Radiation effects in water ice: a near-edge x-ray absorption fine structure study

The changes in the structure and composition of vapor-deposited ice films irradiated at 20 K with soft x-ray photons (3-900 eV) and their subsequent evolution with temperatures between 20 and 150 K have been investigated by near-edge x-ray absorption fine structure spectroscopy (NEXAFS) at the oxygen K edge. We observe the hydroxyl OH, the atomic oxygen O, and the hydroperoxyl HO(2) radicals, as well as the oxygen O(2) and hydrogen peroxide H(2)O(2) molecules in irradiated porous amorphous solid water (p-ASW) and crystalline (I(cryst)) ice films. The evolution of their concentrations with the temperature indicates that HO(2), O(2), and H(2)O(2) result from a simple step reaction fuelled by OH, where O(2) is a product of HO(2) and HO(2) a product of H(2)O(2). The local order of ice is also modified, whatever the initial structure is. The crystalline ice I(cryst) becomes amorphous. The high-density amorphous phase (I(a)h) of ice is observed after irradiation of the p-ASW film, whose initial structure is the normal low-density form of the amorphous ice (I(a)l). The phase I(a)h is thus peculiar to irradiated ice and does not exist in the as-deposited ice films. A new "very high density" amorphous phase-we call I(a)vh-is obtained after warming at 50 K the irradiated p-ASW ice. This phase is stable up to 90 K and partially transforms into crystalline ice at 150 K.     

Apparent mismatch between extended x-ray absorption fine structure and diffraction structures of crystalline metastable WO3 phases

The local structure of monoclinic, monohydrate, hexagonal, and pyrochlore WO3 phases was investigated by the extended x-ray absorption fine structure spectroscopy as preliminary studies of model compounds of amorphous and thin film WO3 based electrochromic species. In the four cases, we found a large W-O distribution of distances ranging from 1.70 to 2.35 A. The apparent discrepancy of these results and previously published crystal structures are discussed and interpreted as the detection of vacancies and local distortion disorder.     

Local structure of Pt and Pd ions in Ce(1-x)TixO2: x-ray diffraction, x-ray photoelectron spectroscopy, and extended x-ray absorption fine structure

Ce(1-x-y)Ti(x)Pt(y)O(2-delta) (x=0.15; y=0.01) and Ce(1-x-y)Ti(x)Pd(y)O(2-delta) (x=0.25; y=0.02 and 0.05) are found to be good CO oxidation catalysts [T. Baidya et al., J. Phys. Chem. B 110, 5262 (2006); T. Baidya et al., J. Phys. Chem. C 111, 830 (2007)]. A detailed structural study of these compounds has been carried out by extended x-ray absorption fine structure along with x-ray diffraction and x-ray photoelectron spectroscopy. The gross cubic fluorite structure of CeO(2) is retained in the mixed oxides. Oxide ion sublattice around Ti as well as Pt and Pd ions is destabilized in the solid solution. Instead of ideal eight coordinations, Ti, Pd, and Pt ions have 4+3, 4+3, and 3+4 coordinations creating long and short bonds. The long Ti-O, Pd-O, and Pt-O bonds are approximately 2.47 A (2.63 A for Pt-O) which are much higher than average Ce-O bonds of 2.34 A.     

Oxygen K-edge fine structures of water by x-ray Raman scattering spectroscopy under pressure conditions

Fine structure of the oxygen K edge was investigated for water at ambient pressure, 0.16, 0.21, 0.27, 0.47, and 0.60 GPa using x-ray Raman scattering spectroscopy (XRS). Similarity in near-edge structures at 0.16 and 0.60 GPa suggests little difference in the electronic state of oxygen in the low-pressure and high-pressure forms of water. Yet, we observed significant variation of preedge structure of the XRS spectra with compression. The intensity of the preedge peak at 535.7 eV has a minimal value at around 0.3 GPa, indicating that the number of hydrogen bonding increases first and then decreases as a function of pressure.     

Dipole-induced structure in aromatic-terminated self-assembled monolayers: a study by near edge x-ray absorption fine structure spectroscopy

The structure of self-assembled monolayers presenting aromatic rings at a surface is studied by near edge x-ray absorption fine structure spectroscopy (NEXAFS). Fluorine substitution at asymmetric positions in the aromatic rings is used to generate a layer of dipoles at the surface of the monolayer. We find that fluorine substituted aromatic rings are more ordered than unsubstituted aromatic rings by a factor of two based on the polarization dependence of the lowest C 1s to pi* transition, which is associated with transitions from phenyl carbons attached to hydrogens. This result is consistent with the influence of dipole-dipole interactions and quadrupolar interactions between the aromatic groups due to the substitution of fluorine atoms. The work also serves to illustrate how subtle variations in the orientation of an end group of a self-assembled monolayer can be determined by using NEXAFS.     

High-sensitivity x-ray absorption fine structure investigation of arsenic shallow implant in silicon

High-sensitivity fluorescence-yield x-ray absorption fine structure spectroscopy (XAFS) has been investigated to characterize the local structure around arsenic shallow implant in silicon. Fluorescence-yield XAFS experiments were performed using a high-brilliance synchrotron radiation beam from an in-vacuum-type undulator in a third-generation light source. In addition to investigating the efficiency of high-brilliance undulator x-rays during the fluorescence-yield XAFS measurements, we compared the analytical performance of both the wavelength dispersive spectrometer (WDS) and the energy dispersive spectrometer (EDS) based on the silicon drift detector (SDD). It was confirmed that the WDS reduces the influence of scattering background due to the high spectral resolution. Another advantage of the WDS is high counting rate measurements. It was found that fluorescence-yield XAFS using undulator x-rays combined with the WDS permits superior sensitivity measurements.     

sp hybridization in free carbon nanoparticles--presence and stability observed by near edge X-ray absorption fine structure spectroscopy

The presence and stability of sp hybridized atoms in free carbon nanoparticles was investigated by NEXAFS spectroscopy. The experiments show that a predominant fraction of carbon atoms is found in linear sp-chains and that conversion into sp(2) structures proceeds already at low temperature and in the gas phase.     

Probing the local structure of liquid water by X-ray absorption spectroscopy

It was recently suggested that liquid water primarily comprises hydrogen-bonded rings and chains, as opposed to the traditionally accepted locally tetrahedral structure (Wernet et al. Science 2004, 304, 995). This controversial conclusion was primarily based on comparison between experimental and calculated X-ray absorption spectra (XAS) using computer-generated ice-like 11-molecule clusters. Here we present calculations which conclusively show that when hydrogen-bonding configurations are chosen randomly, the calculated XAS does not reproduce the experimental XAS regardless of the bonding model employed (i.e., rings and chains vs tetrahedral). Furthermore, we also present an analysis of a recently introduced asymmetric water potential (Soper, A. K. J. Phys.: Condens. Matter 2005, 17, S3273), which is representative of the rings and chains structure, and make comparisons with the standard SPC/E potential, which represents the locally tetrahedral structure. We find that the calculated XAS from both potentials is inconsistent with the experimental XAS. However, we also show the calculated electric field distribution from the rings and chains structure is strongly bimodal and highly inconsistent with the experimental Raman spectrum, thus casting serious doubt on the validity of the rings and chains model for liquid water.     

X-ray absorption near edge structure and extended X-ray absorption fine structure analysis of Fe(II) aqueous and acetone solutions

X-ray absorption spectroscopy measurements were used to determine the structure of the first coordination shell of Fe(II) ions in aqueous and acetone based solutions. Extended X-ray absorption fine structure analysis coupled with ab initio X-ray absorption near edge structure calculations confirms the octahedral coordination of the iron ion in water based solution. Data collected for acetone rich solutions can be reproduced assuming coexistence of the octahedral Fe(H(2)O)(6)(2+) and tetrahedral [FeCl(4)](2-) complexes. Distortion of the tetrahedral coordination of ion was detected in some of the acetone based solutions.     

铒甘氨酸配位化合物和铒组氨酸配位化合物的EXAFS谱研究

本文用EXAFS谱研究了三个固体铒甘氨基酸配位化合物, 得到铒甘氨酸和铒组氨酸的第一配位层Er-O键长分别为2.35和2.32A, 配位数分别为8.3和8.0. 并进一步用EXAFS径向结构函数图, 讨论了与其结构类型的关系, 推测出铒氨基酸配位化合物晶体的所属可能结构类型。     

Comparison between Einstein and Debye models for an amorphous Ni46Ti54 alloy produced by mechanical alloying investigated using extended x-ray absorption fine structure and cumulant expansion

We investigated an amorphous Ni(46)Ti(54) alloy produced by mechanical alloying using extended x-ray absorption fine structure (EXAFS) technique and cumulant expansion considering Einstein and Debye models for the temperature dependence of the cumulants. Results obtained from both models were compared and very similar values were obtained. From them, we found information about the structure of the alloy besides thermal and structural disorder, anharmonicity, thermal expansion, and asymmetry of the partial distribution functions g(ij)(r). The cumulants C(1)(*), C(2)(*), and C(3)(*) also allowed us to reconstruct the g(ij)(r, T) functions from EXAFS.     

The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements

X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ～61% and ～71% higher than in bulk water.     

X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations

Full potential x-ray spectroscopy simulations of hexagonal ice and liquid water are performed by means of the newly implemented methodology based on the Gaussian augmented plane waves formalism. The computed spectra obtained within the supercell approach are compared to experimental data. The variations of the spectral distribution determined by the quality of the basis set, the size of the sample, and the choice of the core-hole potential are extensively discussed. The second part of this work is focused on the understanding of the connections between specific configurations of the hydrogen bond network and the corresponding contributions to the x-ray absorption spectrum in liquid water. Our results confirm that asymmetrically coordinated molecules, in particular, those donating only one or no hydrogen bond, are associated with well identified spectral signatures that differ significantly from the ice spectral profile. However, transient local structures, with half formed hydrogen bonds, may still give rise to spectra with dominant postedge contributions and relatively weaker oscillator strengths at lower energy. This explains why by averaging the spectra over all the O atoms of liquid instantaneous configurations extracted from ab initio molecular dynamics trajectories, the spectral features indicating the presence of weak or broken hydrogen bonds turn out to be attenuated and sometimes not clearly distinguishable.     

Sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) of thiol and thioether compounds

The speciation and quantification of sulfur species based on sulfur K-edge x-ray absorption spectroscopy is of wide interest, particularly for biological and petroleum science. These tasks require a firm understanding of the sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of relevant species. To this end, we have examined the gas phase sulfur 1s NEXAFS spectra of a group of simple thiol and thioether compounds. These high-resolution gas phase spectra are free of solid-state broadening, charging, and saturation effects common in the NEXAFS spectra of solids. These experimental data have been further analyzed with the aid of improved virtual orbital Hartree-Fock ab initio calculations. The experimental sulfur 1s NEXAFS spectra show fine features predicted by calculation, and the combination of experiment and calculation has been used to improve assignment of spectroscopic features relevant for the speciation and quantification of the sulfur compounds.     

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study

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.     

Temperature effect of the local structure in liquid Sb studied with x-ray absorption spectroscopy

The temperature dependence of the local structure of liquid Sb has been studied by x-ray absorption spectroscopy. It is shown that about 10% of the atoms with coordination of 3 and weak Peierls distortion exist in liquid Sb just above its melting point. The Peierls distortion weakens gradually with increasing temperature and vanishes at about 750 degrees C. This structural variation in liquid Sb is different from the normal liquid-liquid phase transition. This work reveals the relationship between the variation in the local structure and the change in the physical properties, such as the electrical resisitvity of liquid Sb, with temperature. The complete agreement between the measured electrical resistivity values during heating and cooling processes suggests that the structural units with the features of a rhombohedron appear above the melting point of Sb during solidification.     

The local structure of protonated water from x-ray absorption and density functional theory

We present a combined x-ray absorption spectroscopy/computational study of water in hydrochloric acid (HCl) solutions of varying concentration to address the structure and bonding of excess protons and their effect on the hydrogen bonding network in liquid water. Intensity variations and energy shifts indicate changes in the hydrogen bonding structure in water as well as the local structure of the protonated complex as a function of the concentration of protons. In particular, in highly acidic solutions we find a dominance of the Eigen form, H(3)O(+), while the proton is less localized to a specific water under less acidic conditions.     

The structure,thermodynamic properties and infrared spectra of liquid water and ice

Monte Carlo simulations are used, together with models of the intramolecular and intermolecular potential surfaces, to model liquid water and several phases of ice. Intramolecular relaxation makes important contributions to both thermodynamic and structural properties. A quantum local mode analysis of the Monte Carlo configurations is used to predict the density of states and infrared absorption intensities for the intramolecular bending and stretching vibrations. The large shifts from the gas phase OH stretch frequencies observed experimentally in the liquid and solid phases are due to anharmonic terms in the intramolecular surface rather than to harmonic intermolecular coupling. A significant contribution to observed changes in IR intensity on condensation arises from the large molecular polarisability.