Interfacial electrostatics of self-assembled monolayers of alkane thiolates on Au(111): work function modification and molecular level alignments

We have isolated at T < 150 K a weakly adsorbed dimethyl disulfide (DMDS) layer on Au(111) and studied how the vibrational states, S core hole level shifts, valence band photoemission, and work function measurements evolve upon transforming this system into chemisorbed methylthiolate (MT) self-assembled monolayers (SAM) by heating above 200 K. By combining these observations with detailed theoretical electronic structure simulations, at the density functional level, we have been able to obtain a detailed picture of the electronic interactions at the interface between Au and adsorbed thiolates and disulfides. All of our measurements may be interpreted with a simple model where MT is bound to the Au surface with negligible charge transfer. Interfacial dipoles arising from Pauli repulsion between molecule and metal surface electrons are present for the weakly adsorbed DMDS layer but not for the chemisorbed species. Instead, for the chemisorbed species, interfacial dipoles are exclusively controlled by the molecular dipole, its interaction with the dipoles on neighboring molecules, and its orientation to the surface. The ramifications of these results for alignment of molecular levels and interfacial properties of this class of materials are discussed.     

Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets

Molecular beacons are sensitive fluorescent probes hybridizing selectively to designated DNA and RNA targets. They have recently become practical tools for quantitative real-time monitoring of single-stranded nucleic acids. Here, we comparatively study the performance of a variety of such probes, stemless and stem-containing DNA and PNA (peptide nucleic acid) beacons, in Tris-buffer solutions containing various concentrations of NaCl and MgCl(2). We demonstrate that different molecular beacons respond differently to the change of salt concentration, which could be attributed to the differences in their backbones and constructions. We have found that the stemless PNA beacon hybridizes rapidly to the complementary oligodeoxynucleotide and is less sensitive than the DNA beacons to the change of salt thus allowing effective detection of nucleic acid targets under various conditions. Though we found stemless DNA beacons improper for diagnostic purposes due to high background fluorescence, we believe that use of these DNA and similar RNA constructs in molecular-biophysical studies may be helpful for analysis of conformational flexibility of single-stranded nucleic acids. With the aid of PNA "openers", molecular beacons were employed for the detection of a chosen target sequence directly in double-stranded DNA (dsDNA). Conditions are found where the stemless PNA beacon strongly discriminates the complementary versus mismatched dsDNA targets. Together with the insensitivity of PNA beacons to the presence of salt and DNA-binding/processing proteins, the latter results demonstrate the potential of these probes as robust tools for recognition of specific sequences within dsDNA without denaturation and deproteinization of duplex DNA.     

Chiral structures of 6,12-dibromochrysene on Au(111) and Cu(111) surfaces

Nanoscale low-dimensional chiral architectures are increasingly receiving scientific interest, because of their potential applications in many fields such as chiral recognition, separation and transformation. Using 6,12-dibromochrysene (DBCh), we successfully constructed and characterized the large-area two-dimensional chiral networks on Au(111) and one-dimensional metal-liganded chiral chains on Cu(111) respectively. The reasons and processes of chiral transformation of chiral networks on Au(111) were analyzed. We used scanning tunneling spectroscopy (STS) to analyze the electronic state information of this chiral structure. This work combines scanning tunneling microscopy (STM) with non-contact atomic force microscopy (nc-AFM) techniques to achieve ultra-high-resolution characterization of chiral structures on low-dimensional surfaces, which may be applied to the bond analysis of functional nanofilms. Density functional theory (DFT) was used to simulate the adsorption behavior of the molecular and energy analysis in order to verify the experimental results.     

Self-assembly of chiral molecular honeycomb networks on Au(111)

Self-assembly of the specifically designed 3-fold symmetric 1,3,5-trikis(4'-carboxylphenyl)-2,4,6-trikis(4'-tert-butylphenyl)-benzene molecule on a Au(111) surface is investigated by means of in situ ultrahigh vacuum scanning tunneling microscopy. A variety of chiral honeycomb networks with increasing interpore distance is observed. Experiments and force field calculations reveal that the formation of the two-dimensional hexagonal porous networks is driven by a balance of molecular close-packing within half-unit cells and cyclic hydrogen bonding dimerization between half-unit cells. The honeycomb networks are shown to be chiral owing to asymmetric molecular close-packing within the half-unit cells.     

Controlling chiral organization of molecular rods on Au(111) by molecular design

Chiral self-assembled structures formed from organic molecules adsorbed on surfaces have been the subject of intense investigation in the recent decade, owing both to relevance in applications such as enantiospecific heterogeneous catalysis or chiral separation as well as to fundamental interest, for example, in relation to the origin of biomolecular homochirality. A central target is rational design of molecular building blocks allowing transfer of chirality from the molecular to the supramolecular level. We previously studied the surface self-assembly of a class of linear compounds based on an oligo(phenylene ethynylene) backbone, which were shown to form a characteristic windmill adsorption pattern on the Au(111) surface. However, since these prochiral compounds were intrinsically achiral, domains with oppositely oriented windmill motifs and related conformational surface enantiomers were always realized in equal proportion. Here we report on the enantioselective, high yield chemical synthesis of a structurally related but intrinsically chiral compound in which two peripheral tert-butyl substituents are replaced by sec-butyl groups, each containing an (S) chiral center. Using scanning tunneling microscopy under ultrahigh vacuum conditions, we characterize the adsorption structures formed from this compound on the Au(111) surface. The perturbation introduced by the modified molecular design is found to be sufficiently small so structures form that are closely analogous to those observed for the original tert-butyl substituted compound. However, as demonstrated from careful statistical analysis of high-resolution STM images, the introduction of the two chiral (S)-sec-butyl substituents leads to a strong preference for windmill motifs with one orientation, demonstrating control of the chiral organization of the molecular backbones through rational molecular design.     

Molecular dynamics simulation study on a monolayer of half [2]rotaxane self-assembled on Au(111)

The self-assembled monolayer (SAM) structure of the tetrathiafulvalene-side half of the Stoddart-Heath type [2]rotaxane on Au(111) surface was investigated using molecular dynamics (MD) simulations. We find that the orientation of the cyclobis(paraquat-p-phenylene) (CBPQT) ring depends dramatically on the coverage, changing in order to obtain highly packed SAMs. The ring lies with its large hollow parallel to the surface at lower coverage (up to one CBPQT per 27 surface Au atoms with a footprint of 1.9 nm(2); 1/27) when free space is available around it, but as the coverage increases (up to one CBPQT per 12 surface Au atoms with a footprint of 0.9 nm(2); 1/12), it tilts completely around its axis and lies with its smaller side (paraquat or phenyl ring) parallel to the surface to accommodate the reduced area available. We find that the best packing densities correspond to one CBPQT per 12-18 surface Au atoms (1/18-1/12) with footprints in the range between 0.9 nm(2) and 1.3 nm(2).     

4-Mercaptopyridine on Au(111): a scanning tunneling microscopy and spectroscopy study

The adsorption of 4-mercaptopyridine (4MPy) molecules on reconstructed Au(111) is investigated by Scanning Tunneling Microscopy (STM) and Spectroscopy (STS) at low temperature and under ultra-high vacuum (UHV) conditions. As made visible by STM, at low coverage (<10%) 4MPy adsorbs preferentially at elbow sites of the Herringbone reconstruction and at step edges of the Au(111). Increasing coverage (but still <30%) results in formation of molecular chains followed, at even higher coverage, by a 3-dimensional growth. Detailed analysis of z-V spectroscopy (ramping the tunneling bias V while keeping the tunneling current constant) provides information on the bias dependent apparent height of a single 4MPy/Au(111) as well as on the local density of states (LDOS) of single and chain 4MPy molecules in comparison to the bare Au(111) surface revealing a significant shift of the lowest unoccupied molecular orbital (LUMO) towards lower energy for molecules within chains. Additionally, the data provide no evidence that for these samples prepared in UHV the adsorption of 4MPy on Au(111) requires mediating Au adatoms. Also, clear indications are given that the adsorption does not induce a strong reduction of the Au DOS close to its Fermi energy. Finally, in context of the apparent STM height of 4MPy molecules, the behavior of the differential barrier height Φ(diff)(V) = (?(z)?(V)I/?(V)I)(2) on bare Au(111) and 4MPy/Au(111) is analyzed and the corresponding experimental values are applied to recover the LDOS of the molecule for unoccupied states according to a previously published numerical recipe [B. Koslowski, H. Pfeifer and P. Ziemann, Phys. Rev. B, 2009, 80, 165419 and M. Ziegler, N. Néel, A. Sperl, J. Kr?ger, and R. Berndt, Phys. Rev. B, 2009, 80, 125402]. In this way, one obtains a spectrum comprising a constant DOS of the Shockley-like surface state of Au(111) and a Lorentzian line attributed to the LUMO of 4MPy.     

Self-assembled monolayers of alkanethiols on Au(111): surface structures, defects and dynamics

The surface structures, defects and dynamics of self-assembled monolayers (SAMs) on Au(111) are reviewed. In the case of the well-known c(4 x 2) and radical 3 x radical 3 R30 degrees surface structures, the present discussion is centered on the determination of the adsorption sites. A more complex scenario emerges for the striped phases, where a variety of surface structures that depends on surface coverage are described. Recently reported surface structures at non-saturation coverage show the richness of the self-assembly process. The study of surface dynamics sheds light on the relative stability of some of these surface structures. Typical defects at the alkanethiol monolayer are shown and discussed in relation to SAMs applications.     

Decorated Ru/Au(111) and Os/Au(111) surfaces: An in situ STM and electrochemistry study

The structure and reactivity of bimetallic electrodes obtained by spontaneous deposition of Ru and Os on Au(111) single-crystal surfaces are studied. In situ electrochemical STM and cyclic voltammetry are used to characterize a wide range of surface morphologies thus produced. The STM results on Ru/Au(111) demonstrate a pronounced step decoration, while a random distribution of Ru nuclei, quite uniform in size, occurs on terraces. Osmium deposits show a slight preference for deposition on steps, but it also occurs readily on terraces. However, many of the Os islands grow into multilayer heights. The coverage of the Au(111) by the deposited Ru or Os islands for a particular solution concentration depends on the deposition time. Nanostructures of Ru and Os are tested for catalytic behavior and correlated to CO oxidation activity as measured by CO stripping voltammetry. Published in Russian in Elektrokhimiya, 2006, Vol. 42, No. 11, pp. 1385–1392. Based on the report delivered at the 8th International Frumkin Symposium “Kinetics of the Electrode Processes,” October 18–22, 2005, Moscow. The text was submitted by the authors in English.     

A molecular dynamics study of nanoindentation on a methyl methacrylate ultrathin film on a Au(111) substrate: interface and thickness effects

The molecular dynamics simulation model of nanoindentation is proposed in order to study the mechanical and structural deformation properties of an ultrathin MMA (methyl methacrylate) film on a Au(111) surface. First, the significant differences in the structural arrangement of MMA thin films with different thicknesses are observed. Two layers are apparent in the thinnest MMA thin film next to the Au(111) surface, while three layer structures are apparent in the thicker film. Second, this study examines the indentation tip that penetrates the MMA thin film into the Au(111) substrate in order to understand the influence of the interface on the properties and deformation behavior in both the thin film and substrate. The result shows that the indentation force is influenced both by the layer structure and by the thickness of the MMA film. The thinnest case exhibits different deformation behavior from that of the thicker cases. In addition, the deformation of MMA molecules becomes significant at the interface between the MMA film and the Au(111) surface with the increase of film thickness, and detailed deformation behavior of the Au surface for different thicknesses of MMA film is reported in this paper. Finally, both the rigid and the active models for the indentation tip are utilized in the simulation to examine the interaction differences between the tip and the film and the deformation mechanism.     

Supramolecular structures of coronene and alkane acids at the Au(111)-solution interface: a scanning tunneling microscopy study

Scanning tunneling microscopy (STM) is utilized to study the solution-solid interface formed between Au(111) and solutions of coronene in hexanoic, heptanoic, and octanoic acids. In all three cases adsorbed coronene is observed and lays flat on the metal surface. Heptanoic and hexanoic acid solutions produce a hexagonal symmetry monolayer. For the heptanoic and hexanoic cases, dipole-image dipole interactions and H bonding stabilize a surface structure in which 12 acid molecules surround each coronene and produce a coronene spacing of 1.45 nm. In the case of octanoic acid as solvent, the incorporation of the solvent into the monolayer is not as strongly favored. The coronene spacing can range from close-packed (1.2 nm) with no solvent presumed present in the monolayer, to 1.50 nm with up to 12 solvent molecules surrounding each coronene. The close-packed regions have hexagonal symmetry, as do those with the largest (1.5 nm) spacing. Heptanoic acid solutions give the clearest STM images and are associated with the most stable two-component monolayer. The present paper demonstrates that non-covalent interactions at the solution-metal interface can lead to complex multicomponent monolayer structures.     

High-density DNA alignment on an Au(111) surface starting from folded DNA

High-density uniform DNA alignment on a metal substrate is essential for creating sensitive DNA devices. We develop a self-sensing DNA alignment process starting from folded DNA to achieve high-density, uniform DNA alignment on an Au(111) surface. We demonstrate that folded DNA plays a critical role in avoiding DNA aggregation and distributing the DNA uniformly on an Au(111) surface at the greatest density and quality ever attained. We also verify that the distributed, folded DNA can be stimulated to align only when the appropriate buffer flow is applied. This selective self-sensing DNA alignment on an Au surface will be a key technology for creating dynamic DNA sensors and switches.     

Dipolar and nonpolar altitudinal molecular rotors mounted on an Au(111) surface

We describe the preparation of a compound whose molecules consist of two metal sandwich stands carrying tentacles with affinity to metal surfaces and holding an axle that carries a dipolar or a nonpolar rotator. The dipolar rotor exists as three pairs of enantiomers, rapidly interconverting at room temperature. When mounted on a gold surface, each molecule represents a chiral altitudinal rotor, with the rotator axle parallel to the surface. The surface-mounted rotor molecules are characterized by several spectroscopic and imaging techniques. At any one time, in about one-third of the dipolar rotors the rotator is free to turn and the direction of its dipole can be flipped by the electric field applied by an STM tip, as revealed by differential barrier height imaging. Molecular dynamics calculations suggest that electric field normal to the surface causes members of one pair of enantiomers to rotate unidirectionally.     

Thiol- and disulfide-modified oligonucleotide monolayer structures on polycrystalline and single-crystal Au(111) surfaces

We provide a comprehensive study of single- (ss) and double-strand (ds) oligonucleotides with either 25 or 10 bases or base pairs (bp) immobilized on polycrystalline and single-crystal Au(111) surfaces. The study is based on X-ray photoelectron spectroscopy, cyclic and differential pulse voltammetry, interfacial capacitance data, and electrochemical scanning tunnelling microscopy (in situ STM). The sequences used were the 25-bp sequence from the BRCA1 gene (25-mer), while the 10-bp oligonucleotides contained solely linear adenine and thymine sequences. The oligonucleotides were modified by the dimethoxytrityl group (DMT) via a disulfide group [DMT-S-S-ss25-mer and DMT-S-S-ds(AT)₁₀], a pure disulfide group (A₁₀-S-S-T₁₀), or a thiol group [HS-ss25-mer and HS-ds-(AT)₁₀], all via a hexamethylene linker. The overall pattern suggests strategies for controlled adsorption of DNA-based molecules and recognition of complementary strands or other molecules.     

氧化锌有序结构在Au(111)和Cu(111)上的生长

利用NO₂或O₂作为氧化剂,研究了氧化锌在Au(111)和Cu(111)上的生长和结构。NO₂表现了更好的氧化性能,有利于有序氧化锌纳米结构或薄膜的生长。在Au(111)和Cu(111)这两个表面上,化学计量比氧化锌都形成非极性的平面化ZnO(0001)的表面结构。在Au(111)上,NO₂气氛下室温沉积锌倾向于形成双层氧化锌纳米结构;而在更高的沉积温度下,在NO₂气氛中沉积锌则可同时观测到单层和双层氧化锌纳米结构。O₂作为氧化剂时可导致形成亚化学计量比的ZnO_x结构。由于铜和锌之间的强相互作用会促进锌的体相扩散,并且铜表面可以被氧化形成表面氧化物,整层氧化锌在Cu(111)上的生长相当困难。我们通过使用NO₂作为氧化剂解决了这个问题,生长出了覆盖Cu(111)表面的满层有序氧化锌薄膜。这些有序氧化锌薄膜表面显示出莫尔条纹,表明存在一个ZnO和Cu(111)之间的莫尔超晶格。实验上观察到的超晶格结构与最近理论计算提出的Cu(111)上的氧化锌薄膜结构相符,具有最小应力。我们的研究表明,氧化锌薄膜的表界面结构可能会随氧化程度或氧化剂的不同而变化,而Cu(111)的表面氧化也可能影响氧化锌的生长。当Cu(111)表面被预氧化成铜表面氧化物时,ZnO_x的生长模式会发生变化,锌原子会受到铜氧化物晶格的限域形成单位点锌。我们的研究表明了氧化锌的生长需要抑制锌向金属基底的扩散,并阻止亚化学计量比ZnO_x的形成。因此,使用原子氧源有利于在Au(111)和Cu(111)表面上生长有序氧化锌薄膜。     

Organic probe molecule adsorption on extended Au(111) surface: a theoretical DFT study

Research on Chemical Intermediates - The cluster approach has been applied to mimic the interactions of probe trans-1,2-bis-(4-pyridyl) ethylene on a gold surface with the aim of discriminating the...     

Ammonia adsorption on iron phthalocyanine on Au(111): influence on adsorbate-substrate coupling and molecular spin

The adsorption of ammonia on Au(111)-supported monolayers of iron phthalocyanine has been investigated by x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory calculations. The ammonia-induced changes of the x-ray photoemission lines show that a dative bond is formed between ammonia and the iron center of the phthalocyanine molecules, and that the local spin on the iron atom is quenched. This is confirmed by density functional theory, which also shows that the bond between the iron center of the metalorganic complex and the Au(111) substrate is weakened upon adsorption of ammonia. The experimental results further show that additional adsorption sites exist for ammonia on the iron phthalocyanine monolayer.     

Influence of molecular geometry on the adsorption orientation for oligophenylene-ethynylenes on Au(111)

The adsorption structures formed from a class of oligophenylene-ethynylenes on Au(111) under ultrahigh vacuum conditions is compared based on high-resolution scanning tunneling microscopy (STM) measurements. The molecules consist of three or four benzene rings connected by ethynylene spokes and are all functionalized identically with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Compounds with the conjugated spokes placed in the para, meta, and threefold configurations were previously found to exclusively form molecular layers with flat-lying adsorption geometries. In contrast, the associated compound with spokes in the ortho configuration surprisingly differs in its adsorption by forming only structures with an upright adsorption orientation. The packing density for the structures formed by the compound with the ortho configuration is less dense than that in conventional self-assembled monolayers while still keeping the conducting backbone in an upright orientation. These structures are thus interesting from the perspective of performing single-molecule conduction measurements on the oligophenylene-ethynylene backbones.     

Methylthiolate on Au(111): adsorption and desorption kinetics

Low energy electron diffraction, Auger electron spectroscopy, X-ray photoelectron spectroscopy and line of sight mass spectrometry have been used to study the adsorption and desorption of dimethyldisulfide (DMDS) on Au(111). At 300 K adsorption is dissociative, forming a chemisorbed adlayer of methylthiolate with a 1/3 ML, (sq rt 3 x sq rt 3)R30 degrees, structure. At 100 K adsorption is molecular, with dissociation to form the 1/3 ML (sq rt 3 x sq rt 3)R30 degrees methylthiolate structure occurring at 138-160 K. A physisorbed DMDS layer, with a coverage of 1/6 ML of DMDS, forms on top of the (sq rt 3 x sq rt 3)R30 degrees chemisorbed MT surface for T < or = 180 K, with multilayers forming for T < or = 150 K. In temperature programmed desorption, multilayers of DMDS desorbed with zero order kinetics and an activation energy of 41 kJ mol(-1); the physisorbed layer desorbed with first order kinetics, exhibiting repulsive lateral interactions with an activation energy which varied from 63 kJ mol(-1) (theta = 0) to 51 kJ mol(-1) (theta = 1); the chemisorbed methylthiolate layer desorbed associatively as DMDS via the physisorbed layer, the activation energy for the reaction, 2 methylthiolate --> physisorbed DMDS, exhibiting repulsive lateral interactions with an activation energy which varied from 65 kJ mol(-1) (theta = 0) to 61 kJ mol(-1) (theta = 1). The physisorbed disulfide layer explains the pre-cursor state adsorption kinetics observed in sticking probability measurement, while its relatively facile formation provides a mechanism by which thiolate self-assembled monolayers can become mobile at room temperature.