How Precisely Can Individual Molecules Be Analyzed? A Case Study on Locally Quantifying Forces and Energies Using Scanning Probe Microscopy

Recent advances in scanning probe microscopy methodology have enabled the measurement of tip-sample interactions with picometer accuracy in all three spatial dimensions, thereby providing a detailed site-specific and distance-dependent picture of the related properties. This paper explores the degree of detail and accuracy that can be achieved in locally quantifying probe-molecule interaction forces and energies for adsorbed molecules. Toward this end, cobalt phthalocyanine (CoPc), a promising CO2 reduction catalyst, was studied on Ag(111) as a model system using low-temperature, ultrahigh vacuum noncontact atomic force microscopy. Data were recorded as a function of distance from the surface, from which detailed three-dimensional maps of the molecule's interaction with the tip for normal and lateral forces as well as the tip-molecule interaction potential were constructed. The data were collected with a CO molecule at the tip apex, which enabled a detailed visualization of the atomic structure. Determination of the tip-substrate interaction as a function of distance allowed isolation of the molecule-tip interactions; when analyzing these in terms of a Lennard-Jones-type potential, the atomically resolved equilibrium interaction energies between the CO tethered to the tip and the CoPc molecule could be recovered. Interaction energies peaked at less than 160 meV, indicating a physisorption interaction. As expected, the interaction was weakest at the aromatic hydrogens around the periphery of the molecule and strongest surrounding the metal center. The interaction, however, did not peak directly above the Co atom but rather in pockets surrounding it.

Molecular sensitised probe for amino acid recognition within peptide sequences

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.

Ultrafast Dynamics Revealed with Time-Resolved Scanning Tunneling Microscopy: A Review

A scanning tunneling microscope (STM) capable of performing pump-probe spectroscopy integrates unmatched atomic-scale resolution with high temporal resolution. In recent years, the union of electronic, terahertz, or visible/near-infrared pulses with STM has contributed to our understanding of the atomic-scale processes that happen between milliseconds and attoseconds. This time-resolved STM (TR-STM) technique is evolving into an unparalleled approach for exploring the ultrafast nuclear, electronic, or spin dynamics of molecules, low-dimensional structures, and material surfaces. Here, we review the recent advancements in TR-STM; survey its application in measuring the dynamics of three distinct systems, nucleus, electron, and spin; and report the studies on these transient processes in a series of materials. Besides the discussion on state-of-the-art techniques, we also highlight several emerging research topics about the ultrafast processes in nanoscale objects where we anticipate that the TR-STM can help broaden our knowledge.

Orbital and Skeletal Structure of a Single Molecule on a Metal Surface Unveiled by Scanning Tunneling Microscopy

Atomic-scale spatial characteristics of a phthalocyanine orbital and skeleton are obtained on a metal surface with a scanning tunneling microscope and a CO-functionalized tip. Intriguingly, the high spatial resolution of the intramolecular electronic patterns is achieved without resonant tunneling into the orbital and despite the hybridization of the molecule with the reactive Cu substrate. The resolution can be fine-tuned by the tip-molecule distance, which controls the p-wave and s-wave contribution of the molecular probe to the imaging process. The detailed structure is deployed to minutely track the translation of the molecule in a reversible interconversion of rotational variants and to quantify relaxations of the adsorption geometry. Entering into the Pauli repulsion imaging mode, the intramolecular contrast loses its orbital character and reflects the molecular skeleton instead. The assignment of pyrrolic-hydrogen sites becomes possible, which in the orbital patterns remains elusive.

Flexible plasmonic nanocavities: a universal platform for the identification of molecular orientations

The molecular orientation provides fundamental images to understand molecular behaviors in chemistry. Herein, we propose and demonstrate sandwich plasmonic nanocavities as a surface-selection ruler to illustrate the molecular orientations by surface-enhanced Raman spectroscopy (SERS). The field vector in the plasmonic nanocavity presents a transverse spinning feature under specific excitations, allowing the facile modulation of the field polarizations to selectively amplify the Raman modes of the target molecules. It does not require the knowledge of the Raman spectrum of a bare molecule as a standard and thus can be extended as a universal ruler for the identification of molecular orientations. We investigated the most widely used Raman probe, Rhodamine 6G (R6G) on the Au surface and tried to clarify the arguments about its orientations from our perspectives. The experimental results suggest concentration-dependent adsorption configurations of R6G: it adsorbs on Au primarily via an ethylamine group with the xanthene ring lying flatly on the metal surface at low concentrations, and the molecular orientation gradually changes from "flat" to "upright" with the increase of molecular concentrations.

Observation of electron orbital signatures of single atoms within metal-phthalocyanines using atomic force microscopy

Resolving the electronic structure of a single atom within a molecule is of fundamental importance for understanding and predicting chemical and physical properties of functional molecules such as molecular catalysts. However, the observation of the orbital signature of an individual atom is challenging. We report here the direct identification of two adjacent transition-metal atoms, Fe and Co, within phthalocyanine molecules using high-resolution noncontact atomic force microscopy (HR-AFM). HR-AFM imaging reveals that the Co atom is brighter and presents four distinct lobes on the horizontal plane whereas the Fe atom displays a "square" morphology. Pico-force spectroscopy measurements show a larger repulsion force of about 5 pN on the tip exerted by Co in comparison to Fe. Our combined experimental and theoretical results demonstrate that both the distinguishable features in AFM images and the variation in the measured forces arise from Co's higher electron orbital occupation above the molecular plane. The ability to directly observe orbital signatures using HR-AFM should provide a promising approach to characterizing the electronic structure of an individual atom in a molecular species and to understand mechanisms of certain chemical reactions.

Atomic-Scale Rectification and Inelastic Electron Tunneling Spectromicroscopy

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

Unravelling the robustness of magnetic anisotropy of a nickelocene molecule in different environments: a first-principles-based study

Recent scanning tunneling spectroscopy with single metallocene molecule-functionalized tips have proved to be a powerful tool to probe and control individual spins and spin-spin exchange interactions due to the robustness of the magnetic properties of the metallocene molecule in different surroundings. However, accurate prediction of such robustness at a first-principles-based level by the conventional density functional theory (DFT) has remained challenging. In this paper, we have performed a detailed investigation of the evolution of electronic and magnetic properties of a nickelocene molecule (NiCp₂) in different environments, i.e., free-standing, adsorbed on Cu(100) and as a functionalized tip apex. Using an embedding method, which combines DFT and the complete active space self-consistent field (CASSCF) method recently developed, we demonstrate that the nickelocene molecule almost preserves its spin and magnetic anisotropy upon adsorption on Cu(100), and also in the position of the tip apex. In particular, the cyclic π* orbital of the Cp rings could hybridize with the singly occupied d_π orbitals of the Ni center of the molecule, protecting these orbitals from external states. Hence the molecular spin maintains S = 1, the same as in the free-standing case, and its magnetic anisotropy is also robust with energies of 3.56, 3.34, and 3.51 meV in free-standing, adsorbed on Cu(100), and functionalized tip apex states, respectively, in good agreement with previous theoretical and experimental results. This work thus provides a first-principles-based understanding of the relevant experiments. Such agreement between theoretical simulations and experimental measurements highlights the potential usefulness of the method for investigating the local electronic and spin states of organometallic molecule-surface composite systems.

Direct transformation of n-alkane into all-trans conjugated polyene via cascade dehydrogenation

Selective C(sp³) −H activation is of fundamental importance in processing alkane feedstocks to produce high-value-added chemical products. By virtue of an on-surface synthesis strategy, we report selective cascade dehydrogenation of n-alkane molecules under surface constraints, which yields monodispersed all-trans conjugated polyenes with unprecedented length controllability. We are also able to demonstrate the generality of this concept for alkyl-substituted molecules with programmable lengths and diverse functionalities, and more importantly its promising potential in molecular wiring.

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.

Atomic Force Extrema Induced by the Bending of a CO-Functionalized Probe

The control and observation of reactants forming a chemical bond at the single-molecule level is a long-standing challenge in quantum physics and chemistry. Using a single CO molecule adsorbed at the apex of an atomic force microscope tip together with a Cu(111) surface, bending of the molecular probe is induced by torques due to van der Waals attraction and Pauli repulsion. As a result, the vertical force between CO and Cu(111) exhibits a characteristic dip-hump evolution with the molecule-surface separation, which depends sensitively on the initial tilt angle the CO axis encloses with the surface normal. The experimental force data are reproduced by model calculations that consider the CO deflection in a harmonic potential and the molecular orientation in the Pauli repulsion term of the Lennard-Jones potential. The presented findings shed new light on vertical-force extrema that can occur in scanning probe experiments with functionalized tips.

Gold Chain Formation via Local Lifting of Surface Reconstruction by Hot Electron Injection on H2(D2)/Au(111)

The hexagonal close packed surface of gold shows a 22 × 3 "herringbone" surface reconstruction which makes it unique among the (111) surfaces of all metals. This long-range energetically favored dislocation pattern appears in response to the strong tensile stress that would be present on the unreconstructed surface. Adsorption of molecular and atomic species can be used to tune this surface stress and lift the herringbone reconstruction. Here we show that herringbone reconstruction can be controllably lifted in ultrahigh vacuum at cryogenic temperatures by precise hot electron injection in the presence of hydrogen molecules. We use the sharp tip of a scanning tunneling microscope (STM) for charge carrier injection and characterization of the resulting chain nanostructures. By comparing STM images, rotational spectromicroscopy and ab initio calculations, we show that formation of gold atomic chains is associated with release of gold atoms from the surface, lifting of the reconstruction, dissociation of H₂ molecules, and formation of surface hydrides. Gold hydrides grow in a zipper-like mechanism forming chains along the [11̅0] directions of the Au(111) surface and can be manipulated by further electron injection. Finally, we demonstrate that Au(111) terraces can be transformed with nearly perfect terrace selectivity over distances of hundreds of nanometers.

The Kondo Effect of a Molecular Tip As a Magnetic Sensor

A single molecule offers to tailor and control the probing capability of a scanning tunneling microscope when placed on the tip. With the help of first-principles calculations, we show that on-tip spin sensitivity is possible through the Kondo ground state of a spin S = 1/2 cobaltocene molecule. When attached to the tip apex, we observe a reproducible Kondo resonance, which splits apart upon tuning the exchange coupling of cobaltocene to an iron atom on the surface. The spin-split Kondo resonance provides quantitative information on the exchange field and on the spin polarization of the iron atom. We also demonstrate that molecular vibrations cause the emergence of Kondo side peaks, which, unlike the Kondo resonance, are sensitive to cobaltocene adsorption.

Surface-controlled reversal of the selectivity of halogen bonds

Intermolecular halogen bonds are ideally suited for designing new molecular assemblies because of their strong directionality and the possibility of tuning the interactions by using different types of halogens or molecular moieties. Due to these unique properties of the halogen bonds, numerous areas of application have recently been identified and are still emerging. Here, we present an approach for controlling the 2D self-assembly process of organic molecules by adsorption to reactive vs. inert metal surfaces. Therewith, the order of halogen bond strengths that is known from gas phase or liquids can be reversed. Our approach relies on adjusting the molecular charge distribution, i.e., the σ-hole, by molecule-substrate interactions. The polarizability of the halogen and the reactiveness of the metal substrate are serving as control parameters. Our results establish the surface as a control knob for tuning molecular assemblies by reversing the selectivity of bonding sites, which is interesting for future applications.

Imaging strain-localized excitons in nanoscale bubbles of monolayer WSe2 at room temperature

In monolayer transition-metal dichalcogenides, localized strain can be used to design nanoarrays of single photon sources. Despite strong empirical correlation, the nanoscale interplay between excitons and local crystalline structure that gives rise to these quantum emitters is poorly understood. Here, we combine room-temperature nano-optical imaging and spectroscopic analysis of excitons in nanobubbles of monolayer WSe₂ with atomistic models to study how strain induces nanoscale confinement potentials and localized exciton states. The imaging of nanobubbles in monolayers with low defect concentrations reveals localized excitons on length scales of around 10 nm at multiple sites around the periphery of individual nanobubbles, in stark contrast to predictions of continuum models of strain. These results agree with theoretical confinement potentials atomistically derived from the measured topographies of nanobubbles. Our results provide experimental and theoretical insights into strain-induced exciton localization on length scales commensurate with exciton size, realizing key nanoscale structure-property information on quantum emitters in monolayer WSe₂.

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.

An Endergonic Synthesis of Single Sondheimer-Wong Diyne by Local Probe Chemistry

Recent advances in scanning probe microscopy on surface enable not only direct observation of molecular structures but also local probe reactions, in which unstable short-lived products have been synthesized and analyzed. Now, an endergonic reaction to synthesize a single Sondheimer-Wong diyne from 6,13-dibromopentaleno[1,2-b:4,5-b']dinaphthalene by local probe chemistry on a ultra-thin film of NaCl formed on a Cu(111) surface at 4.3 K is presented. The structures of the precursor, two intermediates, and the final product were directly identified by the differential conductance imaging with a CO functionalized tip. DFT calculations revealed that the multiple-step reaction, being endergonic overall, is facilitated by temporal charging and discharging of the molecule placed in the nanometric junction between the Cu tip and the Cu substrate underneath the ultra-thin NaCl film. This local probe reaction expands possibilities to synthesize nanocarbon materials in a bottom-up manner.

Probing the intermolecular coupled vibrations in a water cluster with inelastic electron tunneling spectroscopy

The hydrogen-bonding networks of water have strong intra- and intermolecular vibrational coupling which influences the energy dissipation and proton transfer in water. Disentangling and quantitative characterization of different coupling effects in water at a single-molecular level still remains a great challenge. Using tip-enhanced inelastic electron tunneling spectroscopy (IETS) based on low-temperature scanning tunneling microscopy, we report the direct quantitative assessment of the intermolecular coupling constants of the OH-stretch vibrational bands of an isolated water tetramer adsorbed on a Au(111)-supported NaCl(001) bilayer film. This is achieved by distinguishing various coupled modes of the H-bonded O-H stretching vibrations through tip-height dependent IET spectra. In contrast, such vibrational coupling is negligible in the half-deuterated water tetramer owing to the large energy mismatch between the OH and OD stretching modes. Not only do these findings advance our understanding on the effects of local environment on the intermolecular vibrational coupling in water, but also open up a new route for vibrational spectroscopic studies of extended H-bonded network at the single-molecular level.

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.

The theory of scanning quantum dot microscopy

Electrostatic forces are among the most common interactions in nature and omnipresent at the nanoscale. Scanning probe methods represent a formidable approach to study these interactions locally. The lateral resolution of such images is, however, often limited as they are based on measuring the force (gradient) due to the entire tip interacting with the entire surface. Recently, we developed scanning quantum dot microscopy (SQDM), a new technique for the imaging and quantification of surface potentials which is based on the gating of a nanometer-size tip-attached quantum dot by the local surface potential and the detection of charge state changes via non-contact atomic force microscopy. Here, we present a rigorous formalism in the framework of which SQDM can be understood and interpreted quantitatively. In particular, we present a general theory of SQDM based on the classical boundary value problem of electrostatics, which is applicable to the full range of sample properties (conductive versus insulating, nanostructured versus homogeneously covered). We elaborate the general theory into a formalism suited for the quantitative analysis of images of nanostructured but predominantly flat and conductive samples.

Probing surface mediated configurations of nonplanar regioisomeric adsorbates using ultrahigh vacuum tip-enhanced Raman spectroscopy

The ability to directly probe the adsorption configurations of organic regioisomeric molecules, specifically nonplanar isomers, on well-defined substrates holds promise to revolutionize fields dependent on nanoscale processes, such as catalysis, surface science, nanotechnology and modern day electronic applications. Herein, the adsorption configurations and surface sensitive interactions of two nonplanar regioisomer, trans- and cis-tetrakispentafluorophenylporphodilactone (trans- and cis-H₂F₂₀TPPDL), molecules on (100) surfaces of Ag, Cu and Au were studied and investigated using high resolution scanning tunneling microscopy (STM), combined with ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS). Depending on molecule-substrate interactions, similar "phenyl-up" configurations were observed for these molecules on Ag(100) and Au(100), while a "phenyl-flat" configuration was discovered on a Cu(100) surface. With the help of surface selection rules of TERS, we explain the spectral discrepancies recorded on the Ag and Cu substrate. Furthermore, the intermolecular interactions were addressed using STM analysis on these surfaces after the configurations were determined by TERS. This study sheds light on the distinct configurations of regioisomeric porphodilactone systems (at interfaces) for near-infrared (NIR) photosensitizers and molecular electronics in the near future.

Visually constructing the chemical structure of a single molecule by scanning Raman picoscopy

The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial resolution, it is anticipated that full vibrational imaging of a molecule could be achieved to reveal molecular structural details. Here we demonstrate full Raman images of individual vibrational modes at the ångström level for a single Mg-porphine molecule, revealing distinct characteristics of each vibrational mode in real space. Furthermore, by exploiting the underlying interference effect and Raman fingerprint database, we propose a new methodology for structural determination, which we have called ‘scanning Raman picoscopy’, to show how such ultrahigh-resolution spectromicroscopic vibrational images can be used to visually assemble the chemical structure of a single molecule through a simple Lego-like building process.

Borophene-graphene heterostructures

Integration of dissimilar two-dimensional (2D) materials is essential for nanoelectronic applications. Compared to vertical stacking, covalent lateral stitching requires bottom-up synthesis, resulting in rare realizations of 2D lateral heterostructures. Because of its polymorphism and diverse bonding geometries, borophene is a promising candidate for 2D heterostructures, although suitable synthesis conditions have not yet been demonstrated. Here, we report lateral and vertical integration of borophene with graphene. Topographic and spatially resolved spectroscopic measurements reveal nearly atomically sharp lateral interfaces despite imperfect crystallographic lattice and symmetry matching. In addition, boron intercalation under graphene results in rotationally commensurate vertical heterostructures. The rich bonding configurations of boron suggest that borophene can be integrated into a diverse range of 2D heterostructures.

Ion-Selective, Atom-Resolved Imaging of a 2D Cu2N Insulator: Field and Current Driven Tip-Enhanced Raman Spectromicroscopy Using a Molecule-Terminated Tip

Tip-enhanced Raman scattering (TERS) with a cobalt tetraphenylporphyrin (CoTPP)- terminated silver tip is used to obtain ion-selective, atomically resolved images of an insulating Cu₂N monolayer grown on Cu(100). Ion selective images are obtained through vibrational frequency shift maps using CoTPP vibrations with oppositely signed Stark tuning rates (STR). The images allow a quantitative analysis of the electrostatic field of the ionic lattice using in situ calibrated STRs. Both intensity and Stark shift maps yield atomically resolved images in the tunneling regime of plasmons. We show that the CoTPP is bonded to the Ag tip through its central Co atom, whereby TERS taps into intramolecular currents and polarizations. The bias dependence of vibrational line intensities shows diode-like response with opposite polarity for current carrying modes of opposite polarization phase. The phase sensitive detection of vibrational lines and their voltage gating is explained in terms of distinct field- and phototunneling current-driven Raman, offering an alternate paradigm for the long-sought optoelectronic rectifier in molecular electronics.

Probing and imaging spin interactions with a magnetic single-molecule sensor

Magnetic single atoms and molecules are receiving intensifying research focus because of their potential as the smallest possible memory, spintronic, and qubit elements. Scanning probe microscopes used to study these systems have benefited greatly from new techniques that use molecule-functionalized tips to enhance spatial and spectroscopic resolutions and enable new sensing capabilities. We demonstrate a microscopy technique that uses a magnetic molecule, Ni(cyclopentadienyl)₂, adsorbed at the apex of a scanning probe tip, to sense exchange interactions with another molecule adsorbed on a Ag(110) surface in a continuously tunable fashion in all three spatial directions. We further used the probe to image contours of exchange interaction strength, revealing angstrom-scale regions where the quantum states of two magnetic molecules strongly mix. Our results pave the way for new nanoscale imaging capabilities based on magnetic single-molecule sensors.

Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space

All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.

Detection and Characterization of Anharmonic Overtone Vibrations of Single Molecules on a Metal Surface

Inelastic electron tunneling spectroscopy (IETS) with the scanning tunneling microscope (STM) is a powerful technique used to characterize the vibration and spin states at the single-molecule level. While IETS lacks hard selection rules, historically it has been assumed that vibrational overtones are rarely seen or even absent. Here we provide definitive experimental evidence that the hindered rotation overtone excitation of carbon monoxide molecules adsorbed on Ag(110) can be detected with STM-IETS via isotope substitution. We also demonstrate that the anharmonicity of the overtone excitation can be characterized and compared between adsorption sites and find evidence of anisotropy in the vibrational anharmonicity for CO adsorbed on the [11[over ¯]0] step edge.

Bond-Selected Photodissociation of Single Molecules Adsorbed on Metal Surfaces

We report the photoassisted activation of selected C─H bonds in individual molecules adsorbed on metal surfaces within the junction of a scanning tunneling microscope. Photons can couple to the C─H bond activation of specific hydrocarbons through a resonant photoassisted tunneling process. The molecule to be activated can be selected by positioning the tip with subangstrom resolution. Furthermore, structural tomography of the molecule and its dissociation products are imaged at different heights by the inelastic tunneling probe. The demonstration of single bond dissociation induced by resonant photoassisted tunneling electrons implies the attainment of atomic scale spatial resolution for bond-selected photochemistry.

Nitrous oxide as an effective AFM tip functionalization: a comparative study

We investigate the possibility of functionalizing Au tips by N2O molecules deposited on a Au(111) surface and their further use for imaging with submolecular resolution. First, we characterize the adsorption of the N2O species on Au(111) by means of atomic force microscopy with CO-functionalized tips and density functional theory (DFT) simulations. Subsequently we devise a method of attaching a single N2O to a metal tip apex and benchmark its high-resolution imaging and spectroscopic capabilities using FePc molecules. Our results demonstrate the feasibility of high-resolution imaging. However, we find an inherent asymmetry of the N2O probe-particle adsorption on the tip apex, in contrast to a CO tip reference. These findings are consistent with DFT calculations of the N2O- and CO tip apexes.

Interface Characterization and Control of 2D Materials and Heterostructures

2D materials and heterostructures have attracted significant attention for a variety of nanoelectronic and optoelectronic applications. At the atomically thin limit, the material characteristics and functionalities are dominated by surface chemistry and interface coupling. Therefore, methods for comprehensively characterizing and precisely controlling surfaces and interfaces are required to realize the full technological potential of 2D materials. Here, the surface and interface properties that govern the performance of 2D materials are introduced. Then the experimental approaches that resolve surface and interface phenomena down to the atomic scale, as well as strategies that allow tuning and optimization of interfacial interactions in van der Waals heterostructures, are systematically reviewed. Finally, a future outlook that delineates the remaining challenges and opportunities for 2D material interface characterization and control is presented.

Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene

Nitrogen doping of graphene significantly affects its chemical properties, which is particularly important in molecular sensing and electrocatalysis applications. However, detailed insight into interaction between N-dopant and molecules at the atomic scale is currently lacking. Here we demonstrate control over the spin state of a single iron(II) phthalocyanine molecule by its positioning on N-doped graphene. The spin transition was driven by weak intermixing between orbitals with z-component of N-dopant (pz of N-dopant) and molecule (dxz, dyz, dz2) with subsequent reordering of the Fe d-orbitals. The transition was accompanied by an electron density redistribution within the molecule, sensed by atomic force microscopy with CO-functionalized tip. This demonstrates the unique capability of the high-resolution imaging technique to discriminate between different spin states of single molecules. Moreover, we present a method for triggering spin state transitions and tuning the electronic properties of molecules through weak non-covalent interaction with suitably functionalized graphene.

In Situ Electrochemical Tip-Enhanced Raman Spectroscopy with a Chemically Modified Tip

Chemically modified tips in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) have been used to improve the imaging resolution or provide richer chemical information, mostly in ultrahigh vacuum (UHV) environments. Tip-enhanced Raman spectroscopy (TERS) is a nanoscale spectroscopic technique that already provides chemical information and can provide subnanometer spatial resolution. Chemical modification of TERS tips has mainly been focused on increasing their lifetimes for ambient and in situ experiments. Under UHV conditions, chemical functionalization has recently been carried out to increase the amount of chemical information provided by TERS. However, this strategy has not yet been extended to in situ electrochemical (EC)-TERS studies. The independent control of the tip and sample potentials offered by EC-STM allows us to prove the in situ functionalization of a tip in EC-STM-TERS. Additionally, the Raman response of chemically modified TERS tips can be switched on and off at will, which makes EC-STM-TERS an ideal platform for the development of in situ chemical probes on the nanoscale.

Assigning the absolute configuration of single aliphatic molecules by visual inspection

Deciphering absolute configuration of a single molecule by direct visual inspection is the next step in compound identification, with far-reaching implications for medicinal chemistry, pharmacology, and natural product synthesis. We demonstrate the feasibility of this approach utilizing low temperature atomic force microscopy (AFM) with a CO-functionalized tip to determine the absolute configuration and orientation of a single, adsorbed [123]tetramantane molecule, the smallest chiral diamondoid. We differentiate between single enantiomers on Cu(111) by direct visual inspection, and furthermore identify molecular dimers and molecular clusters. The experimental results are confirmed by a computational study that allowed quantification of the corresponding intermolecular interactions. The unique toolset of absolute configuration determination combined with AFM tip manipulation opens a route for studying molecular nucleation, including chirality-driven assembly or reaction mechanisms.

Microscopy with a single-molecule scanning electrometer

The vibrational spectrum of a single carbon monoxide molecule, adsorbed on the tip apex of a scanning tunneling microscope, is used to image electrostatic fields with submolecular spatial resolution. The method takes advantage of the vibrational Stark effect to image local electrostatic fields and the single-molecule sensitivity of tip-enhanced Raman scattering (TERS) to optically relay the signal. We apply the method to single metalloporphyrins adsorbed on Au(111) to image molecular charges, intramolecular polarization, local photoconductivity, atomically resolved hydrogen bonds, and surface electron density waves.

Vibrations of a molecule in an external force field

The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

Probing of sub-picometer vertical differential resolutions using cavity plasmons

Plasmon rulers can be used for resolving ultrasmall environmental, dimensional, and material changes owing to their high sensitivity associated with a light-scattering spectral shift in response to changes in the separation between plasmonic nanostructures. Here, we show, in several experimental setups, how cavity plasmons in a metal nanowire-on-mirror setup can be used to probe vertical dimensional changes with sub-picometer differential resolutions using two carefully chosen material systems. Specifically, we monitor the dielectric layer thickness changes in response to growth using atomic-layer deposition and to thermal expansion, demonstrating a sensitivity of 14-nm spectral shift per Ångström thickness change and 0.58 pm of vertical differential resolution, respectively. The findings confirm theoretical predictions and highlight the potential use of cavity plasmons in some ultrasensitive sensing applications.

Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy

Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.

Scanning probe microscopy has been extensively applied to probe interfacial water but the probes tend to disturb the structure of water easily. Here, the authors report submolecular-resolution imaging of water clusters within the nearly non-invasive region by qPlus noncontact atomic force microscopy.

Tip-Enhanced Raman Spectromicroscopy on the Angstrom Scale: Bare and CO-Terminated Ag Tips

The tip is key to the successful execution of tip-enhanced Raman scattering (TERS) measurements in the single molecule limit. We show that nanoscopically smooth silver tips, batch produced through field-directed sputter sharpening, reliably attain TERS with enhancement factors that reach 10¹³, as measured by the Raman spectra of single CO molecules attached to the tip apex. We validate the bare tips by demonstrating spectromicroscopy with submolecular spatial resolution and underscore that TERS is a near-field effect that does not obey simple selection rules. As a more gainful analytical approach, we introduce TERS-relayed molecular force microscopy using CO-terminated tips. By taking advantage of the large Stark tuning rate of the CO stretch, molecular structure and charges can be imaged with atomic resolution. As illustration, we image a single Ag atom adsorbed on Au(111) and show that the adatom carries +0.2e charge.

Atomically precise graphene nanoribbon heterojunctions from a single molecular precursor

The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.

Submolecular Resolution by Variation of the Inelastic Electron Tunneling Spectroscopy Amplitude and its Relation to the AFM/STM Signal

Here we show scanning tunneling microscopy (STM), noncontact atomic force microscopy (AFM), and inelastic electron tunneling spectroscopy (IETS) measurements on an organic molecule with a CO-terminated tip at 5 K. The high-resolution contrast observed simultaneously in all channels unambiguously demonstrates the common imaging mechanism in STM/AFM/IETS, related to the lateral bending of the CO-functionalized tip. The IETS spectroscopy reveals that the submolecular contrast at 5 K consists of both renormalization of vibrational frequency and variation of the amplitude of the IETS signal. This finding is also corroborated by first principles simulations. We extend accordingly the probe-particle AFM/STM/IETS model to include these two main ingredients necessary to reproduce the high-resolution IETS contrast. We also employ the first principles simulations to get more insight into a different response of frustrated translation and rotational modes of the CO tip during imaging.