Computational prediction of L_{3} EXAFS spectra of gold nanoparticles from classical molecular dynamics simulations

We present a computational approach for the simulation of extended x-ray absorption fine structure (EXAFS) spectra of nanoparticles directly from molecular dynamics simulations without fitting any of the structural parameters of the nanoparticle to experimental data. The calculation consists of two stages. First, a molecular dynamics simulation of the nanoparticle is performed and then the EXAFS spectrum is computed from “snapshots” of structures extracted from the simulation. A probability distribution function approach calculated directly from the molecular dynamics simulations is used to ensure a balanced sampling of photoabsorbing atoms and their surrounding scattering atoms while keeping the number of EXAFS calculations that need to be performed to a manageable level. The average spectrum from all configurations and photoabsorbing atoms is computed as an Au L3-edge EXAFS spectrum with the FEFF 8.4 package, which includes the self-consistent calculation of atomic potentials. We validate and apply this approach in simulations of EXAFS spectra of gold nanoparticles with sizes between 20 and 60 Å. We investigate the effect of size, structural anisotropy, and thermal motion on the gold nanoparticle EXAFS spectra and we find that our simulations closely reproduce the experimentally determined spectra

Early diagenetic vivianite [Fe-3(PO4)(2) center dot 8H(2)O] in a contaminated freshwater sediment and insights into zinc uptake: a mu-EXAFS, mu-XANES and Raman study

The sediments in the Salford Quays, a heavily-modified urban water body, contain high levels of organic matter, Fe, Zn and nutrients as a result of past contaminant inputs. Vivianite [Fe3(PO4)2 · 8H2O] has been observed to have precipitated within these sediments during early diagenesis as a result of the release of Fe and P to porewaters. These mineral grains are small (<100 μm) and micron-scale analysis techniques (SEM, electron microprobe, μ-EXAFS, μ-XANES and Raman) have been applied in this study to obtain information upon the structure of this vivianite and the nature of Zn uptake in the mineral. Petrographic observations, and elemental, X-ray diffraction and Raman spectroscopic analysis confirms the presence of vivianite. EXAFS model fitting of the FeK-edge spectra for individual vivianite grains produces Fe–O and Fe–P co-ordination numbers and bond lengths consistent with previous structural studies of vivianite (4O atoms at 1.99–2.05 Å; 2P atoms at 3.17–3.25 Å). One analysed grain displays evidence of a significant Fe3+ component, which is interpreted to have resulted from oxidation during sample handling and/or analysis. EXAFS modelling of the Zn K-edge data, together with linear combination XANES fitting of model compounds, indicates that Zn may be incorporated into the crystal structure of vivianite (4O atoms at 1.97 Å; 2P atoms at 3.17 Å). Low levels of Zn sulphate or Zn-sorbed goethite are also indicated from linear combination XANES fitting and to a limited extent, the EXAFS fitting, the origin of which may either be an oxidation artifact or the inclusion of Zn sulphate into the vivianite grains during precipitation. This study confirms that early diagenetic vivianite may act as a sink for Zn, and potentially other contaminants (e.g. As) during its formation and, therefore, forms an important component of metal cycling in contaminated sediments and waters. Furthermore, for the case of Zn, the EXAFS fits for Zn phosphate suggest this uptake is structural and not via surface adsorption

EXAFS Analysis of Size-Constrained Semiconducting Materials

Semiconducting materials such as CdSe, CdS, PbS and GaP are included in crystalline zeolite Y and mordenite and structurally flexible ethylene-methacrylic acid copolymer solid matrices. EXAFS analysis reveals formation of species with dimensions of molecular size up to ca. 13 A in the crystalline hosts, while the polymer matrices allow agglomeration of larger semiconducting particles. Zeolite anchored structures are distinctively different to small particles with bulk crystal structure as usually found in colloidal systems

Data analysis in extended x-ray-absorption fine structure: Determination of the background absorption and the threshold energy

Two approaches for the determination of the background absorption (μ_0) in the extended x-ray-absorption fine structure (EXAFS) are presented. Both methods, experimental and computational, take advantage of the damping of the EXAFS amplitude resulting from the convolution with Gaussian functions of different widths. In the experimental method two or more spectra are collected with the use of different spectrometer slit widths, resulting in spectra of different resolutions for the same sample. In the computational approach the convolution is accomplished via a convolution algorithm. The intersection points of the resulting spectra are used to generate μ_0. At the absorption edge, the spectra intersect at a unique point, which is shown to be a measure of the threshold energy, E_0. Illustration of the two methods for background removal is given for a copper-foil sample. The computational approach is superior to the experimental method of damping the EXAFS spectra to give μ_0

EXAFS study of nickel exchanged into zeolite Y

EXAFS and near edge spectroscopy were used to monitor changes i n Ni coordination as a function of treatment conditions after aqueous exchange into zeolite Y. Our results suggest that after calcination and dehydration under the conditions of this study, major site occupancy for Ni appears to be in the tri-coordinate exchange sites , and not i n the hexagonal prisms as suggested by previous x-ray diffraction results

LOCAL DISTORTIONS AND VOLUME CHANGES IN SEMICONDUCTORS - DONORS IN SILICON

Experiments giving impurity-induced lattice distortion can measure quite distinct quantities. In particular EXAFS (extended X-ray fine structure) measures nearest-neighbour distances, whereas both volume changes and recent spectroscopic data measure long-range displacements. The relationship between the two depends strongly on the inter-atomic potential. The authors analyse this for impurities in silicon by adopting a variety of current potentials. There is a significant contradiction between the EXAFS results and the other experiments for all of the inter-atomic potentials. This problem may be associated with the high oxygen concentrations of Czochralski crystals used in the EXAFS study

Local structure of REFeAsO (RE=La, Pr, Nd, Sm) oxypnictides studied by Fe K-edge EXAFS

Local structure of REOFeAs (RE=La, Pr, Nd, Sm) system has been studied as a function of chemical pressure varied due to different rare-earth size. Fe K-edge extended X-ray absorption fine structure (EXAFS) measurements in the fluorescence mode has permitted to compare systematically the inter-atomic distances and their mean square relative displacements (MSRD). We find that the Fe-As bond length and the corresponding MSRD hardly show any change, suggesting the strongly covalent nature of this bond, while the Fe-Fe and Fe-RE bond lengths decrease with decreasing rare earth size. The results provide important information on the atomic correlations that could have direct implication on the superconductivity and magnetism of REOFeAs system, with the chemical pressure being a key ingredient

Is There a Negative Thermal Expansion in Supported Metal Nanoparticles? An In-Situ X-ray Absorption Study Coupled with Neural Network Analysis

Interactions with their support, adsorbates and unique structural motifs are responsible for the many intriguing properties and potential applications of supported metal nanoparticles (NPs). At the same time, they complicate the interpretation of experimental data. In fact, the methods and approaches that work well for the ex situ analysis of bulk materials may be inaccurate or introduce artifacts in the in situ analysis of nanomaterials. Here we revisit the controversial topic of negative thermal expansion and anomalies in the Debye temperature reported for oxide-supported metal NPs. In situ X-ray absorption experimental data collected for Pt NPs in ultrahigh vacuum and an advanced data analysis approach based on an artificial neural network demonstrate that Pt NPs do not exhibit intrinsic negative thermal expansion. Similarly as for bulk materials, in the absence of adsorbates the bond lengths in metal NPs increase with temperature. The previously reported anomalies in particle size-dependent Debye temperatures can also be linked to the artifacts in the interpretation of conventional X-ray absorption data of disordered materials such as NPs