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.     

pH dependence of the electronic structure of glycine

The carbon, nitrogen, and oxygen K-edge spectra were measured for aqueous solutions of glycine by total electron yield near-edge X-ray absorption fine structure (TEY NEXAFS) spectroscopy. The bulk solution pH was systematically varied while maintaining a constant amino acid concentration. Spectra were assigned through comparisons with both previous studies and ab initio computed spectra of isolated glycine molecules and hydrated glycine clusters. Nitrogen K-edge solution spectra recorded at low and moderate pH are nearly identical to those of solid glycine, whereas basic solution spectra strongly resemble those of the gas phase. The carbon 1s --> pi*(C=O) transition exhibits a 0.2 eV red shift at high pH due to the deprotonation of the amine terminus. This deprotonation also effects a 1.4 eV red shift in the nitrogen K-edge at high pH. Two sharp preedge features at 401.3 and 402.5 eV are also observed at high pH. These resonances, previously observed in the vapor-phase ISEELS spectrum of glycine, have been reassigned as transitions to sigma* bound states. The observation of these peaks indicates that the amine moiety is in an acceptor-only hydrogen bond configuration at high pH. At low pH, the oxygen 1s --> pi*(C=O) transition exhibits a 0.25-eV red shift due to the protonation of the carboxylic acid terminus. These spectral differences indicate that the variations in electronic structure observed in the NEXAFS spectra are determined by the internal charge state and hydration environment of the molecule in solution.     

Orbital-resolved partial charge transfer from the methoxy groups of substituted pyrenes in complexes with tetracyanoquinodimethane--a NEXAFS study

It is demonstrated that the near-edge X-ray absorption fine structure (NEXAFS) provides a powerful local probe of functional groups in novel charge transfer (CT) compounds and their electronic properties. Microcrystals of tetra-/hexamethoxypyrene as donors with the strong acceptor tetracyano-p-quinodimethane (TMP/HMP-TCNQ) were grown by vapor diffusion. The oxygen and nitrogen K-edge spectra are spectroscopic fingerprints of the functional groups in the donor and acceptor moieties, respectively. The orbital selectivity of the NEXAFS pre-edge resonances allows us to precisely elucidate the participation of specific orbitals in the charge transfer process. Upon complex formation, the intensities of several resonances change substantially and a new resonance occurs in the oxygen K-edge spectrum. This gives evidence of a corresponding change of hybridization of specific orbitals in the functional groups of the donor (those derived from the frontier orbitals 2e and 6a(1) of the isolated methoxy group) and acceptor (orbitals b(3g), a(u), b(1g), and b(2u), all located at the cyano group) with π*-orbitals of the ring systems. Along with this intensity effect, the resonance positions associated with the oxygen K-edge (donor) and nitrogen K-edge (acceptor) shift to higher and lower photon energies in the complex, respectively. A calculation based on density functional theory qualitatively explains the experimental results. NEXAFS measurements shine light on the action of the functional groups and elucidate charge transfer on a submolecular level.     

Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy

Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.     

X-ray spectroscopy of heterocyclic biochemicals: xanthine, hypoxanthine, and caffeine

The electronic structures of the purine derivatives xanthine, hypoxanthine and caffeine have been investigated in the gas phase using C, N, and O 1s X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results have been interpreted by means of ab initio calculations using the third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Green's function and the second-order ADC method (ADC(2)) for the polarization propagator. The carbon, nitrogen and oxygen K-edge NEXAFS spectra of xanthine and caffeine are very similar, since the molecules differ only by substitution of three hydrogen atoms by methyl groups. For hypoxanthine, the electronic structure and spectra differ considerably from xanthine as the purine ring is more highly conjugated, and there is one less oxo group. Effects due to oxo-hydroxy tautomerism were not observed. However, the two oxo tautomeric forms of hypoxanthine oxo-N(9)-H and oxo-N(7)-H are populated in the gas phase, and the C 1s spectra can be simulated only by taking account of these two tautomers, with appropriate Boltzmann population ratios which we have also calculated. For xanthine and caffeine, single tautomeric forms were observed.     

Decoration of nitrogen vacancies by oxygen atoms in boron nitride nanotubes

Decoration of nitrogen vacancies by oxygen atoms has been studied by near-edge X-ray absorption fine structure (NEXAFS) around B K-edge in several boron nitride (BN) structures, including bamboo-like and multi-walled BN nanotubes. Breaking of B-N bonds and formation of nitrogen vacancies under low-energy ion bombardment reduces oxidation resistance of BN structures and promotes an efficient oxygen-healing mechanism, in full agreement with some recent theoretical predictions. The formation of mixed O-B-N and B-O bonds is clearly identified by well-resolved peaks in NEXAFS spectra of excited boron atoms.     

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.     

The electronic structure and adsorption geometry of L-histidine on Cu(110)

The adsorption of L-histidine on clean and oxygen-covered Cu(110) surfaces has been studied by soft X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The valence band spectra, carbon, nitrogen and oxygen 1 s XPS and N K edge absorption spectra were measured for submonolayer, monolayer, and multilayer films. The spectra provide a detailed picture of the electronic structure and adsorption geometry at each coverage. In the monolayer, the histidine molecules are randomly oriented, in contrast to the submonolayer regime, where the molecules are coordinated to the copper surface with the imidazole functional group nearly parallel to, and strongly interacting with, the surface. The pi*/sigma* intensity ratio in NEXAFS spectra at the nitrogen edge varies strongly with angle, showing the imidazole ring is oriented. Adsorption models are proposed.     

Surface sensitive study to determine the reactivity of soot with the focus on the European emission standards IV and VI

Diesel soot (Euro IV and Euro VI) was investigated with spectroscopic methods such as near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoemission spectroscopy (XPS). C and O K-edge NEXAFS show that structural disorder on the surface is accompanied by a higher amount of oxygen functional groups. O K-edge NEXAFS and O1s XPS results are discussed with the aim to elucidate the nature of the oxygen surface species. The analysis of the data presented here allows the postulation of a hypothetical structure for soot samples emitted by diesel engines.     

Investigating the electronic structure and bonding in uranyl compounds by combining NEXAFS spectroscopy and quantum chemistry

The nature of the reactivity of the "yl" oxygens has been a subject of constant interest for a long time in uranyl chemistry. Thus, the electron-donor ability of the equatorial ligands plays an important role in the nature of the uranyl U=O bond. In this paper, a combination of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and both ground-state and time-dependent density functional theory (DFT) calculations have been used to examine the effect of equatorial plane ligation on the U=O bonding in two uranyl complexes: [UO(2)(py)(3)I(2)] and [UO(2)(CN)(5)][NEt(4)](3). By coupling experimental data and theory, spectral features observed in the oxygen K-edge NEXAFS spectra have been assigned. Despite the inert character of the U=O bond, we observe that the electron-donating or withdrawing character of the equatorial ligands has a measurable effect on features in the NEXAFS spectra of these species and thereby on the unoccupied molecular orbitals of {UO(2)}(2+).     

Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: experiment and theory

The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288 eV photon energy, due to absorption to pi* virtual orbitals, and broader structures at higher energy, involving sigma* virtual orbitals. The sharp absorption structures to the pi* empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of pi* symmetry, from the six chemically shifted C 1s core orbitals.     

Acetone adsorption on ice investigated by X-ray spectroscopy and density functional theory

Using a combination of X-ray photoemission and near-edge X-ray absorption spectroscopy (NEXAFS) as well as density-functional theory (DFT), we have investigated the adsorption of acetone on ice in the temperature range from 218 to 245 K. The adsorption enthalpy determined from experiment (45 kJ mol(-1)) agrees well with the adsorption energy predicted by theory (41 to 44 kJ mol(-1)). Oxygen K-edge NEXAFS spectra indicate that the presence of acetone at the ice surface does not induce the formation of a pre-melted layer at temperatures up to 243 K. DFT calculations show that the energetically most favored adsorption geometry for acetone on ice is with the molecular plane almost parallel to the surface.     

Electronic structure of copper phthalocyanine: an experimental and theoretical study of occupied and unoccupied levels

An experimental and theoretical study of the electronic structure of copper phthalocyanine (CuPc) molecule is presented. We performed x-ray photoemission spectroscopy (XPS) and photoabsorption [x-ray absorption near-edge structure (XANES)] gas phase experiments and we compared the results with self-consistent field, density functional theory (DFT), and static-exchange theoretical calculations. In addition, ultraviolet photoelectron spectra (UPS) allowed disentangling several outer molecular orbitals. A detailed study of the two highest occupied orbitals (having a(1u) and b(1g) symmetries) is presented: the high energy resolution available for UPS measurements allowed resolving an extra feature assigned to vibrational stretching in the pyrrole rings. This observation, together with the computed DFT electron density distributions of the outer valence orbitals, suggests that the a(1u) orbital (the highest occupied molecular orbital) is mainly localized on the carbon atoms of pyrrole rings and it is doubly occupied, while the b(1g) orbital, singly occupied, is mainly localized on the Cu atom. Ab initio calculations of XPS and XANES spectra at carbon K edge of CuPc are also presented. The comparison between experiment and theory revealed that, in spite of being formally not equivalent, carbon atoms of the benzene rings experience a similar electronic environment. Carbon K-edge absorption spectra were interpreted in terms of different contributions coming from chemically shifted C 1s orbitals of the nonequivalent carbon atoms on the inner ring of the molecule formed by the sequence of CN bonds and on the benzene rings, respectively, and also in terms of different electronic distributions of the excited lowest unoccupied molecular orbital (LUMO) and LUMO+1. In particular, the degenerate LUMO appears to be mostly localized on the inner pyrrole ring.     

Polyaniline films electrodeposited on iron from oxalic acid solution: linear dichroism of X-ray absorption and molecular arrangement

Journal of Solid State Electrochemistry - The linear dichroism in the near-edge X-ray absorption fine structure (NEXAFS) spectra measured at the K edges of carbon and nitrogen was used to analyze...     

pH-dependent x-ray absorption spectra of aqueous boron oxides

Near edge x-ray absorption fine structure (NEXAFS) spectra at the boron K-edge were measured for aqueous boric acid, borate, and polyborate ions, using liquid microjet technology, and compared with simulated spectra calculated from first principles density functional theory in the excited electron and core hole (XCH) approximation. Thermal motion in both hydrated and isolated molecules was incorporated into the calculations by sampling trajectories from quantum mechanics∕molecular mechanics simulations at the experimental temperature. The boron oxide molecules exhibit little spectral change upon hydration, relative to mineral samples. Simulations reveal that water is arranged nearly isotropically around boric acid and sodium borate, but the calculations also indicate that the boron K-edge NEXAFS spectra are insensitive to hydrogen bonding, molecular environment, or salt interactions.     

Human fibrinogen adsorption onto single-walled carbon nanotube films

The adsorption behavior of human fibrinogen (Hfg) on single-walled carbon nanotube (SWNT) films was investigated using scanning electron microscopy (SEM) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. It was shown in the SEM images that fibrinogen was adsorbed strongly on the surface of SWNT when the samples were incubated in the Hfg solutions for 10 min. The dependence of adsorption on the concentration of fibrinogen was also investigated and it was found that adsorption increased with increasing concentration. In order to further explore the adsorption of fibrinogen on SWNT surface, NEXAFS spectra were obtained at the N K-edge and the C K-edge. The results confirmed the conclusion regarding the dependence of adsorption on fibrinogen concentration. It is demonstrated that, due to its high sensitivity to the surface elements, NEXAFS spectroscopy is a powerful tool to investigate the adsorption of fibrinogen on SWNT films.     

Molecular orientation in electrodeposited polypyrrole films

The molecular arrangement in electrodeposited polypyrrole films was studied by means of linear dichroism in the near-edge X-ray absorption fine structure (NEXAFS) spectra measured at the K absorption edges of carbon and nitrogen. It has been found that the change of the exciting radiation incidence from normal to grazing leads to an increase in the intensity of π*-related resonances with simultaneous decrease in the intensity of σ*-related resonances in the spectra. Similar changes in the spectra measured for both absorption edges indicate a pronounced conjugation of π-bonds in the polypyrrole chains in the grown films. Preferential in-plane orientation of pyrrole rings relative to the substrate surface is observed for all the deposited films. The linear dichroism is more pronounced at the initial stages of deposition (2D growth) than at later stages characterized by “cauliflower”-like morphology of the grown film.     

Hydrogen bonding in methanol clusters probed by inner-shell photoabsorption spectroscopy in the carbon and oxygen K-edge regions

Hydrogen bonding in methanol clusters has been investigated by using inner-shell photoabsorption spectroscopy and density functional theory (DFT) calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of H(CH(3)OH)(n)(+) were measured as the soft x-ray absorption spectra of methanol clusters. The first resonance peak in the PIY curves, which is assigned to the sigma*(O-H) resonance transition, exhibits a 1.20 eV blueshift relative to the total-ion-yield (TIY) curves of molecular methanol in the oxygen K-edge region, while it exhibits a shift of only 0.25 eV in the carbon K-edge region. Decreased intensities of the transitions to higher Rydberg orbitals were observed in the PIY curves of the clusters. The drastic change in the sigma*(O-H) resonance transition is interpreted by the change in the character of the sigma*(O-H) molecular orbital at the H-donating OH site due to the hydrogen-bonding interaction.     

NEXAFS measurements of the molecular ordering in the boundary layers of liquid crystalline free standing films

By near edge X-ray absorption fine-structure (NEXAFS) spectroscopy a finite molecular tilt angle in the surface layer of a free standing film in the liquid crystalline smectic A phase of C7 was directly detected. Analysis of the angular dependent intensities of the oxygen K edge NEXAFS spectra leads to an average tilt angle of the molecules in the surface layer of about 34°, which is characteristic for the bulk smectic C* phase of C7.