Recent advances in submolecular resolution with scanning probe microscopy

Recent Progress of Imaging Chemical Bonds by Scanning Probe Microscopy: A Review

In the past decades, the invention of scanning probe microscopy (SPM) as the versatile surface-based characterization of organic molecules has triggered significant interest throughout multidisciplinary fields. In particular, the bond-resolved imaging acquired by SPM techniques has extended its fundamental function of not only unraveling the chemical structure but also allowing us to resolve the structure-property relationship. Here, we present a systematical review on the history of chemical bonds imaged by means of noncontact atomic force microscopy (nc-AFM) and bond-resolved scanning tunneling microscopy (BR-STM) techniques. We first summarize the advancement of real-space imaging of covalent bonds and the investigation of intermolecular noncovalent bonds. Beyond the bond imaging, we also highlight the applications of the bond-resolved SPM techniques such as on-surface synthesis, the determination of the reaction pathway, the identification of molecular configurations and unknown products, and the generation of artificial molecules created via tip manipulation. Lastly, we discuss the current status of SPM techniques and highlight several key technical challenges that must be solved in the coming years. In comparison to the existing reviews, this work invokes researchers from surface science, chemistry, condensed matter physics, and theoretical physics to uncover the bond-resolved SPM technique as an emerging tool in exploiting the molecule/surface system and their future applications.

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

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

Tunable Magnetic Coupling in Graphene Nanoribbon Quantum Dots

Carbon-based quantum dots (QDs) enable flexible manipulation of electronic behavior at the nanoscale, but controlling their magnetic properties requires atomically precise structural control. While magnetism is observed in organic molecules and graphene nanoribbons (GNRs), GNR precursors enabling bottom-up fabrication of QDs with various spin ground states have not yet been reported. Here the development of a new GNR precursor that results in magnetic QD structures embedded in semiconducting GNRs is reported. Inserting one such molecule into the GNR backbone and graphitizing it results in a QD region hosting one unpaired electron. QDs composed of two precursor molecules exhibit nonmagnetic, antiferromagnetic, or antiferromagnetic ground states, depending on the structural details that determine the coupling behavior of the spins originating from each molecule. The synthesis of these QDs and the emergence of localized states are demonstrated through high-resolution atomic force microscopy (HR-AFM), scanning tunneling microscopy (STM) imaging, and spectroscopy, and the relationship between QD atomic structure and magnetic properties is uncovered. GNR QDs provide a useful platform for controlling the spin-degree of freedom in carbon-based nanostructures.

Automated Structure Discovery for Scanning Tunneling Microscopy

Scanning tunneling microscopy (STM) with a functionalized tip apex reveals the geometric and electronic structures of a sample within the same experiment. However, the complex nature of the signal makes images difficult to interpret and has so far limited most research to planar samples with a known chemical composition. Here, we present automated structure discovery for STM (ASD-STM), a machine learning tool for predicting the atomic structure directly from an STM image, by building upon successful methods for structure discovery in noncontact atomic force microscopy (nc-AFM). We apply the method on various organic molecules and achieve good accuracy on structure predictions and chemical identification on a qualitative level while highlighting future development requirements for ASD-STM. This method is directly applicable to experimental STM images of organic molecules, making structure discovery available for a wider scanning probe microscopy audience outside of nc-AFM. This work also allows more advanced machine learning methods to be developed for STM structure discovery.

Sterically Selective [3 + 3] Cycloaromatization in the On-Surface Synthesis of Nanographenes

Surface-catalyzed reactions have been used to synthesize carbon nanomaterials with atomically predefined structures. The recent discovery of a gold surface-catalyzed [3 + 3] cycloaromatization of isopropyl substituted arenes has enabled the on-surface synthesis of arylene-phenylene copolymers, where the surface activates the isopropyl substituents to form phenylene rings by intermolecular coupling. However, the resulting polymers suffered from undesired cross-linking when more than two molecules reacted at a single site. Here we show that such cross-links can be prevented through steric protection by attaching the isopropyl groups to larger arene cores. Upon thermal activation of isopropyl-substituted 8,9-dioxa-8a-borabenzo[fg]tetracene on Au(111), cycloaromatization is observed to occur exclusively between the two molecules. The cycloaromatization intermediate formed by the covalent linking of two molecules is prevented from reacting with further molecules by the wide benzotetracene core, resulting in highly selective one-to-one coupling. Our findings extend the versatility of the [3 + 3] cycloaromatization of isopropyl substituents and point toward steric protection as a powerful concept for suppressing competing reaction pathways in on-surface synthesis.

Diboraperylene Diborinic Acid Self-Assembly on Ag(111)-Kagome Flat Band Localized States Imaged by Scanning Tunneling Microscopy and Spectroscopy

Replacement of sp2-hybridized carbon in polycyclic aromatic hydrocarbons (PAHs) by boron affords electron-deficient π-scaffolds due to the vacant pz-orbital of three-coordinate boron with the potential for pronounced electronic interactions with electron-rich metal surfaces. Using a diboraperylene diborinic acid derivative as precursor and a controlled on-surface non-covalent synthesis approach, we report on a self-assembled chiral supramolecular kagome network on an Ag(111) surface stabilized by intermolecular hydrogen-bonding interactions at low temperature. Scanning tunneling microscopy (STM) and spectroscopy (STS) reveal a flat band at ca. 0.33 eV above the Fermi level which is localized at the molecule center, in good agreement with tight-binding model calculations of flat bands characteristic for kagome lattices.

Highly Selective On-Surface Ring-Opening of Aromatic Azulene Moiety

Controllable ring-opening of polycyclic aromatic hydrocarbons plays a crucial role in various chemical and biological processes. However, breaking down aromatic covalent C-C bonds is exceptionally challenging due to their high stability and strong aromaticity. This study presents a seminal report on the precise and highly selective on-surface ring-opening of the seven-membered ring within the aromatic azulene moieties under mild conditions. The chemical structures of the resulting products were identified using bond-resolved scanning probe microscopy. Furthermore, through density functional theory calculations, we uncovered the mechanism behind the ring-opening process and elucidated its chemical driving force. The key to achieving this ring-opening process lies in manipulating the local aromaticity of the aromatic azulene moiety through strain-induced internal ring rearrangement and cyclodehydrogenation. By precisely controlling these factors, we successfully triggered the desired ring-opening reaction. Our findings not only provide valuable insights into the ring-opening process of polycyclic aromatic hydrocarbons but also open up new possibilities for the manipulation and reconstruction of these important chemical structures.

Toward conformational identification of molecules in 2D and 3D self-assemblies on surfaces

The design of supramolecular networks based on organic molecules deposited on surfaces, is highly attractive for various applications. One of the remaining challenges is the expansion of monolayers to well-ordered multilayers in order to enhance the functionality and complexity of self-assemblies. In this study, we present an assessment of molecular conformation from 2D to 3D supramolecular networks adsorbed onto a HOPG surface under ambient conditions utilizing a combination of scanning probe microscopies and atomic force microscopy- infrared (AFM-IR). We have observed that the infrared (IR) spectra of the designed molecules vary from layer to layer due to the modifications in the dihedral angle between the C=O group and the neighboring phenyl ring, especially in the case of a 3D supramolecular network consisting of multiple layers of molecules.

Emergence of π-Magnetism in Fused Aza-Triangulenes: Symmetry and Charge Transfer Effects

On-surface synthesis has paved the way toward the fabrication and characterization of conjugated carbon-based molecular materials that exhibit π-magnetism such as triangulenes. Aza-triangulene, a nitrogen-substituted derivative, was recently shown to display rich on-surface chemistry, offering an ideal platform to investigate structure-property relations regarding spin-selective charge transfer and magnetic fingerprints. Herein, we study electronic changes upon fusion of single molecules into larger dimeric derivatives. We show that the closed-shell structure of aza-triangulene on Ag(111) leads to closed-shell dimers covalently coupled through sterically accessible carbon atoms. Meanwhile, its open-shell structure on Au(111) leads to coupling via atoms displaying a high spin density, resulting in symmetric or asymmetric products. Interestingly, whereas all dimers on Au(111) exhibit similar charge transfer properties, only asymmetric ones show magnetic fingerprints due to spin-selective charge transfer. These results expose clear relationships among molecular symmetry, charge transfer, and spin states of π-conjugated carbon-based nanostructures.

Dynamic Friction Unraveled by Observing an Unexpected Intermediate State in Controlled Molecular Manipulation

The pervasive phenomenon of friction has been studied at the nanoscale via a controlled manipulation of single atoms and molecules with a metallic tip, which enabled a precise determination of the static friction force necessary to initiate motion. However, little is known about the atomic dynamics during manipulation. Here, we reveal the complete manipulation process of a CO molecule on a Cu(110) surface at low temperatures using a combination of noncontact atomic force microscopy and density functional theory simulations. We found that an intermediate state, inaccessible for the far-tip position, is enabled in the reaction pathway for the close-tip position, which is crucial to understanding the manipulation process, including dynamic friction. Our results show how friction forces can be controlled and optimized, facilitating new fundamental insights for tribology.

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. Bottom-up engineering of carbohydrate materials demands an atomic-level understanding of their molecular structures and interactions in condensed phases. Here, high-resolution scanning tunneling microscopy (STM) is used to visualize at submolecular resolution the three-dimensional structure of cellulose oligomers assembled on Au(1111) and the interactions that drive their assembly. The STM imaging, supported by ab initio calculations, reveals the orientation of all glycosidic bonds and pyranose rings in the oligomers, as well as details of intermolecular interactions between the oligomers. By comparing the assembly of D- and L-oligomers, these interactions are shown to be enantioselective, capable of driving spontaneous enantioseparation of cellulose chains from its unnatural enantiomer and promoting the formation of engineered carbohydrate assemblies in the condensed phases.

Structural Expansion of Cyclohepta[def]fluorene towards Azulene-Embedded Non-Benzenoid Nanographenes

Non-benzenoid non-alternant nanographenes (NGs) have attracted increasing attention on account of their distinct electronic and structural features in comparison to their isomeric benzenoid counterparts. In this work, we present a series of unprecedented azulene-embedded NGs on Au(111) during the attempted synthesis of cyclohepta[def]fluorene-based high-spin non-Kekulé structure. Comprehensive scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM) evidence the structures and conformations of these unexpected products. The dynamics of the precursor bearing 9-(2,6-dimethylphenyl)anthracene and dihydro-dibenzo-cyclohepta[def]fluorene units and its reaction products on the surface are analyzed by density functional theory (DFT) and molecular dynamics (MD) simulations. Our study sheds light on the fundamental understanding of precursor design for the fabrication of π-extended non-benzenoid NGs on a metal surface.

Orbital-symmetry effects on magnetic exchange in open-shell nanographenes

Open-shell nanographenes appear as promising candidates for future applications in spintronics and quantum technologies. A critical aspect to realize this potential is to design and control the magnetic exchange. Here, we reveal the effects of frontier orbital symmetries on the magnetic coupling in diradical nanographenes through scanning probe microscope measurements and different levels of theoretical calculations. In these open-shell nanographenes, the exchange energy exhibits a remarkable variation between 20 and 160 meV. Theoretical calculations reveal that frontier orbital symmetries play a key role in affecting the magnetic coupling on such a large scale. Moreover, a triradical nanographene is demonstrated for investigating the magnetic interaction among three unpaired electrons with unequal magnetic exchange, in agreement with Heisenberg spin model calculations. Our results provide insights into both theoretical design and experimental realization of nanographene materials with different exchange interactions through tuning the orbital symmetry, potentially useful for realizing magnetically operable graphene-based nanomaterials.

First-Principles Simulations of Tip Enhanced Raman Scattering Reveal Active Role of Substrate on High-Resolution Images

Tip-enhanced Raman scattering (TERS) has emerged as a powerful tool to obtain subnanometer spatial resolution fingerprints of atomic motion. Theoretical calculations that can simulate the Raman scattering process and provide an unambiguous interpretation of TERS images often rely on crude approximations of the local electric field. In this work, we present a novel and first-principles-based method to compute TERS images by combining Time Dependent Density Functional Theory (TD-DFT) and Density Functional Perturbation Theory (DFPT) to calculate Raman cross sections with realistic local fields. We present TERS results on free-standing benzene and C60 molecules, and on the TCNE molecule adsorbed on Ag(100). We demonstrate that chemical effects on chemisorbed molecules, often ignored in TERS simulations of larger systems, dramatically change the TERS images. This observation calls for the inclusion of chemical effects for predictive theory-experiment comparisons and an understanding of molecular motion at the nanoscale.

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.

Ba+2 ion trapping using organic submonolayer for ultra-low background neutrinoless double beta detector

If neutrinos are their own antiparticles the otherwise-forbidden nuclear reaction known as neutrinoless double beta decay can occur. The very long lifetime expected for these exceptional events makes its detection a daunting task. In order to conduct an almost background-free experiment, the NEXT collaboration is investigating novel synthetic molecular sensors that may capture the Ba dication produced in the decay of certain Xe isotopes in a high-pressure gas experiment. The use of such molecular detectors immobilized on surfaces must be explored in the ultra-dry environment of a xenon gas chamber. Here, using a combination of highly sensitive surface science techniques in ultra-high vacuum, we demonstrate the possibility of employing the so-called Fluorescent Bicolor Indicator as the molecular component of the sensor. We unravel the ion capture process for these molecular indicators immobilized on a surface and explain the origin of the emission fluorescence shift associated to the ion trapping.

AFM advanced modes for dental and biomedical applications

Several analytical methods have been employed to elucidate bonding mechanisms between dental hard tissues, luting agents and restorative materials. Atomic Force Microscopy (AFM) imaging that has been extensively used in materials science, but its full capabilities are poorly explored by dental research community. In fact, commonly used to obtain topographic images of different surfaces, it turns out that AFM is an underestimated technique considering that there are dozens of basic and advanced modes that are scarcely used to explain properties of biomaterials. Thus, this paper addresses the use of phase-contrast imaging, force-distance curves, nanomechanical and Kelvin probe force techniques during AFM analysis to explore topological, nanomechanical and electrical properties of Y-TZP samples modified by different surface treatments, which has been widely used to promote adhesive enhancements to such substrate. The AFM methods are capable of access erstwhile inaccessible properties of Y-TZP which allowed us to describe its adhesive properties correctly. Thus, AFM technique emerges as a key tool to investigate the complex nature of biomaterials and highlighting its inherent interdisciplinarity that can be successfully used for bridging fragmented disciplines such as solid-state physics, microbiology and dental sciences.

Small molecule binding to surface-supported single-site transition-metal reaction centres

Despite dominating industrial processes, heterogeneous catalysts remain challenging to characterize and control. This is largely attributable to the diversity of potentially active sites at the catalyst-reactant interface and the complex behaviour that can arise from interactions between active sites. Surface-supported, single-site molecular catalysts aim to bring together benefits of both heterogeneous and homogeneous catalysts, offering easy separability while exploiting molecular design of reactivity, though the presence of a surface is likely to influence reaction mechanisms. Here, we use metal-organic coordination to build reactive Fe-terpyridine sites on the Ag(111) surface and study their activity towards CO and C₂H₄ gaseous reactants using low-temperature ultrahigh-vacuum scanning tunnelling microscopy, scanning tunnelling spectroscopy, and atomic force microscopy supported by density-functional theory models. Using a site-by-site approach at low temperature to visualize the reaction pathway, we find that reactants bond to the Fe-tpy active sites via surface-bound intermediates, and investigate the role of the substrate in understanding and designing single-site catalysts on metallic supports.

Chemically identifying single adatoms with single-bond sensitivity during oxidation reactions of borophene

The chemical interrogation of individual atomic adsorbates on a surface significantly contributes to understanding the atomic-scale processes behind on-surface reactions. However, it remains highly challenging for current imaging or spectroscopic methods to achieve such a high chemical spatial resolution. Here we show that single oxygen adatoms on a boron monolayer (i.e., borophene) can be identified and mapped via ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) with ~4.8 Å spatial resolution and single bond (B–O) sensitivity. With this capability, we realize the atomically defined, chemically homogeneous, and thermally reversible oxidation of borophene via atomic oxygen in UHV. Furthermore, we reveal the propensity of borophene towards molecular oxygen activation at room temperature and phase-dependent chemical properties. In addition to offering atomic-level insights into the oxidation of borophene, this work demonstrates UHV-TERS as a powerful tool to probe the local chemistry of surface adsorbates in the atomic regime with widespread utilities in heterogeneous catalysis, on-surface molecular engineering, and low-dimensional materials.

On-surface synthesis of triangulene trimers via dehydration reaction

Triangulene and its homologues are of considerable interest for molecular spintronics due to their high-spin ground states as well as the potential for constructing high spin frameworks. Realizing triangulene-based high-spin system on surface is challenging but of particular importance for understanding π-electron magnetism. Here, we report two approaches to generate triangulene trimers on Au(111) by using surface-assisted dehydration and alkyne trimerization, respectively. We find that the developed dehydration reaction shows much higher chemoselectivity thus resulting in significant promotion of product yield compared to that using alkyne trimerization approach, through cutting the side reaction path. Combined with spin-polarized density functional theory calculations, scanning tunneling spectroscopy measurements identify the septuple (S = 3) high-spin ground state and quantify the collective ferromagnetic interaction among three triangulene units. Our results demonstrate the approaches to fabricate high-quality triangulene-based high spin systems and understand their magnetic interactions, which are essential for realizing carbon-based spintronic devices.

Chemically imaging nanostructures formed by the covalent assembly of molecular building blocks on a surface with ultrahigh vacuum tip-enhanced Raman spectroscopy

Surface-bound reactions have become a viable method to develop nanoarchitectures through bottom-up assembly with near atomic precision. However, the bottom-up fabrication of nanostructures on surfaces requires careful consideration of the intrinsic properties of the precursors and substrate as well as the complex interplay of any interactions that arise in the heterogeneous two-dimensional (2D) system. Therefore, it becomes necessary to consider these systems with characterization methods sensitive to such properties with suitable spatial resolution. Here, low temperature ultrahigh vacuum scanning tunneling microscopy (STM) and tip-enhanced Raman spectroscopy (TERS) were used to investigate the formation of 2D covalent networks via coupling reactions of tetra(4-bromophenyl)porphyrin (Br₄TPP) molecules on a Ag(100) substrate. Through the combination of STM topographic imaging and TERS vibrational fingerprints, the conformation of molecular precursors on the substrate was understood. Following the thermally activated coupling reaction, STM and TERS imaging confirm the covalent nature of the 2D networks and suggest that the apparent disorder arises from molecular flexibility.

Field emission microscope for a single fullerene molecule

Applying strong direct current (DC) electric fields on the apex of a sharp metallic tip, electrons can be radially emitted from the apex to vacuum. Subsequently, they magnify the nanoscopic information on the apex, which serves as a field emission microscope (FEM). When depositing molecules on such a tip, peculiar electron emission patterns such as clover leaves appear. These phenomena were first observed seventy years ago. However, the source of these emission patterns has not yet been identified owing to the limited experimental information about molecular configurations on a tip. Here, we used fullerene molecules and characterized the molecule-covered tip by an FEM. In addition to the experiments, simulations were performed to obtain optimized molecular configurations on a tip. Both results indicate that the molecules, the source of the peculiar emission patterns, appear on a molecule layer formed on the tip under strong DC electric fields. Furthermore, the simulations revealed that these molecules are mostly isolated single molecules forming single-molecule-terminated protrusions. Upon the excellent agreements in both results, we concluded that each emission pattern originates from a single molecule. Our work should pave the way to revive old-fashioned electron microscopy as a powerful tool for investigating a single molecule.

Two 'braking mechanisms' for tin phthalocyanine molecular rotors on dipolar iron oxide surfaces

Manipulation of artificial molecular rotors/motors is a key issue in the field of molecular nanomachines. Here we assemble non-planar SnPc molecules on an FeO film to form two kinds of rotors with different apparent morphologies, rotational speeds and stabilities. Both kinds of rotors can switch to each other via external field stimulation and the switch depends on the polarity of the applied bias voltage. Furthermore, we reveal that the molecular fragment has a great influence on the motions of molecules. Combining scanning tunneling microscopy and DFT calculations, two braking mechanisms are addressed for molecular rotors. One is the transformation of adsorption configurations under the external electric field stimulus that enables the molecular rotor to stop/restart its rotation. The other is the introduction of embedded molecular fragments that act as a brake pad and can stop the molecular rotation. We find that the rotation can be recovered by separating the molecule from the fragments. Our study suggests a good system for manipulating molecular rotors' properties in nanophysics and has important value for the design of controllable molecular machines.

Topographic signatures and manipulations of Fe atoms, CO molecules and NaCl islands on superconducting Pb(111)

Topological superconductivity emerging in one- or two-dimensional hybrid materials is predicted as a key ingredient for quantum computing. However, not only the design of complex heterostructures is primordial for future applications but also the characterization of their electronic and structural properties at the atomic scale using the most advanced scanning probe microscopy techniques with functionalized tips. We report on the topographic signatures observed by scanning tunneling microscopy (STM) of carbon monoxide (CO) molecules, iron (Fe) atoms and sodium chloride (NaCl) islands deposited on superconducting Pb(111). For the CO adsorption a comparison with the Pb(110) substrate is demonstrated. We show a general propensity of these adsorbates to diffuse at low temperature under gentle scanning conditions. Our findings provide new insights into high-resolution probe microscopy imaging with terminated tips, decoupling atoms and molecules by NaCl islands or tip-induced lateral manipulation of iron atoms on top of the prototypical Pb(111) superconducting surface.

On-Surface Synthesis of a Dicationic Diazahexabenzocoronene Derivative on the Au(111) Surface

The atomically precise control over the size, shape and structure of nanographenes (NGs) or the introduction of heteroatom dopants into their sp2 -carbon lattice confer them valuable electronic, optical and magnetic properties. Herein, we report on the design and synthesis of a hexabenzocoronene derivative embedded with graphitic nitrogen in its honeycomb lattice, achieved via on-surface assisted cyclodehydrogenation on the Au(111) surface. Combined scanning tunnelling microscopy/spectroscopy and non-contact atomic force microscopy investigations unveil the chemical and electronic structures of the obtained dicationic NG. Kelvin probe force microscopy measurements reveal a considerable variation of the local contact potential difference toward lower values with respect to the gold surface, indicative of its positive net charge. Altogether, we introduce the concept of cationic nitrogen doping of NGs on surfaces, opening new avenues for the design of novel carbon nanostructures.

Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images

High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.

Breaking the Fundamental Limitations of Nanoscale Ferroelectric Characterization: Non-Contact Heterodyne Electrostrain Force Microscopy

Perceiving nanoscale ferroelectric phenomena from real space is of great importance for elucidating underlying ferroelectric physics. During the past decades, nanoscale ferroelectric characterization has mainly relied on the Piezoresponse Force Microscopy (PFM) invented in 1992, however, the fundamental limitations of PFM have made the nanoscale ferroelectric studies encounter significant bottlenecks. In this study, a high-resolution non-contact ferroelectric measurement, named Non-Contact Heterodyne Electrostrain Force Microscopy (NC-HEsFM), is introduced. It is demonstrated that NC-HEsFM can operate on multiple eigenmodes to perform ideal high-resolution ferroelectric domain mapping, standard ferroelectric hysteresis loop measurement, and controllable domain manipulation. By using a quartz tuning fork (QTF) sensor, multi-frequency operation, and heterodyne detection schemes, NC-HEsFM achieves a real non-contact yet non-destructive ferroelectric characterization with negligible electrostatic force effect and hence breaks the fundamental limitations of the conventional PFM. It is believed that NC-HEsFM can be extensively used in various ferroelectric or piezoelectric studies with providing substantially improved characterization performance. Meanwhile, the QTF-based force detection makes NC-HEsFM highly compatible for high-vacuum and low-temperature environments, providing ideal conditions for investigating the intrinsic ferroelectric phenomena with the possibility of achieving an atomically resolved ferroelectric characterization.

Atomically resolved single-molecule triplet quenching

The nonequilibrium triplet state of molecules plays an important role in photocatalysis, organic photovoltaics, and photodynamic therapy. We report the direct measurement of the triplet lifetime of an individual pentacene molecule on an insulating surface with atomic resolution by introducing an electronic pump-probe method in atomic force microscopy. Strong quenching of the triplet lifetime is observed if oxygen molecules are coadsorbed in close proximity. By means of single-molecule manipulation techniques, different arrangements with oxygen molecules were created and characterized with atomic precision, allowing for the direct correlation of molecular arrangements with the lifetime of the quenched triplet. Such electrical addressing of long-lived triplets of single molecules, combined with atomic-scale manipulation, offers previously unexplored routes to control and study local spin-spin interactions.

On-Surface Synthesis of Nitrogen-Doped Kagome Graphene

Nitrogen-doped Kagome graphene (N-KG) has been theoretically predicted as a candidate for the emergence of a topological band gap as well as unconventional superconductivity. However, its physical realization still remains very elusive. Here, we report on a substrate-assisted reaction on Ag(111) for the synthesis of two-dimensional graphene sheets possessing a long-range honeycomb Kagome lattice. Low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM) with a CO-terminated tip supported by density functional theory (DFT) are employed to scrutinize the structural and electronic properties of the N-KG down to the atomic scale. We demonstrate its semiconducting character due to the nitrogen doping as well as the emergence of Kagome flat bands near the Fermi level which would open new routes towards the design of graphene-based topological materials.

Ultrahigh-yield on-surface synthesis and assembly of circumcoronene into a chiral electronic Kagome-honeycomb lattice

On-surface synthesis has revealed remarkable potential in the fabrication of atomically precise nanographenes. However, surface-assisted synthesis often involves multiple-step cascade reactions with competing pathways, leading to a limited yield of target nanographene products. Here, we devise a strategy for the ultrahigh-yield synthesis of circumcoronene molecules on Cu(111) via surface-assisted intramolecular dehydrogenation of the rationally designed precursor, followed by methyl radical-radical coupling and aromatization. An elegant electrostatic interaction between circumcoronenes and metallic surface drives their self-organization into an extended superlattice, as revealed by bond-resolved scanning probe microscopy measurements. Density functional theory and tight-binding calculations reveal that unique hexagonal zigzag topology of circumcoronenes, along with their periodic electrostatic landscape, confines two-dimensional electron gas in Cu(111) into a chiral electronic Kagome-honeycomb lattice with two emergent electronic flat bands. Our findings open up a new route for the high-yield fabrication of elusive nanographenes with zigzag topologies and their superlattices with possible nontrivial electronic properties.

Hypothetical Efficiency of Electrical to Mechanical Energy Transfer during Individual Stochastic Molecular Switching Events

There are now many examples of single molecule rotors, motors, and switches in the literature that, when driven by photons, electrons, or chemical reactions, exhibit well-defined motions. As a step toward using these single molecule devices to perform useful functions, one must understand how they interact with their environment and quantify their ability to perform work on it. Using a single molecule rotary switch, we examine the transfer of electrical energy, delivered via electron tunneling, to mechanical motion and measure the forces the switch experiences with a noncontact q-plus atomic force microscope. Action spectra reveal that the molecular switch has two stable states and can be excited resonantly between them at a bias of 100 mV via a one-electron inelastic tunneling process which corresponds to an energy input of 16 zJ. While the electrically induced switching events are stochastic and no net work is done on the cantilever, by measuring the forces between the molecular switch and the AFM cantilever, we can derive the maximum hypothetical work the switch could perform during a single switching event, which is ∼55 meV, equal to 8.9 zJ, which translates to a hypothetical efficiency of ∼55% per individual inelastic tunneling electron-induced switching event. When considering the total electrical energy input, this drops to 1 × 10^-7% due to elastic tunneling events that dominate the tunneling current. However, this approach constitutes a general method for quantifying and comparing the energy input and output of molecular-mechanical devices.

Atomically Precise Synthesis and Characterization of Heptauthrene with Triplet Ground State

By virtue of multitunable spin structures upon designing the π-electron topologies, phenalenyl-based nanographenes are of substantial interest in fundamental science and for potential applications in spintronics. Heptauthrene, as one of the well-known phenalenyl diradicals, is composed of one benzene-fused bisphenalenyls in mirror symmetry and expected to have a triplet ground state. However, the synthesis of unsubstituted heptauthrene remains very challenging due to the high reactivity of triplet diradicals. Here, we report a combined in-solution and on-surface synthesis of unsubstituted heptauthrene, whose chemical structure is characterized through bond-resolved atomic force microscopy. Combined with mean-field Hubbard model calculations, its triplet ground state is unambiguously confirmed by the underscreened Kondo resonance in response to the magnetic field, as well as the engineered spin-state switching upon extra hydrogen atom addition and dissociation on the radical site. Our results provide access to phenalenyl-based nanographenes with high-spin ground state, potentially useful in constructing high-spin networks.

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.

Real-Space Imaging of a Single-Molecule Monoradical Reaction

Organic radicals consisting of light elements exhibit a low spin-orbit coupling and weak hyperfine interactions with a long spin coherence length, which are crucial for future applications in molecular spintronics. However, the synthesis and characterization of these organic radicals have been a formidable challenge due to their chemical instability arising from unpaired electrons. Here, we report a direct imaging of the surface chemical transformation of an organic monoradical synthesized via the monodehydrogenation of a chemically designed precursor. Bond-resolved scanning tunneling microscopy unambiguously resolves various products formed through a complex structural dissociation and rearrangement of organic monoradicals. Density functional theory calculations reveal detailed reaction pathways from the monoradical to different cyclized products. Our study provides unprecedented insights into complex surface reaction mechanisms of organic radical reactions at the single molecule level, which may guide the design of stable organic radicals for future quantum technology applications.

Substrate induced strain for on-surface transformation and synthesis

Intermolecular strain has long been used to steer and promote chemical reactions towards desired products in wet chemical synthesis. However, similar protocols have not been adopted for the on-surface synthesis on solid substrates due to the complexity of reaction processes. Recent advances in the sub-molecular resolution with scanning probe microscopy allow us to capture on-surface reaction pathways and to gain substantial insights into the role of strain in chemical reactions. The primary focus of this review is to highlight the recent findings on strain-induced on-surface reactions. Such substrate-induced processes can be applied to alter the chemical reactivity and to drive on-surface chemical reactions in different manners, which provides a promising alternative approach for on-surface synthesis. This review aims to shed light on the utilization of substrate-induced strain for on-surface transformation and synthesis of atomically-precise novel functional nanomaterials.

Automated structure discovery in atomic force microscopy

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

Orbitals and the Interpretation of Photoelectron Spectroscopy and (e,2e) Ionization Experiments

Electron momentum spectroscopy, scanning tunneling microscopy, and photoelectron spectroscopy provide unique information about electronic structure, but their interpretation has been controversial. This essay discusses a framework for interpretation. Although this interpretation is not new, we believe it is important to present this framework in light of recent publications. The key point is that these experiments provide information about how the electron distribution changes upon ionization, not how electrons behave in the pre-ionized state. Therefore, these experiments do not lead to a "selection of the correct orbitals" in chemistry and do not overturn the well-known conclusion that both delocalized molecular orbitals and localized molecular orbitals are useful for interpreting chemical structure and dynamics. The two types of orbitals can produce identical total molecular electron densities and therefore molecular properties. Different types of orbitals are useful for different purposes.

Atomically precise bottom-up synthesis of π-extended [5]triangulene

The zigzag-edged triangular graphene molecules (ZTGMs) have been predicted to host ferromagnetically coupled edge states with the net spin scaling with the molecular size, which affords large spin tunability crucial for next-generation molecular spintronics. However, the scalable synthesis of large ZTGMs and the direct observation of their edge states have been long-standing challenges because of the molecules' high chemical instability. Here, we report the bottom-up synthesis of π-extended [5]triangulene with atomic precision via surface-assisted cyclodehydrogenation of a rationally designed molecular precursor on metallic surfaces. Atomic force microscopy measurements unambiguously resolve its ZTGM-like skeleton consisting of 15 fused benzene rings, while scanning tunneling spectroscopy measurements reveal edge-localized electronic states. Bolstered by density functional theory calculations, our results show that [5]triangulenes synthesized on Au(111) retain the open-shell π-conjugated character with magnetic ground states.

Controlling the optical properties of carbon nanotubes with organic colour-centre quantum defects

Previously unwelcome, defects are emerging as a new frontier of research, providing a molecular focal point to study the coupling of electrons, excitons, phonons and spin in low-dimensional materials. This opportunity is particularly intriguing in semiconducting single-walled carbon nanotubes, in which covalently bonding organic functional groups to the sp 2 carbon lattice can produce tunable sp 3 quantum defects that fluoresce brightly in the shortwave IR, emitting pure single photons at room temperature. These novel physical properties have made such synthetic defects, or 'organic colour centres', exciting new systems for chemistry, physics, materials science, engineering and quantum technologies. This Review examines progress in this emerging field and presents a unified description of this new family of quantum emitters, as well as providing an outlook of the rapidly expanding research and applications of synthetic defects.

Exclusion principle repulsion effects on the covalent bond beyond the Born-Oppenheimer approximation

The changes in the covalent bond of the hydrogen molecule limited in space by a spherical hard boundary are studied. The sphere is moved along an axis parallel or orthogonal to the molecular axis. The diffusion Monte Carlo approach is used to solve the Schrödinger equation with the relevant boundary conditions and to evaluate the changes in the bond energy versus the location of the sphere. The vertical and lateral quantum forces exerted on the sphere are evaluated by calculating the energy derivative versus the distances to the sphere. The results show that the quantum forces present an important dependence on the distance and vanish rapidly as the separation between the sphere and the molecule increases. In the limiting case the molecular bond breaks due to the electronic depletion induced in the covalent bond. An application of this study is the modelisation of the forces exerted on the passivated cantilever of an atomic force microscope probing the electron cloud in the contact mode in the Pauli exclusion regime.

Analysis of the Frequency Shift versus Force Gradient of a Dynamic AFM Quartz Tuning Fork Subject to Lennard-Jones Potential Force

A self-sensing and self-actuating quartz tuning fork (QTF) can be used to obtain its frequency shift as function of the tip-sample distance. Once the function of the frequency shift versus force gradient is acquired, the combination of these two functions results in the relationship between the force gradient and the tip-sample distance. Integrating the force gradient once and twice elucidates the values of the interaction force and the interatomic potential, respectively. However, getting the frequency shift as a function of the force gradient requires a physical model which can describe the equations of motion properly. Most papers have adopted the single harmonic oscillator model, but encountered the problem of determining the spring constant. Their methods of finding the spring constant are very controversial in the research community and full of discrepancies. By circumventing the determination of the spring constant, we propose a method which models the prongs and proof mass as elastic bodies. Through the use of Hamilton's principle, we can obtain the equations of motion of the QTF, which is subject to Lennard-Jones potential force. Solving these equations of motion analytically, we get the relationship between the frequency shift and force gradient.

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

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