Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.     

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study

The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.     

1, 1, 2, 3, 4, 5-六苯基硅杂环戊二烯X射线谱的理论研究

近年来苯基硅杂环戊二烯作为一类高效的有机发光二极管材料被广泛研究。本工作利用密度泛函理论结合芯态空穴近似研究了1, 1, 2, 3, 4, 5-六苯基硅杂环戊二烯分子中碳原子K壳层和硅原子L壳层的X射线光电子能谱和近边X射线吸收精细结构谱,与实验谱线符合较好。通过理论结果对实验测量的1, 1, 2, 3, 4, 5-六苯基硅杂环戊二烯分子的X射线谱进行了分析和标定。我们发现碳原子K壳层X射线光电子能谱在低能区283.8eV处的谱峰是由于与硅原子成键的两个电负性较强的碳原子导致的。碳原子K壳层近边X射线吸收精细结构谱中最强的吸收峰与苯分子的吸收峰类似。硅原子L壳层近边X射线吸收精细结构谱两个主要吸收峰分别来自于σ_Si-C^*和π_Si-Ph^*跃迁。     

Polyaniline films electrodeposited on iron from oxalic acid solution: linear dichroism of X-ray absorption and molecular arrangement

Journal of Solid State Electrochemistry - The linear dichroism in the near-edge X-ray absorption fine structure (NEXAFS) spectra measured at the K edges of carbon and nitrogen was used to analyze...     

Structural characterization of nickel oxide nanowires by X-ray absorption near-edge structure spectroscopy

Nickel oxide nanowires modified by poly(vinylpyrrolidone) (PVP) were synthesized via a simple chemical pattern. For the first time NiO nanowires with diameters ranging from 40 to 100 nm with the expected ratio (length vs diameter) ranging from 54 to 90 were grown using a simple solution-phase approach (mild method). These nickel nanowires exhibited unique photoluminescence features and displayed a significant UV luminescence. X-ray absorption near-edge spectroscopy has been used to characterize the local Ni environment and identify the electronic structure. Comparing experimental and theoretical spectra at the Ni and O K edges, we determine the lattice distortion via the analysis of the characteristic preedge features and the multiple-scattering structures detected in the X-ray absorption near-edge structure spectra. The correlation between experimental features and the disordered or distorted local structures is also discussed.     

Calculation of near-edge X-ray absorption fine structure with the CIS(D) method

We report an investigation into the calculation of near-edge X-ray absorption fine structure with the CIS(D) method. Core excitation energies computed with time-dependent density functional theory using standard exchange-correlation functionals are systematically underestimated. CIS(D) predicts core excitation energies that are closer to experiment. However, excitation energies for Rydberg states are too low with respect to valence states, and for some systems spectra that are qualitatively incorrect are obtained. A scaled opposite spin only approach is proposed that reduces the error in the computed core excitation energies, and results in spectra that are in good agreement with experiment.     

Determination of CoSi2 self-aligned nanostructures with grazing incidence X-ray absorption spectroscopy

Self-aligned nanostructures (SAN) made by reacting Co nanoparticles with crystalline Si substrates at high temperatures were studied with grazing incidence X-ray absorption spectroscopy (GI-XAS). The results from extended X-ray absorption fine structure (EXAFS) analysis and X-ray absorption near-edge spectroscopy (XANES) were used to identify SAN as crystalline CoSi2. Theoretical calculations of EXAFS and XANES spectra of several crystalline cobalt silicides were performed with the FEFF8 package. On the basis of these studies, the SAN samples were determined to contain nearly pure CoSi2.     

Structural Characterization of Chemical Species in Solution by a Theoretical Analysis of XANES Spectra

A theoretical analysis method using a discrete variational X (DV-X) molecular orbital (MO) calculation, based on electron transition from an inner orbital to an unoccupied orbital, is introduced to analyze X-ray absorption near-edge structure (XANES) spectra in a lower energy region below the X-ray absorption edge. The computational procedure is described in detail and the evaluation of an obtained result is also explained. Applications of this method are presented for Cu(II) ions in liquid ammonia, macrocyclic Cu(II) complex in aqueous solution, and Al(III) ions in aqueous solution.     

Characterization of monolayer formation on aluminum-doped zinc oxide thin films

The optical and electronic properties of aluminum-doped zinc oxide (AZO) thin films on a glass substrate are investigated experimentally and theoretically. Optical studies with coupling in the Kretschmann configuration reveal an angle-dependent plasma frequency in the mid-IR for p-polarized radiation, suggestive of the detection of a Drude plasma frequency. These studies are complemented by oxygen depletion density functional theory studies for the calculation of the charge carrier concentration and plasma frequency for bulk AZO. In addition, we report on the optical and physical properties of thin film adlayers of n-hexadecanethiol (HDT) and n-octadecanethiol (ODT) self-assembled monolayers (SAMs) on AZO surfaces using reflectance FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), contact angle, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Our characterization of the SAM deposition onto the AZO thin film reveals a range of possible applications for this conducting metal oxide.     

In situ X-ray absorption fine structure studies of amorphous and crystalline polyoxovanadate cluster cathodes for lithium batteries

Amorphous and crystalline MetfV10 electrodes for lithium ion batteries were prepared by mixing MetfV10 with different binders: polyvinylidenefluoride (PVDF) or polytetrafluoroethylene (PTFE). The amorphous MetfV10 cathode demonstrates a higher specific capacity than the crystalline cathode. The reaction mechanism was studied using in situ X-ray absorption fine structure (XAFS) and impedance measurements. The X-ray absorption near-edge structure (XANES) results exhibited a 10-electron reduction per the formula of MetfV10 during discharge, resulting in a large capacity. Extended X-ray absorption fine structure (EXAFS) analyses suggested a slight expansion in the molecular size of MetfV10. The impedance measurements reveal that an increase of discharge capacities for the amorphous cathode is due to lower resistance than in the crystalline cathode. This study presents a rational selection of amorphous or crystalline cathode materials for high power and high energy density lithium batteries.     

Accurate measurement and physical insight: The X-ray extended range technique for fundamental atomic physics,condensed matter research and biological sciences

Research in core physics or atomic and condensed matter science is increasingly relevant for diverse fields and are finding application in chemistry, engineering and biological sciences, linking to experimental research at synchrotrons, reactors and specialised facilities. Over recent synchrotron experiments and publications we have developed methods for measuring the absorption coefficient far from the edge and in the XAFS (X-ray absorption fine structure) region in neutral atoms, simple compounds and organometallics reaching accuracies of below 0.02%. This is 50–500 times more accurate than earlier methods, and 50–250 times more accurate than claimed uncertainties in theoretical computations for these systems. The data and methodology are useful for a wide range of applications, including major synchrotron and laboratory techniques relating to fine structure, near-edge analysis and standard crystallography. Experiments are sensitive to theoretical and computational issues, including correlation between convergence of electronic and atomic orbitals and wavefunctions. Hence, particularly in relation to the popular techniques of XAFS and XANES (X-ray absorption near-edge structure), this development calls for strong theoretical involvement but has great applications in solid state structural determination, catalysis and enzyme environments, active centres of biomolecules and organometallics, phase changes and fluorescence investigations and others. We discuss key features of the X-ray extended range technique (XERT) and illustrate applications.     

Study of the chemical mechanism involved in the formation of tungstite in benzyl alcohol by the advanced QEXAFS technique

Insight into the complex chemical mechanism for the formation of tungstite nanoparticles obtained by the reaction of tungsten hexachloride with benzyl alcohol is presented herein. The organic and inorganic species involved in the formation of the nanoparticles were studied by time-dependent gas chromatography and X-ray diffraction as well as by time-resolved in situ X-ray absorption near-edge structure and extended X-ray absorption fine structure spectroscopy. Principal component analysis revealed two intermediates, which were identified as WCl(4) and WOCl(4) by using linear combination analysis. Quick-scanning extended X-ray absorption fine structure spectroscopy enabled the time-dependent evolution of the starting compound, the intermediates and the product to be monitored over the full reaction period. The reaction starts with fast chlorine substitution and partial reduction during the dissolution of the tungsten hexachloride in benzyl alcohol followed by the generation of intermediates with W=O double bonds and finally the construction of the W-O-W network of the tungstite structure.     

Characterization of Sol-Gel-synthesized LiFePO4 by multiple scattering XAFS

X-ray absorption spectroscopy (XAS) was used to investigate the local structure arrangements of submicrocrystalline lithium iron phosphate and its precursors. The former material, proven to be very promising as active cathode material in lithium metal and lithium-ion batteries, was synthesized through a new procedure that combines a simple sol-gel precipitation with a moderate temperature (e.g., low cost) heat treatment. X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra taken at the Fe K-edge pointed out the modification of the Fe site during the synthesis steps that allow one to produce the submicrometer size crystalline LiFePO4 (active material) useful for batteries applications. The XAS investigation has shown that such a material is different from the conventional crystalline LiFePO4 on the short-range order. The difference is attributed to the synthesis procedure.     

Surface sensitive study to determine the reactivity of soot with the focus on the European emission standards IV and VI

Diesel soot (Euro IV and Euro VI) was investigated with spectroscopic methods such as near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoemission spectroscopy (XPS). C and O K-edge NEXAFS show that structural disorder on the surface is accompanied by a higher amount of oxygen functional groups. O K-edge NEXAFS and O1s XPS results are discussed with the aim to elucidate the nature of the oxygen surface species. The analysis of the data presented here allows the postulation of a hypothetical structure for soot samples emitted by diesel engines.     

Analysis of x-ray Ni Kβ emission,xanes, xps,Ni 2p,and optical spectra of nickel(II) spinels and structure inference

X-ray absorption near-edge structure, X-ray Ni Kβ emission, X-ray photoelectron Ni 2p, and optical spectra are reported for NiM₂O₄ spinels (M = Al,Cr,Ga,Fe,Mn). The characteristic parameters of the Ni(II)-O chemical bond may be correlated with the structural properties (cation repartition and charge distribution).     

Solvation of Copper(II) Ions in Liquid Ammonia

X-ray absorption fine structure (XAFS) measurements have been performed at -50 degrees C on a 0.4 mol dm(-)(3) copper(II) nitrate solution in liquid ammonia. Extended X-ray absorption fine structure (EXAFS) spectroscopy was used to determine the coordination number and bond distances for the solvated copper(II) ion in solution. The equatorial ammonia nitrogens are located 2.00 ? from the copper and the axial nitrogen 2.19 ? from the copper. However, it was not possible from the EXAFS analysis alone to conclude whether there was one or two axial nitrogens. Therefore, X-ray absorption near-edge structure (XANES) spectroscopy was combined with discrete variational Xalpha (DV-Xalpha) molecular orbital calculations for a series of five- and six-coordinated models to determine the coordination number and the geometry. The experimental XANES spectrum was best reproduced by a model where the copper(II) ion is pentacoordinated in liquid ammonia in a square pyramidal geometry with the copper(II) ion lifted above the average nitrogen plane.     

Synthesis of Iron-Oxygen Nanostructures on Silicon and Analysis of Their Structure by NEXAFS Spectroscopy

The near-edge fine structure of the Fe2p and Si2p X-ray absorption spectra (NEXAFS) of iron-oxygen nanolayers on the surface of single-crystal silicon (100) was studied for the first time. The structure of the quasi-2D iron-oxygen nanosystems synthesized by molecular layering was considered on this basis.     

Colloidal gold nanoparticles as catalyst for carbon-carbon bond formation: application to aerobic homocoupling of phenylboronic acid in water

Gold nanoparticles (<2 nm) stabilized by poly(N-vinyl-2-pyrrolidone) (Au:PVP NPs) were prepared by reduction of AuCl4- with NaBH4 in the presence of PVP and characterized via an array of methods including optical absorption spectroscopy, transmission electron microscopy, X-ray diffraction, X-ray absorption near-edge structure, extended X-ray absorption fine structure, and X-ray photoelectron spectroscopy. We demonstrate for the first time that the Au:PVP NPs act as catalyst toward homocoupling of phenylboronic acid in water under aerobic conditions. Suppression of biphenyl formation under anaerobic conditions indicates that molecular oxygen dissolved in water is intimately involved in the coupling reactions. A mechanism of the aerobic homocoupling catalyzed by the Au:PVP NPs is proposed on the basis of a crucial role of dissolved oxygen, steric effects on the product yields, and the well-established mechanism for the Pd(II)-based catalysts.     

Structural study on highly oxidized states of a water oxidation complex [RuIII(bpy)2(H2O)]2(mu-O)4+ by ruthenium K-edge X-ray absorption fine structure spectroscopy

The oxidation-induced structural change of a water-oxidizing diruthenium complex, [(bpy)(2)(H(2)O)Ru(III)(micro-O)Ru(III)(OH(2))(bpy)(2)](4+) (bpy = 2,2'-bipyridine), was investigated by means of X-ray absorption spectroscopy. Ru K-edge XANES (X-ray absorption near-edge structure) spectra from the acidic solution and solid precipitates obtained by oxidation showed that the absorption edge shifts toward higher energy with a preedge feature slightly more enhanced than those of the lower oxidation states. This indicates that the higher oxidation state has a lower symmetry due to shortening of the Ru-O bonds that originated from the water ligands. The EXAFS (extended X-ray absorption fine structure) spectra were similar to those of the lower oxidation states, whose analysis revealed the existence of short Ru-O double bonds and an almost linear Ru-O-Ru angle (169 +/- 2 degrees ). Ab initio EXAFS simulations for several possible structural models suggest that the dimeric structure is maintained during the water oxidation reaction.     

Evidence for sevenfold coordination in the first solvation shell of Hg(II) aqua ion

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C2 symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species. This picture is fully consistent with X-ray absorption near-edge structure experimental data which unambiguously show the preference for a sevenfold instead of a sixfold coordination.