Conformational changes of single molecules induced by scanning tunneling microscopy manipulation: a route to molecular switching

DNA-based molecular wires: multiple emission pathways of individual constructs

The extent of photon energy transfer through individual DNA-based molecular wires composed of five dyes is investigated at the single molecular level. Combining single-molecule spectroscopy and pulse interleaved excitation imaging, we have directly resolved the time evolution spectral response of individual constructs, while simultaneously probing DNA integrity. Our data clearly show that intact wires exhibit photon-transfer efficiencies close to 100% across five dyes. Dynamical and multiple pathways for the photon emission resulting from conformational freedom of the wire are readily uncovered. These results provide the basis for guiding the synthesis of DNA-based supramolecular arrays with improved photon transport at the nanometer scale.

Electron-triggered motions in technomimetic molecules

Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with motions triggered by electrons. The first part is devoted to our work in the field of molecular switches: after having demonstrated the possibility of controlling an intramolecular electron transfer by photoisomerisation, we are now trying to control the isomerisation, either by electrochemistry, or by embedding the photochromic compound in a self-assembled monolayer and testing the electrical conduction with a STM tip. In a second part, we present our strategy on controlling the rotation in a molecular rotary motor and the family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active groups, so that addressing the molecule with nano-electrodes would trigger rotation. The electrical control of the charge state of a molecule by a STM tip is developed in a final part.

Statistical analysis of intensity fluctuations in single molecule SERS spectra

We have investigated the fluctuations of the intensity and the line intermittency in the surface enhanced Raman spectra of a single iron-protoporphyrin IX molecule. A statistical analysis has revealed a high correlation between the intensity of each frequency couple in the spectrum. Removal of the continuum background has led to a suppression of the correlation at those frequencies where no Raman lines are present. Conversely, we have observed the persistence of a strong correlation at the intensities corresponding to the vibrational modes of the molecule. Further evidence of correlation between the intensities and the background signal indicates that the background is involved in the enhancement mechanism. Moreover, analysis of the Raman line intermittency reveals a random activation of the different molecular vibrational modes. These results can be generally put into relationship to the presence of two different contributions to the intensity fluctuations: one, strictly related to the continuum background, and affecting the whole spectrum, and another one which selectively acts on the various vibrational modes of the molecule.

Exploring the interatomic forces between tip and single molecules during STM manipulation

The interaction between a single molecule and the STM tip during intramolecular manipulation is investigated in detail. We show that the conformational change of complex organic molecules can be induced reversibly and very reliably by using exclusively attractive forces. By studying the dependence of this process on the bias voltage and the tip position, the driving forces are characterized. Different regimes of tip-molecule interactions are observed as a function of the distance.

Observation of Single Dinuclear Metal-Complex Molecules Using Scanning Tunneling Microscopy

We report a scanning tunneling microscopy (STM) investigation of a dinuclear organometallic molecule, trans-[Cl(dppe)2Ru(C[triple bond]C)6Ru(dppe)2Cl] (Ru2), absorbed on a Au(111) surface; this molecule is a potential candidate for use in molecular quantum-dot cellular automata (QCA) devices. Isolated Ru2 molecules were observed under ultra-high-vacuum conditions. Submolecular structure was clearly discernible in the STM images, with a bright feature corresponding to each of the two Ru-ligand complexes within the Ru2 molecule. Rotation and translation of the Ru2 molecules were observed to be induced by the STM tip under some tunneling conditions.

Dependence of single-molecule junction conductance on molecular conformation

Since it was first suggested that a single molecule might function as an active electronic component, a number of techniques have been developed to measure the charge transport properties of single molecules. Although scanning tunnelling microscopy observations under high vacuum conditions can allow stable measurements of electron transport, most measurements of a single molecule bonded in a metal-molecule-metal junction exhibit relatively large variations in conductance. As a result, even simple predictions about how molecules behave in such junctions have still not been rigorously tested. For instance, it is well known that the tunnelling current passing through a molecule depends on its conformation; but although some experiments have verified this effect, a comprehensive mapping of how junction conductance changes with molecular conformation is not yet available. In the simple case of a biphenyl--a molecule with two phenyl rings linked by a single C-C bond--conductance is expected to change with the relative twist angle between the two rings, with the planar conformation having the highest conductance. Here we use amine link groups to form single-molecule junctions with more reproducible current-voltage characteristics. This allows us to extract average conductance values from thousands of individual measurements on a series of seven biphenyl molecules with different ring substitutions that alter the twist angle of the molecules. We find that the conductance for the series decreases with increasing twist angle, consistent with a cosine-squared relation predicted for transport through pi-conjugated biphenyl systems.

Electrical switching of DNA monolayers investigated by surface plasmon resonance

The switching of DNA monolayers between a "lying" and a "standing" state initiated by applying electric field, and the subsequent DNA hybridization at different states were investigated in a contactless, label-free mode by surface plasmon resonance (SPR) technique. The results showed that the strength of the electric field and surface coverage could influence the switching of DNA monolayers. In addition, it was found that DNA hybridization efficiency could be enhanced or decreased when DNA probes stood straight up or lay flat on the gold surface, depending on the potential of the gold substrate. The enhancement of DNA hybridization efficiency reached the maximum when surface coverage reached 5.87 x 10(12) molecules/cm(2) and the potential of gold substrate was more negative than -0.7 V (versus ITO-coated glass). The research may be helpful for the construction of sensitive biosensors, biochips, and nanoscale electronic devices.

Self-assembly and conformation of tetrapyridyl-porphyrin molecules on Ag(111)

We present a low-temperature scanning tunneling microscopy (STM) study on the supramolecular ordering of tetrapyridyl-porphyrin (TPyP) molecules on Ag(111). Vapor deposition in a wide substrate temperature range reveals that TPyP molecules easily diffuse and self-assemble into large, highly ordered chiral domains. We identify two mirror-symmetric unit cells, each containing two differently oriented molecules. From an analysis of the respective arrangement it is concluded that lateral intermolecular interactions control the packing of the layer, while its orientation is induced by the coupling to the substrate. This finding is corroborated by molecular mechanics calculations. High-resolution STM images recorded at 15 K allow a direct identification of intramolecular features. This makes it possible to determine the molecular conformation of TPyP on Ag(111). The pyridyl groups are alternately rotated out of the porphyrin plane by an angle of 60 degrees.

SCANNING TUNNELING MICROSCOPY MANIPULATION OF COMPLEX ORGANIC MOLECULES ON SOLID SURFACES

Organic molecules adsorbed on solid surfaces display a fascinating variety of new physical and chemical phenomena ranging from self-assembly and molecular recognition to nonlinear optical properties and current rectification. Both the fundamental interest in these systems and the promise of technological applications have motivated a strong research effort in understanding and controlling these properties. Scanning tunneling microscopy (STM) and, in particular, its ability to manipulate individual adsorbed molecules, has become a powerful tool for studying the adsorption geometry and the conformation and dynamics of single molecules and molecular aggregates. Here we review selected case studies demonstrating the enormous capabilities of STM manipulations to explore basic physiochemical properties of adsorbed molecules. In particular, we emphasize the role of STM manipulations in studying the coupling between the multiple degrees of freedom of adsorbed molecules, the phenomenon of molecular molding, and the possibility of creating and breaking individual chemical bonds in a controlled manner, i.e., the concept of single-molecule chemistry.

Lateral manipulation of atomic size defects on the CaF(2)(111) surface

Atomic scale manipulation on insulating surfaces is one of the great challenges of non-contact atomic force microscopy. Here we demonstrate lateral manipulation of defects occupying single ionic sites on a calcium fluoride (111)-surface. Defects stem from the interaction of the residual gas with the surface. The process of surface degradation is briefly discussed. Manipulation is performed over a wide range of path lengths ranging from tens of nanometres down to a few lattice constants. We introduce a simple manipulation protocol based on line-by-line scanning of a surface region containing defects to be manipulated, and record tip-surface distance and cantilever resonance frequency detuning as a function of the manipulation pathway in real time. We suggest a hopping model to describe manipulation where the tip-defect interaction is governed by repulsive forces.

A reversible molecular switch based on pattern-change in chlorobenzene and toluene on a Si(111)-(7x7) surface

A reversible molecular switch is proposed, based on an observed change in a physisorbed pattern of chlorobenzene or toluene at Si(111)-(7x7), from "triangles" to "circles". Electronic excitation, at an applied surface voltage of Vs = -2.0 V, caused molecular migration, by one atomic site, from under the tip (switch "off"). Thereafter, the adsorbate pattern reverted thermally from circles to triangles (switch "on") across a measured activation barrier of Ea = 0.3 eV for chlorobenzene and 0.2 eV for toluene.

A Directly Fused Tetrameric Porphyrin Sheet and Its Anomalous Electronic Properties That Arise from the Planar Cyclooctatetraene Core

Oxidation of a directly meso-meso linked cyclic porphyrin tetramer 2 gave a porphyrin sheet 3. The symmetric square structure of 3 is indicated by its simple 1H NMR spectrum that exhibits only two signals for the porphyrin beta-protons. The absorption spectrum of 3 displays characteristic Soret-like broad bands and weak Q-bands, and its magnetic circular dichroism (MCD) spectrum exhibits a negative Faraday A term at the 762 nm band as a rare case, indicating the absorption as a transition from a nondegenerate level to a degenerate level. A slightly longer S1-state (1.1 ps) and smaller TPA cross section (2750 GM) than a tetrameric linear porphyrin tape also indicate its unique electronic properties. The porphyrin sheet 3 forms stable 1:2 complexes with guest molecules G1 and G2, whose 1H NMR spectra exhibit remarkable downfield shifts for the guest protons that are located just above the cyclooctatetraene (COT) core of 3, whereas the imidazolyl protons bound to the zinc(II) porphyrin local cores are observed at slightly upfield positions. These results have been qualitatively accounted for in terms of the presence of a strong paratropic ring current around the COT core that propagates through the whole pi-electronic network of 3, hence competing with and cancelling the weak diatropic ring currents of the local zinc(II) porphyrins. This explanation was supported by DFT calculation performed at the GIAO-B3LYP/6-31G level, which indicated large positive NICS values within the COT core and small NICS values within the local zinc(II) porphyrins.

Chiral switching by spontaneous conformational change in adsorbed organic molecules

Self-assembly of adsorbed organic molecules is a promising route towards functional surface nano-architectures, and our understanding of associated dynamic processes has been significantly advanced by several scanning tunnelling microscopy (STM) investigations. Intramolecular degrees of freedom are widely accepted to influence ordering of complex adsorbates, but although molecular conformation has been identified and even manipulated by STM, the detailed dynamics of spontaneous conformational change in adsorbed molecules has hitherto not been addressed. Molecular surface structures often show important stereochemical effects as, aside from truly chiral molecules, a large class of so-called prochiral molecules become chiral once confined on a surface with an associated loss of symmetry. Here, we investigate a model system in which adsorbed molecules surprisingly switch between enantiomeric forms as they undergo thermally induced conformational changes. The associated kinetic parameters are quantified from time-resolved STM data whereas mechanistic insight is obtained from theoretical modelling. The chiral switching is demonstrated to enable an efficient channel towards formation of extended homochiral surface domains. Our results imply that appropriate prochiral molecules may be induced (for example, by seeding) to assume only one enantiomeric form in surface assemblies, which is of relevance for chiral amplification and asymmetric heterogenous catalysis.

Current-induced rotation of helical molecular wires

We show that electric current running through a nanojunction with a biased helical molecule can induce unidirectional rotation of the molecular component. In an electric field, conduction electrons injected into the molecule are accelerated along the helical path going through its body, thereby gaining directed angular momentum. Conservation laws require that an angular momentum of the same size but opposite sense is imparted to the rigid-body rotation of the helix. We describe the angular momentum exchange processes that underlie the operation of the nanorotor, discuss factors limiting its efficiency, and propose potential applications.

Deposition of Thermally Unstable Molecules with the Spray-Jet Technique on Au(111) Surface

A porphyrin derivative (5,15-bis(4-ethynylphenyl)-10,20-bis(3,5-di-tert-butylphenyl)porphyrin: trans-BETBPP) possessing chemically reactive substituents was successfully deposited on an Au(111) surface with a new molecular beam deposition system with use of a spray-jet technique (Spray-jet-MBD) without denaturing the molecules. The deposited molecular overlayers were observed at 77 K under ultrahigh vacuum condition by scanning tunneling microscopy (STM). They form two different overlayer structures: a linear arrangement and a square lattice structure. In these overlayers, some molecules were accidentally moved by STM tip agitation, which indicates that the molecules were not polymerized during the deposition process.

Carbocyanine dyes as efficient reversible single-molecule optical switch

We demonstrate that commercially available unmodified carbocyanine dyes such as Cy5 (usually excited at 633 nm) can be used as efficient reversible single-molecule optical switch, whose fluorescent state after apparent photobleaching can be restored at room temperature upon irradiation at shorter wavelengths. Ensemble photobleaching and recovery experiments of Cy5 in aqueous solution irradiating first at 633 nm, then at 337, 488, or 532 nm, demonstrate that restoration of absorption and fluorescence strongly depends on efficient oxygen removal and the addition of the triplet quencher beta-mercaptoethylamine. Single-molecule fluorescence experiments show that individual immobilized Cy5 molecules can be switched optically in milliseconds by applying alternating excitation at 633 and 488 nm between a fluorescent and nonfluorescent state up to 100 times with a reliability of >90% at room temperature. Because of their intriguing performance, carbocyanine dyes volunteer as a simple alternative for ultrahigh-density optical data storage. Measurements on single donor/acceptor (tetramethylrhodamine/Cy5) labeled oligonucleotides point out that the described light-driven switching behavior imposes fundamental limitations on the use of carbocyanine dyes as energy transfer acceptors for the study of biological processes.

Proposal for quantum gates in permanently coupled antiferromagnetic spin rings without need of local fields

We propose a scheme for the implementation of quantum gates which is based on the qubit encoding in antiferromagnetic molecular rings. We show that a proper engineering of the intercluster link would result in an effective coupling that vanishes as far as the system is kept in the computational space, while it is turned on by a selective excitation of specific auxiliary states. These are also shown to allow the performing of single-qubit and two-qubit gates without an individual addressing of the rings by means of local magnetic fields.

Lévy statistics of vibrational mode fluctuations of single molecules from surface-enhanced Raman scattering

Surface-enhanced Raman spectra of a single Fe-protoporphyrin IX molecule display drastic fluctuations in frequency and intensity. When analyzed in their temporal evolution, the vibrational modes of the molecule undergo an on-off switching behavior that is shown to follow a Lévy statistics. Such a time dependent process may encode both the dynamics of the molecule-environment interactions and the intrinsic gating or activation of the mode emission mechanism.

Octyl-Decorated Fréchet-Type Dendrons: A General Motif for Visualisation of Static and Dynamic Behaviour Using Scanning Tunnelling Microscopy?

A detailed STM study of monolayers of 3,5-bis[(3,5-bisoctyloxyphenyl)methyloxy]benzaldehyde and 3,5-bis[(3,5-bisoctyloxyphenyl)methyloxy]benzyl alcohol adsorbed on graphite is presented. Very highly resolved scanning tunnelling microscopy images are observed at room temperature in air allowing the analysis of the conformation of the adsorbed molecules. These long-chain alkyl-decorated Fréchet-type dendrons are a powerful assembly motif and initially form a pattern based on trimeric units, assembled into hexagonal host structures with a pseudo-unit cell of seven molecules, one of which remains highly mobile. Over time, the supramolecular ordering changes from a trimeric into a dimeric pattern. The chirality arising from the adsorption onto a surface of the dendrons is discussed.

High-Resolution Scanning Tunneling Microscopy Images of Molecular Overlayers Prepared by a New Molecular Beam Deposition Apparatus with Spray-Jet Technique

We developed a new molecular beam deposition apparatus using a spray-jet technique for high-quality thin film preparation of nonsublimable molecules. The apparatus was used to deposit chloro[tri-tert-butyl-subphthalocyaninato]boron(III) (TBSubPc) molecules on an Au(111) surface for analysis by low-temperature scanning tunneling microscopy (STM). Highly resolved images, in which tert-butyl groups in a TBSubPc molecule were clearly identifiable, were obtained. The image quality and the resolution of these images compared favorably well to STM images taken on reference samples which were sublimed onto Au (111) from a heated crucible.

Synthesis of technomimetic molecules: towards rotation control in single-molecular machines and motors

Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with rotary motions, including gears, wheelbarrows and motors. Following the bottom-up approach the synthesis of technomimetic molecules grants access to the study of mechanical properties at the molecular level. These molecules are designed to operate as single molecules on surfaces under the control of the tip of a scanning tunneling microscope or atomic force microscope.

Conformation selective assembly of carboxyphenyl substituted porphyrins on Au (111)

The selective assembly of carboxyphenyl substituted porphyrins on the Au (111) surface has been studied using scanning tunneling microscopy. We find that conformational isomers of the porphyrins are induced upon adsorption and are selectively assembled into hydrogen-bonded supramolecular clusters or wires on the surface. The conformation selective assembly is attributed to the coplanar intermolecular interactions between hydrogen-bonded carboxyphenyl groups.

Mechanisms of reversible conformational transitions in a single molecule

The reversible interconversion between two nonplanar conformations of single Zn(II) Etioporphyrin I molecules adsorbed on a NiAl(110) surface at 13 K was induced by a scanning tunneling microscope (STM). The threshold voltage for the conformational change at negative sample bias depends linearly on the tip-sample distance, suggesting an electrostatic force mechanism. The reverse conversion involves inelastic electron tunneling via a molecular electronic resonance at 1.25 eV. In contrast with the photon-induced conformational changes, an electrically induced mechanism is realized with the STM.

The scanning tunnelling microscope as an operative tool: doing physics and chemistry with single atoms and molecules

The scanning tunnelling microscope, initially invented to image surfaces down to the atomic scale, has been further developed in the last few years to an operative tool, with which atoms and molecules can be manipulated at will at low substrate temperatures in different manners to create and investigate artificial structures, whose properties can be investigated employing spectroscopic dI/dV measurements. The tunnelling current can be used to selectively break chemical bonds, but also to induce chemical association. These possibilities give rise to startling new opportunities for physical and chemical experiments on the single atom and single molecule level. Here we provide a short overview on recent results obtained with these techniques.

Molecular assembly and self-assembly: molecular nanoscience for future technologies

In this review the emerging science of single molecules is discussed in the perspective of nanoscale molecular functions and devices. New methods for the controlled assembly of well-defined molecular nanostructures are presented: self assembly and single molecular positioning. The observation and selective modification of conformation, electronics, and molecular mechanics of individual molecules and molecular assemblies by scanning probes is demonstrated. To complement this scientific review, some of the possible consequences and visions for future developments are discussed, as far as they derive from the presented systems. The prospects of nanoscale science to stimulate technological evolution are exemplified.

Coherent electron transport through an azobenzene molecule: a light-driven molecular switch

We apply a first-principles computational approach to study a light-sensitive molecular switch. The molecule that comprises the switch can convert between a trans and a cis configuration upon photoexcitation. We find that the conductance of the two isomers varies dramatically, which suggests that this system has potential application as a molecular device. A detailed analysis of the band structure of the metal leads and the local density of states of the system reveals the mechanism of the switch.