Iron L-Edge X-ray Absorption Spectroscopy of Myoglobin Complexes and Photolysis Products

FeOOH with Low Spin State Iron as Electron Acceptors for High Yield Rate Electrosynthesis of Urea from Nitrate and Carbon Dioxide

Co electroreduction of carbon dioxide and nitrate to synthesize urea provides an alternative strategy to high energy-consumption traditional methods. However, the complexity of the reaction mechanism and the high energy barrier of nitrate reduction result in a diminished production of urea. Herein, a convenient electrodeposition technique to prepare the FeOOH with low spin state iron that increases the yield rate of urea efficiently is employed. According to soft X-ray Absorption Spectroscopy and theoretical calculations, the unique configuration of low spin state iron as electron acceptors can effectively induce electron pair transfer from the occupied σ orbitals of intermediate * NO to empty d orbitals of iron. This σ→d donation mechanism leads to a reduction in the energy barrier associated with the rate-determining step (* NOOH→* NO + * OH), hence augmenting the urea generation. The low spin state iron presents a high urea yield rate of 512 µg h-1  cm-2 , representing approximately two times compared to the medium spin state iron. The key intermediates (* NH2 and * CO) in the formation of C─N bond are detected with in situ Fourier transform infrared spectroscopy. The coupling of * NH2 and * CO contributes to the formation of * CONH2 , which subsequently endures multi-step proton-coupled electron transfer to generate urea.

Europium-151 and iron-57 nuclear resonant vibrational spectroscopy of naturally abundant KEu(III)Fe(II)(CN)6 and Eu(III)Fe(III)(CN)6 complexes

We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] complexes. Comparison of the observed 151Eu vs.57Fe NRVS spectroscopic features confirms that Eu(III) in both KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] occupies a position outside the [Fe(CN)6] core and coordinates to the N atoms of the CN- ions, whereas Fe(III) or Fe(II) occupies the site inside the [Fe(CN)6]4- core and coordinates to the C atoms of the CN- ions. In addition to the spectroscopic interest, the results from this study provide invaluable insights for the design and evaluation of the nanoparticles of such complexes as potential cellular contrast agents for their use in magnetic resonance imaging. The combined 151Eu and 57Fe NRVS measurements are also among the first few explorations of bi-isotopic NRVS experiments.

X-ray multi-probe data acquisition: A novel technique for laser pump x-ray transient absorption spectroscopy

We report the development and implementation of a novel data acquisition (DAQ) technique for synchrotron-based laser pump X-ray Transient Absorption (XTA) spectroscopy, called X-ray Multi-Probe DAQ (XMP DAQ). This technique utilizes high performance analog to digital converters and home-built software to efficiently measure and process the XTA signal from all x-ray pulses between laser excitations. XMP DAQ generates a set of time resolved x-ray absorption spectra at thousands of different pump-probe time delays simultaneously. Two distinct XMP DAQ schemes are deployed to accommodate different synchrotron storage ring filling patterns. Current Integration (CI) DAQ is a quasi-analog technique that implements a fitting procedure to extract the time resolved absorption intensity from the averaged fluorescence detector response. The fitting procedure eliminates issues associated with small drifts in the voltage baseline and greatly enhances the accuracy of the technique. Photon Counting (PC) DAQ is a binary technique that uses a time resolved histogram to calculate the XTA spectrum. While PC DAQ is suited to measure XTA data with closely spaced x-ray pulses (∼10 ns) and a low count rate (<1 detected photon/pulse), CI DAQ works best for widely spaced pulses (tens of ns or greater) with a high count rate (>1 detected photon/pulse). XMP DAQ produces a two-dimensional XTA dataset, enabling efficient quantitative analysis of photophysical and photochemical processes from the sub-nanosecond timescale to 100 μs and longer.

Coordination Geometry Changes in Amorphous Cyanide-Bridged Metal-Organic Frameworks upon Water Adsorption

Amorphous coordination polymers and metal-organic frameworks (MOFs) have attracted much attention owing to their various functionalities. Here, we demonstrate the tunable water adsorption behavior of a series of amorphous cyanide-bridged MOFs with different metals (M[Ni(CN)₄]: MNi; M = Mn, Fe, and Co). All three compounds adsorb up to six water molecules at a certain vapor pressure (P_ads) and undergo conversion to crystalline Hofmann-type MOFs, M(H₂O)₂[Ni(CN)₄]·4H₂O (MNi-H₂O; M = Mn, Fe, and Co). The P_ads of MnNi, FeNi, and CoNi for water adsorption is P/P₀ = 0.4, 0.6, and 0.9, respectively. Although the amorphous nature of these materials prevented structural elucidation using X-ray crystallography techniques, the local-scale structure around the N-coordinated M²⁺ centers was analyzed using L_2,3-, K-edge X-ray absorption fine structure, and magnetic measurements. Upon hydration, the coordination geometry of these metal centers changed from tetrahedral to octahedral, resulting in significant reorganization of the MOF local structure. On the other hand, Ni[Ni(CN)₄] (NiNi) containing square-planar Ni²⁺ centers did not undergo significant structural transformation and therefore abruptly adsorbed H₂O in the low-pressure region. We could thus define how changes in the bond lengths and coordination geometry are related to the adsorption properties of amorphous MOF systems.

Atomic-level insight into super-efficient electrocatalytic oxygen evolution on iron and vanadium co-doped nickel (oxy)hydroxide

It is of great importance to understand the origin of high oxygen-evolving activity of state-of-the-art multimetal oxides/(oxy)hydroxides at atomic level. Herein we report an evident improvement of oxygen evolution reaction activity via incorporating iron and vanadium into nickel hydroxide lattices. X-ray photoelectron/absorption spectroscopies reveal the synergistic interaction between iron/vanadium dopants and nickel in the host matrix, which subtly modulates local coordination environments and electronic structures of the iron/vanadium/nickel cations. Further, in-situ X-ray absorption spectroscopic analyses manifest contraction of metal-oxygen bond lengths in the activated catalyst, with a short vanadium-oxygen bond distance. Density functional theory calculations indicate that the vanadium site of the iron/vanadium co-doped nickel (oxy)hydroxide gives near-optimal binding energies of oxygen evolution reaction intermediates and has lower overpotential compared with nickel and iron sites. These findings suggest that the doped vanadium with distorted geometric and disturbed electronic structures makes crucial contribution to high activity of the trimetallic catalyst.

L-edge sum rule analysis on 3d transition metal sites: from d10 to d0 and towards application to extremely dilute metallo-enzymes

According to L-edge sum rules, the number of 3d vacancies at a transition metal site is directly proportional to the integrated intensity of the L-edge X-ray absorption spectrum (XAS) for the corresponding metal complex. In this study, the numbers of 3d holes are characterized quantitatively or semi-quantitatively for a series of manganese (Mn) and nickel (Ni) complexes, including the electron configurations 3d10→ 3d0. In addition, extremely dilute (<0.1% wt/wt) Ni enzymes were examined by two different approaches: (1) by using a high resolution superconducting tunnel junction X-ray detector to obtain XAS spectra with a very high signal-to-noise ratio, especially in the non-variant edge jump region; and (2) by adding an inert tracer to the sample that provides a prominent spectral feature to replace the weak edge jump for intensity normalization. In this publication, we present for the first time: (1) L-edge sum rule analysis for a series of Mn and Ni complexes that include electron configurations from an open shell 3d0 to a closed shell 3d10; (2) a systematic analysis on the uncertainties, especially on that from the edge jump, which was missing in all previous reports; (3) a clearly-resolved edge jump between pre-L3 and post-L2 regions from an extremely dilute sample; (4) an evaluation of an alternative normalization standard for L-edge sum rule analysis. XAS from two copper (Cu) proteins measured using a conventional semiconductor X-ray detector are also repeated as bridges between Ni complexes and dilute Ni enzymes. The differences between measuring 1% Cu enzymes and measuring <0.1% Ni enzymes are compared and discussed. This study extends L-edge sum rule analysis to virtually any 3d metal complex and any dilute biological samples that contain 3d metals.

K- and L-edge X-ray Absorption Spectroscopy (XAS) and Resonant Inelastic X-ray Scattering (RIXS) Determination of Differential Orbital Covalency (DOC) of Transition Metal Sites

Continual advancements in the development of synchrotron radiation sources have resulted in X-ray based spectroscopic techniques capable of probing the electronic and structural properties of numerous systems. This review gives an overview of the application of metal K-edge and L-edge X-ray absorption spectroscopy (XAS), as well as K resonant inelastic X-ray scattering (RIXS), to the study of electronic structure in transition metal sites with emphasis on experimentally quantifying 3d orbital covalency. The specific sensitivities of K-edge XAS, L-edge XAS, and RIXS are discussed emphasizing the complementary nature of the methods. L-edge XAS and RIXS are sensitive to mixing between 3d orbitals and ligand valence orbitals, and to the differential orbital covalency (DOC), that is, the difference in the covalencies for different symmetry sets of the d orbitals. Both L-edge XAS and RIXS are highly sensitive to and enable separation of and donor bonding and back bonding contributions to bonding. Applying ligand field multiplet simulations, including charge transfer via valence bond configuration interactions, DOC can be obtained for direct comparison with density functional theory calculations and to understand chemical trends. The application of RIXS as a probe of frontier molecular orbitals in a heme enzyme demonstrates the potential of this method for the study of metal sites in highly covalent coordination sites in bioinorganic chemistry.

Electronic State of Sodium trans-[Tetrachloridobis(1H-indazole)ruthenate(III)] (NKP-1339) in Tumor, Liver and Kidney Tissue of a SW480-bearing Mouse

Ruthenium complexes are promising candidates for anticancer agents, especially NKP-1339 (sodium trans-[tetrachloridobis(1H-indazole)ruthenate(III)]), which is on the edge to clinical applications. The anticancer mechanism seems to be tightly linked to the redox chemistry but despite progress in human clinical trials the in vivo Ru oxidation state and the coordination of Ru remains unclear. The Ru-based anticancer drug NKP-1339 was studied applying XANES (Cl K- and Ru L_2,3-edges) in tumor, kidney and liver tissue of a SW480 bearing mouse. Based on coordination charge and 3D XANES plots containing a series of model compounds as well as pre-edge analysis of the ligand Cl K-edge it is suggested that NKP-1339 remains in its +III oxidation state after 24 hours and at least one of the four chlorido ligands remain covalently bound to the Ru ion showing a biotransformation from Ru^IIIN₂Cl₄ to Ru^IIICl_x(N/O)_6−x (X = 1 or 2).

Probing Framework-Restricted Metal Axial Ligation and Spin State Patterns in a Post-Synthetically Reduced Iron-Porphyrin-Based Metal-Organic Framework

An iron-porphyrin-based metal organic framework PCN-222(Fe) is investigated upon postsynthetic reduction with piperidine. Fe K-edge X-ray absorption and Kβ mainline emission spectroscopy measurements reveal the local coordination geometry, oxidation, and spin state changes experienced by the Fe sites upon reaction with this axially coordinating reducing agent. Analysis and fitting of these data confirm the binding pattern predicted by a space-filling model of the structurally constrained pore environments. These results are further supported by UV-vis diffuse reflectance, IR, and resonance Raman spectroscopy data.

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.

Synchrotron ultrafast techniques for photoactive transition metal complexes

In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.

Ligand discrimination of myoglobin in solution: an iron L-edge X-ray absorption study of the active centre

Iron L-edge X-ray absorption spectra of the active centre of myoglobin in the met-form, in the reduced form and upon ligation to O₂, CO, NO and CN are presented.

Septate-tubular textures in 2.0-Ga pillow lavas from the Pechenga Greenstone Belt: a nano-spectroscopic approach to investigate their biogenicity

Pillow lava rims and interpillow hyaloclastites from the upper part of the Pechenga Greenstone Belt, Kola Peninsula, N-Russia contain rare tubular textures 15-20 μm in diameter and up to several hundred μm long in prehnite-pumpellyite to lower greenschist facies meta-volcanic glass. The textures are septate with regular compartments 5-20 μm across and exhibit branching, stopping and no intersecting features. Synchrotron micro-energy dispersive X-ray was used to image elemental distributions; scanning transmission X-ray microscopy, Fe L-edge and C K-edge were used to identify iron and carbon speciation at interfaces between the tubular textures and the host rock. In situ U-Pb radiometric dating by LA-MC-ICP-MS (laser ablation multicollector inductively coupled plasma mass spectrometry) of titanite from pillow lavas yielded a metamorphic age of 1790 ± 89 Ma. Focused ion-beam milling combined with transmission electron microscopy was used to analyze the textures in three dimensions. Electron diffraction showed that the textures are mineralized by orientated pumpellyite. On the margins of the tubes, an interface between mica or chlorite and the pumpellyite shows evidence of dissolution reactions where the pumpellyite is replaced by mica/chlorite. A thin poorly crystalline Fe-phase, probably precipitated out of solution, occurs at the interface between pumpellyite and mica/chlorite. This sequence of phases leads to the hypothesis that the tubes were initially hollow, compartmentalized structures in volcanic glass that were mineralized by pumpellyite during low-grade metamorphism. Later, a Fe-bearing fluid mineralized the compartments between the pumpellyite and lastly the pumpellyite was partially dissolved and replaced by chlorite during greenschist metamorphism. The most plausible origin for a septate-tubular texture is a progressive etching of the host matrix by several generations of microbes and subsequently these tubes were filled by authigenic mineral precipitates. This preserves the textures in the rock record over geological time. The micro textures reported here thus represent a pumpellyite-mineralized trace fossil that records a Paleoproterozoic sub-seafloor biosphere.

Fe L-edge X-ray absorption spectroscopy determination of differential orbital covalency of siderophore model compounds: electronic structure contributions to high stability constants

Most bacteria and fungi produce low-molecular-weight iron chelators called siderophores. Although different siderophore structures have been characterized, the iron-binding moieties often contain catecholate or hydroxamate groups. Siderophores function because of their extraordinarily high stability constants (K(STAB) = 10(30)-10(49)) and selectivity for Fe(III), yet the origin of these high stability constants has been difficult to quantify experimentally. Herein, we utilize Fe L-edge X-ray absorption spectroscopy to determine the differential orbital covalency (i.e., the differences in the mixing of the metal d-orbitals with ligand valence orbitals) of a series of siderophore model compounds. The results enable evaluation of the electronic structure contributions to their high stability constants in terms of sigma- and pi-donor covalent bonding, ionic bonding, and solvent effects. The results indicate substantial differences in the covalent contributions to stability constants of hydroxamate and catecholate complexes and show that increased sigma as well as pi bonding contributes to the high stability constants of catecholate complexes.

X-ray absorption spectroscopy of biomimetic dye molecules for solar cells

Dye-sensitized solar cells are potentially inexpensive alternatives to traditional semiconductor solar cells. In order to optimize dyes for solar cells we systematically investigate the electronic structure of a variety of porphyrins and phthalocyanines. As a biological model system we use the heme group in cytochrome c which plays a role in biological charge transfer processes. X-ray absorption spectroscopy of the N 1s and C 1s edges reveals the unoccupied molecular orbitals and the orientation of the molecules in thin films. The transition metal 2p edges reflect the oxidation state of the central metal atom, its spin state, and the ligand field of the surrounding N atoms. The latter allows tuning of the energy position of the lowest unoccupied orbital by several tenths of an eV by tailoring the molecules and their deposition. Fe and Mn containing phthalocyanines oxidize easily from +2 to +3 in air and require vacuum deposition for obtaining a reproducible oxidation state. Chlorinated porphyrins, on the other hand, are reduced from +3 to +2 during vacuum deposition at elevated temperatures. These findings stress the importance of controlled thin film deposition for obtaining photovoltaic devices with an optimum match between the energy levels of the dye and those of the donor and acceptor electrodes, together with a molecular orientation for optimal overlap between the pi orbitals in the direction of the carrier transport.

Probing the electronic structure of the hemoglobin active center in physiological solutions

Soft-x-ray absorption spectroscopy at the L_{2,3} edge of the iron center in bovine hemoglobin and hemin under physiological conditions is reported for the first time. Spectra of the same compounds in solid form are presented for comparison. Striking differences in the electronic structure of the metalloporphyrin are observed between the liquid and solid compounds. We unambiguously show that hemoglobin and hemin are in a high-spin ferric state in solution, and that the 2p spin-orbit coupling decreases for hemin compared to the hemoglobin, while this is not the case in solids. The spectra were simulated using ligand field multiplet theory, in good agreement with the experiment, allowing quantification of the amount of charge transfer between the porphyrin and Fe3+ ion in hemoglobin and in hemin.

Observing photochemical transients by ultrafast x-ray absorption spectroscopy

Accurate determination of the transient electronic structures, which drive photochemical reactions, is crucial in chemistry and biology. We report the detection of transient chemical changes on the picosecond time scale by x-ray-absorption near-edge structure of photoexcited aqueous [Ru(bpy)(3)](2+). Upon ultrashort laser pulse excitation a charge transfer excited state having a 300 ns lifetime is formed. We detect the change of oxidation state of the central Ru atom at its L3 and L2 edges, at a temporal resolution of 100 ps with the zero of time unambiguously determined.

Structure of the manganese complex in photosystem II: insights from X-ray spectroscopy

We have used Mn K-edge absorption and Kbeta emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X-ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K-edge energies (1s to 4p, ca. 6550 eV) to obtain L-edge-like spectra (2p to 3d, ca. 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X-ray absorption fine structure data from the S(0) and S(3) states and observed heterogeneity in the Mn-Mn distances leading us to conclude that there may be three rather than two di-mu-oxo-bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X-ray spectroscopy that provide evidence for a heteronuclear Mn-Ca cluster. The possibility of three di-mu-oxo-bridged Mn-Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X-ray spectroscopy results.

Capturing a photoexcited molecular structure through time-domain x-ray absorption fine structure

The determination of the structure of transient molecules, such as photoexcited states, in disordered media (such as in solution) usually requires methods with high temporal resolution. The transient molecular structure of a reaction intermediate produced by photoexcitation of NiTPP-L2 (NiTPP, nickeltetraphenylporphyrin; L, piperidine) in solution was determined by x-ray absorption fine structure (XAFS) data obtained on a 14-nanosecond time scale from a third-generation synchrotron source. The XAFS measurements confirm that photoexcitation leads to the rapid removal of both axial ligands to produce a transient square-planar intermediate, NiTPP, with a lifetime of 28 nanoseconds. The transient structure of the photodissociated intermediate is nearly identical to that of the ground state NiTPP, suggesting that the intermediate adopts the same structure as the ground state in a noncoordinating solvent before it recombines with two ligands to form the more stable octahedrally coordinated NiTPP-L2.