Direct Imaging of Intermolecular Bonds in Scanning Tunneling Microscopy

Automated Structure Discovery for Scanning Tunneling Microscopy

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

Atomic imaging of zeolite-confined single molecules by electron microscopy

Single-molecule imaging with atomic resolution is a notable method to study various molecular behaviours and interactions^1-5. Although low-dose electron microscopy has been proved effective in observing small molecules^6-13, it has not yet helped us achieve an atomic understanding of the basic physics and chemistry of single molecules in porous materials, such as zeolites^14-16. The configurations of small molecules interacting with acid sites determine the wide applications of zeolites in catalysis, adsorption, gas separation and energy storage^17-21. Here we report the atomic imaging of single pyridine and thiophene confined in the channel of zeolite ZSM-5 (ref. ²²). On the basis of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM)^23-25, we directly observe the adsorption and desorption behaviours of pyridines in ZSM-5 under the in situ atmosphere. The adsorption configuration of single pyridine is atomically resolved and the S atoms in thiophenes are located after comparing imaging results with calculations. The strong interactions between molecules and acid sites can be visually studied in real-space images. This work provides a general strategy to directly observe these molecular structures and interactions in both the static image and the in situ experiment, expanding the applications of electron microscopy to the further study of various single-molecule behaviours with high resolution.

Real-Space Investigation of the Multiple Halogen Bonds by Ultrahigh-Resolution Scanning Probe Microscopy

The chemical bond is of central interest in chemistry, and it is of significance to study the nature of intermolecular bonds in real-space. Herein, non-contact atomic force microscopy (nc-AFM) and low-temperature scanning tunneling microscopy (LT-STM) are employed to acquire real-space atomic information of molecular clusters, i.e., monomer, dimer, trimer, tetramer, formed on Au(111). The formation of the various molecular clusters is due to the diversity of halogen bonds. DFT calculation also suggests the formation of three distinct halogen bonds among the molecular clusters, which originates from the noncovalent interactions of Br-atoms with the positive potential H-atoms, neutral potential Br-atoms, and negative potential N-atoms, respectively. This work demonstrates the real-space investigation of the multiple halogen bonds by nc-AFM/LT-STM, indicating the potential use of this technique to study other intermolecular bonds and to understand complex supramolecular assemblies at the atomic/sub-molecular level.

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.

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

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

Optical scanning tunneling microscopy based chemical imaging and spectroscopy

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

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.

Two-Dimensional Hydrogen-Bonded Nanoarchitecture Composed of Rectangular 3,4,9,10-Perylenetetracarboxylic Diimide and Boomerang-Shaped Molecules Resulting from the Dissociation of 1,3,5-Tris(4-aminophenyl)benzene

The self-assembly of 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) with the star-shaped 1,3,5-tris(4-aminophenyl)benzene (TAPB) on Au(111) is investigated using scanning tunneling microscopy. PTCDI forms a compact canted arrangement on the gold surface. When TAPB is sublimated at a high temperature, the molecule dissociates into a 4-aminophenyl group and a boomerang-shaped compound. The boomerang molecule self-assembles with PTCDI to create a two-dimensional (2D) nanoarchitecture stabilized by N-H···O-C hydrogen bonds between the dissociated TAPB and PTCDI. The molecular ratio of this multicomponent structure is 1:1.

Self-ordering of chemisorbed PTCDA molecules on Ge(001) driven by repulsive forces

Realization of future hybrid electronic devices combining organic and inorganic semiconductors requires a well-defined interface between both components. Such an interface can be formed generally by self-ordering of organic molecules on inorganic substrates, which is usually hindered by strong covalent bonds to the semiconductor surface. In this paper, the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecules were unexpectedly found to form a locally self-ordered monolayer on a strongly interacting semiconductor surface of the Ge(001). Molecular arrangements with preferential separations between the molecules were observed by the scanning tunneling microscopy at various coverages of the molecules and substrate temperatures, suggesting strong inter-molecular interaction. Atomic structures of two paired molecules and their inter-molecular interaction energies in five different configurations were calculated by density functional theory. Simple Monte Carlo simulations show that mobility of molecules activated only by the inter-molecular interactions is sufficient to reproduce the local self-ordering. A dominant inter-molecular interaction between neighboring chemisorbed molecules has mostly positive energy (destabilizing) except for a single configuration, which leads to the formation of one-dimensional chains of the molecules and finally a periodic two-dimensional array by increasing the coverage.

Bond-Selected Photodissociation of Single Molecules Adsorbed on Metal Surfaces

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

Two-dimensional black phosphorus: its fabrication, functionalization and applications

Phosphorus, one of the most abundant elements in the Earth (∼0.1%), has attracted much attention in the last five years since the rediscovery of two-dimensional (2D) black phosphorus (BP) in 2014. The successful scaling down of BP endows this 'old material' with new vitality, resulting from the intriguing semiconducting properties in the atomic scale limit, i.e. layer-dependent bandgap that covers from the visible light to mid-infrared light spectrum as well as hole-dominated ambipolar transport characteristics. Intensive research effort has been devoted to the fabrication, characterization, functionalization and application of BP and other phosphorus allotropes. In this review article, we summarize the fundamental properties and fabrication techniques of BP, with particular emphasis on the recent progress in molecular beam epitaxy growth of 2D phosphorus. Subsequently, we highlight recent progress in BP (opto)electronic device applications achieved via customized manipulation methods, such as interface, defect and bandgap engineering as well as forming Lego-like stacked heterostructures.

Interface Characterization and Control of 2D Materials and Heterostructures

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

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.

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-Ångström spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds^1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs ^1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation^8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip^13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule

We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

High resolution SPM imaging of organic molecules with functionalized tips

One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.

Ordered Superstructures of a Molecular Electron Donor on Au(111)

The molecular donor tetraphenyldibenzoperiflanthene (DBP) forms coverage-dependent superstructures on Au(111). At submonolayer coverage, the molecules align parallel to each other. They arrange in row-like structures, which exhibit a nearly rectangular primitive unit cell. By contrast, the molecular monolayer is characterized by a herringbone-type DBP arrangement spanned by an almost square unit cell containing two molecules. Both superstructures occur simultaneously in a narrow coverage range close to completion of the molecular monolayer. The adsorbate-substrate interaction is similar to other physisorbed molecular films on Au(111), but differs for the two adsorption phases as inferred from the different modification of the Au(111) surface reconstruction. Structural properties were consistently probed in real and reciprocal space by scanning tunneling microscopy and low-energy electron diffraction, respectively.

Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy

The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.

Self-assembly of electronically abrupt borophene/organic lateral heterostructures

Two-dimensional boron sheets (that is, borophene) have recently been realized experimentally and found to have promising electronic properties. Because electronic devices and systems require the integration of multiple materials with well-defined interfaces, it is of high interest to identify chemical methods for forming atomically abrupt heterostructures between borophene and electronically distinct materials. Toward this end, we demonstrate the self-assembly of lateral heterostructures between borophene and perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA). These lateral heterostructures spontaneously form upon deposition of PTCDA onto submonolayer borophene on Ag(111) substrates as a result of the higher adsorption enthalpy of PTCDA on Ag(111) and lateral hydrogen bonding among PTCDA molecules, as demonstrated by molecular dynamics simulations. In situ x-ray photoelectron spectroscopy confirms the weak chemical interaction between borophene and PTCDA, while molecular-resolution ultrahigh-vacuum scanning tunneling microscopy and spectroscopy reveal an electronically abrupt interface at the borophene/PTCDA lateral heterostructure interface. As the first demonstration of a borophene-based heterostructure, this work will inform emerging efforts to integrate borophene into nanoelectronic applications.

Passivation of Black Phosphorus via Self-Assembled Organic Monolayers by van der Waals Epitaxy

An effective passivation approach to protect black phosphorus (BP) from degradation based on multi-scale simulations is proposed. The self-assembly of perylene-3,4,9,10-tetracarboxylic dianhydride monolayers via van der Waals epitaxy on BP does not break the original electronic properties of BP. The passivation layer thickness is only 2 nm. This study opens up a new pathway toward fine passivation of BP.

Characteristic Contrast in Δfmin Maps of Organic Molecules Using Atomic Force Microscopy

Scanning tunneling microscopy and atomic force microscopy can provide detailed information about the geometric and electronic structure of molecules with submolecular spatial resolution. However, an essential capability to realize the full potential of these techniques for chemical applications is missing from the scanning probe toolbox: chemical recognition of organic molecules. Here, we show that maps of the minima of frequency shift-distance curves extracted from 3D data cubes contain characteristic contrast. A detailed theoretical analysis based on density functional theory and molecular mechanics shows that these features are characteristic for the investigated species. Structurally similar but chemically distinct molecules yield significantly different features. We find that the van der Waals and Pauli interaction, together with the specific adsorption geometry of a given molecule on the surface, accounts for the observed contrast.

Resonance frequencies of AFM cantilevers in contact with a surface

To make the forces in an Atomic Force Microscope that operates in a dynamic mode with one or multiple vibrations applied to the cantilever, quantitative, one needs to relate a change in resonance frequency of the cantilever to a specific tip-sample interaction. Due to the time dependence of the force between the tip and sample caused by the vibrations, this task is not only difficult, but in fact only possible to solve for certain limiting cases, if one follows common theoretical approaches with a Taylor expansion around the deflection point. Here, we present an analytical method for calculating the resonance frequencies of the cantilever that is valid for any tip-sample interaction. Instead of linearizing the tip-sample interaction locally, we calculate an averaged, weighted linearization taking into account all positions of the tip while vibrating. Our method bridges, therefore, the difficult gap between a free oscillating cantilever and a cantilever that is pushed infinitely hard into contact with a surface, which describes a clamped-pinned boundary condition. For a correct description of the cantilever dynamics, we take into account both the tip mass and the tip moment of inertia. Applying our model, we show that it is possible to calculate the modal response of a cantilever as a function of the tip-sample interaction strength. Based on these modal vibration characteristics, we show that the higher resonance frequencies of a cantilever are completely insensitive to the strength of the tip-sample interaction.

Imaging the Bonds of Dehalogenated Benzene Radicals on Cu(111) and Au(111)

Dissociative adsorption of doubly substituted benzene molecules leads to formation of benzyne radicals. In this study, co-adsorbed hydrogen molecules are used in scanning tunneling hydrogen microscopy to enhance the contrast of the meta- and the para-isomers of these radicals on Cu(111) and Au(111). Up to three hydrogen molecules are attached to one radical. One hydrogen molecule reveals the orientation of the carbon ring and its adsorption site, allowing discrimination between the two radicals. Two hydrogen molecules reflect the bond picture of the carbon skeleton and reveals that adsorption on Cu(111) distorts the meta- isomer differently from its gas-phase distortion. Three hydrogen molecules allow us to determine the bond picture of a minor species.

Monolayer Phases of a Dipolar Perylene Derivative on Au(111) and Surface Potential Build-Up in Multilayers

9-(Bis-p-tert-octylphenyl)-amino-perylene-3,4-dicarboxy anhydride (BOPA-PDCA) is a strongly dipolar molecule representing a group of asymmetrically substituted perylenes that are employed in dye-sensitized solar cells and hold great promise for discotic liquid crystal applications. Thin BOPA-PDCA films with orientated dipole moments can potentially be used to tune the energy-level alignment in electronic devices and store information. To help assessing these prospects, we here elucidate the molecular self-assembly and electronic structure of BOPA-PCDA employing room temperature scanning tunneling microscopy and spectroscopy in combination with ultraviolet and X-ray photoelectron spectroscopies. BOPA-PCDA monolayers on Au(111) exclusively form in-plane antiferroelectric phases. The molecular arrangements, the increase of the average number of molecules per unit cell via ripening, and the rearrangement upon manipulation with the STM tip indicate an influence of the dipole moment on the molecular assembly and the rearrangement. A slightly preferred out-of-plane orientation of the molecules in the multilayer induces a surface potential of 1.2 eV. This resembles the giant surface potential effect that was reported for vacuum-deposited tris(8-hydroxyquinoline)aluminum and deemed applicable for data storage. Notably, the surface potential in the case of BOPA-PDCA can in part be reversibly removed by visible light irradiation.

Theoretical study of carbon-based tips for scanning tunnelling microscopy

Motivated by recent experiments, we present here a detailed theoretical analysis of the use of carbon-based conductive tips in scanning tunnelling microscopy. In particular, we employ ab initio methods based on density functional theory to explore a graphitic, an amorphous carbon and two diamond-like tips for imaging with a scanning tunnelling microscope (STM), and we compare them with standard metallic tips made of gold and tungsten. We investigate the performance of these tips in terms of the corrugation of the STM images acquired when scanning a single graphene sheet. Moreover, we analyse the impact of the tip-sample distance and show that it plays a fundamental role in the resolution and symmetry of the STM images. We also explore in depth how the adsorption of single atoms and molecules in the tip apexes modifies the STM images and demonstrate that, in general, it leads to an improved image resolution. The ensemble of our results provides strong evidence that carbon-based tips can significantly improve the resolution of STM images, as compared to more standard metallic tips, which may open a new line of research in scanning tunnelling microscopy.

Complex Stoichiometry-Dependent Reordering of 3,4,9,10-Perylenetetracarboxylic Dianhydride on Ag(111) upon K Intercalation

Alkali metal atoms are frequently used for simple yet efficient n-type doping of organic semiconductors and as an ingredient of the recently discovered polycyclic aromatic hydrocarbon superconductors. However, the incorporation of dopants from the gas phase into molecular crystal structures needs to be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into the pristine 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low-temperature scanning tunneling microscopy, scanning tunneling hydrogen microscopy (ST[H]M), and low-energy electron diffraction as a function of the stoichiometry. The analysis of the measurements is corroborated by density functional theory calculations. These turn out to be essential for a correct interpretation of the experimental ST[H]M data. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Ångström precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend rather sensitively on the mutual alignment between donor atoms and acceptor molecules. Our results demonstrate that only the combination of experimental and theoretical approaches allows for an unambiguous explanation of the pronounced reordering of KxPTCDA/Ag(111) upon changing the K content.

Organic Monolayer Protected Topological Surface State

Perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA)/Bi2Se3 and Fe/PTCDA/Bi2Se3 heterointerfaces are investigated using scanning tunneling microscopy and spectroscopy. The close-packed self-assembled PTCDA monolayer possesses big molecular band gap and weak molecule-substrate interactions, which leaves the Bi2Se3 topological surface state intact under PTCDA. Formation of Fe-PTCDA hybrids removes interactions between the Fe dopant and the Bi2Se3 surface, such as doping effects and Coulomb scattering. Our findings reveal the functionality of PTCDA to prevent dopant disturbances in the TSS and provide an effective alternative for interface designs of realistic TI devices.

Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H₂ molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

Intramolecular Force Contrast and Dynamic Current-Distance Measurements at Room Temperature

Scanning probe microscopy can be used to probe the internal atomic structure of flat organic molecules. This technique requires an unreactive tip and has, until now, been demonstrated only at liquid helium and liquid nitrogen temperatures. We demonstrate intramolecular and intermolecular force contrast at room temperature on PTCDA molecules adsorbed on a Ag/Si(111)-(√[3]×√[3]) surface. The oscillating force sensor allows us to dynamically measure the vertical decay constant of the tunneling current. The precision of this method is increased by quantifying the transimpedance of the current to voltage converter and accounting for the tip oscillation. This measurement yields a clear contrast between neighboring molecules, which we attribute to the different charge states.

Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule

A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j=0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.

The smallest resonator arrays in atmosphere by chip-size-grown nanowires with tunable Q-factor and frequency for subnanometer thickness detection

A chip-size vertically aligned nanowire (NW) resonator arrays (VNRs) device has been fabricated with simple one-step lithography process by using grown self-assembled zinc oxide (ZnO) NW arrays. VNR has cantilever diameter of 50 nm, which breakthroughs smallest resonator record (>100 nm) functioning in atmosphere. A new atomic displacement sensing method by using atomic force microscopy is developed to effectively identify the resonance of NW resonator with diameter 50 nm in atmosphere. Size-effect and half-dimensional properties of the NW resonator have been systematically studied. Additionally, VNR has been demonstrated with the ability of detecting nanofilm thickness with subnanometer (<10(-9)m) resolution.

Real-space Wigner-Seitz cells imaging of potassium on graphite via elastic atomic manipulation

Atomic manipulation in the scanning tunnelling microscopy, conventionally a tool to build nanostructures one atom at a time, is here employed to enable the atomic-scale imaging of a model low-dimensional system. Specifically, we use low-temperature STM to investigate an ultra thin film (4 atomic layers) of potassium created by epitaxial growth on a graphite substrate. The STM images display an unexpected honeycomb feature, which corresponds to a real-space visualization of the Wigner-Seitz cells of the close-packed surface K atoms. Density functional simulations indicate that this behaviour arises from the elastic, tip-induced vertical manipulation of potassium atoms during imaging, i.e. elastic atomic manipulation, and reflects the ultrasoft properties of the surface under strain. The method may be generally applicable to other soft e.g. molecular or biomolecular systems.

On-surface self-organization of a robust metal–organic cluster based on copper(i) with chloride and organosulphur ligands

Vacuum sublimation of a metal–organic cluster leading to supramolecular wires on surfaces.

Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips

Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complemented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbon monoxide (CO) molecule positioned at the apex of a scanning tunneling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending a model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of its frustrated translation mode in response to changes of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM, and IETS-STM images can deliver information about the charge distribution within molecules deposited on a surface. To demonstrate this, we extend our mechanical model by taking into account electrostatic forces acting on the decorated tip in the surface Hartree potential.

Intermolecular contrast in atomic force microscopy images without intermolecular bonds

Intermolecular features in atomic force microscopy images of organic molecules have been ascribed to intermolecular bonds. A recent theoretical study [P. Hapala et al., Phys. Rev. B 90, 085421 (2014)] showed that these features can also be explained by the flexibility of molecule-terminated tips. We probe this effect by carrying out atomic force microscopy experiments on a model system that contains regions where intermolecular bonds should and should not exist between close-by molecules. Intermolecular features are observed in both regions, demonstrating that intermolecular contrast cannot be directly interpreted as intermolecular bonds.

Mapping the force field of a hydrogen-bonded assembly

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Resolving molecular orbitals self-decoupled from semiconductor surfaces

Molecular orbitals of chemisorbed nitrosobenzene are electronically decoupled from a clean semiconductor substrate and resolved by STM.