Alkanethiol/Au(111) self-assembled monolayers contain gold adatoms: scanning tunneling microscopy before and after reaction with atomic hydrogen

Alkanethiol self-assembled monolayers on Au(111) are widely studied, yet the exact nature of the sulfur-gold bond is still debated. Recent studies suggest that Au(111) is significantly reconstructed, with alkanethiol molecules binding to gold adatoms on the surface. These adatoms are observed using scanning tunneling microscopy before and after removing the organic monolayer with an atomic hydrogen beam. Upon monolayer removal, changes in the gold substrate are seen in the formation of bright, triangularly shaped islands, decreasing size of surface vacancy islands, and faceting of terrace edges. A 0.143 +/- 0.033 increase in gold coverage after monolayer removal shows that there is one additional gold adatom for every two octanethiol molecules on the surface.     

Collision-induced annealing of octanethiol self-assembled monolayers by high-kinetic-energy xenon atoms

Collisions with high-energy xenon atoms (1.3 eV) induce structural changes in octanethiol self-assembled monolayers on Au(111). These changes are characterized at the molecular scale using an in situ scanning tunneling microscope. Gas-surface collisions induce three types of structural transformations: domain boundary annealing, vacancy island diffusion, and phase changes. Collision-induced changes that occur tend to increase order and create more stable structures on the surface. We propose a mechanism where monolayer transformations are driven by large amounts of vibrational energy localized in the alkanethiol molecules. Because we monitor incremental changes over small regions of the surface, we can obtain structural information about octanethiol monolayers that cannot be observed directly in scanning tunneling microscopy images.     

Surface functionalization of electro-deposited nickel

A new in situ electrochemical method of functionalizing an oxide-free Ni surface is demonstrated using octanethiol. Initial adsorption results in a multilayer molecular film, which blocks both the hydrogen evolution reaction (HER) and re-oxidation of the Ni by ambient oxygen. However, excess octanethiol can be removed by rinsing with ethanol, leaving behind a monolayer that continues to protect against re-oxidation but gives rise to an unexpected enhancement in the HER, with a greater enhancement for longer film formation times. The presence of an octanethiol monolayer on the surface was confirmed by spectroscopic observation of the CH(2), CH(3) and thiolate groups using infra red spectroscopy, while X-ray photo-electron spectroscopy demonstrated the effectiveness of the thiol layer as a barrier to surface oxidation. The electrochemically prepared octanethiol film impedes oxidation of the Ni in air more effectively than a film formed by immersion in a solution of octanethiol in ethanol.     

Scanning electrochemical microscopy determination of organic soluble MPC electron-transfer rates

In this paper, we describe a novel method for measuring the forward heterogeneous electron-transfer rate constant (kf) through the thiol monolayer of gold monolayer protected clusters (MPCs) in solution using scanning electrochemical microscopy (SECM). Applying the equations for mixed mass-transfer and electron-transfer processes, we develop a new formula using only the diffusion coefficient and the tip radius and use it as part of a new method for evaluating SECM approach curves. This method is applied to determine the electron-transfer rates from a series of SECM approach curves for monodisperse hexanethiol MPCs and for polydisperse hexanethiol, octanethiol, decanethiol, dodecanethiol, and 2-phenyethylthiol gold MPCs. Our results show that as the alkanethiol length increases the rate of electron transfer decreases in a manner consistent with the previously proposed tunneling mechanism for the electron transfer in MPCs. However, the effective tunneling coefficient, Beta, is found to be only 0.41 A-1 for alkanethiol passivated MPCs compared to typical values of 1.1 A-1 for alkanethiols as self-assembled monolayers on two-dimensional gold substrates. Similar SECM approach curve results for Pt and Au MPCs indicate that the electron-transfer rate is dependent mostly on the composition of the thiol layer and not on differences in the core metal.     

Assembly dynamics and detailed structure of 1-propanethiol monolayers on Au(111) surfaces observed real time by in situ STM

1-Propanethiol is chosen as a model alkanethiol to probe detailed mechanisms of the self-assembled monolayer (SAM) formation at aqueous/Au(111) interfaces. The assembly processes, including initial physi- and chemisorption, pit formation, and domain growth, were recorded into movies in real-time with high resolution by in situ scanning tunneling microscopy (STM) under potential control. Two major adsorption steps were disclosed in the propanethiol SAM formation. The first step involves weak interactions accompanied by the lift of the Au(111) surface reconstruction, which depends reversibly on the electrochemical potentials. The second step is chemisorption to form a dense monolayer, accompanied by formation of pits as well as structural changes in the terrace edges. Pits emerged at the stage of the reconstruction lift and increased to a maximum surface coverage of 4.0 +/- 0.4% at the completion of the SAM formation. Well-defined triangular pits in the SAM were found on the large terraces (more than 300 nm wide), whereas few and small pinholes appeared at the terrace edge areas. Smooth edges were converted into saw-like structural features during the SAM formation, primarily along the Au(111) atomic rows. These observations suggest that shrinking and rearrangement of gold atoms are responsible for both formation of the pits and the shape changes of the terrace edges. STM images disclose a (2 square root 3 x 3)R30 degrees periodic lattice within the ordered domains. Along with electrochemical measurements, each lattice unit is assigned to contain four propanethiol molecules exhibiting different electronic contrasts, which might originate in different surface orientations of the adsorbed molecules.     

Heat-stabilized glycosphingolipid films for biosensing applications

We have investigated a means of producing thin, oriented lipid monolayers which are stable under repeated washing and which may be useful in biosensing or surface-coating applications. Phosphatidylcholine and the glycosphingolipid GM1 were used as representative lipids for this work. Initially, a mixed self-assembled monolayer of octanethiol and hexadecanethiol was produced on a gold surface. This hydrophobic monolayer was then brought into contact with a thin lipid film that had been assembled at the liquid/air interface of a solution, allowing the lipid to deposit on the gold surface through hydrophobic interactions. The lipid layer was then heated to cause intermingling of the fatty acid and alkanethiol chains and cooled to form a highly stable film which withstood repeated rinsing and solution exposure. Presence and stability of the film were confirmed via ellipsometry, Fourier transform infrared spectroscopy, and quartz crystal microbalance (QCM), with an average overall film thickness of approximately 3.5 nm. This method was then utilized to produce GM1 layers on gold-coated QCM crystals for affinity sensing trials with cholera toxin. For these sensing elements, the lower detection limit of cholera toxin was found to be approximately 0.5 microg/mL, with a logarithmic relationship between toxin concentration and frequency response spanning over several orders of magnitude. Potential sites for nonspecific adsorption were blocked using serum albumin without sacrificing toxin specificity.     

Investigation of the interactions between alkanethiol self-assembled monolayers and a liquid overlayer using impedance spectroscopy

We report on changes in the complex impedance response of a quartz crystal microbalance (QCM) that result from the growth of an alkanethiol monolayer on the electrodes of the device. The purpose of this work is to understand the evolution of the interactions between alkanethiol-gold monolayers and a liquid overlayer as a function of time after initial deposition by evaluating the position, shape, and linewidth of the impedance spectra associated with the monolayer formation. We relate the complex impedance response of the QCM to the mass and viscosity of the monolayer through an established equivalent circuit model. The data show the organization of alkanethiol SAMs occurs at approximately the same rate for aliphatic chain lengths in the range of C(9)-C(16), as long as the thiol is readily soluble in the solvent system used. Our data are consistent with SAM annealing being mediated by the sulfur-gold adsorption and desorption equilibrium. Additionally, we have found that examination of a C(18) SAM is limited by the deposition conditions and thiol solubility. Bulk deposition was confirmed visually and related to the evolution of the peak position and shape changes with deposition time.     

Template synthesis of metal nanowires containing monolayer molecular junctions

Metal nanowires containing in-wire monolayer junctions of 16-mercaptohexanoic acid were made by replication of the pores of 70 nm diameter polycarbonate track etch membranes. Au was electrochemically deposited halfway through the 6 microm long pores and a self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid was adsorbed on top. A thin layer of Au was then electrolessly grown to form a metal cap separated from the bottom part of the wire by the SAM. Electron micrographs showed that the bottom and top metal segments were separated by an approximately 2 nm thick organic monolayer. Current-voltage measurements of individual nanowires confirmed that the organic monolayer could be contacted electrically on the top and bottom by the metal nanowire segments without introducing electrical short circuits that penetrate the monolayer. The values of the electrical properties for zero-bias resistance, current density, and breakdown field strength were within the ranges expected for a well-ordered alkanethiol SAM of this thickness.     

Time‐of‐flight secondary ion mass spectrometry and gas chromatography–mass spectrometry studies of alkanethiol self‐assembled monolayers on nanoporous gold surfaces

The dimerization of alkanethiol mixtures (hexanethiol, octanethiol, and dodecanethiol) to form self‐assembled monolayers (SAMs) from headspace on nanoporous gold surfaces was studied for the first time using gas chromatography (GC/MS) and time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS). The nanoporous gold surfaces were obtained by an acidic etching of a 585‐gold alloy. Field emission scanning electron microscopy (FE‐SEM) was utilized to study the change of the surface geometry and porosity of the gold surfaces before and after etching. Alkanethiols were deposited from the vapor phase above the thiol solutions (headspace) on nanoporous gold plates and nanoporous gold solid‐phase vmicroextraction (SPME) fibers. The nanoporous gold substrates were analyzed by TOF‐SIMS and GC/MS, respectively. The TOF‐SIMS spectra exhibited various gold–sulfur ion clusters and specific peaks related to the adsorption of thiols such as deprotonated monomers, thiolate–Au, dimers (e.g., dialkyl sulfides–Au and dialkyl disulfides–Au). The GC/MS analysis of headspace extractions of alkanethiol mixtures by nanoporous gold SPME fibers showed a high extraction efficiency of alkanethiol, dialkyl sulfide, and dialkyl disulfide when compared with the commercial SPME fibers (DVB‐CAR‐PDMS and CAR‐PDMS). Different GC/MS optimization factors were studied including the extraction time and desorption temperature.     

Mixed adlayer of alkanethiol and peptide on GaAs(100): quantitative characterization by X-ray photoelectron spectroscopy

Homogeneous and mixed adlayers composed of an alkanethiol (1-octadecanethiol, ODT) and a peptide (CGISYGRKKRRQRRR) on GaAs(100) were formed in two different solvent systems: phosphate-buffered saline (PBS) and N,N-dimethylformamide (DMF). The chemical composition of each adlayer was characterized by X-ray photoelectron spectroscopy (XPS). The data showed that the makeup of the adlayer and its stability largely depends on the solvent used. Angle-resolved XPS also revealed that the adlayer thickness and tilt angles were different from values obtained from ellipsometry measurements and vastly varied between the two solvents used. The coverage data extracted from the XPS measurements indicated that homogeneous adlayers of peptide in PBS buffer form a multilayered film. Homogeneous alkanethiol adlayers exhibited monolayer coverage under all solvent treatments. Coadsorbed layers containing both alkanethiol and peptide have fractional monolayer coverage in both solvents.     

Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.     

Surface plasmon microscopy of biotin-streptavidin binding reactions on UV-photopatterned alkanethiol self-assembled monolayers

We report surface plasmon imaging of streptavidin binding to photopatterned biotinylated alkanethiol self-assembled monolayers (SAMs) on gold. Micrometer-scale patterns of a mixed biotin- and hydroxyl-terminated monolayer were formed in an inert, hydroxy-terminated alkanethiol monolayer using a UV-photopatterning procedure. Using surface plasmon microscopy, contrast is readily observed between the mixed biotin- and hydroxy-terminated SAM region after specific binding of streptavidin has occurred and the pure hydroxy-terminated region where nonspecific binding of streptavidin is negligible. Surface plasmon microscopy was also able to monitor in situ and in real time the binding of streptavidin to the patterned SAMs. The ability of surface plasmon microscopy to detect and spatially resolve 2-dimensional monolayer binding events may prove useful in diagnostic applications involving the parallel interrogation at surface biomolecular arrays.     

Inelastic scattering dynamics of Ar from a perfluorinated self-assembled monolayer surface

Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are represented as single pseudoatoms. Additionally the nonbonded interactions in both models are different. The simulations show the three limiting mechanisms expected for collisions of rare gas atoms (or small molecules) with SAMs, that is, direct scattering, physisorption, and penetration. Surface penetration results in a translational energy distribution, P(Ef), that can be approximately fit to the Boltzmann for thermal desorption, suggesting that surface accommodation is attained to a large extent. Fluorination of the alkanethiol monolayer leads to less energy transfer in Ar collisions. This results from a denser and stiffer surface structure in comparison with that of the alkanethiol SAM, which introduces constraints for conformational changes which play a significant role in the energy-transfer process. The trajectory simulations predict P(Ef) distributions in quite good agreement with those observed in the experiments. The results obtained with the EA and UA models are in reasonably good agreement, although there are some differences.     

Formation of alkanethiol and alkanedithiol monolayers on GaAs(001)

The formation of alkanethiol (H-(CH2)n-SH, n = 8-18) and 1,8-octanedithiol (HS-(CH2)8-SH) monolayer films on n-type GaAs(001) has been systematically studied. We observed a nonlinear dependence of the film thickness on molecular length, which is drastically different from monolayer films of the same molecules on metals. For 8 < or = n < or = 14, the films are only 3-4.5 A thick, significantly smaller than the corresponding molecular length. For n = 16 and 18, the measured film thicknesses were 9 and 11 A, respectively, consistent with molecules orienting with a tilt angle of approximately 60 degrees from the surface normal. Unlike the alkanethiols, the thickness of the 1,8-octanedithiol monolayer is almost the same as its molecular length, indicating that dithiol molecules orient vertically with only one thiol end group bound to the GaAs surface. Additional support for this conclusion comes from the fact that X-ray photoelectron spectroscopy of the 1,8-octanedithiol monolayer clearly resolves two types of S atoms in the monolayer: those bound to the GaAs surface and those existing as free thiols. A suggestion was made on the mechanisms for alkanethiol and alkanedithiol monolayer formation.     

Anisotropic polymerization of a long-chain diacetylene derivative Langmuir-Blodgett film on a step-bunched SiO2/Si surface

Alternating facet/terrace nanostructures were fabricated on a SiO2 surface by step-bunching and thermal oxidation of a vicinal Si(111) substrate, and their influence upon the polymerization direction of a long-chain diacetylene derivative monolayer film was investigated by angle-dependent polarized near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. It was found that the peak intensity of the C 1s-pi transition was stronger when the electric vector plane of the incident X-ray was parallel to the direction of the periodic facet/terrace structures rather than perpendicular to them. On the contrary, a polymer film fabricated on a flat SiO2 surface showed no in-plane anisotropy of the peak intensity. These results indicate that the diacetylene groups in the diacetylene derivative monolayer are preferentially photopolymerized in the direction not across but along the periodic one-dimensional structures on the step-bunched and thermally oxidized SiO2/Si(111) surface.     

Tunneling Electron Induced Fluorescence from Single Porphyrin Molecules Decoupled by Striped-Phase Octanethiol Self-assembled Monolayer

We investigate tunneling electron induced luminescence from isolated single porphyrin molecules that are decoupled by striped-phase self-assembled monolayer of octanethiol from the underneath Au(111) substrate. Intrinsic single-molecule electroluminescence has been realized by such decoupling at both bias polarities. The photon emission intensity acquired from the molecular lobe is found stronger than that from the molecular center. These re-sults provide useful information on the understanding of electroluminescent behavior and mechanism in molecular tunnel junctions.     

Water-soluble amphiphilic gold nanoparticles with structured ligand shells

Highly water-soluble mixed monolayer protected "rippled" gold nanoparticles were synthesized through a one step reaction with sodium 11-mercaptoundecanesulfonate and octanethiol ligands at various ratios.     

DC photoelectric signals from bacteriorhodopsin adsorbed on lipid monolayers and thiol/lipid bilayers supported by mercury

Purple membrane (PM) fragments were adsorbed on a dioleoylphosphatidylcholine (DOPC) monolayer and on a mixed alkanethiol/DOPC bilayer supported by mercury to investigate the kinetics of light-driven proton transport by bacteriorhodopsin (bR). The light-on and light-off capacitive currents on an alkanethiol/DOPC bilayer at pH 6.4 were interpreted on the basis of a simple equivalent circuit. The pH dependence of the biphasic decay kinetics of the light-on currents was analyzed to estimate the pK(a) values for the transitions releasing protons to, and taking up protons from, the solution. The linear dependence of the stationary light-on current of bR on a DOPC monolayer self-assembled on mercury upon the applied potential was interpreted on the basis of an equivalent circuit.     

Mechanical properties of alkanethiol monolayers studied by force spectroscopy

The mechanical properties of alkanethiol monolayers on Au(111) in KOH solution have been studied by force spectroscopy. The analysis of the vertical force versus penetration curves showed that monolayer penetration is a stepped process that combines elastic regions with sudden penetration events. The structural meaning of these events can be explained both by the creation of gauche defects on the hydrocarbon chains and by a cooperative molecular tilting model proposed by Barrena et al. [J. Chem. Phys. 113, 2413 (2000)]. The validity of these models for alkanethiol monolayers of different compactness and chain length has been discussed. The Young's modulus (E) of the monolayers has been calculated by using a recently developed model which considers the thickness of the monolayer as a parameter, thus allowing a decoupling of the mechanical properties of the thiol layer from those of the Au(111) substrate. As a result, the calculated E values are in the range of 50-150 Pa, which are remarkably lower than those previously reported in the literature.     

1-Dodecanethiol self-assembled monolayers on cobalt

Cobalt and its alloys are used in a broad range of application fields. However, the use of this metal is especially limited by its strongly oxidizable nature. The use of alkanethiol self-assembled monolayers (SAMs) is a very efficient way to protect against such oxidation and/or to inhibit corrosion. This surface modification method has been particularly applied to oxidizable metals such as copper or nickel, yet the modification of cobalt surfaces by alkanethiol SAMs received limited attention up to now. In this work, we study the influence of parameters by which to control the self-assembly process of 1-dodecanethiol monolayers on cobalt: nature of the surface pretreatment, solvent, immersion time, and concentration. Each of these parameters has been optimized to obtain a densely packed and stable monolayer able to efficiently prevent the reoxidation of the modified cobalt substrates. The obtained monolayers were characterized by X-ray photoelectron spectroscopy (XPS), polarization modulation infrared reflection-absorption spectroscopy, and contact angle measurements. The stability of the optimized 1-dodecanethiol monolayer upon air exposure for 28 days has been confirmed by XPS.