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.     

Identification of color centers on MgO(001) thin films with scanning tunneling microscopy

Localized electronic defects on the surface of a 4 monolayer (ML) thin MgO(001) film deposited on Ag(001) have been investigated by low-temperature scanning tunneling microscopy and spectroscopy. Depending on the location of the defect, we observe for the first time different defect energy levels in the band gap of MgO. The charge state of defects can be manipulated by interactions with the scanning tunneling microscope tip. Comparison with ground state energy levels of color centers on the MgO surface obtained from embedded cluster calculations corroborates the assignment of the defects to singly and doubly charged color centers.     

Sexithiophene adlayer growth on vicinal gold surfaces

We have investigated the initial stages of vacuum-deposited sexithiophene (alpha-6T) adlayer formation on Au(111) vicinal surfaces at room temperature. The in situ scanning tunneling microscopy (STM) and photoemission spectroscopy (PES) reveal a step edge-driven growth of alpha-6T on the Au(111) vicinal surfaces that first leads to the formation of an ordered monolayer, comprising two phases with the molecular major axes aligned along the step edges. The monolayer formation is then followed by the appearance of a single-phase 2D superstructure at a two-monolayer coverage. The results highlight the potential of using vicinal metal surfaces as templates for generating organized organic nanostructures over macroscopic areas for applications in organic electronics and moletronics.     

Adsorption of water on reconstructed rutile TiO2(011)-(2 x 1): Ti=O double bonds and surface reactivity

Recent combined experimental and theoretical studies (Beck et al., Phys. Rev. Lett. 2004, 93, 036104) have provided evidence for Ti=O double-bonded titanyl groups on the reconstructed rutile TiO(2)(011)-(2 x 1) surface. The adsorption of water on the same surface is now investigated to further probe the properties of these groups, as well as to confirm their existence. Ultraviolet photoemission experiments show that water is adsorbed in molecular form at a sample temperature of 110 K. At the same time, the presence of a 3sigma state in the photoemission spectra and work function measurements indicate a significant amount of hydroxyls within the first monolayer of water. At room temperature, scanning tunneling microscopy (STM) suggests that dissociated water is present, and about 30% of the surface active sites are hydroxylated. These findings are well explained by total energy density functional theory calculations and Car-Parrinello molecular dynamics simulations for water adsorption on the titanyl model of TiO(2)(011)-(2 x 1). The theoretical results show that a mixed molecular/dissociative layer is the most stable configuration in the monolayer regime at low temperatures, while complete dissociation takes place at 250 K. The arrangement of the protonated mono-coordinated oxygens in the mixed molecular/dissociated layer is consistent with the observed short-range order of the hydroxyls in the STM images.     

Self-assembly of L-tryptophan on Cu(111) studied by low-temperature scanning tunneling microscopy

The self-assembly of L-tryptophan on Cu(111) is investigated by an ultrahigh vacuum scanning tunneling microscope (STM) at 4.4 K. A series of novel supramolecular structures have been prepared with different annealing temperatures.     

Self-assembly of l-tryptophan on Cu(111) studied by low-temperature scanning tunneling microscopy

The self-assembly of l-tryptophan on Cu(111) is investigated by an ultrahigh vacuum scanning tunneling microscope (STM) at 4.4 K. When deposited onto the substrate at around 120 K with a coverage of 0.1 monolayer, molecular trimers, tetramers, hexamers, and chains coexist on Cu(111). Then almost all molecules self-assemble into chiral hexamers after being annealed at room temperature. When increasing molecular coverage to the full layer, a new type of chain is observed on the surface. Based on the high-resolution STM images at sub-molecular level, we suggest that the l-tryptophan molecules are present in neutral, zwitterionic or anionic states in these structures.     

Scanning probe microscopic studies of the oriented attachment and membrane reconstitution of cytochrome C oxidase to a gold electrode

Scanning probe microscopy was used to monitor the resulting surface of the oriented incorporation of cytochrome c oxidase into electrode supported lipid bilayer at four crucial stages with molecular resolution. We were able to reveal the formation of a densely packed monolayer of the active ester dithio(succiniimidylepropionate) (DTSP) and the covalent linkage of the nitrilotriacetic acid (NTA) to the thiol anchored DTSP by scanning tunneling microscopy. Atomic force microscopy investigations showed that the detergent solubilized oxidase is immobilized as monomers and small aggregates via histidine residues. Finally, the reconstitution of the proteins within the supported membrane was verified. The amount of oxidase immobilized within the solid supported membrane was estimated.     

Rectification in Supramolecular Zinc Porphyrin/Fulleropyrrolidine Dyads Self‐Organized on Gold(111)

Self‐assembled donor/acceptor dyads are of current interest as they are biomimetic to the natural photosynthetic conversion system. Herein, we present an ultrahigh‐vacuum scanning tunneling microscopy and scanning tunneling spectroscopy (UHV‐STM/STS) study of ex situ self‐assembled supramolecular dyads consisting of fulleropyrrolidines (PyC₂C₆₀) axially ligated to zinc(II) tetraphenylporphyrin (ZnTPP), self organized on a 4‐aminothiophenol (4‐ATP) self‐assembled monolayer on gold(111). These dyads show both bias‐polarity‐dependent apparent height in STM images and highly rectifying behavior in tunneling spectroscopy. First‐principles density functional theory calculations clarify the conformational and electronic properties of the 4‐ATP/ZnTPP/PyC₂C₆₀ system. Interestingly, we find easier tunneling for electrons moving from the acceptor side of the dyads to the donor side, in the inverse‐rectifying sense with respect to previously reported molecular rectifiers. Such behavior cannot be explained as an elastic resonant tunneling process, but it can by using a model based on the Aviram–Ratner mechanism.     

Tris-cis-tris-trans-dodeca[organo(dimethylorganosiloxy)]cyclododecasiloxanes {RSi(O)[OSiMe2R']}12. Self-ordering features

The molecular order and thermotropic transitions of tris-cis-tris-trans-dodeca- [organo(dimethylorganosiloxy)]cyclododecasiloxanes {RSi(O)[OSiMe(2)R']}(12) (R = Ph, R' = Me, CH(2)Cl, Vi; R = Me, Et, Vi, R' = Me) have been investigated using differential scanning calorimetry, thermogravimetric analysis, and X-ray scattering. The cyclododecasiloxanes with phenyl side groups (R = Ph) can form mesomorphic structures within a very wide temperature range. Compounds with R = Me and Vi are liquids and exhibit microphase separation above their glass transition temperature because of the different nature and structure of the organic R and trimethylsiloxy OSiMe(3) side groups. When the side group R = Et, a mesomorphic structure is formed in a substantially more narrow temperature region than that for cycles containing phenyl groups. Thus, the type of side group R in organocyclododecasiloxanes determines their ability for self-ordering into mesomorphic structures and the thermal stability of the mesomorphic state.     

Noncontact to contact tunneling microscopy in self-assembled monolayers of alkylthiols on gold

The mechanical interaction between a scanning tunneling microscopy (STM) probe and hexadecane (C16) alkylthiol molecules in a self-assembled monolayer was investigated by sensing the force during constant current mode STM imaging. The force regime changed from attractive to repulsive over the insulating molecule islands under feedback control of the current. The repulsive force on the molecule was strongly dependent on the setpoint value of the current during STM operation. In our experiments, the threshold for contact was found at a tunneling current of 1 pA when the sample bias is 2 V. At higher current, the apparent height of molecular islands changed logarithmically with current. In addition, the current as a function of applied load revealed a stepwise increase, indicative of discrete molecular tilting events. A tunneling decay constant beta of =0.53+/-0.02 A(-1) was obtained based on the measurement of the height of molecules and the tunneling current.     

Self-assembly of small polycyclic aromatic hydrocarbons on graphite: a combined scanning tunneling microscopy and theoretical approach

Self-assembled monolayers of chrysene and indene on graphite have been observed and characterized individually with scanning tunneling microscopy (STM) at 80 K under low-temperature, ultrahigh vacuum conditions. These molecules are small, polycyclic aromatic hydrocarbons (PAHs) containing no alkyl chains or functional groups that are known to promote two-dimensional self-assembly. Energy minimization and molecular dynamics simulations performed for small groups of the molecules physisorbed on graphite provide insight into the monolayer structure and forces that drive the self-assembly. The adsorption energy for a single chrysene molecule on a model graphite substrate is calculated to be 32 kcal/mol, while that for indene is 17 kcal/mol. Two distinct monolayer structures have been observed for chrysene, corresponding to high- and low-density assemblies. High-resolution STM images taken of chrysene with different bias polarities reveal distinct nodal structure that is characteristic of the molecular electronic state(s) mediating the tunneling process. Density functional theory calculations are utilized in the assignment of the observed electronic states and possible tunneling mechanism. These results are discussed within the context of PAH and soot particle formation, because both chrysene and indene are known reaction products from the combustion of small hydrocarbons. They are also of fundamental interest in the fields of nanotechnology and molecular electronics.     

Dependence of the molecular aggregation state of octadecylsiloxane monolayers on preparation methods

The molecular aggregation state of octadecylsiloxane monolayers on Si-wafer substrate surfaces prepared from octadecyltrimethoxysilane (OTMS) or octadecyltrichlorosilane (OTS) was investigated on the basis of grazing incidence X-ray diffraction (GIXD), Fourier transform infrared spectroscopy (FT-IR), contact angle measurement, field emission scanning electron microscopy (FE-SEM), and scanning force microscopy (SFM). The OTMS monolayer was prepared by using the chemical vapor adsorption (CVA) method, and the OTS monolayers, which were used as reference samples, were prepared either by chemisorption (OTS-S) or by the water-cast method (OTS-W). The GIXD, FT-IR, lateral force microscopic (LFM) measurements, and FE-SEM observation revealed that the alkyl chains in the OTMS monolayers prepared using the CVA method are in an amorphous state at room temperature. According to the LFM measurement, the transition temperature from the hexagonal crystalline phase to the amorphous phase was found to be ca. 333 K for the OTS-S monolayer prepared by the chemisorption method. However, the phase transition was not observed in the OTMS monolayer prepared by the CVA method. Also, the atomic force microscopic (AFM) observation and the contact angle measurement showed that the OTMS monolayer prepared by the CVA method has a uniform surface when compared to the OTS monolayers. These results indicated that organosilane compounds in the monolayer prepared by the CVA method were immobilized on the Si-wafer substrate surface in an amorphous state, which was quite different from the hexagonal crystalline state obtained by the chemisorption and water-cast methods.     

Ge(001) as a template for long-range assembly of π-stacked coronene rows

The adsorption of coronene molecules (C(24)H(12)) on the Ge(001) surface has been studied by means of scanning tunnelling microscopy (STM). Upon room temperature deposition, the coronene molecules adsorb in an upright geometry forming compact layers patterned in rows for coverages of one monolayer and less, being the only example investigated so far in which a pure aromatic hydrocarbon forms a well-ordered monolayer on a non-passivated semiconductor surface. At half monolayer, the molecular rows consist of long chains of π-stacked molecules and the distance between molecular planes is 8 ?. This configuration is maintained upon cooling the system below the transition temperature of Ge(001) (~220 K), but the molecular layer experiences also a transition from rows perpendicular to rows parallel to the Ge dimer rows. We interpret our observations in terms of a weak bonging between molecules and substrate, which facilitates the formation of large ordered domains of molecules, revealing Ge(001) as an ideal template for the growth of this and other aromatic hydrocarbons.     

Low-temperature orientationally ordered structures of two-dimensional C60

Orientationally ordered structures of two-dimensional (2D) C(60) at low temperature have been investigated theoretically and experimentally. Using total energy optimization with a phenomenological potential, we find the ground state is a close packed hexagonal lattice in which all the molecules have the same orientation. Several local minima of the potential energy surface are found to be associated with other 1 x 1 lattices as well as 2 x 2 lattices. The energies of the orientational domain boundaries of the 1x1 lattices are also computed, and two kinds of which yield negative values. A majority of these theoretical findings are confirmed by our low-temperature scanning tunneling microscopy study of a 2D C(60) array supported on a self-assembled monolayer.     

Electronic mechanism of STM-induced diffusion of hydrogen on Si(100)

We have observed a scanning tunneling microscopy (STM) induced lateral transfer of a single hydrogen atom on the Si(100) surface. The transfer rate of the hydrogen atom is proportional to the electron dose, indicating an electron-assisted transfer mechanism. Measurements of the relations between the transfer rate and the sample bias and temperature give further support for an electronic mechanism. The bias dependence of the transfer rate shows a peak, and from a first principles electronic structure calculation we show that the position of the peak is related to the energy of a localized surface resonance. We propose that the hydrogen transfer is related to inelastic hole scattering with this surface resonance. We develop a microscopic model for the hydrogen transfer, and using the experimental data we extract information on the resonance lifetime and the transfer yield per resonant electron. The transfer takes place by tunneling through a small excited state transfer barrier. The transfer rate is increased if the hydrogen atom before the resonant excitation is vibrationally excited, and this gives rise to an increasing transfer rate with increasing sample temperature.     

The frontier orbitals of a push-pull azobenzene adsorbed on a metal surface in different bonding geometries investigated by scanning tunneling spectroscopy and spectroscopy mapping

The electronic structure of 4-anilino-4'-nitroazobenzene superstructures formed on Au(111) at 250 K is investigated by low temperature scanning tunneling microscopy, scanning tunneling spectroscopy, and dI/dV mapping at 5 K. Changes in the dI/dV maps of this push-pull molecule reflect the spatial distribution of the frontier orbitals on the molecular scale. Spectra of the trans- and the cis?-isomer differ between themselves and in different parts of supramolecular assemblies. The relative importance of these differences is discussed.     

Thermodynamical equilibrium of binary supramolecular networks at the liquid-solid interface

Coadsorption of two different carboxylic acids, benzenetribenzoic acid and trimesic acid, was studied at the liquid-solid interface in two different solvents (heptanoic and nonanoic acid). Independent alteration of both concentrations in binary solutions resulted in six nondensely packed monolayer phases with different structures and stoichiometries, as revealed by means of scanning tunneling microscopy (STM). All of these structures are stabilized by intermolecular hydrogen bonding between the carboxylic acid functional groups. Moreover, phase transitions of the monolayer structures, accompanied by an alteration of the size and shape of cavity voids in the 2D molecular assembly, could be achieved by in situ dilution. The emergence of the various phases could be described by a simple thermodynamic model.     

Asymmetry of electron transmission through monolayers of helical polyalanine adsorbed on gold surfaces

Polyalanine derivatives containing cysteamine linker R-(Ala)14NH-(CH2)2-SH, where R is ferrocenecarbonyl or hydrogen, were synthesized and then used to form self-assembled monolayers on gold. The tilt angles and the packing density of the molecules within monolayer assemblies were determined by FTIR spectroscopy and scanning tunneling microscopy, respectively. Electrochemical properties of monolayer-modified electrodes were studied using cyclic voltammetry and impedance spectroscopy. Measurements of electron-transfer rates using electrochemical techniques and scanning tunneling spectroscopy revealed asymmetry dependent on the applied voltage. It is suggested that the observed electron-transfer behavior is connected with the electric field generated by the molecular dipole of the polyalanine helix.     

Chirality in supramolecular self-assembled monolayers of achiral molecules on graphite: formation of enantiomorphous domains from arachidic anhydride

The molecular arrangement and chirality of the self-assembled arachidic anhydride monolayer on graphite were investigated using scanning tunneling microscopy (STM). This molecule has two identical alkyl chains, linked by an anhydride group in the middle. In its extended form, one alkyl chain is shifted, with respect to the other, along the molecular backbone. Upon adsorption on graphite, this achiral anhydride spontaneously forms two types of homogeneous domains (denoted as m and m') with mirror symmetry. The angle from the molecular chain to the row-packing direction is 98.0 degrees +/- 0.5 degrees and 82.0 degrees +/- 0.5 degrees for domains m and m', respectively. Domain m is the mirror image of m'. The molecular arrangement of this self-assembled monolayer shows that domains m and m' are two-dimensional enantiomers with opposite chiralities. This new molecular packing motif is confirmed by line-profile analyses along the molecule-chain and the row-packing directions. This finding demonstrates the spontaneous formation of highly ordered homogeneous enantiomorphous domains on graphite resulting only from weak van der Waals forces between the achiral arachidic anhydride molecules.