X-ray-absorption spectroscopy and n-body distribution functions in condensed matter. II. Data analysis and applications

In-Depth XANES and EXAFS Characterization of the Ag+ Ion Coordination in Dimethyl Sulfoxide Solution

X-ray absorption near-edge structure (XANES) spectroscopy has been used, in conjunction with extended X-ray absorption fine structure (EXAFS), to determine the coordination structure of the Ag+ ion in a dimethyl sulfoxide (DMSO) solution. From the EXAFS data analysis, the Ag-O first shell distance in DMSO was found to be 2.31(3) Å, with 4.1(5) oxygen atoms surrounding the Ag+ ion, in fair agreement with previous results. This technique did not allow us to determine the geometry of the 4-fold coordination complex and a quantitative analysis of the XANES region was carried out to shed light on this issue. The XANES data analysis confirmed the presence of a four-coordinated complex, unambiguously showing that a regular tetrahedral [Ag(DMSO)4]+ complex is formed when silver triflate is dissolved in DMSO solution.

Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure

An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4-8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ4-8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that CuII is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ4-8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ4-16 peptide. Robust investigations of XAS provide structural details of CuII binding with a very different bis-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ4-12/16 imply that both CuII and CuIII are accommodated in an ATCUN-like binding site. Hypotheses for these CuI, CuII and CuIII geometries were proven and disproven using the novel data and statistical analysis including F tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems.

Structural and electronic transformations of GeSe2 glass under high pressures studied by X-ray absorption spectroscopy

Pressure-induced transformations in an archetypal chalcogenide glass (GeSe2) have been investigated up to 157 GPa by X-ray absorption spectroscopy (XAS) and molecular dynamics (MD) simulations. Ge and Se K-edge XAS data allowed simultaneous tracking of the correlated local structural and electronic changes at both Ge and Se sites. Thanks to the simultaneous analysis of extended X-ray absorption fine structure (EXAFS) signals of both edges, reliable quantitative information about the evolution of the first neighbor Ge-Se distribution could be obtained. It also allowed to account for contributions of the Ge-Ge and Se-Se bond distributions (chemical disorder). The low-density to high-density amorphous-amorphous transformation was found to occur within 10 to 30 GPa pressure range, but the conversion from tetrahedral to octahedral coordination of the Ge sites is completed above [Formula: see text] 80 GPa. No convincing evidence of another high-density amorphous state with coordination number larger than six was found within the investigated pressure range. The number of short Ge-Ge and Se-Se "wrong" bonds was found to increase upon pressurization. Experimental XAS results are confirmed by MD simulations, indicating the increase of chemical disorder under high pressure.

Artificial neural network for deciphering the structural transformation of condensed ZnO by extended x-ray absorption fine structure spectroscopy

Pressure-induced structural phase transitions play a pivotal role in unlocking novel material functionalities and facilitating innovations in materials science. Nonetheless, unveiling the mechanisms of densification, which relies heavily on precise and comprehensive structural analysis, remains a challenge. Herein, we investigated the archetypalB4 →B1 phase transition pathway in ZnO by combining x-ray absorption fine structure (XAFS) spectroscopy with machine learning. Specifically, we developed an artificial neural network (NN) to decipher the extended-XAFS spectra by reconstructing the partial radial distribution functions of Zn-O/Zn pairs. This provided us with access to the evolution of the structural statistics for all the coordination shells in condensed ZnO, enabling us to accurately track the changes in the internal structural parameteruand the anharmonic effect. We observed a clear decrease inuand an increased anharmonicity near the onset of theB4 →B1 phase transition, indicating a preference for the iT phase as the intermediate state to initiate the phase transition that can arise from the softening of shear phonon modes. This study suggests that NN-based approach can facilitate a more comprehensive and efficient interpretation of XAFS under complexin-situconditions, which paves the way for highly automated data processing pipelines for high-throughput and real-time characterizations in next-generation synchrotron photon sources.

EXAFS investigations on the pressure induced local structural changes of GeSe2glass under different hydrostatic conditions

Pressure-induced transformations in glassy GeSe₂have been studied using the x-ray absorption spectroscopy. Experiments have been carried out at the scanning-energy beamline BM23 (European Synchrotron Radiation Facility) providing a micrometric x-ray focal spot up to pressures of about 45 GPa in a diamond anvil cell. Both Se and Ge K-edge experiments were performed under different hydrostatic conditions identifying the metallization onsets by accurate determinations of the edge shifts. The semiconductor-metal transition was observed to be completed around 20 GPa when neon was used as a pressure transmitting medium (PTM), while this transition was slightly shifted to lower pressures when no PTM was used. Accurate double-edge extended x-ray absorption fine structure (EXAFS) refinements were carried out using advanced data-analysis methods. EXAFS data-analysis confirmed the trend shown by the edge shifts for this disordered material, showing that the transition from tetrahedral to octahedral coordination for Ge sites is not fully achieved at 45 GPa. Results of present high pressure EXAFS experiments have shown the absence of significant neon incorporation into the glass within the pressure range up to 45 GPa.

How Nanoparticles Modify Adsorbed Proteins: Impact of Silica Nanoparticles on the Hemoglobin Active Site

The adsorption of proteins on surfaces has been studied for a long time, but the relationship between the structural and functional properties of the adsorbed protein and the adsorption mechanism remains unclear. Using hemoglobin adsorbed on silica nanoparticles, we have previously shown that hemoglobin's affinity towards oxygen increases with adsorption. Nevertheless, it was also shown that there were no significant changes in the quaternary and secondary structures. In order to understand the change in activity, we decided in this work to focus on the active sites of hemoglobin, the heme and its iron. After measuring adsorption isotherms of porcine hemoglobin on Ludox silica nanoparticles, we analyzed the structural modifications of adsorbed hemoglobin by X-ray absorption spectroscopy and circular dichroism spectra in the Soret region. It was found that upon adsorption, there were modifications in the heme pocket environment due to changes in the angles of the heme vinyl functions. These alterations can explain the greater affinity observed.

Design of Single-Atom Catalysts and Tracking Their Fate Using Operando and Advanced X-ray Spectroscopic Tools

The potential of operando X-ray techniques for following the structure, fate, and active site of single-atom catalysts (SACs) is highlighted with emphasis on a synergetic approach of both topics. X-ray absorption spectroscopy (XAS) and related X-ray techniques have become fascinating tools to characterize solids and they can be applied to almost all the transition metals deriving information about the symmetry, oxidation state, local coordination, and many more structural and electronic properties. SACs, a newly coined concept, recently gained much attention in the field of heterogeneous catalysis. In this way, one can achieve a minimum use of the metal, theoretically highest efficiency, and the design of only one active site-so-called single site catalysts. While single sites are not easy to characterize especially under operating conditions, XAS as local probe together with complementary methods (infrared spectroscopy, electron microscopy) is ideal in this research area to prove the structure of these sites and the dynamic changes during reaction. In this review, starting from their fundamentals, various techniques related to conventional XAS and X-ray photon in/out techniques applied to single sites are discussed with detailed mechanistic and in situ/operando studies. We systematically summarize the design strategies of SACs and outline their exploration with XAS supported by density functional theory (DFT) calculations and recent machine learning tools.

Disclosing the Redox Pathway Behind the Excellent Performance of CuS in Solid-State Batteries

Copper sulfide has attracted increasing attention as conversion-type cathode material for, especially, solid-state lithium-based batteries. However, the reaction mechanism behind its extraordinary electroactivity is not well understood, and the various explanations given by the scientific community are diverging. Herein, the CuS reaction dynamics are highlighted by examining the occurring redox processes via a cutting-edge methodology combining X-ray absorption fine structure spectroscopy, and chemometrics to overcome X-ray diffraction limitations posed by the poor material's crystallinity. The mathematical approach rules out the formation of intermediates and clarifies the direct conversion of CuS to Cu in a two-electron process during discharge and reversible oxidation upon delithiation. Two distinct voltage regions are identified corresponding to Cu- as well as the S-redox mechanisms occurring in the material.

Direct Observation of Contact Ion-Pair Formation in La3+ Methanol Solution

An approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to carry out a comparative study about the solvation properties of dilute La(NO₃)₃ solutions in water and methanol, with the aim of elucidating the still elusive coordination of the La³⁺ ion in the latter medium. The comparison between these two systems enlightened a different behavior of the nitrate counterions in the two environments: while in water the La(NO₃)₃ salt is fully dissociated and the La³⁺ ion is coordinated by water molecules only, the nitrate anions are able to enter the metal first solvation shell to form inner-sphere complexes in methanol solution. The speciation of the formed complexes showed that the 10-fold coordination is preferential in methanol solution, where the nitrate anions coordinate the La³⁺ cations in a monodentate fashion and the methanol molecules complete the solvation shell to form an overall bicapped square antiprism geometry. This is at variance with the aqueous solution where a more balanced situation is observed between the 9- and 10-fold coordination. An experimental confirmation of the MD results was obtained by La K-edge XAS measurements carried out on 0.1 M La(NO₃)₃ solutions in the two solvents, showing the distinct presence of the nitrate counterions in the La³⁺ ion first solvation sphere of the methanol solution. The analysis of the extended X-ray absorption fine structure (EXAFS) part of the absorption spectrum collected on the methanol solution was carried out starting from the MD results and confirmed the structural arrangement observed by the simulations.

The formation of contact ion pairs between the La³⁺ ions and the nitrate anions has been demonstrated in diluted methanol solution using a combined approach using Molecular Dynamics simulations and X-ray absorption spectroscpy.

Solubilization and coordination of the HgCl2 molecule in water, methanol, acetone, and acetonitrile: an X-ray absorption investigation

X-ray absorption spectroscopy (XAS) has been employed to carry out structural characterization of the local environment around mercury after the dissolution of the HgCl₂ molecule. A combined EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near edge structure) data analysis has been performed on the Hg L₃-edge absorption spectra recorded on 0.1 M HgCl₂ solutions in water, methanol (MeOH), acetone and acetonitrile. The Hg-Cl distance determined by EXAFS (2.29(2)-2.31(2) Å) is always comparable to that found in the HgCl₂ crystal (2.31(2) Å), demonstrating that the HgCl₂ molecule dissolves in these solvents without dissociating. A small sensitivity of EXAFS to the solvent molecules interacting with HgCl₂ has been detected and indicates a high degree of configurational disorder associated with this contribution. XANES data analysis, which is less affected by the disorder, was therefore carried out for the first time on these systems to shed light into the still elusive structural arrangement of the solvent molecules around HgCl₂. The obtained results show that, in aqueous and MeOH solutions, the XANES data are compatible with three solvent molecules arranged around the HgCl₂ unit to form a trigonal bipyramidal structure. The determination of the three-body Cl-Hg-Cl distribution shows a certain degree of uncertainty around the average 180° bond angle value, suggesting that the HgCl₂ molecule probably vibrates in the solution around a linear configuration.

Synergistic Effect of Co and Mn Co-Doping on SnO2 Lithium-Ion Anodes

The incorporation of transition metals (TMs) such as Co, Fe, and Mn into SnO2 substantially improves the reversibility of the conversion and the alloying reaction when used as a negative electrode active material in lithium-ion batteries. Moreover, it was shown that the specific benefits of different TM dopants can be combined when introducing more than one dopant into the SnO2 lattice. Herein, a careful characterization of Co and Mn co-doped SnO2 via transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy and X-ray diffraction including Rietveld refinement is reported. Based on this in-depth investigation of the crystal structure and the distribution of the two TM dopants within the lattice, an ex situ X-ray photoelectron spectroscopy and ex situ X-ray absorption spectroscopy were performed to better understand the de-/lithiation mechanism and the synergistic impact of the Co and Mn co-doping. The results specifically suggest that the antithetical redox behaviour of the two dopants might play a decisive role for the enhanced reversibility of the de-/lithiation reaction.

Advances in modelling X-ray absorption spectroscopy data using reverse Monte Carlo

Modern extended X-ray absorption fine structure (EXAFS) analysis is based on multiple-scattering calculations. Those calculations are carried out for fixed atomic configurations and proper account of the thermal and static disorder, corresponding to well-defined pair and higher-order distribution functions, can be obtained using different methods. The application of the Reverse Monte Carlo (RMC) method is able to provide tridimensional models of the atomic structure compatible with a given set of experimental data, producing useful and consistent structural models. This method has been proposed and applied also to EXAFS data by several authors in the last 25 years and has been fully implemented in the framework of the RMC-GnXAS method for EXAFS data-analysis. Here we present the extension and application of this method to multiple-edge studies of molecules, crystalline solids and liquids, including the long-range constraints provided by other techniques (e.g. diffraction). The potential and possible weaknesses of the RMC method are discussed, as well as the importance of accounting for the effect of noise levels in XAFS data. Results of RMC refinements are reported for several exemplary cases including Br₂ and GeI₄ molecular gases, crystalline Ge and AgBr, amorphous Ge and liquid AgBr. Those applications show the general interest for this method, and the importance of combining multiple set of data for improving the accuracy of the structural refinement both at short and long range.

Aggregates Sealed by Ions

The chapter draws a line connecting some recent results where the role of ions is found essential in sealing more or less pre-organized assemblies of macromolecules. We draw some dots along the line that starts from the effect of the ionic atmosphere and ends with the chemical bonds formed by multivalent ions acting as bridges between macromolecules. Many of these dots involve structurally disordered peptides and disordered regions of proteins. A broad perspective of the role of multivalent ions in assisting the assembly process, shifting population in polymorphic states, and sealing protein aggregates, is suggested.

Symmetry Breaking in Solution-Phase [Cu(tsc)2(H2O)2]2+: Emergent Asymmetry in Cu-S Distances and in Covalence

The structure of aqueous Cu(II)-bis-thiosemicarbazide, [Cu(tsc)₂]²⁺, is reported following EXAFS and MXAN analyses of the copper K-edge X-ray absorption (XAS) spectrum. The rising K-edge feature at 8987.1 eV is higher energy than those of crystalline models, implying unique electronic and structural solution states. EXAFS analysis (k = 2-13 Å^-1; 2 × Cu-N = 2.02 ± 0.01 Å; 2 × Cu-S = 2.27 ± 0.01 Å; Cu-O_ax = 2.41 ± 0.04 Å) could not resolve 5- versus 6-coordinate models. However, MXAN fits converged to an asymmetric broken symmetry 6-coordinate model with cis-disposed TSC ligands (Cu-O_ax = 2.07 and 2.54 Å; Cu-N = 1.94 Å, 1.98 Å; Cu-S = 2.20 Å, 2.41 Å). Transition dipole integral evaluation of the sulfur K-edge XAS 1s → 3p valence transition feature at 2470.7 eV yielded a Cu-S covalence of 0.66 e^-, indicating Cu^1.34+. The high Cu-S covalence and short Cu-S bond in aqueous [Cu(tsc)₂(H₂O)₂]²⁺ again contradict the need for a protein rack to explain the unique structure of the blue copper active site. MXAN models of dissolved Cu(II) complex ions have invariably featured broken centrosymmetry. The potential energy ground state for dissolved Cu(II) evidently includes the extended solvation field, providing a target for improved physical theory. A revised solvation model for aqueous Cu(II), |[Cu(H₂O)₅]·14H₂O|²⁺, is presented.

Revisiting the Extended X-ray Absorption Fine Structure Fitting Procedure through a Machine Learning-Based Approach

A novel approach for the analysis of extended X-ray absorption fine structure (EXAFS) spectra is developed exploiting an inverse machine learning-based algorithm. Through this approach, it is possible to explore and account for, in a precise way, the nonlinear geometry dependence of the photoelectron backscattering phases and amplitudes of single and multiple scattering paths. In addition, the determined parameters are directly related to the 3D atomic structure, without the need to use complex parametrization as in the classical fitting approach. The applicability of the approach, its potential and the advantages over the classical fit were demonstrated by fitting the EXAFS data of two molecular systems, namely, the KAu (CN)₂ and the [RuCl₂(CO)₃]₂ complexes.

Cross-Investigation on Copper Nitroprusside: Combining XRD and XAS for In-Depth Structural Insights

The emerging energy demand and need to develop sustainable energy storage systems have drawn extensive attention to fundamental and applied research. Anion redox processes were proposed in cathodic materials in addition to traditional transition metal redox to boost the specific capacity and the electrochemical performance. Alternatively, copper nitroprusside (CuNP) features an electroactive nitrosyl ligand alongside the two structural metals (Fe, Cu), representing an alternative to anion redox in layered oxides. Here, a deep structural investigation is carried out on CuNP by complementing the long-range order sensitivity of X-ray diffraction (XRD) and the local atomic probe of X-ray absorption (XAS). Two different CuNP materials are studied, the hydrated and dehydrated forms. A new phase for hydrated CuNP not reported in the literature is solved, and Rietveld refined. The XAS spectra of the two materials at the Cu and Fe K-edges show a similar yet different atomic environment. The extended XAS spectra (EXAFS) analysis is accomplished by considering three- and four-body terms due to the high collinearity of the atomic chains and gives accurate insight into the first-, second-, and third-shell interatomic distances. Both materials are mounted in Li-ion and Na-ion cells to explore the link between structure and electrochemical performance. As revealed by the charge/discharge cycles, the cyclability in Na-ion cells is negatively affected by interstitial water. The similarity in the local environment and the electrochemical differences suggest a long-range structural dependence on the electrochemical performance.

Coordination of the Co2+ and Ni2+ Ions in Tf2N- Based Ionic Liquids: A Combined X-ray Absorption and Molecular Dynamics Study

Molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) have been combined to study the coordination of the Co2+ and Ni2+ ions in ionic liquids (ILs) based on the bis(trifluoromethylsulfonyl)imide ([Tf2N]-) anion and having different organic cations, namely, 1-butyl-3-methylimidazolium ([C4mim]+), 1,8-bis(3-methylimidazolium-1-yl)octane ([C8(mim)2]2+), N,N,N-trimethyl-N-(2-hydroxyethyl)ammonium ([choline]+), and butyltrimethylammonium ([BTMA]+). Co and Ni K-edge XAS data have been collected on 0.1 mol L-1 Co(Tf2N)2 and Ni(Tf2N)2 solutions and on the metallic salts. MD simulations have been carried out to obtain structural information on the metal ion coordination. The analysis of the extended X-ray absorption fine structure (EXAFS) spectra of the solutions has been carried out based on the atomistic description provided by MD, and the studied ILs have been found to be able to dissolve both the Co(Tf2N)2 and Ni(Tf2N)2 salts giving rise to a different structural arrangement around the metal ions as compared to the solid state. The combined EXAFS and MD results showed that the Co2+ and Ni2+ ions are surrounded by a first solvation shell formed by six [Tf2N]- anions, each coordinating in a monodentate fashion by means of the oxygen atoms. The nature of the IL organic cation has little or no influence on the overall spatial arrangement of the [Tf2N]- anions, so that stable octahedral complexes of the type [M(Tf2N)6]4- (M = Co, Ni) have been observed in all the investigated ILs.

Extracting Local Symmetry of Mono-Atomic Systems from Extended X-ray Absorption Fine Structure Using Deep Neural Networks

In recent years, neural networks have become a new method for the analysis of extended X-ray absorption fine structure data. Due to its sensitivity to local structure, X-ray absorption spectroscopy is often used to study disordered systems and one of its more interesting property is the sensitivity not only to pair distribution function, but also to three-body distribution, which contains information on the local symmetry. In this study, by considering the case of Ni, we show that by using neural networks, it is possible to obtain not only the radial distribution function, but also the bond angle distribution between the first nearest-neighbors. Additionally, by adding appropriate configurations in the dataset used for training, we show that the neural network is able to analyze also data from disordered phases (liquid and undercooled state), detecting small changes in the local ordering compatible with results obtained through other methods.

Relativistic Corrections to Phase Shift Calculation in the GNXAS Package

Modern XAFS (X-ray Absorption Fine Structure) data-analysis is based on accurate multiple-scattering (MS) calculations of the x-ray absorption cross-section. In this paper, we present the inclusion and test of relativistic corrections for the multiple-scattering calculations within the GnXAS suite of programs, which is relevant to the treatment of the XAFS signals when atoms with high atomic number are contained into the system. We present a suitable strategy for introducing relativistic corrections without altering the basic structure of the programs. In particular, this is realized by modifying only the Phagen program calculating the atomic absorption cross sections and scattering t-matrices for the selected cluster. The modification incorporates a pseudo-Schrödinger Equation (SE) replacing the Dirac relativistic form. The phase-shift calculations have been put to a test in two known molecular and crystalline cases: molecular bromine Br2 and crystalline Pb. Calculations in an extended energy range have been shown to be very close to the non-relativistic case for Br2 (Br K-edge) while corrections have been found to exceed 25% for amplitude and phases of the XAFS multiple-scattering signals (Pb L3-edge). Benefits in the structural refinement using relativistic corrections are discussed for crystalline Pb at room temperature.

Zinc determines dynamical properties and aggregation kinetics of human insulin

Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.

Elusive Coordination of the Ag+ Ion in Aqueous Solution: Evidence for a Linear Structure

X-ray absorption spectroscopy (XAS) has been employed to study the coordination of the Ag⁺ ion in aqueous solution. The conjunction of extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) data analysis provided results suggesting the preference for a first shell linear coordination with a mean Ag-O bond distance of 2.34(2) Å, different from the first generally accepted tetrahedral model with a longer mean Ag-O bond distance. Ab initio molecular dynamics simulations with the Car-Parrinello approach (CPMD) were also performed and were able to describe the coordination of the hydrated Ag⁺ ion in aqueous solution in very good agreement with the experimental data. The high sensitivity for the closest environment of the photoabsorber of the EXAFS and XANES techniques, together with the long-range information provided by CPMD and large-angle X-ray scattering (LAXS), allowed us to reconstruct the three-dimensional model of the coordination geometry around the Ag⁺ ion in aqueous solution. The obtained results from experiments and theoretical simulations provided a complex picture with a certain amount of water molecules with high configurational disorder at distances comprised between the first and second hydration spheres. This evidence may have caused the proliferation of the coordination numbers that have been proposed so far for Ag⁺ in water. Altogether these data show how the description of the hydration of the Ag⁺ ion in aqueous solution can be complex, differently from other metal species where hydration structures can be described by clusters with well-defined geometries. This diffuse hydration shell causes the Ag-O bond distance in the linear [Ag(H₂O)₂]⁺ ion to be ca. 0.2 Å longer than in isolated ions in solid state.

THORONDOR: a software for fast treatment and analysis of low-energy XAS data

THORONDOR is a data treatment software with a graphical user interface (GUI) accessible via the browser-based Jupyter notebook framework. It aims to provide an interactive and user-friendly tool for the analysis of NEXAFS spectra collected during in situ experiments. The program allows on-the-fly representation and quick correction of large datasets from single or multiple experiments. In particular, it provides the possibility to align in energy several spectral profiles on the basis of user-defined references. Various techniques to calculate background subtraction and signal normalization have been made available. In this context, an innovation of this GUI involves the usage of a slider-based approach that provides the ability to instantly manipulate and visualize processed data for the user. Finally, the program is characterized by an advanced fitting toolbox based on the lmfit package. It offers a large selection of fitting routines as well as different peak distributions and empirical ionization potential step edges, which can be used for the fit of the NEXAFS rising-edge peaks. Statistical parameters describing the goodness of a fit such as χ² or the R-factor together with the parameter uncertainty distributions and the related correlations can be extracted for each chosen model.

Effect of Water and Alkali-Ion Content on the Structure of Manganese(II) Hexacyanoferrate(II) by a Joint Operando X-ray Absorption Spectroscopy and Chemometric Approach

Manganese hexacyanoferrate (MnHCF) is made of earth-abundant elements by a safe and easy synthesis. The material features a higher specific capacity at a higher potential than other Prussian blue analogs. However, the effect of hydration is critical to determine the electrochemical performance as both the electrochemical behavior and the reaction dynamics are affected by interstitial/structural water and adsorbed water. In this study, the electrochemical activity of MnHCF is investigated by varying the interstitial ion content through a joint operando X-ray absorption spectroscopy and chemometric approach, with the intent to assess the structural and electronic modifications that occur during Na release and Li insertion, as well as the overall dynamic evolution of the system. In MnHCF, both the Fe and Mn centers are electrochemically active and undergo reversible oxidation during the interstitial ion extraction (Fe2+ /Fe3+ and Mn2+ /Mn3+ ). The adsorption of water results in irreversible capacity during charge but only on the Fe site, which is suggested by our chemometric analysis. The local environment of Mn experiences a substantial yet reversible Jahn-Teller effect upon interstitial ion removal because of the formation of trivalent Mn, which is associated with a decrease of the equatorial Mn-N bond lengths by 10 %.

Carbon-Nanotube-Supported Copper Polyphthalocyanine for Efficient and Selective Electrocatalytic CO2 Reduction to CO

Electroreduction of CO₂ to CO is one of the simplest ways to valorise CO₂ as a source of carbon. Herein, a cheap, robust, Cu-based hybrid catalyst consisting of a polymer of Cu phthalocyanine coated on carbon nanotubes, which proved to be selective for CO production (80 % faradaic yield) at relatively low overpotentials, was developed. Polymerisation of Cu phthalocyanine was shown to have a drastic effect on the selectivity of the reaction because molecular Cu phthalocyanine was instead selective for proton reduction under the same conditions. Although the material only showed isolated Cu sites in phthalocyanine-like CuN₄ coordination, in situ and operando X-ray absorption spectroscopy showed that, under operating conditions, the Cu atoms were fully converted to Cu nanoparticles, which were likely the catalytically active species. Interestingly, this restructuring of the metal sites was reversible.

Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain

Prions are pathological isoforms of the cellular prion protein that is responsible for transmissible spongiform encephalopathies (TSE). Cellular prion protein interacts with copper, Cu(II), through octarepeat and nonoctarepeat (non-OR) binding sites. The molecular details of Cu(II) coordination within the non-OR region are not well characterized yet. By the means of small angle x-ray scattering and x-ray absorption spectroscopic methods, we have investigated the effect of Cu(II) on prion protein folding and its coordination geometries when bound to the non-OR region of recombinant prion proteins (recPrP) from mammalian species considered resistant or susceptible to TSE. As the prion resistant model, we used ovine recPrP (OvPrP) carrying the protective polymorphism at residues A136, R154, and R171, whereas as TSE-susceptible models, we employed OvPrP with V136, R154, and Q171 polymorphism and bank vole recPrP. Our analysis reveals that Cu(II) affects the structural plasticity of the non-OR region, leading to a more compacted conformation. We then identified two Cu(II) coordination geometries: in the type 1 coordination observed in OvPrP at residues A136, R154, and R171, the metal is coordinated by four residues; conversely, the type 2 coordination is present in OvPrP with V136, R154, and Q171 and bank vole recPrP, where Cu(II) is coordinated by three residues and by one water molecule, making the non-OR region more exposed to the solvent. These changes in copper coordination affect the recPrP amyloid aggregation. This study may provide new insights into the molecular mechanisms governing the resistance or susceptibility of certain species to TSE.

EXAFS wavelet transform analysis of Cu-MOR zeolites for the direct methane to methanol conversion

An innovative approach in EXAFS analysis and fitting using wavelet transforms reveals local structure and nuclearity of Cu-species in zeolites.

Evidence for an egg-box-like structure in iron(ii)–polygalacturonate hydrogels: a combined EXAFS and molecular dynamics simulation study

The coordination of Fe(ii) with polygalacturonic acid (polyGalA) in Fe(ii)–polyGalA hydrogels exhibits an octahedral geometry that follows the “egg-box model”.

Copper and silver gas diffusion electrodes performing CO2 reduction studied through operando X-ray absorption spectroscopy

A guide on operando XAS for high current density CO₂ reduction and a detailed analysis of the obtained XAS data.

Solvation structure of lanthanide(iii) bistriflimide salts in acetonitrile solution: a molecular dynamics simulation and EXAFS investigation

Lanthanide³⁺ ions in acetonitrile solutions of bistriflimide salts form 10-fold coordination complexes composed of both solvent molecules and counterions

Solvation of Zn2+ ion in 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids: a molecular dynamics and X-ray absorption study

Molecular dynamics simulations and X-ray absorption spectroscopy were employed to study Zn²⁺ ions in [C_nmim][Tf₂N] (n = 2, 4).

Operando XAFS and XRD Study of a Prussian Blue Analogue Cathode Material: Iron Hexacyanocobaltate

The reversible electrochemical lithiation of potassium iron hexacyanocobaltate (FeCo) was studied by operando X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS) assisted by chemometric techniques. In this way, it was possible to follow the system dynamics and retrieve structural and electronic transformations along cycling at both Fe and Co sites. These analyses confirmed that FeCo features iron as the main electroactive site. Even though the release of potassium ions causes a local disorder around the iron site, the material exhibits an excellent structural stability during the alkali ion deinsertion/insertion processes. An independent but interrelated analysis approach offers a good strategy for data treatment and provides a time-resolved picture of the studied system.

Thermodynamic stability and structure in aqueous solution of the [Cu(PTA)4]+ complex (PTA = aminophosphine‑1,3,5‑triaza‑7‑phosphaadamantane)

The chemistry of copper(I) with water-soluble phosphines is an emergent area of study which has the objective of finding ligands that stabilize copper in its lower oxidation state. Cu(I) has been found relevant in the mechanism of copper transports into cells, and the accessibility of this oxidation state has implications in oxidative stress processes. For these reasons the possibility to deal with stable, water soluble copper(I) is an attractive approach for devising new biologically relevant metal-based drugs and chelating agents. Here we present the X-ray absorption spectroscopy (XAS) and UV-visible spectrophotometric study of the [Cu(PTA)₄]BF₄ complex (PTA = aminophosphine‑1,3,5‑triaza‑7‑phosphaadamantane). In particular, we have studied the stability of the [Cu(PTA)_n]⁺ species (n = 2-4) in aqueous medium, and their speciation as a function of the total [Cu(PTA)₄]BF₄ concentration by means of competitive UV-visible spectrophotometric titrations using metallochromic indicators. Also, the structure in solution of the Cu(I)/PTA species and the nature of the first coordination sphere of the metal were studied by transformed XAS. Both techniques allowed to study samples with total [Cu(PTA)₄]BF₄ concentration down to 68-74 μM, possibly relevant for biological applications. Overall, our data suggest that the [Cu(PTA)_n]⁺ species are stable in solution, among which [Cu(PTA)₂]⁺ has a remarkable thermodynamic stability. The tendency of this last complex to form adducts with N-donor ligands is demonstrated by the spectrophotometric data. The biological relevance of PTA towards Cu(I), especially in terms of chemotreatments and chelation therapy, is discussed on the basis of the speciation model the Cu(I)/PTA system.

A biological perspective towards a standard for information exchange and reporting in XAS

The complex structural landscape of biological samples and their sensitivity to X-ray exposure leads to specific challenges in biological X-ray absorption spectroscopy (bio-XAS) research, which in turn has necessitated standardization of various aspects of bio-XAS data measurement, analysis and interpretation. The bio-XAS community is therefore well suited for the development of a data-reporting standard with the specific aim of creating a feedback loop for improving/standardizing data analysis protocols and optionally to make published data available to collaborators/researchers in a meaningful and quantitative format. The XIF (XAFS information file) reporting format presented here contains key experimental and analysis parameters, useful in developing a consistent platform for bio-XAS research worldwide. Such a reporting standard, enforced by the user community and publishing groups alike, can be an important step towards the standardization of data measurement and analysis techniques in bio-XAS.

Propagation of uncertainty in experiment: structures of Ni (II) coordination complexes

Accurate experimental XAFS (X-ray absorption fine-structure) data including uncertainties are required during analysis for valid comparison of results and conclusions of hypothesis testing on structural determinations. Here an approach is developed to investigate data without standard interpolation of experimental data and with minimal loss of information content in the raw data. Nickel coordination complexes bis(i-n-propylsalicylaldiminato)nickel(II) (i-pr) and bis(N-n-propylsalicylaldiminato)nickel(II) (n-pr) are investigated. The additional physical insight afforded by the correct propagation of experimental uncertainty is used to determine newly refined structures for the innermost co-ordination shell. Two sets of data are investigated for each complex; one optimized for high point accuracy and one optimized for high point density. Clearly both are important and in this investigation the quality of the physical insight from each is directly provided by measured and propagated uncertainties to fairly represent the relevant accuracies. The results provide evidence for an approximate tetrahedral geometry for the i-pr Ni complex that is more symmetric than previously concluded, with our high point accuracy data yielding ligand lengths of 2.017 ± 0.006 Å and 2.022 ∓ 0.006 Å for Ni-N and Ni-O bonds, respectively, and an even more skewed square-planar (i.e. rhombohedral) arrangement for the n-pr complex with corresponding bond lengths of 2.133 ± 0.004 Å and 1.960 ∓ 0.003 Å. The ability to distinguish using hypothesis testing between the subtle differences in XAFS spectra arising from the approximate local tetrahedral and square-planar geometries of the complexes is also highlighted. The effect of standard interpolation on experimental XAFS spectra prior to fitting with theoretical model structures is investigated. While often performed as a necessary step for Fourier transformation into position space, this will nonetheless skew the fit away from actual data taken, and fails to preserve the information content within the data uncertainty. The artificial effects that interpolation imposes on χr2 are demonstrated. Finally, a method for interpolation is introduced which locally preserves the χr2 and thus information content, when a regular grid is required, e.g for further analysis in r-space.

On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents

The structures of the N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), and N,N-dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that equilibria between different coordination numbers and geometries exist in these systems. Structural information of the alkali, alkaline earth, and selected transition metal and lanthanoid(iii) ions, and the halide ions in water, methanol, ethanol, dimethylsulfoxide, formamide, dmf and dma has been combined with previously reported standard partial molar volumes, V0. The ionic radii and charge densities (charge/ionic volume), and corresponding V0 values have been used to gain information on the relationship between structural and volumetric properties. For the structure-breaking ions, i.e. the alkali metal and halide ions, there is an almost linear relationship between the ionic radius and V0. On the other hand, for the structure-making ions, here the alkaline earth, transition metal and lanthanoid(iii) ions, a linear relationship is observed between the charge density and V0. Solvents with a well-defined bulk structure through hydrogen bonding, specifically, water, methanol and ethanol, will be more contracted through solvation than aprotic solvents, as the space between the solvent molecules is lost as a result of the hydrogen bonding. In this respect, methanol stands out as the most compressed solvent participating in solvation compared to its bulk structure.