Theoretical study of melamine superstructures and their interaction with the Au(111) surface

Using a systematic method, based on considering all possible hydrogen bond connections between two melamine molecules, and ab initio density functional theory (DFT) calculations, we consider the possible planar superstructures that the molecules can form in two dimensions. This is relevant to the assembly of melamine on flat metal surfaces with a small lateral corrugation of the molecule-surface interaction energy. The structures considered include small clusters as well as periodic structures, such as one-dimensional filaments and two-dimensional monolayers. Then, the interaction of melamine structures with the Au(111) surface is considered in detail to elucidate the possible effect of the surface on the formed structures, including the influence of the van der Waals interaction, which is not taken into account in DFT-based methods. The problem of commensurability between the lattices of the gas-phase monolayer and of the substrate is also discussed.     

A study on adsorption of acetonitrile on gold nanorods by non-resonant Raman measurements and density functional theory calculations

Adsorption of acetonitrile (Ac) molecules on gold (Au) nanorods has been investigated by Raman spectroscopic measurements and density functional theory (DFT) calculations. DFT calculations provide a valuable insight into the underlying structure of the metal-molecule complex. From the best agreement between the observed and the calculated Raman frequencies and also from other spectroscopic observations, we propose that Ac molecules interact with Au nanorods and form an [Ac+2Au](0)-like complex on the surface of nanostructures. The environmental effect has also been taken into consideration to explain the Raman activity of the complex.     

Assembling of redox proteins on Au(111) surfaces: A scanning probe microscopy investigation for application in bio-nanodevices

The morphology and conductive properties of azurin molecules, chemically attached to sulfhydryl terminated alkanethiol monolayer assembled on Au(111) surface, are mapped at single molecule level and compared with those observed for the same molecule immobilised on bare Au(111). High-resolution Tapping Mode Atomic Force Microscopy shows that the protein molecules immobilised on modified gold, better reproduces the crystallographic height of the protein, than that immobilised on bare gold. Such a height recovering is also found in the Scanning Tunnelling Microscopy images. Consistently, a good tunnelling conduction of azurins on the modified gold electrode is demonstrated by Tunnelling Spectroscopy. Cyclic voltammetry measurements show, in addition, that the redox activity of azurin molecules covalently immobilised on sulfhydryl functionalised Au(111) surface is retained. These results are discussed in connection with possible use of this linker in the assembling of nano-hybrid systems.     

Microcantilever-based sensors: effect of morphology, adhesion, and cleanliness of the sensing surface on surface stress

The surface stress response of micromechanical cantilever-based sensors was studied as a function of the morphology, adhesion, and cleanliness of the gold sensing surface. Two model systems were investigated: the adsorption of alkanethiol self-assembled monolayers at the gas-solid interface and the potential-controlled adsorption of anions at the liquid-solid interface. The potential-induced surface stress, on a smooth and continuous polycrystalline Au(111)-textured microcantilever in 0.1 M HClO4, is in excellent agreement with macroscopic Au(111) single-crystal electrode results. It is shown that ambient contaminants on the sensing surface dramatically alter the surface stress-potential response. This observation can be misinterpreted as evidence that for polycrystalline Au(111) microcantilever electrodes, surface stress is dominated by surface energy change. Results for anions adsorption on gold are in contrast to the gas-phase model system. We demonstrate that the average grain size of the gold sensing surface strongly influences the magnitude of the surface stress change induced by the adsorption of octanethiol. A 25-fold amplification of the change in surface stress is observed on increasing the average gold grain size of the sensing surface from 90 to 500 nm.     

Zinc porphyrin-driven assembly of gold nanofingers

Nanofingers of gold covered by porphyrins are prepared by a combination of atomic manipulation and surface self-organization. A submonolayer of zinc(II) 5,10,15,20-tetrakis(4-tert-butylphenyl)-porphyrin (ZnTBPP) axially ligated to a self-assembled monolayer of 4-aminothiophenol (4-ATP) on Au(111) is prepared and studied using a combination of ultrahigh vacuum techniques. Under the electric field produced by the STM tip, the relatively weakly bound Au surface atoms along the discommensuration lines become mobile due to the strong bond to 4-ATP, while the tendency of the porphyrins towards self-assembly result in a collective motion of gold clusters. The clusters diffuse onto the surface following well-defined pathways along the [112] direction and then reach the step edges where they assembled, thus forming nanofingers. First-principles density functional theory calculations demonstrate the reduction of the binding energies between the surface gold clusters and the substrate induced by adsorption of thiols. Scanning tunneling microscopy images show assemblies across three adjacent discommensuration lines of the Au(111)-(22 x square root 3) reconstruction, which collectively diffuse along these lines to form islands nucleated at step edges.     

Catalytic role of gold nanoparticle in GaAs nanowire growth: a density functional theory study

The energetics of Ga, As, and GaAs species on the Au(111) surface (employed as a model for Au nanoparticles) is investigated by means of density functional calculations. Apart from formation of the compound Au(7)Ga(2), Ga is found to form a surface alloy with gold with comparable ΔH ~ -0.5 eV for both processes. Dissociative adsorption of As(2) is found to be exothermic by more than 2 eV on both clean Au(111) and AuGa surface alloys. The As-Ga species formed by reaction of As with the surface alloy is sufficiently stable to cover the surface of an Au particle in vacuo in contact with a GaAs substrate. The results of the calculations are interpreted in the context of Au-catalyzed growth of GaAs nanowires. We argue that arsenic is supplied to the growth zone of the nanowire mainly by impingement of molecules on the gold particle and identify a regime of temperatures and As(2) partial pressures suitable for Au-catalyzed nanowire growth in molecular beam epitaxy.     

Cyano‐Functionalized Triarylamines on Au(111): Competing Intermolecular versus Molecule/Substrate Interactions

The self‐assembly of cyano‐substituted triarylamine derivatives on Au(111) is studied with scanning tunneling microscopy and density functional theory calculations. Two different phases, each stabilized by at least two different cyano bonding motifs are observed. In the first phase, each molecule is involved in dipolar coupling and hydrogen bonding, while in the second phase, dipolar coupling, hydrogen bonding and metal‐ligand interactions are present. Interestingly, the metal–ligand bond is already observed for deposition of the molecules with the sample kept at room temperature leaving the herringbone reconstruction unaffected. It is proposed that for establishing this bond, the Au atoms are slightly displaced out of the surface to bind to the cyano ligands. Despite the intact herringbone reconstruction, the Au substrate is found to considerably interact with the cyano ligands affecting the conformation and adsorption geometry, as well as leading to correlation effects on the molecular orientation.     

Surface Supported Gold–Organic Hybrids: On‐Surface Synthesis and Surface Directed Orientation

The surface‐assisted synthesis of gold–organic hybrids on Au (111) and Au (100) surfaces is repotred by thermally initiated dehalogenation of chloro‐substituted perylene‐3,4,9,10‐tetracarboxylic acid bisimides (PBIs). Structures and surface‐directed alignment of the Au–PBI chains are investigated by scanning tunnelling microscopy in ultra high vacuum conditions. Using dichloro‐PBI as a model system, the mechanism for the formation of Au–PBI dimer is revealed with scanning tunnelling microscopy studies and density functional theory calculations. A PBI radical generated from the homolytic C‐Cl bond dissociation can covalently bind a surface gold atom and partially pull it out of the surface to form stable PBI‐Au hybrid species, which also gives rise to the surface‐directed alignment of the Au–PBI chains on reconstructed Au (100) surfaces.     

Direct Imaging of the Induced‐Fit Effect in Molecular Self‐Assembly

Molecular recognition is a crucial driving force for molecular self‐assembly. In many cases molecules arrange in the lowest energy configuration following a lock‐and‐key principle. When molecular flexibility comes into play, the induced‐fit effect may govern the self‐assembly. Here, the self‐assembly of dicyanovinyl‐hexathiophene (DCV6T) molecules, a prototype specie for highly efficient organic solar cells, on Au(111) by using low‐temperature scanning tunneling microscopy and atomic force microscopy is investigated. DCV6T molecules assemble on the surface forming either islands or chains. In the islands the molecules are straight—the lowest energy configuration in gas phase—and expose the dicyano moieties to form hydrogen bonds with neighbor molecules. In contrast, the structure of DCV6T molecules in the chain assemblies deviates significantly from their gas‐phase analogues. The seemingly energetically unfavorable bent geometry is enforced by hydrogen‐bonding intermolecular interactions. Density functional theory calculations of molecular dimers quantitatively demonstrate that the deformation of individual molecules optimizes the intermolecular bonding structure. The intermolecular bonding energy thus drives the chain structure formation, which is an expression of the induced‐fit effect.     

Interplay of adsorbate-adsorbate and adsorbate-substrate interactions in self-assembled molecular surface nanostructures

The adsorption of 2,6-naphthalenedicarboxylic acid (NDCA) molecules on the Ag(110), Cu(110), and Ag(111) surfaces at room temperature has been studied by means of scanning tunnelling microscopy (STM). Further supporting results were obtained using X-ray photoelectron spectroscopy (XPS) and soft X-ray absorption spectroscopy (XAS). On the Ag(110) support, which had an average terrace width of only 15 nm, the NDCA molecules form extended one-dimensional (1-D) assemblies, which are oriented perpendicular to the step edges and have lengths of several hundred nanometres. This shows that the assemblies have a large tolerance to monatomic surface steps on the Ag(110) surface. The observed behaviour is explained in terms of strong intermolecular hydrogen bonding and a strong surface-mediated directionality, assisted by a sufficient degree of molecular backbone flexibility. In contrast, the same kind of step-edge crossing is not observed when the molecules are adsorbed on the isotropic Ag(111) or more reactive Cu(110) surfaces. On Ag(111), similar 1-D assemblies are formed to those on Ag(110), but they are oriented along the step edges. On Cu(110), the carboxylic groups of NDCA are deprotonated and form covalent bonds to the surface, a situation which is also achieved on Ag(110) by annealing to 200 °C. These results show that the formation of particular self-assembled molecular nanostructures depends significantly on a subtle balance between the adsorbate-adsorbate and adsorbate-substrate interactions and that kinetic factors play an important role.      

Long-range order induced by cobalt porphyrin adsorption on aminothiophenol-functionalized Au(111): the influence of the induced dipole

Porphyrins are useful in materials science for optical, photoelectrochemical and chemical sensor applications. Solid films of oriented porphyrins on gold can be realized through a simple procedure and without synthesizing thiol-derivatized porphyrins. In order to immobilize the porphyrin rings on the surface, we prepared a 4-aminothiophenol (4-ATP) self-assembled monolayer (SAM) on gold(111) followed by axial legation, in situ, of cobalt(II) 5,10,15,20-tetrakis(4-tert-butylphenyl)-porphyrin (CoTBPP). Ultrahigh vacuum (UHV) Scanning Tunneling Microscopy (STM) studies performed on the SAMs revealed the Au(111) herringbone structure reconstruction, probably due to adsorption/desorption processes of molecules. STM images and Scanning Tunneling Spectroscopy (STS) measurements clearly showed that the immobilization of molecules also induced an electronic perturbation on the gold surface. This effect is ascribed to the presence of oriented molecular dipole layers between the metal and the organic material.     

Low-bias conductance of single benzene molecules contacted by direct Au-C and Pt-C bonds

The electronic transport properties of a single benzene molecule connected to gold and platinum electrodes through the direct Au-C or Pt-C bond are investigated by using a self-consistent ab initio approach that combines the non-equilibrium Green's function (NEGF) formalism with density functional theory (DFT). Our calculations show that the benzene molecule can bind to the Au(111) surface via direct Au-C bond at the adatom, atop and bridge sites. The largest zero-bias conductance is calculated for the bridge site but it is only G = 0.37G(0) (G(0) = 2e(2)/h). In contrast benzene binds to the Pt(111) surface via direct Pt-C bond only at the adatom and atop sites. When the binding site is the adatom a stable molecular junction forms with a zero-bias conductance as large as 1.15G(0). This originates from the efficient coupling between the extended π-type highest occupied molecular orbital of benzene and the conducting states of the Pt electrodes via the 5d(xz) atomic orbital of the adatoms. The calculated transmission is robust to the choice of DFT functionals, illustrating the potential of the Pt-C bond for constructing future molecular electronic devices.     

Initial epitaxial growth of (111) Au/(111) Cu and (111) Cu/(111) Au

The room temperature modes of growth of Au/(111) Cu and Cu/(111) Au are described. For the former growth mode initial deposits (2.4 Å) of gold on copper form smooth flat islands delineated by coincidence lattice misfit dislocations. For 6.0 Å of gold deposit, both thick and thin gold areas were observed with almost complete substrate coverage. For a 10 Å deposit, surface coverage was complete. Strain measurements and dislocation densities obtained on the (111) Au/(111) Cu films suggest the presence of two separate misfit dislocation networks at the interface. The coincidence lattice networks were large enough for transmission electron microscopy observation but contributed little to total overlayer strain. The (van der Merwe) natural lattice misfit dislocations were too closely spaced for direct observation but their presence was inferred because of the strain measurements. The initial epitaxy of Cu/(111) Au was similar to the Stranski-Krastanov model: the initial monolayer of copper (also delineated by coincidence misfit dislocations) grew smoothly on the gold; additional copper formed essentially stress-free “nuclei” on top of the initial copper layer.     

Nonepitaxial Gold‐Tipped ZnSe Hybrid Nanorods for Efficient Photocatalytic Hydrogen Production

For the first time, colloidal gold (Au)–ZnSe hybrid nanorods (NRs) with controlled size and location of Au domains are synthesized and used for hydrogen production by photocatalytic water splitting. Au tips are found to grow on the apices of ZnSe NRs nonepitaxially to form an interface with no preference of orientation between Au(111) and ZnSe(001). Density functional theory calculations reveal that the Au tips on ZnSe hybrid NRs gain enhanced adsorption of H compared to pristine Au, which favors the hydrogen evolution reaction. Photocatalytic tests reveal that the Au tips on ZnSe NRs effectively enhance the photocatalytic performance in hydrogen generation, in which the single Au‐tipped ZnSe hybrid NRs show the highest photocatalytic hydrogen production rate of 437.8 µmol h^?1 g^?1 in comparison with a rate of 51.5 µmol h^?1 g^?1 for pristine ZnSe NRs. An apparent quantum efficiency of 1.3% for hydrogen evolution reaction for single Au‐tipped ZnSe hybrid NRs is obtained, showing the potential application of this type of cadmium (Cd)‐free metal–semiconductor hybrid nanoparticles (NPs) in solar hydrogen production. This work opens an avenue toward Cd‐free hybrid NP‐based photocatalysis for clean fuel production.     

Discrete charging effects in gold nanoclusters grown on self-assembled monolayers

Single electron charging effects were observed for gold nanoclusters grown on octanedithiol self-assembled monolayers by scanning tunneling microscopy and X-ray photoelectron spectroscopy (XPS). Strong interaction of gold with the terminal sulfur atoms of dithiol molecules on Au(111) suppresses effectively the penetration of deposited gold atoms through the dithiol layer and results in the formation of uniform metal nanoclusters. Decoupling of the clusters from Au(111) by the octanedithiol layer and the small self-capacitance of the nanoclusters realize the observation of the Coulomb blockade in scanning tunneling spectroscopy and the Au 4f core level shifts in XPS at room temperature. Both phenomena originate from a common physics, the Coulomb energy of charged particles.     

An alkyl spacer effect on the structure of 4-fluorobenzenethiol and 4-fluorobenzenemethanethiol self-assembled monolayers on Au(111)

Self-assembled monolayers (SAMs) formed by the adsorption of 4-fluorobenzenethiol (4-FBT) and 4-fluorobenzenemethanethiol (4-FBMT) on Au(111) were examined by scanning tunneling microscopy (STM) to understand the effect of a flexible methylene spacer between the sulfur head-group and phenyl group and the effect of solution temperature on the formation and structure of the SAMs. Although the adsorption of 4-FBT on Au(111) at room temperature for 24 h generated only disordered phase SAMs containing gold adatom islands, 4-FBT at 75 degrees C for 2 h formed mixed SAMs: disordered phases and ordered (2 x 12√(2))R10 degrees superlattice with a rectangular unit cell containing six adsorbed molecules. On the other hand, SAMs formed from 4-FBMT, with a methylene spacer, at room temperature for 24 h on Au(111) had irregularly ordered phases containing uniformly distributed VIs with lateral dimensions of 2-5 nm; SAMs formed from 4-FBMT at 75 degrees C for 2 h were composed of slightly improved ordered phases and larger VIs with lateral dimensions of 5-12 nm as a result of Ostwald ripening. From this study, we found that the methylene spacer plays an important role in controlling the structure of SAMs formed from p-substituted fluorinated aromatic thiols.     

Discrete charging effects in gold nanoclusters grown on self-assembled monolayers

Single electron charging effects were observed for gold nanoclusters grown on octanedithiol self-assembled monolayers by scanning tunneling microscopy and X-ray photoelectron spectroscopy (XPS). Strong interaction of gold with the terminal sulfur atoms of dithiol molecules on Au(111) suppresses effectively the penetration of deposited gold atoms through the dithiol layer and results in the formation of uniform metal nanoclusters. Decoupling of the clusters from Au(111) by the octanedithiol layer and the small self-capacitance of the nanoclusters realize the observation of the Coulomb blockade in scanning tunneling spectroscopy and the Au 4f core level shifts in XPS at room temperature. Both phenomena originate from a common physics, the Coulomb energy of charged particles.     

NaCl multi-layer islands grown on Au(111)-([Formula: see text]) probed by scanning tunneling microscopy

The growth of multi-layer NaCl islands on Au(111)-([Formula: see text]) surfaces was investigated using scanning tunneling microscopy (STM). We observed that the aspect of the NaCl islands drastically differs depending on the tunneling conditions. It is therefore possible to observe the layers forming an NaCl island or to image the gold reconstruction below the first NaCl layer. Atomically resolved STM images obtained on the first NaCl layer demonstrate that NaCl grows as an epitaxial crystalline film on Au(111)-([Formula: see text]). STM images also suggest that some NaCl layers can be non-crystalline.     

Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated into multiscale simulations including quantum mechanical, molecular and the microfluidic continuum regimes. The results may also be useful in extending existing macroscopic empirical models of DNA response dynamics in shear flows.     

Construction of two-dimensional hydrogen clusters on Au（111） directed by phthalocyanine molecules

Low-dimensional H2 aggregates have been successfully fabricated on Au（111） surfaces and investigated by means of low temperature scanning tunneling microscopy. We use manganese phthalocyanine （MnPc） molecules anchored on the Au（111） surface to efficiently collect and pin hydrogen molecules. A two-dimensional （2D） molecular hydrogen cluster is formed around the MnPc. The hydrogen cluster exhibits bias-dependent topography and spatial-dependent conductance spectra, which are rationalized by the exponentially decreasing threshold energy with distance from the central MnPc to activate the motion of the H2 molecules. This exponential drop reveals an interfacial phase behavior in the 2D cluster.