Source of Image Contrast in STM Images of Functionalized Alkanes on Graphite: A Systematic Functional Group Approach

Stability of n-alkanes and n-perfluoroalkanes against horizontal displacement on a graphite surface

The stability of adsorbed molecules on surfaces is fundamental and important for various applications, such as coating, lubrication, friction, and self-assembled structure formation. In this study, we investigated the structures and interaction energies (Eint) of propane, n-pentane, n-heptane, perfluoropropane, n-perfluoropentane, and n-perfluoroheptane adsorbed on the surface of C96H24 (a model surface of graphite). The changes in Eint (ΔEint = Eint - Eint(0)) associated with the horizontal displacement from the stable position were calculated using dispersion-corrected density functional theory (DFT; B3LYP-D3), where Eint(0) is the Eint at the stable position. The maximum value of ΔEint (ΔEint(max)) associated with the horizontal displacement increased as the chain length increased. The ΔEint(max) for the three n-alkanes were 1.10, 1.82, and 2.35 kcal mol-1, respectively. The values for n-perfluoroalkanes were 0.57, 0.83, and 1.04 kcal mol-1, respectively. The ΔEint(max) values for the n-alkanes were significantly larger than those for the corresponding n-perfluoroalkanes. The Eint(max) value per carbon atom of the n-alkanes (ca. 0.30 kcal mol-1) is approximately 2.5 times as large as that of n-perfluoroalkanes (ca. 0.12 kcal mol-1). The ΔEint associated with the horizontal displacement of propane and perfluoropropane on circumcoronene (C54H18) obtained by the B3LYP-D3 calculations are close to those obtained by the second order Møller-Plesset (MP2) and dispersion-corrected double hybrid DFT calculations, suggesting the sufficient accuracy of the ΔEint obtained by the B3LYP-D3. Thus, our quantitative analysis revealed the higher stability of n-alkanes against horizontal displacement on a graphite surface than that of n-perfluoroalkanes.

Nanoscale visualization of phase separation in binary supported lipid monolayer using tip-enhanced Raman spectroscopy

Supported lipid membranes are an important model system to study the phase separation behavior at the nanoscale. However, the conventional nanoanalytical tools often fail to provide reliable chemical characterization of the phase separated domains in a non-destructive and label-free manner. This study demonstrates the application of scanning tunneling microscopy-based tip-enhanced Raman spectroscopy (TERS) to study the nanoscale phase separation in supported d62-DPPC : DOPC lipid monolayers. Hyperspectral TERS imaging successfully revealed a clear segregation of the d62-DPPC-rich and DOPC-rich domains. Interestingly, nanoscale deposits of d62-DPPC were observed inside the DOPC-rich domains and vice versa. High-resolution TERS imaging also revealed the presence of a 40-120 nm wide interfacial region between the d62-DPPC-rich and DOPC-rich domains signifying a smooth transition rather than a sharp boundary between them. The novel insights obtained in this study demonstrate the effectiveness of TERS in studying binary lipid monolayers at the nanoscale.

Nonuniform STM Contrast of Self-Assembled Tri-n-octyl-triazatriangulenium Tetrafluoroborate on HOPG

We have assembled 4,8,12-tri-n-octyl-4,8,12-triazatrianguleniumtetrafluoroborate (TATA-BF4) on highly oriented pyrolytic graphite (HOPG) and have studied the structure and tunneling properties of this self-assembled monolayer (SAM) using scanning tunneling microscopy (STM) under ambient conditions. We show that the triazatriangulenium cations TATA+ form hexagonally packed structures driven by the interaction between the aromatic core and the HOPG lattice, as evidenced by density functional theory (DFT) modeling. According to the DFT results, the three alkyl chains of the platform tend to follow the main crystallographic directions of HOPG, leading to a different STM appearance. The STM contrast of the SAM shows that the monolayer is formed by two types of species, namely, TATA+ with BF4- counterions on top and without them. The cationic TATA+ platform gives rise to a seemingly higher appearance than neutral TATA-BF4, in contrast to observations made on metallic substrates. The variation of the STM tunneling parameters does not change the relative difference of contrast, revealing the stability of both species on HOPG. DFT calculations show that TATA-BF4 on HOPG has sufficient binding energy to resist dissociation into TATA+ and BF4-, which might occur under the action of the electric field in the tunneling gap during STM scanning.

Two-dimensional molecular networks at the solid/liquid interface and the role of alkyl chains in their building blocks

Nanoarchitectonics has attracted increasing attention owing to its potential applications in nanomachines, nanoelectronics, catalysis, and nanopatterning, which can contribute to overcoming global problems related to energy and environment, among others. However, the fabrication of ordered nanoarchitectures remains a challenge, even in two dimensions. Therefore, a deeper understanding of the self-assembly processes and substantial factors for building ordered structures is critical for tailoring flexible and desirable nanoarchitectures. Scanning tunneling microscopy is a powerful tool for revealing the molecular conformations, arrangements, and orientations of two-dimensional (2D) networks on surfaces. The fabrication of 2D assemblies involves non-covalent interactions that play a significant role in the molecular arrangement and orientation. Among the non-covalent interactions, dispersion interactions that derive from alkyl chain units are believed to be weak. However, alkyl chains play an important role in the adsorption onto substrates, as well as in the in-plane intermolecular interactions. In this review, we focus on the role of alkyl chains in the formation of ordered 2D assemblies at the solid/liquid interface. The alkyl chain effects on the 2D assemblies are introduced together with examples documented in the past decades.

Effect of non-oxidative plasma treatments on the surface properties of poly(p-phenylene terephthalamide) (PPTA) and poly(p-phenylene benzobisoxazole) (PBO) fibres as measured by inverse gas chromatography

It has been shown in previous works that the interfacial adhesion in PPTA- and PBO-epoxy composites can be improved by modifying the surface properties of these high-performance fibres upon exposure to non-oxidative plasma treatments. In this work, the effects developed on both types of polymer surface were examined as a function of treatment gas nature (He or N₂) and exposure time (one or four minutes) using inverse gas chromatography at infinite dilution (IGC). From the adsorption of n-alkanes, it has been proved that non-oxidative plasma treatments led to energetically heterogeneous surfaces in the case of PPTA, and to low-energy surfaces in the case of PBO. Nevertheless, it was proved with the 1-min plasma treatments (either under helium or under nitrogen) that chemical reactivity was enhanced on the PBO surface. Such a behaviour was ascribed to the presence of low-molecular weight oxidized materials. The mechanisms involved in surface activation of PPTA were not equivalent under He or N₂ exposure. Nitrogen plasma exposure led to a PPTA surface that is chemically reactive as a result of polarity enhancement. Helium plasma-treated PPTA surface was characterized by the presence of branched arrangements that intensified the number of chemical contacts onto reactive sites. Finally, for both fibre sets, if the purpose is to enhance the chemical surface reactivity, it makes no sense to increase the plasma exposure time from 1 to 4 min.

Substrate-Assisted Visualization of Surfactant Micelles via Transmission Electron Microscopy

The visualization of the micellar morphological evolution for surfactant has drawn much attention due to its self-assemble ability to fold into various structures. However, the direct observation of the soft materials with low atomic number has been hampered because of the poor scattering contrast and complex staining process by the traditional transmission electron microscopy (TEM) techniques. Herein, we reported a novel strategy to the visualization of surfactant micelles with the assistance of layered double hydroxides (LDHs) via TEM. Owing to the uniformly distributed metal ions and positive charges in the LDHs, the surfactant at the micelle-water interface reacted with LDHs to form a stabilized architecture through electrostatic and hydrogen-bond interactions. The morphologies of the surfactant can be clearly observed through the surfactant-LDHs architectures, exhibiting high contrast by TEM techniques. Significantly, the micellar evolutions involving the spherical, rodlike, and wormlike shapes were successfully distinguished. Our results may provide great possibilities and inspirations for the visualization for morphology of soft matters.

Potential Driven Non-Reactive Phase Transitions of Ordered Porphyrin Molecules on Iodine-Modified Au(100): An Electrochemical Scanning Tunneling Microscopy (EC-STM) Study

The modelling of long-range ordered nanostructures is still a major issue for the scientific community. In this work, the self-assembly of redox-active tetra(N-methyl-4-pyridyl)-porphyrin cations (H2TMPyP) on an iodine-modified Au(100) electrode surface has been studied by means of Cyclic Voltammetry (CV) and in-situ Electrochemical Scanning Tunneling Microscopy (EC-STM) with submolecular resolution. While the CV measurements enable conclusions about the charge state of the organic species, in particular, the potentio-dynamic in situ STM results provide new insights into the self-assembly phenomena at the solid-liquid interface. In this work, we concentrate on the regime of positive electrode potentials in which the adsorbed molecules are not reduced yet. In this potential regime, the spontaneous adsorption of the H2TMPyP molecules on the anion precovered surface yields the formation of up to five different potential-dependent long-range ordered porphyrin phases. Potentio-dynamic STM measurements, as a function of the applied electrode potential, show that the existing ordered phases are the result of a combination of van der Waals and electrostatic interactions.

Bias-Dependent Scanning Tunneling Microscopy Signature of Bridging-Oxygen Vacancies on Rutile TiO2(110)

The rutile TiO₂(110) surface has long-served as a well-characterized, prototypical transition-metal oxide surface used in heterogeneous catalysis and photocatalytic water splitting. Naturally occurring defects on this surface, called bridging-oxygen (BO) vacancies, are important as they determine the overall reactivity of the surface. Herein, we report a bias-dependent, scanning tunneling microscopy (STM) signature of the BO vacancies on TiO₂(110): for sample bias voltages past a threshold of +3 V, the bright vacancies are flanked on either side (along the oxygen row) by two dark spots approximately shaped like half-moons. The BO vacancies have a bright aspect below the threshold bias also but are not surrounded by half-moon dark depressions. Using generalized gradient approximation calculations with Hubbard correction (GGA + U) for projected density of states (DOS) and simulated STM images, we find that the bias-dependent STM signature originates from (i) local DOS maxima of all BOs (lighter background that occurs above the threshold bias) and (ii) the increased separation between the first and second BO atoms neighboring the vacancy which leads to an apparent dip between these neighboring oxygens. These results offer a new striking example of the STM signature that appears without switching the polarity of the bias. Similar approaches can be employed for seeking distinguishing features on the surfaces of other large band gap semiconductors and insulators.

Computational insight into the origin of unexpected contrast in chiral markers as revealed by STM

Internal substituents can serve the double purpose of generating stereogenic centers and (potentially) being identifiable with Scanning Tunneling Microscopy (STM) in 2D self-assembled molecular layers. We investigate computationally the origin of stark contrast variations in STM images of chirally substituted self-assembled organic films. STM images of alkyl derivatives with secondary -CH₃ and -OH groups have been simulated. Density functional theory calculations reveal bias-dependent contrast reversals in the substituent regions: a lack of local density of states in the relevant energy regime results in 'dark spots' in the simulated STM images, which turn bright upon increasing the bias voltage.

Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers

Porphyrins and phthalocyanines are ubiquitous in modern science and technology. Their stability, redox properties, and photoresponse make them candidates for numerous applications. Many of these applications rely on thin films, and these are critically dependent on the first monolayer. In this article, we focus on noncovalently bound self-assembled monolayers of porphyrins and phthalocyanines at the solution-solid interface with special emphasis on the kinetic and thermodynamic processes that define the films and their reaction chemistry. We first discuss the difference between film-formation kinetics and desorption kinetics from fully formed films. We then present evidence that many of these monolayers are controlled by adsorption kinetics and are not in thermodynamic equilibrium. Measurement of the solution-solid interface desorption energy by scanning tunneling microscopy is discussed, and data is presented for cobalt, nickel, and free base octaethylporphyrin. The activation energy for the desorption of these compounds into phenyloctane is about half of the computed desorption energy in vacuum, and this is discussed in terms of the role of the solvent. Preexponential factors are very low compared to desorption into vacuum, and this is attributed to a reduction in the entropy of activation due to the participation of solvent in the transition state. An example of the use of relative desorption kinetics to create a new binary surface structure is given. It is suggested that this is a synthesis route that may have been missed because of the large difference in solution concentrations required to drive binary film formation. Attention then turns to the axial reaction chemistry of metalloporphyrins and metallophthalocyanines supported on conducting surfaces. We show several examples of chemistry unique to the supported complexes: cases where the metal binds ligands more readily and cases where the substrate induces ligand loss. Understanding this new axial coordination chemistry is of great importance in catalysis, sensing, and the growth of 3D materials from a self-assembled template.

Odd–even effect in two dimensions induced by the bicomponent blends of isobutenyl compounds

The bicomponent blends in isobutenyl compounds showed 2D structural modulation due to odd–even effect as well as blend ratio-dependent 2D structural change.

Solvent-mediated conductance increase of dodecanethiol-stabilized gold nanoparticle monolayers

Gold nanoparticle monolayers provide convenient templates to study charge transport in organic molecules beyond single junction techniques. Conductance is reported to increase by several orders of magnitude following immersion of alkanethiol-stabilized gold nanoparticle monolayers in a solution containing conjugated thiol-functionalized molecules. Typically, this observation is attributed to molecular exchange. Less attention has been paid to the role of the solvent alone. Here, we report on an increase in conductance of dodecanethiol-stabilized gold nanoparticle monolayers on Si/SiO₂ by an average factor of 36 and 22 after immersion in pure ethanol (EtOH) and tetrahydrofuran (THF), respectively. Analysis by scanning electron microscopy (SEM) and small-angle X-ray scattering (SAXS) reveals a solvent-induced decrease in lattice constant of close-packed monolayers. We compare the conductance of the monolayer after molecular exchange with two different oligophenylenes to shed light on the respective contribution of the solvent-induced structural change and the molecular exchange itself on the conductance increase.

Monolayer Phases of a Dipolar Perylene Derivative on Au(111) and Surface Potential Build-Up in Multilayers

9-(Bis-p-tert-octylphenyl)-amino-perylene-3,4-dicarboxy anhydride (BOPA-PDCA) is a strongly dipolar molecule representing a group of asymmetrically substituted perylenes that are employed in dye-sensitized solar cells and hold great promise for discotic liquid crystal applications. Thin BOPA-PDCA films with orientated dipole moments can potentially be used to tune the energy-level alignment in electronic devices and store information. To help assessing these prospects, we here elucidate the molecular self-assembly and electronic structure of BOPA-PCDA employing room temperature scanning tunneling microscopy and spectroscopy in combination with ultraviolet and X-ray photoelectron spectroscopies. BOPA-PCDA monolayers on Au(111) exclusively form in-plane antiferroelectric phases. The molecular arrangements, the increase of the average number of molecules per unit cell via ripening, and the rearrangement upon manipulation with the STM tip indicate an influence of the dipole moment on the molecular assembly and the rearrangement. A slightly preferred out-of-plane orientation of the molecules in the multilayer induces a surface potential of 1.2 eV. This resembles the giant surface potential effect that was reported for vacuum-deposited tris(8-hydroxyquinoline)aluminum and deemed applicable for data storage. Notably, the surface potential in the case of BOPA-PDCA can in part be reversibly removed by visible light irradiation.

Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach

A self-consistent framework based on modeling and statistical mechanics for the theoretical interpretation of self-assembly at surfaces and interfaces is presented.

Grain Structures and Boundaries on Microcrystalline Copper Covered with an Octadecanethiol Monolayer Revealed by Sum Frequency Generation Microscopy

An octadecanethiol (ODT) self-assembled monolayer on microcrystalline copper was investigated by sum frequency generation (SFG) imaging microscopy. The crystal grain and grain boundaries of the copper surface were mapped in the SFG image based on the strong brightness contrast of the SFG signal across the boundary. Local SFG spectra reveal significant difference with each other as well as the average SFG spectra, indicating the heterogeneity of the copper surface resulting from copper grains with distinct crystallographic facets and orientations. It is demonstrated that the SFG signal of crystalline domain areas contains azimuthal anisotropy with respect to the plane of incidence. In addition, the statistical orientation analyses of amplitude ratio of CH3-sym/CH3-asym and corresponding contour maps imply that the orientation of ODT molecules is affected by the underlying copper.

Self-assembled monolayers of cholesterol and cholesteryl esters on graphite

The molecular arrangements of self-assembled monolayers (SAMs) of cholesterol, cholesteryl laurate, and cholesteryl stearate adsorbed on a graphite surface were studied using scanning tunneling microscopy (STM) at the liquid-solid interface. The STM images of the SAMs showed two-dimensional periodic arrays of bright regions that corresponded to the sterol rings. However, individual sterol rings could not be observed in the bright regions in the STM images of the cholesterol monolayers. Nevertheless, by comparing the STM images and the crystallographic data, it is concluded that the cholesterol molecules are arranged in pairs oriented head-to-head owing to the hydrogen bonds between the hydroxyl groups. These dimers, in turn, are oriented parallel to each other, owing to the interactions between the sterol rings. The STM images of cholesteryl ester monolayers had molecular resolution and showed pairs of cholesteryl ester molecules oriented in an antiparallel manner, with their fatty acid chains located in the central regions. Furthermore, the fatty acid chains of cholesteryl stearate were observed to be oriented in the (1120) zigzag direction of the graphite lattice, whereas those of cholesteryl laurate were oriented in the (1010) armchair direction. These observations reveal that the interactions between the fatty acid chains affect the structure of the SAMs. The molecular arrangements also depend on the lengths of the fatty acid chains of the cholesterol esters and hence on the interactions between the alkyl chains and the graphite surface. The self-assembly at the liquid-solid interface is therefore controlled by the interactions between sterol rings, between alkyl chains, and between alkyl chains and the substrate.

Monolayer patterning using ketone dipoles

The self-assembly of multi-component monolayers with designed patterns requires molecular recognition among components. Dipolar interactions have been found to influence morphologies of self-assembled monolayers and can affect molecular recognition functions. Ketone groups have large dipole moments (2.6 D) and are easily incorporated into molecules. The potential of ketone groups for dipolar patterning has been evaluated through synthesis of two 1,5-disubstituted anthracenes bearing mono-ketone side chains, STM characterization of monolayers self-assembled from their single and two component solutions and molecular mechanics simulations to determine their self-assembly energetics. The results reveal that (i) anthracenes bearing self-repulsive mono-ketone side chains assemble in an atypical monolayer morphology that establishes dipolar attraction, instead of repulsion, between ketones in adjacent side chains; (ii) pairs of anthracene molecules whose self-repulsive ketone side chains are dipolar complementary spontaneously assemble compositionally patterned monolayers, in which the two components segregate into neighboring, single component columns, driven by side chain dipolar interactions; (iii) compositionally patterned monolayers also assemble from dipolar complementary anthracene pairs that employ different dipolar groups (ketones or CF2 groups) in their side chains; (iv) the ketone group, with its larger dipole moment and size, provides comparable driving force for patterned monolayer formation to that of the smaller dipole, and smaller size, CF2 group.

Supramolecular self-assembled network formation containing N⋯Br halogen bonds in physisorbed overlayers

The formation of a halogen bonded self-assembled co-crystal physisorbed monolayer containing N⋯Br interactions is reported for the first time.

Polypyrrole-modified tips for functional group recognition in scanning tunneling microscopy

Tailored chemical modification of scanning tunneling microscopy (STM) tips is a promising method for the recognition of specific chemical species and functional groups in STM images. The present study shows for the first time that tips modified with polypyrrole can be used to measure STM images with molecular resolution. A high conductivity of the polypyrrole film was found to be important for the observation of STM images, while the thickness of the polymer film did not affect the images significantly. Furthermore, it was shown that recognition of functional groups in STM images is possible with tips coated with conductive polypyrroles. 1-Octadecanol and 1-octadecanoic acid monolayers with polypyrrole-modified tips gave high-resolution STM images in which aligned OH and COOH residues were represented by easily recognizable elevated bands. These selective contrast enhancements resemble those observed by us previously with gold tips modified with self-assembled monolayers (SAMs) and seem to be due to hydrogen bond interactions between functional groups of the tip-modifying molecules and the sample. The reproducibility of contrast enhancements in this study was significantly higher than for SAM-modified tips, suggesting that polymer modification of STM tips is particularly promising for specific functional group recognition with chemically modified STM tips.

To mix or not to mix: 2D crystallization and mixing behavior of saturated and unsaturated aliphatic primary amides

Physisorbed monolayers based on relatively weak noncovalent interactions can serve as excellent model systems for understanding crystallization of materials in reduced dimensionality. Here we employ a powerful combination of scanning tunneling microscopy (STM), differential scanning calorimetry (DSC), and computational modeling to reveal two-dimensional (2D) crystallization and mixing behavior of saturated and unsaturated (cis as well as trans) aliphatic primary amides. The foundation of the present work is laid by DSC measurements, which reveal characteristic adsorption and mixing behavior of aliphatic amides. These results are further supported by STM visualization of the adlayers. STM reveals, at submolecular resolution, the adsorption as well as the two-component 2D phase behavior of these molecules at the liquid-solid interface. The saturated and trans-unsaturated amides exhibit random mixing in view of their size and shape complementarity. Binary mixtures of saturated and cis-unsaturated amides, on the other hand, display unprecedented mixing behavior. The linear saturated and bent cis-unsaturated amide molecules are found to mix surprisingly better at the liquid-solid interface than might have been expected on account of the dissimilarity in their shapes. Strong, directional intermolecular hydrogen-bonding interactions as well as the relative stabilization energies of the adlayers are responsible for such unusual mixing behavior. Computational modeling provides additional insight into all the possible interactions in 2D assemblies and their impact on stabilization energies of the supramolecular networks. This study provides a model for understanding the effect of nanoscale cocrystallization on the thin film structure at interfaces and demonstrates the importance of molecular geometry and hydrogen bonding in determining the coadsorption behavior.

Control and induction of surface-confined homochiral porous molecular networks

Homochirality is essential to many biological systems, and plays a pivotal role in various technological applications. The generation of homochirality and an understanding of its mechanism from the single-molecule to supramolecular level have received much attention. Two-dimensional chirality is a subject of intense interest due to the unique possibilities and consequences of confining molecular self-assembly to surfaces or interfaces. Here, we report the perfect generation of two-dimensional homochirality of porous molecular networks at the liquid-solid interface in two different ways: (i) by self-assembly of homochiral building blocks and (ii) by self-assembly of achiral building blocks in the presence of a chiral modifier via a hierarchical structural recognition process, as revealed by scanning tunnelling microscopy. The present results provide important impetus for the development of two-dimensional crystal engineering and may afford opportunities for the utilization of chiral nanowells in chiral recognition processes, as nanoreactors and as data storage systems.

Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy

The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.

High-resolution atomic force microscopy study of hexaglycylamide epitaxial structures on graphite

Two types of hexaglycylamide (HGA) epitaxial lamellar structures coexisting on the surface of highly oriented pyrolytic graphite (HOPG) exposed to water solutions were studied by high-resolution atomic force microscopy (AFM). Lamellae are distinguished by growth direction and by morphology. The lamellae of the first type (L1) produced by depositions from more dilute solutions are close-packed with a period of ∼5.2 nm, twice the HGA molecular length, and form highly ordered domains morphologically similar to the lamellar domains of alkanes. The less-ordered lamellae of the second type (L2) appear at intermediate and large HGA concentrations and demonstrate variable lamellar width, morphological diversity, and a tendency to merge. The interlamellar separation in the domains of close-packed L2 lamellae varies with the discrete increment ∼2.5 nm; the most frequently observed value is ∼7.5-8.0 nm corresponding to the triple HGA molecular length. The growth directions of lamellae of each type have sixfold rotational symmetry indicating epitaxy with graphite; however, the rosettes of L1 and L2 lamellae orientations are misaligned by 30°. The molecular modeling of possible HGA epitaxial packing arrangements on graphite and their classification have been conducted, and the energetically preferable structures are selected. On this basis, the structural models of the L1 and L2 lamellae are proposed explaining the experimentally observed peculiarities as follows: (1) the L1 and L2 lamellae are respectively parallel and antiparallel β-sheets with two HGA molecules in the unit cell oriented normally to the lamellae boundaries, (2) HGA molecules in L1 and L2 lamellae have different orientations with respect to the graphite lattice, respectively along the directions <1120> and <1010>, (3) L1 lamella is the assembly of two hydrogen-bonded parallel β-sheets oriented head-to-head, (4) L2 lamellae are assemblies of several molecular rows (antiparallel β-sheets) cross-linked by hydrogen bonds. The AFM observations indicate that the covering of the hydrophobic graphite by the dense, closely packed, well-ordered monolayers of hydrophilic oligopeptide is possible.

Molecular level studies on binding modes of labeling molecules with polyalanine peptides

In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(II) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO(3)Na)(4))) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO(3)Na)(4) display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.

Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite

The atomic structure of the chains of an alkyl porphyrin (5,10,15,20-tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.

Higher-order complexity through R-group effects in self-assembled tripeptide monolayers

Self-assembled monolayers of tri-L-leucine and tri-L-valine formed on highly ordered pyrolytic graphite (HOPG) substrates have been examined using scanning tunneling microscopy. These monolayers exhibit markedly different structures, even though the tripeptides differ by only a minor change in the amino acid R-group. This minor change in R-group apparently affects the balance between hydrogen bonding and van der Waals interactions that control the monolayer structures. Implications of this effect for evolution of molecular complexity in prebiotic synthesis on environmental surfaces are discussed.

Near-metallic behavior of warm holoferritin molecules on a gold(111) surface

Ferritin, the iron-storage protein, holds great potential for bioelectronic applications because of the presence of an electronically conducting iron core. We have applied scanning tunneling microscopy (STM), a high-resolution imaging method based on direct tunneling, to visualize the ferritin molecules both in the iron-containing holo form and in the iron-free apo form, and we have probed the electron flow through the two forms of this protein by measuring the current-voltage response using scanning tunneling spectroscopy (STS). Clear distinctions could be made among the current-voltage responses of the metallic gold(111) substrate surface, holoferritin molecules, and apoferritin molecules at room temperature. When warmed to the near-physiological temperature of 40 °C, the current-voltage response of the holoferritin molecules exhibited no band gap resembling near-metallic behavior, and the apoferritin molecules exhibited only a reduced band gap.

Two-dimensional self-assembly of a porphyrin-polypyridyl ruthenium(II) hybrid on hopg surface through metal-ligand interactions

The synthesis and self-assembly behavior of porphyrin-polypyridyl ruthenium(II) hybrid, which consists of a flexible alkyl chain attached with two conjugated moieties is described. The electronic absorption spectrum and emission spectra show that the [C(8)-TPP-(ip)Ru(phen)(2)](ClO(4))(2), abbreviated as (C(8)ip)TPPC has optical properties. Scanning tunneling microscopy (STM) studies found that the pi-pi interaction and metal-ligand interaction allow (C(8)ip)TPPC to form self-assembled structure and have an edge-on orientation on the highly oriented pyrolytic graphite (HOPG) surface. The multidentate structure in (C(8)ip)TPPC molecules act as linkers between the molecules and form metal-ligand coordination, which forces the assembly process in the direction of stable columnar arrays. In addition, although the sample was stored for two months in ambient conditions, STM experiments showed that the order of (C(8)ip)TPPC self-assembly only slightly decreased which indicates that the self-assembled monolayer is stable. This work demonstrates that introducing a metal-ligand in the porphyrin-polypyridyl compound is a useful strategy to obtain novel surface assemblies.

Modulated self-assembly of 4,4'-diphenyltetrathiafulvalene molecules on highly oriented pyrolytic graphite by n-tetradecane solvent

We report the formation of a binary-component self-assembled monolayer (SAM) comprising 4,4'-diphenyltetrathiafulvalene (DP-TTF) and n-tetradecane (n-C(14)H(30)) molecules with periodic strip-like phase separation structures on a highly oriented pyrolytic graphite (HOPG) surface. Scanning tunneling microscopy (STM) imaging reveals that ordered DP-TTF single- and double-lamella are periodically tuned by ordered n- C(14)H(30) single- and double-lamella, respectively. This finding can be qualitatively understood in terms of a phase field model, in which the interplay of three ingredients, including free energy of the binary-component solution monolayer, phase boundary energy and surface stress, determines the final equilibrium sizes of the ordered DP-TTF and n- C(14)H(30) phases in the binary-component SAM. Furthermore, anisotropy of the surface stress breaks the symmetry of the substrate and causes the n- C(14)H(30) molecules to arrange along preferential substrate 010 directions. The orientation of the n-C(14)H(30) molecule stripes further guides the directions of the DP-TTF lamellar structures. In addition, scanning tunneling spectra (STS) of the individual DP-TTF and n- C(14)H(30) molecules in the ordered monolayer show a remarkable difference in I(V) curves on the HOPG substrate.

The partially degraded hydrophilic silane pattern and its application in studying the structures of long chain alkane films

We developed a protocol to fabricate hydrophilic patterns over an octadecyltrichlorosilane (OTS) film surface with an atomic force microscope (AFM). Through a local probe oxidation under a 100% humidity environment, the OTS was converted into a hydrophilic, carboxylic acid-terminated surface (OTSpd). The OTSpd pattern grew with the voltage dwell time applied on the conducting AFM probe. Eighty nanometer to submillimeter sized OTSpd patterns could be fabricated with a single scanning probe. The OTSpd patterns were used to study the spreading of long chain alkanes. Hexatriacontane (C36H74) was dip-coated on an OTSpd pattern. Subsequently, an additional hydrophilic OTSpd region was fabricated surrounding the coated C36H74. The alkane spread over this newly created region when heated above its melting point. After cooling to room temperature, the shape and structures of the solidified alkane patterns were characterized. On the methyl-terminated, low-energy surface, the alkane molecules stood directly on the surface. In contrast, on the hydrophilic, high-energy surface, the alkane formed seaweed-shaped patterns after spreading. On the OTSpd surface, the alkane molecules initially adsorbed on the hydrophilic surface with their alkyl chains parallel to the surface. Additional alkane molecules stood vertically or tilted on top of the parallel layer, forming the seaweed-shaped layer. The seaweed patterns were previously thought to consist of only vertically standing alkane molecules. We found that three additional tilted phases existed in the seaweed-shaped structures.

Amyloid beta (1-42) folding multiplicity and single-molecule binding behavior studied with STM

The fine folding and assembling characteristics of amyloid beta (Abeta) peptides are important to pharmaceutical studies of drug molecules and to the pathological analysis of neurodegenerative disorders such as Alzheimer's disease at the molecular level. Here we present observations of the multiple folding characteristics of amyloid peptide Abeta(42) lamellae using scanning tunneling microscopy. Molecularly resolved core regions of Abeta(42) hairpins and unfolded peptide assembly structures are identified. The parallel assembling characteristics of Abeta(42) hairpins can be confirmed in the study. In addition, single-molecule binding characteristics of Congo red and thioflavin T have been shown to bind at the groove regions of peptide assemblies. This study demonstrates a complementary venue for studying molecular heterogeneity of peptide assemblies, as well as the binding characteristics of molecular modulators.

Dipolar side chain control of monolayer morphology: symmetrically substituted 1,5-(mono- and diether) anthracenes at the solution-HOPG interface

Scanning tunneling microscopy (STM) is used to determine the 2-D unit cell parameters of monolayers self-assembled by twelve symmetrical, 1,5-bis(linear aliphatic ether side chain) anthracenes at the solution-graphite interface. The standard morphology assembled by 1,5-bis(alkyloxymethyl) anthracenes consists of single-lamella domains containing columns of anthracene cores alternating with columns of interdigitated, aliphatic side chains. Adjacent side chains within the aliphatic columns adsorb in antiparallel orientations. The terminal methyl (omega-position) of each side chain lies in registration with the 2-positions of its two neighboring chains ((omega <--> 2)-packing). Anthracenes with diether side chains can generate repulsive or attractive dipole-dipole interactions between proximate ethers of adjacent aliphatic chains. Anthracenes bearing even length side chains with oxygens at the 2- and omega-1 positions or at the 3- and omega-2 positions do not assemble (omega <--> 2)-packed monolayers. Repulsive dipolar interactions between ethers in adjacent side chains raise the energy of (omega <--> 2) morphologies. These "self-repulsive" side chains drive assembly of (omega <--> l)- or (omega <--> 3)-packed morphologies, which enjoy stabilizing dipolar interactions between ethers in adjacent side chains. In stark contrast, anthracenes bearing odd length diether side chains assemble (omega <--> 2)-packed morphologies, regardless of whether adjacent chains suffer zero, one, or two sets of proximate dipole-dipole repulsions. The intrinsic energy gap from (omega <--> 2)- to non-(omega <--> 2)-packed morphologies of odd length side chain anthracenes is, apparently, larger than for even length side chain anthracenes. Overall, the twelve compounds self-assemble seven different morphologies. Distinguishing morphologies, understanding polymorphism within the monolayers, and evaluating the morphological consequences of side chain dipolar interactions is facilitated by viewing the monolayers as assemblies of 1-D, molecular tapes.