Oxygen K-edge X-ray Research Articles

Formation mechanism of iron-catechol complexes in the colored periostracum of Corbicula spp.

The shell color of Corbicula clams, which are globally distributed, is roughly divided into yellowish and blackish depending on the environmental conditions of the sediment. The formation of an iron-L-3,4-dihydroxyphenylalanine (DOPA) complex in a thin organic layer, called the periostracum, on a calcareous layer causes the blackening of the clamshell. However, the iron-DOPA complex formation mechanism is unclear. To reveal how the iron is transported from the aquatic environment to the periostracum, cross-sectional analyses of the shell were conducted using an electron probe microanalyzer (EPMA) and Raman spectroscopy to investigate the distribution and structure of iron in the shell. Iron was only present in the periostracum, excluding deposition, and all iron was in the form of an iron-DOPA complex. Attenuated total reflection infrared spectroscopy and oxygen K-edge X-ray absorption fine structure spectroscopy revealed that the molecular structure of the native periostracum is independent of shell color. These results indicate that dissolved iron-organic complexes diffuse from the aqueous environment to the periostracum, forming iron-DOPA complex through ligand exchange. Because the iron-DOPA complex color depends on the pH, the shell color can serve as a historical indicator of the shell's growth environment.

Atomistic Interpretation of the Oxygen K-Edge X-ray Absorption Spectra of Layered Li-Ion Battery Cathode Materials.

Core loss spectroscopies can provide powerful element-specific insight into the redox processes occurring in Li-ion battery cathodes, but this requires an accurate interpretation of the spectral features. Here, we systematically interpret oxygen K-edge core loss spectra of layered lithium transition-metal (TM) oxides (LiMO2, where M = Co, Ni, Mn) from first principles using density-functional theory (DFT). Spectra are simulated using three exchange-correlation functionals, comprising the generalized gradient approximation (GGA) functional PBE, the DFT-PBE + Hubbard U method, and the meta-GGA functional rSCAN. In general, rSCAN provides a better match to experimentally observed excitation energies of spectral features compared to both PBE and PBE + U, especially at energies close to the main edge. Projected density of states of core-hole calculations show that the O orbitals are better described by rSCAN. Hybridization, structural distortions, chemical composition, and magnetism significantly influence the spectra. The O K-edge spectrum of LiNiO2 obtained using rSCAN shows a closer match to the experimental X-ray absorption spectroscopy (XAS) when derived from a simulation cell which includes a Jahn-Teller distortion, showing that the DFT-calculated pre-edge feature contains information about not only chemical species but also geometric distortion. Core loss spectra derived from DFT can also differentiate between materials with the same structure and magnetic configuration but comprising different TMs; these differences are comparable to those observed in experimental XAS from the same materials. This foundational work helps establish the extent to which DFT can be used to bridge the interpretation gap between experimental spectroscopic signatures and ab initio methods describing complex battery materials, such as lithium nickel manganese cobalt oxides.

Exact-Two-Component Complete Active Space Method with Variational Treatment of Magnetic Field and Spin-Orbit Coupling: Application to X-ray Magnetic Circular Dichroism Spectroscopy.

We introduce an exact-two-component complete active space self-consistent-field (X2C-CASSCF) method formulated under the restricted-magnetic-balance condition. This framework allows for the nonperturbative treatment of static magnetic fields using gauge-including atomic orbitals (GIAOs). The GIAO-X2C-CASSCF methodology effectively captures all microstates within the same 2J + 1-degenerate manifold and their splitting in a static magnetic field, which are not accessible through single-reference-based methods. We also present mathematical recursive expressions for evaluating one-electron relativistic integrals by using GIAOs in the presence of a finite magnetic field. Benchmark studies include oxygen and nitrogen K-edge X-ray magnetic circular dichroism spectroscopy (XMCD) for closed-shell organic compounds, as well as L-edge XMCD spectroscopy for the high-spin open-shell transition metal ion Mn2+ and the tetrahedral Mn(II)O46- complex.

Probing Isolated Water Molecules in Aqueous Acetonitrile Solutions Using Oxygen K-Edge X-ray Absorption Spectroscopy.

Oxygen K-edge X-ray absorption spectroscopy (XAS) of an aqueous acetonitrile solution exhibited a sharp peak at approximately 537 eV, which was similar to that of water vapor and was not observed in liquid water. The inner-shell spectra of isolated water molecules and water clusters of different sizes surrounded by acetonitrile molecules were obtained by extracting these water structures from the liquid structures of aqueous acetonitrile solutions, as calculated using molecular dynamics simulations. The sharp peak profiles of the O K-edge XAS spectra were derived not from water clusters but from isolated water molecules surrounded by acetonitrile molecules. The present study proposes that isolated water molecules are easily formed in aqueous acetonitrile solutions and that the electronic structures of the isolated water molecules can be analyzed using O K-edge XAS spectra, which separates the contributions of small water clusters.

Are 4f-Orbitals Engaged in Covalent Bonding Between Lanthanides and Triphenylphosphine Oxide? An Oxygen K-Edge X-ray Absorption Spectroscopy and Density Functional Theory Study.

The bonding covalency between trivalent lanthanides (Ln = La, Pr, Nd, Eu, Gd) and triphenylphosphine oxide (TPPO) is studied by X-ray absorption spectra (XAS) and density functional theory (DFT) calculations on the LnCl3(TPPO)3 complexes. The O, P, and Cl K-edge XAS for the single crystals of LnCl3(TPPO)3 were collected, and the spectra were interpreted based on DFT calculations. The O and P K-edge XAS spectra showed no significant change across the Ln series in the LnCl3(TPPO)3 complexes, unlike the Cl K-edge XAS spectra. The experimental O K-edge XAS spectra suggest no mixing between the Ln 4f- and the O 2p-orbitals in the LnCl3(TPPO)3 complexes. DFT calculations indicate that the amount of the O 2p character per Ln-O bond is less than 0.1% in the Ln 4f-based orbitals in all of the LnCl3(TPPO)3 complexes. The experimental spectra and theoretical calculations demonstrate that Ln 4f-orbitals are not engaged in the covalent bonding of lanthanides with TPPO, which contrasts the involvement of U 5f-orbitals in covalent bonding in the UO2Cl2(TPPO)2 complex. Results in this work reinforce our previous speculation that bonding covalency is potentially responsible for the extractability of monodentate organophosphorus ligands toward metal ions.

Mechanism of poly(N-isopropylacrylamide) cononsolvency in aqueous methanol solutions explored via oxygen K-edge X-ray absorption spectroscopy.

The cononsolvency mechanism of poly(N-isopropylacrylamide) (PNIPAM), dissolving in pure methanol (MeOH) and water (H2O) but being insoluble in MeOH-H2O mixtures, was investigated by O K-edge X-ray absorption spectroscopy (XAS). The cononsolvency emerges from the aggregation of PNIPAM with MeOH clusters, leading to the collapse of the hydrophobic hydration of PNIPAM.

Exploring the impact of ions on oxygen K-edge X-ray absorption spectroscopy in NaCl solution using the GW-Bethe-Salpeter-equation approach.

X-ray absorption spectroscopy (XAS) is a powerful experimental tool to probe the local structure in materials with the core hole excitations. Here, the oxygen K-edge XAS spectra of the NaCl solution and pure water are computed by using a recently developed GW-Bethe-Salpeter equation approach, based on configurations modeled by path-integral molecular dynamics with the deep-learning technique. The neural network is trained on abinitio data obtained with strongly constrained and appropriately normed density functional theory. The observed changes in the XAS features of the NaCl solution, compared to those of pure water, are in good agreement between experimental and theoretical results. We provided detailed explanations for these spectral changes that occur when NaCl is solvated in pure water. Specifically, the presence of solvating ion pairs leads to localization of electron-hole excitons. Our theoretical XAS results support the theory that the effects of the solvating ions on the H-bond network are mainly confined within the first hydration shell of ions, however beyond the shell the arrangement of water molecules remains to be comparable to that observed in pure water.

Engineering Sub-Nanometer Hafnia-Based Ferroelectrics to Break the Scaling Relation for High-Efficiency Piezocatalytic Water Splitting.

Reversible control of ferroelectric polarization is essential to overcome the heterocatalytic kinetic limitation. This can be achieved by creating a surface with switchable electron density; however, owing to the rigidity of traditional ferroelectric oxides, achieving polarization reversal in piezocatalytic processes remains challenging. Herein, sub-nanometer-sized Hf0.5 Zr0.5 O2 (HZO) nanowires with a polymer-like flexibility are synthesized. Oxygen K-edge X-ray absorption spectroscopy and negative spherical aberration-corrected transmission electron microscopy reveal an orthorhombic (Pca21 ) ferroelectric phase of the HZO sub-nanometer wires (SNWs). The ferroelectric polarization of the flexible HZO SNWs can be easily switched by slight external vibration, resulting in dynamic modulation of the binding energy of adsorbates and thus breaking the "scaling relationship" during piezocatalysis. Consequently, the as-synthesized ultrathin HZO nanowires display superb water-splitting activity, with H2 production rate of 25687µmolg-1 h-1 under 40kHz ultrasonic vibration, which is 235and 41times higher than those of non-ferroelectric hafnium oxides and rigid BaTiO3 nanoparticles, respectively. More strikingly, the hydrogen production rates can reach 5.2µmolg-1 h-1 by addition of stirring exclusively.

Site selective analysis of water in hydrogen bond network of aqueous dimethyl sulfoxide solutions by oxygen K-edge X-ray absorption spectroscopy

Hydrogen bond (HB) network in aqueous dimethyl sulfoxide (DMSO) solutions at different concentrations has been observed by oxygen K-edge X-ray absorption spectroscopy with a site selective analysis that separates donor and acceptor sites of water (H2O), where the S=O π* peak in DMSO reflects the donor site of H2O and the 4a1 peak in H2O reflects the acceptor site of H2O, respectively. From the comparison of the XAS experiments with molecular dynamics simulations and inner-shell quantum chemical calculations, we have revealed that the HB network in aqueous DMSO solutions is influenced with not only the HB interaction of the S=O group with the donor site of H2O but also the dipole interaction of the S atom with the acceptor site of H2O, which breaks the HB network between H2O. Four concentration regions were found in the HB network of aqueous DMSO solutions, which would be related to the anomalies of physical properties and solvent effects in chemical and biological reactions.

Hole Dynamics in Photoexcited Hematite Studied with Femtosecond Oxygen K-edge X-ray Absorption Spectroscopy

Hematite (α-Fe2O3) is a photoelectrode for the water splitting process because of its relatively narrow bandgap and abundance in the earth’s crust. In this study, the photoexcited state of a hematite thin film was investigated with femtosecond oxygen K-edge X-ray absorption spectroscopy (XAS) at the PAL-XFEL in order to follow the dynamics of its photoexcited states. The 200 fs decay time of the hole state in the valence band was observed via its corresponding XAS feature.

Involvement of 5f Orbitals in the Covalent Bonding between the Uranyl Ion and Trialkyl Phosphine Oxide: Unraveled by Oxygen K-Edge X-ray Absorption Spectroscopy and Density Functional Theory.

Monodentate organophosphorus ligands have been used for the extraction of the uranyl ion (UO22+) for over half a century and have exhibited exceptional extractability and selectivity toward the uranyl ion due to the presence of the phosphoryl group (O═P). Tributyl phosphate (TBP) is the extractant of the world-renowned PUREX process, which selectively recovers uranium from spent nuclear fuel. Trialkyl phosphine oxide (TRPO) shows extractability toward the uranyl ion that far exceeds that for other metal ions, and it has been used in the TRPO process. To date, however, the mechanism of the high affinity of the phosphoryl group for UO22+ remains elusive. We herein investigate the bonding covalency in a series of complexes of UO22+ with TRPO by oxygen K-edge X-ray absorption spectroscopy (XAS) in combination with density functional theory (DFT) calculations. Four TRPO ligands with different R substituents are examined in this work, for which both the ligands and their uranyl complexes are crystallized and investigated. The study of the electronic structure of the TRPO ligands reveals that the two TRPO molecules, irrespective of their substituents, can engage in σ- and π-type interactions with U 5f and 6d orbitals in the UO2Cl2(TRPO)2 complexes. Although both the axial (Oyl) and equatorial (Oeq) oxygen atoms in the UO2Cl2(TRPO)2 complexes contribute to the X-ray absorption, the first pre-edge feature in the O K-edge XAS with a small intensity is exclusively contributed by Oeq and is assigned to the transition from Oeq 1s orbitals to the unoccupied molecular orbitals of 1b1u + 1b2u + 1b3u symmetries resulting from the σ- and π-type mixing between U 5f and Oeq 2p orbitals. The small intensity in the experimental spectra is consistent with the small amount of Oeq 2p character in these orbitals for the four UO2Cl2(TRPO)2 complexes as obtained by Mulliken population analysis. The DFT calculations demonstrate that the U 6d orbitals are also involved in the U-TRPO bonding interactions in the UO2Cl2(TRPO)2 complexes. The covalent bonding interactions between TRPO and UO22+, especially the contributions from U 5f orbitals, while appearing to be small, are sufficiently responsible for the exceptional extractability and selectivity of monodentate organophosphorus ligands for the uranyl ion. Our results provide valuable insight into the fundamental actinide chemistry and are expected to directly guide actinide separation schemes needed for the development of advanced nuclear fuel cycle technologies.

Oxygen K-edge X-ray absorption spectra of liquids with minimization of window contamination.

Oxygen K-edge X-ray absorption spectroscopy is used routinely to study a range of solid materials. However, liquid samples are studied less frequently at the oxygen K-edge due to the combined challenges of high-vacuum conditions and oxygen contamination of window materials. A modular sample holder design with a twist-seal sample containment system that provides a simple method to encapsulate liquid samples under high-vacuum conditions is presented. This work shows that pure silicon nitride windows have lower oxygen contamination than both diamond- and silicon-rich nitride windows, that the levels of oxygen contamination are related to the age of the windows, and provides a protocol for minimizing the background oxygen contamination. Acid-washed 100 nm-thick silicon nitride windows were found to give good quality oxygen K-edge data on dilute liquid samples.

Temperature dependent structural, electrical and electronic investigation of VO2 (B) thin film

Vanadium dioxide can exist in several polymorphs and among these the layered polymorph VO2 (B) with monoclinic symmetry has numerous applications. In this work, VO2 (B) phase thin film was prepared on quartz substrate via sputtering technique and its temperature dependent structural, electrical and electronic properties were investigated. We have witnessed a broader structural phase transition around 220 K; which encounter significant changes in the lattice constants yet the monoclinic symmetry is retained over a temperature range from 100 K to 380 K. Temperature dependent resistance measurement also exhibited a semi-metal to insulator like transition near 220 K displaying over 2 order of magnitude change in resistance across the transition. Small changes in the oxygen K-edge x-ray absorption spectrum were seen with change in temperature. At low temperature, an additional peak (d|| band) has emerged in the XAS spectra at energy higher than the σ* peak. The appearance of d|| band density of states is associated to the enhanced electron correlation effects driven by the localization of V–V pair's interactions at low temperature.

Publisher’s Note

Abstract Vanadium dioxide can exist in several polymorphs and among these the layered polymorph VO2 (B) with monoclinic symmetry has numerous applications. In this work, VO2 (B) phase thin film was prepared on quartz substrate via sputtering technique and its temperature dependent structural, electrical, and electronic properties were investigated. We have witnessed a broader structural phase transition around 220 K; which encounter significant changes in the lattice constants yet the monoclinic symmetry is retained over a temperature range from 100 K to 380 K. Temperature dependent resistance measurement also exhibited a semi-metal to insulator like transition near 220K displaying over 2 order of magnitude change in resistance across the transition. Small changes in the oxygen K-edge x-ray absorption spectrum were seen with change in temperature. At low temperature, an additional peak (d|| band) has emerged in the XAS spectra at energy higher than the σ* peak. The appearance of d|| band density of states is associated with the enhanced electron correlation effects driven by the localization of V–V pair's interactions at low temperature.

Role of Oxygen Vacancy Sites on the Temperature-Dependent Photoluminescence of SnO2 Nanowires

The role of oxygen vacancies in temperature-dependent photoluminescence of SnO2 nanowires was investigated by X-ray absorption spectroscopy. Two types of oxygen vacancies are present in the nanowires: at out-of-plane sites and at in-plane sites; both play crucial roles in the temperature dependence of the photoluminescence. Oxygen vacancies at in-plane sites participate in photon emission at low temperature, whereas those at out-of-plane sites result in photoluminescence at room temperature. Accordingly, the luminescence color changes from orange (630 nm, 1.93 eV) to green (515 nm, 2.4 eV) at 100 K. The color change is accompanied with a notable change in the oxygen K-edge X-ray absorption spectra. The scanning transmission X-ray microscopy results indicate that more oxygen vacancies at in-plane sites are present in the surface region than in the bulk region, whereas more oxygen vacancies at out-of-plane sites are present in the bulk region than in the surface region. Overall, the results demonstrate that oxygen-vacancy-mediated fluorescence properties of SnO2 nanowires are temperature-dependent; i.e., the photoluminescence mechanisms of the nanowires are mediated by oxygen vacancies at different sites, and the bicolor fluorescence originates from charge transfer between the states.

Aqueous-phase behavior of glyoxal and methylglyoxal observed with carbon and oxygen K-edge X-ray absorption spectroscopy

Abstract. Glyoxal (CHOCHO) and methylglyoxal (CH3C(O)CHO) are well-known components of atmospheric particles and their properties can impact atmospheric chemistry and cloud formation. To get information on their hydration states in aqueous solutions and how they are affected by the addition of inorganic salts (sodium chloride (NaCl) and sodium sulfate (Na2SO4)), we applied carbon and oxygen K-edge X-ray absorption spectroscopy (XAS) in transmission mode. The recorded C K-edge spectra show that glyoxal is completely hydrated in the dilute aqueous solutions, in line with previous studies. For methylglyoxal, supported by quantum chemical calculations we identified not only C–H, C=O and C–OH bonds, but also fingerprints of C–OH(CH2) and C=C bonds. The relatively low intensity of C=O transitions implies that the monohydrated form of methylglyoxal is not favored in the solutions. Instead, the spectral intensity is stronger in regions where products of aldol condensation and enol tautomers of the monohydrates contribute. The addition of salts was found to introduce only very minor changes to absorption energies and relative intensities of the observed absorption features, indicating that XAS in the near-edge region is not very sensitive to these intermolecular organic–inorganic interactions at the studied concentrations. The identified structures of glyoxal and methylglyoxal in an aqueous environment support the uptake of these compounds to the aerosol phase in the presence of water and their contribution to secondary organic aerosol formation.

Oxygen K-edge X-ray Absorption Spectra.

We review oxygen K-edge X-ray absorption spectra of both molecules and solids. We start with an overview of the main experimental aspects of oxygen K-edge X-ray absorption measurements including X-ray sources, monochromators, and detection schemes. Many recent oxygen K-edge studies combine X-ray absorption with time and spatially resolved measurements and/or operando conditions. The main theoretical and conceptual approximations for the simulation of oxygen K-edges are discussed in the Theory section. We subsequently discuss oxygen atoms and ions, binary molecules, water, and larger molecules containing oxygen, including biomolecular systems. The largest part of the review deals with the experimental results for solid oxides, starting from s- and p-electron oxides. Examples of theoretical simulations for these oxides are introduced in order to show how accurate a DFT description can be in the case of s and p electron overlap. We discuss the general analysis of the 3d transition metal oxides including discussions of the crystal field effect and the effects and trends in oxidation state and covalency. In addition to the general concepts, we give a systematic overview of the oxygen K-edges element by element, for the s-, p-, d-, and f-electron systems.

Electronic structure of dense solid oxygen from insulator to metal investigated with X-ray Raman scattering

Electronic structures of dense solid oxygen have been investigated up to 140 GPa with oxygen K-edge X-ray Raman scattering spectroscopy with the help of ab initio calculations based on density functional theory with semilocal metageneralized gradient approximation and nonlocal van der Waals density functionals. The present study demonstrates that the transition energies (Pi*, Sigma*, and the continuum) increase with compression, and the slopes of the pressure dependences then change at 94 GPa. The change in the slopes indicates that the electronic structure changes at the metallic transition. The change in the Pi* and Sigma* bands implies metallic characteristics of dense solid oxygen not only in the crystal a-b plane but also parallel to the c axis. The pressure evolution of the spectra also changes at ∼40 GPa. The experimental results are qualitatively reproduced in the calculations, indicating that dense solid oxygen transforms from insulator to metal via the semimetallic transition.

Hydroxyl-Group Identification Using O K-Edge XAFS in Porous Glass Fabricated by Hydrothermal Reaction and Low-Temperature Foaming.

Porous glass was prepared by the hydrothermal reaction of sodium borosilicate glass, and oxygen-ion characterization was used to identify the hydroxyl groups in its surface area. A substantial amount of “water” was introduced into the ionic structure as either OH− groups or H2O molecules through the hydrothermal reaction. When the hydrothermally treated glass was reheated at normal pressures, a porous structure was formed due to the low-temperature foaming resulting from the evaporation of H2O molecules and softening of the glass. Although it was expected that the OH− groups would remain in the porous glass, their distribution required clarification. Oxygen K-edge X-ray absorption fine structure (XAFS) spectroscopy enables the bonding states of oxygen ions in the surface area and interior to be characterized using the electron yield (EY) and fluorescence yield (FY) mode, respectively. The presence of OH− groups was detected in the O K-edge XAFS spectrum of the porous glass prepared by hydrothermal reaction with a corresponding pre-edge peak energy of 533.1 eV. In addition, comparison of the XAFS spectra obtained in the EY and FY modes revealed that the OH− groups were mainly distributed in the surface area (depths of several tens of nanometers).

Density functional investigation of structural, electronic, optical and thermodynamic properties of Zn1−xBexO semiconductor

Based on the first principles calculations using a full potential linearized augmented plane wave (FP-LAPW) method in the modified Becke–Johnson (mBJ) approximation, we calculated the electronic, optical and thermodynamic properties of $$ {\text{Zn}}_{1 - x} {\text{Be}}_{x} {\text{O}} $$ for different Be concentrations ( $$ 0 \le x \le 1 $$ ). The calculated structure of $$ {\text{Zn}}_{1 - x} {\text{Be}}_{x} {\text{O}} $$ for $$ x = 0.25, x = 0.5\;{\text{and}}\;x = 0.75 $$ was changed compared to the end structures ( $$ x = 0\;{\text{and}}\;x = 1 $$ ) and passed from wurtzite to orthorhombic structures, while most of the previous works show that the structures of ZnO remained unchanged after doping with Be. Our result shows that the orthorhombic lattices have lower formation energies than wurtzite. The calculated band structures show an increase in energy bandgap with increasing Be concentrations and present a gap bowing close to 10 eV. The electronic structure was studied by oxygen k-edge X-ray emission (XES) and X-ray absorption (XAS). Moreover, the calculated absorption coefficient indicates that the $$ {\text{Zn}}_{1 - x} {\text{Be}}_{x} {\text{O}} $$ exhibit more interesting properties in UV region main absorption. The thermodynamic stability of these compounds has also been well studied and confirms well the previous experimental results. The calculations show that if the Be doping quantity increases, the doping system absorption spectrum blueshift becomes more significant, the energy loss peak moves towards the direction of high energy and the plasmon frequency $$ \omega_{\text{p}} $$ become stronger in the case of BeO.