STM control of chemical reaction: single-molecule synthesis

Cryogen-free modular scanning tunneling microscope operating at 4-K in high magnetic field on a compact ultra-high vacuum platform

One of the daunting challenges in modern low temperature scanning tunneling microscopy (STM) is the difficulty of combining atomic resolution with cryogen-free cooling. Further functionality needs, such as ultra-high vacuum (UHV), high magnetic field (HF), and compatibility with μm-sized samples, pose additional challenges to an already ambitious build. We present the design, construction, and performance of a cryogen-free, UHV, low temperature, and high magnetic field system for modular STM operation. An internal vibration isolator reduces vibrations in this system, allowing for atomic resolution STM imaging while maintaining a low base temperature of ∼4 K and magnetic fields up to 9 T. Samples and tips can be conditioned in situ utilizing a heating stage, an ion sputtering gun, an e-beam evaporator, a tip treater, and sample exfoliation. In situ sample and tip exchange and alignment are performed in a connected UHV room temperature stage with optical access. Multisite operation without breaking vacuum is enabled by a unique quick-connect STM head design. A novel low-profile vertical transfer mechanism permits transferring the STM between room temperature and the low temperature cryostat.

Single-Molecule Identification of the Isomers of a Lipidic Antibody Activator

Molecular structural elucidation can be accomplished by different techniques, such as nuclear magnetic resonance or X-ray diffraction. However, the former does not give information about the three-dimensional atomic arrangement, and the latter needs crystallizable solid samples. An alternative is direct, real-space visualization of the molecules by cryogenic scanning tunneling microscopy (STM). This technique is usually limited to thermally robust molecules because an annealing step is required for sample deposition. A landmark development has been the coupling of STM with electrospray deposition (ESD), which smooths the process and widens the scope of the visualization technique. In this work, we present the on-surface characterization of air-, light-, and temperature-sensitive rhamnopolyene with relevance in molecular biology. Supported by theoretical calculations, we characterize two isomers of this flexible molecule, confirming the potential of the technique to inspect labile, non-crystallizable compounds.

Quick-connect scanning tunneling microscope head with nested piezoelectric coarse walkers

To meet changing research demands, new scanning tunneling microscope (STM) features must constantly evolve. We describe the design, development, and performance of a modular plug-in STM, which is compact and stable. The STM head is equipped with a quick-connect socket that is matched to a universal connector plug, enabling it to be transferred between systems. This head can be introduced into a vacuum system via a load-lock and transferred to various sites equipped with the connector plug, permitting multi-site STM operation. Its design allows for reliable operation in a variety of experimental conditions, including a broad temperature range, ultra-high vacuum, high magnetic fields, and closed-cycle pulse-tube cooling. The STM's compact size is achieved by a novel nested piezoelectric coarse walker design, which allows for large orthogonal travel in the X, Y, and Z directions, ideal for studying both bulk and thin film samples ranging in size from mm to μm. Its stability and noise tolerance are demonstrated by achieving atomic resolution under ambient conditions on a laboratory desktop with no vibrational or acoustic isolation. The operation of the nested coarse walkers is demonstrated by successful navigation to a μm-sized 2D sample.

Exploring the Role of Metal in the Biointeraction of Metallacarboranes with C. elegans Embryos

Cobaltabis(dicarbollides), ferrabis(dicarbollide), and their halogenated derivatives are the most studied metallacarboranes with great medical potential. These versatile compounds and their iodinated derivatives can be used in chemotherapy, radiotherapy, particle therapy, and bioimaging when isotopes are used. These metallacarboranes have been evaluated in vitro and recently in vivo with complex animal models. Lately, these studies have been complemented using the invertebrate Caenorhabditis elegans (C. elegans), a nematode largely used in toxicology. When evaluated at the L4 stage, cobaltabis(dicarbollides), ([o-COSAN]- and [8,8'-I2 -o-COSAN]- ), exhibited a higher mean lethal dose (LD50 ) than ferrabis(dicarbollides) ([o-FESAN]- and [8,8'-I2 -o-FESAN]- ). In this work, we used the C. elegans embryos since they are a complex biological barrier with concentric layers of polysaccharides and proteins that protect them from the environment. We assessed if the metal atom changes their biointeraction with the C. elegans embryos. First, we assessed the effects on embryo development for metallacarboranes and their di-iodinated derivatives. We observed changes in color and in their surface structure. An exhaustive physicochemical characterization was performed to understand better this interaction, revealing a stronger interaction of ferrabis(dicarbollide) compounds with C. elegans embryos than the cobaltabis(dicarbollide) molecules. Unveiling the biological interaction of these compounds is of great interest for their future biomedical applications.

Experimental and Theoretical Investigations of the Fragmentation of Ethylenediamine Induced by Low-Energy (<10 eV) Electrons

Ethylenediamine is industrially used as an intermediate for the fabrication of many products. The development of new methodologies for synthesis compatible with the environment and sustainability, such as cold plasma processes, implicates reactions induced by nonthermal electrons. In this contribution, we study the interaction of low-energy (<10 eV) electrons with ethylenediamine. We show that electrons induce the fragmentation of the molecule into various anion fragments and associated neutral counterparts via dissociative electron attachment. The fragmentation mechanisms and energetics are discussed in the frame of DFT calculations. The fragmentation processes are quantified by the estimation of the cross sections and the branching ratios for competitive accessible dissociation routes.

Driving a Third Generation Molecular Motor with Electrons Across a Surface

Excitation of single molecules with electrons tunneling between a sharp metallic tip of a scanning tunneling microscope and a metal surface is one way to study and control dynamics of molecules on surfaces. Electron tunneling induced dynamics may lead to hopping, rotation, molecular switching, or chemical reactions. Molecular motors that convert rotation of subgroups into lateral movement on a surface can in principle also be driven by tunneling electrons. For such surface-bound motor molecules the efficiency of motor action with respect to electron dose is still not known. Here, the response of a molecular motor containing two rotor units in the form of overcrowded alkene groups to inelastic electron tunneling has been examined on a Cu(111) surface in ultrahigh vacuum at 5 K. Upon vibrational excitation, switching between different molecular conformations is observed, including conversion of enantiomeric states of chiral conformations. Tunneling at energies in the range of electronic excitations causes activation of motor action and movement across the surface. The expected unidirectional rotation of the two rotor units causes forward movements but with a low degree of translational directionality.

Spatially Resolved Stimulation for the Controlled Debromination in Single Molecules on a Surface

A controlled chemical reaction on a specific bond in a single molecule is an inevitable step toward atomic engineering and fabrication. Here, we explored the debromination of a single 9,10-dibromoanthracene (DBA) molecule on a surface as stimulated by the voltage pulse through the tip of a scanning tunneling microscope (STM). A voltage threshold of about 2.2 V is obtained, and the nature of single-electron process is revealed. The spatially resolved debromination yield is obtained as a function of the pulse magnitude, which presents strong asymmetry for the two C-Br bonds. The optimal stimulation parameters including the pulse magnitude and the tip locations are suggested. The distinct dynamics in dissociation of the two bonds are illustrated by their energy diagrams and recoil paths, as derived by the first-principles density functional theory (DFT) calculation. The influence of the local electric field due to the STM tip on the dissociation of the C-Br bond has also been discussed. The study presents detailed practice for the controlled debromination in a single DBA molecule, which may lead to automated atomic engineering and fabrication of artificial nanostructures in the future.

Confinement-Induced Catalytic Dissociation of Hydrogen Molecules in a Scanning Tunneling Microscope

The catalytic scission of single chemical bonds has been induced by the nanoscale confinement in a scanning tunneling microscope (STM) junction. Individual hydrogen molecules sandwiched between the STM tip and a copper substrate can be dissociated solely by the reciprocating movement of the tip. The reaction rate depends sensitively on the local molecular environment, as exemplified by the effects of a nearby carbon monoxide molecule or a gold adatom. Detailed mechanisms and the nature of the transition states are revealed by density functional theory (DFT) calculations. This work provides insights into chemical reactions at the atomic scale induced by localized confinement applied by the STM tip. Furthermore, a single diatomic molecule can act as a molecular catalyst to enhance the reaction rate on a surface.

Electrostatic Potential Field Effects on Amine Macrocyclizations within Yoctoliter Spaces: Supramolecular Electron Withdrawing/Donating Groups

The central role of Coulombic interactions in enzyme catalysis has inspired multiple approaches to sculpting electrostatic potential fields (EPFs) for controlling chemical reactivity, including ion gradients in water microdroplets, the tips of STMs, and precisely engineered crystals. These are powerful tools because EPFs can affect all reactions, even those whose mechanisms do not involve formal charges. For some time now, supramolecular chemists have become increasingly proficient in using encapsulation to control stoichiometric and catalytic reactions. However, the field has not taken advantage of the broad range of nanocontainers available to systematically explore how EPFs can affect reactions within their inner-spaces. With that idea in mind, previously, we reported on how positively and negatively charged supramolecular capsules can modulate the acidity and reactivity of thiol guests bound within their inner, yoctoliter spaces (Cai, X.; Kataria, R.; Gibb, B. C. J. Am. Chem. Soc. 2020, 142, 8291–8298; Wang, K.; Cai, X.; Yao, W.; Tang, D.; Kataria, R.; Ashbaugh, H. S.; Byers, L. D.; Gibb, B. C. J. Am. Chem. Soc.2019, 141, 6740–6747). Building on this, we report here on the cyclization of 14-bromotetradecan-1-amine inside these yoctoliter containers. We examine the rate and activation thermodynamics of cyclization (Eyring analysis), both in the absence and presence of exogenous salts whose complementary ion can bind to the outside of the capsule and hence attenuate its EPF. We find the cyclization rates and activation thermodynamics in the two capsules to be similar, but that for either capsule attenuation of the EPF slows the reaction down considerably. We conclude the capsules behave in a manner akin to covalently attached electron donating/withdrawing groups in a substrate, with each capsule enforcing their own deviations from the idealized S_N2 mechanism by moving electron density and charge in the activated complex and TS, and that the idealized S_N2 mechanism inside the theoretical neutral host is relatively difficult because of the lack of solvation of the TS.

Manipulation of Molecular Spin State on Surfaces Studied by Scanning Tunneling Microscopy

The adsorbed magnetic molecules with tunable spin states have drawn wide attention for their immense potential in the emerging fields of molecular spintronics and quantum computing. One of the key issues toward their application is the efficient controlling of their spin state. This review briefly summarizes the recent progress in the field of molecular spin state manipulation on surfaces. We focus on the molecular spins originated from the unpaired electrons of which the Kondo effect and spin excitation can be detected by scanning tunneling microscopy and spectroscopy (STM and STS). Studies of the molecular spin-carriers in three categories are overviewed, i.e., the ones solely composed of main group elements, the ones comprising 3d-metals, and the ones comprising 4f-metals. Several frequently used strategies for tuning molecular spin state are exemplified, including chemical reactions, reversible atomic/molecular chemisorption, and STM-tip manipulations. The summary of the successful case studies of molecular spin state manipulation may not only facilitate the fundamental understanding of molecular magnetism and spintronics but also inspire the design of the molecule-based spintronic devices and materials.

Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science

The ultimate limit of analytical chemistry is single-molecule detection, which allows one to visualize the dynamic processes of chemical/biological interactions with single-molecule or single-event sensitivity and hence enables the study of stochastic fluctuations under equilibrium conditions and the observation of time trajectories and reaction pathways of individual species in nonequilibrated systems. In addition, such studies may also allow the direct observation of novel microscopic quantum effects and fundamental discoveries of underlying molecular mechanisms in organic reactions and biological processes that are not accessible in ensemble experiments, thus providing unique opportunities to solve the key problems of physical, chemical, and life sciences. Consequently, the field of single-molecule detection has received considerable attention and has witnessed tremendous advances in different directions in combination with other disciplines. This Account describes our ongoing work on the development of groundbreaking methods (termed "single-molecule electrical approaches") of translating the detailed processes of chemical reactions or biological functions into detectable electrical signals at the single-event level on the platform of single-molecule electronic devices, with a particular focus on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) and silicon-nanowire-based single-molecule electrical nanocircuits. These nanocircuit-based architectures are complementary to conventional optical or mechanical techniques but exhibit obvious advantages such as the absence of problems associated with bleaching and fluorescent labeling. Dash-line lithography (DLL) is an efficient lithographic method of cutting graphene and forming carboxylic-acid-functionalized nanogapped graphene point contact arrays developed to address the formidable challenges of molecular device fabrication difficulty and poor stability. Molecules of interest terminated by amines on both ends can be covalently sandwiched between graphene point contacts to create high-throughput robust GMG-SMJs containing only one molecule as the conductive element. In conjunction with the ease of device fabrication and device stability, this feature distinguishes GMG-SMJs as a new testbed platform for single-molecule analysis characterized by high temporal resolution and superior signal-to-noise ratios. By exploiting the DLL method, we have fabricated molecular devices that are sensitive to external stimuli and are capable of transducing chemical/biochemical events into electrical signals at the single-molecule level, with notable examples including host-guest interaction, hydrogen bond dynamics, DNA intercalation, photoinduced conformational transition, carbocation formation, nucleophilic addition, and stereoelectronic effect. In addition to GMG-SMJs and considering compatibility with the silicon-based industry, we have also developed a reliable method of point-functionalizing silicon-nanowire-based nanotransistors to afford single-molecule electrical nanocircuits. This approach proved to be a robust platform for single-molecule electrical analysis capable of probing fast dynamic processes such as single-protein detection, DNA hybridization/polymorphism, and motor rotation dynamics. The above systematic investigations emphasize the importance and unique advantages of universal single-molecule electrical approaches for realizing direct, label-free, real-time electrical measurements of reaction dynamics with single-event sensitivity. These approaches promise a fascinating mainstream platform to explore the dynamics of stochastic processes in chemical/biological systems as well as gain information in fields ranging from reaction chemistry for elucidating the intrinsic mechanisms to genomics or proteomics for accurate molecular and even point-of-care clinical diagnoses.

Surface modification on MoO2+x/Mo(110) induced by a local electric potential

Oxygen adatoms on the MoO_2+x/Mo(110) surface are observed to be removed when a sufficiently large bias is applied between the scanning tunneling microscope tip and the surface. Experimental observations, such as the bias polarity dependence of adatom removal and the observation of an intermediate state, indicate that the adatom penetrates the surface oxide layer. Through the comparison of finite element method simulations with various experimental relationships, the electric field is concluded to be the sole contributor to adatom penetration into the surface oxide layer. The energetic barrier to this process is estimated to be approximately 0.45 eV in magnitude. Furthermore, the resolution of this phenomenon is on the atomic scale: individual adatoms can undergo surface penetration whilst their nearest neighbour adatoms, separated by 5 Å, are unaffected. The mechanism reported here has the advantages of not strongly influencing the substrate and is exceptionally localised, which can be beneficial for the synthesis of single atom devices.

Controlling a Chemical Coupling Reaction on a Surface: Tools and Strategies for On-Surface Synthesis

On-surface synthesis is appearing as an extremely promising research field aimed at creating new organic materials. A large number of chemical reactions have been successfully demonstrated to take place directly on surfaces through unusual reaction mechanisms. In some cases the reaction conditions can be properly tuned to steer the formation of the reaction products. It is thus possible to control the initiation step of the reaction and its degree of advancement (the kinetics, the reaction yield); the nature of the reaction products (selectivity control, particularly in the case of competing processes); as well as the structure, position, and orientation of the covalent compounds, or the quality of the as-formed networks in terms of order and extension. The aim of our review is thus to provide an extensive description of all tools and strategies reported to date and to put them into perspective. We specifically define the different approaches available and group them into a few general categories. In the last part, we demonstrate the effective maturation of the on-surface synthesis field by reporting systems that are getting closer to application-relevant levels thanks to the use of advanced control strategies.

Distance-regulating surface plasmon catalyzed coupling reaction of p-nitrophenyl disulfide

In this study, we attempted to regulate the intermolecular distance of PNTP molecules on the surface of silver foil by breaking the S-S bond of NPDS. Though changing the laser wavelength and power, SERS conditions, the Raman spectra of NPDS and PNTP with different concentrations were compared. We found that, under SERS conditions, NPDS converted more efficiently than PNTP to DMAB at low-concentration with low-power and low-energy irradiation. The results indicate that the distance between molecules plays a significant role in the reaction of PNTP to form DMAB.

Electronic effects and fundamental physics studied in molecular interfaces

Scanning probe instruments in conjunction with a very low temperature environment have revolutionized the ability of building, functionalizing, and analysing two dimensional interfaces in the last twenty years. In addition, the availability of fast, reliable, and increasingly sophisticated methods to simulate the structure and dynamics of these interfaces allow us to capture even very small effects at the atomic and molecular level. In this review we shall focus largely on metal surfaces and organic molecular compounds and show that building systems from the bottom up and controlling the physical properties of such systems is no longer within the realm of the desirable, but has become day to day reality in our best laboratories.

Alloy-assisted deposition of three-dimensional arrays of atomic gold catalyst for crystal growth studies

Large-scale assembly of individual atoms over smooth surfaces is difficult to achieve. A configuration of an atom reservoir, in which individual atoms can be readily extracted, may successfully address this challenge. In this work, we demonstrate that a liquid gold–silicon alloy established in classical vapor–liquid–solid growth can deposit ordered and three-dimensional rings of isolated gold atoms over silicon nanowire sidewalls. We perform ab initio molecular dynamics simulation and unveil a surprising single atomic gold-catalyzed chemical etching of silicon. Experimental verification of this catalytic process in silicon nanowires yields dopant-dependent, massive and ordered 3D grooves with spacing down to ~5 nm. Finally, we use these grooves as self-labeled and ex situ markers to resolve several complex silicon growths, including the formation of nodes, kinks, scale-like interfaces, and curved backbones.

Parallel patterning of atoms over a large surface would represent a major advance over current serial methods of single atom manipulation. Here, the authors explore a periodic instability from liquid alloy droplets for high-throughput atom printing.

Molecular Graph Paper

We present a self-assembled template that consists of tetraphenylmethane derivatives and adopts a periodic lateral arrangement on a Au(111) surface with acetyl groups sticking out of the molecular film. By using the tip of a scanning tunneling microscope, these acetyl groups can be removed in a spatially controlled way without significantly affecting the remaining molecular assembly. The chemically modified molecules can be readily distinguished from the original ones such that information can be engraved in the molecular film. Both the modified nature of an individual molecule and the order of the molecular film are shown to persist at room temperature. The mesh size of this molecular graph paper can be tuned by varying the length of the molecular spacer so that writing and reading information on the nanoscale with variable letter sizes becomes possible.

Surface-Assisted Cyclodehydrogenation; Break the Symmetry, Enhance the Selectivity

Selectivity in chemical reactions is a major objective in industrial processes to minimize spurious byproducts and to save scarce resources. In homogeneous catalysis the most important factor which determines selectivity is structural symmetry. However, a transfer of the symmetry concept to heterogeneous catalysis still requires a detailed comprehension of the underlying processes. Here, we investigate a ring-closing reaction in surface-confined meso-substituted porphyrin molecules by scanning tunneling microscopy, temperature-programmed desorption, and computational modeling. The identification of reaction intermediates enables us to analyze the reaction pathway and to conclude that the symmetry of the porphyrin core is of pivotal importance regarding product yields.

Dynamics of tungsten hexacarbonyl, dicobalt octacarbonyl, and their fragments adsorbed on silica surfaces

Tungsten and cobalt carbonyls adsorbed on a substrate are typical starting points for the electron beam induced deposition of tungsten or cobalt based metallic nanostructures. We employ first principles molecular dynamics simulations to investigate the dynamics and vibrational spectra of W(CO)6 and W(CO)5 as well as Co2(CO)8 and Co(CO)4 precursor molecules on fully and partially hydroxylated silica surfaces. Such surfaces resemble the initial conditions of electron beam induced growth processes. We find that both W(CO)6 and Co2(CO)8 are stable at room temperature and mobile on a silica surface saturated with hydroxyl groups (OH), moving up to half an Angström per picosecond. In contrast, chemisorbed W(CO)5 or Co(CO)4 ions at room temperature do not change their binding site. These results contribute to gaining fundamental insight into how the molecules behave in the simulated time window of 20 ps and our determined vibrational spectra of all species provide signatures for experimentally distinguishing the form in which precursors cover a substrate.

Towards single molecule switches

Scanning tunneling microscope (STM) controlled reversible switching of a single-dipole molecule imbedded in hydrogen-bonded binary molecular networks on graphite.

A new variable temperature solution-solid interface scanning tunneling microscope

We present a new solution-solid (SS) interface scanning tunneling microscope design that enables imaging at high temperatures with low thermal drift and with volatile solvents. In this new design, distinct from the conventional designs, the entire microscope is surrounded in a controlled-temperature and controlled-atmosphere chamber. This allows users to take measurements at high temperatures while minimizing thermal drift. By incorporating an open solution reservoir in the chamber, solvent evaporation from the sample is minimized; allowing users to use volatile solvents for temperature dependent studies at high temperatures. The new design enables the user to image at the SS interface with some volatile solvents for long periods of time (>24 h). An increase in the nonlinearity of the piezoelectric scanner in the lateral direction as a function of temperature is addressed. A temperature dependent study of cobalt(II) octaethylporphyrin (CoOEP) at the toluene/Au(111) interface has been performed with this instrument. It is demonstrated that the lattice parameters remain constant within experimental error from 24 °C to 75 °C. Similar quality images were obtained over the entire temperature range. We report the unit cell of CoOEP at the toluene/Au(111) interface (based on two molecules per unit cell) to be A = (1.36 ± 0.04) nm, B = (2.51 ± 0.04) nm, and α = 97° ± 2°.

Tip-induced C-H activation and oligomerization of thienoanthracenes

The tip of a scanning tunneling microscope (STM) can be used to dehydrogenate freely-diffusing tetrathienoanthracene (TTA) molecules on Cu(111), trapping the molecules into metal-coordinated oligomeric structures. The process proceeds at bias voltages above ~3 V and produces organometallic structures identical to those resulting from the thermally-activated cross-coupling of a halogenated analogue. The process appears to be substrate dependent: no oligomerization was observed on Ag(111) or HOPG. This approach demonstrates the possibility of controlled synthesis and nanoscale patterning of 2D oligomer structures on selected surfaces.

Charged-molecule physics

Commonly, chemical modification is considered to be the ultimate way to tune properties of graphene for new devices. The work of Riss and colleagues reported in this issue of ACS Nano demonstrates a reverse approach that enables tuning of molecular properties with graphene. When a back-gate voltage is used, the Fermi level of graphene is shifted with respect to the electronic states of the molecules. This extra electric field opens fascinating new routes toward ultimate sensitive sensors or experimental devices for studying new molecular physics.

Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors

The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by 'plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply 'hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry.

Solution preparation of two-dimensional covalently linked networks by polymerization of 1,3,5-Tri(4-iodophenyl)benzene on Au(111)

The polymerization of 1,3,5-tri(4-iodophenyl)benzene (TIPB) on Au(111) through covalent aryl-aryl coupling is accomplished using a solution-based approach and investigated by scanning tunneling microscopy. Drop-casting of the TIPB monomer onto Au(111) at room temperature results in poorly ordered noncovalent arrangements of molecules and partial dehalogenation. However, drop-casting on a preheated Au(111) substrate yields various topologically distinct covalent aggregates and networks. Interestingly, some of these covalent nanostructures do not adsorb directly on the Au(111) surface, but are loosely bound to a disordered layer of a mixture of chemisorbed iodine and molecules, a conclusion that is drawn from STM data and supported by X-ray photoelectron spectroscopy. We argue that the gold surface becomes covered by a strongly chemisorbed iodine monolayer which eventually inhibits further polymerization.

Substrate-, wavelength-, and time-dependent plasmon-assisted surface catalysis reaction of 4-nitrobenzenethiol dimerizing to p,p'-dimercaptoazobenzene on Au, Ag, and Cu films

In this article, we experimentally investigate the substrate, wavelength, and time dependence of the plasmon-assisted surface-catalyzed dimerization of 4-nitrobenzenethiol to form p,p'-dimercaptoazobenzene on Au, Ag, and Cu films. We provide direct experimental evidence that surface plasmon resonance plays the most important role in these surface-catalyzed reactions. It is found that the reaction is strongly dependent on the substrate, the wavelength of the laser, and the reaction timescales. Our experimental results revealed that optimal experimental conditions can be rationally chosen to control (accelerate or restrain) this reaction. The experimental results are also confirmed by theoretical calculations.

Tip- or electron beam-induced surface polymerization

Control on the formation of a two-dimensional polymer could be achieved in two different ways. Manipulation with the tip of a scanning tunneling microscope allowed for assigning the localization of the polymerization reaction. Additionally, electron irradiation could accelerate greatly the reaction kinetics.

Recent trends in surface characterization and chemistry with high-resolution scanning force methods

The current status and future prospects of non-contact atomic force microscopy (nc-AFM) and Kelvin probe force microscopy (KPFM) for studying insulating surfaces and thin insulating films in high resolution are discussed. The rapid development of these techniques and their use in combination with other scanning probe microscopy methods over the last few years has made them increasingly relevant for studying, controlling, and functionalizing the surfaces of many key materials. After introducing the instruments and the basic terminology associated with them, state-of-the-art experimental and theoretical studies of insulating surfaces and thin films are discussed, with specific focus on defects, atomic and molecular adsorbates, doping, and metallic nanoclusters. The latest achievements in atomic site-specific force spectroscopy and the identification of defects by crystal doping, work function, and surface charge imaging are reviewed and recent progress being made in high-resolution imaging in air and liquids is detailed. Finally, some of the key challenges for the future development of the considered fields are identified.

A new mechanism of atomic manipulation: bond-selective molecular dissociation via thermally activated electron attachment

We report a new mechanism of (bond-selective) atomic manipulation in the scanning tunneling microscope (STM). We demonstrate a channel for one-electron-induced C-Cl bond dissociation in chlorobenzene molecules chemisorbed on the Si(111)-7 × 7 surface, at room temperature and above, which is thermally activated. We find an Arrhenius thermal energy barrier to one-electron dissociation of 0.8 ± 0.2 eV, which we correlate explicitly with the barrier between chemisorbed and physisorbed precursor states of the molecule. Thermal excitation promotes the target molecule from a state where one-electron dissociation is suppressed to a transient state where efficient one-electron dissociation, analogous to the gas-phase negative-ion resonance process, occurs. We expect the mechanism will be obtained in many surface systems, and not just in STM manipulation, but in photon and electron beam stimulated (selective) chemistry.

Insight into action spectroscopy for single molecule motion and reactions through inelastic electron tunneling

We propose a versatile formula that describes action spectra for vibrationally mediated reactions of single molecules with a scanning tunneling microscope. Spectral fitting of the formula to CO hopping and the configurational change of the cis-2-butene molecule on Pd(110) enables us to determine the vibrational energy, reaction order, and transition rate associated with anharmonic coupling between the modes excited by tunneling electrons and the reaction-coordinate modes. The formula proposed here is general and easy to apply to any vibrationally mediated motion and reaction of single molecules.

Unambiguous determination of the adsorption geometry of a metal--organic complex on a bulk insulator

Individual molecules of Co-Salen, a small chiral paramagnetic metal--organic Schiff base complex, were deposited on NaCl(001) and subsequently imaged with noncontact atomic force microscopy employing Cr coated tips in a cryogenic ultrahigh vacuum environment. Images were obtained in which both the position and orientation of the adsorbed molecules and the atomic structure of the surface are resolved simultaneously, enabling the determination of the exact adsorption site. Density functional theory calculations were used to identify the ionic sublattice resolved with the Cr tip and also to confirm the adsorption site and orientation of the molecule on the surface. These calculations show that the central Co atom of the molecule physisorbs on top of a Cl ion and is aligned along 110-directions in its lowest energy configuration. In addition, a local energy minimum exists along 100-directions. Due to the chirality of the molecule, two mirror symmetric configurations rotated by approximately +/-5 degrees away from these directions are energetically equivalent. The resulting 16 low energy configurations are observed in the experimental images.

Single-molecule synthesis and characterization of metal-ligand complexes by low-temperature STM

We present scanning tunneling microscopy (STM)-based single-molecule synthesis of linear metal-ligand complexes starting from individual metal atoms (iron or nickel) and organic molecules (9,10-dicyanoanthracene) deposited on an ultrathin insulating film. We directly visualize the frontier molecular orbitals by STM orbital imaging, from which, in conjunction with detailed density functional theory calculations, the electronic structure of the complexes is inferred. Our studies show how the order of the molecular orbitals and the spin-state of the complex can be engineered through the choice of the metal atom. The high-spin iron complex has a singly occupied delocalized orbital with a large spin-splitting that points to the use of these engineered complexes as modular building blocks in molecular spintronics.

Time-resolved scanning tunnelling microscopy for molecular science

Time-resolved scanning tunnelling microscopy (STM) and its application in molecular science are reviewed. STM can image individual atoms and molecules and thus is able to observe the results of molecular processes such as diffusion, desorption, configuration switching, bond-breaking and chemistry, on the atomic scale. This review will introduce time-resolved STM, its experimental limitations and implementations with particular emphasis on thermally activated and tunnelling current induced molecular processes. It will briefly examine the push towards ultrafast imaging. In general, results achieved by time-resolved STM demonstrate the necessity of both space and time resolution for fully characterizing molecular processes on the atomic scale.

The monomer-to-dimer transition and bimodal growth of Co-salen on NaCl(001): a high resolution atomic force microscopy study

Molecules of Co-salen, a paramagnetic metal-organic Schiff base complex, self-assemble into two different well ordered morphologies on a NaCl(001) substrate: nanowires, which form networks, and compact nanocrystallites. Their growth can be controlled by adjusting the deposition parameters. It turns out that the nanowires are metastable. Molecular resolution images suggest that the packing in both morphologies is the same as in bulk Co-salen single crystals. Only the orientation of the c-axis with respect to the substrate is different. The origin of this intriguing bimodal growth is associated with a monomer-to-dimer transition, which probably takes place during initial nucleation at step edges.