Pre-edge Intensity Research Articles

Elucidating the Protonation Site of Vanadium Peroxide Complexes and the Implications for Biomimetic Catalysis

Coordination complexes of vanadium(5+) played a key role in understanding the structure and mechanism of vanadium-dependent haloperoxidases, particularly the effects of protonation on peroxide coordination to dioxovanadium(5+) species, and in the activation of the peroxo-oxovanadium(5+) complex for substrate oxidation. There has been no spectroscopic evidence that could test the presence of a hydroxo intermediate in a catalytically active oxovanadium(5+) complex. Herein we report the use of the pre-edge transition in X-ray absorption spectroscopy as a spectroscopic signature for V=O bonding. Displacement of oxo donors with hydrogen peroxide or chloride donors dramatically decreases the pre-edge intensity, confirming that the source of the intense pre-edge feature is closely related to the -bonding associated with the V=O. Protonation of a catalytically active tripodal amine oxovanadium(5+) complex has no affect on the pre-edge intensity and, therefore, rules out the possibility of a hydroxo intermediate in the catalytic cycle.

Oxygen K-edge XANES investigation of Ni cMg 1 − cO solid solutions

A series of Ni c Mg 1 − c O solid solutions are characterized by means of synchrotron radiation X-ray diffraction and X-ray absorption near-edge-structure spectroscopy at oxygen K-edge (532 eV). A dramatic drop of the pre-edge peak intensity is observed in the Ni c Mg 1 − c O system upon dilution. It can be attributed to a decrease of 3d 8(Ni 2+)–2p(O 2−) mixing upon dilution with magnesium ions due to a decrease of the number of 3d vacancies as nickel ion is replaced by magnesium ion. Similarly, the decrease of the number of 4s and 4p vacancies also leads to a decrease of 4s4p(Ni 2+)–2p(O 2−) hybridization, and hence a drop of intensities of features B and C. The features E and F are more sensitive to the increase of the degree of disorder upon dilution than feature D, revealing that the latter is mainly dependent by the medium-range order.

Assignment of pre-edge features in the Ru K-edge X-ray absorption spectra of organometallic ruthenium complexes

The nature of the lowest energy bound-state transition in the Ru K-edge X-ray absorption spectra for a series of Grubbs-type ruthenium complexes was investigated. The pre-edge feature was unambiguously assigned as resulting from formally electric dipole forbidden Ru 4d ← 1s transitions. The intensities of these transitions are extremely sensitive to the ligand environment and the symmetry of the metal centre. In centrosymmetric complexes the pre-edge is very weak since it is limited by the weak electric quadrupole intensity mechanism. By contrast, upon breaking centrosymmetry, Ru 5p–4d mixing allows for introduction of electric dipole allowed character resulting in a dramatic increase in the pre-edge intensity. The information content of this approach is explored as it relates to complexes of importance in olefin metathesis and its relevance as a tool for the study of reactive intermediates.

Studies on Reduction Dynamics of Nickel Atoms Incorporated in MCM-41 by XANES with Two-Dimensional Correlation Spectroscopy Approaches

The reduction kinetics of Ni cations incorporated in MCM-41 was investigated by in situ XANES measurements performed at a dispersive beamline. The detailed analysis of XANES spectra was conducted by perturbation-correlation moving-window 2D correlation spectroscopy (PCMW2D) and generalized 2D correlation spectroscopy (2DCORA) formalisms. PCMW2D results showed important changes on white-line intensities associated with water desorption and dehydroxilation during the heating process. PCMW2D successfully located the onset of nickel reduction during H2-TPR and characterized the pattern of changes on white-line and preedge intensities from rapid to gradual. The contributive character of progressive 2D correlation analysis calculations induced neglecting of variations on rate of spectral feature changes. To circumvent this limitation, we employed an alternative approach, calculating contributions to the 2D correlation function using a subset of spectra to take into account the temporal complexity structure of i...

Effects of local atomic order on the pre-edge structure in theTiKx-ray absorption spectra of perovskiteCaTi1−xZrxO3

The effects of local B-cation (Ti, Zr) distribution and octahedral tilting on the pre-edge structure in the Ti X-ray absorption K-spectra of the CaTi1-xZrxO3 perovskite solid solutions were investigated. Experimental spectra for the disordered CaTi1-xZrxO3 samples revealed systematic variations of the pre-edge peak intensities with the x-values. Multiple-scattering calculations using 75-atom clusters Ti(TiO6)6-n(ZrO6)nCa8O24 were conducted to interpret these differences. The origin of the lowest unoccupied states in the conduction band of the CaTi1-xZrxO3 was determined from the analyses of X-ray absorption near-edge structure of the O K-edge. The calculations reproduced the experimental spectra and demonstrated that the differences in the intensities of certain pre-edge feature are dominated by the probability of finding a Zr atom in the first B-cation coordination sphere around the absorbing Ti. The pre-edge structure appeared to be sensitive to small changes in the value of this probability, so that the pre-edge intensities could be used effectively to compare the extent of local B-site order in perovskite solid solution samples having similar chemical composition but processed differently.

The Iron-Sulfur Cluster-free Hydrogenase (Hmd) Is a Metalloenzyme with a Novel Iron Binding Motif

The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing cofactor of yet unknown structure. X-ray absorption spectroscopy of the active, as isolated enzyme from Methanothermobacter marburgensis (mHmd) and of the active, reconstituted enzyme from Methanocaldococcus jannaschii (jHmd) revealed the presence of mononuclear iron with two CO, one sulfur and one or two N/O in coordination distance. In jHmd, the single sulfur ligand is most probably provided by Cys176, as deduced from a comparison of the activity and of the x-ray absorption and Mössbauer spectra of the enzyme mutated in any of the three conserved cysteines. In the isolated Hmd cofactor, two CO, one sulfur, and two nitrogen/oxygen atoms coordinate the iron, the sulfur ligand being most probably provided by mercaptoethanol, which is absolutely required for the extraction of the iron-containing cofactor from the holoenzyme and for the stabilization of the extracted cofactor. In active mHmd holoenzyme, the number of iron ligands increased by one when one of the Hmd inhibitors (CO or KCN) were present, indicating that in active Hmd, the iron contains an open coordination site, which is proposed to be the site of H2 interaction.

Quantification and thickness correction of EFTEM phosphorus maps

We describe a method for correcting plural inelastic scattering effects in elemental maps that are acquired in the energy filtering transmission electron microscope (EFTEM) using just two energy windows, one above and one below a core edge in the electron energy loss spectrum (EELS). The technique is demonstrated for mapping low concentrations of phosphorus in biological samples. First, the single-scattering EELS distributions are obtained from specimens of pure carbon and plastic embedding material. Then, spectra are calculated for different specimen thicknesses t, expressed in units of the inelastic mean free path λ. In this way, standard curves are generated for the ratio k 0 of post-edge to pre-edge intensities at the phosphorus L 2,3 excitation energy, as a function of relative specimen thickness t/λ. Thickness effects in a two-window phosphorus map are corrected by successive acquisition of zero-loss and unfiltered images, from which it is possible to determine a t/λ image and hence a background k 0-ratio image. Knowledge of the thickness-dependent k 0-ratio at each pixel thus enables a more accurate determination of the phosphorus distribution in the specimen. Systematic and statistical errors are calculated as a function of specimen thickness, and elemental maps are quantified in terms of the number of phosphorus atoms per pixel. Further analysis of the k 0-curve shows that the EFTEM can be used to obtain reliable two-window phosphorus maps from specimens that are considerably thicker than previously possible.

Charge Distribution in Chromium and Vanadium Catecholato Complexes: X-ray Absorption Spectroscopic and Computational Studies

Transition-metal complexes with redox-active catecholato ligands are of interest as models of bioinorganic systems and as potential molecular materials. This work expands our recent X-ray absorption spectroscopic (XAS) studies of Cr(V/IV/III) triscatecholato complexes (Levina, A.; Foran, G. J.; Pattison, D. I.; Lay, P. A. Angew. Chem., Int. Ed. 2004, 43, 462-465) to a Cr(III) monocatecholato complex, [Cr(tren)(cat)]+ (tren = tris(2-aminoethyl)amine, cat = catecholato2-), and its oxidized analogue, as well as to a series of V(V/IV/III) triscatecholato complexes ([VL3]n-, where L = cat, 3,5-di-tert-butylcatecholato2-, or tetrachlorocatecholato2-, and n = 1-3). Various oxidation states of these complexes in solutions were generated by bulk electrolysis directly in the XAS cell. Increases in the edge energies and pre-edge absorbance intensities in XANES spectra, as well as decreases in the average M-O bond lengths (M = Cr or V) revealed by XAFS data analyses, are consistent with predominantly metal-based oxidations in both the Cr(V/IV/III) and V(V/IV/III) triscatecholato series, but the degree of electron delocalization between the metal ion and the ligands was higher in the case of Cr complexes. By contrast, oxidation of [Cr(III)(tren)(cat)]+ was mainly ligand-based and led to [Cr(III)(tren)(sq)]2+ (sq = semiquinonato-), as shown by the absence of significant changes in the pre-edge and edge features and by an increase in the average Cr-O bond length. The observed differences in electron-density distribution in various oxidation states of Cr and V mono- and triscatecholato complexes have been discussed on the basis of the results of density functional calculations. A crystal and molecular structure of (Et3NH)2[V(IV)(cat)3] has been determined at 25 K and the same complex with an acetonitrile of crystallization at 150 K.

A New Structural Motif for Biological Iron: Iron K-Edge XAS Reveals a [Fe4-μ-(OR)5(OR)9-10] Cluster in the Ascidian Perophora annectens

The Phlebobranch ascidian Perophora annectens surprisingly exhibited a biological Fe/V ratio of approximately 15:1 on multichannel X-ray fluorescence analysis of two independent collections of organisms. Iron K-edge X-ray absorption spectroscopy (XAS) indicated a single form of iron. The XAS K-edge of the first collection of blood cells was shifted approximately +1 eV relative to that of the second, indicating redox activity with average iron oxidation states of 2.67+ and 2.60+. The first-derivative iron XAS K-edge features at 7120.5, 7124, and 7128 eV resembled the XAS of magnetite but not of ferritin or of dissolved Fe(II) or Fe(III). Pseudo-Voigt fits to blood-cell iron K-edge XAS spectra yielded 12.4 integrated units of preedge intensity, indicating a noncentrosymmetric environment. The non-phase-corrected extended X-ray absorption fine structure (EXAFS) Fourier transform spectrum showed a first-shell O/N peak at 1.55 angstroms and an intense Fe-Fe feature at 2.65 angstroms. Fits to the EXAFS required a split first shell with two O at 1.93 angstroms and three O at 2.07 angstroms, consistent with terminal and bridging alkoxide ligands, respectively. More distant shells included three C at 2.87 angstroms, two Fe at 3.08 angstroms, three O at 3.29 angstroms, and one Fe at 3.8 angstroms. Structural models consistent with these findings include a [Fe4(OR)13](2-/3-) broken-edged Fe4O5 cuboid or a [Fe4(OR)14](3-/4-) "Jacob's ladder" with three edge-fused Fe2(OR)2 rhombs. Either of these models represents an entirely new structural motif for biological iron. Vanadium domination of blood-cell metals cannot be a defining trait of Phlebobranch tunicates so long as P. annectens is included among them.

Sulfur K-Edge XAS and DFT Calculations on P450 Model Complexes: Effects of Hydrogen Bonding on Electronic Structure and Redox Potentials

Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.

ASFMS: A program package for ab initio calculation of absorption spectra by full multiple scattering

The program package ASFMS for ab initio self-consistent field (SCF) all-electron full multiple scattering (MS) computations of electron structure and absorption spectra of large systems was developed. ASFMS can compute the X-ray absorption fine structure (XAFS) and near-edge structure (XANES) spectra. Unlike other programs ASFMS can be applied to calculations of pre-edge structure and transition intensity in ultraviolet region. Another advantage of ASFMS consists in using additional cluster boundary conditions for modeling of ionic and covalent solids. Effective algorithms are implemented to reduce the time of the computation and storage.

Effects of Alkali Metal Halide Salts on the Hydrogen Bond Network of Liquid Water

Measurements of the oxygen K-edge X-ray absorption spectrum (XAS) of aqueous sodium halide solutions demonstrate that ions significantly perturb the electronic structure of adjacent water molecules. The addition of halide salts to water engenders an increase in the preedge intensity and a decrease in the postedge intensity of the XAS, analogous to those observed when increasing the temperature of pure water. The main-edge feature exhibits unique behavior and becomes more intense when salt is added. Density functional theory calculations of the XAS indicate that the observed red shift of the water transitions as a function of salt concentration arises from a strong, direct perturbation of the unoccupied molecular orbitals on water by anions, and does not require significant distortion of the hydrogen bond network beyond the first solvation shell. This contrasts the temperature-dependent spectral variations, which result primarily from intensity changes of specific transitions due to geometric rearrangement of the hydrogen bond network.

Ordering of Hydrogen Bonds in High-Pressure Low-TemperatureH2O

The near K-edge structure of oxygen in liquid water and ices III, II, and IX at 0.25 GPa and several low temperatures down to 4 K has been studied using inelastic x-ray scattering at 9884.7 eV with a total energy resolution of 305 and 175 meV. A marked decrease of the preedge intensity from the liquid phase and ice III to ices II and IX is attributed to ordering of the hydrogen bonds in the proton-ordered lattice of the latter phases. Density functional theory calculations including the influence of the Madelung potential of the ice IX crystal correctly account for the remaining preedge feature. Furthermore, we obtain spectroscopic evidence suggesting a possible new phase of ice at temperatures between 4 and 50 K.

A study of transition metal K absorption pre-edges by resonant inelastic x-ray scattering (RIXS)

The K absorption pre-edge structure arises from excitations into the lowest unoccupied states that are partly formed by metal 3d orbitals. The pre-edge energy position, intensity and spectral shape can give valuable insight into the metal site symmetry and electronic configuration. The excited electronic states that form the absorption pre-edge subsequently decay radiatively. This fluorescence decay can be recorded using a crystal spectrometer that has a similar energy bandwidth as the incident beam. Plotting the fluorescence intensity versus incoming and outgoing energy yields three-dimensional plots that offer numerous possibilities for further analysis. In this paper we show that resonant inelastic x-ray scattering (RIXS) considerably facilitates separation of the K pre-edge structure from the strong dipole allowed transitions at higher incident energies. Previously unobserved spectral features could be revealed. The spectra along the energy transfer axis contain information on the electronic structure that is complementary to K-edge absorption spectroscopy.

Metal and Ligand K-Edge XAS of Organotitanium Complexes: Metal 4p and 3d Contributions to Pre-edge Intensity and Their Contributions to Bonding

Titanium cyclopentadienyl (Cp) complexes play important roles as homogeneous polymerization catalysts and have recently received attention as potential anticancer agents. To systematically probe the contribution of the Cp to bonding in organotitanium complexes, Ti K-edge XAS has been applied to TiCl(4) and then to the mono- and bis-Cp complexes, TiCpCl(3) and TiCp(2)Cl(2). Ti K-edge XAS is used as a direct probe of metal 3d-4p mixing and provides insight into the contribution of the Cp to bonding. These data are complimented by Cl K-edge XAS data, which provide a direct probe of the effect of the Cp on the bonding to the spectator chloride ligand. The experimental results are correlated to DFT calculations. A model for metal 3d-4p mixing is proposed, which is based on covalent interactions with the ligands and demonstrates that metal K-pre-edge intensities may be used as a measure of ligand-metal covalency in molecular Ti(IV) systems in noncentrosymmetric environments.

Determination of the iron oxidation state in basaltic glasses using XANES at the K-edge

Fe K-edge X-ray absorption near edge structure (XANES) and Mössbauer spectra were collected on synthetic glasses of basaltic composition and of glasses on the sodium oxide–silica binary to establish a relation between the pre-edge of the XANES at the K-edge and the Fe oxidation state of depolymerised glasses. Charges of sample material were equilibrated at ambient pressure, superliquidus temperatures and oxygen fugacities that were varied over a range of about 15 orders of magnitude. Most experiments were carried out in gas-flow furnaces, either with pure oxygen, air, or different CO/CO 2 mixtures. For the most reduced conditions, the samples charges were enclosed together with a pellet of the IQF oxygen buffer in an evacuated silica glass ampoule. Fe 3+/∑Fe×100 of the samples determined by Mössbauer spectroscopy range between 0% and 100%. Position and intensity of the pre-edge centroid position vary strongly depending on the Fe oxidation state. The pre-edge centroid position and the Fe oxidation state determined by Mössbauer spectroscopy are nonlinearly related and have been fitted by a quadratic polynomial. Alternatively, the ratio of intensities measured at positions sensitive to Fe 2+ and Fe 3+, respectively, provides an even more sensitive method. Pre-edge intensities of the sample suite indicate average Fe co-ordination between 4 and 6 for all samples regardless of oxidation state. A potential application of the calibration given here opens the possibility of determining Fe oxidation state in glasses of similar compositions with high spatial resolution by use of a Micro-XANES setup (e.g., glass inclusions in natural minerals).

Changes in electronic structure of the electrochemically Li-ion deintercalated LiMn 2O 4 system investigated by soft X-ray absorption spectroscopy

The electronic structure of the electrochemically Li-ion deintercalated Li 1− x Mn 2O 4 system has been investigated for various Li compositions using soft X-ray absorption spectroscopy (XAS) for oxygen K-edge and Mn L II,III-edge. To get reasonably good XAS spectra for the electrochemically Li-ion deintercalated Li 1− x Mn 2O 4 system, we made a binder free LiMn 2O 4 film electrode using electrostatic spray deposition (ESD) technique. From the Mn L II,III-edge XAS, it is found that the peak shifts to higher energy with the Li-ion deintercalation and this is due to the increase of the average oxidation state of the Mn ion. From the oxygen K-edge XAS, the Li-ion deintercalation gives rise to a gradual increase in pre-edge peak intensity but mostly does not effect its peak shape.

Comparison of V 2 O 5 Xerogels Prepared by the Vanadate and Alkoxide Routes Using X-Ray Absorption and other Methods

X-ray absorption near edge spectroscopy (XANES), Brunauer-Emmett-Teller surface area, Fourier transform infrared (FTIR), and thermogravimetric analysis were used to characterize two xerogels of prepared using the vanadate hydrolysis (i.e., the material) or the vanadyl tris(isopropoxide) hydrolysis (i.e., the material) synthetic routes. XANES spectra were obtained and analyzed for samples at varying degrees of lithiation that were either bathed in 0.5 M carbonate (PC) supporting electrolyte (i.e., in situ) or from which the solvent had been removed by treatment under high vacuum (i.e., ex situ), as judged by FTIR analysis. The pre-edge, main edge, and edge resonance peak intensities were examined to track the symmetry around the vanadium center. The results for the in situ samples made by both synthetic routes showed that the local symmetry around vanadium did not change significantly for x values ranging from 0 to 0.98, where x represents the degree of reduction in the formulation For the ex situ samples, substantial distortion was observed on going from either the hydrated or PC-swollen states to states in which solvent was absent. Further, the XANES spectrum for an unlithiated ex situ material showed very substantial distortion around vanadium compared to the material, presumably due to the rapidity of polymerization in the alkoxide synthetic procedure. The galvanostatic intermittent titration technique was used to obtain the apparent diffusion coefficient in both materials, revealing diffusion in the material that appeared to be more than two orders of magnitude faster than in the material. The origin of that observation is discussed. © 2003 The Electrochemical Society. All rights reserved.

Comparison of Interfacial Chemistry at Cu/α-Alumina and Cu/γ-Alumina Interfaces

Abstract Different alumina polymorphs (alpha, gamma and a transient phase) are formed in a copper matrix by oxidation of (Cu, Al) at 900°C, at an oxygen activity of aO2 = 10−13. Spatially resolved electron energy loss spectroscopy is used to determine bonding and electronic structure at the different interfaces. Compared to adjacent bulk phases, at the interfaces, the near edge fine structures are modified. Cu L2,3 shows an increased intensity compared to metallic copper and a chemical shift to higher energy. The size of both varies for the different interfaces, smallest chemical shift and highest L2,3 intensity are observed at {111} γ-alumina//{111}Cu interfaces, while larger chemical shift and smaller L2,3 intensities are found for α-alumina/Cu interfaces in the order of {112¯0}α-alumina//{100}Cu, {0001}α-alumina//{001}Cu, {112¯3}α-alumina//Cu. In the interfacial OK edge, an additional pre-edge intensity is observed. For γ-alumina//Cu, it appears as a clear pre-peak, indicating hybridization with strong...

Spectroscopic studies of the effect of ligand donor strength on the Fe-NO bond intradiol dioxygenases.

The geometric and electronic structure of NO bound to reduced protocatechuate 3,4-dioxygenase and its substrate (3,4-dihydroxybenzoate, PCA) complex have been examined by X-ray absorption (XAS), UV-vis absorption (Abs), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The results are compared to those previously published on model complexes described as [FeNO]7 systems in which an S = 5/2 ferric center is antiferromagnetically coupled to an S = 1 NO-. XAS pre-edge analysis indicates that the Fe-NO units in FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] lack the greatly increased pre-edge intensity representative of most [FeNO]7 model sites. Furthermore, from extended X-ray absorption fine structure (EXAFS) analysis, the FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] active sites are shown to have an Fe-NO distance of at least 1.91 A, approximately 0.2 A greater than those found in the model complexes. The weakened Fe-NO bond is consistent with the overall lengthening of the bond lengths and the fact that VTVH MCD data show that NO(-)-->FeIII CT transitions are no longer polarized along the z-axis of the zero-field splitting tensor. The weaker Fe-NO bond derives from the strong donor interaction of the endogenous phenolate and substrate catecholate ligands, which is observed from the increased intensity in the CT region relative to that of [FeNO]7 model complexes, and from the shift in XAS edge position to lower energy. As NO is an analogue of O2, the effect of endogenous ligand donor strength on the Fe-NO bond has important implications with respect to O2 activation by non-heme iron enzymes.