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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 L 3 -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 60Å. 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.

The structural parameters of the first five coordination shells of an Au bulk obtained from high accuracy L(3)-edge extended x-ray absorption fine structure (EXAFS) spectra in the temperature range 20-300 K are reported. Good agreement with previously reported studies is found. The effective second and third order force constants evaluated using EXAFS data are compatible with those calculated from phonon dispersion curves. A careful comparison of the variations of the EXAFS first shell distance with x-ray diffraction data provided the mean squared relative displacement of the atomic vibrations perpendicular to the first interatomic bond. An alternative new approach that is useful in achieving this parameter when x-ray diffraction data are not available is proposed.

Lead (Pb) and other heavy metals represent a great source of concern in agriculture because they may disperse from polluted sources and accumulate in crop organs. This research study was performed with three edible crops and one pasture species (lettuce: Lactuca sativa L. cv. Romana; radish: Raphanus sativus L. var. radicicola; tomato: Lycopersicon lycopersicum L. Karst.; Italian ryegrass: Lolium multiflorum Lam). It was aimed at (1) assessing how species affect Pb distribution among plant organs, (2) determining the extent to which Pb is localized in edible organs, and (3) ascertaining whether it could be possible to distinguish which compounds are responsible for the transport of Pb from one plant organ to another and which compounds are responsible for the accumulation of this metal inside each plant organ. The experiment was conducted in the greenhouse. Plants were grown in plastic pots using a Pb-spiked sandy soil as substrate. Total Pb concentrations in different plant organs and in soil were determined. Within plants, the maximum accumulation of Pb was found in roots while the remaining part of Pb was mainly located in leaves. Pb L-III edge XANES (X-ray Absorption Near Edge Spectroscopy) was applied to identify the principal Pb carrier molecules in the different plant organs. The data suggest that in roots Pb immobilization is mainly due to the complexing ability of histidine, which binds the metal and, to a lesser extent, to precipitation of Pb as carbonate. The transport to the upper plant organs is mainly attributed to Pb complexes with organic acids. In stems and leaves, Pb bonding is mainly carboxylic and amino acid-like, thus confirming the role of these substances in promoting Pb mobility. Thio amino acidic (glutathione and cysteine-like) Pb complexes, which in this study were only found in stems, can also be held responsible for Pb long-distance transport from roots to shoots

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