. XPS measurements were performed using laboratory spectrometers with sample charge compensation, and Near Edge X-ray Absorption Fine Structure (NEXAFS) studies using the Russian–German dipole beamline (RGBL) synchrotron radiation at BESSY-II. The studied samples were tested by scanning and transmission electron microscopy, X-ray diffractometry, Raman scattering and NEXAFS spectroscopy. It was shown that the interface between MWCNT and the pyrolytic coating of tungsten carbide has a three-layer structure: (i) an interface layer consisting of the outer graphene layer carbon atoms, forming bonds with oxygen atoms from the oxides adsorbed on the MWCNT surface, and tungsten atoms from the coating layer; (ii) a non-stoichiometric tungsten carbide WC1-x nanoscale particles layer; (iii) a 3.3 nm thick non-stoichiometric tungsten oxide WO3-x layer on the WC1-x/MWCNT nanocomposite outer surface, formed in air. The tungsten carbide nanosized particle’s adhesion to the nanotube outer surface is ensured by the formation of a chemical bond between the carbon atoms from the MWCNT upper layer and the tungsten atoms from the coating layer.

In situ XAFS study of highly reducible mixed oxide catalysts Ce0.9Pd0.1O2-δ and Ce0.7Yb0.2Pd0.1O2-δ

Abstract Within this paper the simultaneous local structural analysis of the highly reducible mixed oxides catalysts Ce0.9Pd0.1O2-δ and Ce0.7Yb0.2Pd0.1O2-δ is presented under reduction and oxidation conditions at elevated temperatures up to 500 °C. In situ X-ray Absorption Fine Structure characterization shows that during the reduction up to 80 °C no changes are observed in both of the exemplarily studied samples. The oxidation of the Ce1-xPdxO2-δ sample continuously introduces changes in the structure over the whole temperature range while for the Ce0.7Yb0.2Pd0.1O2-δ sample oxidation is completed already at 200 °C. The metallic palladium cluster formation in both studied samples was followed by Extended X-ray Absorption Fine Structure (EXAFS) studies. The presence of the Yb atoms affects the formation time and the Pd cluster size. It was found that during the reduction process the palladium cluster creation is initiated at higher temperatures for the Ce0.9Pd0.1O2-δ sample than for the Ce0.7Yb0.2Pd0.1O2-δ sample. The higher percentage of Pd atoms creates metallic palladium clusters in the Ce0.9Pd0.1O2-δ sample.

Structure of amorphous BaTiO3 by molecular dynamics simulations using a shell model

We studied the structure of amorphous BaTiO3 by molecular dynamics (MD) simulations. The local bonding units (LBUs) were mainly TiO6 in agreement with an X-ray absorption fine-structure (XAFS) study. An LBU was linked to its neighboring ones with their apexes, edges, and/or faces shared. The first peak of the Ti–Ti radial distribution function (g(r)) was located at ~ 3 Å with a trimodal distribution that results from the three linkage types, supporting extended X-ray absorption fine structure (EXAFS) experiments. If the number of Ba atoms around a Ti atom was larger than the average, the number of non-bridging oxygen (NBO; [1]O) atoms was larger around that Ti atom. In the opposite case, the number of tricluster oxygen (TO; [3]O) atoms was increased around it, and the number of edge or face-sharing linkages with the neighboring Ti atoms was also increased.

Electronic properties of Ga-In-Zn-O (GIZO) thin films: Effect of post-annealing

Effect of post annealing temperature on electronic properties of Ga-In-Zn-O (GIZO) have quantitatively studied by using reflection electron energy loss spectroscopy (REELS), x-ray photoelectron spectroscopy (XPS), and x-ray absorption fine structure (XAFS) spectra. The band gap values of GIZO are 3.1 eV, 3.5 eV, and 3.8 eV, at room temperature (as deposited), post-annealing at 600 °C, and 700 °C, respectively. The composition of Ga increased and Zn reduced with increasing post-annealing temperature. The formation of Ga-(Ga,Zn) and Zn-(Zn,Ga) bonds in GIZO thin film annealed at 700 °C was confirmed by XAFS study. The electronic properties of GIZO thin films strongly affected by the bonding formation of Zn-O and Ga-O as the effect of annealing temperature.

XAFS studies on battery materials: Data analysis supported by a chemometric approach

The large amount of data collected during a typical operando X-ray absorption fine structure (XAFS) experiment and the interest to thoroughly investigate and comprehend a redox process occurring in a Li-ion battery need an advanced data analysis approach. In this context, multivariate curve resolution (MCR) has gained attention as chemometric technique that allows the identification of the number of the species and their existence range without any a priori information on the studied system. The call for an advanced data treatment is answered by a joint XAFS-MCR approach, able to unveil the local structural dynamics of the selected species, providing a quick and efficient data interpretation.

XAFS study on single-atomic-site Cu1/N-graphene catalyst for oxygen reduction reaction

Heteroatom-doped homogeneous M-N-C catalysts are recently emerging as a promising substitute to replace platinum-based noble metal catalysts for highly efficient oxygen reduction reaction (ORR). Here we construct an electrocatalyst with atomically dispersed Cu atoms confined in N-doped graphene by a facile pyrolysis process. The extended X-ray absorption fine structure (XAFS) spectroscopy validates that the intrinsically active center is composed of a mixture of Cu-N2 and Cu-N4 moieties. The designed catalyst exhibits outstanding ORR activity with onset (Eonset) and half-wave potential (E1/2) at 0.869 V and 0.779 V respectively, and a smaller Tafel slope of 74 mV decade−1, superior to the commercial Pt/C catalysts.

Laboratory EXAFS determined structure of the stable complexes in the ternary Ni(ii)-EDTA-CN- system.

Aqueous solutions of the ternary system Ni(ii)-EDTA-CN- are investigated with X-ray Absorption Spectroscopy (XAS) as a function of cyanide concentration with an enhanced laboratory von Hámos X-ray spectrometer. The near-edge structure of the spectra identifies unambiguously the formation of the pentacyanidonickel(ii) complex at excess CN- concentrations. An analysis of the extended energy range of the XAS spectra reveals the molecular structure of the distinct molecular components present and provides a detailed description of the barely detectable mixed ligand [NiEDTA(CN)]3- complex. This thorough Extended X-ray Absorption Fine Structure (EXAFS) study demonstrates the potential of the emerging laboratory XAS spectrometers to become routine probes in various areas of chemistry, materials science, physics and related disciplines.

High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes

We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition...

Operando Time-Resolved X-ray Absorption Fine Structure Study for Pt Oxidation Kinetics on Pt/C and Pt3Co/C Cathode Catalysts by Polymer Electrolyte Fuel Cell Voltage Operation Synchronized with Rapid O2 Exposure

The oxidation of a cathode catalyst surface is one of the major factors for cathode catalyst degradation under polymer electrolyte fuel cell (PEFC) operating conditions; however, the oxidation kinetics of Pt cathode catalysts in a membrane electrode assembly with O2 has not been investigated. We have investigated operando Pt LIII-edge time-resolved X-ray absorption fine structure analysis for the Pt oxidation processes on Pt/C and Pt3Co/C cathode catalysts controlled by transient PEFC voltage operation (0.4 V → 0.7–1.0 V) synchronized with the rapid exchange of cathode gas (N2 → 10% O2 in N2). We plotted Pt valence and the coordination numbers of Pt–Pt and Pt–O bonds every 20 ms, and the rate constants of the structural parameters for the Pt oxidation were successfully estimated. The structural kinetics of the Pt oxidation at the cathode suggested differences in the Pt oxidation kinetics between the Pt/C and Pt3Co/C cathode catalysts, showing the kinetic control of the Pt oxidation rate by the alloying wi...

Towards understanding the correlation between UO22+ extraction and substitute groups in 2,9-diamide-1,10-phenanthroline

2,9-Diamide-1,10-phenanthroline (DAPhen) ligands represent a new family of tetradentate extractants given their strong affinity to actinides and the CHON principle. Among this family, N,N′-diethyl-N,N′-ditolyl-2,9-diamide-1,10-phenanthroline (Et-Tol-DAPhen), initially reported by us, exhibits excellent selectivity towards actinides (U, Th, Am, Pu) over lanthanides and thus can be potentially applied in the group actinide extraction (GANEX) process for the group separation of actinides. In this article, by tailoring the lengths of alkyl chains, we synthesized other four DAPhen ligands with different substitute groups in the diamide moieties, and characterized the relationship between properties and substitute groups of DAPhen ligand. The extraction results show that three of the ligands exhibit high performance in UO22+ extraction from an acidic solution and the extracted UO22+ can be easily stripped by only using ultrapure water. Spectrophotometry titration confirms that UO22+ combined with all the four ligands in 1:1 mode. The extended X-ray absorption finestructure (EXAFS) study shows that six donor atoms comprise the first equatorial shell of the UO22+ ions bonded by the DAPhen ligands, among which two nitrogen and two oxygen atoms are from the DAPhen ligand, while other two oxygen atoms are from one nitrate ions. This article promises to provide basic data for assessing the feasibility of this kind of DAPhen ligands applied in actinides separation from nuclear wastes.

Correlation of structural ordering with magnetic properties of pulsed laser deposited Co2FeGa Heusler alloy thin films

In the present contribution, structural and magnetic properties of Pulsed laser deposited (PLD) Co2FeGa (CFG) thin films have been studied as a function of substrate temperature. Structural investigation carried out by X-Ray Diffraction (XRD) measurement reveals mixed phase cubic structure of the films which changes from a nearly ordered to highly disordered phase with an increase in substrate temperature. Grazing Incidence X-Ray Diffraction (GIXRD) study shows the presence of disordered A2 phase similar to the bulk target. Grazing Incidence X-Ray Reflectivity (GIXR) measurement reveals the formation of bi-layer structure in the films with different density and thickness though the overall thickness remains same. Field Emission Scanning Electron Microscopy (FESEM) study shows the formation of a droplet-like morphology of the films. Extended X-ray Absorption Fine Structure (EXAFS) study serves a major role in complementing the XRD results and also shows a strong hybridization of Co with Ga maintaining the half metallicity. A novel approach in analyzing the EXAFS data additionally gives quantitative estimation of the different kinds of disorders present in the samples at the atomic level. In addition to this, magnetization result suggests that the films grown at lower substrate temperatures acts as proper ferromagnet following the well known spin wave theory with higher value of spontaneous magnetization in comparison to other samples. A lesser value of saturation magnetization in the films compared to bulk also supports the presence of antisite disorders.

Nitrogen doped heat treated and activated hydrothermal carbon: NEXAFS examination of the carbon surface at different temperatures

Hydrothermal carbons have been shown to have controllable surface functionalization through various post-treatment techniques, which indicates these materials may be tuned for specific applications. For this reason, Near Edge X-ray Absorption Fine Structure (NEXAFS) studies have been conducted on a series of nitrogen doped and non-doped heat treated and activated hydrothermal carbons to further understand the changes in surface functionality with treatment. The NEXAFS carbon K-edge spectrum of the non-doped samples displayed a loss of oxygen functionalities (CO and COH) as well as the furan ring structure with increasing temperature, while CC bonds from graphitic groups increased. This effect was amplified further upon the addition of phosphoric acid (H3PO4) during activation. The doped hydrothermal carbons displayed similar functionality to the non-doped, although the effect of both heat treatment and activation was diminished. The nitrogen K-edge displayed characteristic peaks for pyridine and imines/amides, with pyrroles located under the broad ionization step. This work represents the first time a series of heat treated and activated hydrothermal carbons have been examined via NEXAFS spectroscopy. Additionally, difference analysis has been applied to the NEXAFS spectra to obtain a deeper understanding in the changes in surface functionality, a previously unused technique for these materials.

Polarization-dependent Total Reflection Fluorescence X-ray Absorption Fine Structure (PTRF-XAFS) Studies on the Structure of a Pt Monolayer on Au(111) Prepared by the Surface-limited Redox Replacement Reaction

We studied the initial stage of a Pt monolayer produced by surface-limited redox replacement (SLRR) using polarization-dependent total reflection fluorescence X-ray absorption fine structure (PTRF-XAFS). Different from the widely accepted understanding that a metallic monolayer island is formed, our XAFS showed that the Pt monolayer, initially present on the Au(111) substrate, was mainly in the form of a planar [PtCl4]2- complex with its molecular plane parallel to the Au(111). This result provides a new insight into the mechanism of SLRR.

Structural and magnetic characterization of the Ni55Fe19Ga26 shape memory alloy thin film

The structural evolution of the Pulsed Laser Deposited Ni55Fe19Ga26 ferromagnetic Heusler alloy thin films has been studied as a function of substrate temperature. Room temperature Grazing Incidence X-Ray Diffraction (GIXRD) measurement reveals the polycrystalline nature of the films consisting of cubic austenite and non-cubic martensite phases. The cubic phase consists of the mixture of an ordered (L21) and disordered (γ) phases, the disordered phase gets suppressed with an increase in the substrate temperature while low temperature X-Ray Diffraction study shows structural modification of the samples. Field Emission Scanning Electron Microscopy (FESEM) study shows the droplet-like morphology of the films. Extended X-ray Absorption Fine Structure (EXAFS) study agrees with the X-ray diffraction results about the phase evaluation and further reveals the local structure information of the constituent atoms which leads to the hybridization effect and finally govern the macroscopic properties of the material. In addition, magnetization studies show the ferromagnetic nature of the film with a mixture of anti-ferromagnetic ordering arising due to antisite disorder of the atoms revealed by the EXAFS measurements.

Synchrotron based NEXAFS study on nitrogen doped hydrothermal carbon: Insights into surface functionalities and formation mechanisms

Synchrotron-based Near-Edge X-ray Absorption Fine Structure (NEXAFS) studies have been conducted on two hydrothermally produced carbon (HTC) structures and their main surface structural features are reported. The two HTCs were produced respectively from sucrose, and sucrose with added (NH4)2SO4, under subcritical water conditions. The NEXAFS carbon K-edge spectra reveal the presence of CC, COC (furan), CO and COH functionalities on the surface of the sucrose derived HTC. For the nitrogen-doped HTC, the carbon K-edge spectra indicate an increase in CC and COH functionalities, as well as the inclusion of CN and CN functionalities. Additionally, the nitrogen K-edge for the doped hydrothermal carbon displayed characteristic peaks for pyridinic, pyrrolic and tertiary amine nitrogen surface groups. Furthermore, a mechanistic pathway to inclusion of nitrogen atoms in the HTC-SAS structure is postulated.