Self-assembled structures of 4′-([2,2′:6′,2″-terpyridine]-4′-yl)-[1,1′-phenyl]-4-carboxylic acid molecules induced by metal atoms on ag(111) surface

The self-assembled supramolecular structures of 4′-([2,2′:6′,2″-terpyridine]-4′-yl)-[1,1′-phenyl]-4-carboxylic acid (Y) molecules on Ag(111) surface induced by metal elements have been studied by scanning tunneling microscopy. After annealing, the as-deposited monolayer of Y molecules shows four kinds of well-ordered structures due to the competition between dipole interaction, hydrogen bonding and Van der Waals interaction. Introduced Cu atoms drive ordered monolayer into a self-assembled supramolecular structure with bright spots. Deposited Ag atoms cause the monolayer change to a windmill shape self-assembled supramolecular structure. Though the Cu and Ag are in the same group of the periodic table, a Cu atom connects two COOH groups and an Ag atom trends to bind to three COOH groups during the formation of metal-organic bonding within both induced structures. Such result suggests that the self-assembled structures formed by metal-organic coordination bonding can be controlled by choosing the number of metal-organic coordination bonds, which can be helpful to design metal-organic molecular architectures comprising functional building blocks.     

Hydrogen bonds induced supramolecular self-assembly of azobenzene derivatives on the highly oriented pyrolytic graphite surface

The self-assembly of azobenzene derivatives (C_nAzCOOH) with various lengths of peripheral alkyl chains (with carbon number of n = 8, 10, 12, 14, 16) were observed by scanning tunneling microscopy on highly oriented pyrolytic graphite (HOPG) surface. The effect of van der Waals interactions and the intermolecular hydrogen bonding on the two-dimensional self-assembly was systematically studied. No alkyl-chain length effect was observed according to the STM images. All kinds of C_nAzCOOH adopting the same pattern self-assembled on the HOPG surface, suggesting the formation of the two-dimensional structures was dominated by the hydrogen bonding of the functional groups. It could be found that two C_nAzCOOH molecules formed a hydrogen-bonded dimer with “head-to-head” fashion as expected; however, the dimers organized themselves in the form of relative complex lamellae. Three dimers as a group arranged side by side and formed a well-defined stripe with periodic dislocations due to the registry mechanism of the alkyl chain with the underlying HOPG surface. The hydrogen bonds between the adjacent dimers in one lamella were formed and dominated the self-assembled pattern.     

Self-assembly of lamella-forming diblock copolymers confined in nanochannels: Effect of confinement geometry

The self-assembly of symmetric diblock copolymers confined in the channels of variously shaped cross sections(regular triangles, squares, and ellipses) is investigated using a simulated annealing technique. In the bulk, the studied symmetric diblock copolymers form a lamellar structure with period LL. The geometry and surface property of the confining channels have a large effect on the self-assembled structures and the orientation of the lamellar structures. Stacked perpendicular lamellae with period LLare observed for neutral surfaces regardless of the channel shape and size, but each lamella is in the shape of the corresponding channel’s cross section. In the case of triangle-shaped cross sections, stacked parallel lamellae are the majority morphologies for weakly selective surfaces, while morphologies including a triangular-prism-shaped B-cylinder and multiple tridentate lamellae are obtained for strongly selective surfaces. In the cases of square-shaped and ellipse-shaped cross sections, concentric lamellae are the signature morphology for strongly selective surfaces, whereas for weakly selective surfaces, stacked parallel lamellae, and several types of folding lamellae are obtained in the case of square-shaped cross sections, and stacked parallel lamellae are the majority morphologies in the case of ellipse-shaped cross sections when the length of the minor axis is commensurate with the bulk lamellar period. The mean-square endto-end distance, the average contact number between different species and the surface concentration of the A-monomers are computed to elucidate the mechanisms of the formation of the different morphologies. It is found that the resulting morphology is a consequence of competition among the chain stretching, interfacial energy, and surface energy. Our results suggest that the self-assembled morphology and the orientation of lamellae can be manipulated by the shape, the size, and the surface property of the confining channels.     

Electron tunneling in the presence of adsorbed molecules

We perform ab initio density functional theory calculations of the tunneling current through an electrode-molecule-electrode system with four different small organic molecules, benzenedithiol (BDT), benzenedimethanethiol (XYL), diethynylbenzene (DEB) and dodecanethiol (C12), sandwiched between two gold (1 1 1) electrodes. For the XYL molecule, we test the effect of alternate bonding types and sites. Although this reduces the current considerably, it does not account for the orders of magnitude differences between experimental and theoretical results in the literature. We also model a typical STM experimental setup with a gold nanoparticle absorbed on a self-assembled monolayer (SAM) of the molecule with a gap between the nanoparticle and probing tip and show that such a gap could account for these differences. Finally, we describe the effect that the gap has on the ability of STS measurements to distinguish between the i(V) characteristics and thicknesses of self-assembled monolayers of different molecules.     

Vacuum vapour deposition of phenylphosphonic acid on amorphous alumina

A study of the growth of phenylphosphonic acid (PPOA) on amorphous alumina thin films on top of polycrystalline aluminium foil is presented. The self-assembled monolayer (SAM) of the acid was grown in ultra high vacuum via vapour phase deposition, which allows us to investigate the molecular growth process in situ by photoelectron spectroscopy. The acid adlayer was deposited on the alumina surface at 300 K from an evaporator consisting of a ceramic tube heated by a tungsten wire. On adsorption of the PPOA acid on the alumina surface the anchoring properties of the phosphonic group lead to the formation of an ordered layer with an outward phenyl ring group and a phosphonate interface. The C 1s, P 2s, P 2p, Al 2p and O 1s core level spectra were analysed as a function of the deposition time. The acid adsorption occurs in two ranges: formation of an initial monolayer phase, followed by saturation coverage where the P 2s peak intensity is constant with deposition time. It was confirmed that the phenylphosphonic acid molecules react with the alumina surface forming P-O-Al bonds. It was shown that the SAM formation is driven by the evolution of acid molecular coverage on the alumina surface. The results on the vapour deposited PPOA SAM monolayer on the amorphous alumina surface are consistent with previous findings for a number of phosphonic acids SAMs prepared through immersion of the alumina surfaces in an acid solution.     

A direct observation on the surface assembling and ordering of coumarin derivatives on the graphite surface

The 2D monolayer structures of two coumarin derivatives, 4-heptadecyl-7-hydroxycoumarin (HHC) 1 and 3-(2-benzo thiazolyl)-7-octadecyloxy-coumarin (BOC) 2, have been studied by STM and different sensitivity to thermal annealing for these two systems has been observed. The results show that the arrangements of these two molecules are obviously different in the self-assembled monolayer at 20 °C on the graphite surface. Furthermore, only BOC is sensitive to thermal annealing. The assembly of BOC becomes more stable and ordered after annealing at 65 °C for 1 h.     

Preparation and properties of binary metal monolayers: I. Pb and Bi on Cu(100)

LEED and AES have been used to monitor the coadsorption of lead and bismuth vapour on the (100) face of copper. Breaks in the plots of substrate and adsorbate Auger signals as a function of deposition time, correlated with the appearance of various LEED patterns, permit a calibration of the spectrometer. For bismuth adsorbed alone a break before the completion of the dense monolayer is ascribed to a sudden change in the sticking probability; after the monolayer a second layer starts to form. The binary monolayers form with a maximum compactness compatible with the structures of the pure monolayers. The LEED patterns for these binary layers show that separate “domains” of each adsorbate are formed, each having the dense monolayer structure. Adsorption of lead causes a dispersed low-coverage structure of bismuth to condense into islands. For lead-rich layers the “surface melting” behaviour of the lead structure is influenced by the presence of bismuth.     

Chemisorption of 4-(4-amino-phenylazo) benzoic acid molecule on the Si(0 0 1)-(4 × 2) surface

Structural and electronic properties of self-assembled monolayer with 4-(4-amino-phenylazo) benzoic acid (APABA) on the Si(0 0 1)-(4 × 2) surface are investigated by ab initio calculation based on density functional theory. For the APABA chemisorption on the silicon surface, we have assumed two different binding sites: (i) amino group of molecule and (ii) carboxyl group of molecule. Considering amino-site, we have assumed two possible models for the chemisorption of molecules on the Si(0 0 1)-(4 × 2) surface: (i) an intrarow position between two neighboring Si dimers in the same dimer row (Model I), (ii) on-dimer position (Model II). We have found that Model II is 1.10 eV energetically more favorable than Model I. The Si-N bond length was calculated as 1.85 Å which is in excellent agreement with the sum of the corresponding covalent radii of 1.87 Å. Considering carboxyl-site, we have assumed exactly the same model as mentioned above. Again we have found that Model II is energetically favorable than Model I. The calculated bond lengths for Si-O and O-C are 1.76 and 1.35 Å, respectively.     

Two-dimensional self-assembly of esters with different configurations at the liquid-solid interface

Self-assembled monolayers of hexadecyl palmitate (HP) and 3,3′-thiodipropionic acid di-n-octadecyl ester (TADE) physisorbed on highly oriented pyrolytic graphite (HOPG) are investigated using scanning tunneling microscope (STM) and computer simulation. Both molecules form alkane-like linear shapes to maximize the interactions with substrate when they adsorb on HOPG surface. The HP molecules self-assemble into lamellae with the chain-trough angle of 48°, which is the result of a shifting 3/2 units from the adjacent molecule in a lamella. Based on the simulation insights combined with STM images, we confirm that a perpendicular orientation appears in which the HP molecular backbone is rotated 90° with respect to the substrate such that the carbonyl points away from the HOPG surface. TADE molecules form three kinds of configurations with chain-trough angles of 90°, 72° and 60° by shifting 0, 1/2 and 1 units from their adjacent molecules, respectively. The bright stripes in STM images reveal the electron density distribution of the part between two ester groups. The energy differences of three TADE adsorption configurations by molecular mechanics (MM) simulation are used to explain the structural coexistence phenomenon. It is also shown that lattice match between alkyl chain of molecules and HOPG substrate could change molecular conformation upon self-assembly.     

Infrared spectroscopy of self-assembled monolayer films on silicon

Infrared vibrational spectroscopy in an attenuated total reflection (ATR) geometry has been employed to investigate the presence of organic thin layers on Si-wafer surfaces. The phenomena have been simulated to show there can be a field enhancement with the presented single-reflection ATR (SR-ATR) approach which is substantially larger than for conventional ATR or specular reflection. In SR-ATR, a discontinuity of the field normal to the film contributes a field enhancement in the lower index thin film causing a two order of magnitude increase in sensitivity. SR-ATR was employed to characterize a single monolayer of undecylenic acid self-assembled on Si(1 1 1) and to investigate a two monolayer system obtained by adding a monolayer of bovine serum albumin protein.     

Synthesis and characterization of a fatty acid self-assembled monolayer on CeO2 nanoparticles: to explore solution-state property of a SAM

Decanoic acid self-assembled monolayer (SAM) in the quasi-crystalline state was prepared on the surface of the cubic CeO₂ nanoparticles (6.5 ± 1.1 nm) by hydrothermal synthesis. The purification method to obtain quasi-crystalline SAM without residual (free) decanoic acid was developed. The SAM was carefully washed (purified) and characterized carefully by FT-IR, TG, DSC, and NMR. The obtained results showed that good agreement with the property of the dry state SAM. The solution state properties of the SAM were also examined by the CeO₂ nanoparticles. It turned out that the quasi-crystalline SAM could be swollen by its good solvents, cyclohexane, and chloroform; however, the quasi-crystalline SAM showed that a size exclusion effect to the solvent, trans-decalin. In addition, it turned out that the molecular motion of the decanoic acids in the SAM was highly restricted even in the swollen state depending on the distance from the grafting point to the CeO₂ surface. The strong osmosis was also observed. The solvent molecules were not easily released from the SAM even after the solvent molecules outside of the SAM were frozen.     

Molecular gated transistors: Role of self-assembled monolayers

In order to understand the biosensing mechanism of field-effect based biosensors and optimize their performance, the effect of each of its molecular building block must be understood. In this work the gating effect of self-assembled linker molecules on field-effect transistor was studied in detail. We have combined Kelvin probe force microscopy, current-voltage measurements, capacitance-voltage measurements, equivalent circuit modeling and device simulations in order to trace the mechanism of silicon-on-insulator biological field-effect transistors. The measurements were conducted on the widely used linker molecules (3-aminopropyl)-trimethoxysilane (APTMS) and 11-aminoundecyl-triethoxysilane (AUTES), which were self-assembled on ozone activated silicon oxide surface covering the transistor channel. In a dry environment, the work function of the modified silicon oxide decreased by more than 1.5 eV, and the transistor threshold voltage increased by about 30 V following the self-assembly. A detailed analysis indicates that these changes are due to negative induced charges on the top dielectric layer, and an effective dipole due to the polar monolayer. However, the self-assembly did not change the silicon flat-band voltage when in contact with an electrolyte. This is attributed to electrostatic screening by the electrolyte.     

A switch based on self-assembled thymine

The DNA base thymine is deposited at 100?K on Cu(111) and investigated and manipulated by low-temperature scanning tunneling microscopy at 5?K. At submonolayer coverage paired rows are observed. At monolayer coverage a hexagonal commensurate self-assembled layer with the methyl group pointing away from the surface forms. A reversible local manipulation of molecules within the self-assembled layer is demonstrated. This manipulation is interpreted as an out-of-plane relaxation of molecules within the layer induced by the change of the adsorption geometry of individual molecules between two meta-stable orientations. A positive field of 2-4?V leads to this local change in the molecular arrangement, while a field larger than 4?V restores the original geometry.     

Correlation between iodide dosimetry and terephthalic acid dosimetry to evaluate the reactive radical production due to the acoustic cavitation activity

Acoustic cavitation plays an important role in sonochemical processes and the rate of sonochemical reaction is influenced by sonication parameters. There are several methods to evaluate cavitation activity such as chemical dosimetry. In this study, to comparison between iodide dosimetry and terephthalic acid dosimetry, efficacy of sonication parameters in reactive radical production has been considered by iodide and terephthalic acid dosimetries. For this purpose, efficacy of different exposure parameters on cavitations production by 1 MHz ultrasound has been studied. The absorbance of KI dosimeter was measured by spectrophotometer and the fluorescence of terephthalic acid dosimeter was measured using spectrofluorometer after sonication. The result of experiments related to sonication time and intensity showed that with increasing time of sonication or intensity, the absorbance is increased. It has been shown that the absorbance for continuous mode is remarkably higher than for pulsing mode (p-value < 0.05). Also results show that with increasing the duty cycles of pulsed field, the inertial cavitation activity is increased. With compensation of sonication time or intensity in different duty cycles, no significant absorbance difference were observed unless 20% duty cycle. A significant correlation between the absorbance and fluorescence intensities (count) at different intensity (R = 0.971), different sonication time (R = 0.999) and different duty cycle (R = 0.967) were observed (p-value < 0.05). It is concluded that the sonication parameters having important influences on reactive radical production. These results suggest that there is a correlation between iodide dosimetry and terephthalic acid dosimetry to examine the acoustic cavitation activity in ultrasound field.     

Structural ordering of ω-ferrocenylalkanethiol monolayers on Au(1 1 1) studied by scanning tunneling microscopy

The self-assembly of ω-ferrocenylalkanethiols (FcCnSH) with different alkyl-spacer lengths on Au(1 1 1) substrates has been studied by scanning tunneling microscopy (STM). Upon deposition at room temperature FcCnSH molecules tend to form multilayers, while by thermal treatment monolayer formation, a rearrangement of the molecules and the formation of ordered domains is achieved. The surface structure of the resulting full coverage self-assembled monolayers is resolved with molecular resolution by STM. The ordered monolayer structure of ω-ferrocenylpropanethiol is discussed in comparison with its bulk crystal structure, derived from single crystal X-ray analysis. Based on these results a monolayer structure of ω-ferrocenylalkanethiols with longer alkyl chains closely related to the bulk crystal structure of the shorter alkyl-spacer derivates is suggested. Our results provide detailed insight into the self-assembly of FcCnSH on gold substrates.     

Reactions of small gold cluster cations with propylene, methane, and hydrogen: permissive and competitive coadsorption effects

Coadsorption effects of molecular hydrogen and small hydrocarbons, CH₄ and C₃H₆, on free Au₃ ⁺ and Au₅ ⁺ were investigated in an octopole ion trap under multi-collision conditions. For hydrogen and methane the observations indicate that both molecules coadsorb on the same adsorption site, i.e., the same atom of the cluster. This type of molecular adsorption on free clusters is termed permissive coadsorption, in contrast to competitive coadsorption, in which two molecules compete for the same adsorption site. The latter case was observed for hydrogen and propylene: already trace amounts of propylene were able to completely saturate the clusters preventing the coadsorption of H₂. The size dependent adsorbate coverage is discussed and implications on the cluster structure are deduced from time and temperature dependent reaction measurements.     

Investigation of monolayer dispersion of benzoic acid supported on the surface of H-titanate nanotubes

Benzoic acid (BA) can disperse spontaneously onto the surface of H-titanate nanotubes (HTNTs) in a sub-monolayer state by heating mechanical mixtures method. The structure of BA-HTNTs system has been characterized by X-ray diffraction (XRD), thermogravimetric (TG), Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) in detail. The results show that the H-bond association structure among BA molecules collapses and the carboxyl groups react with the surface hydroxyl group of HTNTs to form a salt-like structure on the surface after dispersion. The monolayer dispersion capacity determined by XRD is ca. 0.305 g BA g⁻¹ HTNTs, which is lower than the utmost monolayer dispersion capacity 0.550 g BA g⁻¹ HTNTs calculated according to a model that the benzene ring in BA molecules is perpendicular to the surface of HTNTs. At the same time, the dispersion capacity is also measurement by the fit of C 1s XPS peak at various BA loadings at first time.     

Adsorption of bovine serum albumin (BSA) on polystyrene (PS) and its acid copolymer

The effect of surface polarity on the adsorption of bovine serum albumin (BSA) on polystyrene (PS), 7% polystyrene-co-maleic anhydride (7%PSMAn) and 50% polystyrene-co-maleic acid (50%PSMA), at pH 7.4, was investigated. Polystyrene represented the non-polar surface while 7%PSMAn and 50%PSMA represented a low and high acid content copolymer. The amount of the adsorbed BSA depended on the amount of the acid content in the copolymer. BSA formed a monolayer with a side-on orientation on the low polarity PS surface, a mixed side-on and end-on orientation on 7%PSMAn and a predominantly side-on orientation on 50%PSMA. The thickness of adsorbed BSA, measured with an atomic force microscope (AFM), varied from 3 nm to 5 nm for the side-on orientation and from 10 nm to 15 nm for the end-on orientation. The average area occupied per BSA molecule was consistent with the proposed orientation, and was 34.8 nm², 27.8 nm² and 18.0 nm² for PS, 7%PSMAn and 50%PSMA, respectively. The adsorption showed a concentration dependency following the Freundlich isotherm, which indicated the interactions among adsorbed BSA molecules on the polymer surface. The adsorption took place as an island-like morphology and started to fuse into a patch-like morphology at higher concentrations before achieving a complete monolayer formation. A non-uniform surface coverage and defects were observed in all cases. It is recommended that for an effective blocking of PS, 7%PSMAn and 50%PSMA, the BSA concentration should be higher than 3 mg/mL.     

Structure of dioctadecyl l-glutamide-derived lipid self-assembled monolayers on Au(1 1 1) surface

An l-glutamic acid-derived lipid with a terminal thiol has been synthesized and its corresponding self-assembled structure on Au(1 1 1) surfaces described. The surface morphology of the lipid self-assembled monolayer (SAM) exhibits nano-order patterning, where the height of the monolayer (approximately 1.5 nm) could be interpreted as due to the monolayer structure estimated from molecular models. The molecular orientation in the monolayer is almost perpendicular to the Au(1 1 1) surface depending on the three-point hydrogen-bonding sites in the molecule.