Chemical Information in the L3 X-ray Absorption Spectra of Molybdenum Compounds by High-Energy-Resolution Detection and Density Functional Theory.

X-ray spectroscopy using high-energy-resolution fluorescence detection (HERFD) has critically increased the information content in X-ray spectra. We extend this technique to the tender X-ray range and present a study at the L3-edge of molybdenum. We show how information on the oxidation state, phase composition, and local environment in molybdenum-based compounds can be obtained by analyzing the HERFD L3 X-ray absorption near-edge structure (XANES). We demonstrate that the chemical shift of the L3-edge HERFD spectra follows a parabolic dependence on the oxidation state and show that a qualitative analysis of high-resolution spectra can help to estimate parameters such as distortion of a ligand environment and radial order of atoms around the absorber. In certain cases, the spectra allow disentangling the contributions from bond lengths and angles to the distortion of the ligand polyhedron. Comparison of the high-resolution spectra with theoretical simulations shows that the single-electron approximation is able to reproduce the spectral shape. The results of this work may be useful in every branch of physics, inorganic and organometallic chemistry, catalysis, materials science, biochemistry, and mineralogy where observed changes in performance or chemical properties of Mo-based compounds, accompanied by small changes in spectral shape, are to be related to the details of electronic structure and local atomic environment.

The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26.

X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.

TEXS: in-vacuum tender X-ray emission spectrometer with 11 Johansson crystal analyzers.

The design and first results of a large-solid-angle X-ray emission spectrometer that is optimized for energies between 1.5 keV and 5.5 keV are presented. The spectrometer is based on an array of 11 cylindrically bent Johansson crystal analyzers arranged in a non-dispersive Rowland circle geometry. The smallest achievable energy bandwidth is smaller than the core hole lifetime broadening of the absorption edges in this energy range. Energy scanning is achieved using an innovative design, maintaining the Rowland circle conditions for all crystals with only four motor motions. The entire spectrometer is encased in a high-vacuum chamber that allocates a liquid helium cryostat and provides sufficient space for in situ cells and operando catalysis reactors.

A Solvent-Exposed Cysteine Forms a Peculiar NiII -Binding Site in the Metallochaperone CooT from Rhodospirillum rubrum.

In Rhodospirillum rubrum, the maturation of carbon monoxide dehydrogenase (CODH) requires three nickel chaperones, namely RrCooC, RrCooT and RrCooJ. Recently, the biophysical characterisation of the RrCooT homodimer and the X-ray structure of its apo form revealed the existence of a solvent-exposed NiII -binding site at the dimer interface, involving the strictly conserved Cys2. Here, a multifaceted approach that used NMR and X-ray absorption spectroscopies, complemented with structural bio-modelling methodologies, was used to characterise the binding mode of NiII in RrCooT. This study suggests that NiII adopts a square-planar geometry through a N2 S2 coordinating environment that comprises the two thiolate and amidate groups of both Cys2 residues at the dimer interface. The existence of a diamagnetic mononuclear NiII centre with bis-amidate/bis-thiolate ligands, coordinated by a single-cysteine motif, is unprecedented in biology and raises the question of its role in the activation of CODH at the molecular level.

Mercury(II) Binding to Metallothionein in Mytilus edulis revealed by High Energy-Resolution XANES Spectroscopy.

Of all divalent metals, mercury (HgII ) has the highest affinity for metallothioneins. HgII is considered to be enclosed in the α and ß domains as tetrahedral α-type Hg4 Cys11-12 and ß-type Hg3 Cys9 clusters similar to CdII and ZnII . However, neither the four-fold coordination of Hg nor the existence of Hg-Hg atomic pairs have ever been demonstrated, and the HgII partitioning among the two protein domains is unknown. Using high energy-resolution XANES spectroscopy, MP2 geometry optimization, and biochemical analysis, evidence for the coexistence of two-coordinate Hg-thiolate complex and four-coordinate Hg-thiolate cluster with a metacinnabar-type (ß-HgS) structure in the α domain of separate metallothionein molecules from blue mussel under in vivo exposure is provided. The findings suggest that the CXXC claw setting of thiolate donors, which only exists in the α domain, acts as a nucleation center for the polynuclear complex and that the five CXC motifs from this domain serve as the cluster-forming motifs. Oligomerization is driven by metallophilic Hg⋅⋅⋅Hg interactions. Our results provide clues as to why Hg has higher affinity for the α than the ß domain. More generally, this work provides a foundation for understanding how metallothioneins mediate mercury detoxification in the cell under in vivo conditions.

Divalent Mercury in Dissolved Organic Matter Is Bioavailable to Fish and Accumulates as Dithiolate and Tetrathiolate Complexes.

The freshwater cyprinid Tanichthys albonubes was used to assess the bioavailability of divalent mercury (Hg(II)) complexed in dissolved organic matter (DOM) to fish. The fish acquired 0.3 to 2.2 µg Hg/g dry weight after 8 weeks in aquaria containing DOM from a Carex peat with complexed mercury at initial concentrations of 14 nM to 724 nM. Changes in the relative proportions of dithiolate Hg(SR)2 and nanoparticulate ß-HgS in the DOM, as quantified by high energy-resolution XANES (HR-XANES) spectroscopy, indicate that Hg(SR)2 complexes either produced by microbially induced dissolution of nanoparticulate ß-HgS in the DOM or present in the original DOM were the forms of mercury that entered the fish. In the fish with 2.2 µg Hg/g, 84 ± 8% of Hg(II) was bonded to two axial thiolate ligands and one or two equatorial N/O electron donors (Hg[(SR)2+(N/O)1-2] coordination), and 16% had a Hg(SR)4 coordination, as determined by HR-XANES. For comparison, fish exposed to Hg2+ from 40 nM HgCl2 contained 10.4 µg Hg/g in the forms of dithiolate (20 ± 10%) and tetrathiolate (23 ± 10%) complexes, and also Hg xS y clusters (57 ± 15%) having a ß-HgS-type local structure and a dimension that exceeded the size of metallothionein clusters. There was no evidence of methylmercury in the fish or DOM within the 10% uncertainty of the HR-XANES. Together, the results indicate that inorganic Hg(II) bound to DOM is a source of mercury to biota with dithiolate Hg(SR)2 complexes as the immediate species bioavailable to fish, and that these complexes transform in response to cellular processes.

Solid and Aqueous Speciation of Yttrium in Passive Remediation Systems of Acid Mine Drainage.

Yttrium belongs to the rare earth elements (REEs) together with lanthanides and scandium. REEs are commonly used in modern technologies, and their limited supply has made it necessary to look for new alternative resources. Acid mine drainage (AMD) is a potential resource since it is moderately enriched in REEs. In fact, in passive remediation systems, which are implemented to minimize the environmental impacts of AMD, REEs are mainly retained in basaluminite, an aluminum hydroxysulfate precipitate. In this study, the solid and liquid speciation and the local structure of yttrium are studied in high-sulfate aqueous solutions, basaluminite standards, and samples from remediation columns using synchrotron-based techniques and molecular modeling. Pair distribution function (PDF) analyses and ab initio molecular dynamics density functional theory models of the yttrium sulfate solution show that the YSO4+ ion pair forms a monodentate inner-sphere complex. Extended X-ray absorption fine structure (EXAFS) and PDF analyses show that Y is retained by basaluminite, forming a monodentate inner-sphere surface complex on the aluminum hydroxide surface. EXAFS of the column samples shows that more than 72% of their signal is represented by the signal of basaluminite with which YSO4+ forms an inner-sphere complex. The atomic view of the REE configuration in AMD environments could facilitate a deeper research of REE recovery from waste generated in AMD remediation systems.

Biogenesis of Mercury-Sulfur Nanoparticles in Plant Leaves from Atmospheric Gaseous Mercury.

Plant leaves serve both as a sink for gaseous elemental mercury (Hg) from the atmosphere and a source of toxic mercury to terrestrial ecosystems. Litterfall is the primary deposition pathway of atmospheric Hg to vegetated soils, yet the chemical form of this major Hg input remains elusive. We report the first observation of in vivo formation of mercury sulfur nanoparticles in intact leaves of 22 native plants from six different species across two sampling areas from China. The plants grew naturally in soils from a mercury sulfide mining and retorting region at ambient-air gaseous-Hg concentrations ranging from 131 ± 19 to 636 ± 186 ng m-3 and had foliar Hg concentration between 1.9 and 31.1 ng Hg mg-1 dry weight (ppm). High energy resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy shows that up to 57% of the acquired Hg is nanoparticulate, and the remainder speciated as a bis-thiolate complex (Hg(SR)2). The fractional amount of nanoparticulate Hg is not correlated with Hg concentration. Variation likely depends on leaf age, plant physiology, and natural variability. Nanoparticulate Hg atoms are bonded to four sulfide or thiolate sulfur atoms arranged in a metacinnabar-type (ß-HgS) coordination environment. The nanometer dimension of the mercury-sulfur clusters outmatches the known binding capacity of plant metalloproteins. These findings give rise to challenging questions on their exact nature, how they form, and their biogeochemical reactivity and fate in litterfall, whether this mercury pool is recycled or stored in soils. This study provides new evidence that metacinnabar-type nanoparticles are widespread in oxygenated environments.

Drastic Change in Zinc Speciation during Anaerobic Digestion and Composting: Instability of Nanosized Zinc Sulfide.

Zinc (Zn) is a potentially toxic trace element that is present in large amounts in organic wastes (OWs) spread on agricultural lands as fertilizer. Zn speciation in OW is a crucial parameter to understand its fate in soil after spreading and to assess the risk associated with agricultural recycling of OW. Here, we investigated changes in Zn speciation from raw OWs up to digestates and/or composts for a large series of organic wastes sampled in full-scale plants. Using extended X-ray absorption fine structure, we show that nanosized Zn sulfide (nano-ZnS) is a major Zn species in raw liquid OWs and a minor species in raw solid OWs. Whatever the characteristics of the raw OW, anaerobic digestion always favors the formation of nano-ZnS (>70% of zinc in digestates). However, after 1 to 3 months of composting of OWs, nano-ZnS becomes a minor species (<10% of zinc). In composts, Zn is mostly present as amorphous Zn phosphate and Zn sorbed to ferrihydrite. These results highlight (i) the influence of OW treatment on Zn speciation and (ii) the chemical instability of nano-ZnS formed in OW in anaerobic conditions.

High-Energy Resolution Fluorescence Detected X-Ray Absorption Spectroscopy: A Powerful New Structural Tool in Environmental Biogeochemistry Sciences.

The study of the speciation of highly diluted elements by X-ray absorption spectroscopy (XAS) is extremely challenging, especially in environmental biogeochemistry sciences. Here we present an innovative synchrotron spectroscopy technique: high-energy resolution fluorescence detected XAS (HERFD-XAS). With this approach, measurement of the XAS signal in fluorescence mode using a crystal analyzer spectrometer with a ∼1-eV energy resolution helps to overcome restrictions on sample concentrations that can be typically measured with a solid-state detector. We briefly describe the method, from both an instrumental and spectroscopic point of view, and emphasize the effects of energy resolution on the XAS measurements. We then illustrate the positive impact of this technique in terms of detection limit with two examples dealing with Ce in ecologically relevant organisms and with Hg species in natural environments. The sharp and well-marked features of the HERFD-X-ray absorption near-edge structure spectra obtained enable us to determine unambiguously and with greater precision the speciation of the probed elements. This is a major technological advance, with strong benefits for the study of highly diluted elements using XAS. It also opens new possibilities to explore the speciation of a target chemical element at natural concentration levels, which is critical in the fields of environmental and biogeochemistry sciences.

Chemical Forms of Mercury in Human Hair Reveal Sources of Exposure.

Humans are contaminated by mercury in different forms from different sources. In practice, contamination by methylmercury from fish consumption is assessed by measuring hair mercury concentration, whereas exposure to elemental and inorganic mercury from other sources is tested by analysis of blood or urine. Here, we show that diverse sources of hair mercury at concentrations as low as 0.5 ppm can be individually identified by specific coordination to C, N, and S ligands with high energy-resolution X-ray absorption spectroscopy. Methylmercury from seafood, ethylmercury used as a bactericide, inorganic mercury from dental amalgams, and exogenously derived atmospheric mercury bind in distinctive intermolecular configurations to hair proteins, as supported by molecular modeling. A mercury spike located by X-ray nanofluorescence on one hair strand could even be dated to removal of a single dental amalgam. Chemical forms of other known or putative toxic metals in human tissues could be identified by this approach with potential broader applications to forensic, energy, and materials science.

Molybdenum Speciation and its Impact on Catalytic Activity during Methane Dehydroaromatization in Zeolite ZSM-5 as Revealed by Operando X-Ray Methods.

Combined high-resolution fluorescence detection X-ray absorption near-edge spectroscopy, X-ray diffraction, and X-ray emission spectroscopy have been employed under operando conditions to obtain detailed new insight into the nature of the Mo species on zeolite ZSM-5 during methane dehydroaromatization. The results show that isolated Mo-oxo species present after calcination are converted by CH4 into metastable MoCx Oy species, which are primarily responsible for C2 Hx /C3 Hx formation. Further carburization leads to MoC3 clusters, whose presence coincides with benzene formation. Both sintering of MoC3 and accumulation of large hydrocarbons on the external surface, evidenced by fluorescence-lifetime imaging microscopy, are principally responsible for the decrease in catalytic performance. These results show the importance of controlling Mo speciation to achieve the desired product formation, which has important implications for realizing the impact of CH4 as a source for platform chemicals.

Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations.

We present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular natural organic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree-Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0-3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is -5 kcal/mol per RSR ligand. Detection of distant ligands beyond the first coordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accurate calculation of spectra for representative molecular models. The combined experimental and theoretical approaches described here for Hg can be applied to other closed-shell atoms, such as Ag(I) and Au(I). To facilitate further calculation of XANES spectra, experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computed models, and examples of input files are provided as Supporting Information .

Hyper-accumulation of vanadium in animals: Two sponges compete with urochordates.

Vanadium (V) concentrations in organisms are usually very low. To date, among animals, only some urochordate and annelid species contain very high levels of V in their tissues. A new case of hyper-accumulation of V in a distinct animal phylum (Porifera), namely, the two homoscleromorph sponge species Oscarella lobularis and O. tuberculata is reported. The measured concentrations (up to 30 g/kg dry weight) exceed those reported previously and are not found in all sponge classes. In both Oscarella species, V is mainly accumulated in the surface tissues, and in mesohylar cells, as V(IV), before being partly reduced to V(III) in the deeper tissues. Candidate genes from Bacteria and sponges have been identified as possibly being involved in the metabolism of V. This finding provides clues for the development of bioremediation strategies in marine ecosystems and/or bioinspired processes to recycle this critical metal.

Novel high-pressure/high-temperature reactor cell for in situ and operando x-ray absorption spectroscopy studies of heterogeneous catalysts at synchrotron facilities.

This paper presents the development of a novel high-pressure/high-temperature reactor cell dedicated to the characterization of catalysts using synchrotron x-ray absorption spectroscopy under operando conditions. The design of the vitreous carbon reactor allows its use as a plug-flow reactor, monitoring catalyst samples in a powder form with a continuous gas flow at high-temperature (up to 1000 °C) and under high pressure (up to 1000 bar) conditions, depending on the gas environment. The high-pressure/high-temperature reactor cell incorporates an automated gas distribution system and offers the capability to operate in both transmission and fluorescence detection modes. The operando x-ray absorption spectroscopy results obtained on a bimetallic InCo catalyst during CO2 hydrogenation reaction at 300 °C and 50 bar are presented, replicating the conditions of a conventional microreactor. The complete setup is available for users and permanently installed on the Collaborating Research Groups French Absorption spectroscopy beamline in Material and Environmental (CRG-FAME) sciences and French Absorption spectroscopy beamline in Material and Environmental sciences at ultra-high dilution (FAME-UHD) beamlines (BM30 and BM16) at the European Synchrotron Radiation Facility in Grenoble, France.

Biological Samples Preparation for Speciation at Cryogenic Temperature using High-Resolution X-Ray Absorption Spectroscopy.

The study of elements with X-ray absorption spectroscopy (XAS) is of particular interest when studying the role of metals in biological systems. Sample preparation is a key and often complex procedure, particularly for biological samples. Although X-ray speciation techniques are widely used, no detailed protocol has been yet disseminated for users of the technique. Further, chemical state modification is of concern, and cryo-based techniques are recommended to analyze the biological samples in their near-native hydrated state to provide the maximum preservation of chemical integrity of the cells or tissues. Here, we propose a cellular preparation protocol based on cryo-preserved samples. It is demonstrated in a high energy resolution fluorescence detected X-ray absorption spectroscopy study of selenium in cancer cells and a study of iron in phytoplankton. This protocol can be used with other biological samples and other X-ray techniques that can be damaged by irradiation.

Pinus nigra bark from a mercury mining district studied with high resolution XANES spectroscopy.

Tree bark near former mercury (Hg) mines and roasting plants is known to have exceptionally high (up to several mg kg-1) Hg concentrations. This study explores the change of Hg speciation with depth (down to 25-30 mm from the outermost surface) in black pine (Pinus nigra) bark by means of high-resolution X-ray absorption near edge structure (HR-XANES) spectroscopy at the Hg LIII-edge. Principal component analysis and linear combination fitting applied to the HR-XANES spectra suggested that in the outermost layer (∼0-2 mm from the surface), roughly 50% of Hg is in the form of nanoparticulate metacinnabar (nano-ß-HgS). A progressive increase in Hg-organic species (Hg bound to thiol groups) is found in deeper bark layers, while nano-ß-HgS may decrease below the detection limit in the deepest layers. Notably, bark layers did not contain cinnabar (α-HgS), which was found in the nearby soils along with ß-HgS (bulk), nor Hg0, which is the main Hg species in the atmosphere surrounding the sampled trees. These observations suggested that nano-ß-HgS, at least in part, does not originate from mechanically trapped wind-blown particulates from the surrounding soil, but may be the product of biochemical reactions between gaseous elemental Hg and the bark tissue.

Bad neighbour, good neighbour: how magnetic dipole interactions between soft and hard ferrimagnetic nanoparticles affect macroscopic magnetic properties in ferrofluids.

Fluids responding to magnetic fields (ferrofluids) offer a scene with no equivalent in nature to explore long-range magnetic dipole interactions. Here, we studied the very original class of binary ferrofluids, embedding soft and hard ferrimagnetic nanoparticles. We used a combination of X-ray magnetic spectroscopy measurements supported by multi-scale experimental techniques and Monte-Carlo simulations to unveil the origin of the emergent macroscopic magnetic properties of the binary mixture. We found that the association of soft and hard magnetic nanoparticles in the fluid has a considerable influence on their inherent magnetic properties. While the ferrofluid remains in a single phase, magnetic interactions at the nanoscale between both types of particles induce a modification of their respective coercive fields. By connecting the microscopic properties of binary ferrofluids containing small particles, our findings lay the groundwork for the manipulation of magnetic interactions between particles at the nanometer scale in magnetic liquids.

High energy-resolution x-ray spectroscopy at ultra-high dilution with spherically bent crystal analyzers of 0.5 m radius.

We present the development, manufacturing, and performance of spherically bent crystal analyzers (SBCAs) of 100 mm diameter and 0.5 m bending radius. The elastic strain in the crystal wafer is partially released by a "strip-bent" method where the crystal wafer is cut into strips prior to the bending and the anodic bonding process. Compared to standard 1 m SBCAs, a gain in intensity is obtained without loss of energy resolution. The gain ranges between 2.5 and 4.5, depending on the experimental conditions and the width of the emission line measured. This reduces the acquisition times required to perform high energy-resolution x-ray absorption and emission spectroscopy on ultra-dilute species, accessing concentrations of the element of interest down to, or below, the ppm (ng/mg) level.

Detailed Characterization of a Nanosecond-Lived Excited State: X-ray and Theoretical Investigation of the Quintet State in Photoexcited [Fe(terpy)2]2.

Theoretical predictions show that depending on the populations of the Fe 3d xy , 3d xz , and 3d yz orbitals two possible quintet states can exist for the high-spin state of the photoswitchable model system [Fe(terpy)2]2+. The differences in the structure and molecular properties of these 5B2 and 5E quintets are very small and pose a substantial challenge for experiments to resolve them. Yet for a better understanding of the physics of this system, which can lead to the design of novel molecules with enhanced photoswitching performance, it is vital to determine which high-spin state is reached in the transitions that follow the light excitation. The quintet state can be prepared with a short laser pulse and can be studied with cutting-edge time-resolved X-ray techniques. Here we report on the application of an extended set of X-ray spectroscopy and scattering techniques applied to investigate the quintet state of [Fe(terpy)2]2+ 80 ps after light excitation. High-quality X-ray absorption, nonresonant emission, and resonant emission spectra as well as X-ray diffuse scattering data clearly reflect the formation of the high-spin state of the [Fe(terpy)2]2+ molecule; moreover, extended X-ray absorption fine structure spectroscopy resolves the Fe-ligand bond-length variations with unprecedented bond-length accuracy in time-resolved experiments. With ab initio calculations we determine why, in contrast to most related systems, one configurational mode is insufficient for the description of the low-spin (LS)-high-spin (HS) transition. We identify the electronic structure origin of the differences between the two possible quintet modes, and finally, we unambiguously identify the formed quintet state as 5E, in agreement with our theoretical expectations.