Self-assembly of heterogeneous bilayers stratified by Au-S and hydrogen bonds on Au(111).

The self-assembly of heterogeneous bilayers on Au substrates was investigated using atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and infrared reflection absorption spectroscopy (IRAS). The formation of a well-defined bilayer including different types of functional groups would be one of the desired goals to create varying surface functionalities. In this study, we examined the assembly of a hydrogen-bonded molecular layer to another functional alkanethiolate self-assembled monolayer (SAM) on the Au(111) surface. The chemical properties and bond strength of the hydrogen bonds at the interlayer differ from those of the Au-S bonds at the anchor of thiolate SAMs, therefore the adsorbed molecules are expected to form a stratified bilayer. In this study, on one hand, we revealed that imidazole-terminated alkanethiolate SAMs (Im-SAMs) have an atomically smooth topography but chemically inhomogeneous Au-S anchors, rather incomplete than n-alkanethiolate SAMs, on the Au(111) surface. On the other hand, we confirmed the self-assembly of the heterogeneous bilayers including Im-SAMs on the Au(111) surface, even in a mixed solution containing two types of molecules. These results show that the self-assembly of the bilayer stratified by H bonds and Au-S bonds is flexible and adaptable.

Formation and structural characterization of two-dimensional wetting water layer on graphite (0001).

Understanding the structure and wettability of monolayer water is essential for revealing the mechanisms of nucleation, growth, and chemical reactivity at interfaces. We have investigated the wetting layer formation of water (ice) on the graphite (0001) surface using a combination of low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM). At around monolayer coverages, the LEED pattern showed a (2 × 2) periodicity and STM revealed a hydrogen-bonded hexagonal network. The lattice constant was about 9% larger than that for ice Ih/Ic crystals, and the packing density was 0.096 Å-2. These results indicate that an extended ice network is formed on graphite, different from that on metal surfaces. Graphite is hydrophobic under ambient conditions due to the airborne contaminant but is considered inherently hydrophilic for a clean surface. In this study, the hydrophilic nature of the clean surface has been investigated from a molecular viewpoint. The formation of a well-ordered commensurate monolayer supports that the interaction of water with graphite is not negligible so that a commensurate wetting layer is formed at the weak substrate-molecule interaction limit.

Formation and regulation of unoccupied hybridized band with image potential states at perylene/graphite interface.

Occupied and unoccupied electronic structures of submonolayer perylene (C20H12) on a graphite surface have been investigated using two-photon photoemission (2PPE) spectroscopy for two phases at room and low temperatures. Low energy electron diffraction measurements indicated that the molecules are disordered at room temperature and form a well-ordered superstructure below 180 K. In 2PPE, a specific unoccupied peak (Lx) was observed at around room temperature (>180 K) but not at low temperature (<180 K). The temperature-dependence of the excitation probability was attributed to a contribution of a diffuse unoccupied state, which is characterized by the molecular orbital extending outside the perylene molecular framework. At around room temperature, perylene adopts a flat-lying molecular orientation so that the diffuse state can hybridize with a free-electron-like unoccupied surface state, image potential states (IPS). As a result, the hybridized Lx state can be excited from the occupied bulk band through the IPS-mediated process. In contrast, hybridization is not efficient in the low-temperature phase due to the standing molecular orientation, which decouples the molecule away from the image plane of the substrate. The size of molecular islands also affects hybridization between the diffuse states and IPS because the two states encounter each other at the edge part of molecular aggregates. The temperature-dependent 2PPE results indicate that the molecular orientation and island size of perylene are directly linked to the formation of hybridized states, and thus, the excitation probability at the interface can be regulated by the morphology on the surface.

Direct visualization of diffuse unoccupied molecular orbitals at a rubrene/graphite interface.

Spectroscopic and nanoscale imaging investigations concerning the spatial extent of molecular orbitals at organic/substrate interfaces have been of intense interest to understand charge dynamics. Here, the spatial extent of unoccupied molecular orbitals of ultrathin rubrene [5,6,11,12-tetraphenyltetracene] films has been investigated with scanning tunneling microscopy and spectroscopy. Based on constant-current distance (z)-voltage (V) measurements, the unoccupied energy levels are elucidated and found to be consistent with previously reported macroscopic two-photon photoemission (2PPE) spectroscopy. In the diffuse unoccupied molecular orbitals reported with 2PPE (J. Phys. Chem. C, 2013, 117, 20098), nanoscale dz/dV spatial maps reveal that the local density of states of the orbitals extends over the rubrene molecules. Delocalization is also observed for the image potential states, which are inherently free-electron-like. This is in contrast to the localized nature of other unoccupied molecular orbitals. A nanoscale understanding of diffuse and delocalized molecular orbitals provides a fundamental insight into low-lying Rydberg states in polycyclic aromatic hydrocarbons.

Strong Hydrogen Bonds at the Interface between Proton-Donating and -Accepting Self-Assembled Monolayers on Au(111).

Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations. Here, we report the formation of the catechol-fused bis(methylthio)tetrathiafulvalene (H2Cat-BMT-TTF) adlayer hydrogen bonding with an imidazole-terminated alkanethiolate self-assembled monolayer (Im-SAM) on Au(111). The heterogeneous bilayer is realized by sequential two-step immersions in solutions for the individual Im-SAM and H2Cat-BMT-TTF adlayer formations. In the measurements by AFM, a grained H2Cat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of H2Cat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between H2Cat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm-1, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm-1). The OH stretching mode frequency and the adsorption strength for the H2Cat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations.

The complex polymorphism and thermodynamic behavior of a seemingly simple system: naphthalene on Cu(111).

Naphthalene, C10H8, is a polycyclic aromatic hydrocarbon (PAH) consisting of two fused benzene rings. From previous studies, it is known to form three different commensurate structures in thin epitaxial films on Cu(111), depending on the preparation conditions. One of these structures even exhibits a chiral motif of molecular rotations within the unit cell. In an attempt to elucidate this polymorphism, we performed in situ low-energy electron diffraction (LEED) as a function of temperature and surface coverage, revealing an unexpected and extraordinarily complex structural and thermodynamic behavior. We present experimental evidence for a phase transition from a two-dimensional gas to a highly ordered molecular solid via an intermediate metastable phase with moderate order (extending over a few lattice constants only) which undergoes a reversible orientational shift upon temperature variation. At monolayer coverage and above, we find that two different point-on-line (POL) coincident epitaxial relations constitute the dominant structures. This is remarkable because, so far, POL structures of naphthalene on Cu(111) and other substrates have either not been recognized or not obtained under the respective experimental conditions. Our results are corroborated by the analysis of characteristic moiré patterns observed in scanning tunneling microscopy (STM), indicative of a noncommensurate epitaxial registry.

Dispersive Electronic States of the π-Orbitals Stacking in Single Molecular Lines on the Si(001)-(2×1)-H Surface.

One-dimensional (1D) molecular assemblies have been considered as one of the potential candidates for miniaturized electronic circuits in organic electronics. Here, we present the quantitative experimental measurements of the dispersive electronic feature of 1D benzophenone molecular assemblies on the Si(001)-(2×1)-H. The well-aligned molecular lines and their certain electronic state dispersion were observed by scanning tunneling microscopy (STM) and angle-resolved ultraviolet photoemission spectroscopy (ARUPS), respectively. Density functional theory (DFT) calculations reproduced not only the experimental STM image but also the dispersive features that originated from the stacking phenyl π-orbitals in the molecular assembly. We obtained the effective mass of 2.0me for the hole carrier along the dispersive electronic state, which was comparable to those of the single-crystal molecules widely used in organic electronic applications. These results ensure the one-dimensionally delocalized electronic states in the molecular lines, which is requisitely demanded for a charge-transport wire.

Dispersions of image potential states on surfaces of clean graphite and lead phthalocyanine film.

Dispersions of image potential states on a graphite surface (denoted IPS1) and on 1 monolayer (ML) film (denoted IPS2) of lead phthalocyanine (PbPc) are investigated by the micro-spot angle-resolved two-photon photoemission (micro-AR-2PPE) spectroscopy. On the graphite surface, whole dispersions of the two members of IPS1 (n = 1 and 2) are observed. The n = 1 IPS1 peak is weakly visible at energy higher than the vacuum level. The effective mass of an electron in the n = 1 IPS1 becomes slightly light at the high momentum region, suggesting the interaction between the IPS1 and the unoccupied σ-band of graphite. On the PbPc film, the IPS2 band forms a band gap and back-folds at the boundary of the Brillouin zone. A 1-dimensional Kronig-Penny model is used to reproduce the effective mass and the shift of binding energy.

Characterization of an organic field-effect thin-film transistor in operation using fluorescence-yield x-ray absorption spectroscopy.

In situ element-specific observation of electronic states of organic films beneath metal electrodes is achieved by x-ray absorption spectroscopy (XAS) in the bulk-sensitive fluorescence-yield (FY) mode. The molecular orientation in Au-covered oligo-thiophene films is confirmed by the C K-edge FY-XAS spectra and the applied bias dependence of the spectra is successfully detected for the first time. The present method can give deeper insights into the electronic-state investigation of various real-device systems under operational conditions.

Systematic study of soft X-ray spectra of poly(Dg).poly(Dc) and poly(Da).poly(Dt) DNA duplexes.

In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG).poly(dC) and poly(dA).poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

The electronic structure of oxygen atom vacancy and hydroxyl impurity defects on titanium dioxide (110) surface.

Introducing a charge into a solid such as a metal oxide through chemical, electrical, or optical means can dramatically change its chemical or physical properties. To minimize its free energy, a lattice will distort in a material specific way to accommodate (screen) the Coulomb and exchange interactions presented by the excess charge. The carrier-lattice correlation in response to these interactions defines the spatial extent of the perturbing charge and can impart extraordinary physical and chemical properties such as superconductivity and catalytic activity. Here we investigate by experiment and theory the atomically resolved distribution of the excess charge created by a single oxygen atom vacancy and a hydroxyl (OH) impurity defects on rutile TiO(2)(110) surface. Contrary to the conventional model where the charge remains localized at the defect, scanning tunneling microscopy and density functional theory show it to be delocalized over multiple surrounding titanium atoms. The characteristic charge distribution controls the chemical, photocatalytic, and electronic properties of TiO(2) surfaces.

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.

Selective chain reaction of acetone leading to the successive growth of mutually perpendicular molecular lines on the si(100)-(2 x 1)-H surface.

The successive growth of mutually perpendicular molecular lines from one dangling-bond (DB) site on the Si(100)-(2 x 1)-H surface has been realized through a substrate-mediated chain reaction at 300 K. Among various molecules, acetone molecules undergo the most facile chain reaction with a DB site, which proceeds selectively on the Si(100)-(2 x 1)-H surface, resulting in only single molecular lines in the parallel-row (parallel to the dimer row) direction. The smaller size and higher reactivity of acetone molecules enable us to successively grow a parallel-row acetone line from the end of a cross-row (perpendicular to the dimer row) allylmercaptan line simply by changing the feed of gas molecules into the reaction chamber. Since the length of a molecular line is controlled by the number of gas molecules impinged, it is possible to turn a chain reaction from the cross-row direction to the parallel-row direction at any desired point on the surface. The reaction path of the adsorbing molecules is discussed. The present study provides a new means of fabricating mutually perpendicular molecular lines through a chain reaction initiating at a preselected DB site on the Si(100)-(2 x 1) surface.

Deposition and crystallization studies of thin amorphous solid water films on Ru(0001) and on CO-precovered Ru(0001).

The deposition and the isothermal crystallization kinetics of thin amorphous solid water (ASW) films on both Ru(0001) and CO-precovered Ru(0001) have been investigated in real time by simultaneously employing helium atom scattering, infrared reflection absorption spectroscopy, and isothermal temperature-programmed desorption. During ASW deposition, the interaction between water and the substrate depends critically on the amount of preadsorbed CO. However, the mechanism and kinetics of the crystallization of approximately 50 layers thick ASW film were found to be independent of the amount of preadsorbed CO. We demonstrate that crystallization occurs through random nucleation events in the bulk of the material, followed by homogeneous growth, for solid water on both substrates. The morphological change involving the formation of three-dimensional grains of crystalline ice results in the exposure of the water monolayer just above the substrate to the vacuum during the crystallization process on both substrates.

First-principles calculations of hydrogen diffusion on rutile TiO2(110) surfaces.

Density functional calculations are performed to study the H-atom diffusion on titanium dioxide (110) surface in the cases of water-molecule dissociation and splitting of the adjacent hydroxyl OH pair. It is shown that, when a water molecule is adsorbed at a surface oxygen-vacancy site, a fragment H atom of the water molecule tends to diffuse toward the nearest-neighboring bridging-oxygen sites by using a straight-line or relay-point path. As the result, a pair of surface hydroxyl OH is formed on the same oxygen row. In a thermal process, on the other hand, such OH pair favorably splits only by using a relay-point path, i.e., by transferring one H atom from a bridging-oxygen site to a next-neighboring one along the same oxygen row by way of another in-plane oxygen site. We found that the latter splitting reaction is activated around room temperature.

Morphological change during crystallization of thin amorphous solid water films on Ru(0001).

The isothermal crystallization process of thin amorphous solid water (ASW) films on Ru(0001) has been investigated in real time by simultaneously employing helium atom scattering, infrared reflection absorption spectroscopy, and isothermal temperature-programmed desorption. The measurements reveal that the crystallization mechanism consists of random nucleation events in the bulk of the ASW films, followed by homogeneous growth. Morphological changes of the solid water film during crystallization expose the water monolayer just above the substrate to the vacuum during the crystallization process.

Competing forward and reversed chain reactions in one-dimensional molecular line growth on the Si(100)-(2 x 1)-H surface.

To explore the role of competing forward and reversed chain reactions in the growth of a one-dimensional (1D) molecular line on the Si(100)-(2 x 1)-H surface, controlled experiments were performed with various alkene molecules by scanning tunneling microscopy (STM) at various temperatures. It was observed that the end dangling bond (DB) of a styrene line, fabricated by a chain reaction on the Si(100)-(2 x 1)-H surface at 300 K, initiated a reverse chain reaction at 400 K, leading to the complete disappearance of the styrene line with zero-order desorption kinetics (rate constant k = 1.17 x 10-2 s-1 at 400 K). In the case of 2,4-dimethylstyrene, the reversed chain reaction was observed even at 300 K. These results suggest that the appearance of a molecular line in an STM image is determined by the rates of competing forward and reversed chain reactions at a given temperature. As predicted, 1D lines formed by the DB-initiated chain reaction of 1-hexene and 1-heptene on Si(100)-(2 x 1)-H were observed at 180 K because of the reduced desorption rate, despite the fact that those molecules showed no line growth at 300 K. These results indicate that the scope of forming 1D molecular lines on the Si(100)-(2 x 1)-H surface with various alkenes is much wider than anticipated in previous studies.

Adsorption of unsaturated hydrocarbon moieties on H:Si(111) by Grignard reaction.

Grafting of unsaturated hydrocarbon moieties (-CH(2)-CH=CH(2), -CH=CH(2), -CH(2)-CH=CH-CH(3), and -CCH) by a C-Si covalent bond was attempted by the Grignard reaction on hydrogen-terminated Si(111) in tetrahydrofuran solutions. The product adsorbates were monitored by vibrational methods of high-resolution electron energy loss spectroscopy and multiple internal infrared reflection absorption spectroscopy, as well as Auger electron spectroscopy. The temperature and the period of reaction were adjusted so as to preserve the unsaturated carbon-carbon bonds. The -CH(2)-CH=CH(2) group was introduced by a mild reaction condition, with the reservation of the C=C double bond confirmed. The unsaturated bonds in -CH(2)-CH=CH-CH(3) and -CCH were also reserved. Only in the case of -CH=CH(2) was the reservation of the C=C double bond not realized. Unsaturated hydrocarbon moieties are applicable for further organic modification to introduce functional groups, and are prospective materials in nanofabrication and biological application on silicon wafer surfaces.

Photoassisted adsorption of allylamine and 1-butene on H:Si(111) studied by surface vibrational spectroscopies.

Ultraviolet photoassisted adsorption of terminally double-bonded molecules, allylamine (CH2=CH-CH2-NH2) and 1-butene (CH2=CH-CH2-CH3), on hydrogen-terminated silicon (111) surface was attempted to obtain adsorbates covalently terminating the surface Si atoms. The adsorption process was monitored by high-resolution electron energy loss spectroscopy, multiple internal infrared reflection-absorption spectroscopy, and Auger electron spectroscopy. Allylamine adsorbates emerged upon delivery of allylamine gas under ultraviolet irradiation. The N-H bonds in allylamine were evidenced to survive over the photoadsorption process by vibrational analysis and by the reaction with ketene. CH3- groups were detected at low coverage, indicating anchoring of the organic moieties by the secondary (sec-) type carbon atoms, which were taken over by the primary (n-) type with increasing coverage. C-D bonds were detected after deposition on deuterium-terminated Si(111) upon incorporation of Si-terminating H into the hydrocarbon part of adsorbates. In the case of 1-butene, not only the C=C end but also the CH3- end of a molecule might attach on Si, resulting in emergence of adsorbates composed of CH2 groups. The newly obtained adsorbates are prospective as a material applied for nanolithography, fine electrochemistry, and nano-biotechnology.

Surface structure and interface dynamics of alkanethiol self-assembled monolayers on Au(111).

Scanning tunneling microscopy (STM) and high-resolution electron energy loss spectroscopy (HREELS) were used to examine the structural transitions and interface dynamics of octanethiol (OT) self-assembled monolayers (SAMs) caused by long-term storage or annealing at an elevated temperature. We found that the structural transitions of OT SAMs from the c(4 x 2) superlattice to the (6 x square root 3) superlattice resulting from long-term storage were caused by both the dynamic movement of the adsorbed sulfur atoms on several adsorption sites of the Au(111) surface and the change of molecular orientation in the ordered layer. Moreover, it was found that the chemical structure of the sulfur headgroups does not change from monomer to dimer by the temporal change of SAMs at room temperature. Contrary to the results of the long-term-stored SAMs, it was found that the annealing process did not modify either the interfacial or chemical structures of the sulfur headgroups or the two-dimensional c(4 x 2) domain structure. Our results will be very useful for a better understanding of the interface dynamics and stability of sulfur atoms in alkanethiol SAMs on Au(111) surfaces.