Calculation of near-edge X-ray absorption fine structure with the CIS(D) method

We report an investigation into the calculation of near-edge X-ray absorption fine structure with the CIS(D) method. Core excitation energies computed with time-dependent density functional theory using standard exchange-correlation functionals are systematically underestimated. CIS(D) predicts core excitation energies that are closer to experiment. However, excitation energies for Rydberg states are too low with respect to valence states, and for some systems spectra that are qualitatively incorrect are obtained. A scaled opposite spin only approach is proposed that reduces the error in the computed core excitation energies, and results in spectra that are in good agreement with experiment.     

Structural study of NO adsorbed on the reconstructed Pt(110)-(1 x 2) surface with X-ray photoelectron diffraction and near-edge X-ray absorption fine structure spectroscopy

The adsorption structure of NO on the reconstructed Pt(110)-(1 x 2) surface was studied with X-ray photoelectron spectroscopy (XPS), X-ray photoelectron diffraction (XPD), low-energy scanned-angle photoelectron diffraction (LESA-PD), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The experiments were performed at 180 K, where no surface lifting from (1 x 2) to (1 x 1) takes place after NO adsorption. XPS indicates that the (1 x 2) unit cell of the Pt(110) surface contains 1.5 NO molecules at the saturated coverage. XPD and LESA-PD analyses allow us to propose a structural model for the NO adlayer, where two-thirds of the NO molecules in the (1 x 2) unit cell are adsorbed on the atop site of the close-packed Pt rows (ridges) along the [10] direction with an inclined geometry and one-third of the NO molecules adsorb on the bridge site between the Pt ridges with an upright configuration. This model is supported by the N K-edge NEXAFS experiments and is consistent with the recently reported model based on the density functional theory (Orita, H.; Nakamura, I.; Fujitani, T. J. Phys. Chem. B 2005, 109, 10312).     

Potential-controlled switching of 2-(2'-thienyl)pyridine adsorbed on Au(111)

Switching between three different adsorbed states was achieved using potential control to separately induce electrochemical behaviour associated with changes in binding and orientation of the thiophene and pyridine moieties of 2-(2'-thienyl)pyridine adsorbed to Au(111) in neutral and basic solution.     

N+NO reaction on Rh(111) surfaces studied with fast near-edge X-ray absorption fine structure spectroscopy: role of NO dimer as an extrinsic precursor

We studied the mechanism of the N+NO reaction on Rh(111) surfaces by means of fast near-edge X-ray absorption fine structure spectroscopy. This reaction is important as a basis of NOx reduction reactions on platinum-group metal surfaces. Atomic nitrogen layers on Rh(111) were titrated with NO at various temperatures. N2O is exclusively formed and desorbs into the gas phase below 350 K. The consumption rate of atomic nitrogen exhibits strange temperature dependence between 100 and 350 K; the reaction proceeds slower with increasing temperature. Reaction kinetics analyses and isotope-controlled experiments have revealed that the surface N atoms do not react with chemisorbed NO molecules but with NO dimers weakly bound on top of the chemisorbed layer, which play a role as an extrinsic precursor. The present results may support the possibility that NO dimers participate in various NO-related synthetic, biochemical, and surface reactions as an intermediate.     

Orientation and bonding of ethylene and ethylidyne on Pt(111) by means of near-edge x-ray absorption fine structure spectroscopy

Near-edge X-ray absorption fine structure (NEXAFS) spectra have been measured for ethylene chemisorbed on Pt(111) at 90 and 300 K. From the polarization dependence of the spectra at 90 K, ethylene is found to lie down with a π bond to the surface. The spectra collected at 300 K indicate a CC bond normal to the surface in ethylidyne, and a SCF Xα calculation was carried out to assign the K-edge transitions in this species. The ethylidyne carboncarbon bond (which is nominally a single bond) appears to be shorter (≈0.03 A) than that for chemisorbed ethylene.     

Solid-state near-edge X-ray absorption fine structure spectra of glycine in various charge states

The experimental solid-state near-edge X-ray absorption fine structure spectra for a series of glycine-related samples including alpha-glycine, beta-glycine, glycinium chloride, glycinium trifluoroacetate, and sodium glycinate at the C, N, and O K-edges measured under identical conditions are reported and compared. An assignment of spectral features for alpha-glycine is proposed on the basis of extended theoretical simulations of polarization-dependent spectra performed within the real-space multiple-scattering formalism explicitly taking into account the intermolecular environment of a glycine molecule in a crystal.     

X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure study of water adsorption on pyridine-terminated thiolate self-assembled monolayers

Adsorption of water on self-assembled monolayers (SAMs) of 4-(4-mercaptophenyl)pyridine on gold at low temperatures under ultrahigh vacuum conditions is studied by synchrotron radiation X-ray photoelectron and absorption spectroscopy. Water adsorption induces a strong modification of the chemical state of the pyridine N atoms at the SAM/ice interface, indicative for strong H bonding and partial proton transfer between water molecules and pyridine moieties. Additionally, the initial molecular orientation within the SAM is changed upon formation of an adsorbed water multilayer.     

Mechanism of the CO oxidation reaction on O-precovered Pt(111) surfaces studied with near-edge x-ray absorption fine structure spectroscopy

The mechanism of CO oxidation reaction on oxygen-precovered Pt(111) surfaces has been studied by using time-resolved near-edge x-ray absorption fine structure spectroscopy. The whole reaction process is composed of two distinct paths: (1) a reaction of isolated oxygen atoms with adsorbed CO, and (2) a reaction of island-periphery oxygen atoms after the CO saturation. CO coadsorption plays a role to induce the dynamic change in spatial distribution of O atoms, which switches over the two reaction paths. These mechanisms were confirmed by kinetic Monte Carlo simulations. The effect of coadsorbed water in the reaction mechanism was also examined.     

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.     

Chemically transformable configurations of mercaptohexadecanoic acid self-assembled monolayers adsorbed on Au(111)

Carboxyl-terminated self-assembled monolayers (SAMs) are commonly used in a variety of applications, with the assumption that the molecules form well-ordered monolayers. In this work, near-edge X-ray absorption fine structure measurements verify that well-ordered monolayers can be formed using acetic acid in the solvent. Disordered monolayers with unbound molecules present in the film result using only ethanol. A stark reorientation occurs upon deprotonation of the end group by rinsing in a KOH solution. This reorientation of the end group is reversible with tilted-over, hydrogen-bound carboxyl groups while the carboxylate ion end groups are upright. C(1s) photoemission shows that SAMs formed and rinsed with acetic acid in ethanol have protonated end groups, while SAMs formed without acetic acid have a large fraction of carboxylate-terminated molecules.     

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.     

Nitrogen 1s near-edge X-ray absorption fine structure spectroscopy of amino acids: Resolving zwitterionic effects

Considerable variation is observed in the near-edge X-ray absorption fine structure (NEXAFS) spectra of amino acids. To unambiguously characterize the chemical origin of this variation, we have acquired the nitrogen 1s NEXAFS spectra of several amino acids and other model compounds and complemented these experimental measurements with ab initio calculations of isolated molecules and molecular clusters. The systematic differences observed between the zwitterionic and un-ionized forms of amino acids arise directly from the structural difference (-NH2 vs -NH3+), which leads to a change in the degree of Rydberg-valence mixing. Further change arises from quenching of this Rydberg character in the spectra of condensed amino acids. Ab initio calculations are used to explore the degree of Rydberg-valence mixing in the solid state.     

Theoretical study of near-edge X-ray absorption fine structure spectra of metal phthalocyanines at C and N K-edges

The inner shell excitation of CuPc, NiPc, and H(2)Pc phthalocyanines at both C and N K-edges has been investigated theoretically by density functional theory calculations. The selected molecules allow one to study the effect on the spectra of the presence and the nature of the atom in the central cavity of the macrocycle. The individual characteristics of the spectra can be rationalized in terms of the position of the unequivalent C and N atomic sites, showing that sensible changes are present in the spectral features deriving from the N atoms directly bound to the atom at the center of the Pc macrocycle. The minor variations present in the spectral C 1s profiles of the phthalocyanines reflect the little perturbation experienced by the peripheral atomic sites.     

Rydberg-valence mixing in the carbon 1s near-edge X-ray absorption fine structure spectra of gaseous alkanes

We have acquired high-resolution carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of methane, ethane, propane, isobutane, and neopentane. These experimental measurements are complemented by high-quality ab initio calculations, performed with the improved virtual orbital approximation. The degree and character of Rydberg-valence mixing in the preedge of the NEXAFS spectra of these species is explored. Significant Rydberg-valence mixing only occurs when there are excited states of valence sigma(C-H) character that have the appropriate symmetry to interact with excited states of Rydberg character. Our results show that this mixing is only present when there are C-H bonds to the core excited carbon atom.     

Electrochemical dimerization of 2-(2'-thienyl)pyridine adsorbed on Au(111) observed by in situ fluorescence

The study of heterodentate molecules adsorbed on metal electrodes provides an opportunity to expand the functionality of modified surfaces while offering insights into the surface and intramolecular electronic interactions of organic adsorbates. The adsorption of 2-(2'-thienyl)pyridine, a molecule containing both pyridine and thiophene moieties, on a Au(111) electrode is reported. Adsorption was characterized by electrochemistry in neutral and basic aqueous electrolyte and was compared to that of pyridine. The aqueous electrochemistry of thiophene on Au(111) was also characterized for comparison purposes. At negative potentials, in the presence of 2-(2'-thienyl)pyridine, a diffuse, pi-bonded monolayer was formed, and a phase transition to a close-packed N- and/or S-bonded configuration was observed near -0.4 V in a 1 mM solution of adsorbate, similar to that seen in pyridine on Au(111). The thiophene-like oxidative dimerization of the molecule was confirmed at positive potentials using in situ fluorescence microscopy by comparison with the spectrum of the chemically synthesized dimer.     

Systematic oxidation of polystyrene by ultraviolet-ozone, characterized by near-edge X-ray absorption fine structure and contact angle

The process of implanting oxygen in polystyrene (PS) via exposure to ultraviolet-ozone (UV-O) was systematically investigated using the characterization technique of near-edge X-ray absorption fine structure (NEXAFS). Samples of PS exposed to UV-O for 10-300 s and washed with isopropanol were analyzed using the carbon and oxygen K-edge NEXAFS partial electron yields, using various retarding bias voltages to depth-profile the oxygen penetration into the surface. Evaluation of reference polymers provided a scale to quantify the oxygen concentration implanted by UV-O treatment. We find that ozone initially reacts with the double bonds on the phenyl rings, forming carbonyl groups, but within 1 min of exposure, the ratio of double to single oxygen bonds stabilizes at a lower value. Oxygen penetrates the film with relative ease, creating a fairly uniform distribution of oxygen within at least the first 4 nm (the effective depth probed by NEXAFS here). Before oxygen accumulates in large concentrations, however, it preferentially degrades the uppermost layer of the film by removing oxygenated low-molecular-weight oligomers. The failure to accumulate high concentrations of oxygen is seen in the nearly constant carbon edge jump, the low concentration of oxygen even at 5 min exposure (58% of that in poly(4-acetoxystyrene), the polymer with the most similarities to UV-O-treated PS), and the relatively high contact angles. At 5 min exposure the oxygen concentration contains ca. 7 atomic % oxygen. The oxygen species that are implanted consist predominantly of single O-C bonds and double O=C bonds but also include a small fraction of O-H. UV-O treatment leads a plateau after 2 min exposure in the water contact angle hysteresis, at a value of 67 +/- 2 degrees , due primarily to chemical heterogeneity. Annealing above T(g) allows oxygenated species to move short distances away from the surface but not diffuse further than 1-2 nm.     

Surface structure and interface dynamics of alkanethiol self-assembled monolayers on Au(111)

Scanning tunneling microscopy (STM) and high-resolution electron energy loss spectroscopy (HREELS) were used to examine the structural transitions and interface dynamics of octanethiol (OT) self-assembled monolayers (SAMs) caused by long-term storage or annealing at an elevated temperature. We found that the structural transitions of OT SAMs from the c(4 x 2) superlattice to the (6 x square root 3) superlattice resulting from long-term storage were caused by both the dynamic movement of the adsorbed sulfur atoms on several adsorption sites of the Au(111) surface and the change of molecular orientation in the ordered layer. Moreover, it was found that the chemical structure of the sulfur headgroups does not change from monomer to dimer by the temporal change of SAMs at room temperature. Contrary to the results of the long-term-stored SAMs, it was found that the annealing process did not modify either the interfacial or chemical structures of the sulfur headgroups or the two-dimensional c(4 x 2) domain structure. Our results will be very useful for a better understanding of the interface dynamics and stability of sulfur atoms in alkanethiol SAMs on Au(111) surfaces.     

Thin film structure of tetraceno[2,3-b]thiophene characterized by grazing incidence X-ray scattering and near-edge X-ray absorption fine structure analysis

Understanding the structure-property relationship for organic semiconductors is crucial in rational molecular design and organic thin film process control. Charge carrier transport in organic field-effect transistors predominantly occurs in a few semiconductor layers close to the interface in contact with the dielectric layer, and the transport properties depend sensitively on the precise molecular packing. Therefore, a better understanding of the impact of molecular packing and thin film morphology in the first few monolayers above the dielectric layer on charge transport is needed to improve the transistor performance. In this Article, we show that the detailed molecular packing in thin organic semiconductor films can be solved through a combination of grazing incidence X-ray diffraction (GIXD), near-edge X-ray absorption spectra fine structure (NEXAFS) spectroscopy, energy minimization packing calculations, and structure refinement of the diffraction data. We solve the thin film structure for 2 and 20 nm thick films of tetraceno[2,3-b]thiophene and detect only a single phase for these thicknesses. The GIXD yields accurate unit cell dimensions, while the precise molecular arrangement in the unit cell was found from the energy minimization and structure refinement; the NEXAFS yields a consistent molecular tilt. For the 20 nm film, the unit cell is triclinic with a = 5.96 A, b = 7.71 A, c = 15.16 A, alpha = 97.30 degrees, beta = 95.63 degrees, gamma = 90 degrees; there are two molecules per unit cell with herringbone packing (49-59 degree angle) and tilted about 7 degrees from the substrate normal. The thin film structure is significantly different from the bulk single-crystal structure, indicating the importance of characterizing thin film to correlate with thin film device performance. The results are compared to the corresponding data for the chemically similar and widely used pentacene. Possible effects of the observed thin film structure and morphology on charge carrier mobility are discussed.     

X-ray absorption near-edge structure (XANES) spectroscopy identifies differential sulfur speciation in corneal tissue

The chemical composition of tissues can influence their form and function. As a prime example, the lattice-like arrangement of collagen fibrils required for corneal transparency is controlled, in part, by sulfated proteoglycans, which, via core proteins, bind to the collagen at specific locations along the fibril axis. However, to date, no studies have been able to directly identify and characterize sulfur (S) in the cornea as a function of tissue location. In this study, X-ray absorption near-edge structure spectroscopy and micro-beam X-ray fluorescence (μ-XRF) chemical contrast imaging were employed to probe the nature of the mature (bovine) cornea as a function of position from the anterior sub-epithelial region into the deep stroma. Data indicate an inhomogeneity in the composition of S species in the first ≈50 μm of stromal depth. In μ-XRF chemical contrast imaging, S did not co-localize with phosphorous (P) in the deep stroma where sulfates are prominent. Rather, P is present only as isolated micrometric spots, presumably identifiable as keratocytes. This study lends novel insights into the elemental physiology of mature cornea, especially in relation to its S distribution; future studies could be applied to human tissues. Moreover, it defines an analytical protocol for the interrogation of S species in biological tissues with micrometric resolution.

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.