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.     

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.     

Changes in the near-edge X-ray absorption fine structure spectra of long-chain diacetylene derivatives through photopolymerization in Langmuir–Blodgett films

Photopolymerization of cadmium 10,12-pentacosadiynoate (CdDA) in Langmuir–Blodgett (LB) films, with the molecular packing well arranged by moderate preannealing, was investigated with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Greenish films of polydiacetylene with an absorption wavelength of 705 nm were obtained through the photopolymerization of preannealed monomer LB films, and this resulted in an extended π-conjugate system based on the well-ordered monomer in a two-dimensional arrangement. The electronic structures of the polydiacetylenes were found to be correlated to the variation of the molecular arrangements in the films from the changes in the NEXAFS spectra through photopolymerization in the LB films. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2329–2336, 2004     

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.     

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.     

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.     

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.     

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.     

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.     

Photoemission and near-edge X-ray absorption fine structure studies of the bacterial surface protein layer of Bacillus sphaericus NCTC 9602

The electronic structure of the regular, two-dimensional bacterial surface protein layer of Bacillus sphaericus NCTC 9602 has been examined by photoemission (PE) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Both the O 1s and the N 1s core-level PE spectra show a single structure, whereas the C 1s core-level spectrum appears manifold, suggesting similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in the different functional groups of the amino acids. This result is supported by the element-specific NEXAFS spectra of the unoccupied valence electronic states, which exhibit a series of characteristic NEXAFS peaks that can be assigned to particular molecular orbitals of the amino acids by applying a phenomenological building-block model. The relative contributions of the C-O, C-N, and C-C bond originating signals into the C 1s PE spectrum are in good agreement with the number ratios of the corresponding bonds calculated from the known primary structure of the bacterial surface protein. First interpretation of the PE spectrum of the occupied valence states is achieved on the basis of electronic density-of-states calculations performed for small peptides. It was found that mainly the pi clouds of the aromatic rings contribute to both the lowest unoccupied and the highest occupied molecular orbitals.     

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.     

Surface structure and chemical switching of thioctic acid adsorbed on Au(111) as observed using near-edge X-ray absorption fine structure

Thioctic acid (alpha-lipoic acid) is a molecule with a large disulfide-containing base, a short alkyl chain with four CH2 units, and a carboxyl termination. Self-assembled monolayer (SAM) films ofthioctic acid adsorbed on Au(111) have been investigated with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS) to determine film quality, bonding, and morphology. Using standard preparation protocols for SAMs, that is, dissolving thioctic acid in ethanol and exposing gold to the solution, results in poor films. These films are highly disordered, contain a mixture of carboxyl and carboxylate terminations, have more than monolayer coverage, and exhibit unbound disulfide. Conversely, forming films by dissolving 1 mmol thioctic acid into 5% acetic acid in ethanol (as previously reported with carboxyl-terminated alkanethiols) forms ordered monolayers with small amounts of unbound sulfur. NEXAFS indicates tilted over endgroups with the carboxyl group normal on average 38 degrees from the surface normal. Slight angle-dependent intensity modulations in other features indicate alkyl chains statistically more upright than prostrate on the surface. Reflection-absorption Fourier transform infrared (RA-FTIR) spectra indicate hydrogen bonding between neighboring molecules. In such well-formed monolayers, a stark reorientation occurs upon deprotonation of the endgroup by rinsing in a KOH solution. The carboxylate plane normal is now about 66 degrees from sample normal, a much more upright orientation. Data indicate this reorientation may also cause a more upright orientation to the alkyl portion of the molecules.     

Structural characterization of nickel oxide nanowires by X-ray absorption near-edge structure spectroscopy

Nickel oxide nanowires modified by poly(vinylpyrrolidone) (PVP) were synthesized via a simple chemical pattern. For the first time NiO nanowires with diameters ranging from 40 to 100 nm with the expected ratio (length vs diameter) ranging from 54 to 90 were grown using a simple solution-phase approach (mild method). These nickel nanowires exhibited unique photoluminescence features and displayed a significant UV luminescence. X-ray absorption near-edge spectroscopy has been used to characterize the local Ni environment and identify the electronic structure. Comparing experimental and theoretical spectra at the Ni and O K edges, we determine the lattice distortion via the analysis of the characteristic preedge features and the multiple-scattering structures detected in the X-ray absorption near-edge structure spectra. The correlation between experimental features and the disordered or distorted local structures is also discussed.     

X-ray absorption near-edge spectroscopic study of nickel catalysts

Ni-isocyanide and Ni-acac complexes have been studied by X-ray absorption spectroscopy. Theoretical analysis has been done using self-consistent full multiple scattering (MS) approach within both muffin-tin (MT) model of the potential and non-MT finite deference method. For the isocyanide complex, it was shown that MS theoretical spectra reproduce all structural details of the X-ray absorption near-edge structure (XANES), but also that it is important to consider the non-MT effects in the potential for a correct simulation of the shape of the pre-edge structures. The contribution of a non-constant potential in the interstitial regions is extremely important for the interpretation of the XANES of Ni(acac)₂.     

Self-assembled carbon nanotubes on gold: polarization-modulated infrared reflection-absorption spectroscopy, high-resolution X-ray photoemission spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study

Recently we reported noncovalent functionalization of nanotubes in an aqueous medium with ionic liquid-based surfactants, 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), resulting in positively charged single-wall carbon nanotube (SWNT)-1,2 composites. Thiolation of SWNTs with 2 provides their self-assembly on gold as well as templating gold nanoparticles on SWNT sidewalls via a covalent -S-Au bond. In this investigation, we studied the electronic structure, intermolecular interactions, and packing within noncovalently thiolated SWNTs and also nanotube alignment in the bulk of SWNT-2 dried droplets and self-assembled submonolayers (SAMs) on gold by high-resolution X-ray photoemission spectroscopy (HRXPS), C K-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). HRXPS data confirmed the noncovalent nature of interactions within the nanocomposite of thiolated nanotubes. In PM-IRRAS spectra of SWNT SAMs on gold, the IR-active vibrational SWNT modes have been observed and identified. According to PM-IRRAS data, the hydrocarbon chains of 2 are oriented with less tilt angle to the bare gold normal in a SAM deposited from an SWNT-2 dispersion than those of 1 deposited from an SWNT-1 dispersion on the mercaptoethanesulfonic acid-primed gold. For both the dried SWNT-2 bulk and the SWNT-2 SAM on gold, the C K-edge NEXAFS spectra revealed the presence of CH-pi interactions between hydrocarbon chains of 2 and the pi electronic nanotube structure due to the highly resolved vibronic fine structure of carbon 1s --> R*/sigma*C-H series of states in the alkyl chain of 2. For the SWNT-2 bulk, the observed splitting and upshift of the SWNT pi* orbitals in the NEXAFS spectrum indicated the presence of pi-pi interactions. In the NEXAFS spectrum of the SWNT-2 SAM on gold, the upshifted values of the photon energy for R*/sigma*C-H transitions indicated close contact of 2 with nanotubes and with a gold surface. The angle-dependent NEXAFS for the SWNT-2 bulk showed that most of the molecules of 2 are aligned along the nanotubes, which are self-organized with orientation parallel to the substrate plane, whereas the NEXAFS for the SWNT-2 SAM revealed a more normal orientation of functionality 2 on gold compared with that in the SWNT-2 bulk.     

X-ray absorption fine structure spectroscopic study of uranium nitrides

Uranium mononitride (UN), sesquinitride (U₂N₃) and dinitride (UN₂) were characterized by extended X-Ray absorption fine structure spectroscopy. Analysis on UN indicate the presence of three uranium shells at distances of 3.46(3), 4.89(5) and 6.01(6) Å and a nitrogen shell at a distance of 2.46(2) Å. For U₂N₃, two absorbing uranium atoms at different crystallographic positions are present in the structure. One of the uranium atoms is surrounded by nitrogen atoms at 2.28(2) Å and by uranium atoms at 3.66(4) and 3.95(4) Å. The second type of uranium atom is surrounded by nitrogen atoms at 2.33(2) and 2.64(3) Å and by uranium atoms at 3.66(4), 3.95(4) and 5.31(5) Å. Results on UN₂ indicate two uranium shells at 3.71(4) and 5.32(5) Å and two nitrogen shells at 2.28(2) and 4.34(4) Å. The lattice parameters of UN, U₂N₃ and UN₂ unit cells were respectively determined to be 4.89(5), 10.62(10) and 5.32(5) Å. Those results are well in agreement with those obtained by X-Ray diffraction analysis.     

X-ray absorption fine structure of artificial antigens for cadmium

Immunoassay technology as a quick and large-scale screening method to detect metal ions in foods and environmental samples has rapidly been developed due to several advantages over conventional instrument-intensive methods. Unlike biomacromolecule, metal ions are haptens without immunogenicity, so successful preparation of artificial antigens is the first critical step for establishing immunoassay methods for them. In the current paper, cadmium ions were conjugated to BSA and OVA, respectively, using bifunctional chelator, p-SCN-Bn-DTPA. The ultraviolet analysis indicated that the maximum absorption peak of Cd–p-SCN-DTPA–BSA and Cd–p-SCN-DTPA–OVA had a small peak shift and an apparent absorbance increase compared to that of BSA and OVA, and the extents of substitution of ?-amino in both conjugates were 51.2% and 58.6%, respectively. In addition, the EXAFS of conjugates implied that Cd²⁺ coordinated with N and O atoms of DTPA in artificial antigens, the coordination type and number of Cd–DTPA, Cd–p-SCN-Bn-DTPA–BSA, Cd–p-SCN-Bn-DTPA–OVA were the same. XANES region and geometries of the three compounds were also same. These results implied that the three antigens had the similar local structure and atomic geometry.This was the first time that the XAFS was attempted for the identification of artificial heavy metal ion antigens.