X-Ray Absorption Spectroscopy of Amorphous Solids, Liquids, and Catalytic and Biochemical Systems?Capabilities and Limitations

Palladium K-edge X-ray Absorption Spectroscopy Studies on Controlled Ligand Systems

X-ray absorption spectroscopy (XAS) is widely used across the life and physical sciences to identify the electronic properties and structure surrounding a specific element. XAS is less often used for the characterization of organometallic compounds, especially for sensitive and highly reactive species. In this study, we used solid- and solution-phase XAS to compare a series of 25 palladium complexes in controlled ligand environments. The compounds include palladium centers in the formal I, II, III, and IV oxidation states, supported by tridentate and tetradentate macrocyclic ligands, with different halide and methyl ligand combinations. The Pd K-edge energies increased not only upon oxidizing the metal center but also upon increasing the denticity of the ligand framework, substituting sigma-donating methyl groups with chlorides, and increasing the charge of the overall metal complex by replacing charged ligands with neutral ligands. These trends were then applied to characterize compounds whose oxidation states were otherwise unconfirmed.

Complementary combinative strategy of defect engineering and graphene coupling for efficient energy-functional materials

The synergetic combination of defect engineering and graphene coupling enables to develop an effective way of exploring efficient bifunctional electrocatalyst/electrode materials. Defect-engineered amorphous MoO₂ -reduced graphene oxide (rGO) nanohybrid was synthesized by soft-chemical reduction of K₂ MoO₄ in graphene oxide colloids. Mo K-edge X-ray absorption spectroscopy clearly demonstrates the rutile-type local atomic structure of amorphous MoO₂ with significant oxygen vacancies and intimate electronic coupling with rGO. The defect-introduced MoO₂ -rGO nanohybrid shows excellent bifunctionality as electrocatalyst for hydrogen evolution reaction and electrode for sodium-ion batteries, which are superior to those of crystalline MoO₂ -rGO homologue. The beneficial effect of simultaneous defect control and rGO coupling can be ascribed to the provision of oxygen vacancies acting as active sites, the increase of electrical conductivity, and the improvement of reaction kinetics.

Deciphering the Phillips Catalyst by Orbital Analysis and Supervised Machine Learning from Cr Pre-edge XANES of Molecular Libraries

Unveiling the nature and the distribution of surface sites in heterogeneous catalysts, and for the Phillips catalyst (CrO₃/SiO₂) in particular, is still a grand challenge despite more than 60 years of research. Commonly used references in Cr K-edge XANES spectral analysis rely on bulk materials (Cr-foil, Cr₂O₃) or molecules (CrCl₃) that significantly differ from actual surface sites. In this work, we built a library of Cr K-edge XANES spectra for a series of tailored molecular Cr complexes, varying in oxidation state, local coordination environment, and ligand strength. Quantitative analysis of the pre-edge region revealed the origin of the pre-edge shape and intensity distribution. In particular, the characteristic pre-edge splitting observed for Cr(III) and Cr(IV) molecular complexes is directly related to the electronic exchange interactions in the frontier orbitals (spin-up and -down transitions). The series of experimental references was extended by theoretical spectra for potential active site structures and used for training the Extra Trees machine learning algorithm. The most informative features of the spectra (descriptors) were selected for the prediction of Cr oxidation states, mean interatomic distances in the first coordination sphere, and type of ligands. This set of descriptors was applied to uncover the site distribution in the Phillips catalyst at three different stages of the process. The freshly calcined catalyst consists of mainly Cr(VI) sites. The CO-exposed catalyst contains mainly Cr(II) silicates with a minor fraction of Cr(III) sites. The Phillips catalyst exposed to ethylene contains mainly highly coordinated Cr(III) silicates along with unreduced Cr(VI) sites.

From IR to x-rays: gaining molecular level insights on metal-organic frameworks through spectroscopy

This topical review focuses on the application of several types of spectroscopy methods to a class of solid state materials called metal organic frameworks (MOFs). MOFs are self-assembled, porous crystalline materials composed of metal cluster nodes linked through coordination bonds with organic or organometallic molecular constituents. Their unique host-guest properties make them attractive for many adsorption-based applications such as gas storage and separation, catalysis, sensing and others. While much research focuses on the development and application of these materials, fundamental studies of MOF properties and molecular level host-guest interactions behind their functionality have become a significant research direction on its own. Spectroscopy methods are now ubiquitous tools in this pursuit. This review focuses on the application of three classes of spectroscopy methods to MOF materials: vibrational, optical electronic and x-ray spectroscopies. Following brief introductions to each method that include pertinent theory and experimental considerations, we present a broad overview of the types of MOF systems that have been studied, with specific examples and important new molecular level insights highlighted along the way. The current status of spectroscopic studies of MOFs is presented at the end along with some perspectives on the future directions in this area of research.

Impact of finite-temperature and condensed-phase effects on theoretical X-ray absorption spectra of transition metal complexes

The impact of condensed-phase and finite-temperature effects on the theoretical X-ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all-electron Gaussian and augmented plane-wave approach, whereas the latter are taken into account by extensive ensemble averaging along second-generation Car-Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite-temperature effects systematically improves the agreement between our simulated X-ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.

Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands

The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.

[Cu(aq)]2+ is structurally plastic and the axially elongated octahedron goes missing

High resolution (k = 18 Å^-1 or k = 17 Å^-1) copper K-edge EXAFS and MXAN (Minuit X-ray Absorption Near Edge) analyses have been used to investigate the structure of dissolved [Cu(aq)]²⁺ in 1,3-propanediol (1,3-P) or 1,5-pentanediol (1,5-P) aqueous frozen glasses. EXAFS analysis invariably found a single axially asymmetric 6-coordinate (CN6) site, with 4×O_eq = 1.97 Å, O_ax1 = 2.22 Å, and O_ax2 = 2.34 Å, plus a second-shell of 4×O_water = 3.6 Å. However, MXAN analysis revealed that [Cu(aq)]²⁺ occupies both square pyramidal (CN5) and axially asymmetric CN6 structures. The square pyramid included 4×H₂O = 1.95 Å and 1×H₂O = 2.23 Å. The CN6 sites included either a capped, near perfect, square pyramid with 5×H₂O = 1.94 ± 0.04 Å and H₂O_ax = 2.22 Å (in 1,3-P) or a split axial configuration with 4×H₂O = 1.94, H₂O_ax1 = 2.14 Å, and H₂O_ax2 = 2.28 Å (in 1,5-P). The CN6 sites also included an 8-H₂O second-shell near 3.7 Å, which was undetectable about the strictly pyramidal sites. Equatorial angles averaging 94° ± 5° indicated significant departures from tetragonal planarity. MXAN assessment of the solution structure of [Cu(aq)]²⁺ in 1,5-P prior to freezing revealed the same structures as previously found in aqueous 1M HClO₄, which have become axially compressed in the frozen glasses. [Cu(aq)]²⁺ in liquid and frozen solutions is dominated by a 5-coordinate square pyramid, but with split axial CN6 appearing in the frozen glasses. Among these phases, the Cu-O axial distances vary across 1 Å, and the equatorial angles depart significantly from the square plane. Although all these structures remove the d_x²-y² , d_z² degeneracy, no structure can be described as a Jahn-Teller (JT) axially elongated octahedron. The JT-octahedral description for dissolved [Cu(aq)]²⁺ should thus be abandoned in favor of square pyramidal [Cu(H₂O)₅]²⁺. The revised ligand environments have bearing on questions of the Cu(i)/Cu(ii) self-exchange rate and on the mechanism for ligand exchange with bulk water. The plasticity of dissolved Cu(ii) complex ions falsifies the foundational assumption of the rack-induced bonding theory of blue copper proteins and obviates any need for a thermodynamically implausible protein constraint.

Simultaneously Quantifying Ferrihydrite and Goethite in Natural Sediments Using the Method of Standard Additions with X-ray Absorption Spectroscopy

The presence of ferrihydrite in sediments/soils is critical to the cycling of iron (Fe) and many other elements but difficult to quantify. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used to speciate Fe in the solid phase, but this method is thought to have difficulties in distinguishing ferrihydrite from goethite and other minerals. In this study, both conventional EXAFS linear combination fitting (LCF) and the method of standard-additions are applied to the same samples in attempt to quantify ferrihydrite and goethite more rigorously. Natural aquifer sediments from Bangladesh and the United States were spiked with known quantities of ferrihydrite, goethite and magnetite, and analyzed by EXAFS. Known mineral mixtures were also analyzed. Evaluations of EXAFS spectra of mineral references and EXAFS-LCF fits on various samples indicate that ferrihydrite and microcrystalline goethite can be distinguished and quantified by EXAFS-LCF but that the choice of mineral references is critical to yield consistent results. Conventional EXAFS-LCF and the method of standard-additions both identified appreciable amount of ferrihydrite in Bangladesh sediments that were obtained from a low-arsenic Pleistocene aquifer. Ferrihydrite was also independently detected by sequential extraction and ⁵⁷Fe Mӧssbauer spectroscopy. These observations confirm the accuracy of conventional EXAFS-LCF and demonstrate that combining EXAFS with additions of reference materials provides a more robust means of quantifying short-range-ordered minerals in complex samples.

Structural properties of iron-phosphate glasses: spectroscopic studies and ab initio simulations

Vitrification is the most effective method for the immobilization of hazardous waste by incorporating toxic elements into a glass structure. Iron phosphate glasses are presently being considered as matrices for the storage of radioactive waste, even of those which cannot be vitrified using conventional borosilicate waste glass. In this study, a structural model of 60P2O5-40Fe2O3 glass is proposed. The model is based on the crystal structure of FePO4 which is composed of [FeO4][PO4] tetrahedral rings. The rings are optimized using the DFT method and the obtained theoretical FTIR and Raman spectra are being compared with their experimental counterparts. Moreover, the proposed model is in very good agreement with X-ray absorption fine structure spectroscopy (XANES/EXAFS) and Mössbauer spectroscopy measurements. According to the calculations the Fe(3+) is in tetrahedral and five-fold coordination. The maximal predicted load of waste constituents into the glass without rebuilding of the structure is 30 mol%. Below this content, waste constituents balance the charge of [FeO4](-) tetrahedra which leads to their strong bonding to the glass resulting in an increase of the chemical durability, transformation and melting temperatures and density.

Structure-kinetic relationship study of organozinc reagents

Phenylzinc reagents prepared from various zinc halides show distinct kinetic features in the palladium-catalyzed Negishi-type oxidative coupling reaction, in which the phenylzinc reagent prepared from ZnI2 gives the highest rate. In situ infrared and X-ray absorption spectroscopy studies show that the higher reaction rate was observed for longer Zn-C bond distances.

HERFD-XAS and valence-to-core-XES: new tools to push the limits in research with hard X-rays?

In this perspective, the HERFD-XANES (high energy resolution fluorescence detected X-ray absorption near edge structure) and Kβ2,5- or V2C-XES (valence-to-core X-ray emission spectroscopy) methods are discussed as new and powerful tools for chemical research with hard X-rays. This includes a brief survey of the underlying physical processes and the introduction of experimental issues. The potential of both methods to overcome limitations of conventional XAS (X-ray absorption spectroscopy) and to push the limits for obtaining new information about the electronic and geometric structures of metal centers, in the solid state structure or heterogeneous catalysts, but also in metal complexes and homogeneous catalysts, is discussed by presenting a survey of representative references and recent own studies, rounded off by a conclusion and outlook.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

EXAFS Spectroscopy – Fundamentals, Measurement Techniques, Data Evaluation and Applications in the Field of Phthalocyanines

EXAFS spectroscopy is a useful method for determining the local structure around a specific atom in disordered systems. This technique provides information about the coordination number, the nature of the scattering atoms surrounding a particular absorbing atom, the interatomic distance between the absorbing atom and the backscattering atoms, and Debye–Waller factor. The measurements are done with high energy X-rays, which are normally generated by synchrotron radiation sources. The data analysis is facilitated by specially developed program packages suitable for evaluation purposes. EXAFS spectroscopy is employed in several fields for a variety of applications. Here the structural characterization of a series of amorphous μ-oxo-bridged metallophthalocyanine dimers is presented. It is found that the phthalocyanine macrocycle has significant influence in the spectra and the results obtained are in agreement with the well-known structure of phthalocyanine complexes.

Crystal-chemical characterization of mixed-valent indium chalcogenides by X-ray absorption spectroscopy (EXAFS)

The mixed-valent indium chalcogenides InTe, In4Se3, In4Te3, In6S7 and In6Se7 were studied together with b-InS3 and TlInS2 by In and Te K-edge EXAFS spectroscopy. These well-characterized crystalline solids were chosen as model systems to assess the general applicability of EXAFS for structural studies of first order mixed-valent solids containing indium. The question was whether the interatomic distances and coordination numbers derived from EXAFS data could be used for a basic structural characterization in the sense of "structural fingerprints" to identify the indium species present in a given sample. Indium species in the samples comprised In+, In3+, (In2)4+ and (In3)5+, with up to 3 of them being simultaneously present. While the analysis of compounds with only one indium species was possible with high accuracy, it was impossible to interpret the EXAFS data of complex mixed-valent solids containing three different indium species (e.g. In+, In3+, (In2)4+) without prior knowledge of the crystal structures. Intermediate cases are those compounds in which two indium species are present, e.g. In3+ in tetrahedral and octahedral coordination or In+ in a highly regular coordination accompanied by In3+. In conclusion, EXAFS measurements alone can be a reliable basis for structural discussions beyond the first coordination sphere only for compounds of moderate complexity. In most cases prior information of structural data from single crystals or other sources is necessary. This is particularly relevant for future experiments with amorphous or poly-crystalline samples that cannot be studied with standard diffraction techniques.

The mineral phase in the cuticles of two species of Crustacea consists of magnesium calcite, amorphous calcium carbonate, and amorphous calcium phosphate

The cuticules (shells) of the woodlice Porcellio scaber and Armadillidium vulgare were analysed with respect to their content of inorganic material. It was found that the cuticles consist of crystalline magnesium calcite, amorphous calcium carbonate (ACC), and amorphous calcium phosphate (ACP), besides small amounts of water and an organic matrix. It is concluded that the cuticle, which constitutes a mineralized protective organ, is chemically adapted to the biological requirements by this combination of different materials.

Orientation of calcium in the Mn4Ca cluster of the oxygen-evolving complex determined using polarized strontium EXAFS of photosystem II membranes

The oxygen-evolving complex of photosystem II (PS II) in green plants and algae contains a cluster of four Mn atoms in the active site, which catalyzes the photoinduced oxidation of water to dioxygen. Along with Mn, calcium and chloride ions are necessary cofactors for proper functioning of the complex. The current study using polarized Sr EXAFS on oriented Sr-reactivated samples shows that Fourier peak II, which fits best to Mn at 3.5 A rather than lighter atoms (C, N, O, or Cl), is dichroic, with a larger magnitude at 10 degrees (angle between the PS II membrane normal and the X-ray electric field vector) and a smaller magnitude at 80 degrees . Analysis of the dichroism of the Sr EXAFS yields a lower and upper limit of 0 degrees and 23 degrees for the average angle between the Sr-Mn vectors and the membrane normal and an isotropic coordination number (number of Mn neighbors to Sr) of 1 or 2 for these layered PS II samples. The results confirm the contention that Ca (Sr) is proximal to the Mn cluster and lead to refined working models of the heteronuclear Mn(4)Ca cluster of the oxygen-evolving complex in PS II.

The Mn cluster in the S(0) state of the oxygen-evolving complex of photosystem II studied by EXAFS spectroscopy: are there three Di-mu-oxo-bridged Mn(2) moieties in the tetranuclear Mn complex?

A key component required for an understanding of the mechanism of the evolution of molecular oxygen by the photosynthetic oxygen-evolving complex (OEC) in photosystem II (PS II) is the knowledge of the structures of the Mn cluster in the OEC in each of its intermediate redox states, or S-states. In this paper, we report the first detailed structural characterization using Mn extended X-ray absorption fine structure (EXAFS) spectroscopy of the Mn cluster of the OEC in the S(0) state, which exists immediately after the release of molecular oxygen. On the basis of the EXAFS spectroscopic results, the most likely interpretation is that one of the di-mu-oxo-bridged Mn-Mn moieties in the OEC has increased in distance from 2.7 A in the dark-stable S(1) state to 2.85 A in the S(0) state. Furthermore, curve fitting of the distance heterogeneity present in the EXAFS data from the S(0) state leads to the intriguing possibility that three di-mu-oxo-bridged Mn-Mn moieties may exist in the OEC instead of the two di-mu-oxo-bridged Mn-Mn moieties that are widely used in proposed structural models for the OEC. This possibility is developed using novel structural models for the Mn cluster in the OEC which are consistent with the structural information available from EXAFS and the recent X-ray crystallographic structure of PS II at 3.8 A resolution.

Calcium carbonate modifications in the mineralized shell of the freshwater snail Biomphalaria glabrata

The mineralized shell (consisting of calcium carbonate) of the tropical freshwater snail Biomphalaria glabrata was investigated with high resolution synchrotron X-ray powder diffractometry and X-ray absorption spectroscopy (EXAFS). Parts from different locations of the snail shell were taken from animals of different age grown under various keeping conditions. Additionally, eggs with ages of 60, 72, 120, and 140 hours were examined. Traces of aragonite were found as first crystalline phase in 120 h old eggs, however, Ca K-edge EXAFS indicated the presence of aragonitic structures already in the X-ray amorphous sample of 72 h age. The main component of the shell of adult animals was aragonite in all cases, but in some cases minor amounts of vaterite (below 1.5%) are formed. The content of vaterite is generally low in the oldest part of the shell (the center) and increases towards the mineralizing zone (the shell margin). In juvenile snails, almost no vaterite was detectable in any part of the shell.

Characterization and X-ray absorption spectroscopic studies of bis[quinato(2-)]oxochromate(V)

A new Cr(V) complex, K[CrVO(qaH3)2].H2O (Ia; qaH3 = quinato = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylato(2-)), synthesized by the reaction of K2Cr2O7 with excess qaH5 in MeOH (Codd, R.; Lay, P. A. J. Am. Chem. Soc. 1999, 121, 7864-7876), has been characterized by microanalyses, electrospray mass spectra, and UV-visible, CD, IR, EPR, and X-ray absorption spectroscopies. This complex is of interest because of its ability to act as both a structural and a biomimetic model for a range of Cr(V) species believed to be generated in vivo during the intracellular reduction of carcinogenic Cr(VI). The Na+ analogue of Ia (Ib) has also been isolated and characterized by microanalyses and IR and X-ray absorption spectroscopies. The reaction of Cr(VI) with MeOH in the presence of qaH5 that leads to I proceeds via a Cr(IV) intermediate (observed by UV-visible spectroscopy), and a mechanism for the formation of I has been proposed. DMF or DMSO solutions of I are stable for several days at 25 degrees C, while I in aqueous solution (pH = 4) disproportionates to Cr(VI) and Cr(III) in minutes. The likely structures in the solid state for Ia (14 K) and Ib (approximately 293 K) have been determined using both single-scattering (Ia,b) and multiple-scattering (Ia) analyses of XAFS data. These analyses have shown the following: (i) In agreement with the results from the other spectroscopic techniques, the quinato ligands are bound to Cr(V) by 2-hydroxycarboxylato moieties, with Cr-O bond lengths of 1.55, 1.82, and 1.94 A for the oxo, alcoholato, and carboxylato O atoms, respectively. (ii) The position of an oxo O atom is somewhat disordered. This is consistent with molecular mechanics modeling of the likely structures. The XAFS, EPR, and IR spectroscopic evidence points to the existence of hydrogen bonds between the oxo ligand and the 3,4,5-OH groups of the quinato ligands in the solid state of I.

Strontium EXAFS Reveals the Proximity of Calcium to the Manganese Cluster of Oxygen-Evolving Photosystem II

The oxygen-evolving complex of Photosystem II (PS II) in green plants and algae contains a cluster of four manganese atoms in the active site, which catalyzes the photoinduced oxidation of water to dioxygen. Along with Mn, calcium and chloride ions are necessary cofactors for proper functioning of the complex. A key unresolved question is whether Ca is close to the Mn cluster, within about 3.5 Å. To further test and verify this finding, we substituted strontium for Ca and probed from the Sr point-of-view for any nearby Mn. Sr has been shown to replace Ca and still maintain enzyme activity (about 40% of normal rate). The extended X-ray absorption fine structure (EXAFS) of Sr-PS II probes the local environment around the Sr cofactor to detect any nearby Mn. We focused on the functional Sr by removing nonessential, loosely bound Sr in the protein environment. For comparison, an inactive sample was prepared by treating the intact PS II with hydroxylamine to disrupt the Mn cluster and to produce nonfunctional enzyme. Sr EXAFS results indicate major differences in the phase and amplitude between the functional (intact) and nonfunctional (NH2OH-treated) samples. In intact samples, the Fourier transform of the Sr EXAFS shows a peak that is missing in inactive samples. This Fourier peak II is best simulated by two Mn neighbors at a distance of 3.5 Å. Thus, with X-ray absorption studies on Sr-reconstituted PS II, we confirm the proximity of Ca (Sr) cofactor to the Mn cluster and show that the active site is a Mn-Ca heteronuclear cluster.