Matrix effects in the carbon 1s near edge x-ray absorption fine structure spectra of condensed alkanes

The carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectra of simple gaseous alkane molecules differ from the spectra of the same alkane molecules in the condensed phase. The origin of these large, systematic differences is poorly understood. The NEXAFS spectra of gaseous alkanes are interpreted as a progression of core-->Rydberg transitions with distinctive vibronic structure. The interpretation of the NEXAFS spectra of condensed phase alkanes is varied. Specifically, the degree of Rydberg character in the pre-edge core excited states of condensed alkanes is controversial. We determined the character of core excited states in condensed alkanes with a combination of experiment and computational study. From this, we have determined the nature of matrix effects for these species. The high-resolution carbon 1s NEXAFS spectrum of gaseous neopentane is dramatically different from its condensed phase spectrum, a striking illustration of the dramatic spectroscopic changes that occur upon condensation. High quality ab initio calculations of a cluster designed to model the solid phase environment provide definitive evidence for the reduction of Rydberg character and support the assignment of sigma*C-H) valence character in the pre-edge features in the NEXAFS spectra of condensed alkanes.     

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C(9)H(10) isomers trans-methylstyrene, alpha-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s-->pi(*) transitions which are explained by different coupling of the pi-electron system of the C(6) ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbed molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.     

Selective adsorption of atomic hydrogen on a h-BN thin film

The adsorption of atomic hydrogen on hexagonal boron nitride (h-BN) is studied using two element-specific spectroscopies, i.e., near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and x-ray photoelectron spectroscopy (XPS). B K-edge NEXAFS spectra show a clear change in the energy region of the π* band before and after reaction with atomic deuterium. On the other hand, N K-edge NEXAFS spectra show only a little change. B 1s XPS spectra show a distinct component at the low binding energy side of a main component, while N 1s XPS spectra show peak broadening at the high binding energy side. These experimental results are analyzed by the discrete variational Xα method with a core-hole effect and are explained by a model in which hydrogen atoms are preferentially adsorbed on the B sites of h-BN. Based on the experimental and theoretical results, we propose a site-selective property of BN material on adsorption of atomic hydrogen.     

Spectral identification of fullerene C82 isomers

Ultraviolet photoelectron spectra (UPS) of C(82) isomers have been calculated using hybrid density functional theory in combination with the Gelius model [Proceedings of the International Conference on Electron spectroscopy, edited by D. A. Shirley (North-Holland, Amsterdam, 1972), p. 311; J. Electron Spectrosc. Relat. Phenom. 5, 985 (1974)]. The calculated UPS spectra are found to be isomer dependent and in good agreement with the experimental counterparts. Near-edge x-ray absorption fine structure (NEXAFS), x-ray photoelectron spectroscopy (XPS), x-ray emission spectroscopy, and the resonant inelastic x-ray scattering (RIXS) spectra of three important isomers [3(C(2)), 6(C(s)), and 9(C(2v))] have also been simulated. Strong isomer dependence has also been found for NEXAFS, XPS, and RIXS spectra.     

Adlayers of dimannoside thiols on gold: surface chemical analysis

Carbohydrate films on gold based on dimannoside thiols (DMT) were prepared, and a complementary surface chemical analysis was performed in detail by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), near-edge X-ray absorption fine structure (NEXAFS), FT-IR, and contact angle measurements in order to verify formation of ω-carbohydrate-functionalized alkylthiol films. XPS (C 1s, O 1s, and S 2p) reveals information on carbohydrate specific alkoxy (C-O) and acetal moieties (O-C-O) as well as thiolate species attached to gold. Angle-resolved synchrotron XPS was used for chemical speciation at ultimate surface sensitivity. Angle-resolved XPS analysis suggests the presence of an excess top layer composed of unbound sulfur components combined with alkyl moieties. Further support for DMT attachment on Au is given by ToF-SIMS and FT-IR analysis. Carbon and oxygen K-edge NEXAFS spectra were interpreted by applying the building block model supported by comparison to data of 1-undecanethiol, poly(vinyl alcohol), and polyoxymethylene. No linear dichroism effect was observed in the angle-resolved C K-edge NEXAFS.     

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.     

Study of CVD diamond C(100) by X-ray absorption spectroscopies

Surface sensitive x-ray absorption fine structure measurements were carried out near the carbon K-edge on chemical vapor deposited (CVD) diamond and natural diamond. Utilizing different methods, namely near edge and extended x-ray absorption fine structure measurements (NEXAFS and EXAFS), features were found in the spectra which were attributed to non-diamond coordination fractions, such as bulk C-H bonds, graphite-like and more diamond-like coordinated amorphous carbon domains. Both techniques show that the non-diamond fractions consist mainly of diamond-like amorphous carbon.     

A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface

The adsorption of alanine on the mixed-terminated ZnO(10 ?10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ?10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ?10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ?10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.     

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.     

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.     

Adsorption and charge transfer dynamics of bi-isonicotinic acid on Au(111)

The interaction of bi-isonicotinic acid (4,4(')-dicarboxy-2,2(')-bipyridine) with the Au(111) surface has been investigated using electron spectroscopic techniques. Near edge x-ray absorption fine structure (NEXAFS) spectra show that monolayers of the molecule lie flat to the surface and also reveal that the monolayer is sensitive to the preparation conditions employed. Core level x-ray photoelectron spectroscopy (XPS) shows that the adsorbed molecule does not undergo deprotonation upon adsorption. The "core-hole clock" implementation of resonant photoemission has been used to probe the coupling between molecule and substrate. This technique has revealed the possibility of ultrafast backtransfer from the substrate into the molecule upon resonant excitation of a N 1s core level electron. This is supported by a NEXAFS and XPS investigation of energy level alignments in the system.     

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.     

Substituent effects in the iron 2p and carbon 1s edge near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of ferrocene compounds

The iron 2p and carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of substituted ferrocene compounds (Fe(Cp-(CH3)5)2, Fe(Cp)(Cp-COOH), Fe(Cp-COOH)2, and Fe(Cp-COCH3)2) are reported and are interpreted with the aid of extended Hückel molecular orbital (EHMO) theory and density functional theory (DFT). Significant substituent effects are observed in both the Fe 2p and C 1s NEXAFS spectra. These effects can be related to the electron donating/withdrawing properties of the cyclopentadienyl ligands and their substituents as well as the presence of pi* conjugation between the cyclopentadienyl ligand and unsaturated substituents.     

Core level study of alanine and threonine

Core level X-ray photoemission spectra (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra of alanine and threonine in the gas phase have been measured at the carbon, nitrogen, and oxygen K edges and interpreted in the light of theoretical calculations. For the computations, a set of approximations is made which allows sufficiently accurate calculations of several conformers to be performed in reasonable computing time. The accuracy has been checked by comparing results obtained for proline to our previous, higher level calculations. The photoemission spectra at the carbon and oxygen edges are assigned and compared. The nitrogen 1s photoemission peaks show anomalous broadening which we relate to the populations and types of conformers. The carbon K-edge NEXAFS spectra of alanine and threonine are compared with our previous data on glycine and resonances assigned accordingly. The nitrogen K-edge NEXAFS spectra of alanine and threonine do not show measurable effects due to the population of conformers, in contrast to the photoemission results. At the oxygen K edge, the spectra of these amino acids are similar with two prominent peaks assigned to transitions of O 1s electrons from the oxo and hydroxyl groups to vacant pi* and sigma* orbitals and additional intensity for threonine due to the second OH group. Conformer effects are observable in photoemission but appear to be more difficult to resolve in photoabsorption. We explain this by energetic shifts of opposite sign for the core hole states and unoccupied orbitals, which causes partial cancelation in NEXAFS but not in photoemission.     

Core excitations of naphthalene: vibrational structure versus chemical shifts

High-resolution x-ray photoelectron emission (XPS) and near-edge x-ray absorption fine structure (NEXAFS) spectra of naphthalene are analyzed in terms of the initial state chemical shifts and the vibrational fine structure of the excitations. Carbon atoms located at peripheral sites experience only a small chemical shift and exhibit rather similar charge-vibrational coupling, while the atoms in the bridging positions differ substantially. In the XPS spectra, C-H stretching modes provide important contributions to the overall shape of the spectrum. In contrast, the NEXAFS spectrum contains only vibrational progressions from particular C-C stretching modes. The accuracy of ab initio calculations of absolute electronic transition energies is discussed in the context of minute chemical shifts, the vibrational fine structure, and the state multiplicity.     

Towards a detailed understanding of the NEXAFS spectra of bulk polyethylene copolymers and related alkanes

High energy resolution C 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of ethylene-1-alkene copolymers with systematic variations in comonomer content and thus systematic changes in branch length, branching ratio, and degree of crystallinity are presented. Spectral changes of the σ^*_C–H/Rydberg and σ^*_C–C features in these ideal model systems provide unambiguous experimental evidence for intermolecular interactions with profound effects on the spectral intensity, but only very small energy shifts. Ab initio calculations reproduce the experimental results in detail. The intermolecular interaction observed suggests that interpretation of NEXAFS spectra based on calculations of isolated molecules can be insufficient even in relatively weakly interacting macromolecules.     

Orientation of pentacene molecules on SiO2: from a monolayer to the bulk

Near edge x-ray absorption fine structure (NEXAFS) spectroscopy is used to study the orientation of pentacene molecules within thin films on SiO2 for thicknesses ranging from monolayers to the bulk (150 nm). The spectra exhibit a strong polarization dependence of the pi* orbitals for all films, which indicates that the pentacene molecules are highly oriented. At all film thicknesses the orientation varies with the rate at which pentacene molecules are deposited, with faster rates favoring a thin film phase with different tilt angles and slower rates leading to a more bulklike orientation. Our NEXAFS results extend previous structural observations to the monolayer regime and to lower deposition rates. The NEXAFS results match crystallographic data if a finite distribution of the molecular orientations is included. Damage to the molecules by hot electrons from soft x-ray irradiation eliminates the splitting between nonequivalent pi* orbitals, indicating a breakup of the pentacene molecule.     

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+).     

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.     

Cl/GaAs(111)表面近边X射线吸收精细结构的多重散射研究

利用多重散射团簇方法（MSC）计算了Cl/GaAs(111)吸附表面的Cl原子k边X射线吸收精细结构谱（NEXAFS）.阐明了NEXAFS谱中各个弱结构的物理起源.根据模型计算的结果与实验比较,求得吸附在顶位的氯原子和最近邻的镓原子的键长为（0.213±0.005）nm.这个结果在0.005 nm的误差范围内将广延X射线吸收精细结构（EXFAS）实验谱的Fourier变换结果（0.217 nm）和Slab模型计算的结果（0.208 nm）合理地联系起来.此外,MSC计算求得衬底表面层Ga－As键长为（0.235±0.005）nm,证实Cl吸附引起GaAs(111)表面驰豫.