Chemistry of Alanine on Pd(1 1 1): Temperature-programmed desorption and X-ray photoelectron spectroscopic study

The adsorption of alanine is studied on a Pd(1 1 1) surface using X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD). It is found that alanine adsorbs into the second and subsequent layers prior to completion of the first monolayer for adsorption at ∼250 K, while at ∼300 K, alanine adsorbs almost exclusively into the first monolayer with almost no second-layer adsorption. Alanine adsorbs onto the Pd(1 1 1) surface in its zwitterionic form, while the multilayer contains about 30-35% neutral alanine, depending on coverage. Alanine is thermally stable on the Pd(1 1 1) surface to slightly above room temperature, and decomposes almost exclusively by scission of the CCOO bond to desorb CO₂ and CO from the COO moiety, and the remaining fragment yields ethylamine and HCN.     

Self-assembly of 2,6-dimethylpyridine on Cu(1 1 0) directed by weak hydrogen bonding

Sequential stages of formation of a self-assembled monolayer of flat-lying 2,6-dimethylpyridine molecules on a single crystal Cu(1 1 0) surface have been observed by low-temperature scanning tunneling microscopy (LT-STM). At an adsorption temperature of 10 K, all of the molecules are randomly distributed at low coverage upon adsorption. The isolated molecules align their molecular axes parallel to the 〈0 0 1〉 azimuth of the Cu lattice. The nitrogen atom in the molecule is located at the four-fold hollow site. Upon annealing to 100 K, the molecules associate to form head-to-head dimers. The dimer units involve a pair of weak hydrogen bonds between methyl group-hydrogen atoms and N moieties on adjacent molecules, forming a core structure for further growth. In a later stage of self-assembly, single head-to-tail weak hydrogen bonds between ring C-H bonds and N moieties form in chains on the periphery of the central cores, leading to larger domains with a c(6 × 2) overlayer structure.     

Configuration of pentacene (C22H14) films on Si(1 0 0)-2 × 1 studied by NEXAFS

Pentacene films on Si(1 0 0)-(2 × 1) surface at 300 K were investigated using near edge X-ray absorption fine structure (NEXAFS) at the carbon K-edge. NEXAFS spectra show that pentacene molecules are chemisorbed on the Si(1 0 0)-(2 × 1) surface for monolayer with flat-laying and predominantly physisorbed on the Si(1 0 0)-(2 × 1) surface for multilayer films with an upright molecular orientation. Absorption angle of pentacene molecules were measured through π^∗ transition. The angles between the double bond and the silicon surface were 35-55°, 65° and 76° at monolayer, 24 and 48 nm pentacene deposited on the Si(1 0 0) surface, respectively. We observed that the intermediate flat-laying phase is favored for monolayer coverage, while the films of molecules standing perpendicular to the Si(1 0 0) surface are favored for multilayer coverage.     

Ammonia on Ni(1 1 1) surface studied by first principles: Bonding, multilayers structure and comparison with experimental IR and XPS data

DFT calculations have been performed on the adsorption of NH₃ on Ni(1 1 1) to obtain information on the structure of the absorbed species, the nature of the chemical interactions between the adsorbate and the surface and the structure of multilayers formed at high coverage. A cluster model, using localized basis functions as well as an approach based on plane waves and periodic boundary conditions have been considered. The two approaches lead to similar results for the relative stabilities of investigated adsorption sites (atop > fcc > hcp) with an adsorption energy of about 15-24 kcal/mol (depending on the coverage). On the atop site, α-ammonia adsorbs molecularly with an equilibrium distance between the nitrogen atom and the surface of 2.03 ± 0.02 Å and a geometry close to the one of the molecule in the gas phase. The good agreement between the two DFT approaches clearly underlines the local nature of the adsorption reaction. The vibrational frequencies computed for NH₃ adsorbed in this site are in good agreement with experimental values. They show that the interaction with the surface leads to a weakening of the strength of the N-H bond while the angular stretching is stronger. Both orbital and topological analyses were used to investigate chemical interactions between the cluster and the molecule. The results strongly suggest an electrostatic (non-covalent) interaction between the substrate and the molecule. Calculations with NH₃ coverages above 0.25 confirm that saturation occurs at a coverage of 0.25. Above the saturation coverage, ammonia molecules in excess form multiple layers (β and γ ammonia) bonded to the first layer by intermolecular hydrogen bonds. N 1s core level shifts calculations performed for the several investigated coverages are also in good agreement with experimental XPS data. It is shown that the H-bond network more than the bond to the surface allows to understand the N 1s core level variations.     

Adsorption of 2-butyne on Si(0 0 1) at room temperature: A valence band photoemission study

We present an angle resolved ultraviolet photoemission spectroscopy study of the adsorption of 2-butyne (CH₃-CC-CH₃) on Si(0 0 1)-2 × 1 at room temperature. We recorded valence band photoemission spectra for two azimuthal positions of a vicinal silicon surface, where all the rows formed by the surface silicon dimers are parallel. The photoemission symmetry selection rules allow the determination of the orientation of the molecular orbitals. The photoemission signal of the HOMO is enhanced when the electric field is parallel to the dimer rows. This showed that the π orbital left intact after the cyclo-addition reaction of the molecule with one silicon dimer is parallel to the dimer rows. This indicates that each 2-butyne molecule adsorbs on one silicon dimer. In spite of the size of the system and the vicinity of the orbitals, the angle resolved study points out that no dispersion of the electronic bands occurs. Not all the surface dimers are reacted so some disorder still exists on the surface preventing the formation of Bloch states.     

Vibrationally-assisted dissociative adsorption of oxygen on Ru(0 0 0 1)-p(2 × 1)-O

Supersonic molecular beam technique combined with high resolution X-ray photoelectron spectroscopy using synchrotron radiation was applied to the study of the dynamics of dissociative adsorption of oxygen on Ru(0 0 0 1) surface in high coverage region. The Ru(0 0 0 1) surface pre-covered with oxygen atoms of 0.5 monolayer, which corresponds to the p(2 × 1)-O structure, was dosed to oxygen molecules with translational energy of 0.5 eV. Oxygen uptake was compared between the cases with and without the beam source heated in order to verify the effects of internal energy of oxygen. We found drastic enhancement in initial sticking probability of oxygen when the beam source was heated to 1400 K. We concluded that the enhancement of sticking probability is mainly caused by molecular vibrational excitation, indicating that dissociation barrier is located in the exit channel on potential energy surface.     

DFT study of NH3 dissociation on Si(1 1 1)-7 × 7. The role of intermolecular interactions

The adsorption of NH₃ molecule on the Si(1 1 1)-7 × 7 surface modelled with a cluster has been studied using density functional theory (DFT). The results indicate the existence of a precursor state for the non-dissociative chemisorption. The active site for the molecular chemisorption is the adatom; while the NH₃ molecule adsorbs on the Si restatom via this preadsorbed state, the adsorption on the Si adatom is produced practically without an energy barrier. The ammonia adsorption on the adatom induces an electron transfer from the dangling bond of this atom to the dangling bond of the adjacent Si restatom, hindering this site for the adsorption of a second NH₃ incoming molecule. However, this second molecule links strongly by means of two H-bonds. The dissociative chemisorption process was studied considering one and two ammonia molecules. For the dissociation of a lonely NH₃ molecule an energy barrier of ∼0.3 eV was calculated, yielding NH₂ on the adatom and H on the restatom. When two molecules are adsorbed, the NH₃-NH₃ interaction yields the weakening of a N-H bond of the ammonia molecule adsorbed closer the Si surface. As a consequence, the dissociation barrier practically disappears. Thus, the presence of a second NH₃ molecule at the adatom-restatom pair of the Si(1 1 1)-7 × 7 surface makes the dissociative reaction self-assisted, the total adsorption process elapsing with a negligible activation barrier (less than 0.01 eV).     

Study of ammonia molecule adsorbing on diamond (1 0 0) surface

The diamond (1 0 0) surface with amino terminations is investigated based on density function theory within the generalized gradient approximation. Our calculated negative electron affinity of diamond (1 0 0) surface with hydrogen termination provides a necessary condition for initiating radical reaction. The results display that the ammonia molecule can form stable C-N covalent bonds on the diamond surface. In addition, due to the lower adsorption energy of one amino group binding on diamond surface, single amino group (SAG) model is easy to be realized in experiment with the comparison of double amino group (DAG) model. The adsorbed ammonia molecule will induce acceptor-like gap states with little change of the valence and conduction band of diamond in SAG model. The adsorption mechanism in the formation of ammonia monolayer on H-terminated diamond (1 0 0) surface, and two possible adsorption structures (SAG and DAG) were especially studied.     

Self-assembly of zwitterionic molecules on a Au(23 23 21) surface at low temperature

The adsorption of zwitterionic (E) 4-methoxy-4′-(3-n-sulfonatopropyl)stilbazolium (MSPS) molecules on the stepped vicinal Au(23 23 21) surface was studied by scanning tunneling microscopy (STM) at low temperature as a function of the molecular coverage. At the sub-half monolayer, a supramolecular network based on MSPS is preferentially adsorbed onto face-centered cubic stacking regions. At the monolayer, a complete periodic supramolecular film is obtained.     

Substrate-induced symmetry reduction of CuPc on Cu(1 1 1): An LT-STM study

The adsorption of copper phthalocyanine (CuPc) on Cu(1 1 1) was studied by means of low-temperature scanning microscopy. At very low coverage, individual molecules are randomly distributed over the surface. Increasing the coverage, the molecules align in chains before forming ordered domains with a rectangular unit cell. The molecules are centered on top of a copper atom aligning two opposite lobes with a principal axis of the substrate. The topographic images of the molecules show a reduction of the fourfold to a twofold symmetry. At negative sample bias, a switching between two states at a typical rate of 500 Hz is observed for isolated molecules, which are neither adsorbed at defects nor forming chains or domains.     

The adsorption of 1,3-butadiene on Ag(1 1 1): A TPD/IRAS study and importance of lateral interactions

Temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS) have been used to study the adsorption, desorption, molecular orientation and conformation of 1,3-butadiene on Ag(1 1 1) at 80 K. Butadiene adsorbs weakly as an s-trans conformer with the first layer oriented parallel to the silver surface and desorbs without decomposition. A very narrow line shape of the out-of-plane modes at low submonolayer coverage indicates molecular ordering within the diluted adsorbed layer, presumably through weak π-bonding interaction with the surface and intermolecular repulsive interaction. Compression within the first layer at coverages above 0.5 ML is driven by repulsive interaction as seen in both TPD and IRAS data. The IR intensity rollover and peak broadening, together with a significant shift in the TPD peak to lower temperature, indicate a reorientation of the butadiene molecule. Adsorption in the second- and multilayer is characterized by distinct IR frequency shifts and crystal field splitting effects similar to those reported for solid butadiene.     

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.     

Ordered arrangement of 9-aminoanthracene on Au(1 1 1) surfaces: A scanning tunneling microscopy study

We present a scanning tunneling microscopy (STM) investigation of 9-aminoanthracene (AA) on the reconstructed Au(1 1 1) surface. The bare Au(1 1 1) surface shows the herringbone reconstruction which is conserved upon deposition of the organic molecules. Most of the AA molecules are found to decorate the regions of fcc-stacking of the gold surface where a periodic linear arrangement is observed. The orientation of the long molecule axis of individual molecules is along the -directions of the Au substrate. In addition, for individual domains of the surface reconstruction, one of the three possible orientations is preferred. On substrate areas which exhibit a high step density, the steps are completely decorated by AA molecules. A detailed analysis of the STM images reveals that the molecules are located on top terrace levels. The fine structure of individual molecules on the terrace shows a clear dependence on the tunneling voltage and resembles the molecular orbitals of the free AA molecule.     

Change in work function during phase transition of Sc-O/W(1 0 0) system at high temperatures

The change in work function during the phase transition of a Sc-O/W(1 0 0) system at high temperatures of 1500-1700 K was investigated in order to elucidate the mechanism of the decrease in the work function of a (1 × 1)-Sc-O/W(1 0 0) surface. For the measurement of the work function using a secondary electron method at high temperatures, a sample holder was uniquely designed in order to suppress contributions of a large number of thermionic electrons emitted from a low-work-function surface. The obtained work function revealed that the change in work function strongly correlates with the coverage of Sc-O complexes, the stoichiometry of which is Sc₁O₁. The higher the coverage of ScO is, the lower the work function is, suggesting that the work function of the (1 × 1)-Sc-O/W(1 0 0) surface is reduced by the formation of ScO electric dipoles. Furthermore, the decrease in work function was modeled in combination with a previously reported kinetic model describing surface phenomena, i.e., the oxidation, oxygen desorption, diffusion and surface segregation of Sc-O complexes, during the phase transition of the Sc-O/W(1 0 0) surface at high temperatures. It was confirmed that the proposed model can explain the experimentally obtained change in work function very well. The value of the dipole moment of a ScO electric dipole was determined to be 2.7 × 10⁻³⁰ C m.     

Photoelectron spectroscopy for probing surface reactions at the CO/K/Cu(1 1 5) interface

The adsorption of carbon monoxide on the potassium modified Cu(1 1 5) surface was investigated using photoelectron spectroscopy based on synchrotron radiation. From detailed analysis of the 1s core levels in combination with existing knowledge, the assignment of surface species is performed. It is demonstrated that in dependence of the alkali coverage, several adsorption states of CO are present on the interface at 135 K. From the temperature dependence of the C 1s and O 1s profiles it is established that surface reactions based on CO dissociation start from 223 K over an interface with a potassium coverage close to half a complete K overlayer. The role of potassium as a reordering environment of adsorbed CO, leading to molecule dissociation and disproportionation is proposed. It is observed that a higher density of potassium on the substrate surface blocks adsorption sites for incoming CO molecules and no dissociation takes place.     

Molecularly resolved studies of the role of basicity in the reaction of amines with oxygen at a Cu(1 1 0) surface

The role of basicity in the surface reactions of amines has been investigated in an STM/XPS study of the oxidation of methylamine, ethylamine and 2,2,2-trifluoroethylamine at a Cu(1 1 0) surface. Methylamine and ethylamine are strongly basic molecules and for sub monolayer concentrations of oxygen form an amine/oxygen complex characterised by a (3 × 1) structure. The complex rapidly decomposes at room temperature to form water and an imide which desorbs via β-elimination. In contrast, 2,2,2-trifluoroethylamine has a relatively low basicity and its reactions with surface oxygen do not involve a stable intermediate.     

Bond polarization and image-potential screening in adsorbed C6F6 on Cu(1 1 1)

The orientation of hexafluorobenzene (C₆F₆) on the Cu(1 1 1) surface has been determined for different coverages with the help of near edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS). The adsorption geometry and the bonding mode of C₆F₆ differ significantly in comparison to its hydrocarbon analog C₆H₆. C₆F₆ is found to adsorb on Cu(1 1 1) with the ring plane parallel to the surface for coverages below 10 ML. Next to the distinct multilayer, bilayer and monolayer phases we also present evidence of sub-monolayer (i.e., 1/2 ML) coverage with different electronic structure. These findings are explained in a phenomenological model based on fluorine’s property as a σ-acceptor and a π-donor and the resulting bond polarization within the molecule, which is stabilized by image-potential screening within the substrate.     

Competition between associative and dissociative adsorption of 1,2-dihalogenated benzenes on Si(1 0 0)2 × 1: Formation of dihalocyclohexadiene, halophenyl and phenylene adstructures

The room temperature (RT) adsorption of 1,2-difluorobenzene (1,2-DFB), 1,2-dichlorobenzene (1,2-DCB) and 1,2-dibromobenzene (1,2-DBB) on Si(1 0 0)2 × 1 have been investigated by X-ray photoelectron spectroscopy (XPS) and temperature programmed desorption (TPD). Both XPS and TPD data show that the relative degree of dissociative to associative adsorption of the dihalogenated benzene (DXB) appears to increase with decreasing electronegativity of the halogen atom (X). In particular, the C 1s intensity ratios for the C-H and C-Si components to the C-X component are found to be 2, 3 and 9.6 for 1,2-DFB, 1,2-DCB and 1,2-DBB, respectively. These results indicate that 1,2-DFB, like benzene, exclusively adsorbs molecularly as a difluorocyclohexadiene adspecies on Si(1 0 0)2 × 1 while 1,2-DBB adsorbs predominantly with double debromination to form 1,2-phenylene. The majority of 1,2-DCB (75%) is found to adsorb molecularly, with the rest (25%) undergone single or double dechlorination to form chlorophenyl and phenylene, respectively. All three DXB molecules appear to have similar coverage as benzene. The two molecular desorption features for 1,2-DFB and 1,2-DCE are observed with desorption maxima at 460 K and 540 K similar to those found for benzene, which suggests that the dihalocyclohexadiene adstructures involve similar bonding through the benzene ring. In accord with the XPS data, no molecular desorption feature is observed for 1,2-DBB on the 2 × 1 surface. Further decomposition of the resulting phenylene adstructures is evident from the desorption fragment, C₂H₂, found at 610 K and 740 K. Recombinative desorption of HCl and HBr above 880 K are also found for 1,2-DCB and 1,2-DBB, respectively. The observed differences between associative and dissociative adsorption for the three DXB adsorbates could be attributed not only to the large difference in the C-X bond strength but also to the relative contributions from inductively withdrawing and resonantly donating electrons exerted by the halogen (X) atoms to the benzene ring.     

Observation of anthraquinone compounds using low temperature scanning tunneling microscopy

Three derivatives of anthraquinone deposited on Cu(1 1 1) have been observed by STM at liquid nitrogen temperature. Adsorption of the three molecules is found to be strongly dependent on the end group (phenyl, thienyl and pyridyl) surrounding the anthraquinone central part. While adsorption of the bi-pyridyl compound yields single molecules on the copper surface, evaporation of the phenyl derivative leads to the formation of stable dimers. The bi-thienyl anthraquinone has an intermediate behaviour with dimer formation and single molecule adsorption. These findings are assumed to result from the polar character of the molecules and from the bond strength of the different substituents with the metallic surface.     

Energetics of oxygen embedment into unreconstructed and reconstructed Cu(1 0 0) surfaces: Density functional theory calculations

Atomic oxygen embedment into a Cu(1 0 0) surface is studied by density functional theory calculation and the nudged elastic band method. As the oxygen coverage increases on the unreconstructed surface from 0.25 monolayer (ML) to 0.75 ML, the energy barrier for oxygen embedment decreases and an energetically favorable sub-surface site is found at 0.75 ML coverage. At a fixed oxygen coverage of 0.5 ML, the oxygen embedment energetics vary with the surface morphology and the embedment is found to be more probable for reconstructed structures compared to the bare surface. On the missing-row reconstructed surface, we find that the energy barrier for atomic oxygen embedment is smaller through the missing-row compared to other paths, suggesting a mechanism for the formation of sub-surface oxygen structures that are consistent with a recent experiment. The energy barrier for sub-surface oxygen diffusion is predicted to be less than that for on-surface diffusion.