K-edge Near-edge X-ray Absorption Research Articles

Characterization of Bisphosphonate Hydrate Crystals by Phosphorus K-Edge X-Ray Absorption Near-Edge Structure Spectroscopy.

X-ray absorption near-edge structure (XANES) spectroscopy is a new method for the characterization of active pharmaceutical ingredients. XANES spectra show unique features depending on the electronic states of the X-ray absorbing elements and provide information about the chemical environment that affects the electronic states. In this study, six bisphosphonate hydrate crystals were used to investigate, for the first time, how the phosphorus K-edge XANES spectra are affected by the interatomic interactions and charged states of phosphonate moieties. Phosphorus K-edge XANES spectra showed several differences among the bisphosphonates. In particular, the chlorine atoms covalently bonded near the phosphonate and the number of electric charges of the phosphonate moieties seemed to have large effects on peak shape in XANES spectra. Unique shapes of the XANES spectra demonstrated that differences in interactions at the oxygen atoms of the phosphonate moieties could change the shapes of the XANES spectrum peaks to the extent that each material was distinguished based on the spectra. Since slight differences in interatomic interactions and charged states lead to variations in the spectra, XANES spectroscopy could be widely applied as the fingerprint method to evaluate active pharmaceutical ingredients.

Generalization of One-Center Nonorthogonal Configuration Interaction Singles to Open-Shell Singlet Reference States: Theory and Application to Valence-Core Pump-Probe States in Acetylacetone.

We formulate a one-center nonorthogonal configuration interaction singles (1C-NOCIS) theory for the computation of core excited states of an initial singlet state with two unpaired electrons. This model, which we refer to as 1C-NOCIS two-electron open-shell (2eOS), is appropriate for computing the K-edge near-edge X-ray absorption spectra (NEXAS) of the valence excited states of closed-shell molecules relevant to pump-probe time-resolved (TR) NEXAS experiments. With the inclusion of core-hole relaxation effects and explicit spin adaptation, 1C-NOCIS 2eOS requires mild shifts to match experiment, is free of artifacts due to spin contamination, and can capture the high-energy region of the spectrum beyond the transitions into the singly occupied molecular orbitals (SOMOs). Calculations on water and thymine illustrate the different key features of excited-state NEXAS, namely, the core-to-SOMO transitions as well as shifts and spin-splittings in the transitions analogous to those of the ground state. Simulations of the TR-NEXAS of acetylacetone after excitation to its π → π* singlet excited state at the carbon K-edge, an experiment carried out recently, showcase the ability of 1C-NOCIS 2eOS to efficiently simulate NEXAS based on nonadiabatic molecular dynamics simulations.

Characterization of Ambroxol and Its Hydrochloride Salt Crystals by Bromine K-Edge X-Ray Absorption Near-Edge Structure Spectroscopy and X-Ray Crystal Structure Analysis.

Polymorphic crystals of ambroxol, forms I and II, and form A ambroxol hydrochloride crystals were characterized with bromine K-edge X-ray absorption near-edge structure (XANES) spectroscopy and single-crystal X-ray structure analysis. The XANES spectra had unique shapes depending on the crystal forms. Refined single-crystal structures revealed different interatomic interactions around bromine atoms, such as C-H…Br and N-H…Br hydrogen bonds, Br…O halogen bonds, and N-H…π interactions. Differences in these weak interactions could affect the electronic states of the bromines, resulting in differences in the XANES spectra. The results demonstrated that weak non-conventional interatomic interactions could alter the shape of XANES spectra. Hence, the spectra could be used for evaluating polymorphs of active pharmaceutical ingredients.

Chemical speciation of phosphorus in farmland soils and soil aggregates around mining areas

Phosphorus (P) speciation determines its bioavailability, mobility, and environmental risk in soils. Farmland soils around mining areas are worldwide distributed, yet the P speciation in such soils remains poorly understood. In this study, we determined the P speciation in the farmland soils and soil aggregates around mining areas from China and evaluated their relationship with soil pH and Fe/Al fractions using chemical extraction, P K-edge X-ray absorption near-edge (XANES) spectroscopy, and correlation analysis. Chemical extraction revealed that soil P was dominated by inorganic P (Pi) (68.0 – 82.5%) largely associated with pedogenic Fe/Al oxides (43.4% – 94.8%). The P was mainly adsorbed and occluded by Fe/Al oxides in acidic soils, while predominantly existed as Ca-P and occluded species in alkaline soils. The presence of heavy metals appeared to have no significant effect on P speciation in these soils. Compared with the macroaggregates, the available P, total P, and their ratio all increased dramatically in the soil colloids (< 0.002 mm) due to the accumulation of Fe/Al oxides. The XANES analysis indicated that the P speciation in the acidic soils and soil aggregates was dominated by Fe-P, followed by Al-P, and little Ca-P; in contrast, the proportions of Ca-P increased but Fe-P decreased in the alkaline soils and soil aggregates. Compared with the macroaggregates, the proportions of Fe-P increased while Ca-P decreased in the soil colloids. Correlation analysis indicated that amorphous Al and isomorphic substitution Al played critical roles in P immobilization by pedogenic Fe/Al oxides. These new insights into the P speciation are essential for environmental risk assessment and efficient utilization of P in the farmland soils.

Analytical Method for Rubber Materials Using Sulfur K-edge NEXAFS and Its Application

Here, we develop a technique for curve-fitting of the sulfur K-edge near-edge X-ray absorption fine structure (NEXAFS) to analyze the crosslinked structure of vulcanized rubber based on the chemical state of sulfur. The proposed analytical method provides the sulfur chain length (Sx), crosslink density, and sulfur oxide content simultaneously, and it is highly sensitive for the analysis of the depth direction. Furthermore, we verify the aging mechanism of the crosslinked structure using this analytical method. It is found that the sulfur chains, shortened and oxidized by heat aging at 120°C, can cause scission of the S—C bond, thereby decreasing the crosslink density. Long sulfur chains are more susceptible to oxidation, which rapidly decreases the sulfur chain length (Sx) and, in turn, the crosslink density compared with short sulfur chains. By comparing the heat-aging dependence between the S—C bond and S100, it is found that the styrene-butadiene rubber polymer surface can form the C—C crosslink. We present the aging mechanism of the crosslinked structure and establish NEXAFS as a useful analytical method for rubber materials.

Long-range ordered porous carbons produced from C60.

Carbon structures with covalent bonds connecting C60 molecules have been reported1-3, but their production methods typically result in very small amounts of sample, which restrict the detailed characterization and exploration necessary for potential applications. We report the gram-scale preparation of a new type of carbon, long-range ordered porous carbon (LOPC), from C60 powder catalysed by α-Li3N at ambient pressure. LOPC consists of connected broken C60 cages that maintain long-range periodicity, and has been characterized by X-ray diffraction, Raman spectroscopy, magic-angle spinning solid-state nuclear magnetic resonance spectroscopy, aberration-corrected transmission electron microscopy and neutron scattering. Numerical simulations based on a neural network show that LOPC is a metastable structure produced during the transformation from fullerene-type to graphene-type carbons. At a lower temperature, shorter annealing time or by using less α-Li3N, a well-known polymerized C60 crystal forms owing to the electron transfer from α-Li3N to C60. The carbon K-edge near-edge X-ray absorption fine structure shows a higher degree of delocalization of electrons in LOPC than in C60(s). The electrical conductivity is 1.17 × 10-2 S cm-1 at room temperature, and conduction at T < 30 K appears to result from a combination of metallic-like transport over short distances punctuated by carrier hopping. The preparation of LOPC enables the discovery of other crystalline carbons starting from C60(s).

Integrated Experimental and Computational K-Edge X-ray Absorption Near-Edge Structure Analysis of Vanadium Catalysts

Integrated Experimental and Computational K-Edge X-ray Absorption Near-Edge Structure Analysis of Vanadium Catalysts

Relativistic Effects in Modeling the Ligand K-Edge X-ray Absorption Near-Edge Structure of Uranium Complexes.

Accurate modeling of the complex electronic structure of actinide complexes requires full inclusion of relativistic effects. In this study, we examine the effect of explicit inclusion of spin-orbit coupling (SOC) versus scalar relativistic effects on the predicted spectra for heavy-element complexes. In this study, we employ a relativistic two-component Hamiltonian in the X2C form with all of the electrons in the system being considered explicitly to compare and contrast with previous studies that included the relativistic effects by means of relativistic effective core potentials (RECPs). A few uranium complexes are chosen as model systems. Comparison of the computed Cl K-edge X-ray absorption spectra with experimental data shows significantly improved agreement when a variational relativistic treatment of SOC is performed. In particular, we note the importance of SOC terms to obtain not only correct transition energies but also correct intensities for these heavy-element complexes because of the redistribution of ligand bonding character among the valence MOs. While RECPs generally agree well with all-electron scalar relativistic calculations, there are some differences in the predicted spectra of open-shell systems. These methods are still suitable for broad application to analyze the qualitative nature of transitions in X-ray absorption spectra, but caution is recommended for quantitative analysis, as SOC can be non-negligible for both open- and closed-shell heavy-element systems.

Mediation of arsenic mobility by organic matter in mining-impacted sediment from sub\u2010Arctic lakes: implications for environmental monitoring in a warming climate

Arsenic (As) is commonly sequestered at the sediment–water interface (SWI) in mining-impacted lakes through adsorption and/or co-precipitation with authigenic iron (Fe)-(oxy)hydroxides or sulfides. The results of this study demonstrate that the accumulation of organic matter (OM) in near-surface sediments also influences the mobility and fate of As in sub-Arctic lakes. Sediment gravity cores, sediment grab samples, and porewaters were collected from three lakes downstream of the former Tundra gold mine, Northwest Territories, Canada. Analysis of sediment using combined micro-X-ray fluorescence/diffraction, K-edge X-ray Absorption Near-Edge Structure (XANES), and organic petrography shows that As is associated with both aquatic (benthic and planktonic alginate) and terrestrially derived OM (e.g., cutinite, funginite). Most As is hosted by fine-grained Fe-(oxy)hydroxides or sulfide minerals (e.g., goethite, orpiment, lepidocrocite, and mackinawite); however, grain-scale synchrotron-based analysis shows that As is also associated with amorphous OM. Mixed As oxidation states in porewater (median = 62% As (V), 18% As (III); n = 20) and sediment (median = 80% As (-I) and (III), 20% As (V); n = 9) indicate the presence of variable redox conditions in the near-surface sediment and suggest that post-depositional remobilization of As has occurred. Detailed characterization of As-bearing OM at and below the SWI suggests that OM plays an important role in stabilizing redox-sensitive authigenic minerals and associated As. Based on these findings, it is expected that increased concentrations of labile OM will drive post-depositional surface enrichment of As in mining-impacted lakes and may increase or decrease As flux from sediments to overlying surface waters.

The influence of long-term N and P fertilization on soil P forms and cycling in a wheat/fallow cropping system

Efficient phosphorus (P) management is important for crop production and environmental sustainability of cropping systems. The effects of the agricultural management practices of crop rotation and fertilization on soil P forms and cycling were investigated in plots in Swift Current, SK, Canada, under three crop rotation phases [fallow (F), wheat after fallow (WF), and wheat after wheat (WW)], with four nitrogen (N) and/or P fertilizer treatments (+N+P, -N+P, +N-P, and -N-P), using techniques including sequential fractionation, 31P nuclear magnetic resonance (P-NMR), and P K-edge X-ray absorption near-edge (P-XANES). Soil total P (TP) and organic P (Po) concentrations were significantly reduced in F and WW phases compared to WF regardless of fertilization practice. Compared to WW, WF had the highest grain yield and nutrient uptake. Fertilization with N and P significantly influenced soil total carbon (C), total N, TP, and Mehlich 3-P concentrations and acid phosphatase activities, as well as the concentration of some P pools by sequential fractionation and stable P determined by P-XANES. Stopping P fertilization significantly increased the proportions, but not concentrations, of soil Po determined by P-NMR compared to plots still receiving P fertilizers, while the concentration of total diesters increased in plots fertilized with N. Redundancy analysis showed that soil pH and organic C were the significant predictors of P forms in these soils, suggesting that long-term N and P fertilization altered soil P forms by changing soil chemical properties.

Nanographene growth from benzene on Pt(111)

Graphene growth on a Pt(111) substrate exposed to benzene was studied at substrate temperatures between 800 K and 1100 K. The effects of the substrate temperature during benzene exposure and post-annealing were examined. It was revealed that the substrate temperature during benzene exposure determined the graphene size, which was measured using scanning tunneling microscopy (STM). Nanographenes (NGs) of ~10 nm in size. were obtained by exposing the substrate to benzene at 800 K and post-annealing at 1100 K. The presence of a C–Pt bond, which may fix the carbon atoms on the Pt(111) surface and suppress any further growth of graphene, was confirmed by the carbon K-edge near-edge X-ray absorption fine structure spectroscopy (C K NEXAFS) and X-ray photoelectron spectroscopy (XPS) for the NG. Angle resolved photoemission spectroscopy (ARPES) performed on the NG has a reduced density of states at the Fermi level.

Controlling Oxygen Reduction Selectivity through Steric Effects: Electrocatalytic Two-Electron and Four-Electron Oxygen Reduction with Cobalt Porphyrin Atropisomers.

Achieving a selective 2 e- or 4 e- oxygen reduction reaction (ORR) is critical but challenging. Herein, we report controlling ORR selectivity of Co porphyrins by tuning only steric effects. We designed Co porphyrin 1 with meso-phenyls each bearing a bulky ortho-amido group. Due to the resulted steric hinderance, 1 has four atropisomers with similar electronic structures but dissimilar steric effects. Isomers αβαβ and αααα catalyze ORR with n=2.10 and 3.75 (n is the electron number transferred per O2 ), respectively, but ααββ and αααβ show poor selectivity with n=2.89-3.10. Isomer αβαβ catalyzes 2 e- ORR by preventing a bimolecular O2 activation path, while αααα improves 4 e- ORR selectivity by improving O2 binding at its pocket, a feature confirmed by spectroscopy methods, including O K-edge near-edge X-ray absorption fine structure. This work represents an unparalleled example to improve 2 e- and 4 e- ORR by tuning only steric effects without changing molecular and electronic structures.

High-resolution X-ray absorption spectroscopy of alkanethiolate self-assembled monolayers on Au(111) and Ag(111)

High-resolution C K-edge near-edge X-ray absorption fine structure (NEXAFS) spectra of non-substituted alkanethiolate self-assembled monolayers (SAMs) on Au(111) and Ag(111) were studied, with a particular emphasis on their fine structure and temperature dependence. Depending on the orientation of the light polarization with respect to the surface normal, the spectra were either dominated by the 'C−H' band, comprised of several σ*C−H / Rydberg resonances or exhibited several usually "hidden" features, including a sharp pre-edge resonance at ∼286.8 eV, related to the terminal methyl group of the SAM forming molecules and accompanied by a vibronic feature. The spectra exhibit pronounced reversible temperature dependence at going from cryogenic (60−70 K) to room temperature, including a shift of the 'C−H' band to lower energy by 250−300 meV, broadening and decrease in intensity of nearly all resonances, and disappearance of several "fine structure" features. This behavior was attributed to the nuclear motion effects, with the major impact of progressing orientational and conformational disorder in the SAMs, and correlated with the length of the of molecular backbone and specific character of the SAM-ambient interface.

C–H Bond Activation of Methane through Electronic Interaction with Pd(110)

The adsorption and interaction of methane on Pd(110) were investigated by vibrational spectroscopy, synchrotron-based X-ray spectroscopy, and first-principles density functional theory (DFT) calculations. The vibrational modes of methane are significantly perturbed by the interaction with the Pd surface. A redshifted C–H stretching vibration was detected by infrared reflection-absorption spectroscopy, indicating that C–H bonds in methane molecules are softened through the interaction with the Pd(110) surface. The electronic interaction was evidenced by carbon K-edge near-edge X-ray absorption fine structure spectroscopy, which shows the mixing between methane molecular orbitals and the substrate d-band. The adsorption configuration and vibrational modes of methane were calculated by the DFT method. The combined experimental and theoretical studies revealed that the interaction between methane and Pd(110) depends significantly on the adsorbed conformation of methane molecules, which is affected by the intermolecular interaction at a high methane coverage. The methane–substrate interaction is suppressed when oxygen is preadsorbed on Pd(110). The obtained spectroscopic results indicate that the coverage of oxygen is a key factor in the activation of methane on metal catalysts.

Chlorine K-Edge X-ray Absorption Near-Edge Structure Discrimination of Crystalline Solvates and Salts in Organic Molecules

The crystal forms of active pharmaceutical ingredients must be precisely determined to properly regulate their physical properties. In this study, chlorine K-edge X-ray absorption near-edge structu...

Determination of Both Tilting and In-Plane Molecular Rotational Angles for Dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene Using Near-Edge X-ray Absorption Fine Structure

We demonstrate that both in-plane molecular rotational and tilting angles of the molecular orientation can be determined using the σ* resonance of sulfur (S) K-edge near-edge X-ray absorption fine ...

Local Structure Analysis on Si-Containing DLC Films Based on the Measurement of C K-Edge and Si K-Edge X-ray Absorption Spectra

In this paper, the local structure of silicon-containing diamond-like carbon (Si-DLC) films is discussed based on the measurement of C K-edge and Si K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra using the synchrotron radiation of 11 types of Si-DLC film fabricated with various synthesis methods and having different elemental compositions. In the C K-edge NEXAFS spectra of the Si-DLC films, the σ* band shrunk and shifted to the lower-energy side, and the π* peak broadened with an increase in the Si content in the Si-DLC films. However, there were no significant changes observed in the Si K-edge NEXAFS spectra with an increase in the Si content. These results indicate that Si–Si bonding is not formed with precedence in Si-DLC film.

Limited Cu(II) binding to biochar DOM: Evidence from C K-edge NEXAFS and EEM-PARAFAC combined with two-dimensional correlation analysis

Multiple spectroscopic technologies and chemometric analyses were combined to explore the compositional characteristics and Cu binding performance of biochar-derived dissolved organic matter (DOM). The DOM samples were extracted from biochars produced from lignocellulose-rich rapeseed cake (RSC) by pyrolysis at 300, 500, and 700 °C (i.e., RSC300, RSC500, RSC700). Fourier transform infrared spectroscopy (FTIR) and carbon K-edge near-edge X-ray absorption fine structure spectroscopy (NEXAFS) analyses were combined to elucidate the molecular-level C species in the DOM. With the increasing pyrolysis temperature, DOM aromaticity increased, whereas the proportion of metal complexing sites (e.g., carboxyl and phenolic groups) decreased. Fluorescence excitation-emission matrix (EEM) spectroscopy with parallel factor analysis (PARAFAC) indicated that biochar DOM, irrespective of pyrolysis temperature, was mostly composed of three types of humic-like components (C1–C3), and a small amount of a protein-like component (C4). As charring temperature increased, DOM concentrations decreased substantially, but the humic-like C3 with abundant aromatic structures became predominant. Fluorescence quenching experiment and two-dimensional correlation spectroscopy (2D-COS) analysis suggested that the preferential Cu(II) binding fractions of the DOM were the humic-like substances. Moreover, the quenching curve fitting results for individual components indicated that despite the Cu(II) binding affinity was slightly enhanced as the pyrolysis temperature increased, the binding capacities of the four components decreased. In general, the DOM components from RSC biochar exhibited limited Cu(II) binding capacities (2.18–17.7 μmol L−1). Results from this study improved understanding of the mechanisms by which biochar DOM interacts with Cu, and provided tools for fast screening of biochars to reduce their environmental risks.

Molecular-level understanding of phosphorus transformation with long-term phosphorus addition and depletion in an alkaline soil

With the increasing pressure on phosphorus (P) resources and global water eutrophication, the development of sustainable land management is pushed forward by detailed knowledge on the nature and fate of phosphorus (P) in agricultural soils under various long-term fertilizer regimes. Using bulk- (solution 31P nuclear magnetic resonance; P K-edge X-ray absorption near-edge, XANES) and micro- (X-ray fluorescence and XANES) spectroscopic techniques, we investigated the molecular speciation of P in an alkaline soil from plots under wheat-maize rotation with or without chemical P fertilizers for 26 years, since 1990. The long-term experimental results show that P buildup and drawdown were mainly in the inorganic forms in response to P addition and depletion. The added P increased P accumulation in the forms of brushite and deoxyribonucleic acid that preferentially depleted without P addition, indicating that these species were phytoavailable. Although P forms as hydroxyapatite and orthophosphate monoesters were increased under P fertilization, no significant depletions of these P forms were observed when P fertilization was withheld. In contrast, iron-associated P increased with and without P fertilization. These results from this long-term experimental site facilitate understanding of dynamics and availability of fertilizer P and the existing legacy P in soils, with important implications for sustainable P management in these soils and similar soils in other regions.

Zinc K-edge XANES spectroscopy of mineral and organic standards.

Zinc K-edge X-ray absorption near-edge (XANES) spectroscopy was conducted on 40 zinc mineral samples and organic compounds. The K-edge position varied from 9660.5 to 9666.0 eV and a variety of distinctive peaks at higher post-edge energies were exhibited by the materials. Zinc is in the +2 oxidation state in all analyzed materials, thus the variations in edge position and post-edge features reflect changes in zinc coordination. For some minerals, multiple specimens from different localities as well as pure forms from chemical supply companies were examined. These specimens had nearly identical K-edge and post-edge peak positions with only minor variation in the intensity of the post-edge peaks. This suggests that typical compositional variations in natural materials do not strongly affect spectral characteristics. Organic zinc compounds also exhibited a range of edge positions and post-edge features; however, organic compounds with similar zinc coordination structures had nearly identical spectra. Zinc XANES spectral patterns will allow identification of unknown zinc-containing minerals and organic phases in future studies.