Ab-initio calculations and STM observations on tetrapyridyl and Fe(II)-tetrapyridyl-porphyrin molecules on Ag(1 1 1)

We modelled the adsorption of tetra-pyridyl-porphyrin (TPyP) and Fe(II)-tetra-pyridyl- porphyrin (Fe-TPyP) molecules on Ag(1 1 1). TPyP adsorbs in a flat geometry at a distance of 5.6 Å from the surface. The dihedral angle of the pyridyl rings is found to be 70°. The molecular structure remains largely unaffected by the adsorption. The structure of the molecular adlayer should thus be determined mainly by lateral intermolecular interactions. These conclusions are confirmed by scanning tunnelling microscopy observations. Upon metalation spin-polarized states with strong Fe d-character appear in Fe-TPyP near the centre of the gap between the highest occupied and the lowest unoccupied states of a TPyP molecule. We find also that the gap is widened in the presence of Fe. This implies a shift of 0.3 eV of unoccupied states as identified by scanning tunnelling spectroscopy simulations and confirmed by experimental data.     

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.     

Interaction of 2,2,6,6-tetramethyl-3,5-heptanedione with the Si(1 0 0)-2 × 1 surface: Scanning tunneling microscopy and density functional theory study

Room temperature adsorption and reaction of 2,2,6,6-tetramethyl-3,5-heptanedione (dpmH) on the Si(1 0 0)-2 × 1 surface has been studied with ultra-high vacuum scanning tunneling microscopy (UHV-STM) and temperature programmed desorption (TPD). The molecule is found to chemisorb as a mixture of at least five distinct species. Density functional theory (DFT) was used to calculate the structures and adsorption energies of 12 possible addition products. Unique bonding assignments for each experimental feature are proposed by consideration of a common intermediate reaction network, and a comparison of possible reaction pathways leading to the final products. These assignments are: OH inter-dimer dissociation, OH intra-dimer dissociation, 1,5 intra-dimer addition, 1,5 inter-dimer addition, and intra-dimer [2 + 2]CO addition with OH dissociation on an adjacent dimer. TPD and STM results show that the molecule dissociates completely upon annealing to 700 °C with formation of the c(4 × 4) phase at low exposures, and SiC islands for exposures exceeding 0.15 L.     

Electrochemical scanning tunneling microscopy examination of the structures of benzenethiol molecules adsorbed on Au(1 0 0) and Pt(1 0 0) electrodes

In situ electrochemical scanning tunneling microscopy (STM) has been used to examine the structures of benzenethiol adlayers on Au(1 0 0) and Pt(1 0 0) electrodes in 0.1 M HClO₄, revealing the formation of well-ordered adlattices of Au(1 0 0)-(√2 × √5) between 0.2 and 0.9 V and Pt(1 0 0)-(√2 × √2)R45° between 0 and 0.5 V (versus reversible hydrogen electrode), respectively. The coverage of Au(1 0 0)-(√2 × √5) is 0.33, which is identical to those observed for upright alkanethiol admolecules on Au(1 1 1). In comparison, the coverage of Pt(1 0 0)-(√2 × √2)R45° - benzenethiol is 0.5, much higher than those of thiol molecules on gold surfaces. This result suggests that benzenethiol admolecules on Pt(1 0 0) could stand even more upright than those on Au(1 0 0). All benzenethiol admolecules were imaged by the STM as protrusions with equal corrugation heights, suggesting identical molecular registries on Au(1 0 0) and Pt(1 0 0) electrodes, respectively. Modulation of the potential of a benzenethiol-coated Au(1 0 0) electrode resulted in irreversible desorption of admolecules at E ? 0.1 V (vs. reversible hydrogen electrode) and oxidation of admolecules at E ? 0.9 V. In contrast, benzenethiol admolecule was not desorbed from Pt(1 0 0) at potentials as negative as the onset of hydrogen evolution. Raising the potential rendered deposition of more benzenethiol molecules before oxidation of admolecules commenced at E > 0.9 V.     

STM investigations of Au(1 1 1) electrodes coated with vitamin B12 derivatives

Vitamin B₁₂ derivatives immobilized at flame-annealed Au(1 1 1) electrode surfaces have been investigated in close correlation with their structural properties and spatial arrangement at the electrode substrate by scanning tunneling microscopy (STM) in air and in aqueous 0.1 M NaClO₄ solution. The investigated compounds were symmetrical (B₁₂C₁₀S-SC₁₀B₁₂) and nonsymmetrical (B₁₂C₁₀S-SC₁₀) dialkyl disulfide derivatives of vitamin B₁₂, attached to the electrode surfaces by the S-Au bond. The ex situ and in situ STM experiments show the formation of a surface layer, whose packing density and structure is presumably controlled by the spatial arrangement of the large cobyrinate head groups. In presence of the symmetrical B₁₂ compound, a disordered surface layer is observed. Voltammetric investigations show that, in 0.1 M NaClO₄, this layer becomes unstable at potentials approximately ? −1000 mV vs. MSE and is almost completely removed at more negative potentials. The STM imaging properties of the nonsymmetrical B₁₂ surface layer show a significant dependence on the tunneling distance. In particular, at small tunneling distances, a highly regular hexagonal surface pattern is observed that suggests strongly the presence of an ordered surface assembly. Modeling of the B₁₂ head group has been performed to provide information for a structure-related interpretation of the high-resolution STM images. The investigations are first STM results obtained at such B₁₂ modified electrodes.     

Germanium growth on Br-terminated Si(1 0 0)

The consequences of Ge deposition on Br-terminated Si(1 0 0) were studied with scanning tunneling microscopy at ambient temperature after annealing at 650 K. One monolayer of Br was sufficient to prevent the formation of Ge huts beyond the critical thickness of 3 ML. This is possible because Br acts as a surfactant whose presence lowered the diffusivity of Ge adatoms. Hindered mobility was manifest at low coverage through the formation of short Ge chains. Further deposition resulted in the extension and connection of the Ge chains and gave rise to the buildup of incomplete layers. The deposition of 7 ML of Ge resulted in a rough surface characterized by irregularly shaped clusters. A short 800 K anneal desorbed the Br and allowed Ge atoms to reorganize into the more energetically favorable “hut” structures produced by conventional Ge overlayer growth on Si(1 0 0).     

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.     

STM studies of cyclohexene hydrogenation/dehydrogenation and its poisoning by carbon monoxide on Pt(1 1 1)

A scanning tunneling microscope that can be operated in ultra high vacuum (<10⁻⁹ Torr) as well as at high pressures (1 − 10³ Torr) has been utilized to study the structures formed by cyclic C₆ hydrocarbons adsorbed on a platinum (1 1 1) crystal surface. Catalytic reactions of cyclohexene were also studied in the presence of hydrogen at pressures (up to 200 mTorr) and 300 K-350 K temperature range. Cyclohexane and cyclohexene produced the same adsorbed structure, which is attributed to the partially dehydrogenated π-allyl (C₆H₉). 1,3-Cyclohexadiene produced structures similar to those produced by benzene. In contrast 1,4-cyclohexadiene forms a structure that we attribute to intact molecular 1,4-cyclohexadiene. During reaction the STM images appear disordered, indicative of rapid diffusion of surface species. Addition of 5 mTorr of CO stops the catalytic activity and forms an ordered structure on the surface.     

Phase transition of thiophene molecules on Au(1 1 1) in solution

The orientation and packing arrangement of thiophene molecules on a well-defined Au(1 1 1) surface in 0.1 M HClO₄ solution have been investigated as a function of applied potentials by in situ scanning tunneling microscopy (STM) and electrochemical method. Thiophene molecules are found to form highly ordered adlayers in the double layer region. High-resolution STM images reveal different adlayer structures. Thiophene molecules take flat-lying and vertical orientation at 0.3 and 0.6 V, respectively. Compared with the results of electrochemical measurement, we concluded that the phase transition of thiophene on Au(1 1 1) occurs as the potential is changed between 0.1 and 0.65 V.     

Scanning tunneling microscopy investigation of clean (2 1 1) surface of Ta and Mo

Scanning tunneling microscopy was used to obtain images from clean (2 1 1) surfaces of Ta and Mo under the same ultrahigh vacuum conditions. In the case of tantalum the surface is very rough, and single extending atomic chains reach distances up to 100 Å. Those furrows are a surface reconstruction based on creation of (1 1 0) “micro-facets” along the [1 1 1] direction or (1 1 1)fcc micro-facets with a more dense structure than (1 1 0)bcc plane. In contrast, the (2 1 1) surface of Mo is smooth, and single atomic rows are visible on high resolution STM images. Step bunching occurs on the Mo surface, reducing the number of terrace edges.     

Electron-stimulated desorption from an unexpected source: Internal hot electrons for Br-Si(1 0 0)-(2 × 1)

The desorption of Br adatoms from Br-saturated Si(1 0 0)-(2 × 1) was studied with scanning tunneling microscopy as a function of dopant type, dopant concentration, and temperature for 620-775 K. Analysis yields the activation energies and prefactors for desorption, and the former correspond to the energy separation between the Fermi level and Si-Br antibonding states. Thus, electron capture in long-lived states results in Br expulsion via a Franck-Condon transition. Analysis of the prefactors reveals that optical phonons provide the energy needed for the electronic excitation. These results show that desorption induced by an electronic transition can occur in closed system without external stimulus, and they indicate that thermally-excited charge carriers may play a general role in surface reactions.     

Scanning tunneling microscopy luminescence from nanoscale surface of GaAs(1 1 0)

Scanning tunneling microscopy luminescence (STML) was induced from the nanometer scale surfaces of cleaved n-type and p-type GaAs(1 1 0) wafers by using of an ITO-coated optical fiber probe in an ultrahigh-vacuum chamber. The STML from n-type GaAs(1 1 0) surface was induced under negative sample bias when the applied bias exceeds a threshold voltage around −1.5 V. Whereas the STML from p-type GaAs(1 1 0) surface was induced under positive sample bias when the applied bias exceeds a threshold voltage around +1.5 V. The excitation energies at the threshold voltages are consistent with the band gap of GaAs (1.42 eV) at 295 K. The typical quantum efficiencies for n-type and p-type GaAs are about 3 × 10⁻⁵ and 2 × 10⁻⁴ photons/electron, respectively. The observed STML from are attributed to a radiative recombination of electron-hole pairs generated by a hole injection for n-type GaAs under negative sample bias and an electron injection for p-type GaAs under positive sample bias, respectively.     

A theoretical study of the water gas shift reaction mechanism on Cu(1 1 1) model system

The water gas shift (WGS) reaction is an important reaction system and has wide applications in several processes. However, the mechanism of the reaction is still in dispute. In this paper we have investigated the reaction mechanism on the model Cu(1 1 1) system using the density functional method and slab models. We have characterized the kinetics and the thermodynamics of the four reaction pathways containing 24 elementary steps and computed the reaction potential energy surfaces. Calculations show that the formate (HCOO) intermediate mechanism (CO + OH → HCOO → CO₂ + H) and the associative mechanism (CO + OH → CO₂ + H) are kinetically unlikely because of the high formation barrier. On the other hand, the carboxyl (HOCO) intermediate mechanism (CO + OH → HOCO → CO₂ + H) and the redox mechanism (CO + O → CO₂) are demonstrated to be feasible. Our calculations also indicate that surface oxygen atoms can reduce the barriers of both water dissociation and HOCO decomposition significantly. The calculated potential energy surfaces show that the water dissociation which produces OH groups is the rate-determining step at the initial stage of the reaction or in the absence of surface oxygen atoms. With the development of the reaction or in the presence of oxygen atoms on the surface, CO + OH → HOCO and CO + O → CO₂ become the rate-limiting step for the carboxyl and redox mechanisms, respectively.     

Study of vacancy on diamond (1 0 0) (2 × 1) surface from first-principles

Structure and energy related properties of neutral and charged vacancies on relaxed diamond (1 0 0) (2 × 1) surface were investigated by means of density functional theory. Calculations indicate that the diffusion of a single vacancy from the top surface layer to the second layer is not energetically favored. Analysis of energies in charged system shows that neutral state is most stable on diamond (1 0 0) (2 × 1) surface. The multiplicity of possible states can exist on diamond (1 0 0) surface in dependence on the surface Fermi level, which supports that surface diffusion of a vacancy is mediated by the change of vacancy charge states. Analysis of density of states shows surface vacancy can be effectively measured by photoelectricity technology.     

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.     

Formation and characterization of Au/Pd surface alloys on Pd(1 1 1)

The formation of alloys by adsorbing gold on a Pd(1 1 1) single crystal substrate and subsequently annealing to various temperatures is studied in an ultrahigh vacuum by means of Auger and X-ray photoelectron spectroscopy. The nature of the alloy surface is probed by CO chemisorption using temperature-programmed desorption and reflection-absorption infrared spectroscopy. It is found that gold grows in a layer-by-layer fashion on Pd(1 1 1) at 300 K, and starts to diffuse into the bulk after annealing to above ∼600 K. Alloy formation results in a ∼0.5 eV binding energy decrease of the Au 4f XPS signals and a binding energy increase of the Pd 3d features of ∼0.8 eV, consistent with results obtained for the bulk alloy. The experimentally measured CO desorption activation energies and vibrational frequencies do not correlate well with the surface sites expected from the bulk alloy composition but are more consistent with significant preferential segregation of gold to the alloy surface.     

Vertical bonding distances of PTCDA on Au(1 1 1) and Ag(1 1 1): Relation to the bonding type

The vertical bonding distance of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) above the Au(1 1 1) surface has been measured by the normal incidence X-ray standing wave (NIXSW) technique. The carbon skeleton of PTCDA has a vertical distance of D = (3.27 ± 0.02) Å to the Au(1 1 1) substrate. This distance corresponds very nearly to the sum of the van der Waals radii of carbon and gold, suggesting the adsorption to be a physisorptive one. In contrast, the PTCDA/Ag(1 1 1) interface which according to spectroscopic data follows the standard model of chemisorption very closely, shows a considerably smaller bonding distance of D = (2.86 ± 0.01) Å [A. Hauschild, K. Karki, B.C.C. Cowie, M. Rohlfing, F.S. Tautz, M. Sokolowski, Phys. Rev. Lett. 94 (2005) 036106, comment: Rurali et al., Phys. Lett. 95 (2005) 209205, reply: Phys. Rev. Lett. 95 (2005) 209206]. The different vertical adsorption heights of PTCDA on gold and silver are discussed in relation to the different bonding mechanisms on both noble metal surfaces.     

Dynamics of NF3 in a condensed film on Au(1 1 1) as studied by electron-stimulated desorption

We report a low-temperature dynamics study of condensed layers of NF₃ on Au(1 1 1) by time-of-flight electron-stimulated desorption ion angular distribution (TOF-ESDIAD), temperature-programmed desorption (TPD) and low-temperature scanning tunneling microscopy (LT-STM). Upon adsorption at 30 K, molecular NF₃ adsorption occurs first at the step edges and at minor terrace defect sites with the formation of 2D islands. Within the islands, NF₃ is adsorbed in an upright conformation via the nitrogen lone pair electrons projecting fluorine atoms away from the surface as judged by the presence of only a sharp F⁺ central beam in the ESDIAD pattern. At higher coverages, 3D islands start to populate the surface. Electron bombardment of a thick NF₃ (∼6 ML) layer adsorbed on the Au(1 1 1) surface leads to emission of F⁺, N⁺, NF⁺, and ions as observed in the TOF-ESD distribution. Upon heating to ∼37 K, a sudden decrease of the and ion yield, which is not related to thermal desorption, is observed which reflects the surface migration of NF₃ molecules, leading to local thinning of the film. The thinning process occurs at the temperature of onset of molecular rotations and self-diffusion in the bulk NF₃ crystal. In this process, some NF₃ molecules move closer to the surface which results in higher efficiency for ion neutralization by the underlying metal surface. In the TPD spectra, the monolayer desorption is observed to begin at ∼65 K, exhibiting zero-order kinetics with an activation energy of 21 kJ/mol.     

Sulphur overlayers on the Au(1 1 0) surface: LEED and TPD study

The adsorption and desorption of sulphur on the clean reconstructed Au(1 1 0)-(1 × 2) surface has been studied by low energy electron diffraction, Auger electron spectroscopy and temperature programmed desorption. The results obtained show a complex behaviour of the S/Au(1 1 0) system during sulphur desorption at different temperatures. Two structures of the stable ordered sulphur overlayer on the Au(1 1 0) surface, p(4 × 2) and c(4 × 4), were found after annealing the S/Au(1 1 0) system at 630 K and 463 K, respectively. The corresponding sulphur coverage for these overlayers was estimated by AES signal intensity analysis of the Au NOO and S LMM Auger lines to be equal to 0.13 ML and 0.2 ML, respectively. Both sulphur structures appear after removing an excess of sulphur, which mainly desorbs at 358 K as determined from TPD spectra. Furthermore, it was not possible to produce the lower coverage p(4 × 2) sulphur structure by annealing the c(4 × 4) surface. In the case of the p(4 × 2) S overlayer on the Au(1 1 0)-(1 × 2) surface it is proposed that the sulphur is attached to “missing row” sites only. The c(4 × 4) S overlayer arises via desorption of S₂ molecules that are formed on the surface due to mobility of sulphur atoms after a prolonged anneal.     

A theoretical study of Ge adsorption on Si(0 0 1) covered with Bi nanolines

The energetic stability and the equilibrium geometry of Ge adsorption on the Si(0 0 1) surface covered with Bi nanolines were examined by ab initio total energy calculations. We find that there is an energetic preference of Ge atoms lying on the Si(0 0 1) terraces, forming Si^down-Ge^up mixed dimers. Further investigations reveal a repulsive interaction between the mixed dimers and the Bi nanolines, suggesting that the formation of Si^down-Ge^up dimers can be tailored by the presence of the Bi nanolines.