Time-dependent organization and wettability of decanethiol self-assembled monolayer on Au(111) investigated with STM

A detailed study on the time-dependent organization of a decanethiol self-assembled monolayer (SAM) at a designed solution concentration onto a Au(111) surface has been performed with scanning tunneling microscopy (STM). The SAMs were prepared by immersing Au(111) into an ethanol solution containing 1 microM decanethiol with different immersion times. STM images revealed the formation process and adlayer structure of the SAMs. It was found that the molecules self-organized into adlayers from random separation to a well-defined structure. From 10 s, small domains with ordered molecular organization appeared, although random molecules could be observed on Au(111) at the very initial stage. At 30 s, the SAM consisted of uniform short stripes. Each stripe consisted of sets of decanethiol mainly containing eight molecules. With the immersion time increasing, the length of the stripes increased. At 5 min, the alkyl chains overlapped each other between the adjacent stripes, indicating the start of a stacked process. After immersing Au(111) in decanethiol solution for 3 days, a densely packed adlayer with a (radical 3 x radical 3)R30 degrees structure was observed. The formation process and structure of decanethiol SAMs are well related to sample preparation conditions. The wettability of the decanethiolate SAM-modified Au(111) surface was also investigated.     

Structures and displacement of 1-adamantanethiol self-assembled monolayers on Au{111}

We have designed monolayers with weak intermolecular interactions for use as placeholders in intelligent self- and directed-assembly. We have shown that these 1-adamantanethiolate monolayers are labile with respect to displacement by exposing them to dilute solutions of alkanethiols. These self-assembled monolayers (SAMs) of 1-adamantanethiol on Au{111} were probed using ambient scanning tunneling microscopy (STM), and their assembled order was determined. Solution deposition of the molecules results in a highly ordered hexagonally close-packed molecular lattice with a measured nearest neighbor distance of 6.9 +/- 0.4 A. The SAMs exhibit several rotational domains, but lack the protruding domain boundaries typical of alkanethiolate SAMs, and are similarly stable at room temperature. Co-deposition of alkanethiol and 1-adamantanethiol from solution results in alkanethiolate SAMs, except when using extremely low alkanethiol to 1-adamantanethiol concentration ratios. Facile displacement of low interaction strength SAMs can be exploited to enhance patterning using soft nanolithography.     

Reaction of 5-40 eV ions with self-assembled monolayers

The reaction of 5-40 eV O(+) and Ne(+) ions with alkanethiolate and semifluorinated alkanethiolate self-assembled monolayers (SAMs) is studied under ultrahigh vacuum (UHV) conditions. Whereas Ne(+) simply sputters fragments from the surface, O(+) can also abstract surface atoms and break C-C bonds in both the hydrocarbon and fluorocarbon SAM chains. Isotopic labeling experiments reveal that O(+) initially abstracts hydrogen atoms from the outermost two carbon atoms on an alkanethiolate SAM chain. However, the position of the isotopic label quickly becomes scrambled along the chain as the SAM is damaged through continuous ion bombardment. Scanning tunneling microscopy (STM) monitors changes in the SAM conformational structure at various stages during 5 eV ion bombardment. STM images indicate that O(+) reacts less efficiently with dodecanethiolate molecules packed internally within a structural domain than it does with molecules adsorbed at domain boundaries or near defect sites. STM images recorded after Ne(+) bombardment suggest that Ne(+) attacks the SAM exclusively near the domain boundaries. Taken collectively, these experiments advance our understanding of the degradation pathways suffered by polymeric satellite materials in the low-earth orbit (LEO) space environment.     

STM study of mixed alkanethiol/biphenylthiol self-assembled monolayers on Au(111)

A method is presented for depositing mixed self-assembled monolayers (SAMs) of dodecanethiol (C12) and 4'-methyl-1,1'-biphenyl-4-butane (H3C-C6H4-C6H4-(CH2)4-SH, BP4) by insertion of BP4 into a closely packed SAM of dodecanethiol on Au(111). Insertion takes place at defect sites such as domain boundaries or etch pits in the gold surface that are characteristic of C12 monolayers on gold. With a lower probability, insertion also occurs beside defect sites inside dodecanethiol domains. Insertion at defect sites results in domains of BP4, whereas insertion into C12 domains leads to isolated BP4 molecules. The isolated BP4 molecules are shown not to move at room temperature. By comparing the apparent height of the isolated BP4 molecules and BP4 domains, it is proposed that the isolated molecules have the same conformation as in the full-coverage phase. A simple two-layer model is proposed to characterize the current transport through BP4. The decay constant beta for the phenylene groups is deduced from the apparent STM heights of the inserted BP4 islands compared to the STM heights of the C12 closely packed monolayers.     

Formation of highly ordered and orientated gold islands: effect of immersion time on the molecular adlayer structure of pentafluorobenzenethiols (PFBT) SAMs on Au(111)

Self-assembled monolayers (SAMs) of pentafluorobenzenethiol (PFBT) on Au(111) substrates, prepared with different immersion times (ITs) at room temperature, were studied using scanning tunneling microscopy (STM) and infrared reflection-absorption spectroscopy (IRRAS). In the present study, the focus was on several important points of interest in the field of SAMs. First, the gold islands formed upon adsorption of PFBT molecules on the gold surface were monitored at different ITs in terms of their size, density, and shape. After short ITs (5 to 30 min), small gold islands with rounded shape were formed. These gold islands were arranged in a rather regular fashion and found to be quite mobile under the influence of the STM-tip during the scanning. When the IT was increased to 16 h, the results revealed the formation of highly ordered and orientated gold islands with very unusual shapes with straight edges meeting at 60° or 120° running preferentially along the [11(-)0] substrate directions. The density of the gold islands was found to decrease with increasing IT until they almost disappeared from the SAMs prepared after 190 h of IT. On top of the gold islands, the PFBT molecules were found to adopt the closely packed (10√3 × 2) structure. Second, a number of structural defects such as disordered regions at the domain boundaries and dark row(s) of molecules within the ordered domains of the PFBT SAMs were observed at different ITs. The SAMs prepared after 190 h of IT were found to be free of these defects. Third, at low and moderate ITs, a variation in the PFBT molecular contrast was observed. This contrast variation was found to depend mainly on the tunneling parameters. Finally, our results revealed that the organization process of PFBT SAMs is IT-dependent. Consequently, a series of structural phases, namely, α, β, γ, δ, and ε were found. The α-, β-, γ-, and δ-phases were typically accompanied by the ε-phase that appeared on top of gold islands. With increasing IT, the α→β→ γ→δ→ε phase transitions took place. The resulting ε-phase, which covered the entire gold surface after 190 h of IT, yielded well-ordered self-assembled monolayers with large domains having a (10√3 × 2) superlattice structure.     

Ambient-pressure vapor deposition of octanethiol self-assembled monolayers

Scanning tunneling microscopy was used to characterize self-assembled monolayers (SAMs) of octanethiol on Au(111), created using vapor deposition at elevated temperatures and ambient pressure. Monolayers contained large, close-packed ( radical3 x radical3)R30 degrees domains with sizes considerably larger than those typically formed from conventional solution-phase preparation and with crystallographically straight domain boundaries. New striped surface phases were also observed, including a 13 x radical3 phase with a density that was 69% of the close-packed density; these striped phases appeared topographically higher in STM images than close-packed monolayers.     

Two-site adsorption model for the (square root 3 x square root 3)-R30 degrees dodecanethiolate lattice on Au(111) surfaces

The surface structure of dodecanethiolate self-assembled monolayers (SAMs) on Au(111) surfaces, formed from the liquid phase, have been studied by grazing incidence X-ray diffraction (GIXRD), scanning tunneling microscopy (STM), and electrochemical techniques. STM images show that the surface structure consists of (square root 3 x square root 3)-R30 degrees domains with only a few domains of the c(4 x 2) lattice. The best fitting of GIXRD data for the (square root 3 x square root 3)-R30 degrees lattice is obtained with alkanethiolate adsorption at the top sites, although good fittings are also obtained for the fcc and hcp hollow sites. On the basis of this observation, STM data, electrochemical measurements, and previously reported data, we propose a two-site model that implies the formation of incoherent domains of alkanethiolate molecules at top and fcc hollow sites. This model largely improves the fitting of the GIXRD data with respect to those observed for single adsorption sites and, also, for the other possible two-site combinations. The presence of alkanethiolate molecules adsorbed at the less favorable top sites could result from the adsorption pathway that involves an initial physisorption step which, for steric reasons, takes place at on top sites. Once the molecules are chemisorbed, the presence of energy barriers for alkanethiolate surface diffusion, arising mostly from chain-chain interactions, "freezes" some of them at the on top sites, hindering their movement toward fcc hollow sites. By considering the length of the hydrocarbon chain and the adsorption time, the two-site model could be a tool to explain most of the controversial results on this matter reported in the literature.     

Disorder-order phase change of omega-(N-pyrrolyl)alkanethiol self-assembled monolayers on gold induced by STM scans and thermal activation

Molecular ordering of pyrrolyl-terminated alkanethiol self-assembled monolayers (PyC(n)SH SAMs) on Au(111) substrates (n = 11 or 12) was investigated by scanning tunneling microscopy (STM) and various spectroscopic methods. The SAMs, which were in a disordered state when formed at room temperature, could be ordered either globally by thermal annealing at 70 degrees C, or locally via stimulation with repetitive STM scans. The ordered phase was characterized by small domains of molecular rows formed along 112[combining macron] directional set with an inter-row corrugation period close to 1.44 nm, in which defects were abundant. Based on the experimental results, the molecular arrangement in the ordered PyC(n)SH SAM was proposed to be a (5x radical3)rect structure with a molecular deficiency >or=10%. While mechanical interactions between molecules and scanning probe tips had been pointed out as the major cause of scan-induced phase transformations in other SAM systems, electronic or electrostatic factors were thought to affect considerably the scan-induced ordering process in this SAM system. From comparison of surface molecular coverage between disordered and thermally ordered SAMs of PyC(12)SH, it was inferred that the disorder could be ascribed to both kinetic and thermodynamic factors. The kinetic barrier to the ordered phase was supposed to result from strong dipole-dipole interactions among the pyrrolyl endgroups.     

Versatility of aqueous micellar solutions for self-assembled monolayers engineering

Self-assembly of aliphatic as well as aromatic thiol-terminated molecules was achieved onto a variety of gold surfaces using aqueous micellar solutions. Scanning tunneling microscopy experiments allowed us to demonstrate that the increase in the density of self-assembled monolayers (SAMs) prepared from micellar aqueous solvent compared to that prepared from ethanol directly originates from the decrease in defect density in the SAM (etch pits, domain boundaries) and not from a denser local packing of the molecules. Extending the use of such an aqueous solvent to various conjugated molecules, we report for the first time the insertion of these molecules from an aqueous solution in a dodecanethiol (DT) SAM and the ligand-exchange on the surface of DT stabilized gold nanoparticles deposited as a Langmuir-Blodgett film. Finally, we show that aqueous micellar DT solutions allow the preparation of DT SAMs on gold through a micropatterned resist mask. These results make possible the use of water to deliver molecules on a solid substrate to build molecular devices in a way compatible with lithography requirements in microelectronic processes.     

Hierarchical chiral framework based on a rigid adamantane tripod on Au(111)

We have investigated the tripod-shaped bromo adamantane trithiol (BATT) molecule on Au(111) using scanning tunneling microscopy (STM) at 4.7 K. Adsorption of BATT leads to formation of highly ordered self-assembled monolayers (SAMs) with three-point contacts on Au(111). The structure of these SAMs has been found to have a two-tiered hierarchical chiral organization. The self-assembly of achiral monomers produces chiral trimers, which then act as the building blocks for chiral hexagonal supermolecules. SAMs begin to form from the racemic mixture of assembled molecules in ribbon-shaped islands, followed by the transformation to enantiomeric domains when SAM layers develop two-dimensionally across hcp domains. Such a chiral phase transition at the two-dimensional domain can arise from a subtle balance between molecule-substrate and intermolecular interactions. Two structural factors, the S atom (stabilization) and the methylene groups (chirality) located just above the S atom, induce the chiral ordering of BATT on Au(111).     

Formation of ordered self-assembled monolayers by adsorption of octylthiocyanates on Au(111)

Self-assembled monolayers (SAMs) were formed by the spontaneous adsorption of octythiocyanate (OTC) on Au(111) using both solution and ambient-pressure vapor deposition methods at room temperature and 50 degrees C. The surface structures and adsorption characteristics of the OTC SAMs on Au(111) were characterized by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). The STM observation showed that OTC SAMs formed in solution at room temperature have unique surface structures including the formation of ordered and disordered domains, vacancy islands, and structural defects. Moreover, we revealed for the first time that the adsorption of OTC on Au(111) in solution at 50 degrees C led to the formation of SAMs containing small ordered domains, whereas the SAMs formed by vapor deposition at 50 degrees C had long-range ordered domains, which can be described as (radical3 x 2 radical19)R5 degrees structures. XPS measurements of the peaks in the S 2p and N 1s regions for the OTC SAMs showed that vapor deposition is the more effective method as compared to solution deposition for obtaining high-quality SAMs by adsorption of OTC on gold. The results obtained will be very useful in understanding the SAM formation of organic thiocyanates on gold surfaces.     

Scanning tunneling microscopy of template-stripped Au surfaces and highly ordered self-assembled monolayers

Template stripping of Au films in ultrahigh vacuum (UHV) produces atomically flat and pristine surfaces that serve as substrates for highly ordered self-assembled monolayer (SAM) formation. Atomic resolution scanning tunneling microscopy of template-stripped (TS) Au stripped in UHV confirms that the stripping process produces a flat, predominantly 111 textured, atomically clean surface. Octanethiol SAMs vapor deposited in situ onto UHV TS Au show a c(4 x 2) superlattice with (square root 3 x square root 3) R30 degrees basic molecular structure having an ordered domain size up to 100 nm wide. These UHV results validate the TS Au surface as a simple, clean and high-quality surface preparation method for SAMs deposited from both vapor phase and solution phase.     

Molecular-level approach to inhibit degradations of alkanethiol self-assembled monolayers in aqueous media

A molecular-level approach is developed to prevent or inhibit the degradation processes of alkanethiol self-assembled monolayers (SAMs). Previous studies revealed two degradation pathways: direct desorption and oxidation-desorption. By use of scanning tunneling microscopy (STM) and atomic force microscopy (AFM), in situ and time-dependent imaging reveals and confirms that degradations of alkanethiol SAMs on gold mainly initiate at defect sites, such as domain boundaries and vacancy islands, and then propagate into the ordered domains. Our approach targets at attaching small molecules with preferred adhesion to the defects. The best candidates are aqueous media containing a small amount of amphiphilic surfactant molecules, such as N,N-dimethylformamide (DMF) or dimethyl sulfoxide (DMSO). High-resolution studies demonstrate that DMSO and DMF molecules attach to SAM surfaces and more favorably at defect sites, forming relatively stable adsorbates. This attachment increases the activation energy sufficiently to inhibit both degradation pathways. The robustness of this approach has been investigated as a function of surfactant concentration, solution temperature, and the stirring condition. Molecular-level mechanisms and energetics for degradation inhibition of SAMs are also discussed in detail.     

Role of surface heterogeneity and molecular interactions in the charge-transfer process through self-assembled thiolate monolayers on Au(111)

A comparative study of charge-transfer processes from/to methyl-terminated and carboxylate-terminated thiolate-covered Au(111) surfaces to/from immobilized methylene blue (MB) molecules is presented. Scanning tunneling microscopy images with molecular resolution reveal the presence of molecular-sized defects, missing rows, and crystalline domains with different tilts that turn the thickness of the alkanethiolate SAM (the spacer) uncertain. The degree of surface heterogeneity at the SAMs increases as the number of C units (n) in the hydrocarbon chain decreases from n = 6. Defective regions act as preferred paths for MB incorporation into the methyl-terminated SAMs, driven by hydrophobic forces. The presence of negative-charged terminal groups at the SAMs reduces the number of molecules that can be incorporated, immobilizing them at the outer plane of the monolayer. Only MB molecules incorporated into the SAMs close to the Au(111) surface (at a distance < 0.5 nm) are electrochemically active. MB molecules trapped in different defects explain the broad shape and humps observed in the voltammogram of the redox couple. The heterogeneous charge-transfer rate constants for MB immobilized into methyl-terminated thiolate SAMs are higher than those estimated for carboxylate- terminated SAMs, suggesting a different orientation of the immobilized molecule in the thiolate environment.     

Probing the local structure and mechanical response of nanostructures using force modulation and nanofabrication

Nanostructures of self-assembled monolayers (SAMs) are designed and produced using coadsorption and nanografting techniques. Because the structures of these artificially engineered domains are predesigned and well-characterized, a systematic investigation is possible to study the mechanical responses to force modulation under atomic force microscope tips. Force modulation imaging reveals characteristic contrast sensitivity to changes in molecular-level packing, molecule chain lengths, domain boundaries, and surface chemical functionalities in SAMs. By means of actively tuning the driving frequency, the resonances at the tip-surface contact are selectively activated. Therefore, specific surface features, such as the edges of the domains and nanostructures or desired chemical functionalities, can be selectively enhanced in the amplitude images. These observations provide a new and active approach in materials characterization and the study of nanotribology using atomic force microscopy.     

Boundary Effects in the Hexagonal Packing of Rod-Like Molecules Inside a Right Circular Cylindrical Domain. III. The Case of Arbitrarily Oriented Spherocylindrical Molecules

We study the organization of spherocylindrical molecules inside a freely rotating right circular cylindrical domain at the gas/liquid interface. The analysis is made under the assumption that the molecules are rigid and close packed, and that they are oriented parallel to each other. The direction and angle of their common orientation are completely arbitrary. We obtain exact analytic expressions for the lattice of molecular centers and its boundaries as a function of molecular dimensions, molecular orientation, and domain size. As a first application, we derive the number of molecules in a domain, and the packing fraction. The results obtained are essential when attempting to analytically model a Langmuir film where the global order of the film is less than the local order of the domains.     

Analysis of self-assembled monolayers by thermal desorption mass spectrometry: neighborhood interaction and hydrogen/deuterium exchange.

Two ideas for characterizing the local structure in mixed self-assembled monolayers (SAMs) were introduced. First, to use thermal desorption mass spectrometry (TD-MS) to probe nearest neighborhoods in the mixed monolayers. Second, to use hydrogen/deuterium exchange as a probe of the accessibility of acidic protons to exchange. Neighborhood interactions provided an opportunity to observe microscopic phase changes at the SAMs surface as a function of the OH-terminal ratio. H/D exchange between surficial OH-terminal SAMs and D2O was successfully observed. H/D exchange was of importance in characterizing the surface properties and molecular basis interactions for the design of bio-interface structures using self-assembled monolayers.     

Structural characterization of aldehyde-terminated self-assembled monolayers

The structure of aldehyde-terminated alkanethiol self-assembled monolayers (SAMs) on Au(111) is investigated using scanning tunneling microscopy (STM), atomic force microscopy (AFM), and density functional theory (DFT) calculations. For the first time, the structures of aldehyde-terminated SAMs are revealed with molecular resolution. SAMs of 11-mercapto-1-undecanal exhibit the basic (radical3xradical3)R30 degrees periodicity and form various c(4x2) superstructures upon annealing. In conjunction with DFT studies, the models of the (radical3xradical3)R30 degrees and the c(4x2) superstructures are constructed. In comparison with alkanethiol SAMs, the introduction of aldehyde-termini results in smaller domain size, lower degree of long-range order, large coverage of disordered areas, and higher density of missing molecules and other point defects within domains of closely packed molecules. The origin of these structural differences is mainly attributed to the strong dipole-dipole interactions among the aldehyde termini.     

Self-assembled monolayers of alkaneselenolates on (111) gold and silver

Self-assembled monolayers (SAMs) formed from didodecyl diselenide (C12SeSeC12) and didodecyl selenide (C12SeC12) on (111) Au and Ag substrates were extensively characterized by several complementary techniques. C12SeSeC12 was found to form contamination-free, densely packed, and well-ordered C12Se SAMs on both substrates, whereas the adsorption of C12SeC12 occurred only on Au and resulted in the formation of a SAM-like C12SeC12 film with a low packing density and a conformational disorder. The properties of the C12Se SAMs were compared with those of dodecanethiolate (C12S) SAMs. The packing density, orientational order, and molecular inclination in C12Se/Au and C12S/Au were found to be very similar. In contrast, C12Se/Ag exhibited significantly lower packing density, a lower degree of the conformational and orientational order, and a larger molecular inclination than C12S/Ag. The results suggest a sp3 bonding configuration for the selenium atom on Au and Ag and indicate a larger corrugation of the headgroup-substrate binding energy surface in C12Se/Ag than in C12S/Ag.     

Assessing group-based cutoffs and the Ewald method for electrostatic interactions in clusters and in saturated,superheated, and supersaturated vapor phases of dipolar molecules

Monte Carlo simulations in the canonical, isobaric-isothermal, grand canonical, and Gibbs ensembles were used to assess whether the computationally expensive Ewald summation method for the computation of the first-order electrostatic energy can be replaced with a simpler truncation approach for accurate simulations of the saturated, superheated, and supersaturated vapor phases of dipolar and hydrogen-bonding molecules. Rotationally averaged hydrogen fluoride dimer and trimer energies, thermophysical properties and aggregation in the superheated vapor phase of hydrogen fluoride, nucleation free energy barriers for water, and the vapor–liquid coexistence properties of hydrogen fluoride and water were investigated over a wide range of state points. We find that for densities not too close to the critical density, results obtained from simulations using a spherical potential truncation based on neutral groups (molecules or fragments) for the Coulomb interactions are statistically identical to those obtained using the Ewald summation method. Use of the simpler spherical truncation results in a significant reduction of the computational effort for simulations employing molecular mechanics force fields and also allows for straightforward implementation of many-body expansion methods to compute the potential energy from electronic structure calculations of subsystems of the entire vapor-phase system.