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.     

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.     

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.     

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 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.     

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.     

Structure of enantiopure and racemic alanine adlayers on Cu(1 1 0)

Plane wave density functional theory has been employed to analyze the structure of alanine adlayers on the Cu(1 1 0) surface. Alanine forms (3 × 2) adlayers on Cu(1 1 0) that are closely related to the structures of glycine on the same surface. There is essentially no energy difference between the most stable racemic and enantiopure alanine adlayers. This observation implies that adsorption of racemic alanine on Cu(1 1 0) will result in a pseudoracemate adlayer.     

Structural stability and electronic structure of iron adsorption on the GaN(0 0 0 1) surface

In this work, we have investigated by means of first-principles spin-polarized calculations, the electronic and magnetic properties of iron (Fe) adsorption and diffusion on the GaN(0 0 0 1) surface using density functional theory (DFT) within a plane-wave pseudopotential scheme. In the surface adsorption study, results show that the most stable positions of a Fe adatom on GaN(0 0 0 1) surface are the H3 sites and T4 sites, for low and high Fe coverage respectively. We found that the Fe-H3 2 × 2 surface reconstruction exhibits a half-metallic behavior with a spin band gap and stable ferromagnetism ordering, which is a desirable property for high-efficiency magnetoelectronic devices. In addition, confirming previous experimental results, we found that the iron monolayers present a ferromagnetic order and a large thermal stability. This is interesting from a theoretical point of view and for its technological applications.     

Local structure determination of a chiral adsorbate: Alanine on Cu(1 1 0)

N 1s and O 1s scanned-energy mode photoelectron diffraction (PhD) has been used to investigate the local structure of a single enantiomer of deprotonated alanine, alaninate, NH₂CH₃CHCOO-, on Cu(1 1 0) in the (3 × 2) phase. The local site is found to be similar to that of glycinate on Cu(1 1 0), with the N atoms in near-atop sites and the O atoms sites consistent with bonding to single surface Cu atoms but substantially off-atop. Unlike the Cu(1 1 0)(3 × 2)pg-glycinate phase, however, in which the two molecular species per unit mesh are mirror images of one another in identical local sites, the intrinsic chirality of l-alaninate means that the two molecules per unit mesh of the (3 × 2) surface phase occupy slightly different local sites. However, an excellent fit to the PhD data can be achieved by a minor modification of the structure found in DFT calculations by R.B. Rankin and D.S. Sholl [Surf. Sci. 574 (2005) L1] in which the heights of the N and O atoms above the surface are reduced by approximately 0.1 Å. The resulting average N-Cu and O-Cu values are 2.02 and 1.98 Å, respectively, with an estimated precision of ±0.03 Å. These bondlengths are shorter than those obtained from DFT by 0.08 and 0.10 Å, respectively.     

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.     

Dissociative adsorption and adsorbate-induced reconstruction on Fe{2 1 1}

The products of CO, NO, O₂ and N₂ dissociation on Fe{2 1 1} have been studied by means of first-principles density functional theory. Preferred adsorption sites for adatoms C, N and O are identified, and trends in charge transfer and surface magnetism described. An experimentally observed (2 × 1) reconstruction induced by O is confirmed to be energetically stable, and a similar reconstruction induced by N is tentatively predicted. It is argued that these reconstructions may be important not only in the context of the catalytic reactivity of the Fe{2 1 1} surface, but also for the initial stages of surface nitridation and oxidation.     

Density functional theory investigation of CN on Cu(1 1 1), Ni(1 1 1) and Ni(1 0 0)

The adsorption of CN on Cu(1 1 1), Ni(1 1 1) and Ni(1 0 0) has been investigated using density functional theory (DFT). While experimental studies of CN on Cu(1 1 1) show the molecular axis to be essentially parallel to the surface, the normally-preferred DFT approach using the generalised gradient approximation (GGA) yields a lowest energy configuration with the C-N axis perpendicular to the surface, although calculations using the local density approximation (LDA) do indicate that the experimental geometry is energetically favoured. The same conclusions are found for CN on Ni(1 1 1); on both surfaces bonding through the N atom is always unfavourable, in contrast to some earlier published results of ab initio calculations for Ni(1 1 1)/CN and Ni(1 0 0)/CN. The different predictions of the GGA and LDA approaches may lie in subtly different relative energies of the CN 5σ and 1π orbitals, a situation somewhat similar to that for CO adsorbed on Pt(1 1 1) which has proved challenging for DFT calculations. On Ni(1 0 0) GGA calculations favour a lying-down species in a hollow site in a geometry rather similar to that found experimentally and in GGA calculations for CN on Ni(1 1 0).     

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.     

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.     

First principle calculations of benzotriazole adsorption onto clean Cu(1 1 1)

The adsorption of benzotriazole (BTAH or C₆N₃H₅) on a Cu(1 1 1) surface is investigated by using first principle density functional theory calculations (VASP). It is found that BTAH can be physisorbed (<0.1 eV) or weakly chemisorbed (∼0.43 eV) onto Cu(1 1 1), and the chemical bond is formed through nitrogen sp² lone pairs. The weak chemisorption can be stabilized by reaction with neighboring protonphilic radicals, like OH⁻. Furthermore, the geometries and associated energies of intermolecular hydrogen bonds between adsorbates on Cu(1 1 1) are also calculated. A model of the first layer of BTAH/BTA⁻ on Cu(1 1 1) surface is developed based on a hydrogen bond network structure.     

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.     

STM study of l-serine adsorption on Cu(0 0 1)

The adsorption of l-serine on Cu(0 0 1) surface at 310 K was studied by scanning tunneling microscope (STM). l-serine molecules on the Cu(0 0 1) initially formed a domain of thick lines with a order structure along the direction on the terraces regardless of the coverage of serine. The thick lines were partly replaced by thin line along the direction, and completely disappeared in 2 h. It is considered that in these structures hydrogen bonds involved in hydroxymethyl group between adsorbates play some role in addition to intermolecular hydrogen bond between a hydrogen atom of amino group and an oxygen atom of carboxy group for alanine adsorption.     

The adsorption geometry of sulphur on Ir{1 0 0}: A quantitative LEED study

A quantitative low energy electron diffraction (LEED) analysis has been performed for the p(2 × 2)-S and c(2 × 2)-S surface structures formed by exposing the (1 × 1) phase of Ir{1 0 0} to H₂S at 750 K. S is found to adsorb on the fourfold hollow sites in both structures leading to Pendry R-factor values of 0.17 for the p(2 × 2)-S and 0.16 for the c(2 × 2)-S structures. The distances between S and the nearest and next-nearest Ir atoms were found to be similar in both structures: 2.36 ± 0.01 Å and 3.33 ± 0.01 Å, respectively. The buckling in the second substrate layer is consistent with other structural studies for S adsorption on fcc{1 0 0} transition metal surfaces: 0.09 Å for p(2 × 2)-S and 0.02 Å for c(2 × 2)-S structures. The (1 × 5) reconstruction, which is the most stable phase for clean Ir{1 0 0}, is completely lifted and a c(2 × 2)-S overlayer is formed after exposure to H₂S at 300 K followed by annealing to 520 K. CO temperature-programmed desorption (TPD) experiments indicate that the major factor in the poisoning of Ir by S is site blocking.     

Nitrogen adsorption and thin surface nitrides on Cu(1 1 1) from first-principles

Experimental studies of nitrogen adsorbed on a Cu(1 1 1) surface show that the surface layer undergoes a reconstruction to form a pseudo-(1 0 0) structure. We use ab initio techniques to demonstrate the theoretical stability of this reconstructed surface phase over a range of conditions. We systematically investigate the chemisorption of N on the Cu(1 1 1) surface, from 0.06 to 1 ML coverage. A peculiar atomic relaxation of N atoms for 0.75 ML is identified, which results in the formation of a (metastable) “N-trimer cluster” on the surface. We have also investigated surface nitride formation, as suggested from experiments. A surface nitride-like structure similar to the reported pseudo-(1 0 0) reconstruction is found to be highly energetically favored. Using concepts from “ab initio atomistic thermodynamics”, we predict that this surface nitride exists for a narrow range of nitrogen chemical potential before the formation of bulk Cu₃N.     

NO adsorption and diffusion on unreconstructed Pt{1 0 0} surface. A density functional theory investigation

Ab initio density functional theory was used to investigate the adsorption and diffusion of a single NO molecule on the unreconstructed Pt{1 0 0}-(1 × 1) surface. To our knowledge this is the first theoretical study of the NO diffusion activation energy on the Pt{1 0 0} surface. The most stable adsorption position for NO corresponds to the bridge site with the axis of the molecule perpendicular to the surface. The bond of the NO molecule to the surface is through the N-atom. We found that there is a low adsorption energy when the NO molecule is bonded through the O-atom and the axis is perpendicular to the surface, for the three high symmetry sites investigated. NO diffusion between bridge-hollow sites, bridge-atop sites, and hollow-atop sites was also investigated. The barrier for NO diffusion is 0.41 eV, which corresponds to the energy difference between the bridge and hollow sites. This value is around 15% of the highest adsorption energy found on this surface. NO stretch frequencies are also calculated for the three high symmetry sites investigated.