Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

Bridging molecular-scale interfacial science with continuum-scale models

Solid-water interfaces are crucial for clean water, conventional and renewable energy, and effective nuclear waste management. However, reflecting the complexity of reactive interfaces in continuum-scale models is a challenge, leading to oversimplified representations that often fail to predict real-world behavior. This is because these models use fixed parameters derived by averaging across a wide physicochemical range observed at the molecular scale. Recent studies have revealed the stochastic nature of molecular-level surface sites that define a variety of reaction mechanisms, rates, and products even across a single surface. To bridge the molecular knowledge and predictive continuum-scale models, we propose to represent surface properties with probability distributions rather than with discrete constant values derived by averaging across a heterogeneous surface. This conceptual shift in continuum-scale modeling requires exponentially rising computational power. By incorporating our molecular-scale understanding of solid-water interfaces into continuum-scale models we can pave the way for next generation critical technologies and novel environmental solutions.

Electrostatic potentials of atomic nanostructures at metal surfaces quantified by scanning quantum dot microscopy

The discrete and charge-separated nature of matter - electrons and nuclei - results in local electrostatic fields that are ubiquitous in nanoscale structures and relevant in catalysis, nanoelectronics and quantum nanoscience. Surface-averaging techniques provide only limited experimental access to these potentials, which are determined by the shape, material, and environment of the nanostructure. Here, we image the potential over adatoms, chains, and clusters of Ag and Au atoms assembled on Ag(111) and quantify their surface dipole moments. By focusing on the total charge density, these data establish a benchmark for theory. Our density functional theory calculations show a very good agreement with experiment and allow a deeper analysis of the dipole formation mechanisms, their dependence on fundamental atomic properties and on the shape of the nanostructures. We formulate an intuitive picture of the basic mechanisms behind dipole formation, allowing better design choices for future nanoscale systems such as single-atom catalysts.

Direct Observation of Twin van der Waals Molecular Chains

The van der Waals (vdW) assemblies are the most common structures of materials. However, direct mapping of intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedentedly mapped the intermolecular electron cloud of the assemblies of ethanol molecules via ethyl groups with high-resolution atomic force microscopy and scanning tunneling microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on the Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from those of 2D vdW materials. These findings provide an "eye" to see the atomic world of vdW materials.

On-Surface Synthesis and Real-Space Visualization of Aromatic P3 N3

On-surface synthesis is at the verge of emerging as the method of choice for the generation and visualization of unstable or unconventional molecules, which could not be obtained via traditional synthetic methods. A case in point is the on-surface synthesis of the structurally elusive cyclotriphosphazene (P3 N3 ), an inorganic aromatic analogue of benzene. Here, we report the preparation of this fleetingly existing species on Cu(111) and Au(111) surfaces at 5.2 K through molecular manipulation with unprecedented precision, i.e., voltage pulse-induced sextuple dechlorination of an ultra-small (about 6 Å) hexachlorophosphazene P3 N3 Cl6 precursor by the tip of a scanning probe microscope. Real-space atomic-level imaging of cyclotriphosphazene reveals its planar D3h -symmetric ring structure. Furthermore, this demasking strategy has been expanded to generate cyclotriphosphazene from a hexaazide precursor P3 N21 via a different stimulation method (photolysis) for complementary measurements by matrix isolation infrared and ultraviolet spectroscopy.

Molecular Identification from AFM Images Using the IUPAC Nomenclature and Attribute Multimodal Recurrent Neural Networks

Spectroscopic methods─like nuclear magnetic resonance, mass spectrometry, X-ray diffraction, and UV/visible spectroscopies─applied to molecular ensembles have so far been the workhorse for molecular identification. Here, we propose a radically different chemical characterization approach, based on the ability of noncontact atomic force microscopy with metal tips functionalized with a CO molecule at the tip apex (referred as HR-AFM) to resolve the internal structure of individual molecules. Our work demonstrates that a stack of constant-height HR-AFM images carries enough chemical information for a complete identification (structure and composition) of quasiplanar organic molecules, and that this information can be retrieved using machine learning techniques that are able to disentangle the contribution of chemical composition, bond topology, and internal torsion of the molecule to the HR-AFM contrast. In particular, we exploit multimodal recurrent neural networks (M-RNN) that combine convolutional neural networks for image analysis and recurrent neural networks to deal with language processing, to formulate the molecular identification as an imaging captioning problem. The algorithm is trained using a data set─which contains almost 700,000 molecules and 165 million theoretical AFM images─to produce as final output the IUPAC name of the imaged molecule. Our extensive test with theoretical images and a few experimental ones shows the potential of deep learning algorithms in the automatic identification of molecular compounds by AFM. This achievement supports the development of on-surface synthesis and overcomes some limitations of spectroscopic methods in traditional solution-based synthesis.

Visualizing the atomic-scale origin of metallic behavior in Kondo insulators

A Kondo lattice is often electrically insulating at low temperatures. However, several recent experiments have detected signatures of bulk metallicity within this Kondo insulating phase. In this study, we visualized the real-space charge landscape within a Kondo lattice with atomic resolution using a scanning tunneling microscope. We discovered nanometer-scale puddles of metallic conduction electrons centered around uranium-site substitutions in the heavy-fermion compound uranium ruthenium silicide (URu₂Si₂) and around samarium-site defects in the topological Kondo insulator samarium hexaboride (SmB₆). These defects disturbed the Kondo screening cloud, leaving behind a fingerprint of the metallic parent state. Our results suggest that the three-dimensional quantum oscillations measured in SmB₆ arise from Kondo-lattice defects, although we cannot exclude other explanations. Our imaging technique could enable the development of atomic-scale charge sensors using heavy-fermion probes.

Real-space imaging of a phenyl group migration reaction on metal surfaces

The explorations to extend present chemical synthetic methods are of great importance to simplify synthetic routes of chemical species. Additionally, understanding the chemical reaction mechanisms is critical to achieve controllable synthesis for applications. Here, we report the on-surface visualization and identification of a phenyl group migration reaction of 1,4-dimethyl-2,3,5,6-tetraphenyl benzene (DMTPB) precursor on Au(111), Cu(111) and Ag(110) substrates. With the combination of bond-resolved scanning tunneling microscopy (BR-STM), noncontact atomic force microscopy (nc-AFM) and density functional theory (DFT) calculations, the phenyl group migration reaction of DMTPB precursor is observed, forming various polycyclic aromatic hydrocarbons on the substrates. DFT calculations reveal that the multiple-step migrations are facilitated by the hydrogen radical attack, inducing cleavage of phenyl groups and subsequent rearomatization of the intermediates. This study provides insights into complex surface reaction mechanisms at the single molecule level, which may guide the design of chemical species.

Water Structures Reveal Local Hydrophobicity on the In2O3(111) Surface

Clean oxide surfaces are generally hydrophilic. Water molecules anchor at undercoordinated surface metal atoms that act as Lewis acid sites, and they are stabilized by H bonds to undercoordinated surface oxygens. The large unit cell of In₂O₃(111) provides surface atoms in various configurations, which leads to chemical heterogeneity and a local deviation from this general rule. Experiments (TPD, XPS, nc-AFM) agree quantitatively with DFT calculations and show a series of distinct phases. The first three water molecules dissociate at one specific area of the unit cell and desorb above room temperature. The next three adsorb as molecules in the adjacent region. Three more water molecules rearrange this structure and an additional nine pile up above the OH groups. Despite offering undercoordinated In and O sites, the rest of the unit cell is unfavorable for adsorption and remains water-free. The first water layer thus shows ordering into nanoscopic 3D water clusters separated by hydrophobic pockets.

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.

Length-dependent symmetry in narrow chevron-like graphene nanoribbons

We report the structural and electronic properties of narrow chevron-like graphene nanoribbons (GNRs), which depending on their length are either mirror or inversion symmetric. Additionally, GNRs of different length can form molecular heterojunctions based on an unusual binding motif.

Step-Assisted On-Surface Synthesis of Graphene Nanoribbons Embedded with Periodic Divacancies

The bottom-up approach through on-surface synthesis of porous graphene nanoribbons (GNRs) presents a controllable manner for implanting periodic nanostructures to tune the electronic properties of GNRs in addition to bandgap engineering by width and edge configurations. However, owing to the existing steric hindrance in small pores like divacancies, it is still difficult to embed periodic divacancies with a nonplanar configuration into GNRs. Here, we demonstrate the on-surface synthesis of atomically precise eight-carbon-wide armchair GNRs embedded with periodic divacancies (DV8-aGNRs) by utilizing the monatomic step edges on the Au(111) surface. From a single molecular precursor correspondingly following a trans- and cis-coupling, the DV8-aGNR and another porous nanographene are respectively formed at step edges and on terraces at 720 and 570 K. Combining scanning tunneling microscopy/spectroscopy, atomic force microscopy, and first-principles calculations, we determine the out-of-plane conformation, wide bandgap (∼3.36 eV), and wiggly shaped frontier orbitals of the DV8-aGNR. Nudged elastic band calculations further quantitatively reveal that the additional steric hindrance effect in the cyclodehydrogenative reactions has a higher barrier of 1.3 eV than that in the planar porous nanographene, which also unveils the important role played by the monatomic Au step and adatoms in reducing the energy barriers and enhancing the thermodynamic preference of the oxidative cyclodehydrogenation. Our results provide the first case of GNRs containing periodic pores as small as divacancies with a nonplanar configuration and demonstrate the strategy by utilizing the chemical heterogeneity of a substrate to promote the formation of novel carbon nanomaterials.

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.

QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy

This paper introduces Quasar Science Resources-Autonomous University of Madrid atomic force microscopy image data set (QUAM-AFM), the largest data set of simulated atomic force microscopy (AFM) images generated from a selection of 685,513 molecules that span the most relevant bonding structures and chemical species in organic chemistry. QUAM-AFM contains, for each molecule, 24 3D image stacks, each consisting of constant-height images simulated for 10 tip-sample distances with a different combination of AFM operational parameters, resulting in a total of 165 million images with a resolution of 256 × 256 pixels. The 3D stacks are especially appropriate to tackle the goal of the chemical identification within AFM experiments by using deep learning techniques. The data provided for each molecule include, besides a set of AFM images, ball-and-stick depictions, IUPAC names, chemical formulas, atomic coordinates, and map of atom heights. In order to simplify the use of the collection as a source of information, we have developed a graphical user interface that allows the search for structures by CID number, IUPAC name, or chemical formula.

A novel energy level detector for molecular semiconductors

The multifunction of molecule-based devices is always achieved by improving their charge transport characteristics. These characteristics depend strongly on the energy levels of molecular semiconductors, which fundamentally govern the working principle and device performance. Therefore, an accurate measurement of these energy levels is crucial for evaluating the availability of the prepared materials and thus optimizing the device performance. Here, an easy-to-operate three-terminal hot electron transistor has been developed, which comprises a molecular optoelectronic device that records the charge transport. It achieves exceptional properties including the lowest unoccupied molecular orbit level, highest occupied molecular orbit level, higher energy states, and higher electronic bandgap. When compared with existing techniques such as cyclic voltammetry, inverse photoemission spectroscopy, and ultraviolet photoemission spectroscopy, the hot electron transistor provides in-situ characterization and categorizes the measured energy information as intrinsic properties of the molecular semiconductor. Furthermore, we provide an in-depth understanding of the fundamental device-physics, which provides promising guidance for performance optimization.

Electrostatic Discovery Atomic Force Microscopy

While offering high resolution atomic and electronic structure, scanning probe microscopy techniques have found greater challenges in providing reliable electrostatic characterization on the same scale. In this work, we offer electrostatic discovery atomic force microscopy, a machine learning based method which provides immediate maps of the electrostatic potential directly from atomic force microscopy images with functionalized tips. We apply this to characterize the electrostatic properties of a variety of molecular systems and compare directly to reference simulations, demonstrating good agreement. This approach offers reliable atomic scale electrostatic maps on any system with minimal computational overhead.

Pseudo-atomic orbital behavior in graphene nanoribbons with four-membered rings

The incorporation of nonhexagonal rings into graphene nanoribbons (GNRs) is an effective strategy for engineering localized electronic states, bandgaps, and magnetic properties. Here, we demonstrate the successful synthesis of nanoribbons having four-membered ring (cyclobutadienoid) linkages by using an on-surface synthesis approach involving direct contact transfer of coronene-type precursors followed by thermally assisted [2 + 2] cycloaddition. The resulting coronene-cyclobutadienoid nanoribbons feature a narrow 600-meV bandgap and novel electronic frontier states that can be interpreted as linear chains of effective p_x and p_y pseudo-atomic orbitals. We show that these states give rise to exceptional physical properties, such as a rigid indirect energy gap. This provides a previously unexplored strategy for constructing narrow gap GNRs via modification of precursor molecules whose function is to modulate the coupling between adjacent four-membered ring states.

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.

Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy

[Figure: see text].

Colloidal Self-Assembly Approaches to Smart Nanostructured Materials

Colloidal self-assembly refers to a solution-processed assembly of nanometer-/micrometer-sized, well-dispersed particles into secondary structures, whose collective properties are controlled by not only nanoparticle property but also the superstructure symmetry, orientation, phase, and dimension. This combination of characteristics makes colloidal superstructures highly susceptible to remote stimuli or local environmental changes, representing a prominent platform for developing stimuli-responsive materials and smart devices. Chemists are achieving even more delicate control over their active responses to various practical stimuli, setting the stage ready for fully exploiting the potential of this unique set of materials. This review addresses the assembly of colloids into stimuli-responsive or smart nanostructured materials. We first delineate the colloidal self-assembly driven by forces of different length scales. A set of concepts and equations are outlined for controlling the colloidal crystal growth, appreciating the importance of particle connectivity in creating responsive superstructures. We then present working mechanisms and practical strategies for engineering smart colloidal assemblies. The concepts underpinning separation and connectivity control are systematically introduced, allowing active tuning and precise prediction of the colloidal crystal properties in response to external stimuli. Various exciting applications of these unique materials are summarized with a specific focus on the structure-property correlation in smart materials and functional devices. We conclude this review with a summary of existing challenges in colloidal self-assembly of smart materials and provide a perspective on their further advances to the next generation.

Benchmarking atomically defined AFM tips for chemical-selective imaging

Controlling the identity of the tip-terminating atom or molecule in low-temperature atomic force microscopy has led to ground breaking progress in surface chemistry and nanotechnology. Lacking a comparative tip-performance assessment, a profound standardization in such experiments is highly desirable. Here we directly compare the imaging and force-spectroscopy capabilities of four atomically defined tips, namely Cu-, Xe-, CO-, and O-terminated Cu-tips (CuOx-tips). Using a nanostructured copper-oxide surface as benchmark system, we found that Cu-tips react with surface oxygen, while chemically inert Xe- and CO-tips allow entering the repulsive force regime enabling increased resolution. However, their high flexibility leads to imaging artifacts and their strong passivation suppresses the chemical contrast. The higher rigidity and selectively increased chemical reactivity of CuOx-tips prevent tip-bending artifacts and generate a distinct chemical contrast. This result is particularly promising in view of future studies on other metal-oxide surfaces.

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.

A Deep Learning Approach for Molecular Classification Based on AFM Images

In spite of the unprecedented resolution provided by non-contact atomic force microscopy (AFM) with CO-functionalized and advances in the interpretation of the observed contrast, the unambiguous identification of molecular systems solely based on AFM images, without any prior information, remains an open problem. This work presents a first step towards the automatic classification of AFM experimental images by a deep learning model trained essentially with a theoretically generated dataset. We analyze the limitations of two standard models for pattern recognition when applied to AFM image classification and develop a model with the optimal depth to provide accurate results and to retain the ability to generalize. We show that a variational autoencoder (VAE) provides a very efficient way to incorporate, from very few experimental images, characteristic features into the training set that assure a high accuracy in the classification of both theoretical and experimental images.

Significance Of Nuclear Quantum Effects In Hydrogen Bonded Molecular Chains

In hydrogen-bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of π-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to distinctive electronic in-gap states localized at the ends. These findings demonstrate the identification of a class of isomeric hydrogen-bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. This identification is a step toward the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling.

Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning

Scanning probe microscopies allow investigating surfaces at the nanoscale, in real space and with unparalleled signal-to-noise ratio. However, these microscopies are not used as much as it would be expected considering their potential. The main limitations preventing a broader use are the need of experienced users, the difficulty in data analysis and the time-consuming nature of experiments that require continuous user supervision. In this work, we addressed the latter and developed an algorithm that controlled the operation of an Atomic Force Microscope (AFM) that, without the need of user intervention, allowed acquiring multiple high-resolution images of different molecules. We used DNA on mica as a model sample to test our control algorithm, which made use of two deep learning techniques that so far have not been used for real time SPM automation. One was an object detector, YOLOv3, which provided the location of molecules in the captured images. The second was a Siamese network that could identify the same molecule in different images. This allowed both performing a series of images on selected molecules while incrementing the resolution, as well as keeping track of molecules already imaged at high resolution, avoiding loops where the same molecule would be imaged an unlimited number of times. Overall, our implementation of deep learning techniques brings SPM a step closer to full autonomous operation.

Atomic-Level Electronic Properties of Carbon Nitride Monolayers

Heteroatom-doped carbon-based materials are of significance for clean energy conversion and storage because of their fascinating electronic properties, low cost, high durability, and environmental friendliness. Atomically precise fabrication of carbon-based materials with well-defined heteroatom-dopant positions and atomic-scale understanding of their atomic-level electronic properties is a challenge. Herein, we demonstrate the bottom-up on-surface synthesis of 1D and 2D monolayer carbon nitride nanostructures with precise control of the nitrogen-atom doping sites and pore sizes. We also observe an electronic band offset at the C-N heterojunction. Using high-resolution scanning tunneling microscopy, the atomic structure of the as-prepared carbon nitride nanoporous monolayers are revealed, indicating successful and precise control of the structures and N atom doping sites. Furthermore, corroborated by theoretical calculations, scanning tunneling spectroscopy measurements reveal a valence band shift of 140 meV that results in an electric field of 2.9 × 10⁸ V m^-1 at the C-N heterojunction, indicating efficient separation of the electron-hole pair at the N doping site. Our finding offers direct atomic-level insights into the local electronic structure of the heteroatom-doped carbon-based materials.

Electrostatics, Hydrogen Bonding, and Molecular Structure at Polycation and Peptide:Lipid Membrane Interfaces

Polycation and peptide-modified surfaces represent opportunities for developing potentially novel biocidal materials in a growing effort to combat bacterial resistance to traditional bactericides. It is well-known that the positive charge of these compounds is crucial to their function in biofouling prevention and as antimicrobials; however, methods for quantifying the number of positive charges on surface-bound polycations and peptides are necessary to predict, control, and optimize the design and therefore the utility of these compounds. This Spotlight on Applications reports on such an approach that combines second harmonic generation (SHG) spectroscopy, quartz crystal microbalance with dissipation monitoring (QCM-D), and atomistic simulations to obtain mechanistic insight into polycation-membrane interactions using supported lipid bilayers (SLBs) as our model system. We find that at high surface coverage, the large polycations we surveyed feature a considerably smaller percentage of ionization when compared to the smaller polycations and peptides. At these high charge densities, we suspect a pK_a shift of the charged groups to lower charge-charge repulsion as well as the formation of a looplike conformation such that less monomeric units form contact-ion pairs with the bilayer. Our sum frequency generation (SFG) spectroscopy results complement our understanding of the polycation-membrane interaction. At a high density of the polycation poly(allylamine hydrochloride) (PAH), second-order spectral line shapes are consistent with the expulsion of interfacial water molecules possibly due to contact-ion pair formation between PAH and the lipid bilayer. This finding could be essential for understanding the underlying first steps of cell lysis and penetration by polycations and should be explored further.

High resolution noncontact atomic force microscopy imaging with oxygen-terminated copper tips at 78 K

Functionalizing atomic force microscopy (AFM) tips by picking up single inert probe particles like CO or Xe from the surface drastically increase the resolution. In particular, this approach allows imaging organic molecules with submolecular resolution revealing their internal bonding structure. However, due to the weak coupling of these probe particles to both, the surface they are picked up from and the tip apex, these experiments require liquid helium temperatures (i.e.≈5 K). In the present study we demonstrate that functionalizing an AFM tip with an atomically defined O-terminated copper tip (CuOx tip) allows performing such experiments at liquid nitrogen temperatures (i.e.≈78 K) with outstanding quality. We show that it is possible to utilize CuOx tips for chemically selective imaging of a copper oxide nanodomain on a partially oxidized Cu(110) surface in the repulsive force regime at elevated temperatures. Moreover, the high structural and chemical stability of CuOx tips allow even ex situ investigations where these tips are used to perform experiments on other, non-Cu, non-oxidized, substrates. In particular, we present results obtained from a dicoronylene (DCLN) molecule with submolecular resolution. An analysis of inner and peripheral bond lengths of the DCLN molecule shows excellent agreement with theoretical gas phase simulations emphasizing the exceptional imaging properties of CuOx tips also at elevated temperatures.

Elucidating the intramolecular contrast in the STM images of 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules recorded at room-temperature and at the liquid-solid interface

Star-shaped 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules self-assemble at the solid-liquid interface into a compact hexagonal nanoarchitecture on graphite. High resolution scanning tunneling microscopy (STM) images of the molecules reveal intramolecular features. Comparison of the experimental data with calculated molecular charge density contours shows that the molecular features in the STM images correspond to molecular LUMO+2.

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.

On-surface chemical reactions characterised by ultra-high resolution scanning probe microscopy

The impact of high resolution scanning probe microscopy on imaging individual molecules with intramolecular resolution is reviewed.

Fluorescence enhancement of fungicide thiabendazole by van der Waals interaction with transition metal dichalcogenide nanosheets for highly specific sensors

Many molecules quench their fluorescence upon adsorption on surfaces. Herein we show that the interaction of thiabendazole, a widespread used fungicide of the benzimidazole family, with nanosheets of transition metal dichalcogenides, particularly of WS2, leads to a significant increase, more than a factor of 5, of the fluorescence yield. This surprising effect is rationalized by DFT calculations and found to be related to the inhibition of the intramolecular rotation between the benzimidazole and thiazole groups due to a bonding rigidization upon interaction with the MoS2 surface. This non-covalent adsorption leads to a redistribution of the molecular LUMO that blocks the non-radiative energy dissipation channel. This unusual behaviour does not operate either for other molecules of the same benzimidazole family or for other 2D materials (graphene or graphene oxide). Moreover, we found that a linear dependence of the emission with the concentration of thiabendazole in solution, which combined with the specificity of the process, allows the development of a highly sensitive and selective method towards thiabendazole determination that can be applied to real river water samples. An excellent detection limit of 2.7 nM, comparable to the best performing reported methods, is obtained with very good accuracy (Er ≤ 6.1%) and reproducibility (RSD ≤ 4.1%) in the concentration range assayed.

Charge Carrier Injection Electroluminescence with CO-Functionalized Tips on Single Molecular Emitters

We investigate electroluminescence of single molecular emitters on NaCl on Ag(111) and Au(111) with submolecular resolution in a low-temperature scanning probe microscope with tunneling current, atomic force, and light detection capabilities. The role of the tip state is studied in the photon maps of a prototypical emitter, zinc phthalocyanine (ZnPc), using metal and CO-metal tips. CO-functionalization is found to have an impact on the resolution and contrast of the photon maps due to the localized overlap of the p-orbitals on the tip with the molecular orbitals of the emitter. The possibility of using the same CO-functionalized tip for tip-enhanced photon detection and high resolution atomic force is demonstrated. We study the electroluminescence of ZnPc, induced by charge carrier injection at sufficiently high bias voltages. We propose that the distinct level alignment of the ZnPc frontier orbitals with the Au(111) and Ag(111) Fermi levels governs the primary excitation mechanisms as the injection of electrons and holes from the tip into the molecule, respectively. These findings put forward the importance of the tip status in the photon maps and contribute to a better understanding of the photophysics of organic molecules on surfaces.

The theory of scanning quantum dot microscopy

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

Revisiting Kekulene: Synthesis and Single-Molecule Imaging

Four decades after the first (and only) reported synthesis of kekulene, this emblematic cycloarene has been obtained again through an improved route involving the construction of a key synthetic intermediate, 5,6,8,9-tetrahydrobenzo[m]tetraphene, by means of a double Diels-Alder reaction between styrene and a versatile benzodiyne synthon. Ultra-high-resolution AFM imaging of single molecules of kekulene and computational calculations provide additional support for a molecular structure with a significant degree of bond localization in accordance with the resonance structure predicted by the Clar model.

Charge-Induced Structural Changes in a Single Molecule Investigated by Atomic Force Microscopy

Intramolecular structural relaxations occurring upon electron transfer are crucial in determining the rate of redox reactions. Here, we demonstrate that subangstrom structural changes occurring upon single-electron charging can be quantified by means of atomically resolved atomic force microscopy (AFM) for the case of single copper(II)phthalocyanine (CuPc) molecules deposited on an ultrathin NaCl film. Imaging the molecule in distinct charge states (neutral and anionic) reveals characteristic differences in the AFM contrast. In comparison to density functional theory simulations these changes in contrast can be directly related to relaxations of the molecule's geometric structure upon charging. The dominant contribution arises from a nonhomogeneous vertical relaxation of the molecule, caused by a change in the electrostatic interaction with the surface.

Quantitative imaging of electric surface potentials with single-atom sensitivity

Because materials consist of positive nuclei and negative electrons, electric potentials are omnipresent at the atomic scale. However, due to the long range of the Coulomb interaction, large-scale structures completely outshine small ones. This makes the isolation and quantification of the electric potentials that originate from nanoscale objects such as atoms or molecules very challenging. Here we report a non-contact scanning probe technique that addresses this challenge. It exploits a quantum dot sensor and the joint electrostatic screening by tip and surface, thus enabling quantitative surface potential imaging across all relevant length scales down to single atoms. We apply the technique to the characterization of a nanostructured surface, thereby extracting workfunction changes and dipole moments for important reference systems. This authenticates the method as a versatile tool to study the building blocks of materials and devices down to the atomic scale.

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

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

External strain-enhanced cysteine enantiomeric separation ability on alloyed stepped surfaces

Using density functional theory with an accurate treatment of van der Waals interactions, we investigate the enantioselective recognition and separation of chiral molecules on stepped metal surfaces. Our calculations demonstrate that the separation ability of metal substrates can be significantly enhanced by surface decoration and external strain. For example, applying 2% tensile strain to the Ag-alloyed Au(532) surface leads to a dramatic increase (by 89%) in cysteine enantioselectivity as compared to that of pristine Au(532). Analysis on the computed binding energies shows that the interaction energy is the predominant factor that affects the separation efficiency in strongly bound systems. Our study presents a new strategy to modify the enantioselectivity of stepped metal surfaces and paves the way for exploring high efficiency chiral separation technology in pharmaceutical industry.

Geometric imaging of borophene polymorphs with functionalized probes

A common characteristic of borophene polymorphs is the presence of hollow hexagons (HHs) in an otherwise triangular lattice. The vast number of possible HH arrangements underlies the polymorphic nature of borophene, and necessitates direct HH imaging to definitively identify its atomic structure. While borophene has been imaged with scanning tunneling microscopy using conventional metal probes, the convolution of topographic and electronic features hinders unambiguous identification of the atomic lattice. Here, we overcome these limitations by employing CO-functionalized atomic force microscopy to visualize structures corresponding to boron-boron covalent bonds. Additionally, we show that CO-functionalized scanning tunneling microscopy is an equivalent and more accessible technique for HH imaging, confirming the v_1/5 and v_1/6 borophene models as unifying structures for all observed phases. Using this methodology, a borophene phase diagram is assembled, including a transition from rotationally commensurate to incommensurate phases at high growth temperatures, thus corroborating the chemically discrete nature of borophene.

Borophene, or 2D boron, is highly polymorphic with many predicted lattice arrangements, complicating the identification of its atomic structure. Here, the authors use functionalized-tip scanning probe microscopy to directly resolve the atomic lattice structures of several borophene polymorphs.

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

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

Molecular Identification, Bond Order Discrimination, and Apparent Intermolecular Features in Atomic Force Microscopy Studied with a Charge Density Based Method

We introduce an efficient method to simulate high-resolution atomic force microscopy (HR-AFM) images with CO probes. Our model explicitly takes into account the charge densities of the sample and the probe for the calculation of the short-range (SR) interaction and retains ab initio accuracy with only two parameters, that are essentially universal, independent of the number of chemical species and the complexity of the bonding topology. The application to molecular images shows a strong dependence on the stoichiometry and bonding configuration that precludes the chemical identification of individual atoms based on local force-distance curves. However, we have identified features in the 2D images and 3D force maps that reflect the highly anisotropic spatial decay of the molecular charge density and provide a way toward molecular identification. The model treats SR and electrostatics interactions on an equal footing and correctly pinpoints the Pauli repulsion as the underlying interaction responsible for the bond order discrimination in C60. Finally, we settle the controversy regarding the origin of the intermolecular features, discarding the effect of the charge redistribution associated with the H bonds, and linking them with the overlap of the wave functions of the atoms that constitute the bond. This overlap creates saddle regions in the potential energy landscape that are sensed by the probe.

On-surface structural and electronic properties of spontaneously formed Tb2Pc3 single molecule magnets

The single molecule magnet (SMM) bis(phthalocyaninato)terbium(iii) (TbPc2) has received significant and increasing attention as an exemplar system for realizing molecule-based spin electronics. Attaining higher nuclearity via multi-decker TbPc systems has remained an outstanding challenge, as known examples of Tb2Pc3 systems are only those containing Pc rings with substituents (e.g. alkyl, alkoxyl). Here we report on the spontaneous formation of Tb2Pc3 species from TbPc2 precursors via sublimation in ultrahigh vacuum (UHV) onto an Ag(111) surface. The presence of Tb2Pc3 molecules on the surface are inspected using scanning probe microscopy with submolecular resolution supported by density functional theory (DFT) calculations and additional chemical analysis. We observe the selective presence of a Kondo resonance (30 K) in the Tb2Pc3 species, that we attribute to differences in the orientation of the internal molecular ligands. Formation of triple-decker complexes offers new possibilities to study and control magnetic interactions not accessible with standard TbPc2 molecules.

Copper-oxide tip functionalization for submolecular atomic force microscopy

Establishing submolecular imaging in real-space by non-contact atomic force microscopy (NC-AFM) has been a major breakthrough in the field of organic surface chemistry. The key for the drastically increased resolution in these experiments is to functionalize a metallic tip apex with an inert probe particle. However, due to their weak bonding at the metal apex, these probe particles show a pronounced dynamic lateral deflection in the measurements. This constitutes a major limitation of this approach as it involves image distortions, an overestimation of bond lengths, and even artificial bond-like contrast features where actually no bonds exist. In this contribution, recent progress by using an alternative approach by copper-oxide tip functionalization is reviewed. Copper-oxide tips (CuOx tips) consist of a bulk copper apex, terminated by a covalently connected single oxygen atom, which chemically passivates the tip. Such CuOx tips can be identified by contrast analysis at specific surface sites and allow for submolecular resolution. A comparative analysis of data recorded with flexible tips allows a detailed discussion of the contrast mechanisms and related artificial effects. It is concluded with an assessment of limitations, future challenges and opportunities in such experiments.

Iron-based trinuclear metal-organic nanostructures on a surface with local charge accumulation

Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes-where organic ligands bind to several metal atoms-are relevant due to their electronic/magnetic properties and potential for functional reactivity pathways. However, their synthesis remains challenging; few geometries and configurations have been achieved. Here, we synthesise-via supramolecular chemistry on a noble metal surface-one-dimensional metal-organic nanostructures composed of terpyridine (tpy)-based molecules coordinated with well-defined polynuclear iron clusters. Combining low-temperature scanning probe microscopy and density functional theory, we demonstrate that the coordination motif consists of coplanar tpy's linked via a quasi-linear tri-iron node in a mixed (positive-)valence metal-metal bond configuration. This unusual linkage is stabilised by local accumulation of electrons between cations, ligand and surface. The latter, enabled by bottom-up on-surface synthesis, yields an electronic structure that hints at a chemically active polynuclear metal centre, paving the way for nanomaterials with novel catalytic/magnetic functionalities.

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

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

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy

There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δ f and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.

The Pentagonal Nature of Self-Assembled Silicon Chains and Magic Clusters on Ag(110)

The atomic structures of self-assembled silicon nanoribbons and magic clusters on Ag(110) substrate have been studied by high-resolution noncontact atomic force microscopy (nc-AFM) and tip-enhanced Raman spectroscopy (TERS). Pentagon-ring structures in Si nanoribbons and clusters have been directly visualized. Moreover, the vibrational fingerprints of individual Si nanoribbon and cluster retrieved by subnanometer resolution TERS confirm the pentagonal nature of both Si nanoribbons and clusters. This work demonstrates that Si pentagon can be an important element in building silicon nanostructures, which may find important applications for future nanoelectronic devices based on silicon.