Formation of highly ordered organic monolayers by dative bonding: pyridine on ge(100)

The adsorption of pyridine onto the Ge(100) surface has been studied using both real-time scanning tunneling microscopy (STM) and ab initio pseudopotential density functional calculations. The results show that pyridine molecules adsorb on the electron-deficient down-Ge atoms of the Ge=Ge dimers via Ge-N dative bonding, with the pyridine ring tilted to the surface. The electron-rich up-Ge atoms remaining after adsorption of pyridine induce an asymmetric dimer row, which is mainly reconstructed to the c(4 x 2) structure. At pyridine coverage of 0.25 ML, the adsorbed pyridine molecules form a perfectly ordered monolayer. The entire Ge substrate underlying this organic monolayer rearranges into the c(4 x 2) structure.     

Chemical reactions and adsorption geometries of pyrrole on Ge(100)

The adsorption structures of pyrrole (C(4)H(5)N) on a Ge(100) surface at various coverages have been investigated with both scanning tunneling microscopy (STM) and ab initio density-functional theory (DFT) calculations. Three distinct features are observed in the STM images at low coverages. The comparison of the STM images with the simulation reveals that the most dominant flowerlike feature with a dark side is that the adsorbed pyrrole molecules with H dissociated form bridges between two down Ge atoms of neighboring Ge dimer rows through N-Ge bonding and beta-carbon-Ge interaction. The flowerlike feature without a dark side is also observed as a minority, which is identified as nearly the same structure as the most dominant one where a dissociated H is out of the feature. The third feature showing bright protrusions may be due to a C- and N-end-on (CN) configuration, where the pyrrole molecule is located on one dimer row. At higher coverages, the number of localized configurations increases.     

Self-induced 1-D molecular chain growth of thiophene on Ge(100)

The adsorption of thiophene on Ge(100) has been studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculations. Until now, thiophene is known to react with the Ge(100) dimer through a [4 + 2] cycloaddition reaction at room temperature, similar to the case of thiophene on Si(100). However, we found that thiophene has two adsorption geometries on Ge(100) at room temperature, such as a kinetically favorable Ge-S dative bonding configuration and a thermodynamically stable [4 + 2] cycloaddition adduct. Moreover, our STM results show that under 0.25 ML thiophene molecules preferentially produce one-dimensional molecular chain structures on Ge(100) via the Ge-S dative bonding configuration.     

Atomic imaging of nucleation of trimethylaluminum on clean and H2O functionalized Ge(100) surfaces

The direct reaction of trimethylaluminum (TMA) on a Ge(100) surface and the effects of monolayer H(2)O pre-dosing were investigated using ultrahigh vacuum techniques, such as scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and x-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). At room temperature (RT), a saturation TMA dose produced 0.8 monolayers (ML) of semi-ordered species on a Ge(100) surface due to the dissociative chemisorption of TMA. STS confirmed the chemisorption of TMA passivated the bandgap states due to dangling bonds. By annealing the TMA-dosed Ge surface, the STM observed coverage of TMA sites decreased to 0.4 ML at 250?°C, and to 0.15 ML at 450?°C. XPS analysis showed that only carbon content was reduced during annealing, while the Al coverage was maintained at 0.15 ML, consistent with the desorption of methyl (-CH(3)) groups from the TMA adsorbates. Conversely, saturation TMA dosing at RT on the monolayer H(2)O pre-dosed Ge(100) surface followed by annealing at 200?°C formed a layer of Ge-O-Al bonds with an Al coverage a factor of two greater than the TMA only dosed Ge(100), consistent with Ge-OH activation of TMA chemisorption and Ge-H blocking of CH(3) chemisorption. The DFT shows that the reaction of TMA has lower activation energy and is more exothermic on Ge-OH than Ge-H sites. It is proposed that the H(2)O pre-dosing enhances the concentration of adsorbed Al and forms thermally stable Ge-O-Al bonds along the Ge dimer row which could serve as a nearly ideal atomic layer deposition nucleation layer on Ge(100) surface.     

Formation of hydrogen-bridged cytosine dimers on Cu(110)

Cytosine was adsorbed onto a Cu(110) surface under UHV conditions. Annealing to 370 K resulted in the formation of a (6 x 6)gg low energy electron diffraction (LEED) pattern, even at submonolayer coverages. Examination of this structure with scanning tunneling microscopy (STM) revealed islands of zigzag chains at low coverages and large ordered domains at monolayer saturation. Further annealing to 480 K initiated a phase transition to a (6 x 2)gg structure observed both by LEED and STM. High resolution electron energy loss spectroscopy spectra for both overlayer structures exhibited mainly in-plane modes suggesting upright/tilted species on the surface. Based on the experimental data and supported by density functional theory calculations, a model is proposed for the (6 x 2)gg structure, which involves the formation of deprotonated hydrogen bridge-bonded cytosine dimers, adsorbed through the oxygen atoms.     

Chlorine adsorption on Au(111): chlorine overlayer or surface chloride?

We report the first scanning tunneling microscope (STM) investigation, combined with density functional theory calculations, to resolve controversy regarding the bonding and structure of chlorine adsorbed on Au(111). STM experiments are carried out at 120 K to overcome instability caused by mobile species upon chlorine adsorption at room temperature. Chlorine adsorption initially lifts the herringbone reconstruction. At low coverages (<0.33 ML), chlorine binds to the top of Au(111)-(1 x 1) surface and leads to formation of an overlayer with (square root(3) x square root(3))R30 degree structure at 0.33 ML. At higher coverages, packing chlorine into an overlayer structure is no longer favored. Gold atoms incorporate into a complex superlattice of a Au-Cl surface compound.     

Scanning tunneling microscopy study of metal-free phthalocyanine monolayer structures on graphite

Low temperature scanning tunneling microscopy (STM) studies of metal-free phthalocyanine (H2Pc) adsorbed on highly oriented pyrolytic graphite (HOPG) have shown ordered arrangement of molecules for low coverages up to 1 ML. Evaporation of H2Pc onto HOPG and annealing of the sample to 670 K result in a densely packed structure of the molecules. Arrangements of submonolayer, monolayer, and monolayer with additional adsorbed molecules have been investigated. The high resolution of our investigations has permitted us to image single molecule orientation. The molecular plane is found to be oriented parallel to the substrate surface and a square adsorption unit cell of the molecules is reported. In addition, depending on the bias voltage, different electronic states of the molecules have been probed. The characterized molecular states are in excellent agreement with density functional theory ground state simulations of a single molecule. Additional molecules adsorbed on the monolayer structures have been observed, and it is found that the second layer molecules adsorb flat and on top of the molecules in the first layer. All STM measurements presented here have been performed at a sample temperature of 70 K.     

Self-directed chain reaction by small ketones with the dangling bond site on the Si(100)-(2 x 1)-H surface: acetophenone, a unique example

Using scanning tunneling microscope (STM) at 300 K, we studied the growth of one-dimensional molecular assemblies (molecular lines) on the Si(100)-(2 x 1)-H surface through the chain reaction of small ketone (CH 3COCH 3, PhCOPh, and PhCOCH 3) molecules with dangling bond (DB) sites of the substrate. Acetone and benzophenone show the growth of molecular lines exclusively parallel to the dimer row direction. In contrast, acetophenone molecules show some molecular lines perpendicular, in addition to parallel, to the dimer row direction. Most of the molecular lines perpendicular to the dimer row direction were grown by self-turning the propagation direction of a chain reaction from parallel to perpendicular directions relative to the dimer row. A chiral center created upon adsorption of an acetophenone molecule allows the adsorbed molecules to align with identical as well as alternate enantiomeric forms along the dimer row direction, whereas such variations in molecular arrangement are not observed in the case of acetone and benzophenone molecules. The observed molecular lines growth both parallel and perpendicular to dimer row directions appears to be unique to acetophenone among all the molecules studied to date. Hence, the present study opens new possibility for fabricating one-dimensional molecular assemblies of various compositions in both high-symmetry directions on the Si(100)-(2 x 1)-H surface.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.     

Purely site-specific chemisorption and conformation of trimethylamine on Si(100)c(4 x 2)

One of the fundamental points of interest on the Si(100) surface is how the spatial localization of electron density on the buckled silicon dimer controls the site-specific reaction toward different Lewis acid and Lewis base molecules. We have investigated the adsorption of trimethylamine (TMA) on Si(100)c(4x2) using scanning tunneling microscopy (STM) at 80 K. The adsorbed TMA appears as a triangle-shaped bright protrusion in the occupied-state STM image. The triangle-shaped protrusion is ascribed to three methyl groups in the adsorbed TMA. The center of the protrusion is located on the down atom site, which indicates that the adsorption of TMA occurs only on the down dimer atom. Thus, TMA adsorption on Si(100)c(4x2) is found to be purely site-specific on the down dimer atom and can be categorized in Lewis acid-base reaction.     

Single molecule observations of the adsorption sites of methyl isocyanide on Pt(111) by low-temperature scanning tunneling microscopy

Scanning tunneling microscopy (STM) has been used to directly investigate the local structure of methyl isocyanide (CNCH3) adsorbed on Pt(111). At low coverages, CNCH3 is preferentially adsorbed at on-top sites, in agreement with earlier deductions based on vibrational spectroscopy. When dosed at low coverages at 50 K, the molecules tend to adsorb near other CNCH3 molecules with preferred distances of a and a, where a = 2.78 A is the lattice constant of Pt. Annealing the surface to 120 K, however, results in a more uniform separation of the molecules. At higher coverages, the CNCH3 molecules are observed to occupy both on-top and two-fold bridge sites. On the basis of STM image analysis, CNCH3 forms an ordered layer of (2 x 3) periodicity at 0.33 ML. Additional details on the structures of CNCH3 adsorbed at the on-top and two-fold bridge sites are provided by density functional theory (DFT) calculations. At a coverage that saturates the first layer (0.33 ML), the occupation ratio for the on-top and two-fold bridge bonded CNCH3 is 1:1, which is consistent with the results obtained from the combined use of experimental reflection absorption infrared spectroscopy (RAIRS) data and DFT calculations.     

Self-assembly of semifluorinated n-alkanethiols on {111}-oriented Au investigated with scanning tunneling microscopy experiment and theory

The adsorption of semifluorinated alkanethiols on Au/mica was studied by scanning tunneling microscopy (STM). The adlayer structure produced is based on a p(2 x 2) structure though lines of molecules displayed extensive kinks and bends. In addition, a considerable variation in the contrast of molecular features is found. Molecular modeling calculations confirm that, for the fluorinated thiols, inequivalently adsorbed molecules within a p(2 x 2) registry are present, an aspect that endows the local structure of the adlayer with a higher flexibility in comparison to nonfluorinated thiols, where one adsorption site is strongly favored in a (radical 3 x radical 3) R30 degrees structure. Simulated STM imaging on the optimized systems successfully recovered the effects on the molecular feature contrast induced by the flexibility of the fluorinated thiol adlayer.     

Binding structures of propylene glycol stereoisomers on the Si(001)-2×1 surface: a combined scanning tunneling microscopy and theoretical study

The binding configuration of propylene glycol stereoisomer molecules adsorbed on the Si(001)-2×1 surface was investigated using a combination of scanning tunneling microscopy (STM) and density functional theory calculations. Propylene glycol was found to adsorb dissociatively via two hydroxyl groups exclusively as a bridge between the ends of two adjacent dimers along the dimer row. The chirality was preserved during bonding to Si atoms and was identifiable with STM imaging. The large number of propylene glycol conformers in the gas phase was reduced to a single configuration adsorbed on the surface at low molecular coverage.     

A single molecule view of bistilbene photoisomerization on a surface using scanning tunneling microscopy

The advent of scanning tunneling microscopy (STM) has permitted a detailed atomic view of organic molecules adsorbed on solid surfaces. In this work, we make use of the STM to provide an unprecedented direct single-molecule perspective on the cis-trans photoisomerization of stilbene molecules within ordered monolayers physisorbed on the Ag/Ge(111)-( radical3x radical3)R30 degrees surface. The STM view of the molecular structure transformation upon irradiation provides direct evidence for the generally accepted one-bond-flip mechanism proposed for the photoisomerization process. We also find that the surface environment produces a profound effect on the reaction mechanism. The reaction is observed to proceed mainly through pairs of co-isomerizing molecules situated at domain boundaries. To explain these observations, we propose a mechanism whereby excitation migrates to the domain boundary and the reaction occurs through a biexciton reaction pathway.     

Structural determination of the low-coverage phase of Al on Si(001) surface

The atomic structure of Al layer on Si(001)-(2 x 1) surface has been studied by coaxial impact collision ion scattering spectroscopy. When 0.5 monolayer (ML) of Al atoms are adsorbed on Si(001) at room temperature, it is found that Al adatoms are dimerized and Al ad-dimers are oriented parallel to the underlying Si dimers at the position of centering T3 site with a height of 1.02 Angstroms from the first layer of Si(001). The bond length of the Al dimer is 2.67 Angstroms. With increasing Al coverage up to one ML, Al ad-dimers still occupied near T3 site and the next favorable site is near HH site.     

Ab initio surface reaction energetics of SiH4 and Si2H6 on Si(001)-(2 x 2)

First-principles pseudopotential calculations, within a simple dynamically constrained scheme, have been performed to investigate the reaction of 0.25 ML coverage of SiH4 and Si2H6 with the Si(001)-(2 x 2) surface. The silane molecule (SiH4) is adsorbed on to the surface at a number of different sites (on dimer, interrow, or intrarow) with varying barrier heights. Two distinct structures, which are similar in energy, arise from the initial dissociative reaction SiH4-->SiH3(silyl) + H, where the dissociated species are adsorbed either on the same dimer components or on adjacent dimer components. Several further decays of silyl from SiH4 are presented in two separate regimes of high and low ambient hydrogen coverages. The decomposition of silyl can form two different bridging structures: an on top or an intrarow bridging structure in both of the two hydrogen coverage regimes. The disilane molecule (Si2H6) is also adsorbed upon this surface with varying energy barriers, resulting in a dissociation reaction where two SiH3 species are adsorbed on one dimer or in an adjacent dimer configuration. Plausible energy reaction paths for the above models are presented. The stability of the SiH2 species is also discussed.     

Coverage dependent supramolecular structures: C60:ACA monolayers on Ag(111)

The dependence of supramolecular structure on fractional molecular coverage has been investigated for acridine-9-carboxylic acid (ACA) and the C(60):ACA binary molecular system. The coverage-dependent phase diagram for ACA is first determined from room-temperature STM imaging. At low molecular coverages (theta < 0.4 ML, ML = monolayer), ACA forms a 2-D gas phase. Ordered ACA structures appear with increasing coverage: first a chain structure composed of ACA molecules linked by consecutive O-H...N hydrogen bonds (theta > 0.4 ML), then a dimer structure composed of ACA dimers linked by paired carboxyl-carboxyl hydrogen bonds (theta approximately equal to 1.0 ML). Structures of the C(60):ACA binary system depend on the coverage of predeposited ACA. At intermediate (0.4 ML approximately 0.8 ML) ACA coverages, C(60) deposition results in a hexagonal cooperative structure with the C(60) periodicity nearly 3 times that of the normal C(60) 2-D packing of 1 nm and exists in enantiopure domains. At higher ACA coverages, a C(60) quasi-chain structure is formed in which parallel C(60) chains are spaced by ACA dimer domains. The mechanistic role of the initial ACA phase in the formation of C(60):ACA supramolecular structures is described. Chemically intuitive molecular packing models are presented based on the observed STM images.     

Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Phase transformation driven by valence electron concentration: tuning interslab bond distances in Gd5GaxGe4-x

X-ray single crystal and powder diffraction studies on the Gd(5)Ga(x)()Ge(4)(-)(x)() system with 0 < or = x < or = 2.2 reveal dependence of interslab T-T dimer distances and crystal structures themselves on valence electron concentration (T is a mixture of Ga and Ge atoms). While the Gd(5)Ga(x)()Ge(4)(-)(x)() phases with 0 < or = x < or = 0.6 and valence electron concentration of 30.4-31 e(-)/formula crystallize with the Sm(5)Ge(4)-type structure, in which all interslab T-T dimers are broken (distances exceeding 3.4 A), the phases with 1 < or = x < or = 2.2 and valence electron concentration of 28.8-30 e-/formula adopt the Pu(5)Rh(4)- or Gd(5)Si(4)-type structures with T-T dimers between the slabs. An orthorhombic Pu(5)Rh(4)-type structure, which is intermediate between the Gd(5)Si(4)- and Sm(5)Ge(4)-type structures, has been identified for the Gd(5)GaGe(3) composition. Tight-binding linear-muffin-tin-orbital calculations show that substitution of three-valent Ga by four-valent Ge leads to larger population of the antibonding states within the dimers and, thus, to dimer stretching and eventually to dimer cleavage.     

STM observation of a ruthenium dye adsorbed on a TiO2(110) surface

Individual Ru(4,4'-dicarboxy-2,2'-bipyridine)2(NCS)2 molecules, commonly known as N3, adsorbed on a TiO2 surface were visualized with a scanning tunneling microscope (STM) operated in ultrahigh vacuum. A TiO2(110)-(1 x 1) crystal was taken out from the vacuum vessel and immersed into an acetonitrile solution of N3. A monolayer of pivalate ((CH3)3CCOO-) ions was used to protect the (1 x 1) surface from contamination during the wetting process of the N3 adsorption. The N3 molecules adsorbed on the flat terraces protruded by 0.65 nm from the pivalate monolayer. The image height difference of the admolecules could be understood with the assumption that the N3 molecules anchor to the TiO2 surface via two carboxyl groups. The number density of the N3 molecules on the steps was higher than that on the terraces. The poorly coordinated Ti atoms exposed at the step edges form preferential sites where the carboxyl groups can approach, due to a lower steric obstacle or because the structure of the adsorbed N3 molecules suffers less distortion.