c(4x2) structures of alkanethiol monolayers on Au (111) compatible with the constraint of dense packing

Short Ligand, Cysteine-Modified Warnericin RK Antimicrobial Peptides Favor Highly Sensitive Detection of Legionella pneumophila

Culture-based methods for the detection of Legionella pneumophila are prohibitively slow and frequently inadequate. The problem has been addressed with biosensing technology that employs a variety of ligands for the specific capture of bacteria. However, the limited success of the application of mammalian antibodies, aptamers, and nucleic acid-based probes for sensitive biosensing has generated growing interest in exploring alternative biosensing architectures, such as those based on antimicrobial peptides (AMP) that are known for their attractive therapeutic applications. We report on the successful employment of cysteine-modified warnericin RK AMP for the operation of a highly sensitive biosensor of L. pneumophila based on digital photocorrosion of GaAs/AlGaAs nanoheterostructures. The replacement of the relatively cumbersome procedure commonly applied for the attachment of antibodies to COOH-terminated mercaptohexadecanoic acid self-assembled monolayers has allowed for a significant reduction in the distance at which bacteria are immobilized above the biosensor surface. An important consequence of this approach is the attractive limit of detection of L. pneumophila estimated at 2 × 102 CFU/mL. The target bacteria were captured four times more efficiently than P. fluorescens, B. subtilis, and E. coli, which is highly promising for environmental monitoring.

Interaction of the (2√3 × 3)rect. Adsorption-Site Basis and Alkyl-Chain Close Packing in Alkanethiol Self-Assembled Monolayers on Au(111): A Molecular Dynamics Study of Alkyl-Chain Conformation

We show that the adsorption site basis of the (2√3 × 3)rect. phase of n-alkanethiol self-assembled monolayers plays a key role in determining the molecular conformation of the close-packed alkyl chains. Ten proposed reconstructed Au-S interfaces are used to explore the minimized energy alkyl-chain packing of n-decanethiol molecules using molecular dynamics with the all-atom description. In this comparative study, all models have the same alkyl-chain surface density of four molecules per unit cell; thus, differences are due to the headgroup spacing within the 4-molecule basis as opposed to the average surface density. We demonstrate for the first time the 4-molecule-basis twist structure driven by the packing of alkanethiol molecules in a large simulation box (100 molecules, 25 unit cells) using molecular dynamics. Our results validate the prediction put forward by Mar and Klein that to achieve the 4-molecule-basis twist symmetry observed by the experiment, the headgroups must deviate from the high-symmetry (√3 × √3)R30° sites. The key structural parameters: tilt, twist, and end-group height, as well as their spatial order, are compared with experimental results, which we show is a highly sensitive approach that can be used to vet proposed Au-S interfacial models.

Investigation of Local Hydration Structures of Alkanethiol Self-Assembled Monolayers with Different Molecular Structures by FM-AFM

Hydration structures play crucial roles in a wide variety of chemical and biological phenomena. However, the key factors that determine a hydration structure remain an open question. Most recent studies have focused on the electrostatic interactions between the surface charges and dipoles of water molecules, which are determined by the atomic/ionic species of the outermost solid surface, as the dominating factor. The number of studies on the correlation between the hydration structure and the atomic-scale surface corrugation has been limited. In this study, we investigated the hydration structures of alkanethiol self-assembled monolayers terminated with a hydroxyl group using frequency-modulated atomic force microscopy. We observed two molecular structures, namely, the (√3 × √3) R30° structure and the c(4 × 2) superlattice structure, and found that their hydration structures are different mainly because of the slight differences in their molecular arrangements. This result suggests that a slight difference in the molecular/atomic arrangements as well as the atomic/ionic species in the outermost solid surface strongly influences the local hydration structures.

Self-assembled monolayers of thiolates on metals: a review article on sulfur-metal chemistry and surface structures

A review article on fundamental aspects of thiolate self-assembled monolayers (SAMs) on the (111) and (100) surfaces of the Cu and Ni groups is presented.

Identification of parameters through which surface chemistry determines the lifetimes of hot electrons in small Au nanoparticles

This paper describes measurements of the dynamics of hot electron cooling in photoexcited gold nanoparticles (Au NPs) with diameters of ∼3.5 nm, and passivated with either a hexadecylamine or hexadecanethiolate adlayer, using ultrafast transient absorption spectroscopy. Fits of these dynamics with temperature-dependent Mie theory reveal that both the electronic heat capacity and the electron-phonon coupling constant are larger for the thiolated NPs than for the aminated NPs, by 40% and 30%, respectively. Density functional theory calculations on ligand-functionalized Au slabs show that the increase in these quantities is due to an increased electronic density of states near the Fermi level upon ligand exchange from amines to thiolates. The lifetime of hot electrons, which have thermalized from the initial plasmon excitation, increases with increasing electronic heat capacity, but decreases with increasing electron-phonon coupling, so the effects of changing surface chemistry on these two quantities partially cancel to yield a hot electron lifetime of thiolated NPs that is only 20% longer than that of aminated NPs. This analysis also reveals that incorporation of a temperature-dependent electron-phonon coupling constant is necessary to adequately fit the dynamics of electron cooling.

Rapid formation of a dense sulfur layer on gold through use of triphenylmethane sulfenyl chloride as a precursor

The use of triphenylmethane sulfenyl chloride as a new precursor leads to the efficient deposition of sulfur on polycrystalline gold and Au(111) substrates. The modified surfaces are characterized using X-ray photoelectron spectroscopy (XPS), electrochemistry and scanning tunneling microscopy (STM). The XPS data shows the rapid deposition of polymeric sulfur within very short times. Electrochemical stripping cyclic voltammetry (CV) confirms the rapid deposition and shows that high coverage values are achieved. STM imaging shows the formation of a wide range sulfur layer and production of the well-known etch pits. High-resolution STM images confirm the high density of the sulfur layers and show formation of a long-range phase consisting of rhombus structures close to the previously described rectangular structures along with other parallelograms and partial parallelograms. The present results do not show the initial formation of any organic self-assembled monolayer (SAM) indicating that the formation of polymeric sulfur does not result from the decomposition of an initial SAM as previously observed with alkyl and aryl thiolate-based SAMs. The suggested mechanism involves an initial reductive process similar to the one reported for thiocyanates and sulfenyl chlorides. This is followed by the dissociation of the Ph(3)C-S bond, leaving only sulfur on the surface, through a process leading to the recombination of the remaining fragments to yield triphenylmethyl chloride.

Molecular-scale and wide-energy-range tunneling spectroscopy on self-assembled monolayers of alkanethiol molecules

The electronic properties of alkanethiol self-assembled monolayers (alkanethiolate SAMs) associated with their molecular-scale geometry are investigated using scanning tunneling microscopy and spectroscopy (STM/STS). We have selectively formed the three types of alkanethiolate SAMs with standing-up, lying-down, and lattice-gas phases by precise thermal annealing of the SAMs which are conventionally prepared by depositing alkanethiol molecules onto Au(111) surface in solution. The empty and filled states of each SAM are evaluated over a wide energy range covering 6 eV above/below the Fermi level (E(F)) using two types of STS on the basis of tunneling current-voltage and distance-voltage measurements. Electronic states originating from rigid covalent bonds between the thiol group and substrate surface are observed near E(F) in the standing-up and lying-down phases but not in the lattice-gas phase. These states contribute to electrical conduction in the tunneling junction at a low bias voltage. At a higher energy, a highly conductive state stemming from the alkyl chain and an image potential state (IPS) formed in a vacuum gap appear in all phases. The IPS shifts toward a higher energy through the change in the geometry of the SAM from the standing-up phase to the lattice-gas phase through the lying-down phase. This is explained by the increasing work function of alkanethiolate/Au(111) with decreasing density of surface molecules.

Adsorption and electron-induced dissociation of ethanethiol on Au(111)

Dissociation of ethanethiol and the formation of Au-adatom-diethylthiolate rows on the Au(111) surface were investigated using scanning tunneling microscopy (STM) at low temperature. Ethanethiol molecules physisorb on Au(111) at 120 K by sequentially occupation of the elbow site, the fcc domain before covering the whole surface with a semiliquid layer without long-range order. Scanning the physisorbed layer with a sample bias higher than +1.2 V leads to dissociation via cleaving the H-S bond. One of the dissociation products, ethylthiolate, forms a double-row structure with the rows aligned in one of the [112(-)] directions. These double rows arise from the Au-adatom-dithiolate species: CH(3)CH(2)S-Au-SCH(2)CH(3).

Physical structure of standing-up aromatic SAMs revealed by scanning tunneling microscopy

Long-range-ordered aromatic SAMs are formed on Au(111) using 4-nitrophenyl sulfenyl chloride as a precursor. Although the main structure is a √3 × √3 with a molecular density similar to that usually found for aliphatic SAMs, particular spots presenting specific shapes are also observed by STM. These include hexagons, partial hexagons, parallelograms, and zigzags resulting from specific arrangements of adsorbed molecules. These molecular arrangements are reversible as they form and dissociate or "vanish" in various areas on the surface. STM shows that these particular structures provide some order to their surrounding because areas void of these structures look less ordered. More interestingly, STM shows submolecular details of the molecules involved in forming these structures, hence providing direct experimental evidence for the ability of the STM to provide physical structure information of standing up SAMs. This is indeed a heavily debated question, and this work reports the first experimental example where submolecular physical structure is revealed by STM for standing-up SAMs.

Assessment of a nanoparticle bridge platform for molecular electronics measurements

A combination of electron beam lithography, photolithography and focused ion beam milling was used to create a nanogap platform, which was bridged by gold nanoparticles in order to make electrical measurements and assess the platform under ambient conditions. Non-functionalized electrodes were tested to determine the intrinsic response of the platform and it was found that creating devices in ambient conditions requires careful cleaning and awareness of the contributions contaminants may make to measurements. The platform was then used to make measurements on octanethiol (OT) and biphenyldithiol (BPDT) molecules by functionalizing the nanoelectrodes with the molecules prior to bridging the nanogap with nanoparticles. Measurements on OT show that it is possible to make measurements on relatively small numbers of molecules, but that a large variation in response can be expected when one of the metal-molecule junctions is physisorbed, which was partially explained by attachment of OT molecules to different sites on the surface of the Au electrode using a density functional theory calculation. On the other hand, when dealing with BPDT, high yields for device creation are very difficult to achieve under ambient conditions. Significant hysteresis in the I-V curves of BPDT was also observed, which was attributed primarily to voltage induced changes at the interface between the molecule and the metal.

The complex thiol-palladium interface: a theoretical and experimental study

This paper presents a theoretical study of the surface structures and thermodynamic stability of different thiol and sulfide structures present on the palladium surface as a function of the chemical potential of the thiol species. It has been found that as the chemical potential of the thiol is increased, the initially clean palladium surface is covered by a (√3 × √3)R30° sulfur lattice. Further increase in the thiol pressure or concentration leads to the formation of a denser (√7 × √7)R19.1° sulfur lattice, which finally undergoes a phase transition to form a complex (√7 × √7)R19.1° sulfur + thiol adlayer (3/7 sulfur + 2/7 thiol coverage). This transition is accompanied by a strong reconstruction of the Pd(111) surface. The formation of these surface structures has been explained in terms of the catalytic properties of the palladium surface. These results have been compared with X-ray photoelectron spectroscopy results obtained for thiols adsorbed on different palladium surfaces.

On the thermodynamic stability of alpha,omega-alkanedithiols self-assembled monolayers on unreconstructed and reconstructed Au(111)

A comparative study on the thermodynamic stability of the lying down (LD) and standing up (SU) phases of alpha,omega-butanedithiol (BDT) on unreconstructed (U) and on reconstructed (R) Au(111) surfaces is presented. The R surface is made of dithiol-Au adatom units. Density functional calculations (DFT) allow the estimation of the adsorption energy of the LD and SU BDT phases on both substrates. Surface free energies based on the DFT calculations show the coverage of the clean Au(111) surface by the LD phase, and the LD to SU phase transition as the chemical potential of the BDT molecule is increased. The LD and SU phases are more stable on R than on U substrates, suggesting that the Au(111) surface should reconstruct upon BDT adsorption. The stability analysis is extended to longer alpha,omega-dithiols. Results reveal that the LD to SU phase transition is favored as the hydrocarbon chain length of the dithiol molecule is increased. Changes in the hydrogen pressure affect the formation of the LD phase, while they have only minor effects on the LD to SU phase transitions. Our calculations explain the influence of the number of carbon atoms in the hydrocarbon chains, hydrogen pressure and dithiol pressure (or concentration) on dithiol adsorption, and phase transitions. This information is relevant to control the coverage, reactivity, and surface chemistry of the alpha,omega-dithiol self-assembled monolayers on Au surfaces.

Self-assembled monolayers of thiols and dithiols on gold: new challenges for a well-known system

Self-assembled monolayers (SAMs) of alkanethiols and dialkanethiols on gold are key elements for building many systems and devices with applications in the wide field of nanotechnology. Despite the progress made in the knowledge of these fascinating two-dimensional molecular systems, there are still several "hot topics" that deserve special attention in order to understand and to control their physical and chemistry properties at the molecular level. This critical review focuses on some of these topics, including the nature of the molecule-gold interface, whose chemistry and structure remain elusive, the self-assembly process on planar and irregular surfaces, and on nanometre-sized objects, and the chemical reactivity and thermal stability of these systems in ambient and aqueous solutions, an issue which seriously limits their technological applications (375 references).

The role of gold adatoms and stereochemistry in self-assembly of methylthiolate on Au(111)

On the basis of high resolution STM images and DFT modeling, we have resolved low- and high-coverage structures of methylthiolate (CH(3)S) self-assembled on the Au(111) surface. The key new finding is that the building block of all these structures has the same stoichiometry of two thiolate species joined by a gold adatom. The self-arrangement of the methylthiolate-adatom complexes on the surface depends critically on their stereochemical properties. Variations of the latter can produce local ordering of adatom complexes with either (3 x 4) or (3 x 4 square root(3)) periodicity. A possible structural connection between the (3 x 4 square root(3)) structure and commonly observed (square root(3) x square root(3))R30 degrees phase in methylthiolate self-assembled monolayers is developed by taking into account the reduction in the long-range order and stereochemical isomerization at high coverage. We also suggest how the observed self-arrangements of methylthiolate may be related to the c(4 x 2) phase of its longer homologues.