Mixed-Sandwich Titanium(III) Qubits on Au(111): Electron Delocalization Ruled by Molecular Packing

Organometallic sandwich complexes are versatile molecular systems that have been recently employed for single-molecule manipulation and spin sensing experiments. Among related organometallic compounds, the mixed-sandwich S = 1/2 complex (η⁸-cyclooctatetraene)(η⁵-cyclopentadienyl)titanium, here [CpTi(cot)], has attracted interest as a spin qubit because of the long coherence time. Here the structural and chemical properties of [CpTi(cot)] on Au(111) are investigated at the monolayer level by experimental and computational methods. Scanning tunneling microscopy suggests that adsorption occurs in two molecular orientations, lying and standing, with a 3:1 ratio. XPS data evidence that a fraction of the molecules undergo partial electron transfer to gold, while our computational analysis suggests that only the standing molecules experience charge delocalization toward the surface. Such a phenomenon depends on intermolecular interactions that stabilize the molecular packing in the monolayer. This orientation-dependent molecule-surface hybridization opens exciting perspectives for selective control of the molecule-substrate spin delocalization in hybrid interfaces.

Atomic-Scale Rectification and Inelastic Electron Tunneling Spectromicroscopy

The phenomenon of rectification describes the emergence of a DC current from the application of an oscillating voltage. Although the origin of this effect has been associated with the nonlinearity in the current-voltage I(V) relation, a rigorous understanding of the microscopic mechanisms for this phenomenon remains challenging. Here, we show the close connection between rectification and inelastic electron tunneling spectroscopy and microscopy for single molecules with a scanning tunneling microscope. While both techniques are based on nonlinear features in the I(V) curve, comprehensive line shape analyses reveal notable differences that highlight the two complementary techniques of nonlinear conductivity spectromicroscopy for probing nanoscale systems.

Strain-Relief Patterns and Kagome Lattice in Self-Assembled C60 Thin Films Grown on Cd(0001)

We report an ultra-high vacuum low-temperature scanning tunneling microscopy (STM) study of the C₆₀ monolayer grown on Cd(0001). Individual C₆₀ molecules adsorbed on Cd(0001) may exhibit a bright or dim contrast in STM images. When deposited at low temperatures close to 100 K, C₆₀ thin films present a curved structure to release strain due to dominant molecule–substrate interactions. Moreover, edge dislocation appears when two different wavy structures encounter each other, which has seldomly been observed in molecular self-assembly. When growth temperature rose, we found two forms of symmetric kagome lattice superstructures, 2 × 2 and 4 × 4, at room temperature (RT) and 310 K, respectively. The results provide new insight into the growth behavior of C₆₀ films.

Magnetic and defect probes of the SmB6 surface state

The impact of nonmagnetic and magnetic impurities on topological insulators is a central focus concerning their fundamental physics and possible spintronics and quantum computing applications. Combining scanning tunneling spectroscopy with transport measurements, we investigate, both locally and globally, the effect of nonmagnetic and magnetic substituents in SmB₆, a predicted topological Kondo insulator. Around the so-introduced substitutents and in accord with theoretical predictions, the surface states are locally suppressed with different length scales depending on the substituent's magnetic properties. For sufficiently high substituent concentrations, these states are globally destroyed. Similarly, using a magnetic tip in tunneling spectroscopy also resulted in largely suppressed surface states. Hence, a destruction of the surface states is always observed close to atoms with substantial magnetic moment. This points to the topological nature of the surface states in SmB₆ and illustrates how magnetic impurities destroy the surface states from microscopic to macroscopic length scales.

Probing Charge Transport through Peptide Bonds

We measure the conductance of unmodified peptides at the single-molecule level using the scanning tunneling microscope-based break-junction method, utilizing the N-terminal amine group and the C-terminal carboxyl group as gold metal-binding linkers. Our conductance measurements of oligoglycine and oligoalanine backbones do not rely on peptide side-chain linkers. We compare our results with alkanes terminated asymmetrically with an amine group on one end and a carboxyl group on the other to show that peptide bonds decrease the conductance of an otherwise saturated carbon chain. Using a newly developed first-principles approach, we attribute the decrease in conductance to charge localization at the peptide bond, which reduces the energy of the frontier orbitals relative to the Fermi energy and the electronic coupling to the leads, lowering the tunneling probability. Crucially, this manifests as an increase in conductance decay of peptide backbones with increasing length when compared with alkanes.

Manipulation of Origin of Life Molecules: Recognizing Single-Molecule Conformations in β-Carotene and Chlorophyll-a/β-Carotene Clusters

Carotenoids and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how β-carotene and chlorophyll-a form mixed molecular phases on a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five β-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of β-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: β-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.

Probing Single Vacancies in Black Phosphorus at the Atomic Level

Utilizing a combination of low-temperature scanning tunneling microscopy/spectroscopy (STM/STS) and electronic structure calculations, we characterize the structural and electronic properties of single atomic vacancies within several monolayers of the surface of black phosphorus. We illustrate, with experimental analysis and tight-binding calculations, that we can depth profile these vacancies and assign them to specific sublattices within the unit cell. Measurements reveal that the single vacancies exhibit strongly anisotropic and highly delocalized charge density, laterally extended up to 20 atomic unit cells. The vacancies are then studied with STS, which reveals in-gap resonance states near the valence band edge and a strong p-doping of the bulk black phosphorus crystal. Finally, quasiparticle interference generated near these vacancies enables the direct visualization of the anisotropic band structure of black phosphorus.

Single-Molecule Electronics: Chemical and Analytical Perspectives

It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule

A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j=0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.

Structure-dependent electrical conductivity of protein: its differences between alpha-domain and beta-domain structures

Electron transports in the α-domain and β-domain of proteins have been comprehensively investigated. The structure-dependent electron transport of proteins has been experimentally measured and theoretically simulated, and both the theoretical and experimental results demonstrate significant differences in electrical conductivity between the α-domain and β-domain. By controlling the feedback system of the scanning tunneling microscope (STM), the conductance of a single α-domain protein hemoglobin (Hgb) and a β-domain protein superoxide dismutase enzyme (SOD) were measured, respectively. The current signal of Hgb is obviously stronger, indicating that the α-domain is more conductive. To confirm our finding, molecular orbitals of both the β-domain in SOD and α-domain in Hgb have been analyzed based on first-principles calculations. As expected, tunneling transport and hopping in the α-domain are both more efficient, indicating that it is easier for electrons to transport through the α-domain, which are in great agreement with our experimental data. In order to explain our results, molecular structures of α- and β-domains have been carefully analyzed and show that the explanation should lie in the differences in packing mode between the α-domain and β-domain. This research should be very important to application prospects in molecular electronics.

Physical model for recognition tunneling

Recognition tunneling (RT) identifies target molecules trapped between tunneling electrodes functionalized with recognition molecules that serve as specific chemical linkages between the metal electrodes and the trapped target molecule. Possible applications include single molecule DNA and protein sequencing. This paper addresses several fundamental aspects of RT by multiscale theory, applying both all-atom and coarse-grained DNA models: (1) we show that the magnitude of the observed currents are consistent with the results of non-equilibrium Green's function calculations carried out on a solvated all-atom model. (2) Brownian fluctuations in hydrogen bond-lengths lead to current spikes that are similar to what is observed experimentally. (3) The frequency characteristics of these fluctuations can be used to identify the trapped molecules with a machine-learning algorithm, giving a theoretical underpinning to this new method of identifying single molecule signals.

Local measurement of the Eliashberg function of Pb islands: enhancement of electron-phonon coupling by quantum well states

Inelastic tunneling spectroscopy of Pb islands on Cu(111) obtained by scanning tunneling microscopy below 1 K provides a direct access to the local Eliashberg function of the islands with high energy resolution. The Eliashberg function describes the electron-phonon interaction causing conventional superconductivity. The measured Eliashberg function strongly depends on the local thickness of the Pb nanostructures and shows a sharp maximum when quantum well states of the Pb islands come close to the Fermi energy. Ab initio calculations reveal that this is related to enhanced electron-phonon coupling at these thicknesses.

[On the possibility of analysis of biopolymer fragments by tunneling microscopy]

An image of fragmented sequence of biopolymer molecules by example of bacterial DNA in vivo (in atmosphere air) was received by scanning tunneling microscopy. An air adsorbate (mainly water vapors) that covers the molecule's surface gives rise to local tunnel conductivity and by virtue of adsorption selectivity indirectly reflects local conductance of fragments that consist of different rows of various atoms, supporting their tunnel conductivity. Having processed experimental data fragment images are obtained with scaled-up topography characteristics for their further identification.

High-resolution scanning tunneling microscopy imaging of Si(1 1 1)-7 × 7 structure and intrinsic molecular states

We review our achievements in exploring the high resolution imaging of scanning tunneling microscopy (STM) on the surface and adsorbates in a ultra-high vacuum system, by modifying the STM tip or introducing a decoupled layer onto the substrate. With an ultra-sharp tip, the highest resolution of Si(1 1 1)-7 × 7 reconstruction can be achieved, in which all the rest atoms and adatoms are observed simultaneously with high contrast. Further functionalization of STM tips can realize selective imaging of inherent molecular states. The electronic states of perylene and metal-phthalocyanine molecules are resolved with special decorated tips on metal substrates at low temperature. Moreover, we present two kinds of buffer layer: an organic molecular layer and epitaxially grown graphene to decouple the molecular electronic structure from the influence of the underlying metallic substrate and allow the direct imaging of the intrinsic orbitals of the adsorbed molecules. Theoretical calculations and STM simulations, based on first-principle density function theory, are performed in order to understand and verify the mechanism of high-resolution images. We propose that our results provide impactful routes to pursue the goal of higher resolution, more detailed information and extensive properties for future STM applications.

Effect of dissolved LiCl on the ionic liquid-Au(111) interface: an in situ STM study

The structure of the electrolyte/electrode interface plays a significant role in electrochemical processes. To date, most studies are focusing on understanding the interfacial structure in pure ionic liquids. In this paper in situ scanning tunnelling microscopy (STM) has been employed to elucidate the structure of the charged Au(111)-ionic liquid (1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate, [Py1,4]FAP) interface in the presence of 0.1 M LiCl. The addition of the Li salt to the ionic liquid has a strong influence on the interfacial structure. In the first STM scan in situ measurements reveal that Au(111) undergoes the (22 x √3) 'herringbone' reconstruction in a certain potential regime, and there is strong evidence that the gold surface dissolves at negative electrode potentials in [Py1,4]FAP containing LiCl. Bulk deposition of Li is obtained at -2.9 V in the second STM scan.

Effects of plasmon energetics on light emission induced by scanning tunneling microscopy

A theoretical model of plasmon and molecular luminescence induced by scanning tunneling microscopy using a molecule-covered tip on clean metal surfaces is developed. The effects of coupling between molecular exciton and interface plasmon on the luminescence spectra are investigated for variable energy of plasmon modes by means of the nonequilibrium Green's function method. It is found that spectral features arising from interference between the processes of energy absorption by the molecule and interface plasmons appear near the energy of the excitonic mode. For the energy of plasmon above (below) the energy of excitonic mode, an additional peak structure appears in the energy range slightly below (above) the energy of the excitonic mode. Prominent peak and dip structures observed in recent luminescence experiments are interpreted by the developed theory whereby its utility in the fields of plasmonics and nanophotonics is demonstrated.

Morphology of monolayer MgO films on Ag(100): switching from corrugated islands to extended flat terraces

The ability to engineer nearly perfect ultrathin oxide layers, up to the limit of monolayer thickness, is a key issue for nanotechnological applications. Here we face the difficult and important case of ultrathin MgO films on Ag(100), for which no extended and well-ordered layers could thus far be produced in the monolayer limit. We demonstrate that their final morphology depends not only on the usual growth parameters (crystal temperature, metal flux, and oxygen partial pressure), but also on aftergrowth treatments controlling so far neglected thermodynamics constraints. We thus succeed in tuning the shape of the oxide films from irregular, nanometer-sized, monolayer-thick islands to slightly larger, perfectly squared, bilayer islands, to extended monolayers limited apparently only by substrate steps.

Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.

Recovery of nanomolecular electronic states from tunneling spectroscopy: LDOS of low-dimensional phthalocyanine molecular structures on Cu(111)

Organic nanomolecules have become one of the most attractive materials for new nanoelectronics devices. Understanding of the electronic density of states around the Fermi energy of low-dimensional molecules is crucial in designing the electronic properties of molecular devices. The low dimensionality of nanomolecules results in new electronic properties owing to their unique symmetry. Scanning tunneling spectroscopy is one of the most effective techniques for studying the electronic states of nanomolecules, particularly near the Fermi energy (±1.5 eV), whereas these molecular electronic states are frequently buried by the tunneling probability background in tunneling spectroscopy, resulting in incorrect determination of the molecular electronic states. Here, we demonstrate how to recover nanomolecular electronic states from dI/dV curves obtained by tunneling spectroscopy. Precise local density of states (LDOS) peaks for low-dimensional nanostructures (monolayer ultrathin films, one-dimensional chains, and single molecules) of phthalocyanine (H2Pc) molecules grown on noble fcc-Cu(111) were obtained.

A temperature dependent tunneling study of the spin density wave gap in EuFe2As2 single crystals

We report temperature dependent scanning tunneling microscopy and spectroscopy measurements on single crystals of EuFe2As2 in the 15-292 K temperature range. The in situ cleaved crystals show atomic terraces with homogeneous tunnel spectra that correlate well with the spin density wave (SDW) transition at a temperature, TSDW ≈ 186 K. Above TSDW the local tunnel spectra show a small depression in the density of states (DOS) near the Fermi energy (EF). The gap becomes more pronounced upon entering the SDW state with a gap value ∼90 meV at 15 K. However, the zero bias conductance remains finite down to 15 K indicating a finite DOS at the EF in the SDW phase. Furthermore, no noticeable change is observed in the DOS at the antiferromagnetic ordering transition of Eu(2+) moments at 19 K.

A universal scheme to convert aromatic molecular monolayers into functional carbon nanomembranes

Free-standing nanomembranes with molecular or atomic thickness are currently explored for separation technologies, electronics, and sensing. Their engineering with well-defined structural and functional properties is a challenge for materials research. Here we present a broadly applicable scheme to create mechanically stable carbon nanomembranes (CNMs) with a thickness of ~0.5 to ~3 nm. Monolayers of polyaromatic molecules (oligophenyls, hexaphenylbenzene, and polycyclic aromatic hydrocarbons) were assembled and exposed to electrons that cross-link them into CNMs; subsequent pyrolysis converts the CNMs into graphene sheets. In this transformation the thickness, porosity, and surface functionality of the nanomembranes are determined by the monolayers, and structural and functional features are passed on from the molecules through their monolayers to the CNMs and finally on to the graphene. Our procedure is scalable to large areas and allows the engineering of ultrathin nanomembranes by controlling the composition and structure of precursor molecules and their monolayers.

How nanoscience translates into technology: the case of self-assembled monolayers, electron-beam writing, and carbon nanomembranes

One of the great quests in nanotechnology is to translate nanoprecision materials science into practical manufacturing processes. The paper by Angelova et al. in this issue of ACS Nano, which discusses the production of functional carbon-based membranes with a thickness of 0.5 to 3 nm, provides instructive insight into how researchers are pulling together complementary strands from a quarter century of nanoscience research to develop novel, hybrid processing schemes. In this Perspective, we reflect on the progress that is taking place in the two principal component technologies combined in this scheme, namely, (i) control of self-assembled monolayers, including their detailed atomic structures, and (ii) electron-induced manipulation and processing of molecular layers, as well as considering (iii) remaining challenges for thin membrane production in the future.

Mapping image potential states on graphene quantum dots

Free-electron-like image potential states are observed in scanning tunneling spectroscopy on graphene quantum dots on Ir(111) acting as potential wells. The spectrum strongly depends on the size of the nanostructure as well as on the spatial position on top, indicating lateral confinement. Analysis of the substructure of the first state by the spatial mapping of the constant energy local density of states reveals characteristic patterns of confined states. The most pronounced state is not the ground state, but an excited state with a favorable combination of the local density of states and parallel momentum transfer in the tunneling process. Chemical gating tunes the confining potential by changing the local work function. Our experimental determination of this work function allows us to deduce the associated shift of the Dirac point.

Edge scattering of surface plasmons excited by scanning tunneling microscopy

The scattering of electrically excited surface plasmon polaritons (SPPs) into photons at the edges of gold metal stripes is investigated. The SPPs are locally generated by the inelastic tunneling current of a scanning tunneling microscope (STM). The majority of the collected light arising from the scattering of SPPs at the stripe edges is emitted in the forward direction and is collected at large angle (close to the air-glass critical angle, θ(c)). A much weaker isotropic component of the scattered light gives rise to an interference pattern in the Fourier plane images, demonstrating that plasmons may be scattered coherently. An analysis of the interference pattern as a function of excitation position on the stripe is used to determine a value of 1.42 ± 0.18 for the relative plasmon wave vector (kSPP/k0) of the corresponding SPPs. From these results, we interpret the directional, large angle (θ~θ(c)) scattering to be mainly from plasmons on the air-gold interface, and the diffuse scattering forming interference fringes to be dominantly from plasmons on the gold-substrate interface.

Probing the location of displayed cytochrome b562 on amyloid by scanning tunnelling microscopy

Amyloid fibres displaying cytochrome b562 were probed using scanning tunnelling microscopy (STM) in vacuo. The cytochromes are electron transfer proteins containing a haem cofactor and could, in principle, mediate electron transfer between the tip and the gold substrate. If the core fibres were insulating and electron transfer within the 3D haem network was detected, then the electron transport properties of the fibre could be controlled by genetic engineering. Three kinds of STM images were obtained. At a low bias (<1.5 V) the fibres appeared as regions of low conductivity with no evidence of cytochrome mediated electron transfer. At a high bias, stable peaks in tunnelling current were observed for all three fibre species containing haem and one species of fibre that did not contain haem. In images of this kind, some of the current peaks were collinear and spaced around 10 nm apart over ranges longer than 100 nm, but background monomers complicate interpretation. Images of the third kind were rare (1 in 150 fibres); in these, fully conducting structures with the approximate dimensions of fibres were observed, suggesting the possibility of an intermittent conduction mechanism, for which a precedent exists in DNA. To test the conductivity, some fibres were immobilized with sputtered gold, and no evidence of conduction between the grains of gold was seen. In control experiments, a variation of monomeric cytochrome b562 was not detected by STM, which was attributed to low adhesion, whereas a monomeric multi-haem protein, GSU1996, was readily imaged. We conclude that the fibre superstructure may be intermittently conducting, that the cytochromes have been seen within the fibres and that they are too far apart for detectable current flow between sites to occur. We predict that GSU1996, being 10 nm long, is more likely to mediate successful electron transfer along the fibre as well as being more readily detectable when displayed from amyloid.

Design of a scanning gate microscope for mesoscopic electron systems in a cryogen-free dilution refrigerator

We report on our design of a scanning gate microscope housed in a cryogen-free dilution refrigerator with a base temperature of 15 mK. The recent increase in efficiency of pulse tube cryocoolers has made cryogen-free systems popular in recent years. However, this new style of cryostat presents challenges for performing scanning probe measurements, mainly as a result of the vibrations introduced by the cryocooler. We demonstrate scanning with root-mean-square vibrations of 0.8 nm at 3 K and 2.1 nm at 15 mK in a 1 kHz bandwidth with our design. Using Coulomb blockade thermometry on a GaAs/AlGaAs gate-defined quantum dot, we demonstrate an electron temperature of 45 mK.

Dynamics of decanethiol self-assembled monolayers on Au(111) studied by time-resolved scanning tunneling microscopy

We investigated the dynamics of decanethiol self-assembled monolayers on Au(111) surfaces using time-resolved scanning tunneling microscopy at room temperature. The expected ordered phases (β, δ, χ*, and φ) and a disordered phase (ε) were observed. Current-time traces with the feedback loop disabled were recorded at different locations on the surface. The sulfur end group of the decanethiolate molecule exhibits a stochastic two-level switching process when the molecule is adsorbed in a (local) β phase registry. This two-level process is attributed to the diffusion of the Au-thiolate complex between two adjacent adsorption sites. The irregular current jumps in the current-time traces recorded on the tails of decanethiolate molecules in the ordered β, δ, and χ* phases are ascribed to wagging of the alkyl tails. Finally, the disordered phase is characterized by even larger current jumps, which indicates that the tail of the decanethiolate flips up occasionally and makes contact with the tip. Our experiments reveal that the massive dynamics of the self-assembled monolayer is due to diffusion of decanethiol-Au complexes, rather than the diffusion of decanethiolate molecules.

Atomic-scale evidence for potential barriers and strong carrier scattering at graphene grain boundaries: a scanning tunneling microscopy study

We use scanning tunneling microscopy and spectroscopy to examine the electronic nature of grain boundaries (GBs) in polycrystalline graphene grown by chemical vapor deposition (CVD) on Cu foil and transferred to SiO(2) substrates. We find no preferential orientation angle between grains, and the GBs are continuous across graphene wrinkles and SiO(2) topography. Scanning tunneling spectroscopy shows enhanced empty states tunneling conductance for most of the GBs and a shift toward more n-type behavior compared to the bulk of the graphene. We also observe standing wave patterns adjacent to GBs propagating in a zigzag direction with a decay length of ~1 nm. Fourier analysis of these patterns indicates that backscattering and intervalley scattering are the dominant mechanisms responsible for the mobility reduction in the presence of GBs in CVD-grown graphene.

High-temperature scanning tunneling microscopy study of the ordering transition of an amorphous carbon layer into graphene on ruthenium(0001)

The ordering transition of an amorphous carbon layer into graphene was investigated by high-temperature scanning tunneling microscopy. A disordered C layer was prepared on a Ru(0001) surface by chemical vapor deposition of ethylene molecules at ~660 K. The carbon layer grows in the form of dendritic islands that have almost the same density as graphene. Upon annealing of the fully covered surface, residual hydrogen desorbs and a coherent but still disordered carbon layer forms, with almost the same carbon coverage as in graphene. The ordering of this layer into graphene at 920 to 950 K was monitored as a function of time. A unique mechanism was observed that involves small topographic holes in the carbon layer. The holes are mobile, and on the trajectories of the holes the disordered carbon layer is transformed into graphene. The transport of C atoms across the holes or along the hole edges provides a low-energy pathway for the ordering transition. This mechanism is prohibited in a dense graphene layer, which offers an explanation for the difficulty of removing defects from graphene synthesized by chemical methods.

Luttinger liquid behaviour of Li0.9Mo6O17 studied by scanning tunnelling microscopy

Scanning tunnelling spectroscopy (STS) was used to study the Luttinger liquid behaviour of the purple bronze Li(0.9)Mo(6)O(17) in the temperature range 5 K < T < 300 K. In the entire temperature range the suppression of the density of states at the Fermi energy can be fitted very well by a model describing the tunnelling into a Luttinger liquid at ambient temperature. The power-law exponent extracted from these fits reveals a significant increase above 200 K. It changes from α = 0.6 at low temperature to α = 1.0 at room temperature.

Electrochemical scanning tunneling microscopy and spectroscopy for single-molecule investigation

The technique of electrochemical scanning tunneling microscopy (ECSTM) and spectroscopy (ECSTS) for studying electron transport through single redox molecules is here described. Redox molecules of both biological and organic nature have been studied by this technique with the aim of understanding the transport mechanisms ruling the flow of electrons via a single molecule placed in a nanometer-sized gap between two electrodes while elucidating the role of the redox density of states brought about by the molecule. The obtained results provide unique clues to single-molecule transport behavior and support the concept of single-molecule electrochemical gating.

Energy-gap opening in a Bi110 nanoribbon induced by edge reconstruction

Scanning tunnelling microscopy and spectroscopy experiments complemented by first-principles calculations have been conducted to study the electronic structure of 4 monolayer Bi(110) nanoribbons on epitaxial graphene on silicon carbide [4H-SiC(0001)]. In contrast with the semimetal property of elemental bismuth, an energy gap of 0.4 eV is measured at the centre of the Bi(110) nanoribbons. Edge reconstructions, which can facilitate the edge strain energy release, are found to be responsible for the band gap opening. The calculated density of states around the Fermi level are decreased quickly to zero from the terrace edge to the middle of a Bi(110) nanoribbon potentially signifying a spatial metal-to-semiconductor transition. This study opens new avenues for room-temperature bismuth nanoribbon-based electronic devices.

Near-field scanning optical microscopy enables direct observation of Moiré effects at the nanometer scale

This work reports probing the Moiré effect directly at the nanometer scale via near-field scanning optical microscopy (NSOM). Periodic metal nanostructures of Au and Cu have been produced sequentially using particle lithography, and the overlapped regions serve as Moiré patterns at nanometer scale. The Moiré effect in these regions can be directly visualized from NSOM images, from which periodicity and structural details are accurately determined. In addition, the near-field Moiré effect was found to be very sensitive to structural changes, such as lateral displacement and/or rotations of the two basic arrays with respect to each other. Further, nanostructures of Cu exhibited higher photon transmission than Au from NSOM images. Collectively, NSOM enables direct visualization of the Moiré effect at nanoscale levels, from optical read out, and without enhancements or modification of the structures. The results demonstrate the feasibility to extend applications of the Moiré effect-based techniques to nanometer levels.

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.

Covalent attachment of functionalized cardiolipin on a biosensor gold surface allows repetitive measurements of anticardiolipin antibodies in serum

Antiphospholipid antibodies (aPL) are a relevant serological indicator of antiphospholipid syndrome (APS). A solid-state surface with covalently bound ω-amine-functionalized cardiolipin was established and the binding of β2-glycoprotein I (β2-GPI) was investigated either by use of surface plasmon resonance (SPR) biosensor, by electrically switchable DNA interfaces (switchSENSE) and by scanning tunneling microscopy (STM). STM could clearly visualize the attachment of β2-GPI to the cardiolipin surface. Using the switchSENSE sensor, β2-GPI as specific ligand could be identified by increased hydrodynamic friction. The binding of anti-cardiolipin antibodies (aCL) was detected against the ω-amine-functionalized cardiolipin-modified SPR biosensor (aCL biosensor) using sera from healthy donors, APS patients and syphilis patients. Our results showed that the aCL biosensor is a much more sensitive diagnostic device for APS patients compared to previous methods. The specificity between β2-GPI-dependent autoimmune- and β2-GPI-independent infection-associated types of aPLs was also studied and they can be distinguished by the different binding kinetics and patterns.

STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.

Scanning tunneling microscopy reveals single-molecule insights into the self-assembly of amyloid fibrils

Many severe diseases are associated with amyloid fibril deposits in the body caused by protein misfolding. Structural information on amyloid fibrils is accumulating rapidly, but little is known about the assembly of peptides into fibrils at the level of individual molecules. Here we investigate self-assembly of the fibril-forming tetrapeptides KFFE and KVVE on a gold surface under ultraclean vacuum conditions using scanning tunneling microscopy. Combined with restrained molecular dynamics modeling, we identify peptide arrangements with interesting similarities to fibril structures. By resolving individual peptide residues and revealing conformational heterogeneities and dynamics, we demonstrate how conformational correlations may be involved in cooperative fibril growth. Most interestingly, intermolecular interactions prevail over intramolecular interactions, and assembly of the phenyl-rich KFFE peptide appears not to be dominated by π-π interactions. This study offers interesting perspectives for obtaining fundamental single-molecule insights into fibril formation using a surface science approach to study idealized model systems.

Patterning of sub-1 nm dangling-bond lines with atomic precision alignment on H:Si(100) surface at room temperature

We have patterned sub-1 nm dangling-bond (DB) lines on a H-terminated Si(100)-2 × 1 surface aligned with atomic precision at room temperature using a scanning tunneling microscope (STM) to controllably desorb hydrogen atoms from a H:Si(100) surface. In order to achieve continuous and aligned DB lines, we have performed a detailed investigation of the effects of patterning parameters such as the writing voltage, writing current and electron dosage, as well as STM tip apex geometry on the fabrication and alignment of Si DB lines. We show that there exists an optimum set of patterning parameters which enables us to obtain near-perfect Si DB lines and align them with near atomic precision in a highly controllable manner. In addition, our results indicate that the pattern quality is weakly dependent on the STM tip apex quality when the patterning parameters are within the optimum parameter space.

Scanning tunneling microscopy study and nanomanipulation of graphene-coated water on mica

We study interfacial water trapped between a sheet of graphene and a muscovite (mica) surface using Raman spectroscopy and ultrahigh vacuum scanning tunneling microscopy (UHV-STM) at room temperature. We are able to image the graphene-water interface with atomic resolution, revealing a layered network of water trapped underneath the graphene. We identify water layer numbers with a carbon nanotube height reference. Under normal scanning conditions, the water structures remain stable. However, at greater electron energies, we are able to locally manipulate the water using the STM tip.

Growth of silicene layers on Ag(111): unexpected effect of the substrate temperature

The deposition of one silicon monolayer on the silver (111) substrate in the temperature range 150-300 °C gives rise to a mix of (4 × 4), (2√3 × 2√3)R30° and (√13 × √13)R13.9° superstructures which strongly depend on the substrate temperature. We deduced from a detailed analysis of the LEED patterns and the STM images that all these superstructures are given by a quasi-identical silicon single layer with a honeycomb structure (i.e. a silicene-like layer) with different rotations relative to the silver substrate. The morphologies of the STM images are explained from the position of the silicon atoms relative to the silver atoms. A complete analysis of all possible rotations of the silicene layer predicts also a (√7 × √7)R19.1° superstructure which has not been observed so far.

Electronic properties of graphene: a perspective from scanning tunneling microscopy and magnetotransport

This review covers recent experimental progress in probing the electronic properties of graphene and how they are influenced by various substrates, by the presence of a magnetic field and by the proximity to a superconductor. The focus is on results obtained using scanning tunneling microscopy, spectroscopy, transport and magnetotransport techniques.

Formation of nanometer-sized surface platinum oxide clusters on a stepped Pt(557) single crystal surface induced by oxygen: a high-pressure STM and ambient-pressure XPS study

We studied the oxygen-induced restructuring process on a stepped Pt(557) single crystal surface using high-pressure scanning tunneling microscopy (HP-STM) and ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) at O(2) pressures up to 1 Torr. HP-STM has revealed that nanometer-sized clusters are created on Pt(557) at 1 Torr of O(2) and at room temperature. These clusters are identified as surface Pt oxide by AP-XPS. The appearance of clusters is preceded by the formation of 1D chain structures at the step edges. By using a Pt(111) surface as a reference, it was found that the step sites are the nucleation centers for the formation of surface oxide clusters. These surface oxide clusters disappear and the stepped structure is restored on Pt(557) after evacuating O(2) to 10(-8) Torr. Changes in the surface oxide concentration in response to variations in the O(2) gas pressure are repeatable for several cycles. Our results that small clusters are initiated at step sites at high pressures demonstrate the importance of performing in situ characterization of stepped Pt catalysts under reaction conditions.

Visualizing local doping effects of individual water clusters on gold(111)-supported graphene

The local charge carrier density of graphene can exhibit significant and highly localized variations that arise from the interaction between graphene and the local environment, such as adsorbed water, or a supporting substrate. However, it has been difficult to correlate such spatial variations with individual impurity sites. By trapping (under graphene) nanometer-sized water clusters on the atomically well-defined Au(111) substrate, we utilize scanning tunneling microscopy and spectroscopy to characterize the local doping influence of individual water clusters on graphene. We find that water clusters, predominantly nucleated at the atomic steps of Au(111), induce strong and highly localized electron doping in graphene. A positive correlation is observed between the water cluster size and the local doping level, in support of the recently proposed electrostatic-field-mediated doping mechanism. Our findings quantitatively demonstrate the importance of substrate-adsorbed water on the electronic properties of graphene.

Electron-induced dynamics of heptathioether β-cyclodextrin molecules

Variable-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) measurements are performed on heptathioether β-cyclodextrin (β-CD) self-assembled monolayers (SAMs) on Au. The β-CD molecules exhibit very rich dynamical behavior, which is not apparent in ensemble-averaged studies. The dynamics are reflected in the tunneling current-time traces, which are recorded with the STM feedback loop disabled. The dynamics are temperature independent, but increase with increasing tunneling current and sample bias, thus indicating that the conformational changes of the β-CD molecules are induced by electrons that tunnel inelastically. Even for sample biases as low as 10 mV, well-defined levels are observed in the tunneling current-time traces. These jumps are attributed to the excitations of the molecular vibration of the macrocyclic β-CD molecule. The results are of great importance for a proper understanding of transport measurements in SAMs.

Simultaneous determination of conductance and thermopower of single molecule junctions

We report the first concurrent determination of conductance (G) and thermopower (S) of single-molecule junctions via direct measurement of electrical and thermoelectric currents using a scanning tunneling microscope-based break-junction technique. We explore several amine-Au and pyridine-Au linked molecules that are predicted to conduct through either the highest occupied molecular orbital (HOMO) or the lowest unoccupied molecular orbital (LUMO), respectively. We find that the Seebeck coefficient is negative for pyridine-Au linked LUMO-conducting junctions and positive for amine-Au linked HOMO-conducting junctions. Within the accessible temperature gradients (<30 K), we do not observe a strong dependence of the junction Seebeck coefficient on temperature. From histograms of thousands of junctions, we use the most probable Seebeck coefficient to determine a power factor, GS(2), for each junction studied, and find that GS(2) increases with G. Finally, we find that conductance and Seebeck coefficient values are in good quantitative agreement with our self-energy corrected density functional theory calculations.

Effect of bromine and substituted alkyl chain on the interfacial self-assembly of bromobenzene derivatives by scanning tunneling microscopy

The self-assemblies of four compounds, 1-bromo-4-(hexadecyloxy)benzene (BHB-16), 1-bromo-4-(octadecyloxy)benzene (BOB-18), 1-bromo-4-(pentadecyloxy)benzene (BPB-15) and 1,4-dibromo-2,5-(dioctadecyloxy)benzene (DDB-18), have been studied on highly oriented pyrolytic graphite (HOPG) under ambient conditions by scanning tunneling microscopy (STM), with the aim of understanding the influence of the molecular structure and functional groups on the arrangements. It is found that the bromine atoms of the four molecules are in bright contrast and can be identified in STM images. The neighbouring phenyl head groups of the BHB-16, BOB-18 and BPB-15 molecules in one lamella, with an anti-parallel orientation, are interdigitated with different offset distance, while the aromatic cores of DDB-18 molecules in the same row are in a parallel orientation. Moreover, an odd-even effect is observed in the self-assemblies of the former three molecules as expected. The STM images of the four molecules resemble the calculated HOMO electron density contours somewhat with positive surface bias voltage. On the basis of comparative analysis between the STM images, it is suggested that the electrostatic attractions between the neighbouring molecules play an important role in the self-assemblies of BHB-16, BOB-18 and BPB-15, while it is the van der Waals force and the non-covalent halogen-halogen interaction that dominate the structure of DDB-18 adlayer.

Interfacial self-assembly of amino acids and peptides: scanning tunneling microscopy investigation

Proteins play important roles in human daily life. To take advantage of the lessons learned from nature, it is essential to investigate the self-assembly of subunits of proteins, i.e., amino acids and polypeptides. Due to its high resolution and versatility of working environment, scanning tunneling microscopy (STM) has become a powerful tool for studying interfacial molecular assembly structures. This review is intended to reflect the progress in studying interfacial self-assembly of amino acids and peptides by STM. In particular, we focus on environment-induced polymorphism, chiral recognition, and coadsorption behavior with molecular templates. These studies would be highly beneficial to research endeavors exploring the mechanism and nanoscale-controlling molecular assemblies of amino acids and polypeptides on surfaces, understanding the origin of life, unravelling the essence of disease at the molecular level and deeming what is necessary for the "bottom-up" nanofabrication of molecular devices and biosensors being constructed with useful properties and desired performance.

Electrical conduction of organic ultrathin films evaluated by an independently driven double-tip scanning tunneling microscope

The electrical transport properties of organic thin films within the micrometer scale have been evaluated by a laboratory-built independently driven double-tip scanning tunneling microscope, operating under ambient conditions. The two tips were used as point contact electrodes, and current in the range from 0.1 pA to 100 nA flowing between the two tips through the material can be detected. We demonstrated two-dimensional contour mapping of the electrical resistance on a poly(3-octylthiophene) thin films as shown below. The obtained contour map clearly provided an image of two-dimensional electrical conductance between two point electrodes on the poly(3-octylthiophene) thin film. The conductivity of the thin film was estimated to be (1-8) × 10(-6) S cm(-1). Future prospects and the desired development of multiprobe STMs are also discussed.

Quantum point contact microscopy

We introduce quantum point contact microscopy (QPCM) as a novel method for surface characterization, where the conductance through a quantum point contact formed by a metal atom between the tip of a scanning tunneling microscope and the surface is mapped across the surface. Application of QPCM to copper and gold (111) shows reproducibly atomic resolution, on gold (111) the alternating atomic stacking of the surface reconstruction is observed in real space. The perspectives for chemical sensitivity in QPCM images are demonstrated for an iron-platinum surface alloy where we observe local variations of the transport current due to changes in the chemical environment of the point contact.