Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy

Coronene-Based 2D Networks by On-Surface Skeletal Rearrangement of Sumanene Precursors

The design of novel low-dimensional carbon materials is at the forefront of modern chemistry. Recently, on-surface covalent synthesis has emerged as a powerful strategy to synthesize previously precluded compounds and polymers. Here, we report a scanning probe microscopy study, complemented by theoretical calculations, on the sequential skeletal rearrangement of sumanene-based precursors into a coronene-based organometallic network by stepwise intra- and inter-molecular reactions on Au(111). Interestingly, upon higher annealing, the formed organometallic networks evolve into two-dimensional coronene-based covalently linked patches through intermolecular homocoupling reactions. A new reaction mechanism is proposed based on the role of C-Au-C motifs to promote two stepwise carbon-carbon couplings to form cyclobutadiene bridges. Our results pave avenues for the conversion of molecular precursors on surfaces, affording the design of unexplored two-dimensional organometallic and covalent materials.

Advances in the Dynamics of Adsorbate Diffusion on Metal Surfaces: Focus on Hydrogen and Oxygen

Adsorbates on metal surfaces are typically formed from the dissociative chemisorption of molecules occurring at gas-solid interfaces. These adsorbed species exhibit unique diffusion behaviors on metal surfaces, which are influenced by their translational energy. They play crucial roles in various fields, including heterogeneous catalysis and corrosion. This review examines recent theoretical advancements in understanding the diffusion dynamics of adsorbates on metal surfaces, with a specific emphasis on hydrogen and oxygen atoms. The diffusion processes of adsorbates on metal surfaces involve two energy transfer mechanisms: surface phonons and electron-hole pair excitations. This review also surveys new theoretical methods, including the characterization of the electron-hole pair excitation within electronic friction models, the acceleration of quantum chemistry calculations through machine learning, and the treatment of atomic nuclear motion from both quantum mechanical and classical perspectives. Furthermore, this review offers valuable insights into how energy transfer, nuclear quantum effects, supercell sizes, and the topography of potential energy surfaces impact the diffusion behavior of hydrogen and oxygen species on metal surfaces. Lastly, some preliminary research proposals are presented.

Universal inter-molecular radical transfer reactions on metal surfaces

On-surface synthesis provides tools to prepare low-dimensional supramolecular structures. Traditionally, reactive radicals are a class of single-electron species, serving as exceptional electron-withdrawing groups. On metal surfaces, however, such species are affected by conduction band screening effects that may even quench their unpaired electron characteristics. As a result, radicals are expected to be less active, and reactions catalyzed by surface-stabilized radicals are rarely reported. Herein, we describe a class of inter-molecular radical transfer reactions on metal surfaces. With the assistance of aryl halide precursors, the coupling of terminal alkynes is steered from non-dehydrogenated to dehydrogenated products, resulting in alkynyl-Ag-alkynyl bonds. Dehalogenated molecules are fully passivated by detached hydrogen atoms. The reaction mechanism is unraveled by various surface-sensitive technologies and density functional theory calculations. Moreover, we reveal the universality of this mechanism on metal surfaces. Our studies enrich the on-surface synthesis toolbox and develop a pathway for producing low-dimensional organic materials.

Dramatic Acceleration of the Hopf Cyclization on Gold(111): From Enediynes to Peri-Fused Diindenochrysene Graphene Nanoribbons

Hopf et al. reported the high-temperature 6π-electrocyclization of cis-hexa-1,3-diene-5-yne to benzene in 1969. Subsequent studies using this cyclization have been limited by its very high reaction barrier. Here, we show that the reaction barrier for two model systems, (E)-1,3,4,6-tetraphenyl-3-hexene-1,5-diyne (1a) and (E)-3,4-bis(4-iodophenyl)-1,6-diphenyl-3-hexene-1,5-diyne (1b), is decreased by nearly half on a Au(111) surface. We have used scanning tunneling microscopy (STM) and noncontact atomic force microscopy (nc-AFM) to monitor the Hopf cyclization of enediynes 1a,b on Au(111). Enediyne 1a undergoes two sequential, quantitative Hopf cyclizations, first to naphthalene derivative 2, and finally to chrysene 3. Density functional theory (DFT) calculations reveal that a gold atom from the Au(111) surface is involved in all steps of this reaction and that it is crucial to lowering the reaction barrier. Our findings have important implications for the synthesis of novel graphene nanoribbons. Ullmann-like coupling of enediyne 1b at 20 °C on Au(111), followed by a series of Hopf cyclizations and aromatization reactions at higher temperatures, produces nanoribbons 12 and 13. These results show for the first time that graphene nanoribbons can be synthesized on a Au(111) surface using the Hopf cyclization mechanism.

The role of aromaticity in the cyclization and polymerization of alkyne-substituted porphyrins on Au(111)

Aromaticity is an established and widely used concept for the prediction of the reactivity of organic molecules. However, its role remains largely unexplored in on-surface chemistry, where the interaction with the substrate can alter the electronic and geometric structure of the adsorbates. Here we investigate how aromaticity affects the reactivity of alkyne-substituted porphyrin molecules in cyclization and coupling reactions on a Au(111) surface. We examine and quantify the regioselectivity in the reactions by scanning tunnelling microscopy and bond-resolved atomic force microscopy at the single-molecule level. Our experiments show a substantially lower reactivity of carbon atoms that are stabilized by the aromatic diaza[18]annulene pathway of free-base porphyrins. The results are corroborated by density functional theory calculations, which show a direct correlation between aromaticity and thermodynamic stability of the reaction products. These insights are helpful to understand, and in turn design, reactions with aromatic species in on-surface chemistry and heterogeneous catalysis.

Discovery and construction of surface kagome electronic states induced by p-d electronic hybridization in Co3Sn2S2

Kagome-lattice materials possess attractive properties for quantum computing applications, but their synthesis remains challenging. Herein, based on the compelling identification of the two cleavable surfaces of Co3Sn2S2, we show surface kagome electronic states (SKESs) on a Sn-terminated triangular Co3Sn2S2 surface. Such SKESs are imprinted by vertical p-d electronic hybridization between the surface Sn (subsurface S) atoms and the buried Co kagome-lattice network in the Co3Sn layer under the surface. Owing to the subsequent lateral hybridization of the Sn and S atoms in a corner-sharing manner, the kagome symmetry and topological electronic properties of the Co3Sn layer is proximate to the Sn surface. The SKESs and both hybridizations were verified via qPlus non-contact atomic force microscopy (nc-AFM) and density functional theory calculations. The construction of SKESs with tunable properties can be achieved by the atomic substitution of surface Sn (subsurface S) with other group III-V elements (Se or Te), which was demonstrated theoretically. This work exhibits the powerful capacity of nc-AFM in characterizing localized topological states and reveals the strategy for synthesis of large-area transition-metal-based kagome-lattice materials using conventional surface deposition techniques.

Two-Dimensional Crystal Transition from Radialene to Cumulene on Ag(111) via Retro-[2 + 1] Cycloaddition

Two-dimensional (2D) crystal-to-crystal transition is an important method in crystal engineering because of its ability to directly create diverse crystal materials from one crystal. However, steering a 2D single-layer crystal-to-crystal transition on surfaces with high chemo- and stereoselectivity under ultra-high vacuum conditions is a great challenge because the transition is a complex dynamic process. Here, we report a highly chemoselective 2D crystal transition from radialene to cumulene with retention of stereoselectivity on Ag(111) via retro-[2 + 1] cycloaddition of three-membered carbon rings and directly visualize the transition process involving a stepwise epitaxial growth mechanism by the combination of scanning tunneling microscopy and non-contact atomic force microscopy. Using progression annealing, we found that isocyanides on Ag(111) at a low annealing temperature underwent sequential [1 + 1 + 1] cycloaddition and enantioselective molecular recognition based on C-H···Cl hydrogen bonding interactions to form 2D triaza[3]radialene crystals. In contrast, a higher annealing temperature induced the transformation of triaza[3]radialenes to generate trans-diaza[3]cumulenes, which were further assembled into 2D cumulene-based crystals through twofold N-Ag-N coordination and C-H···Cl hydrogen bonding interactions. By combining the observed distinct transient intermediates and density functional theory calculations, we demonstrate that the retro-[2 + 1] cycloaddition reaction proceeds via the ring opening of a three-membered carbon ring, sequential dechlorination/hydrogen passivation, and deisocyanation. Our findings provide new insights into the growth mechanism and dynamics of 2D crystals and have implications for controllable crystal engineering.

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.

Tuning the Diradical Character of Pentacene Derivatives via Non-Benzenoid Coupling Motifs

The development of functional organic molecules requires structures of increasing size and complexity, which are typically obtained by the covalent coupling of smaller building blocks. Herein, with the aid of high-resolution scanning tunneling microscopy/spectroscopy and density functional theory, the coupling of a sterically demanded pentacene derivative on Au(111) into fused dimers connected by non-benzenoid rings was studied. The diradical character of the products was tuned according to the coupling section. In particular, the antiaromaticity of cyclobutadiene as the coupling motif and its position within the structure play a decisive role in shifting the natural orbital occupancies toward a stronger diradical electronic character. Understanding these structure-property relations is desirable not only for fundamental reasons but also for designing new complex and functional molecular structures.

Insights into the Polymerization Reactions on Solid Surfaces Provided by Scanning Tunneling Microscopy

Understanding the polymerization process at the molecular level is essential for the rational design and synthesis of polymers with controllable structures and properties. Scanning tunneling microscopy (STM) is one of the most important techniques to investigate the structures and reactions on conductive solid surfaces, and it has successfully been used to reveal the polymerization process on the surface at the molecular level in recent years. In this Perspective, after a brief introduction of on-surface polymerization reactions and STM, we focus on the applications of STM in the study of the processes and mechanism of on-surface polymerization, from one-dimensional to two-dimensional polymerization reactions. We conclude by a discussion of the challenges and perspectives on this topic.

On-surface synthesis of enetriynes

Belonging to the enyne family, enetriynes comprise a distinct electron-rich all-carbon bonding scheme. However, the lack of convenient synthesis protocols limits the associated application potential within, e.g., biochemistry and materials science. Herein we introduce a pathway for highly selective enetriyne formation via tetramerization of terminal alkynes on a Ag(100) surface. Taking advantage of a directing hydroxyl group, we steer molecular assembly and reaction processes on square lattices. Induced by O₂ exposure the terminal alkyne moieties deprotonate and organometallic bis-acetylide dimer arrays evolve. Upon subsequent thermal annealing tetrameric enetriyne-bridged compounds are generated in high yield, readily self-assembling into regular networks. We combine high-resolution scanning probe microscopy, X-ray photoelectron spectroscopy and density functional theory calculations to examine the structural features, bonding characteristics and the underlying reaction mechanism. Our study introduces an integrated strategy for the precise fabrication of functional enetriyne species, thus providing access to a distinct class of highly conjugated π-system compounds.

On-surface synthesis of non-benzenoid conjugated polymers by selective atomic rearrangement of ethynylarenes

Here, we report a new on-surface synthetic strategy to precisely introduce five-membered units into conjugated polymers from specifically designed precursor molecules that give rise to low-bandgap fulvalene-bridged bisanthene polymers. The selective formation of non-benzenoid units is finely controlled by the annealing parameters, which govern the initiation of atomic rearrangements that efficiently transform previously formed diethynyl bridges into fulvalene moieties. The atomically precise structures and electronic properties have been unmistakably characterized by STM, nc-AFM, and STS and the results are supported by DFT theoretical calculations. Interestingly, the fulvalene-bridged bisanthene polymers exhibit experimental narrow frontier electronic gaps of 1.2 eV on Au(111) with fully conjugated units. This on-surface synthetic strategy can potentially be extended to other conjugated polymers to tune their optoelectronic properties by integrating five-membered rings at precise sites.

The Role of Metal Adatoms in a Surface-Assisted Cyclodehydrogenation Reaction on a Gold Surface

Dehydrogenation reactions are key steps in many metal-catalyzed chemical processes and in the on-surface synthesis of atomically precise nanomaterials. The principal role of the metal substrate in these reactions is undisputed, but the role of metal adatoms remains, to a large extent, unanswered, particularly on gold substrates. Here, we discuss their importance by studying the surface-assisted cyclodehydrogenation on Au(111) as an ideal model case. We choose a polymer theoretically predicted to give one of two cyclization products depending on the presence or absence of gold adatoms. Scanning probe microscopy experiments observe only the product associated with adatoms. We challenge the prevalent understanding of surface-assisted cyclodehydrogenation, unveiling the catalytic role of adatoms and their effect on regioselectivity. The study adds new perspectives to the understanding of metal catalysis and the design of on-surface synthesis protocols for novel carbon nanomaterials.

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.

Selective activation of four quasi-equivalent C-H bonds yields N-doped graphene nanoribbons with partial corannulene motifs

Selective C–H bond activation is one of the most challenging topics for organic reactions. The difficulties arise not only from the high C–H bond dissociation enthalpies but also the existence of multiple equivalent/quasi-equivalent reaction sites in organic molecules. Here, we successfully achieve the selective activation of four quasi-equivalent C–H bonds in a specially designed nitrogen-containing polycyclic hydrocarbon (N-PH). Density functional theory calculations reveal that the adsorption of N-PH on Ag(100) differentiates the activity of the four ortho C(sp³) atoms in the N-heterocycles into two groups, suggesting a selective dehydrogenation, which is demonstrated by sequential-annealing experiments of N-PH/Ag(100). Further annealing leads to the formation of N-doped graphene nanoribbons with partial corannulene motifs, realized by the C–H bond activation process. Our work provides a route of designing precursor molecules with ortho C(sp³) atom in an N-heterocycle to realize surface-induced selective dehydrogenation in quasi-equivalent sites.

Selective activation of C–H bonds is a key challenge in organic reactions. Here, the authors achieve the selective activation of four quasi-equivalent C–H bonds, leading to the formation of N-doped graphene nanoribbons with partial corannulene motifs.

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

A Swiss Army knife for surface chemistry

Voltage pulses offer a way to control single-molecule reactions on a surface

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

Polycyclic hydrocarbons (PHs) share the same hexagonal structure of sp² carbons as graphene but possess an energy gap due to quantum confinement effect. PHs can be synthesized by a bottom-up strategy starting from small building blocks covalently bonded into large 2D organic sheets. Further investigation of the role of the covalent bonding/coupling ways on their electronic properties is needed. Here, we demonstrate a surface-mediated synthesis of hexa-peri-hexabenzocoronene (HBC) and its extended HBC oligomers (dimers, trimers, and tetramers) via single- and triple-coupling ways and reveal the implication of different covalent bonding on their electronic properties. High-resolution low-temperature scanning tunneling microscopy and noncontact atomic force microscopy are employed to in situ determine the atomic structures of as-synthesized HBC oligomers. Scanning tunneling spectroscopy measurements show that the length extension of HBC oligomers narrows the energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Furthermore, the energy gaps of triple-coupling HBC oligomers are smaller and decrease more significantly than that of the single-coupling ones. We hypothesize that the triple coupling promotes a more effective delocalization of π-electrons than the single coupling, according to density functional theory calculations. We also demonstrate that the HBC oligomers can further extend across the substrate steps to achieve conjugated polymers and large-area porous carbon networks.

Chemical bond imaging using torsional and flexural higher eigenmodes of qPlus sensors

Non-contact atomic force microscopy (AFM) with CO-functionalized tips allows visualization of the chemical structure of adsorbed molecules and identify individual inter- and intramolecular bonds. This technique enables in-depth studies of on-surface reactions and self-assembly processes. Herein, we analyze the suitability of qPlus sensors, which are commonly used for such studies, for the application of modern multifrequency AFM techniques. Two different qPlus sensors were tested for submolecular resolution imaging via actuating torsional and flexural higher eigenmodes and via bimodal AFM. The torsional eigenmode of one of our sensors is perfectly suited for performing lateral force microscopy (LFM) with single bond resolution. The obtained LFM images agree well with images from the literature, which were scanned with customized qPlus sensors that were specifically designed for LFM. The advantage of using a torsional eigenmode is that the same molecule can be imaged either with a vertically or laterally oscillating tip without replacing the sensor simply by actuating a different eigenmode. Submolecular resolution is also achieved by actuating the 2^nd flexural eigenmode of our second sensor. In this case, we observe particular contrast features that only appear in the AFM images of the 2^nd flexural eigenmode but not for the fundamental eigenmode. With complementary laser Doppler vibrometry measurements and AFM simulations we can rationalize that these contrast features are caused by a diagonal (i.e. in-phase vertical and lateral) oscillation of the AFM tip.

Experimental analysis of tip vibrations at higher eigenmodes of QPlus sensors for atomic force microscopy

QPlus sensors are non-contact atomic force microscope probes constructed from a quartz tuning fork and a tungsten wire with an electrochemically etched tip. These probes are self-sensing and offer an atomic-scale spatial resolution. Therefore, qPlus sensors are routinely used to visualize the chemical structure of adsorbed organic molecules via the so-called bond imaging technique. This is achieved by functionalizing the AFM tip with a single CO molecule and exciting the sensor at the first vertical cantilever resonance mode. Recent work using higher-order resonance modes has also resolved the chemical structure of single organic molecules. However, in these experiments, the image contrast can differ significantly from the conventional bond imaging contrast, which was suspected to be caused by unknown vibrations of the tip. This work investigates the source of these artefacts by using a combination of mechanical simulation and laser vibrometry to characterize a range of sensors with different tip wire geometries. The results show that increased tip mass and length cause increased torsional rotation of the tuning fork beam due to the off-center mounting of the tip wire, and increased flexural vibration of the tip. These undesirable motions cause lateral deflection of the probe tip as it approaches the sample, which is rationalized to be the cause of the different image contrast. The results also provide a guide for future probe development to reduce these issues.

Anchoring and Reacting On-Surface to Achieve Programmability

On-surface synthesis has developed into a modern method to fabricate low-dimensional molecular nanostructures with atomic precision. It impresses the chemistry community mostly via its simplicity, selectivity, and programmability during the synthesis. However, an insufficient mechanistic understanding of on-surface reactions and the discriminations in methodologies block it out from the conventional cognition of reaction and catalysis, which inhibits the extensive implication of on-surface synthesis. In this Perspective, we summarize the empirical paradigms of conceptually appealing programmability in on-surface synthesis. We endeavor to deliver the message that the impressive programmability is related to chemical heterogeneity which can also be coded at the molecular level and deciphered by the catalytic surfaces in varying chemical environments as specific chemical selectivity. With the assistance of structure-sensitive techniques, it is possible to recognize the chemical heterogeneity on surfaces to provide insight into the programmable on-surface construction of molecular nanoarchitectures and to reshape the correlation between the mechanistic understanding in on-surface synthesis and conventional chemistry.

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.

Order from a Mess: The Growth of 5-Armchair Graphene Nanoribbons

The advent of on-surface chemistry under vacuum has vastly increased our capabilities to synthesize carbon nanomaterials with atomic precision. Among the types of target structures that have been synthesized by these means, graphene nanoribbons (GNRs) have probably attracted the most attention. In this context, the vast majority of GNRs have been synthesized from the same chemical reaction: Ullmann coupling followed by cyclodehydrogenation. Here, we provide a detailed study of the growth process of five-atom-wide armchair GNRs starting from dibromoperylene. Combining scanning probe microscopy with temperature-dependent XPS measurements and theoretical calculations, we show that the GNR growth departs from the conventional reaction scenario. Instead, precursor molecules couple by means of a concerted mechanism whereby two covalent bonds are formed simultaneously, along with a concomitant dehydrogenation. Indeed, this alternative reaction path is responsible for the straight GNR growth in spite of the initial mixture of reactant isomers with irregular metal-organic intermediates that we find. The provided insight will not only help understanding the reaction mechanisms of other reactants but also serve as a guide for the design of other precursor molecules.

On-surface synthesis of organocopper metallacycles through activation of inner diacetylene moieties

The design of organometallic complexes is at the heart of modern organic chemistry and catalysis. Recently, on-surface synthesis has emerged as a disruptive paradigm to design previously precluded compounds and nanomaterials. Despite these advances, the field of organometallic chemistry on surfaces is still at its infancy. Here, we introduce a protocol to activate the inner diacetylene moieties of a molecular precursor by copper surface adatoms affording the formation of unprecedented organocopper metallacycles on Cu(111). The chemical structure of the resulting complexes is characterized by scanning probe microscopy and X-ray photoelectron spectroscopy, being complemented by density functional theory calculations and scanning probe microscopy simulations. Our results pave avenues to the engineering of organometallic compounds and steer the development of polyyne chemistry on surfaces.

The diacetylene skeletons of DNBD precursors are attacked on Cu(111) by copper adatoms resulting in the synthesis of organocopper metallacycles.

Constructing covalent organic nanoarchitectures molecule by molecule via scanning probe manipulation

Constructing low-dimensional covalent assemblies with tailored size and connectivity is challenging yet often key for applications in molecular electronics where optical and electronic properties of the quantum materials are highly structure dependent. We present a versatile approach for building such structures block by block on bilayer sodium chloride (NaCl) films on Cu(111) with the tip of an atomic force microscope, while tracking the structural changes with single-bond resolution. Covalent homo-dimers in cis and trans configurations and homo-/hetero-trimers were selectively synthesized by a sequence of dehalogenation, translational manipulation and intermolecular coupling of halogenated precursors. Further demonstrations of structural build-up include complex bonding motifs, like carbon–iodine–carbon bonds and fused carbon pentagons. This work paves the way for synthesizing elusive covalent nanoarchitectures, studying structural modifications and revealing pathways of intermolecular reactions.

Tailoring the size and connectivity of organic nanostructures is challenging but is often key in molecular electronics for tuning the properties of the quantum materials. Now an approach has been developed for building low-dimensional covalent architectures block by block on a surface by highly selective tip-induced intermolecular reactions.

On-Surface Strain-Driven Synthesis of Nonalternant Non-Benzenoid Aromatic Compounds Containing Four- to Eight-Membered Rings

The synthesis of polycyclic aromatic hydrocarbons containing various non-benzenoid rings remains a big challenge facing contemporary organic chemistry despite a considerable effort made over the last decades. Herein, we present a novel route, employing on-surface chemistry, to synthesize nonalternant polycyclic aromatic hydrocarbons containing up to four distinct kinds of non-benzenoid rings. We show that the surface-induced mechanical constraints imposed on strained helical reactants play a decisive role leading to the formation of products, energetically unfavorable in solution, with a peculiar ring current stabilizing the aromatic character of the π-conjugated system. Determination of the chemical and electronic structures of the most frequent product reveals its closed-shell character and low band gap. The present study renders a new route for the synthesis of novel nonalternant polycyclic aromatic hydrocarbons or other hydrocarbons driven by internal stress imposed by the surface not available by traditional approaches of organic chemistry in solution.

Chemical Identification and Bond Control of π-Skeletons in a Coupling Reaction

Highly unsaturated π-rich carbon skeletons afford versatile tuning of structural and optoelectronic properties of low-dimensional carbon nanostructures. However, methods allowing more precise chemical identification and controllable integration of target sp-/sp²-carbon skeletons during synthesis are required. Here, using the coupling of terminal alkynes as a model system, we demonstrate a methodology to visualize and identify the generated π-skeletons at the single-chemical-bond level on the surface, thus enabling further precise bond control. The characteristic electronic features together with localized vibrational modes of the carbon skeletons are resolved in real space by a combination of scanning tunneling microscopy/spectroscopy (STM/STS) and tip-enhanced Raman spectroscopy (TERS). Our approach allows single-chemical-bond understanding of unsaturated carbon skeletons, which is crucial for generating low-dimensional carbon nanostructures and nanomaterials with atomic precision.

Direct Observation of Amide Bond Formation in a Plasmonic Nanocavity Triggered by Single Nanoparticle Collisions

The real-time observation of chemical bond formation at the single-molecule level is one of the great challenges in the fields of organic and biomolecular chemistry. Valuable information can be gleaned that is not accessible using ensemble-average measurements. Although remarkably sophisticated techniques for monitoring chemical reactions have been developed, the ability to detect the specific formation of a chemical bond in situ at the single-molecule level has remained an elusive goal. Amide bonds are routinely formed from the aminolysis of N-hydroxysuccinimide (NHS) esters by primary amines, and the protocol is widely used for the synthesis, cross-linking, and labeling of peptides and proteins. Herein, a plasmonic nanocavity was applied to study aminolysis reaction for amide bond formation, which was initiated by single nanoparticle collision events between suitably functionalized free-moving gold nanoparticles and a gold nanoelectrode in an aqueous buffer. By means of simultaneous surface enhanced Raman spectroscopy (SERS) and single-entity electrochemistry (EC) measurements, we have probed the dynamic evolution of amide bond formation in the aminolysis reaction with 10 s of millisecond time resolution. Hence, we demonstrate that single-entity EC-SERS is a valuable and sensitive technique by which chemical reactions can be studied at the single-molecule level.

Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions

We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3- (Keggin) and [P2W18O62]6- (Wells-Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W-O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.

Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium

In heterogeneous catalysis, free energy profiles of reactions govern the mechanisms, rates, and equilibria. Energetics are conventionally computed using the harmonic approximation (HA), which requires determination of critical states a priori. Here, we use neural networks to efficiently sample and directly calculate the free energy surface (FES) of a prototypical heterogeneous catalysis reaction-the dissociation of molecular nitrogen on ruthenium-at density-functional-theory-level accuracy. We find that the vibrational entropy of surface atoms, often neglected in HA for transition metal catalysts, contributes significantly to the reaction barrier. The minimum free energy path for dissociation reveals an "on-top" adsorbed molecular state prior to the transition state. While a previously reported flat-lying molecular metastable state can be identified in the potential energy surface, it is absent in the FES at relevant reaction temperatures. These findings demonstrate the importance of identifying critical points self-consistently on the FES for reactions that involve considerable entropic effects.

Reassessing Alkyne Coupling Reactions While Studying the Electronic Properties of Diverse Pyrene Linkages at Surfaces

The combination of alkyne and halogen functional groups in the same molecule allows for the possibility of many different reactions when utilized in on-surface synthesis. Here, we use a pyrene-based precursor with both functionalities to examine the preferential reaction pathway when it is heated on an Au(111) surface. Using high-resolution bond-resolving scanning tunneling microscopy, we identify multiple stable intermediates along the prevailing reaction pathway that initiate with a clearly dominant Glaser coupling, together with a multitude of other side products. Importantly, control experiments with reactants lacking the halogen functionalization reveal the Glaser coupling to be absent and instead show the prevalence of non-dehydrogenative head-to-head alkyne coupling. We perform scanning tunneling spectroscopy on a rich variety of the product structures obtained in these experiments, providing key insights into the strong dependence of their HOMO-LUMO gaps on the nature of the intramolecular coupling. A clear trend is found of a decreasing gap that is correlated with the conversion of triple bonds to double bonds via hydrogenation and to higher levels of cyclization, particularly with nonbenzenoid product structures. We rationalize each of the studied cases.

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.

Aryl Triflates in On-Surface Chemistry

The reactivity of aryl triflates in on-surface C-C coupling is reported. It is shown that the triflate group in aryl triflates enables regioselective homo coupling with preceding or concomitant hydrodetriflation on Cu(111). Three different symmetrical π-systems with two and three triflate functionalities were used as monomers leading to oligomeric conjugated π-systems. The cascade, comprising different intermediates at different reaction temperatures as observed for one of the molecules, proceeds via initial removal of the trifluoromethyl sulfonyl group to give an aryloxy radical which in turn is deoxygenated to the corresponding aryl radical. Thermodynamically driven regioselective 1,2-hydrogen atom transfer leads to a translocated aryl radical which in turn undergoes coupling. For a sterically more hindered bistriflate, where one ortho position was blocked, dehydrogenative coupling occurred at remote position with good regioselectivity. Starting materials, intermediates as well as products were analyzed by scanning tunneling microscopy. Structures and suggested mechanism were further supported by DFT calculations.

Manipulable Metal Catalyst for Nanographene Synthesis

Performing bottom-up synthesis by using molecules adsorbed on a surface is an effective method to yield functional polycyclic aromatic hydrocarbons (PAHs) and nanocarbon materials. The intramolecular cyclodehydrogenation of hydrocarbons is a critical process in this synthesis; however, thus far, its elementary steps have not been elucidated thoroughly. In this study, we utilize the metal tip of a low-temperature noncontact atomic force microscope as a manipulable metal surface to locally activate dehydrogenation for PAH-forming cyclodehydrogenation. This method leads to the dissociation of a H atom of an intermediate to yield the cyclodehydrogenated product in a target-selective and reproducible manner. We demonstrate the metal-tip-catalyzed dehydrogenation for both benzenoid and nonbenzonoid PAHs, suggesting its universal applicability as a catalyst for nanographene synthesis.

Imaging oxygen molecular adsorption and dissociation on the Ti site of rutile TiO2(110) surface with real configuration at 78 K by atomic force microscopy

Understanding oxygen adsorption and dissociation on the five-fold coordinated titanium (Ti5c) site of the rutile TiO2 surface is important in clarifying chemical reaction processes. Accordingly, three different configurations of molecularly adsorbed O2, including parallel side-on, inclined side-on and end-on configurations, and their dissociation were directly observed with atomic resolution at 78 K by atomic force microscopy. Our results experimentally demonstrated that the three adsorbed O2 configurations could be changed by electric field stimulation. The initial configurations of the adsorbed O2 and transition of O2 configurations were related to their coverage. On the other hand, the tunneling current stimulation could dissociate these O2 species, indicating that they are precursors for the O adatom (Oad). It is proposed that the effect of electric field stimulation contributes to the transition of these three adsorbed O2 configurations, and the effect of the tunneling current is the main factor for the dissociation of the adsorbed O2. In addition, based on the atomic contrast and height histograms of Oad, different charge states of Oad were observed, which could coexist on the surface region. The present study demonstrates an intuitional observation of O2 adsorption and dissociation on the Ti5c site, and thus is expected to be useful to understand the surface reactions on the oxide surface.

On-Surface Synthesis of a Five-Membered Carbon Ring from a Terminal Alkynyl Bromide: A [4 + 1] Annulation

We report an on-surface synthesis of five-membered carbon ring via a [4 + 1] annulation reaction, starting from a simple terminal alkynyl bromide, 4-(bromoethynyl)biphenyl, on Ag(110). The combination of scanning tunneling microscopy (STM), synchrotron radiation photoemission spectroscopy (SRPES), and density functional theory (DFT) calculations unravel the reaction pathway and mechanism. Three basic reaction steps are involved, successively including the formation of alkynyl-Ag-alkynyl bridged organometallic dimer, the generation of alkylidene carbene intermediate, and the final [4 + 1] annulation involving a hydrogen transfer step.

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.

On-Surface Synthesis of Cumulene-Containing Polymers via Two-Step Dehalogenative Homocoupling of Dibromomethylene-Functionalized Tribenzoazulene

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on-surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well-controlled ultrahigh-vacuum conditions. Here we report the on-surface synthesis of a polymer linked by cumulene-like bonds on a Au(111) surface via sequential thermally activated dehalogenative C-C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene-like pentagon-pentagon and heptagon-heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X-ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on-surface synthesis of cumulene-containing compounds, as well as protocols relevant to the stepwise fabrication of carbon-carbon bonds on surfaces.

Steering alkyne homocoupling with on-surface synthesized metal-organic complexes

We report a multi-step on-surface synthesis strategy. The first step consists in the surface-supported synthesis of metal-organic complexes, which are subsequently used to steer on-surface alkyne coupling reactions. In addition, we analyze and compare the electronic properties of the different coupling motifs obtained.

Thermally induced intra-molecular transformation and metalation of free-base porphyrin on Au(111) surface steered by surface confinement and ad-atoms

We investigated chemical transformations of a fluorinated free-base porphyrin, 5,10,15,20-tetrakis(4-fluorophenyl)-21,23H-porphyrin (2H-4FTPP) under a Au(111) surface confinement and including gold adatoms by using an experiment and density functional theory based first-principles calculations. Annealing of 2H-4FTPP led to cyclodehydrogenation of the molecule to a π-extended fused aromatic planar compound, 2H-4FPP, and metallation of the porphyrin ring by Au atoms to Au-4FPP complex. Noticeable lowering of bond-dissociation energies of the pyrrole's C-H bonds of the Au(111) supported molecule with respect to their values in the gas phase explained the observed on-surface planarization. Our findings also indicate that Au adatoms may catalyze cleavage of C-H/F bonds in temperature-initiated processes on Au surfaces. BDEs and explicit inclusion of Au adatoms helps to rationalize thermally induced chemical reactions on the respective surface.

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.

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.