Single-molecule chemistry

Atomically Precise Control of Topological State Hybridization in Conjugated Polymers

Realization of topological quantum states in carbon nanostructures has recently emerged as a promising platform for hosting highly coherent and controllable quantum dot spin qubits. However, their adjustable manipulation remains elusive. Here, we report the atomically accurate control of the hybridization level of topologically protected quantum edge states emerging from topological interfaces in bottom-up-fabricated π-conjugated polymers. Our investigation employed a combination of low-temperature scanning tunneling microscopy and spectroscopy, along with high-resolution atomic force microscopy, to effectively modify the hybridization level of neighboring edge states by the selective dehydrogenation reaction of molecular units in a pentacene-based polymer and demonstrate their reversible character. Density functional theory, tight binding, and complete active space calculations for the Hubbard model were employed to support our findings, revealing that the extent of orbital overlap between the topological edge states can be finely tuned based on the geometry and electronic bandgap of the interconnecting region. These results demonstrate the utility of topological edge states as components for designing complex quantum arrangements for advanced electronic devices.

Charge-transfer dipole low-frequency vibronic excitation at single-molecular scale

Scanning tunneling microscopy (STM) vibronic spectroscopy, which has provided submolecular insights into electron-vibration (vibronic) coupling, faces challenges when probing the pivotal low-frequency vibronic excitations. Because of eigenstate broadening on solid substrates, resolving low-frequency vibronic states demands strong decoupling. This work designs a type II band alignment in STM junction to achieve effective charge-transfer state decoupling. This strategy enables the successful identification of the lowest-frequency Hg(ω1) (Raman-active Hg mode) vibronic excitation within single C60 molecules, which, despite being notably pronounced in electron transport of C60 single-molecule transistors, has remained hidden at submolecular level. Our results show that the observed Hg(ω1) excitation is "anchored" to all molecules, irrespective of local geometry, challenging common understanding of structural definition of vibronic excitation governed by Franck-Condon principle. Density functional theory calculations reveal existence of molecule-substrate interfacial charge-transfer dipole, which, although overlooked previously, drives the dominant Hg(ω1) excitation. This charge-transfer dipole is not specific but must be general at interfaces, influencing vibronic coupling in charge transport.

Atomic-Resolution Vibrational Mapping of Bilayer Borophene

The successful synthesis of borophene beyond the monolayer limit has expanded the family of two-dimensional boron nanomaterials. While atomic-resolution topographic imaging has been previously reported, vibrational mapping has the potential to reveal deeper insight into the chemical bonding and electronic properties of bilayer borophene. Herein, inelastic electron tunneling spectroscopy (IETS) is used to resolve the low-energy vibrational and electronic properties of bilayer-α (BL-α) borophene on Ag(111) at the atomic scale. Using a carbon monoxide (CO)-functionalized scanning tunneling microscopy tip, the BL-α borophene IETS spectra reveal unique features compared to single-layer borophene and typical CO vibrations on metal surfaces. Distinct vibrational spectra are further observed for hollow and filled boron hexagons within the BL-α borophene unit cell, providing evidence for interlayer bonding between the constituent borophene layers. These experimental results are compared with density functional theory calculations to elucidate the interplay between the vibrational modes and electronic states in bilayer borophene.

Selective excitation of vibrations in a single molecule

The capability to excite, probe, and manipulate vibrational modes is essential for understanding and controlling chemical reactions at the molecular level. Recent advancements in tip-enhanced Raman spectroscopies have enabled the probing of vibrational fingerprints in a single molecule with Ångström-scale spatial resolution. However, achieving controllable excitation of specific vibrational modes in individual molecules remains challenging. Here, we demonstrate the selective excitation and probing of vibrational modes in single deprotonated phthalocyanine molecules utilizing resonance Raman spectroscopy in a scanning tunneling microscope. Selective excitation is achieved by finely tuning the excitation wavelength of the laser to be resonant with the vibronic transitions between the molecular ground electronic state and the vibrational levels in the excited electronic state, resulting in the state-selective enhancement of the resonance Raman signal. Our approach contributes to setting the stage for steering chemical transformations in molecules on surfaces by selective excitation of molecular vibrations.

Light switching for product selectivity control in photocatalysis

Artificial switchable catalysis is a new, rapidly expanding field that offers great potential advantages for both homogeneous and heterogeneous catalytic systems. Light irradiation is widely accepted as the best stimulus to artificial switchable chemical systems. In recent years, tremendous progress has been made in the synthesis and application of photo-switchable catalysts that can control when and where bond formation and dissociation take place in reactant molecules. Photo-switchable catalysis is a niche area in current catalysis, on which systematic analysis and reviews are still lacking in the scientific literature, yet it offers many intriguing and versatile applications, particularly in organic synthesis. This review aims to highlight the recent advances in photo-switchable catalyst systems that can result in two different chemical product outcomes and thus achieve a degree of control over organic synthetic reactions. Furthermore, this review evaluates different approaches that have been employed to achieve dynamic control over both the catalytic function and the selectivity of several different types of synthesis reactions, along with the remaining challenges and potential opportunities. Owing to the great diversity of the types of reactions and conditions adopted, a quantitative comparison of efficiencies between considered systems is not the focus of this review, instead the review showcases how insights from successful adopted strategies can help better harness and channel the power of photoswitchability in this new and promising area of catalysis research.

Impact of Single-Melamine Tautomerization on the Excitation of Molecular Vibrations in Inelastic Electron Tunneling Spectroscopy

Vibrational quanta of melamine and its tautomer are analyzed at the single-molecule level on Cu(100) with inelastic electron tunneling spectroscopy. The on-surface tautomerization gives rise to markedly different low-energy vibrational spectra of the isomers, as evidenced by a shift in mode energies and a variation in inelastic cross sections. Spatially resolved spectroscopy reveals the maximum signal strength on an orbital nodal plane, excluding resonant inelastic tunneling as the mechanism underlying the quantum excitations. Decreasing the probe-molecule separation down to the formation of a chemical bond between the melamine amino group and the Cu apex atom of the tip leads to a quenched vibrational spectrum with different excitation energies. Density functional and electron transport calculations reproduce the experimental findings and show that the shift in the quantum energies applies to internal molecular bending modes. The simulations moreover suggest that the bond formation represents an efficient manner of tautomerizing the molecule.

Effect of Bystander Hydrogen Atoms on Hydrogen Desorption on Single-Atom Alloy Surfaces: Insights from Simulated Temperature-Programmed Desorption Spectra

Single-atom alloy (SAA) catalysts exhibit unique and excellent catalytic properties in heterogeneous hydrogenation/dehydrogenation reactions. A thorough understanding of the microscopic surface processes is essential to improve the catalytic performance. Here, from a new perspective of the temperature-programmed desorption (TPD) spectra of hydrogen (H) on two common SAA surfaces, Pt@Cu(111) and Pd@Cu(111), we reveal and confirm the key influence of H atoms attached to Pt/Pd dopants, i.e., the H atom bystander, on the desorption process of surface H atoms. It is found that only after considering the effect of the H atom bystander can the simulated TPD spectra well reproduce the experimentally observed higher desorption temperature on Pt@Cu(111) than on Pd@Cu(111) and the leftward shift of the TPD peak with increasing H atom coverage; otherwise, the features are inconsistent with experiments. Our work provides direct evidence for the effect of bystander H atoms from a simulation perspective.

Molecular-Scale Visualization of Steric Effects of Ligand Binding to Reconstructed Au(111) Surfaces

Direct imaging of single molecules at nanostructured interfaces is a grand challenge with potential to enable new, precise material architectures and technologies. Of particular interest are the structural morphology and spectroscopic signatures of the adsorbed molecule, where modern probes are only now being developed with the necessary spatial and energetic resolution to provide detailed information at the molecule-surface interface. Here, we directly characterize the adsorption of individual m-terphenyl isocyanide ligands on a reconstructed Au(111) surface through scanning tunneling microscopy and inelastic electron tunneling spectroscopy. The site-dependent steric pressure of the various surface features alters the vibrational fingerprints of the m-terphenyl isocyanides, which are characterized with single-molecule precision through joint experimental and theoretical approaches. This study provides molecular-level insights into the steric-pressure-enabled surface binding selectivity as well as its effect on the chemical properties of individual surface-binding ligands.

A scanning probe microscope compatible with quantum sensing at ambient conditions

We designed and built up a new type of ambient scanning probe microscope (SPM), which is fully compatible with state-of-the-art quantum sensing technology based on the nitrogen-vacancy (NV) centers in diamond. We chose a qPlus-type tuning fork (Q up to ∼4400) as the current/force sensor of SPM for its high stiffness and stability under various environments, which yields atomic resolution under scanning tunneling microscopy mode and 1.2-nm resolution under atomic force microscopy mode. The tip of SPM can be used to directly image the topography of nanoscale targets on diamond surfaces for quantum sensing and to manipulate the electrostatic environment of NV centers to enhance their sensitivity up to a single proton spin. In addition, we also demonstrated scanning magnetometry and electrometry with a spatial resolution of ∼20 nm. Our new system not only paves the way for integrating atomic/molecular-scale color-center qubits onto SPM tips to produce quantum tips but also provides the possibility of fabricating color-center qubits with nanoscale or atomic precision.

Local heating and Raman thermometry in a single molecule

Because of the nonequilibrium nature of thermal effects at the nanoscale, the characterization of local thermal effects within a single molecule is highly challenging. Here, we demonstrate a way to characterize the local thermal properties of a single fullerene (C60) molecule during current-induced heating processes through tip-enhanced anti-Stokes Raman spectroscopy. Although the measured vibron populations are far from equilibrium with the environment, we can still define an "effective temperature (Teff)" statistically via a Bose-Einstein distribution, suggesting a local equilibrium within the molecule. With increased current heating, Teff is found to rise up to about 1150 K until the C60 cage is decomposed. Such a decomposition temperature is similar to that reported for ensemble C60 samples, thus justifying the validity of our methodology. Moreover, the possible reaction pathway and product can be identified because of the chemical sensitivity of Raman spectroscopy. Our findings provide a practical method for noninvasively detecting the local heating effect inside a single molecule under nonequilibrium conditions.

Adsorbate motors for unidirectional translation and transport

Artificial molecular motors are designed to transform external energy into useful work in the form of unidirectional motion1. They have been studied mainly in solution2-4, but also on solid surfaces5,6, which provide fixed reference points, allowing for tracking of their movement. However, these molecules require sophisticated design and synthesis, because the motor function must be imprinted into the chemical structure, and show reduced functionality on surfaces compared with in solution5-8. DNA walkers9,10, on the other hand, impart high directionality as they include the surface as part of the motor function, but they require chemical surface patterning and sequential solvent modification for motor activation. Here we show how efficient motors can operate at much smaller length scales on a homogeneous metal surface without any liquid. This is realized by combining a surface with a simple molecule, which, by itself, does not contain any motor unit. The motion, which is tracked at the single-molecule level, is triggered by intramolecular proton transfer with a corresponding modulation of the potential energy surface. Each molecule moves with 100 percent unidirectionality along an atomically defined straight line. Proof of the motor performing meaningful work is shown by controlled transport of single carbon monoxide molecules. This simplistic concept could form the basis for the controlled bottom-up assembly of nanostructures at the atomic scale.

Probing surface properties of organic molecular layers by scanning tunneling microscopy

In view of the relevance of organic thin layers in many fields, the fundamentals, growth mechanisms, and dynamics of thin organic layers, in particular thiol-based self-assembled monolayers (SAMs) on Au(111) are systematically elaborated. From both theoretical and practical perspectives, dynamical and structural features of the SAMs are of great intrigue. Scanning tunneling microscopy (STM) is a remarkably powerful technique employed in the characterization of SAMs. Numerous research examples of investigation about the structural and dynamical properties of SAMs using STM, sometimes combined with other techniques, are listed in the review. Advanced options to enhance the time resolution of STM are discussed. Additionally, we elaborate on the extremely diverse dynamics of various SAMs, such as phase transitions and structural changes at the molecular level. In brief, the current review is expected to supply a better understanding and novel insights regarding the dynamical events happening in organic SAMs and how to characterize these processes.

Enhancement of Graphene Phonon Excitation by a Chemically Engineered Molecular Resonance

The abstraction of pyrrolic hydrogen from a single phthalocyanine on graphene turns the molecule into a sensitive probe for graphene phonons. The inelastic electron transport measured with a scanning tunneling microscope across the molecular adsorbate and graphene becomes strongly enhanced for a graphene out-of-plane acoustic phonon mode. Supporting density functional and transport calculations elucidate the underlying physical mechanism. A molecular orbital resonance close to the Fermi energy controls the inelastic current while specific phonon modes of graphene are magnified due to their coupling to symmetry-equivalent vibrational quanta of the molecule.

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.

Combining grating-coupled illumination and image recognition for stable and localized optical scanning tunneling microscopy

Combining scanning tunneling microscopy (STM) and optical excitation has been a major objective in STM for the last 30 years to study light-matter interactions on the atomic scale. The combination with modern pulsed laser systems even made it possible to achieve a temporal resolution down to the femtosecond regime. A promising approach toward a truly localized optical excitation is featured by nanofocusing via an optical antenna spatially separated from the tunnel junction. Until now, these experiments have been limited by thermal instabilities introduced by the laser. This paper presents a versatile solution to this problem by actively coupling the laser and STM, bypassing the vibration-isolation without compromising it. We utilize optical image recognition to monitor the position of the tunneling junction and compensate for any movement of the microscope relative to the laser setup with up to 10 Hz by adjusting the beamline. Our setup stabilizes the focus position with high precision (<1 μm) on long timescales (>1 h) and allows for high resolution STM under intense optical excitation with femtosecond pulses.

Hierarchical equations of motion approach for accurate characterization of spin excitations in quantum impurity systems

Recent technological advancement in scanning tunneling microscopes has enabled the measurement of spin-field and spin-spin interactions in single atomic or molecular junctions with an unprecedentedly high resolution. Theoretically, although the fermionic hierarchical equations of motion (HEOM) method has been widely applied to investigate the strongly correlated Kondo states in these junctions, the existence of low-energy spin excitations presents new challenges to numerical simulations. These include the quest for a more accurate and efficient decomposition for the non-Markovian memory of low-temperature environments and a more careful handling of errors caused by the truncation of the hierarchy. In this work, we propose several new algorithms, which significantly enhance the performance of the HEOM method, as exemplified by the calculations on systems involving various types of low-energy spin excitations. Being able to characterize both the Kondo effect and spin excitation accurately, the HEOM method offers a sophisticated and versatile theoretical tool, which is valuable for the understanding and even prediction of the fascinating quantum phenomena explored in cutting-edge experiments.

Tautomerization of single asymmetric oxahemiporphycene molecules on Cu(111)

We have studied 22-oxahemiporphycene molecules by a combination of scanning tunneling microscopy at low temperatures and density functional theory calculations. In contrast to other molecular switches with typically two switching states, these molecules can in principle exist in three different tautomers, due to their asymmetry and three inequivalent binding positions of a hydrogen atom in their macrocycle. Different tautomers are identified from the typical appearance on the surface and tunneling electrons can be used to tautomerize single molecules in a controllable way with the highest rates if the STM tip is placed close to the hydrogen binding positions in the cavity. Characteristic switching processes are explained by the different energy pathways upon adsorption on the surface. Upon applying higher bias voltages, deprotonation occurs instead of tautomerization, which becomes evident in the molecular appearance.

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.

Joule Heating in Single-Molecule Point Contacts Studied by Tip-Enhanced Raman Spectroscopy

Heating and cooling in current-carrying molecular junctions is a crucial issue in molecular electronics. The microscopic mechanism involves complex factors such as energy inputs, molecular properties, electrode materials, and molecule-electrode coupling. To gain an in-depth understanding, it is a desired experiment to assess vibrational population that represents the energy distribution stored within the molecule. Here, we demonstrate the direct observation of vibrational heating in a single C₆₀ molecule by means of tip-enhanced Raman spectroscopy (TERS). The heating of respective vibrational modes is monitored by anti-Stokes Raman scattering in the TERS spectra. The precise control of the gap distance in the single-molecule junction allows us to reveal a qualitatively different heating mechanism in distinct electron transport regimes, namely, the tunneling and single-molecule point contact (SMPC) regimes. Strong Joule heating via inelastic electron-vibration scattering occurs in the SMPC regime, whereas optical heating is predominant in the tunneling regime. The strong Joule heating at the SMPC also leads to a pronounced red shift of the Raman peak position and line width broadening. Furthermore, by examining the SMPC with several types of contact surfaces, we show that the heating efficiency is related to the current density at the SMPC and the vibrational dissipation channels into the electrode.

Nanoscale Heating of an Ultrathin Oxide Film Studied by Tip-Enhanced Raman Spectroscopy

We report on the nanoscale heating mechanism of an ultrathin ZnO film using low-temperature tip-enhanced Raman spectroscopy. Under the resonance condition, intense Stokes and anti-Stokes Raman scattering can be observed for the phonon modes of a two-monolayer (ML) ZnO on an Ag(111) surface, enabling us to monitor local heating at the nanoscale. It is revealed that the local heating originates mainly from inelastic electron tunneling through the electronic resonance when the bias voltage exceeds the conduction band edge of the 2-ML ZnO. When the bias voltage is lower than the conduction band edge, the local heating arises from two different contributions, namely direct optical excitation between the interface state and the conduction band of 2-ML ZnO or injection of photoexcited electrons from an Ag tip into the conduction band. These optical heating processes are promoted by localized surface plasmon excitation. Simultaneous mapping of tip-enhanced Raman spectroscopy and scanning tunneling spectroscopy for 2-ML ZnO including an atomic-scale defect demonstrates visualizing a correlation between the heating efficiency and the local density of states, which further allows us to analyze the local electron-phonon coupling strength with ∼2  nm spatial resolution.

Resonance conditions, detection quality, and single-molecule sensitivity in fluorescence-encoded infrared vibrational spectroscopy

Fluorescence-encoded Infrared (FEIR) spectroscopy is a vibrational spectroscopy technique that has recently demonstrated the capability of single-molecule sensitivity in solution without near-field enhancement. This work explores the practical experimental factors that are required for successful FEIR measurements in both the single-molecule and bulk regimes. We investigate the role of resonance conditions by performing measurements on a series of coumarin fluorophores of varying electronic transition frequencies. To analyze variations in signal strength and signal to background between molecules, we introduce an FEIR brightness metric that normalizes out measurement-specific parameters. We find that the effect of the resonance condition on FEIR brightness can be reasonably well described by the electronic absorption spectrum. We discuss strategies for optimizing detection quality and sensitivity in bulk and single-molecule experiments.

Direct imaging of single-molecule electrochemical reactions in solution

Chemical reactions tend to be conceptualized in terms of individual molecules transforming into products, but are usually observed in experiments that probe the average behaviour of the ensemble. Single-molecule methods move beyond ensemble averages and reveal the statistical distribution of reaction positions, pathways and dynamics^1-3. This has been shown with optical traps and scanning probe microscopy manipulating and observing individual reactions at defined locations with high spatial resolution^4,5, and with modern optical methods using ultrasensitive photodetectors^3,6,7 that enable high-throughput single-molecule measurements. However, effective probing of single-molecule solution chemistry remains challenging. Here we demonstrate optical imaging of single-molecule electrochemical reactions⁷ in aqueous solution and its use for super-resolution microscopy. The method utilizes a chemiluminescent reaction involving a ruthenium complex electrochemically generated at an electrode⁸, which ensures minimal background signal. This allows us to directly capture single photons of the electrochemiluminescence of individual reactions, and to develop super-resolved electrochemiluminescence microscopy for imaging the adhesion dynamics of live cells with high spatiotemporal resolution. We anticipate that our method will advance the fundamental understanding of electrochemical reactions and prove useful for bioassays and cell-imaging applications.

Unraveling current-induced dissociation mechanisms in single-molecule junctions

Understanding current-induced bond rupture in single-molecule junctions is both of fundamental interest and a prerequisite for the design of molecular junctions, which are stable at higher-bias voltages. In this work, we use a fully quantum mechanical method based on the hierarchical quantum master equation approach to analyze the dissociation mechanisms in molecular junctions. Considering a wide range of transport regimes, from off-resonant to resonant, non-adiabatic to adiabatic transport, and weak to strong vibronic coupling, our systematic study identifies three dissociation mechanisms. In the weak and intermediate vibronic coupling regime, the dominant dissociation mechanism is stepwise vibrational ladder climbing. For strong vibronic coupling, dissociation is induced via multi-quantum vibrational excitations triggered either by a single electronic transition at high bias voltages or by multiple electronic transitions at low biases. Furthermore, the influence of vibrational relaxation on the dissociation dynamics is analyzed and strategies for improving the stability of molecular junctions are discussed.

Electron stimulated desorption of vanadyl-groups from vanadium oxide thin films on Ru(0001) probed with STM

Low-temperature scanning tunnelling microscopy (STM) is employed to study electron-stimulated desorption of vanadyl groups from an ultrathin vanadium oxide film. The vanadia patches are prepared by reactive vapour deposition of V onto a Ru(0001) surface and comprise a highly ordered network of six and twelve membered V-O rings, some of them terminated by upright V[double bond, length as m-dash]O groups. The vanadyl units can be desorbed via electron injection from the STM tip in a reliable fashion. From hundreds of individual experiments, desorption rates are determined as a function of bias voltage and tunnelling current. Data analysis reveals a distinct threshold behaviour with bias onsets at +3.3 V and -2.6 V for positive and negative polarity, respectively. The desorption rate varies quadratically (cubically) with the tunnelling current at positive (negative) sample bias, indicating that V[double bond, length as m-dash]O desorption is a many-electron process. Based on our findings, a mechanism for desorption is proposed that includes resonant tunnelling into anti-bonding or out of bonding orbitals, followed by vibrational ladder climbing in the binding potential of the V[double bond, length as m-dash]O ad-system. The underlying electronic states can be identified directly in the STM conductance spectra taken on the oxide surface.

Superconducting Scanning Tunneling Microscope Tip to Reveal Sub-millielectronvolt Magnetic Energy Variations on Surfaces

Combining the complex ordering ability of molecules with their local magnetic properties is a little-explored technique to tailor spin structures on surfaces. However, revealing the molecular geometry can be demanding. Nickelocene (Nc) molecules present a large spin-flip excitation leading to clear changes of conductance at the excitation-threshold bias. Using a superconducting tip, we have the energy resolution to detect small shifts of the Nc spin-flip excitation thresholds, permitting us to reveal the different individual environments of Nc molecules in an ordered layer. This knowledge allows us to reveal the adsorption configuration of a complex molecular structure formed by Nc molecules in different orientations and positions. As a consequence, we infer that Nc layers present a strong noncollinear magnetic-moment arrangement.

On-Surface Synthesis and Molecular Engineering of Carbon-Based Nanoarchitectures

On-surface synthesis via covalent coupling of adsorbed precursor molecules on metal surfaces has emerged as a promising strategy for the design and fabrication of novel organic nanoarchitectures with unique properties and potential applications in nanoelectronics, optoelectronics, spintronics, catalysis, etc. Surface-chemistry-driven molecular engineering (i.e., bond cleavage, linkage, and rearrangement) by means of thermal activation, light irradiation, and tip manipulation plays critical roles in various on-surface synthetic processes, as exemplified by the work from the Ernst group in a prior issue of ACS Nano. In this Perspective, we highlight recent advances in and discuss the outlook for on-surface syntheses and molecular engineering of carbon-based nanoarchitectures.

Raman Detection of Bond Breaking and Making of a Chemisorbed Up-Standing Single Molecule at Single-Bond Level

Probing bond breaking and making as well as related structural changes at the single-molecule level is of paramount importance for understanding the mechanism of chemical reactions. In this work, we report in situ tracking of bond breaking and making of an up-standing melamine molecule chemisorbed on Cu(100) by subnanometer resolved tip-enhanced Raman spectroscopy (TERS). We demonstrate a vertical detection depth of about 4 Å with spectral sensitivity at the single chemical-bond level, which allows us not only to justify the up-standing configuration involving a dehydrogenation process at the bottom upon chemisorption, but also to specify the breaking of top N-H bonds and the transformation to its tautomer during photon-induced hydrogen transfer reactions. Our results indicate the chemical and structural sensitivity of TERS for single-molecule recognition beyond flat-lying planar molecules, providing new opportunities for probing the microscopic mechanism of molecular adsorption and surface reactions at the chemical-bond level.

Lanthanide-Based Nanosensors: Refining Nanoparticle Responsiveness for Single Particle Imaging of Stimuli

Lanthanide nanoparticles (LNPs) are promising sensors of chemical, mechanical, and temperature changes; they combine the narrow-spectral emission and long-lived excited states of individual lanthanide ions with the high spatial resolution and controlled energy transfer of nanocrystalline architectures. Despite considerable progress in optimizing LNP brightness and responsiveness for dynamic sensing, detection of stimuli with a spatial resolution approaching that of individual nanoparticles remains an outstanding challenge. Here, we highlight the existing capabilities and outstanding challenges of LNP sensors, en-route to nanometer-scale, single particle sensor resolution. First, we summarize LNP sensor read-outs, including changes in emission wavelength, lifetime, intensity, and spectral ratiometric values that arise from modified energy transfer networks within nanoparticles. Then, we describe the origins of LNP sensor imprecision, including sensitivity to competing conditions, interparticle heterogeneities, such as the concentration and distribution of dopant ions, and measurement noise. Motivated by these sources of signal variance, we describe synthesis characterization feedback loops to inform and improve sensor precision, and introduce noise-equivalent sensitivity as a figure of merit of LNP sensors. Finally, we project the magnitudes of chemical and pressure stimulus resolution achievable with single LNPs at nanoscale resolution. Our perspective provides a roadmap for translating ensemble LNP sensing capabilities to the single particle level, enabling nanometer-scale sensing in biology, medicine, and sustainability.

The Expanding Frontiers of Tip-Enhanced Raman Spectroscopy

Fundamental understanding of chemistry and physical properties at the nanoscale enables the rational design of interface-based systems. Surface interactions underlie numerous technologies ranging from catalysis to organic thin films to biological systems. Since surface environments are especially prone to heterogeneity, it becomes crucial to characterize these systems with spatial resolution sufficient to localize individual active sites or defects. Spectroscopy presents as a powerful means to understand these interactions, but typical light-based techniques lack sufficient spatial resolution. This review describes the growing number of applications for the nanoscale spectroscopic technique, tip-enhanced Raman spectroscopy (TERS), with a focus on developments in areas that involve measurements in new environmental conditions, such as liquid, electrochemical, and ultrahigh vacuum. The expansion into unique environments enables the ability to spectroscopically define chemistry at the spatial limit. Through the confinement and enhancement of light at the apex of a plasmonic scanning probe microscopy tip, TERS is able to yield vibrational fingerprint information of molecules and materials with nanoscale resolution, providing insight into highly localized chemical effects.

Binding Behavior of Carbonmonoxide to Gold Atoms on Ag(001)

The adsorption behavior of single CO molecules at 4 K bound to Au adatoms on a Ag(001) metal surface is studied with scanning tunneling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). In contrast to earlier observations two different binding configurations are observed—one on top of a Au adatom and the other one adsorbed laterally to Au on Ag(001). Moreover, IETS reveals different low-energy vibrational energies for the two binding sites as compared to the one for a single CO molecule bound to Ag(001). Density functional theory (DFT) calculations of the adsorption energies, the diffusion barriers, and the vibrational frequencies of the CO molecule on the different binding sites rationalize the experimental findings.

Multifaceted aspects of charge transfer

Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.

Innovative optofluidics and microscopy-based rapid analysis of pathogens

The timely knowledge and prescription of the most suitable antibiotic to treat bacterial infections is critical for the recovery of patients battling life-threatening bacterial infections. Unfortunately, current standard-of-care approaches relies on the empiric prescription of an antibiotic, as determination of the most effective antibiotic requires multiple time-consuming steps. These steps often include culturing of the bacterium responsible for infection and subsequent antibiotic susceptibility testing. Here we introduce an optofluidic technology that allows us to capture bacterial cells efficiently and rapidly from different biological samples and use the captured cells for rapid antibiotic selection thereby bypassing the need to culture the bacterium.

Optical scanning tunneling microscopy based chemical imaging and spectroscopy

Through coupling optical processes with the scanning tunneling microscope (STM), single-molecule chemistry and physics have been investigated at the ultimate spatial and temporal limit. Electrons and photons can be used to drive interactions and reactions in chemical systems and simultaneously probe their characteristics and consequences. In this review we introduce and review methods to couple optical imaging and spectroscopy with scanning tunneling microscopy. The integration of the STM and optical spectroscopy provides new insights into individual molecular adsorbates, surface-supported molecular assemblies, and two-dimensional materials with subnanoscale resolution, enabling the fundamental study of chemistry at the spatial and temporal limit. The inelastic scattering of photons by molecules and materials, that results in unique and sensitive vibrational fingerprints, will be considered with tip-enhanced Raman spectroscopy. STM-induced luminescence examines the intrinsic luminescence of organic adsorbates and their energy transfer and charge transfer processes with their surroundings. We also provide a survey of recent efforts to probe the dynamics of optical excitation at the molecular level with scanning tunneling microscopy in the context of light-induced photophysical and photochemical transformations.

Rigid Double-Stranded DNA Linkers for Single Molecule Enzyme-Drug Interaction Measurements Using Molecular Recognition Force Spectroscopy

Single-molecule studies can reveal the distribution of states and interactions between ligand-enzyme complexes not accessible for most studies that measure a large ensemble average response of many molecules. Furthermore, in some biological applications, the information regarding the outliers, not the average of measured properties, can be more important. The high spatial and force resolution provided by atomic force microscopy (AFM) under physiological conditions has been utilized in this study to quantify the force-distance relations of enzyme-drug interactions. Different immobilization techniques of the protein to a surface and the drug to AFM tip were quantitatively compared to improve the accuracy and precision of the measurement. Protein that is directly bound to the surface, forming a monolayer, was compared to enzyme molecules bound to the surface with rigid double-stranded (ds) DNA spacers. These surfaces immobilization techniques were studied with the drug bound directly to the AFM tip and drug bound via flexible poly(ethylene glycol) and rigid dsDNA linkers. The activity of the enzyme was found to be not significantly altered by immobilization methods relative to its activity in solution. The findings indicate that the approach for studying drug-enzyme interaction based on rigid dsDNA linker on the surface and either flexible or rigid linker on the tip affords straightforward, highly specific, reproducible, and accurate force measurements with a potential for single-molecule level studies. The method could facilitate in-depth examination of a broad spectrum of biological targets and potential drugs.

Excited-State Imaging of Single Particles on the Subnanometer Scale

At the intersection of spectroscopy and microscopy lie techniques that are capable of providing subnanometer imaging of excited states of individual molecules or nanoparticles. Such approaches are particularly important for imaging macromolecules or nanoparticles large enough to have a high probability of containing a defect. These inevitable defects often control properties and function despite an otherwise ideal structure. We discuss real-space imaging techniques such as using scanning tunneling microscopy tips to enhance optical measurements and electron energy-loss spectroscopy in a scanning transmission electron microscope, which is based on focused electron beams to obtain high-resolution spatial information on excited states. The outlook for these methods is bright, as they will provide critical information for the characterization and improvement of energy-switching, electron-switching, and energy-harvesting materials.

Vibrational Excitation Mechanism in Tunneling Spectroscopy beyond the Franck-Condon Model

Vibronic spectra of molecules are typically described within the Franck-Condon model. Here, we show that highly resolved vibronic spectra of large organic molecules on a single layer of MoS_{2} on Au(111) show spatial variations in their intensities, which cannot be captured within this picture. We explain that vibrationally mediated perturbations of the molecular wave functions need to be included into the Franck-Condon model. Our simple model calculations reproduce the experimental spectra at arbitrary position of the scanning tunneling microscope's tip over the molecule in great detail.

Inelastic Electron Tunneling in 2H-Ta_{x}Nb_{1-x}Se_{2} Evidenced by Scanning Tunneling Spectroscopy

We report a detailed study of tunneling spectra measured on 2H-Ta_{x}Nb_{1-x}Se_{2} (x=0∼0.1) single crystals using a low-temperature scanning tunneling microscope. The prominent gaplike feature, which has not been understood for a long time, was found to be accompanied by some "in-gap" fine structures. By investigating the second-derivative spectra and their temperature and magnetic field dependencies, we were able to prove that inelastic electron tunneling is the origin of these features and obtain the Eliashberg function of 2H-Ta_{x}Nb_{1-x}Se_{2} at an atomic scale, providing a potential way to study the local Eliashberg function and the phonon spectra of the related transition-metal dichalcogenides.

Energy, Particle, and Photon Fluxes in Molecular Junctions

Electroluminescence from a current-carrying molecular junction at steady state is simulated. (Charge) particle conservation and energy conservation are satisfied by a perturbative expansion in the radiation/matter coupling. Our approach makes it possible to adopt standard tools of traditional (equilibrium) spectroscopy to study signals from open systems such as molecular junctions. The nonperturbative analysis of spontaneous light emission signals coincides with the perturbative approach for weak molecule-field coupling.

Spontaneous Light Emission from Molecular Junctions: Theoretical Analysis of Upconversion Signal

Spontaneous light emission from a current-carrying molecular junction is analyzed. There are two leading processes, fluorescence and electroluminescence, as defined using Liouville space diagrams within the perturbative method, that contribute to the light emission from junctions. This allows us to identify a general mechanism that explains the origin of the so-called upconversion electroluminescence (UCEL) signal, which has been observed in a variety of molecular junctions [Umera et al. Chem. Phys. Lett. 2007, 448, 232; Dong et al. Nat. Photonics 2010, 4, 50]. Here, we show that a double-peak signal, one at energy less than the applied bias and the other at higher energy (UCEL), is generated due to overlap between two processes: one is electron transfer to create the required excited state, and the other is radiative relaxation of the excited state. The lifetimes induced by the lead interactions play a crucial role in determining the required overlap between these processes. Our analysis shows that, unlike the higher-energy signal, the lower-energy peak is sensitive to the applied bias and does not correspond to any optical resonance in the junction. The signal at higher energy is enhanced as the temperature is increased. We demonstrate our findings using nonperturbative analytic results for a model system.

Radio frequency filter for an enhanced resolution of inelastic electron tunneling spectroscopy in a combined scanning tunneling- and atomic force microscope

The combination of inelastic electron tunneling spectroscopy (IETS), also used for IET spectrum based on scanning tunneling microscopy with atomic force microscopy (AFM) enables us to measure the vibrational energies of a single molecule along with the force exerted by the tip of a microscope, which deepens our understanding on the interaction between the tip and the molecule on a surface. The resolution of IETS is a crucial factor in determining the vibrational energies of a molecule. However, radio frequency (RF) noise from the environment significantly deteriorates the resolution. We introduce an RF noise filtering technique, which enables high resolution IETS while maintaining uncompromised AFM performance, demonstrated by vibrational measurements of a CO molecule on a copper surface.

Magneto-transport properties of a single molecular transistor in the presence of electron-electron and electron-phonon interactions and quantum dissipation

A single molecular transistor is considered in the presence of electron-electron interaction, electron-phonon interaction, an external magnetic field and dissipation. The quantum transport properties of the system are investigated using the Anderson-Holstein Hamiltonian together with the Caldeira-Leggett model that takes care of the damping effect. The phonons are first removed from the theory by averaging the Hamiltonian with respect to a coherent phonon state and the resultant electronic Hamiltonian is finally solved with the help of the Green function technique due to Keldysh. The spectral function, spin-polarized current densities, differential conductance and spin polarization current are determined.

Orientation-specific switching of inelastic electron tunneling in an oxygen-pyridine complex adsorbed onto an Ag(110) surface

Here, we report the development of a molecular rotary switch (a "stator-rotor" consisting of a single oxygen molecule as a stator and a single pyridine molecule as a rotor) on a silver surface. The pyridine molecule was bonded to the oxygen molecule and was found to rotate to enable "ON" or "OFF" vibrational conductance through the oxygen molecule. Four stable sites around the oxygen molecule were observed, and vibration conductance turned on and off depending on the site at which the pyridine molecule bonded. The spatially resolved mapping of the vibrational change revealed two locations of maximal vibration intensity, separated by ∼3 Å. These positions acted as two conducting channels. The two distinct vibrational energy levels were associated with the switching process. Adsorption-induced electron transfer between the silver layers and the molecules enhanced the local interactions between the molecules. The two vibration modes were excited by resonant tunneling despite substantial interactions between the molecules, which resulted in a decrease in tunneling conductance. An independent pathway exists for the vibrational excitation process by tunneling electrons and intermolecular interactions.

Unraveling the molecular conformations of a single ruthenium complex adsorbed on the Ag(111) surface by calculations

The tris(dibenzoylmethanato)ruthenium (Ru(dbm)3) molecule has recently been characterized by scanning tunneling microscopy (STM) experiments upon adsorption on Ag(111). The adsorbed Ru(dbm)3 molecule shows two conformations with respect to the [11[combining macron]0] direction of the substrate, one with a three-lobed feature and the other one with a bi-lobed structure. For each of these structures, the molecule can take two geometries (states). Molecular mechanics calculations in a semi-empirical framework and STM calculated images reveal that these states on the substrate originate from the enantiomer of the Ru(dbm)3 molecule in the case of three-lobed structure and from the rotation of the two phenyls in the top dbm moities for the bi-lobed form.

Force-conductance spectroscopy of a single-molecule reaction

We demonstrate how simultaneous measurements of conductance and force can be used to monitor the step-by-step progress of a mechanically-activated cis-to-trans isomerization single-molecule reaction, including events that cannot be distinguished using force or conductance alone. To do so, we simulated the force-conductance profile of cyclopropane oligomers connected to graphene nanoribbon electrodes that undergo a cis-to-trans isomerization during mechanical elongation. This was done using a combination of classical molecular dynamics simulation of the pulling using a reactive force field, and Landauer transport computations of the conductance with nonequilibrium Green's function methods. The isomerization events can be distinguished in both force and conductance profiles. However, the conductance profile during the mechanical elongation distinguishes between reaction intermediates that cannot be resolved using force. In turn, the force signals non-reactive deformations in the molecular backbone which are not visible in the conductance profile. These observations are shown to be robust to the choice of electrode and Hamiltonian model. The computations exemplify the potential of the integration of covalent mechanochemistry with molecular conductance to investigate chemical reactivity at the single-entity limit.