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.     

Single-molecule conductance of redox molecules in electrochemical scanning tunneling microscopy

Experimental data and theoretical notions are presented for 6-[1'-(6-mercapto-hexyl)-[4,4']bipyridinium]-hexane-1-thiol iodide (6V6) "wired" between a gold electrode surface and tip in an in situ scanning tunneling microscopy configuration. The viologen group can be used to "gate" charge transport across the molecular bridge through control of the electrochemical potential and consequently the redox state of the viologen moiety. This gating is theoretically considered within the framework of superexchange and coherent two-step notions for charge transport. It is shown here that the absence of a maximum in the Itunneling versus electrode potential relationship can be fitted by a "soft" gating concept. This arises from large configurational fluctuations of the molecular bridge linked to the gold contacts by flexible chains. This view is incorporated in a formalism that is well-suited for data analysis and reproduces in all important respects the 6V6 data for physically sound values of the appropriate parameters. This study demonstrates that fluctuations of isolated configurationally "soft" molecules can dominate charge transport patterns and that theoretical frameworks for compact monolayers may not be directly applied under such circumstances.     

A single molecule view of bistilbene photoisomerization on a surface using scanning tunneling microscopy

The advent of scanning tunneling microscopy (STM) has permitted a detailed atomic view of organic molecules adsorbed on solid surfaces. In this work, we make use of the STM to provide an unprecedented direct single-molecule perspective on the cis-trans photoisomerization of stilbene molecules within ordered monolayers physisorbed on the Ag/Ge(111)-( radical3x radical3)R30 degrees surface. The STM view of the molecular structure transformation upon irradiation provides direct evidence for the generally accepted one-bond-flip mechanism proposed for the photoisomerization process. We also find that the surface environment produces a profound effect on the reaction mechanism. The reaction is observed to proceed mainly through pairs of co-isomerizing molecules situated at domain boundaries. To explain these observations, we propose a mechanism whereby excitation migrates to the domain boundary and the reaction occurs through a biexciton reaction pathway.     

Spectroscopic scanning tunneling microscopy studies of single surface-supported free-base corroles

Corroles are versatile chemically active agents in solution. Expanding their applications toward surface-supported systems requires a fundamental knowledge of corrole-surface interactions. We employed the tip of a low-temperature scanning tunneling microscope as local probe to investigate at the single-molecule level the electronic and geometric properties of surface-supported free-base corrole molecules. To provide a suitable reference for other corrole-based systems on surfaces, we chose the archetypal 5,10,15-tris(pentafluorophenyl)corrole [H(3)(TpFPC)] as model system, weakly adsorbed on two surfaces with different interaction strengths. We demonstrate the nondissociative adsorption of H(3)(TpFPC) on pristine Au(111) and on an intermediate organic layer that provides sufficient electronic decoupling to investigate geometric and frontier orbital electronic properties of almost undisturbed H(3)(TpFPC) molecules at the submolecular level. We identify a deviating adsorption behavior of H(3)(TpFPC) compared to structurally similar porphyrins, characterized by a chiral pair of molecule-substrate configurations.     

Quantitative imaging of ion transport through single nanopores by high-resolution scanning electrochemical microscopy

Here we report on the unprecedentedly high resolution imaging of ion transport through single nanopores by scanning electrochemical microscopy (SECM). The quantitative SECM image of single nanopores allows for the determination of their structural properties, including their density, shape, and size, which are essential for understanding the permeability of the entire nanoporous membrane. Nanoscale spatial resolution was achieved by scanning a 17 nm radius pipet tip at a distance as low as 1.3 nm from a highly porous nanocrystalline silicon membrane in order to obtain the peak current response controlled by the nanopore-mediated diffusional transport of tetrabutylammonium ions to the nanopipet-supported liquid-liquid interface. A 280 nm × 500 nm image resolved 13 nanopores, which corresponds to a high density of 93 nanopores/μm(2). A finite element simulation of the SECM image was performed to assess quantitatively the spatial resolution limited by the tip diameter in resolving two adjacent pores and to determine the actual size of a nanopore, which was approximated as an elliptical cylinder with a depth of 30 nm and major and minor axes of 53 and 41 nm, respectively. These structural parameters were consistent with those determined by transmission electron microscopy, thereby confirming the reliability of quantitative SECM imaging at the nanoscale level.     

Coherent transport through spin-crossover single molecules

Coherent quantum transport calculations were performed for high- and low-spin states of a mononuclear Fe(II) complex showing spin-crossover behavior using density functional theory methods combined with the non-equilibrium Green functions procedure. The high-spin state has a larger conductivity than the low-spin state; furthermore, it behaves as a spin filter, giving a β-polarized current.     

Determination of relative binding affinities of labeling molecules with amino acids by using scanning tunneling microscopy

The binding behaviour of labeling molecule copper phthalocyanine tetrasulfonate sodium (PcCu(SO(3)Na)(4)) on the assemblies of representative polyamino acids has been studied by using scanning tunneling microscopy (STM). By directly visualizing the adsorption and distribution of the labeling species on the peptide assemblies in STM images, one could obtain relative binding affinities of the labeling molecule with different amino acid residues.     

Single carbon dioxide molecules on surfaces studied by low-temperature scanning tunneling microscopy

The chemical conversion of carbon dioxide (\(\hbox {CO}_2\)) has been intensively studied because the molecule is responsible for global warming. Rational design of catalysts plays an important role in converting \(\hbox {CO}_2\) into value-added compounds. Understanding the interaction between \(\hbox {CO}_2\) and surfaces of catalysts is a prerequisite to preparing high-performance catalysts. This review focuses on the investigations of \(\hbox {CO}_2\) molecules on single crystalline surfaces studied by low-temperature scanning tunneling microscopy. Molecular adsorption, diffusion, and conversion on metal surfaces, metal oxide surfaces, and surfaces decorated by metal-organic frameworks are summarized.     

Selective internal manipulation of a single molecule by scanning tunneling microscopy

We have studied the adsorption of the polyaromatic molecule 1,4"-paratriphenyldimethylacetone, which we have nicknamed Trima. The originality of this linear molecule is that it was designed and synthesized to have two functionalities. First, chemisorb itself to the surface by its two ends rather like a bridge. Second, the central part of the molecule could then be rotated by injecting electrons with the tip of the scanning tunneling microscope (STM). The length of the molecule corresponds exactly to the spacing between five dimers in a row on the Si(100)-2 x 1 surface. We found that the molecule adsorbs as expected on the clean silicon surface by using complementary STM and synchrotron radiation studies. Manipulation of individual molecules with the STM tip showed selective internal modifications that were highly voltage dependent. These manipulations were found to be compatible with an electronic excitation of the pi-pi* transition of the molecule.     

Sequence modulation of tunneling barrier and charge transport across histidine doped oligo-alanine molecular junctions

Series tunneling across peptides composed of various amino acids is one of the main charge transport mechanisms for realizing the function of protein. Histidine, more frequently found in redox active proteins, has been proved to be efficient tunneling mediator. While how it exactly modulates charge transport in a long peptide sequence remains poorly explored. In this work, we studied charge transport of a model peptide junction, where oligo-alanine peptide was doped by histidine at different position, and the series of peptides were self-assembled into a monolayer on gold electrode with soft EGaIn as top electrode to form molecular junction. It was found that histidine increased the overall conductance of the peptide, meanwhile, its position modulated the conductance as well. Quantitative analysis by transport model and ultraviolet photoelectron spectroscopy (UPS) indicated a sequence dependent energy landscape of the tunneling barrier of the junction. Density-functional theory (DFT) calculation on the electronic structure of histidine doped oligo-alanine peptides revealed localized highest occupied molecular orbital (HOMO) on imidazole group of the histidine, which decreased charge transport barrier.     

Observation of DNA transport through a single carbon nanotube channel using fluorescence microscopy

DNA transport through a single multiwall carbon nanotube (MWNT) channel was directly observed via fluorescence microscopy.     

Mapping the placement of oligonucleotide molecules using scanning probe microscopy

The successful development of novel bio-inspired devices requires the ability to place specific biomolecules on a substrate with nanometre precision, in such a way so that their bioactivity is retained. A method is required that can verify this bio-modification. Scanning probe microscopy (SPM) can image and probe a surface in a liquid environment with nanometre resolution. Using short chain complementary oligonucleotides as the bioactive molecules we have modified continuous and patterned gold substrates and SPM probes. We demonstrated that the attached oligonucleotides retained their biological activity after surface attachment with a hybridization interaction force that varies between 50 and 400pN as measured by SPM force measurements. Finally, the position of the attached oligonucleotides was determined with nanometre resolution. Thus we have demonstrated the capabilities of SPM in the application of the development of substrates and templates suitable for forming the basis of novel and innovative devices.     

Electrochemical electron transfer and its relation to charge transport in single molecule junctions

Ability to control charge transport at nanometer scale lies in the heart of design of fast reliable electronic devices. Molecular electronics thrive to use functional molecules for such transport. If the molecule contains redox center(s), a diode-like or transistor-like behavior can be easily explored by controlling not only the voltage difference between two metallic contacts of the molecular junction but also the potential of one of the contacting electrodes with respect to some reference. Thus, one needs to understand the relationship between electrochemical electron transfer and charge transport in metal–molecule–metal junctions. This review presents latest theoretical approaches toward understanding of such relationship and discusses pivotal experimental works to validate them. Tunneling and hopping pathways may operate in parallel (two-channel model), but experimental conditions dictate the channel preference.     

Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.     

Solvent effects on two-dimensional molecular self-assemblies investigated by using scanning tunneling microscopy

Self-assembly structures investigated by using scanning tunneling microscopy (STM) at liquid/solid interface have been a topic of broad interest in surface science, molecular materials, molecular electronics. The delicate balance among the adsorbate–solvent, adsorbate–adsorbate, solvent–solvent interactions would give rise to the coadsorption or competitive deposition of solvent with adsorbate. The solvents at the interface enable dynamic absorption and desorption of the adsorbates leading to the controlled assembly of the molecular architectures. The solvent-induced polymorphism, coadsorption effect, as well as solvent effects on chirality and electronic structures are discussed in this report in view of the polarity, solubility and viscosity of the solvent, the hydrogen bonding formation between solute and solvent, and the solvophobic and solvophilic effects. The systematic studies on the solvent effects would shed light on better control of assembly structures for design of new molecular materials and molecular electronics.     

Visualization of atomic processes on ruthenium dioxide using scanning tunneling microscopy.

The visualization of surface reactions on the atomic scale provides direct insight into the microscopic reaction steps taking place in a catalytic reaction at a (model) catalyst's surface. Employing the technique of scanning tunneling microscopy (STM), we investigated the CO oxidation reaction over the RuO2(110) and RuO2(100) surfaces. For both surfaces the protruding bridging O atoms are imaged in STM as bright features. The reaction mechanism is identical on both orientations of RuO2. CO molecules adsorb on the undercoordinated surface Ru atoms from where they recombine with undercoordinated O atoms to form CO2 at the oxide surface. In contrast to the RuO2(110) surface, the RuO2(100) surface stabilizes also a catalytically inactive c(2 x 2) surface phase onto which CO is not able to adsorb above 100 K. We argue that this inactive RuO2(100)-c(2 x 2) phase may play an important role in the deactivation of RuO2 catalysts in the electrochemical Cl2 evolution and other heterogeneous reactions.     

Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy

Hydrogen(H)-bond dynamics are involved in many elementary processes in chemistry and biology. Because of its fundamental importance, a variety of experimental and theoretical approaches have been employed to study the dynamics in gas, liquid, solid phases, and their interfaces. This review describes the recent progress of direct observation and control of H-bond dynamics in several model systems on a metal surface by using low-temperature scanning tunneling microscopy (STM). General aspects of H-bond dynamics and the experimental methods are briefly described in chapter 1 and 2. In the subsequent four chapters, I present direct observation of an H-bond exchange reaction within a single water dimer (chapter 3), a symmetric H bond (chapter 4) and H-atom relay reactions (chapter 5) within water–hydroxyl complexes, and an intramolecular H-atom transfer reaction (tautomerization) within a single porphycene molecule (chapter 6). These results provide novel microscopic insights into H-bond dynamics at the single-molecule level, and highlight significant impact on the process from quantum effects, namely tunneling and zero-point vibration, resulting from the small mass of H atom. Additionally, local environmental effect on H-bond dynamics is also examined by using atom/molecule manipulation with the STM.     

Imaging and vibrational spectroscopy of single pyridine molecules on Ag(110) using a low-temperature scanning tunneling microscope

A scanning tunneling microscope (STM) was used to extract the images of single, isolated pyridine molecules adsorbed on Ag(110) and to record their vibrational spectrum at 13 K. On the STM image, the pyridine molecule appears as an elongated protrusion along the [001] direction on top of a silver atom, indicating that it is bonded through its nitrogen lone pair electrons. STM inelastic electron tunneling spectroscopy of the adsorbed pyridine revealed C-D and C-H stretch modes at 282 and 378 meV, respectively.