Project description:The L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.
Project description:Simulation of Ni K-edge X-ray absorption near edge structure (XANES) spectra in LiNi0.5Co0.2Mn0.3O2 (NCM523) was performed. The structure of NCM523 was optimized by first-principles calculation based on density functional theory and XANES spectrum simulation via the finite difference method. The calculated Ni K-edge XANES spectra of NCM523 with Li amounts of 1.0 and 0.5 showed good agreement with the measured spectra. The bond length between Ni and O shortened as the valence of Ni increased. Distortion of the structure resulting from Jahn-Teller distortion was observed with Ni3+. The XANES spectra of the Ni K-edge of Ni2+, Ni3+, and Ni4+ were calculated. In NCM523 with a Li amount of 1.0, the spectrum of Ni3+ shifts towards the higher energy side compared to that of Ni2+; at a Li amount of 0.5 the absorption edge of Ni2+, Ni3+, and Ni4+ shifts toward a higher energy as valence increases. Even at the same Ni valence number, the XANES spectra were different when the Li amounts were 1.0 and 0.5. Cation mixing of Li/Ni readily occurs at a Li amount of 1.0, more than that of 0.5 because of the super exchange interaction. The K-edge XANES spectrum of the Ni of the Li site did not change the position of the absorption edge of the Ni site Ni2+ XANES spectrum; a difference in shape of the shoulder peak and the pre-edge peak appeared. From these results, the Ni valence, bonding state, and cation mixing effect of Li/Ni on the Ni K-edge XANES spectrum in NCM523 were clarified.
Project description:Laboratory-based X-ray absorption spectroscopy (XAS) and especially X-ray absorption near-edge structure (XANES) offers new opportunities in catalyst characterization and presents not only an alternative, but also a complementary approach to precious beamtime at synchrotron facilities. We successfully designed a laboratory-based setup for performing operando, quasi-simultaneous XANES analysis at multiple K-edges, more specifically, operando XANES of mono-, bi-, and trimetallic CO2 hydrogenation catalysts containing Ni, Fe, and Cu. Detailed operando XANES studies of the multielement solid catalysts revealed metal-dependent differences in the reducibility and re-oxidation behavior and their influence on the catalytic performance in CO2 hydrogenation. The applicability of operando laboratory-based XANES at multiple K-edges paves the way for advanced multielement catalyst characterization complementing detailed studies at synchrotron facilities.
Project description:We used soft X-ray three-dimensional imaging to quantify the mass of superparamagnetic iron oxide nanoparticles (SPION) within whole cells, by exploiting the iron oxide differential absorption contrast. Near-edge absorption soft X-ray nanotomography (NEASXT) combines whole-cell 3D structure determination at 50 nm resolution, with 3D elemental mapping and high throughput. We detected three-dimensional distribution of SPIONs within cells with 0.3 g/cm(3) sensitivity, sufficient for detecting the density corresponding to a single nanoparticle.
Project description:The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.
Project description:Fluorescence-yield X-ray absorption fine structure (FY-XAFS) is extensively used for investigating atomic-scale local structures around specific elements in functional materials. However, conventional FY-XAFS instruments frequently cannot cover trace light elements, for example dopants in wide gap semiconductors, because of insufficient energy resolution of semiconductor X-ray detectors. Here we introduce a superconducting XAFS (SC-XAFS) apparatus to measure X-ray absorption near-edge structure (XANES) of n-type dopant N atoms (4 ×10(19) cm(-3)) implanted at 500°C into 4H-SiC substrates annealed subsequently. The XANES spectra and ab initio multiple scattering calculations indicate that the N atoms almost completely substitute for the C sites, associated with a possible existence of local CN regions, in the as-implanted state. This is a reason why hot implantation is necessary for dopant activation in ion implantation. The SC-XAFS apparatus may play an important role in improving doping processes for energy-saving wide-gap semiconductors and other functional materials.
Project description:The toxicity and bioavailability of arsenic is heavily dependent on its speciation. Therefore, robust and accurate methods are needed to determine arsenic speciation profiles for materials related to public health initiatives, such as food safety. Here, X-ray spectroscopies are attractive candidates as they provide in situ, nondestructive analyses of solid samples without perturbation to the arsenic species therein. This work provides a speciation analysis for three certified reference materials for the food chemistry community, whose assigned values may be used to assess the merit of the X-ray spectroscopy results. Furthermore, extracts of SRM 3232 Kelp Powder, which is value-assigned for arsenic species, are measured to provide further evidence of its efficacy. These analyses are performed on the results of As K-edge X-ray Absorption Near Edge Structure (XANES) measurements collected on each sample. Notably, such analyses have traditionally relied on linear combination fitting of a minimal subset of empirical standards selected by stepwise regression. This is known to be problematic for compounds with meaningfully collinear spectra and can yield overestimates of the accuracy of the analysis. Therefore, the least absolute shrinkage and selection operator (lasso) regression method is used to reduce the risk of overfitting and increase the interpretability of statistical inferences. As this is a biased statistical method, results and uncertainties are estimated using a bootstrap method accounting for the dominant sources of variability. Finally, this method does not separate model and data selection from regression analysis. Indeed, a survey of many spectral influences is presented including changes in the: state of methylation, state of protonation, oxidation state, coordination geometry, and sample phase. These compounds were all included in the model's training set, preventing model over-simplification and enabling high-throughput and robust analyses.
Project description:Analyzing coordination environments using X-ray absorption spectroscopy has broad applications in solid-state physics and material chemistry. Here, we show that random forest models trained on 190,000 K-edge X-ray absorption near-edge structure (XANES) spectra can identify the main atomic coordination environment with a high accuracy of 85.4% and all associated coordination environments with a high Jaccard score of 81.8% for 33 cation elements in oxides, significantly outperforming other machine-learning models. In a departure from prior works, the coordination environment is described as a distribution over 25 distinct coordination motifs with coordination numbers ranging from 1 to 12. More importantly, we show that the random forest models can be used to predict coordination environments from experimental K-edge XANES with minimal loss in accuracy. A drop-variable feature importance analysis highlights the key roles that the pre-edge and main-peak regions play in coordination environment identification.
Project description:This study addresses the need for methods that validate the surface chemistry leading to the immobilization of biomolecules and provide information about the resulting structural configurations. We report on the use of near-edge X-ray absorption fine structure spectroscopy (NEXAFS) to characterize a widely employed immobilization chemistry that leads to the covalent attachment of a biologically relevant oligopeptide to a surface. The oligopeptide used in this study is a kinase substrate of the epidermal growth factor receptor (EGFR), a protein that is a common target for cancer therapeutics. By observing changes in the pi* and sigma* orbitals of specific nitrogen and carbon atoms (amide, imide, carbonyl), we are able to follow the sequential reactions leading to immobilization of the oligopeptide. We also show that it is possible to use NEXAFS to extend this characterization method to submonolayer densities that are relevant to biological assays. Such an element-specific chemical characterization of small peptides on surfaces fills an unmet need and establishes NEXAFS as useful technique for characterizing the immobilization of small biomolecules on surfaces.
Project description:Collagen type I fibrils are the major building blocks of connective tissues. Collagen fibrils are anisotropic supramolecular structures, and their orientation can be revealed by polarized light microscopy and vibrational microspectroscopy. We hypothesized that the anisotropy of chemical bonds in the collagen molecules, and hence their orientation, might also be detected by X-ray photoemission electron spectromicroscopy (X-PEEM) and X-ray absorption near-edge structure (XANES) spectroscopy, which use linearly polarized synchrotron light. To test this hypothesis, we analyzed sections of rat-tail tendon, composed of parallel arrays of collagen fibrils. The results clearly indicate that XANES-PEEM is sensitive to collagen fibril orientation and, more specifically, to the orientations of carbonyl and amide bonds in collagen molecules. These data suggest that XANES-PEEM is a promising technique for characterizing the chemical composition and structural organization at the nanoscale of collagen-based connective tissues, including tendons, cartilage, and bone.