XPS and NEXAFS studies of aliphatic and aromatic amine species on functionalized surfaces

The chemical constitution of functionalized supports is an important parameter that determines their performance in a broad range of applications, e.g. for immobilization of biomolecules. Supports with amino functionalized surfaces are also often used for DNA microarray experiments. However, spectral data which have been reported for surfaces with amino functionalities suffer from some inconsistencies. In this article a detailed XPS (X-ray photoelectron spectroscopy) and NEXAFS (Near edge X-ray absorption fine structure) database for amino functionalized surfaces is presented. Amino-terminated surfaces prepared from aliphatic and aromatic aminosilanes or aminothiols and a field sample are considered. Effects of aging in air and damage by radiation are addressed as well.     

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.     

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.     

Adsorption and reaction of formaldehyde on thin-film cerium oxide

Formaldehyde adsorption and reaction have been studied on cerium oxide thin films that were vapor deposited on Ru(0 0 0 1). The formaldehyde behavior was examined as a function of temperature, exposure and Ce oxidation state. Formaldehyde chemisorbs on fully oxidized CeO₂ as dioxymethylene, CH₂O₂. The dioxymethylene decomposes and desorbs as formaldehyde between 200 K and 400 K. No other products are formed. On reduced ceria, formaldehyde also adsorbs as dioxymethylene. In addition to the formaldehyde desorption between 200 K and 400 K, a more strongly bound form of dioxymethylene is formed that produces formaldehyde at 440 K. Above 400 K, some of the dioxymethylene reacts to form formate and methoxy on the surface. These species decompose to produce H₂, CO and CH₂O above 500 K.     

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.     

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.     

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.     

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.     

Identification of the vanadyl terminated V2O3(0 0 0 1) surface by NEXAFS spectroscopy: A combined theoretical and experimental study

In this work we present results from density functional theory (DFT) cluster studies to determine polarization-dependent near edge X-ray absorption fine structure (NEXAFS) spectra of the vanadyl termination of the V₂O₃(0 0 0 1) surface. The oxygen K edge spectra are calculated for the relaxed surface geometry where geometric parameters are taken from recent periodic DFT work. A detailed analysis of energetic peak positions, relative intensities, and final state orbitals allows a deep understanding of the complex angular dependence of the calculated spectra on the basis of the local binding environment of differently coordinated oxygen species. Further, our theoretical analysis can assign and explain various spectral details in the experimental NEXAFS data, in particular, those related to vanadyl oxygen. This allows us to support the experimentally suggested vanadyl surface termination.     

Molecular orientation of thiol-derivatized tetraphenylporphyrin on gold studied by XPS and NEXAFS

Tetraphenylporphyrins bearing four linkers consisting of thioacetyl-functionalized carbon chains were immobilized on a gold surface via thiolate-gold bonds using two different preparation routes. The structure of these molecular layers was characterized in detail with synchrotron radiation based core-level spectroscopy, X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results show that the geometry of the molecular layers and the number of linkers that bind to the gold surface depends on the preparation schemes. The deprotection of the linkers through removal of the terminal acetyl group before the molecular adsorption (deprotected systems) resulted in porphyrins bound to the gold surface with on the average three linkers, their normal axis being tilted ∼38° with respect to the surface normal. On the other hand, porphyrin layers prepared directly with the acetyl group still in place on the linkers (protected systems) are made of molecules bound to the gold surface via two linkers on the average. The resulting orientation is more upright, with the normal axis of the porphyrin plane tilted ∼50° with respect to the surface normal. Moreover, NEXAFS measurements revealed that the acetyl deprotected porphyrin layers have a higher degree of ordering than the protected systems.     

H2O induced structural modification of pentacene crystal

Water is one of the obstacles for prolonged life-time of organic based field-effect-transistors (OFETs). Here, we show how H₂O molecules adsorb and affect pentacene crystal by using photoelectron spectroscopic methods. Diffusion into the crystal is accompanied with accumulation of H₂O onto the crystal. Valence band, core level, and X-ray absorption spectra show that H₂O molecules physisorb on the pentacene surface via oxygen, resulting in the increase of the hole-injection barrier. The diffused molecules results in the deteriorated crystallinity, and they reflect the weakening inter-molecular interactions of pentacene crystal.     

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.     

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.     

苝四甲酸二酐在Au(111)表面的取向生长及电子结构研究

利用X射线光电子能谱(XPS),同步辐射紫外光电子能谱(SRUPS),近边X射线吸收精细结构(NEXAFS)以及原子力显微镜(AFM)等技术研究了苝四甲酸二酐(PTCDA)与Au(111)的界面电子结构、PTCDA分子取向及有机薄膜的表面形貌.SRUPS价带谱显示,伴随PTCDA分子的微量沉积(0·5ML),位于费米能级附近Au的表面电子态迅速消失,但却观察不到明显的界面杂化态,这说明PTCDA分子和Au(111)界面间存在弱电子传输过程,但并没有发生明显的化学反应.角分辨NEXAFS以及SRUPS结果证明PTCDA分子是平铺在衬底表面.根据Au4f7/2和C1s峰积分强度随薄膜厚度的变化以及AFM图像可知,PTCDA分子在Au(111)表面是一种典型的Stranski-Krastanov生长模式,即先层状生长,再岛状生长,并且在层状生长到岛状生长的转变过程中,存在有机分子的去润湿过程.     

Adsorption and reaction of methanol on thin-film cerium oxide

Methanol adsorption and reaction has been studied on cerium oxide thin films that were vapor deposited on Ru(0 0 0 1). The methanol behavior was examined as a function of temperature and Ce oxidation state. Methanol reacts at low temperatures with fully oxidized CeO₂ to produce water at 200 K while formaldehyde and methanol desorb near 560 K. This leads to the reduction of the ceria. On reduced ceria, more methanol can be adsorbed and it undergoes more extensive decomposition producing CO and H₂ near 640 K in addition to formaldehyde and water. As the degree of ceria reduction increases, more H₂ and less H₂O are produced. TPD experiments using isotopically labeled CH₃OD show that deuterated water is produced from the oxidized surface at low temperatures, whereas the deuterium is stabilized on the reduced surface and is incorporated into the dihydrogen that desorbs near 600 K. High resolution C 1s and O 1s XPS and C k-edge NEXAFS measurements were performed to quantify the amount of methanol adsorbed and to identify the adsorbed species.     

Glycine on Pt(111): a TDS and XPS study

The adsorption and desorption of in situ deposited glycine on Pt(111) were investigated with thermal desorption spectroscopy (TDS) and X-ray photoelectron spectroscopy (XPS). Glycine adsorbs intact on Pt(111) at all coverages at temperatures below 250 K. The collected results suggest that the glycine molecules adsorb predominantly in the zwitterionic state both in the first monolayer and in multilayers. Upon heating, intact molecules start to desorb from multilayers around 325 K. The second (and possibly third) layer(s) are somewhat more strongly bound than the subsequent layers. The multilayer desorption follows zero order kinetics with an activation energy of 0.87 eV molecule⁻¹. From the first saturated monolayer approximately half of the molecules desorbs intact with a desorption peak at 360 K, while the other half dissociates before desorption. Below 0.25 monolayer all molecules dissociate upon heating. The dissociation reactions lead to H₂, CO₂, and H₂O desorption around 375 K and CO desorption around 450 K. This is well below the reported gas phase decomposition temperature of glycine, but well above the thermal desorption temperatures of the individual H₂, CO₂, and H₂O species on Pt(111), i.e. the dissociation is catalyzed by the surface and H₂, CO₂, and H₂O immediately desorb upon dissociation. For temperatures above 500 K the remaining residues of the dissociated molecules undergo a series of reactions leading to desorption of, for example, H₂CN, N₂ and C₂N₂, leaving only carbon left on the surface at 900 K. Comparison with previously reported studies of this system show substantial agreement but also distinct differences.     

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.     

The adsorption and stability of sulfur containing amino acids on Cu{5 3 1}

The adsorption of l-cysteine and l-methionine amino acids on a chiral Cu{5 3 1} surface was investigated with high resolution X-ray photoelectron spectroscopy (XPS) and carbon K-edge near edge X-ray absorption fine structure (NEXAFS) Spectroscopy using synchrotron radiation. XPS shows that at 300 K l-cysteine adsorbs through two oxygen, a nitrogen and a sulfur atom, in a four point ‘quadrangular footprint’, whereas l-methionine adsorbs through only two oxygen and a nitrogen atom in a ‘triangular footprint’. NEXAFS was used to clarify the adsorption geometry of both molecules, which suggests a binding orientation to the top layer and second layer atoms in two different orientations associated with adsorption sites on {1 1 0} and {3 1 1} microfacets of the Cu{5 3 1} surface.     

Photon-stimulated ion desorption from DCOO/Si(100) near the O K-edge

Photon-stimulated ion desorption from deuterated formic acid chemisorbed on Si(100) has been studied using pulsed synchrotron radiation in the energy region of the oxygen 1s electron excitation. The O 1s electrons of hydroxyl oxygen and carbonyl oxygen could be selectively excited in the O K-edge region because the chemical environments are different. It is found that the CDO⁺ yield is enhanced at the O 1s(C---O)→σ*(C---O) resonance and the CD⁺ yield at the O 1s(C=O)→σ*(C---O) resonance. The results indicate that ion desorption is related both to the antibonding character of excited molecular orbitals and the local character of core hole orbitals.     

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.