Extended X-ray Absorption Fine Structure Simulation Research Articles

Solvent Dynamics of Aqueous Halides before and after Photoionization.

Electron transfer reactions can be strongly influenced by solvent dynamics. We study the photoionization of halides in water as a model system for such reactions. There are no internal nuclear degrees of freedom in the solute, allowing the dynamics of the solvent to be uniquely identified. We simulate the equilibrium solvent dynamics for Cl-, Br-, I-, and their respective neutral atoms in water, comparing quantum mechanical/molecular mechanical (QM/MM) and classical molecular dynamics (MD) methods. On the basis of the obtained configurations, we calculate the extended X-ray absorption fine structure (EXAFS) spectra rigorously based on the MD snapshots and compare them in detail with other theoretical and experimental results available in the literature. We find our EXAFS spectra based on QM/MM MD simulations in good agreement with their experimental counterparts for the ions. Classical MD simulations for the ions lead to EXAFS spectra that agree equally well with the experiment when it comes to the oscillatory period of the signal, even though they differ from the QM/MM radial distribution functions extracted from the MD. The amplitude is, however, considerably overestimated. This suggests that to judge the reliability of theoretical simulation methods or to elucidate fine details of the atomistic dynamics of the solvent based on EXAFS spectra, the amplitude as well as the oscillatory period need to be considered. If simulations fail qualitatively, as does the classical MD for the aqueous neutral halogen atoms, the resulting EXAFS will also be strongly affected in both oscillatory period and amplitude. The good reliability of QM/MM-based EXAFS simulations, together with clear qualitative differences in the EXAFS spectra found between halides and their atomic counterparts, suggests that a combined theory and experimental EXAFS approach is suitable for elucidating the nonequilibrium solvent dynamics in the photoionization of halides and possibly also for electron transfer reactions in more complex systems.

Local structural modifications of the HfO2 layer in the Al2O3 capped high‐k dielectric films as probed by EXAFS

AbstractThe information on the subtle local structural modifications around the Hf atom in HfO2 high‐k dielectric stacks has been demonstrated to be crucial in determining the resulting electronic properties of the complementary metal oxide (CMOS) devices. In this work, using extended X‐ray‐absorption fine structure (EXAFS) spectroscopy, the local structural characterization of Hf‐based advanced gate stacks thin films were investigated. The thin film stacks used in this project are Al2O3 capped HfO2 thin films deposited on silicon substrates. EXAFS simulations and fits were applied to the data in order to extract crucial structural modifications on these films upon postdeposition annealing (PDA). The local crystal symmetry and coordination around the Hf atom were investigated under various annealing conditions. Specifically, in Hf‐based dielectric thin films on silicon substrates capped with Al2O3 layers, the local crystal symmetry, and coordination around the Hf atom were investigated under various annealing conditions. The questions addressed are the effects of various annealing mechanisms to the diffusion mechanisms in the cap layers and modifications on the emerging local structures around the Hf atom. The diffusion of Al into HfO2 films were monitored through the EXAFS simulations. The non‐linear least‐squares fitting to the EXAFS data revealed that the PDA in NH3 (or N2) ambient after HfO2 deposition had prevented Al diffusion to the HfO2 layers.

The Structure and Bonding of Au25(SR)18 Nanoclusters from EXAFS: The Interplay of Metallic and Molecular Behavior

While recent advances in the synthesis and crystallography of gold–thiolate nanoclusters have led to enormous progress in understanding the structure and bonding of gold thiolate nanomaterials, the changes in structure experienced by these nanomaterials in different conditions, such as low temperature and solvation, is still largely lacking. Herein, we report a temperature- and solvation-dependent extended X-ray absorption fine structure (EXAFS) study of thiolate-protected Au25 nanoclusters. The structural changes experienced by Au25 in response to low temperature and different solvation environments are illustrated in great detail using a site-specific EXAFS fitting approach consisting of one Au–S and three Au–Au shells. EXAFS simulations as well as ab initio calculations of the local density of states are used to support the EXAFS analysis and correlate the structural characteristics of Au25 with its electronic properties. These experimental and theoretical studies point out the existence of the interplay between the “metallic” behavior of the Au13 core and the “molecular” behavior of the six RS–Au–S(R)–Au–SR “staple” units within Au25, which may shed light on its catalytic mechanism and aid in the design and synthesis of other gold–thiolate nanoclusters by balancing the metallic and molecular interactions.

Antimony(V) Incorporation into Synthetic Ferrihydrite, Goethite, and Natural Iron Oxyhydroxides

In this study, we investigated local structures of Sb species in synthetic Sb(V)-coprecipitated and -adsorbed ferrihydrite and goethite, which are common iron(III) oxyhydroxides in environment, at various Sb/Fe molar ratios by extended X-ray absorption fine structure (EXAFS) analyses. The EXAFS analyses showed that Sb(V) is adsorbed on ferrihydrite and goethite by the formation of an inner-sphere surface complex at pH 7.5. In the EXAFS spectra of the coprecipitated ferrihydrite and goethite, some features of the spectra significantly differed from those in the adsorbed samples. The EXAFS simulation indicated that the difference is due to the larger coordination number of the Fe atom to the Sb atom in the coprecipitation samples, indicating a structural incorporation (heterovalent substitution) of Sb(V) into ferrihydrite and goethite. The incorporation of Sb(V) into the structure was also confirmed in natural iron(III) oxyhydroxides in contaminated soil near an Sb mine tailing using mu-EXAFS. This study directly provided the first evidence for the structural incorporation of Sb(V) into the iron(III) oxide structure. Our findings are important for understanding the fate of Sb in the aquatic environment because the behavior of the elements incorporated into solids by such a substitution is not greatly influenced by aquatic factors such as the pH and ionic strength because of isolation of the incorporated metal(loid) ions from the aqueous phase.

Investigation of the copper binding site and the role of histidine as a ligand in riboflavin binding protein.

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 A, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O 3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

Defect structure of highly Zn-doped LiNbO3 single crystal revealed by extended x-ray absorption spectra

To determine the defect structure of ZnO-doped LiNbO3 single crystals with high doping concentrations, we obtain the measurements using the extended x-ray absorption fine structure (EXAFS) at room temperature. It indicates Zn atom is directly substituted on the Li site of the LiNbO3 crystal after Zn doping. EXAFS simulation by way of analyzing the scattering amplitudes also shows that the Zn atom does not substitute the Nb site at highly Zn-doped LiNbO3. Finally, we confirm that VNb5−, a strong charged vacancy, should be considered as an important factors in influencing the physical properties of LiNbO3 beyond 7.5mol% Zn-doped doping concentration.