Soft X-ray Induced Photoreduction of Organic Cu(II) Compounds Probed by X-ray Absorption Near-Edge (XANES) Spectroscopy

Impacts of atmospheric deposition on the heavy metal mobilization and bioavailability in soils amended by lime

Atmospheric deposition is an important source of heavy metal in agricultural soils, but there is limited research on the mobility of these metals in soil and their impact on soil amendment. Here, we performed a dust incubation experiment in soils in the laboratory and a factorial transplant experiment at three field sites with a gradient of atmospheric deposition to examine the impacts of atmospherically deposited heavy metals (Cu, Cd, and Pb) on the mobility and bioavailability in soils with and without lime applications. Results showed that the atmospherically deposited heavy metals showed high mobility and were primarily presented in the soluble ionic fractions in the wet part and acid-exchangeable and reducible fractions in the dry part of atmospheric deposition. Atmospheric dust addition caused the 2p3/2 and 2p1/2 electrons of Cu atoms in uncontaminated soils to transition the 3d vacant states, resulting in similar copper absorption peaks as atmospheric particles by the observation of X-ray absorption near-edge spectroscopy (XANES). In the field, atmospheric deposition can only increase the mobile fractions in the surface soils, but not in the deeper layers. However, the deposition can increase the soluble and diffusive gradients in thin films (DGT)-measured bioavailable fractions in profile along with the soil depth. Lime applications cannot significantly reduce the mobile fractions of heavy metals in the surface soils exposed to atmospheric deposition, but significantly reduce the heavy metal concentrations in soil solutions and the DGT-measured bioavailable concentrations, particularly in the deeper layer (6-10 cm). The major implication is that atmospherically deposited heavy metals can significantly increase their bioavailable concentrations in the plough horizon of soil and constrain the effects of soil amendments on heavy metal immobilization, thereby increasing the risks of crop uptake.

Interpreting the Cu-O2 Antibonding Nature in Two Cu-O2 Complexes from Cu L-Edge X-ray Absorption Spectra

Cu-O2 structures play important roles in bioinorganic chemistry and enzyme catalysis, where the bonding between the Cu and O2 parts serves as a fundamental research concern. Here, we performed a multiconfigurational study on the copper L2,3-edge X-ray absorption spectra (XAS) of two copper enzyme model complexes to gain a better understanding of the antibonding nature from the clearly interpreted structure-spectroscopy relation. We obtained spectra in good agreement with the experiments by using the restricted active space second-order perturbation theory (RASPT2) method, which facilitated reliable chemical analysis. Spectral feature interpretations were supported by computing the spin-orbit natural transition orbitals. All major features were assigned to be mainly from Cu 2p to antibonding orbitals between Cu 3d and O2 π*, Cu 3d-πO-O* (type A), and a few also to mixed antibonding/bonding orbitals between Cu 3d and O2 π, Cu 3d ± πO-O (type M). Our calculations provided a clear illustration of the interactions between Cu 3d and O2 π*/π orbitals that are carried in the metal L-edge XAS.

Differential transformation mechanisms of exotic Cr(VI) in agricultural soils with contrasting physio-chemical and biological properties

The transformation mechanisms of Cr(VI) in agricultural soils at the molecular level remain largely unknown due to the multitude of abiotic and biotic factors. In this study, the different speciation and distribution of Cr in two types of agricultural soil (Ultisol and Fluvo-aquic soils) after two weeks of aging was investigated using synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy, microfocused X-ray fluorescence (μ-XRF) and X-ray transmission microscopy (STXM). The microbial community structure of the two soils was also analyzed via high-throughput sequencing of 16S rRNA. Cr(VI) availability was relatively lower in the Ultisol than in the Fluvo-aquic soil after aging. Cr K-edge bulk XANES and STXM analysis indicated that Cr(VI) was reduced to Cr(III) in both soils. μ-XRF analysis and STXM analysis indicated the predominant association of Cr with Mn/Fe oxides and/or organo-Fe oxides in both soils. Additionally, STXM-coupled imaging and multiedge XANES analyses demonstrated that carboxylic groups were involved in the reduction of Cr(VI) and subsequent retention of Cr(III). 16S rRNA analysis showed considerably different bacterial communities across the two soils. Redundancy analysis (RDA) suggested that soil properties, including the total carbon content, Fe oxide component and pH, were closely linked to Cr(VI)-reducing functional bacteria in the Ultisol, including chromium-reducing bacteria (CRB) (e.g., Bacillus sp.) and dissimilatory iron-reducing (DIRB) (e.g., Shewanella sp.) bacteria, which possibly promoted Cr(VI) reduction. These findings shed light on the molecular-level transformation mechanisms of Cr(VI) in agricultural soils, which facilitates the effective management of Cr-enriched farmland.

What Lies beneath a Metal-Organic Framework Crystal Structure? New Design Principles from Unexpected Behaviors

The rational design principles established for metal-organic frameworks (MOFs) allow clear structure-property relationships, fueling expansive growth for energy storage and conversion, catalysis, and beyond. However, these design principles are based on the assumption of compositional and structural rigidity, as measured crystallographically. Such idealization of MOF structures overlooks subtle chemical aspects that can lead to departures from structure-based chemical intuition. In this Perspective, we identify unexpected behavior of MOFs through literature examples. Based on this analysis, we conclude that departures from ideality are not uncommon. Whereas linker topology and metal coordination geometry are useful starting points for understanding MOF properties, we anticipate that deviations from the idealized crystal representation will be necessary to explain important and unexpected behaviors. Although this realization reinforces the notion that MOFs are highly complex materials, it should also stimulate a broader reexamination of the literature to identify corollaries to existing design rules and reveal new structure-property relationships.

Molecular Mechanisms of Chromium(III) Immobilization by Organo-Ferrihydrite Co-precipitates: The Significant Roles of Ferrihydrite and Carboxyl

The interaction mechanisms of heavy metals with organo-Fe hydroxides co-precipitates (OFC) remain unclear due to the structural complexity of the OFC. In this study, batch experiments were conducted to investigate the immobilization mechanisms of Cr(III) by the OFC, which was prepared by co-precipitating Fe³⁺ with rice/rape straw-derived dissolved organic carbon, through sorption and co-precipitation using synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy and scanning transmission X-ray microscopy (STXM). At an Fe/C molar ratio ≥ 0.3, both the sorption and co-precipitation immobilized the majority of Cr(III), but the co-precipitation desorbed less Cr(III) than the sorption regardless of DOC loadings and sources. In contrast, Cr(III) immobilization was significantly reduced at an Fe/C molar ratio of 0.1 for both reactions. Linear combination fitting of Cr K-edge XANES spectra revealed the predominance of ferrihydrite-bound Cr(III), but enhanced organic Cr(III) occurred with increased organic carbon (OC) loading for both the sorption and co-precipitation. STXM coupled with multi-edge XANES analysis confirmed the primary association of Cr(III) with ferrihydrite and directly probed carboxyl as the binding site for Cr(III) retention on the OC constituents of the OFC. These results provided new molecular-level insights into the Cr(III) retention mechanisms on the OFC, particularly for the interactions of Cr(III) and OC constituents of the OFC, which could benefit the management of Cr-contaminated soils with straw returning.

Arabidopsis thaliana Hcc1 is a Sco-like metallochaperone for CuA assembly in Cytochrome c Oxidase

The assembly of the Cu_A site in Cytochrome c Oxidase (COX) is a critical step for aerobic respiration in COX-dependent organisms. Several gene products have been associated with the assembly of this copper site, the most conserved of them belonging to the Sco family of proteins, which have been shown to perform different roles in different organisms. Plants express two orthologs of Sco proteins: Hcc1 and Hcc2. Hcc1 is known to be essential for plant development and for COX maturation, but its precise function has not been addressed until now. Here, we report the biochemical, structural and functional characterization of Arabidopsis thaliana Hcc1 protein (here renamed Sco1). We solved the crystal structure of the Cu⁺¹ -bound soluble domain of this protein, revealing a tri coordinated environment involving a CxxxCx_n H motif. We show that AtSco1 is able to work as a copper metallochaperone, inserting two Cu⁺¹ ions into the Cu_A site in a model of CoxII. We also show that AtSco1 does not act as a thiol-disulfide oxido-reductase. Overall, this information sheds new light on the biochemistry of Sco proteins, highlighting the diversity of functions among them despite their high structural similarities. DATABASE: PDB entry 6N5U (Crystal structure of Arabidopsis thaliana ScoI with copper bound).

Minimizing experimental artefacts in synchrotron-based X-ray analyses of Fe speciation in tissues of rice plants

Iron (Fe) plays an important role within environmental systems. Synchrotron-based X-ray approaches, including X-ray absorption spectroscopy (XAS), provide powerful tools for in situ analyses of Fe speciation, but beam damage during analysis may alter Fe speciation during its measurement. XAS was used to examine whether experimental conditions affect the analysis of Fe speciation in plant tissues. Even when analyzed in a cryostat at 12 K, it was found that Fe^III can rapidly (within 0.5-1 min) photoreduce to Fe^II, although the magnitude of photoreduction varied depending upon the hydration of the sample, the coordination chemistry of the Fe, as well as other properties. For example, photoreduction of Fe^III was considerably higher for aqueous standard compounds than for hydrated plant-root tissues. The use of freeze-dried samples in the cryostat (12 K) markedly reduced the magnitude of this Fe^III photoreduction, and there was no evidence that the freeze-drying process itself resulted in experimental artefacts under the current experimental conditions, such as through the oxidation of Fe^II, although some comparatively small differences were observed when comparing spectra of hydrated and freeze-dried Fe^II compounds. The results of this study have demonstrated that Fe^III photoreduction can occur during X-ray analysis, and provides suitable conditions to preserve Fe speciation to minimize the extent of beam damage when analyzing environmental samples. All studies utilizing XAS are encouraged to include a preliminary experiment to determine if beam damage is occurring, and, where appropriate, to take the necessary steps (such as freeze drying) to overcome these issues.

Beam-induced redox transformation of arsenic during As K-edge XAS measurements: availability of reducing or oxidizing agents and As speciation

During X-ray absorption spectroscopy (XAS) measurements of arsenic (As), beam-induced redox transformation is often observed. In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam-induced redox reactions as a function of sample properties including the redox state of FeS and the solid-phase As speciation. The beam-induced oxidation of reduced As species was found to be mediated by the atmospheric O₂ and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface-complexed As(III) readily underwent the photo-oxidation upon exposure to the atmospheric O₂ during XAS measurements. With strict O₂ exclusion, however, both As(0) and arsenic sulfide were less prone to the photo-oxidation by Fe(III) (oxyhydr)oxides than NaAsO₂ and/or surface-complexed As(III). In case of unaerated As(V)-reacted FeS samples, surface-complexed As(V) was photocatalytically reduced during XAS measurements, but arsenic sulfide did not undergo the photo-reduction.

Mercury capture on a supported chlorocuprate(ii) ionic liquid adsorbent studied using operando synchrotron X-ray absorption spectroscopy

Mercury scrubbing from gas streams using a supported 1-butyl-3-methylimidazolium chlorocuprate(ii) ionic liquid ([C₄mim]₂[Cu₂Cl₆]) has been studied using operando EXAFS. Initial oxidative capture as [HgCl₃]^- anions was confirmed, this was then followed by the unanticipated generation of mercury(i) chloride through comproportionation with additional mercury from the gas stream. Combining these two mechanisms leads to net one electron oxidative extraction of mercury from the gas with increased potential capacity and efficiency for supported ionic liquid mercury scrubbers.

Promises and Pitfalls of Metal Imaging in Biology

A picture may speak a thousand words, but if those words fail to form a coherent sentence there is little to be learned. As cutting-edge imaging technology now provides us the tools to decipher the multitude of roles played by metals and metalloids in molecular, cellular, and developmental biology, as well as health and disease, it is time to reflect on the advances made in imaging, the limitations discovered, and the future of a burgeoning field. In this Perspective, the current state of the art is discussed from a self-imposed contrarian position, as we not only highlight the major advances made over the years but use them as teachable moments to zoom in on challenges that remain to be overcome. We also describe the steps being taken toward being able to paint a completely undisturbed picture of cellular metal metabolism, which is, metaphorically speaking, the Holy Grail of the discipline.

Radiation chemistry of molecular compounds and polymers by soft X-ray spectroscopy and microscopy

Soft X-ray-induced radiation chemistry in selected Fe molecular compounds and some aliphatic polymers was studied using soft X-ray absorption spectroscopy, and scanning transmission X-ray microscopy. X-ray absorption near-edge structure (XANES) spectroscopy was used to elucidate the radiation chemistry. The results show that damage to the Fe molecular complexes involves Fe-ligand bond breaking, ligand damage, and subsequent photoreduction of Fe(III) if it is not tightly bonded to oxygen. Upon radiation damage, polymer PAN primarily undergoes chemical structure changes without mass loss, PECA experiences chemical structure changes as well as small mass loss, while PPC and PEC suffer large mass loss with chemical structure changes. These studies are not only important to X-ray analysis of radiation sensitive materials but also are valuable to the applications of X-ray lithography and other types of nanofabrication involving photoresist.

Retention Mechanisms of Citric Acid in Ternary Kaolinite-Fe(III)-Citrate Acid Systems Using Fe K-edge EXAFS and L3,2-edge XANES Spectroscopy

Organic carbon (OC) stability in tropical soils is strongly interlinked with multivalent cation interaction and mineral association. Low molecular weight organic acids (LMWOAs) represent the readily biodegradable OC. Therefore, investigating retention mechanisms of LMWOAs in mineral-cation-LMWOAs systems is critical to understanding soil C cycling. Given the general acidic conditions and dominance of kaolinite in tropical soils, we investigated the retention mechanisms of citric acid (CA) in kaolinite-Fe(III)-CA systems with various Fe/CA molar ratios at pH ~3.5 using Fe K-edge EXAFS and L_3,2-edge XANES techniques. With Fe/CA molar ratios >2, the formed ferrihydrite mainly contributed to CA retention through adsorption and/or coprecipitation. With Fe/CA molar ratios from 2 to 0.5, ternary complexation of CA to kaolinite via a five-coordinated Fe(III) bridge retained higher CA than ferrihydrite-induced adsorption and/or coprecipitation. With Fe/CA molar ratios ≤0.5, kaolinite-Fe(III)-citrate complexation preferentially occurred, but less CA was retained than via outer-sphere kaolinite-CA complexation. This study highlighted the significant impact of varied Fe/CA molar ratios on CA retention mechanisms in kaolinite-Fe(III)-CA systems under acidic conditions, and clearly showed the important contribution of Fe-bridged ternary complexation on CA retention. These findings will enhance our understanding of the dynamics of CA and other LMWOAs in tropical soils.

Visualising coordination chemistry: fluorescence X-ray absorption near edge structure tomography

Here we develop a measurement scheme to determine the abundance, distribution, and coordination environment of biological copper complexes in situ, without need for complex sample preparation.

Speciation and distribution of copper in a mining soil using multiple synchrotron-based bulk and microscopic techniques

Molecular-level understanding of soil Cu speciation and distribution assists in management of Cu contamination in mining sites. In this study, one soil sample, collected from a mining site contaminated since 1950s, was characterized complementarily by multiple synchrotron-based bulk and spatially resolved techniques for the speciation and distribution of Cu as well as other related elements (Fe, Ca, Mn, K, Al, and Si). Bulk X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy revealed that soil Cu was predominantly associated with Fe oxides instead of soil organic matter. This agreed with the closest association of Cu to Fe by microscopic X-ray fluorescence (U-XRF) and scanning transmission X-ray microscopy (STXM) nanoanalysis, along with the non-occurrence of photoreduction of soil Cu(II) by quick Cu L3,2-edge XANES spectroscopy (Q-XANES) which often occurs when Cu organic complexes are present. Furthermore, bulk-EXAFS and STXM-coupled Fe L3,2-edge nano-XANES analysis revealed soil Cu adsorbed primarily to Fe(III) oxides by inner-sphere complexation. Additionally, Cu K-edge μ-XANES, L3,2-edge bulk-XANES, and successive Q-XANES results identified the presence of Cu2S rather than radiation-damage artifacts dominant in certain microsites of the mining soil. This study demonstrates the great benefits in use of multiple combined synchrotron-based techniques for comprehensive understanding of Cu speciation in heterogeneous soil matrix, which facilitates our prediction of Cu reactivity and environmental fate in the mining site.

Cu1+ in HKUST-1: selective gas adsorption in the presence of water

Photo-reduced Cu²⁺ in HKUST-1 adsorbs NO over water, underscoring the potential of MOFs with mixed oxidation metals for gas separation.

3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences

The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.

Aqueous Cu(II)-organic complexation studied in situ using soft X-ray and vibrational spectroscopies

In situ aqueous solutions containing copper-ligand mixtures were measured at the Cu L-edge using X-ray absorption near edge structure (XANES) and with attenuated total reflectance infrared (ATR-FTIR) spectroscopies. Copper complexation with environmentally relevant ligands such as EDTA, citrate, and malate provided a bridge between spectroscopic studies and general environmental behavior and will allow for future study of complex environmental samples. XANES results show that the lowest unoccupied molecular orbital (LUMO) energy is governed by the ligand field strength and is related to Lewis acid/base properties of the ligand functional groups. Complementary ATR-FTIR studies confirmed the importance of water molecules in the structure of these Cu-ligand complexes and provided in-depth structural analysis to support the XANES data. Copper-malate is shown to have a 5/6-O-ring structure, and Cu-ethylenediaminetetraacetate has pentadentate coordination. Cu L-edge XANES also revealed direct Cu-N coordination in these aqueous solutions with amide functional groups.