X-ray absorption spectroscopy to analyze nuclear geometry and electronic structure of biological metal centers—potential and questions examined with special focus on the tetra-nuclear manganese complex of oxygenic photosynthesis

X-ray absorption spectroscopy (XAS) has become a prominent tool for the element-specific analysis of transition metals at the catalytic center of metalloenzymes. In the present study the information content of X-ray spectra with respect to the nuclear geometry and, in particular, to the electronic structure of the protein-bound metal ions is explored using the manganese complex of photosystem II (PSIII) as a model system. The EXAFS range carries direct information on the number and distances of ligands as well as on the chemical type of the ligand donor function. For first-sphere ligands and second-sphere metals (in multinuclear complexes), the determination of precise distances is mostly straightforward, whereas the determination of coordination numbers clearly requires more effort. The EXAFS section starts with an exemplifying discussion of a PSII spectrum data set with focus on the coordination number problem. Subsequently, the method of linear dichroism EXAFS spectroscopy is introduced and it is shown how the EXAFS data leads to an atomic resolution model for the tetra-manganese complex of PSII. In the XANES section the following aspects are considered: (1) Alternative approaches are evaluated for determination of the metal-oxidation state by comparison with a series of model compounds. (2) The interpretation of XANES spectra in terms of molecular orbitals (MOs) is approached by comparative multiple-scattering calculations and MO calculations. (3) The underlying reasons for the oxidation-state dependence of the XANES spectra are explored. Furthermore, the potential of modern XANES theory is demonstrated by presenting first simulations of the dichroism in the XANES spectra of the PSII manganese complex.     

Np(IV)/Np(V) valence determinations from Np L3 edge XANES/EXAFS

X-ray absorption near edge structure (XANES) spectroscopy for in situ metal valence determination has become a powerful analytical tool in heterogeneous systems. This is in part because it is applicable without prior separation procedures. For some systems, however, determining the oxidation state from XANES spectra is not straightforward and caution must be used. We show that the analysis of L3,2 edge EXAFS (extended X-ray absorption fine structure) spectra is better suited to distinguish between Np(IV) and Np(V) than from their XANES spectra. Whereas evidence for the oxidation of Np(IV) in solution samples from their Np L3 XANES is unclear, their EXAFS data unequivocally reveals Np(V) formation in the solutions.     

X-ray absorption fine structure spectroscopic studies of Octakis(DMSO)lanthanoid(III) complexes in solution and in the solid iodides

Octakis(DMSO)lanthanoid(III) iodides (DMSO = dimethylsulfoxide), [Ln(OS(CH3)2)8]I3, of most lanthanoid(III) ions in the series from La to Lu have been studied in the solid state and in DMSO solution by extended X-ray absorption fine structure (EXAFS) spectroscopy. L3-edge and also some K-edge spectra were recorded, which provided mean Ln-O bond distances for the octakis(DMSO)lanthanoid(III) complexes. The agreement with the average of the Ln-O bond distances obtained in a separate study by X-ray crystallography was quite satisfactory. The crystalline octakis(DMSO)lanthanoid(III) iodide salts have a fairly broad distribution of Ln-O bond distances, ca. 0.1 A, with a few disordered DMSO ligands. Their EXAFS spectra are in excellent agreement with those obtained for the solvated lanthanoid(III) ions in DMSO solution, both of which show slightly asymmetric distributions of the Ln-O bond distances. Hence, all lanthanoid(III) ions are present as octakis(DMSO)lanthanoid(III) complexes in DMSO solution, with the mean Ln-O distances centered at 2.50 (La), 2.45 (Pr), 2.43 (Nd), 2.41 (Sm), 2.40 (Eu), 2.39 (Gd), 2.37 (Tb), 2.36 (Dy), 2.34 (Ho), 2.33 (Er), 2.31 (Tm), and 2.29 A (Lu). This decrease in the Ln-O bond distances is larger than expected from the previously established ionic radii for octa-coordination. This indicates increasing polarization of the LnIII-O(DMSO) bonds with increasing atomic number. However, the S(1s) electron transition energies in the sulfur K-edge X-ray absorption near-edge structure (XANES) spectra, probing the unoccupied molecular orbitals of lowest energy of the DMSO ligands for the [Ln(OS(CH3)2)8](3+) complexes, change only insignificantly from Ln = La to Lu. This indicates that there is no appreciable change in the sigma-contribution to the S-O bond, probably due to a corresponding increase in the contribution from the sulfur lone pair to the bonding.     

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, characterization, and physicochemical properties of manganese(III) and manganese(V)-oxo corrolazines

The structural and physicochemical properties of the manganese-corrolazine (Cz) complexes (TBP8Cz)Mn(V)O (1) and (TBP8Cz)Mn(III) (2) (TBP = p-tert-butylphenyl) have been determined. Recrystallization of 2 from toluene/MeOH resulted in the crystal structure of (TBP8Cz)Mn(III)(CH3OH) (2 x MeOH). The packing diagram of 2 x MeOH reveals hydrogen bonds between MeOH axial ligands and meso N atoms of adjacent molecules. Solution binding studies of 2 with different axial ligands (Cl-, Et3PO, and Ph3PO) reveal strong binding, corroborating the preference of the Mn(III) ion for a five-coordinate environment. High-frequency and field electron paramagnetic resonance (HFEPR) spectroscopy of solid 2 x MeOH shows that 2 x MeOH is best described as a high-spin (S = 2) Mn(III) complex with zero-field splitting parameters typical of corroles. Structural information on 1 was obtained through an X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure (EXAFS) study and compared to XANES/EXAFS data for 2 x MeOH. The XANES data for 1 shows an intense pre-edge transition characteristic of a high-valent metal-oxo species, and a best fit of the EXAFS data gives a short Mn-O bond distance of 1.56 A, confirming the structure of the metal-oxo unit in 1. Detailed spectroelectrochemical studies of 1 and 2 were performed revealing multiple reversible redox processes for both complexes, including a relatively low potential for the Mn(V) --> Mn(IV) process in 1 (near 0.0 V vs saturated calomel reference electrode). Chemical reduction of 1 results in the formation of a Mn(III)Mn(IV)(mu-O) dimer as characterized by electron paramagnetic resonance spectroscopy.     

辽河减压渣油中非卟啉镍的XAFS研究

为获得石油中非卟啉Ni的结构信息，采用荧光法对辽河减压清油中非叶琳Ni的 K边进行了XAFS测试非叶琳Ni第一配位壳层的结构和Ni-四苯基卟啉（NiTPP）的配 位结构类似，也是4个氮原子，呈平面四方构型为0.192nm，在较高的配位壳层，二 者存在一定的差别此外，根据XAFS测试，对石油中非卟啉Ni讨论.     

X-ray absorption spectroscopy of hemes and hemeproteins in solution: multiple scattering analysis

A full quantitative analysis of Fe K-edge X-ray absorption spectra has been performed for hemes in two porphynato complexes, that is, iron(III) tetraphenylporphyrin chloride (Fe(III)TPPCl) and iron(III) tetraphenylporphyrin bis(imidazole) (Fe(III)TPP(Imid)2), in two protein complexes whose X-ray structure is known at atomic resolution (1.0 A), that is, ferrous deoxy-myoglobin (Fe(II)Mb) and ferric aquo-myoglobin (Fe(III)MbH2O), and in ferric cyano-myoglobin (Fe(III)MbCN), whose X-ray structure is known at lower resolution (1.4 A). The analysis has been performed via the multiple scattering approach, starting from a muffin tin approximation of the molecular potential. The Fe-heme structure has been obtained by analyzing independently the Extended X-ray Absorption Fine Structure (EXAFS) region and the X-ray Absorption Near Edge Structure (XANES) region. The EXAFS structural results are in full agreement with the crystallographic values of the models, with an accuracy of +/- 0.02 A for Fe-ligand distances, and +/-6 degrees for angular parameters. All the XANES features above the theoretical zero energy (in the lower rising edge) are well accounted for by single-channel calculations, for both Fe(II) and Fe(III) hemes, and the Fe-N p distance is determined with the same accuracy as EXAFS. XANES evaluations of Fe-5th and Fe-6th ligand distances are determined with 0.04-0.07 A accuracy; a small discrepancy with EXAFS (0.01 to 0.05 A beyond the statistical error), is found for protein compounds. Concerns from statistical correlation among parameters and multiple minima in the parameter space are discussed. As expected, the XANES accuracy is slightly lower than what was found for polarized XANES on Fe(III)MbCN single crystal (0.03-0.04 A), and states the actual state-of-the-art of XANES analysis when used to extract heme-normal parameters in a solution spectrum dominated by heme-plane scattering.     

Preparation, stability, and structural characterization of plutonium(VII) in alkaline aqueous solution

A freshly prepared solution of Pu(VI) in 2 M NaOH was oxidized to Pu(VII), via ozonolysis, while simultaneously collecting X-ray absorption spectra. Analyses of the XANES (X-ray absorption near edge structure) and EXAFS (extended X-ray absorption fine structure) data, acquired throughout the in situ experiments, show a dioxo coordination environment for Pu(VI), PuO(2)(2+), typical for it and the hexavalent actinyl species of U and Np, and its evolution into a tetraoxo-coordination environment for Pu(VII), PuO(4)(-), like that known for Np(VII). The EXAFS data provide average Pu-O distances of 1.79(1) and 1.88(1) ?, respectively. The second coordination shells, also fit as O atoms, provide Pu-O distances of 2.29-2.32 ? that are independent of the Pu oxidation state. The coordination numbers for the distant O atoms in sums with those for the nearest O atoms are consistent with 6-O environments for both Pu(VI) and Pu(VII) ions in accordance with their previously proposed speciation as [Pu(VI)O(2)(OH)(4)](2-) and [Pu(VII)O(4)(OH)(2)](3-), respectively. This solution speciation accounts precisely for the Pu(VI) and Pu(VII) coordination environments reported in various solid state structures. The Pu(VII) tetraoxo-dihydroxo anion was found to have a half-life of 3.7 h. Its instability is attributed to spontaneous reduction to Pu(VI) and not to a measurable extent of disproportionation. We found no direct evidence for Pu(VIII) in the X-ray data and, furthermore, the stoichiometry of the oxidation of Cr(III) by Pu is consistent with that expected for a valence-pure Pu(VII) preparation by ozonation and, in turn, stoichiometrically equivalent to the established Np(VII)/Cr(III) redox reaction.     

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.     

Effect of swift heavy ions in Ni-Al nanocrystalline films studied by X-ray absorption spectroscopy

X-ray absorption spectroscopic measurements have been used to compare the electronic structures of swift heavy ions (100 MeV Si ions) irradiated and pristine Ni-Al nanocrystalline films. Results from X-ray diffraction (XRD), X-ray absorption near-edge structure (XANES) spectra at Al K-, and Ni L(2,3)-edges and extended X-ray absorption fine structure (EXAFS) at Ni K-edges are discussed. The observed XRD peaks indicate the improvement of crystalline nature and Al(111) clustering after the swift heavy ion interactions. While the XANES spectra at Ni L(2,3)-edges show decrease in the intensity of white line strength, the Al K-edge shows increase in intensity after irradiation. Above results imply that swift heavy ions induce low Z (i.e., Al) ion mass transport, changes in Al sp-Ni-d hybridization, and charge transfer. EXAFS results show that crystalline nature is improved after swift heavy irradiation which is consistent with XRD results.     

Characterization of the particulate methane monooxygenase metal centers in multiple redox states by X-ray absorption spectroscopy

The integral membrane enzyme particulate methane monooxygenase (pMMO) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. The 2.8-A resolution pMMO crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. Although not found in the crystal structure, solution samples of pMMO also contain iron. We have used X-ray absorption spectroscopy to analyze the oxidation states and coordination environments of the pMMO metal centers in as-isolated (pMMO(iso)), chemically reduced (pMMO(red)), and chemically oxidized (pMMO(ox)) samples. X-ray absorption near-edge spectra (XANES) indicate that pMMO(iso) contains both Cu(I) and Cu(II) and that the pMMO Cu centers can undergo redox chemistry. Extended X-ray absorption fine structure (EXAFS) analysis reveals a Cu-Cu interaction in all redox forms of the enzyme. The Cu-Cu distance increases from 2.51 to 2.65 A upon reduction, concomitant with an increase in the average Cu-O/N bond lengths. Appropriate Cu2 model complexes were used to refine and validate the EXAFS fitting protocols for pMMO(iso). Analysis of Fe EXAFS data combined with electron paramagnetic resonance (EPR) spectra indicates that Fe, present as Fe(III), is consistent with heme impurities. These findings are complementary to the crystallographic data and provide new insight into the oxidation states and possible electronic structures of the pMMO Cu ions.     

Exploring the capabilities of X-ray absorption spectroscopy for determining the structure of electrolyte solutions: computed spectra for Cr(3+) or Rh(3+) in water based on molecular dynamics

Extended X-ray absorption fine structure (EXAFS) spectra of Cr(3+) and Rh(3+) in aqueous solution are analyzed and compared with computed spectra derived from structural results obtained by molecular dynamics (MD) simulation. This procedure quantifies the reliability of the EXAFS structural determination when applied to ions in solution. It provides guidelines for interpreting experimental spectra of octahedrally coordinated metal cations in aqueous solution. A set of relationships among Debye-Waller factors is proposed on the basis of MD results to reduce the number of independent fit parameters. The determination of the second hydration shell is examined. Calculated XANES spectra compare well with experimental ones. Indeed, the splitting observed on the main peak of the Rh K-edge was anticipated by the calculations. Simulated spectra from MD structures of increasing cluster size show a relationship between the second hydration shell and features of the XANES region at energies just above the edge. The combination of quantum and statistical calculations with the XANES spectrum is found to be very fruitful to get insight into the quantitative estimation of structural properties of electrolyte solutions.     

Investigation of Dienophile-TiCl(4) Complexation by Means of X-ray Absorption and (13)C-NMR Spectroscopies

Extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) techniques, in combination with (13)C-NMR spectroscopy, have been used to study the complexation of methyl acrylate (1), N-acryloylbenzylamine (2), O-acryloyl-(R)-pantolactone (3), methyl N-acryloyl-(S)-prolinate (4), and methyl N-acryloyl-(S)-phenylalaninate (5) with excess TiCl(4) in solution. The results obtained show that TiCl(4) has a great tendency to coordinate with two ester ligands, but this tendency is not so marked with amides, which is related to the greater basicity of the latter. Complexation increases the Ti-Cl bond distance, in comparison with TiCl(4), which is clearly shown by the EXAFS spectra. Chelate complexes are formed with bidentate ligands, but comparison between the EXAFS spectra, obtained with different TiCl(4)/dienophile ratios, shows that chelation is more difficult with methyl N-acryloyl-(S)-phenylalaninate (5).     

Structural characterization study of FeCo alloy nanoparticles in a highly porous aerogel silica matrix

A series of FeCo-SiO(2) nanocomposite aerogels having different FeCo loadings of 3, 5, and 8 wt % were prepared using a novel urea-assisted sol-gel route. The size of the nanoparticles, which was estimated using Scherrer analysis of the main peak of the x-ray diffraction pattern, varies from 3 to 8 nm. X-ray absorption fine structure (EXAFS) and x-ray absorption near edge structure (XANES) techniques at both Fe and Co K edges were used to investigate the structure of the FeCo nanoparticles. EXAFS and XANES show that FeCo nanoparticles have the typical bcc structure. Evidence of oxidation was observed in low FeCo content aerogels. Spatially resolved electron energy loss spectroscopy analysis suggests the formation of a passivation layer of predominantly iron oxide.     

Formation and cation distribution in supported manganese ferrite nanoparticles: an X-ray absorption study

Extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) techniques at both Fe and Mn K-edges were used to investigate the formation of MnFe(2)O(4) nanoparticles embedded in a silica aerogel matrix as a function of calcination temperature (at 450, 750 and 900 degrees C). Up to 450 degrees C, two separated highly-disordered phases of iron and manganese are present. With increasing the temperature (to 750 and 900 degrees C), the structure of aerogel nanoparticles becomes progressively similar to that of the spinel structure MnFe(2)O(4) (jacobsite). Quantitative determination of cations distribution in the spinel structure shows that aerogels calcined at 750 and 900 degrees C have a degree of inversion i = 0.20. A pure jacobsite sample synthesised by co-precipitation and used as a reference compound shows a much higher degree of inversion (i = 0.70). The different distribution of iron and manganese cations in the octahedral and tetrahedral sites in pure jacobsite and in the aerogels can be ascribed to partial oxidation of Mn(2+) to Mn(3+) in pure jacobsite, confirmed by XANES analysis, probably due to the synthesis conditions.     

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.     

Redox chemistry of tantalum clusters on silica characterized by X-ray absorption spectroscopy

SiO(2)-supported clusters of tantalum were synthesized from adsorbed Ta(CH(2)Ph)(5) by treatment in H(2) at 523 K. The surface species were characterized by X-ray absorption spectroscopy (extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray absorption near edge spectroscopy (XANES)) and ultraviolet-visible spectroscopy. The EXAFS data show that SiO(2)-supported tantalum clusters were characterized by a Ta-Ta coordination number of approximately 2, consistent with the presence of tritantalum clusters, on average. When these were reduced in H(2) and reoxidized in O(2), the cluster nuclearity remained essentially unchanged, although reduction and oxidation occurred, respectively, as shown by XANES and UV-vis spectra; in the reoxidation, the tantalum oxidation state change was approximately two electronic charges per tritantalum cluster. The data demonstrate an analogy between the chemistry of group 5 metals on the SiO(2) support and their chemistry in solution, as determined by the group of Cotton.     

A XANES and EXAFS Study of Hydration and Ion Pairing in Ambient Aqueous MnBr<Subscript>2</Subscript> Solutions

Extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) spectroscopies were used to probe the first-shell coordination structure of Mn(II) in aqueous MnBr₂ solutions at ambient conditions from very dilute to the near saturation limit. The Mn K-edge EXAFS spectra for 0.05 and 0.2 m solutions showed that there was no Br(−I) in the first shell, and that the Mn(II) was fully hydrated with six water molecules in an octahedral arrangement. In contrast, for 6 m solution, the coordination number of water was reduced to about 5, and an average of about one bromine atom was present in the first shell as a contact ion pair. The 1s → 4p transition at 6545.5 eV confirmed the observation of Mn–Br contact ion pairs at high concentrations and the 1s → 3d transition at 6539.5 eV showed that the first shell coordination symmetry remained octahedral even in the presence of Mn–Br ion pairs.