Geometrical characterization of adenine and guanine on Cu(1 1 0) by NEXAFS, XPS, and DFT calculation

Adsorption of purine DNA bases (guanine and adenine) on Cu(1 1 0) was studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT) calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed that adenine adsorbates lie almost flat and that guanine adsorbates are tilted up on the surface with the purine ring parallel to the atom rows of Cu(1 1 0). Referring to the previous studies on pyrimidine DNA bases [M. Furukawa, H. Fujisawa, S. Katano, H. Ogasawara, Y. Kim, T. Komeda, A. Nilsson, M. Kawai, Surf. Sci. 532-535 (2003) 261], the isomerization of DNA bases on Cu(1 1 0) was found to play an important role in the adsorption geometry. Guanine, thymine and cytosine adsorption have an amine-type nitrogen next to a carbonyl group, which is dehydrogenated into imine nitrogen on Cu(1 1 0). These bases are bonded by the inherent portion of -NH-CO- altered by conversion into enolic form and dehydrogenation. Adenine contains no CO group and is bonded to Cu(1 1 0) by participation of the inherent amine parts, resulting in nearly flatly-lying position.     

Atom geometry of nanostructured Fe films grown on c(2 × 2)-N/Cu(1 0 0) surface: An investigation by X-ray absorption spectroscopy with multishell analysis

We investigated the growth of Fe nanostructured films on c(2 × 2)-N/Cu(1 0 0) surface with Fe K-edge X-ray absorption fine structure (XAFS) in the near edge and in the extended energy region. The high photon flux of the incident X-rays allowed us to perform multishell analysis of the XAFS oscillations for Fe coverage Θ_Fe < 1 ML. This data analysis yields a detailed investigation of the atom geometry and some insights in the film morphology. At Θ_N < 0.5 ML (N saturation coverage) there is absence of contribution to XAFS from N atoms. First shell analysis of linearly polarized XAFS gives Fe-Fe (or Fe-Cu) bond length values varying between R₁ = 2.526 ± 0.006 Å at the highest Fe coverage (3 ML ) and R₁ = 2.58 ± 0.01 Å at Θ_Fe = 0.5 ML, Θ_N = 0.3 ML, with incidence angle Θ = 35°. These values are different from the case of bcc Fe (R = 2.48 Å), and compatible with fcc Fe (R₁ = 2.52 Å) and fcc Cu (R₁ = 2.55 Å). At the Fe lowest coverage (Θ_Fe = 0.5 ML) the dependence of R₁ on the incidence angle indicates expansion of the outmost layer. Near edge spectra and multishell analysis can be well reproduced by fcc geometry with high degree of static disorder. At N saturation pre-coverage (Θ_N = 0.5 ML) the XAFS analysis has to keep into account the Fe-N bonding. The results suggest two different adsorption sites: one with Fe in a fcc hollow site, surrounded by other metal atoms as nearest neighbours, and one resulting from an exchange with a Cu atom underneath the N layer.     

Thin PTCDA films on Si(0 0 1): 2. Electronic structure

We have studied the thin film formation and the electronic structure of the organic molecular semiconductor 3,4,9,10 perylene tetracarboxylic dianhydride (PTCDA), on clean and on hydrogen-passivated Si(0 0 1) surfaces. The studies were made by means of high resolution X-ray photoelectron spectroscopy (HRXPS), angle-resolved photoelectron spectroscopy (ARPES), near edge X-ray absorption fine structure (NEXAFS) and low energy electron diffraction (LEED). On the H passivated surface the changes in the electronic structure of the substrate and the molecules with increasing film thickness are very small. The molecular orbitals show a dispersive behavior, indicating that the PTCDA layers are ordered. On the reactive clean surface the anhydride groups of the molecule interact with the substrate as indicated by changes in the core level binding energies. This results in a much lower ordering in the film compared to PTCDA on a passivated silicon surface. There is no sign of decomposition of the molecule because of the more reactive substrate.     

Molecular adsorption and growth of naphthalene films on Ag(1 0 0)

The adsorption of naphthalene, vacuum deposited on a Ag(1 0 0) surface, was comprehensively investigated by means of low-energy electron diffraction (LEED), temperature-programmed thermal desorption (TPD) spectroscopy, X-ray photoelectron spectroscopy (XPS), and polarization-dependent near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in the mono- and multilayer regime. A growth of long-range ordered monolayer at 140 K is observed with LEED. The polarization-dependent C 1s NEXAFS shows that the naphthalene molecules in the monolayer lie almost parallel to the Ag(1 0 0) surface. With increasing film thickness, the molecular orientation turns to upright position. Furthermore, NEXAFS measurements show that in the multilayer regime the molecular orientation depends on the substrate temperature during deposition.     

Photoemission, NEXAFS and STM studies of pentacene thin films on Au(1 0 0)

We have investigated the initial stages of the growth of pentacene thin films on the Au(1 0 0) substrate using synchrotron radiation photoelectron spectroscopy (PES), near edge X-ray absorption fine structure (NEXAFS) and scanning tunnelling microscopy (STM). Results indicate a well-ordered structure with the pentacene molecules adopting a predominantly flat orientation with respect to the substrate for coverages of less than three monolayers. NEXAFS and photoemission data indicates the presence of a second molecular orientation for thicker films, with the introduction of a slight tilting away from planar bonding geometry at higher pentacene coverages. STM images of coverages less than three monolayers indicate a well-ordered pentacene structure allowing for the calculation of pentacene unit cell parameters. The pentacene molecular rows adopt a side-by-side bonding arrangement on the surface. For pentacene deposited at room temperature, step edges were observed to act as nucleation centres for film growth. Annealing of the substrate to 373 K was found to remove excess molecules and improve film quality, but did not otherwise change the bonding geometry of the pentacene with respect to the surface.     

Adsorption and structure of methyl mercaptoacetate on Cu(1 1 1) surface by XPS and NEXAFS spectroscopy

Methyl mercaptoacetate (MA) on Cu(1 1 1) surface was investigated using synchrotron radiation-based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. MA adsorbs on the surface via thiolate formation and weak interaction of the carbonyl group with the surface. Two different adsorption states previously reported for methanethiolate and ethanethiolate were confirmed, besides atomic sulfur. NEXAFS measurements support gauche-type conformation of MA whose skeleton lies on the surface.     

A study of the interaction between perylene and the TiO2(1 1 0)-(1 × 1) surface-based on XPS, UPS and NEXAFS measurements

The interaction between a semi-large aromatic hydrocarbon compound (perylene) and the TiO₂(1 1 0)-(1 × 1) surface under ultra high vacuum conditions has been probed by X-ray photoemission spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS) and near-edge X-ray absorption fine structure (NEXAFS) methods. UPS measurements of the adsorbate system have been compared with an experimental UPS spectrum of perylene in the gas phase and a calculated spectrum obtained by means of density functional theory (DFT) methods. NEXAFS results of perylene molecules adsorbed on TiO₂(1 1 0)-(1 × 1) were compared with data from an α-phase perylene single crystal. A novel analysis of the valence data has been employed to show that no strong chemical interaction takes place between perylene and the TiO₂(1 1 0)-(1 × 1) surface. Furthermore, angle-dependent NEXAFS measurements and the growth curve results suggest that the perylene molecules are oriented flat down onto the TiO₂ substrate due to weak van der Waals interactions.     

A DFT periodic study of the vanadyl pyrophosphate (1 0 0) surface

The unique ability of the vanadyl pyrophosphate (1 0 0) surface to activate n-butane and then selectively oxidise the hydrocarbon to maleic anhydride was investigated using modern quantum chemical methods. Bulk (VO)₂P₂O₇, together with stoichiometric and phosphorus-enriched (1 0 0) surfaces, were analysed using periodic density functional theory calculations. Also simulated was surface ionic relaxation from bulk geometry, and surface hydration. Density of states (DOS) plots show that, whether stoichiometric or phosphorus-enriched, bulk terminated or relaxed, bare or hydrated, local covalent reactivity at the (1 0 0) surface is controlled by vanadium species. Terminal P-O oxygen species are the most nucleophilic surface oxygens, as indicated by their predominance of sub-vanadium high-lying valence band levels. A periodic treatment of (VO)₂P₂O₇(1 0 0) hence gives results qualitatively identical to those obtained from earlier cluster calculations. Simulation of surface ionic relaxation shows that in-plane P-O-V oxygens may also be involved in rupture of substrate C-H bonds for mild oxidation, while surface hydration calculations indicate that dissociative chemisorption of water may play a key role in perpetuation of the selective oxidation cycle.     

Thin PTCDA films on Si(0 0 1): 1. Growth mode

We have studied the interface and thin film formation of the organic molecular semiconductor 3,4,9,10 perylene tetracarboxylic dianhydride (PTCDA) on clean and on hydrogen passivated Si(0 0 1) surfaces. The studies were made by means of high resolution X-ray photoelectron spectroscopy (HRXPS), near edge X-ray absorption fine structure (NEXAFS), low energy electron diffraction (LEED), and atomic force microscopy (AFM). On the passivated surface the LEED pattern is somewhat diffuse but reveals that the molecules grow in several ordered domains with equivalent orientations to the substrate. NEXAFS shows that the molecules are lying flat on the substrate. The Si 2p XPS line shape is not affected when the film is deposited so it can be concluded that the interaction at the interface between PTCDA and the substrate is weak. The evolution of the film formation appears to be homogeneous for the first monolayer with a nearly complete coverage of flat lying molecules based on the XPS attenuation. For layer thickness of 0.5-2 monolayers (ML) the molecules start to form islands, attracting the molecules in between, leaving the substrate partly uncovered. For thicker films there is a Stranski-Krastanov growth mode with thick islands and a monolayer thick film in between. For the clean surface the ordering of the film is much lower and angle resolved photoelectron spectroscopy (ARPES) of the molecular orbitals have only a small dependence of the emission angle. NEXAFS shows that the molecules do not lie flat on the surface and also reveal a chemical interaction at the interface.     

The local adsorption geometry and electronic structure of alanine on Cu{1 1 0}

The adsorption of alanine on Cu{1 1 0} was studied by a combination of near edge X-ray absorption fine structure (NEXAFS) spectroscopy, X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Large chemical shifts in the C 1s, N 1s, and O 1s XP spectra were found between the alanine multilayer and the chemisorbed and pseudo-(3 × 2) alaninate layers. From C, N, and O K-shell NEXAFS spectra the tilt angles of the carboxylate group (≈26° in plane with respect to and ≈45° out of plane) and the C-N bond angle with respect to could be determined for the pseudo-(3 × 2) overlayer. Using this information three adsorption geometries could be eliminated from five p(3 × 2) structures which lead to almost identical heats of adsorption in the DFT calculations between 1.40 and 1.47 eV/molecule. Due to the small energy difference between the remaining two structures it is not unlikely that these coexist on the surface at room temperature.     

Electronic structure of octane on Cu(1 1 1) and Ni(1 1 1) studied by near edge X-ray absorption fine structure

The electronic structure of an octane film grown on Cu(1 1 1) and Ni(1 1 1) was studied using C K-edge near edge X-ray absorption fine structure (NEXAFS). A pre-peak was observed on the bulk edge onset for the 1 ML thick octane films on the metal substrates. The pre-peak originated from metal induced gap states (MIGS) in the band gap of octane. The intensity of the pre-peak for octane/Ni(1 1 1) was the same as that of octane/Cu(1 1 1), suggesting that there was little difference in the density of unoccupied MIGS between the octane film on Ni(1 1 1) and Cu(1 1 1). We discuss the metal dependence of the density of unoccupied MIGS on the band structure of the metals.     

Conformational isomers of stilbene on Si(1 0 0)

Stilbene (1,2-diphenylethylene) has shown an intriguing isomerisation behavior and may serve as a model system for “molecular switches” incorporating a CC double bond. To evaluate the possible use of such molecules as molecular switches on semiconductor surfaces, the adsorption of cis- and trans-stilbene on Si(1 0 0) has been investigated. Identification of both isomers is achieved by differences in adsorption geometry as revealed by NEXAFS, and differences in electronic structure in the occupied and unoccupied molecular orbitals. For both isomers, bonding takes place via the CC double bond to the Si dimer atoms allowing for free movement of the aromatic rings, a necessary prerequisite for photoinduced isomerisation on the surface. Our experimental results agree well with theoretical calculations.     

A theoretical study of CH4 dissociation on Pt(1 0 0) surface

Density functional theory calculations have been performed on the adsorption of H and CH₃, and the dissociation of CH₄ on Pt(1 0 0) surface. It was found that H was adsorbed on the top and bridge sites, while CH₃ was adsorbed only on the top site. The coadsorption of methyl and hydrogen which has also been investigated shows that the interaction between the two adsorbates is stabilising. In addition, two distinct pathways were explored, differing by the initial adsorbed state of CH₄. They converge readily to the same transition state corresponding to an activation energy value of 0.53 eV. These results compare favourably with existing data in the literature for Pt(1 1 1) and Pt(1 1 0).     

The structure of the V2O3(0 0 0 1) surface: A scanned-energy mode photoelectron diffraction study

Scanned-energy mode photoelectron diffraction (PhD), using the O 1s and V 2p photoemission signals, together with multiple-scattering simulations, have been used to investigate the structure of the V₂O₃(0 0 0 1) surface. The results support a strongly-relaxed half-metal termination of the bulk, similar to that found in earlier studies of Al₂O₃(0 0 0 1) and Cr₂O₃(0 0 0 1) surfaces based on low energy electron and surface X-ray diffraction methods. However, the PhD investigation fails to provide definitive evidence for the presence or absence of surface vanadyl (VO) species associated with atop O atoms on the surface layer of V atoms. Specifically, the best-fit structure does not include these vanadyl species, although an alternative model with similar relaxations but including vanadyl O atoms yields a reliability-factor within the variance of that of the best-fit structure.     

DFT study of Pt adsorption on low index SrTiO3 surfaces: SrTiO3(1 0 0), SrTiO3(1 1 1) and SrTiO3(1 1 0)

Density Functional Theory has been used to determine the energetically preferred structures of submonolayer, monolayer, and multilayer Pt films on both ideal terminations of SrTiO₃(1 0 0), SrTiO₃(1 1 1), and SrTiO₃(1 1 0). The strength of the resulting metal/metal oxide interfaces was characterized by the adsorption energy of the film and the film’s work of separation. The two polar surfaces, SrTiO₃(1 1 1) and SrTiO₃(1 1 0), form significantly stronger interfaces than the non-polar SrTiO₃(1 0 0) surface. Approximate criteria were applied to predict the growth mode of Pt on each surface.     

An XPS study on the surface reduction of V2O5(0 0 1) induced by Ar ion bombardment

The effect of the irradiation with Al Kα X-rays during an XPS measurement upon the surface vanadium oxidation state of a fresh in vacuum cleaved V₂O₅(0 0 1) crystal was examined. Afterwards, the surface reduction of the V₂O₅(0 0 1) surface under Ar⁺ bombardment was studied. The degree of reduction of the vanadium oxide was determined by means of a combined analysis of the O1s and V2p photoelectron lines. Asymmetric line shapes were needed to fit the V³⁺2p photolines, due to the metallic character of V₂O₃ at ambient temperature. Under Ar⁺ bombardment, the V₂O₅(0 0 1) crystal surface reduces rather fast towards the V₂O₃ stoichiometry, after which a much slower reduction of the vanadium oxide occurs.     

TiO2-rich reconstructions of SrTiO3(0 0 1): a theoretical study of structural patterns

We have recently reported structure solutions for the (2 × 1) and c(4 × 2) reconstructions of SrTiO₃(0 0 1) based on high-resolution electron microscopy, direct methods analysis of diffraction data and density functional theory. Both reconstructions were found to be TiO₂-rich and feature a single overlayer of TiO₂ stoichiometry on top of a bulk-like TiO₂ layer. Qualitatively, the two reconstruction geometries differ in the cation sub-lattice of the overlayer only, where Ti atoms occupy half of the fivefold cation sites. In the present work we use density functional theory to generate a number of variations of this structural motif in search of patterns of stability. We find a reliable predictor for the reconstruction energy in the ability of oxygen atoms to relax vertically out of the overlayer plane to minimize non-bonded oxygen-oxygen repulsions. Out-of-plane relaxation of oxygen atoms in turn is modulated by the number and relative position of coordinating Ti atoms, which yields simple empirical rules as to how cations are distributed in low energy reconstructions.     

STM study of Si(1 1 3) 3 × 2-Ga surface

The Ga-adsorbed structure on Si(1 1 3) surface at low coverage has been studied by scanning tunneling microscopy (STM). The bright protrusion corresponding to the position of the dimer without the interstitial Si atom of the clean surface disappeared in the filled-state STM image after Ga adsorption, although the protrusion due to the Si adatom still remained. On the basis of the adatom-dimer-interstitial (ADI) model, this result indicates that the Ga atom is adsorbed interstitially at the center of another pentamer that does not have the interstitial Si atom. An ab initio calculation was performed and STM images were simulated.     

Ex-situ prepared films of 4-aminothiophenol on Au(1 1 1): photoemission, NEXAFS and STM measurements

Ex-situ prepared films of 4-aminothiophenol (4-ATP) on Au(1 1 1) have been studied by core-level photoemission using synchrotron radiation, ultra-high-vacuum scanning tunneling microscopy and spectroscopy (UHV-STM, STS), and X-ray absorption (NEXAFS). Photoemission measurements suggest that the film contains a relatively low percentage of 4-ATP bonded to the Au surface, with the presence of free 4-ATP, with oxidised and possibly dimerised molecules also present. We find a lower oxide content than has previously been observed, with well-resolved STM images. These images show a disruption of the long range order of the Au(1 1 1)-(22 × √3) reconstruction, with local nucleation of the reconstruction apparently induced by the 4-ATP, and bias-dependent contrast images. This latter effect, together with the asymmetry observed in STS, is ascribed to the presence of oriented molecular dipole layers between the metal and the organic material. NEXAFS data suggest a broadly upright geometry, with, however, considerable uncertainties.     

Reactivity of monolayer V2O5 films on TiO2(1 1 0) produced via the oxidation of vapor-deposited vanadium

The growth, and reactivity of monolayer V₂O₅ films supported on TiO₂(1 1 0) produced via the oxidation of vapor-deposited vanadium were studied using X-ray photoelectron spectroscopy and temperature programmed desorption (TPD). Oxidation of vapor-deposited vanadium in 10⁻⁷ Torr of O₂ at 600 K produced vanadia films that contained primarily V³⁺, while oxidation in 10⁻³ Torr at 400 K produced films that contained primarily V⁵⁺. The reactivity of the supported vanadia layers for the oxidation of methanol to formaldehyde was studied using TPD. The activity for this reaction was found to be a function of the oxidation state of the vanadium cations in the film.