Quantifying molecular stiffness and interaction with lateral force microscopy

Structure and Defect Identification at Self-Assembled Islands of CO2 Using Scanning Probe Microscopy

Understanding how carbon dioxide (CO2) behaves and interacts with surfaces is paramount for the development of sensors and materials to attempt CO2 mitigation and catalysis. Here, we combine simultaneous atomic force microscopy (AFM) and scanning tunneling microscopy (STM) using CO-functionalized probes with density functional theory (DFT)-based simulations to gain fundamental insight into the behavior of physisorbed CO2 molecules on a gold(111) surface that also contains one-dimensional metal-organic chains formed by 1,4-phenylene diisocyanide (PDI) bridged by gold (Au) adatoms. We resolve the structure of self-assembled CO2 islands, both confined between the PDI-Au chains as well as free-standing on the surface and reveal a chiral arrangement of CO2 molecules in a windmill-like structure that encloses a standing-up CO2 molecule and other foreign species existing at the surface. We identify these species by the comparison of height-dependent AFM and STM imaging with DFT-calculated images and clarify the origin of the kagome tiling exhibited by this surface system. Our results show the complementarity of AFM and STM using functionalized probes and their potential, when combined with DFT, to explore greenhouse gas molecules at surface-supported model systems.

Imaging the adsorption sites of organic molecules on metallic surfaces by an adaptive tunnelling current feedback

Atomic force microscopy (AFM) allows submolecular resolution imaging of organic molecules deposited on a surface by using CO-functionalized qPlus sensors under ultrahigh vacuum and low temperature conditions. However, the experimental determination of the adsorption sites of these organic molecules requires the precise identification of the atomic structure of the surface on which they are adsorbed. Here, we develop an automation method for AFM imaging that provides in a single image both, submolecular resolution on organic molecules and atomic resolution on the surrounding metallic surface. The method is based on an adaptive tunnelling current feedback system that is regulated according to the response of the AFM observables, which guarantees that both the molecules and the surface atoms are imaged under optimum conditions. Therewith, the approach is suitable for imaging adsorption sites of several adjacent and highly mobile molecules such as 2-iodotriphenylene on Ag(111) in a single scan. The proposed method with the adaptive feedback system facilitates statistical analysis of molecular adsorption geometries and could in the future contribute to autonomous AFM imaging as it adapts the feedback parameters depending on the sample properties.

Scanning Probe Microscopies for Characterizations of 2D Materials

2D materials are intriguing due to their remarkably thin and flat structure. This unique configuration allows the majority of their constituent atoms to be accessible on the surface, facilitating easier electron tunneling while generating weak surface forces. To decipher the subtle signals inherent in these materials, the application of techniques that offer atomic resolution (horizontal) and sub-Angstrom (z-height vertical) sensitivity is crucial. Scanning probe microscopy (SPM) emerges as the quintessential tool in this regard, owing to its atomic-level spatial precision, ability to detect unitary charges, responsiveness to pico-newton-scale forces, and capability to discern pico-ampere currents. Furthermore, the versatility of SPM to operate under varying environmental conditions, such as different temperatures and in the presence of various gases or liquids, opens up the possibility of studying the stability and reactivity of 2D materials in situ. The characteristic flatness, surface accessibility, ultra-thinness, and weak signal strengths of 2D materials align perfectly with the capabilities of SPM technologies, enabling researchers to uncover the nuanced behaviors and properties of these advanced materials at the nanoscale and even the atomic scale.

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

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

Exploring in-plane interactions beside an adsorbed molecule with lateral force microscopy

Atomic force microscopy with a CO-functionalized tip can be used to directly image the internal structure of a planar molecule and to characterize chemical bonds. However, hydrogen atoms usually cannot be directly observed due to their small size. At the same time, these atoms are highly important, since they can direct on-surface chemical reactions. Measuring in-plane interactions at the sides of PTCDA (3,4,9,10-perylenetetracarboxylic dianhydride) molecules with lateral force microscopy allowed us to directly identify hydrogen atoms via their repulsive signature, which we confirmed with a model incorporating radially symmetric atomic interactions. Additional features were observed in the force data and could not be explained by H-bonding of the CO tip with the PTCDA sides. Instead, they are caused by electrostatic interaction of the large dipole of the metal apex, which we verified with density functional theory. This calculation allowed us to estimate the strength of the dipole at the metal tip apex. To further confirm that this dipole generally affects measurements on weakly polarized systems, we investigated the archetypical surface adsorbate of a single CO molecule. We determined the radially symmetric atomic interaction to be valid over a large solid angle of 5.4 sr, corresponding to 82°. We therefore find that in both the PTCDA and CO systems, the underlying interaction preventing direct observations of H-bonding and causing a collapse of the radially symmetric model is the dipole at the metal apex, which plays a significant role when approaching closer than standard imaging heights.

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.

Revealing CO2 dissociation pathways at vicinal copper (997) interfaces

Size- and shape-tailored copper (Cu) nanocrystals can offer vicinal planes for facile carbon dioxide (CO₂) activation. Despite extensive reactivity benchmarks, a correlation between CO₂ conversion and morphology structure has not yet been established at vicinal Cu interfaces. Herein, ambient pressure scanning tunneling microscopy reveals step-broken Cu nanocluster evolutions on the Cu(997) surface under 1 mbar CO₂(g). The CO₂ dissociation reaction produces carbon monoxide (CO) adsorbate and atomic oxygen (O) at Cu step-edges, inducing complicated restructuring of the Cu atoms to compensate for increased surface chemical potential energy at ambient pressure. The CO molecules bound at under-coordinated Cu atoms contribute to the reversible Cu clustering with the pressure gap effect, whereas the dissociated oxygen leads to irreversible Cu faceting geometries. Synchrotron-based ambient pressure X-ray photoelectron spectroscopy identifies the chemical binding energy changes in CO-Cu complexes, which proves the characterized real-space evidence for the step-broken Cu nanoclusters under CO(g) environments. Our in situ surface observations provide a more realistic insight into Cu nanocatalyst designs for efficient CO₂ conversion to renewable energy sources during C₁ chemical reactions.

Customization of an atomic force microscope for multidimensional measurements under environmental conditions

Atomic force microscopy (AFM) is an analytical surface characterization tool that reveals the surface topography at a nanometer length scale while probing local chemical, mechanical, and even electronic sample properties. Both contact (performed with a constant deflection of the cantilever probe) and dynamic operation modes (enabled by demodulation of the oscillation signal under tip-sample interaction) can be employed to conduct AFM-based measurements. Although surface topography is accessible regardless of the operation mode, the resolution and the availability of the quantified surface properties depend on the mode of operation. However, advanced imaging techniques, such as frequency modulation, to achieve high resolution, quantitative surface properties are not implemented in many commercial systems. Here, we show the step-by-step customization of an atomic force microscope. The original system was capable of surface topography and basic force spectroscopy measurements while employing environmental control, such as temperature variation of the sample/tip, etc. We upgraded this original setup with additional hardware (e.g., a lock-in amplifier with phase-locked loop capacity, a high-voltage amplifier, and a new controller) and software integration while utilizing its environmental control features. We show the capabilities of the customized system with frequency modulation-based topography experiments and automated voltage and/or distance spectroscopy, time-resolved AFM, and two-dimensional force spectroscopy measurements under ambient conditions. We also illustrate the enhanced stability of the setup with active topography and frequency drift corrections. We believe that our methodology can be useful for the customization and automation of other scanning probe systems.

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.

Fundamental and higher eigenmodes of qPlus sensors with a long probe for vertical-lateral bimodal atomic force microscopy

The detection of vertical and lateral forces at the nanoscale by atomic force microscopy (AFM) reveals various mechanical properties on surfaces. The qPlus sensor is a widely used force sensor, which is built from a quartz tuning fork (QTF) and a sharpened metal probe, capable of high-resolution imaging in viscous liquids such as lubricant oils. Although a simultaneous detection technique of vertical and lateral forces by using a qPlus sensor is required in the field of nanotribology, it has still been difficult because the torsional oscillations of QTFs cannot be detected. In this paper, we propose a method to simultaneously detect vertical and lateral force components by using a qPlus sensor with a long probe. The first three eigenmodes of the qPlus sensor with a long probe are theoretically studied by solving a set of equations of motion for the QTF prong and probe. The calculation results were in good agreement with the experimental results. It was found that the tip oscillates laterally in the second and third modes. Finally, we performed friction anisotropy measurements on a polymer film by using a bimodal AFM utilizing the qPlus sensor with a long probe to confirm the lateral force detection.

CO oxidation by Pt2/Fe3O4: Metastable dimer and support configurations facilitate lattice oxygen extraction

Heterogeneous catalysts based on subnanometer metal clusters often exhibit strongly size-dependent properties, and the addition or removal of a single atom can make all the difference. Identifying the most active species and deciphering the reaction mechanism is extremely difficult, however, because it is often not clear how the catalyst evolves in operando. Here, we use a combination of atomically resolved scanning probe microscopies, spectroscopic techniques, and density functional theory (DFT)-based calculations to study CO oxidation by a model Pt/Fe3O4(001) "single-atom" catalyst. We demonstrate that (PtCO)2 dimers, formed dynamically through the agglomeration of mobile Pt-carbonyl species, catalyze a reaction involving the oxide support to form CO2. Pt2 dimers produce one CO2 molecule before falling apart into two adatoms, releasing the second CO. Olattice extraction only becomes facile when both the Pt-dimer and the Fe3O4 support can access metastable configurations, suggesting that substantial, concerted rearrangements of both cluster and support must be considered for reactions occurring at elevated temperature.

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.

Breaking a dative bond with mechanical forces

Bond breaking and forming are essential components of chemical reactions. Recently, the structure and formation of covalent bonds in single molecules have been studied by non-contact atomic force microscopy (AFM). Here, we report the details of a single dative bond breaking process using non-contact AFM. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via quantum-based simulations. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN or by a repulsive force of ~220 pN with a significant contribution of shear forces, accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process.

Mechanical and Chemical Interactions in Atomically Defined Contacts

Providing fundamental insights in atomic interactions, dedicated methods in atomic force microscopy allow measuring the threshold forces needed to move single adsorbed atoms or molecules. However, the chemical and structural properties of the probe-tip can drastically influence the results. Establishing atomically defined contacts in such experiments, the tips in the present study are functionalized with various chemically and structurally different terminations. Xenon atoms are moved along an atomically defined metal/metal-oxide boundary where all tips show a pulling mechanism and slight force variations, which are assigned to polarization effects within the tip-sample junction. Detaching Xe atoms from the boundary involves a significantly higher energy barrier where chemical reactive Cu-tips cause Xe pickup before any lateral manipulation. Passivating the tip by inert probe particles (Xe or CO) allows further approaching the surface Xe atom. Yet, the small vertical attraction and pronounced tip relaxations prevent reaching sufficient threshold forces inducing manipulation. In contrast, the high structural rigidity of oxygen-terminated Cu-tips allows manipulations even beyond the threshold where they evolve from initial pulling, via sliding to pushing mode. The detailed quantitative analysis of the processes in the atomically defined junctions emphasizes the mechanical and chemical interactions for highly controlled experiments with piconewton sensitivity.

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.

Probing the Nature of Chemical Bonds by Atomic Force Microscopy

The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. We review experimental AFM data, covering precise studies of van-der-Waals-, covalent-, ionic-, metallic- and hydrogen bonds as well as bonds between artificial and natural atoms. Further, we discuss some of the density functional theory calculations that are related to the experimental studies of the chemical bonds. A description of frequency modulation AFM, the most precise AFM method, discusses some of the experimental challenges in measuring bonding forces. In frequency modulation AFM, forces between the tip of an oscillating cantilever change its frequency. Initially, cantilevers were made mainly from silicon. Most of the high precision measurements of bonding strengths by AFM became possible with a technology transfer from the quartz watch technology to AFM by using quartz-based cantilevers ("qPlus force sensors"), briefly described here.

Confronting interatomic force measurements

The quantitative interatomic force measurements open a new pathway to materials characterization, surface science, and chemistry by elucidating the tip-sample interaction forces. Atomic force microscopy is the ideal platform to gauge interatomic forces between the tip and the sample. For such quantitative measurements, either the oscillation frequency or the oscillation amplitude and the phase of a vibrating cantilever are recorded as a function of the tip-sample separation. These experimental quantities are subsequently converted into the tip-sample interaction force, which can be compared with interatomic force laws to reveal the governing physical phenomena. Recently, it has been shown that the most commonly applied mathematical conversion techniques may suffer a significant deviation from the actual tip-sample interaction forces. To avoid the assessment of unphysical interatomic forces, the use of either very small (i.e., a few picometers) or very large oscillation amplitudes (i.e., a few nanometers) has been proposed. However, the use of marginal oscillation amplitudes gives rise to another problem as it lacks the feasibility due to the adverse signal-to-noise ratios. Here, we show a new mathematical conversion principle that confronts interatomic force measurements while preserving the oscillation amplitude within the experimentally achievable and favorable limits, i.e., tens of picometers. Our theoretical calculations and complementary experimental results demonstrate that the proposed technique has three major advantages over existing methodologies: (I) eliminating mathematical instabilities of the reconstruction of tip-sample interaction force, (II) enabling accurate conversion deep into the repulsive regime of tip-sample interaction force, and (III) being robust to the uncertainty of the oscillation amplitude and the measurement noise. Due to these advantages, we anticipate that our methodology will be the nucleus of a reliable evaluation of material properties with a more accurate measurement of tip-sample interaction forces.

Determining amplitude and tilt of a lateral force microscopy sensor

In lateral force microscopy (LFM), implemented as frequency-modulation atomic force microscopy, the tip oscillates parallel to the surface. Existing amplitude calibration methods are not applicable for mechanically excited LFM sensors at low temperature. Moreover, a slight angular offset of the oscillation direction (tilt) has a significant influence on the acquired data. To determine the amplitude and tilt we make use of the scanning tunneling microscopy (STM) channel and acquire data without and with oscillation of the tip above a local surface feature. We use a full two-dimensional current map of the STM data without oscillation to simulate data for a given amplitude and tilt. Finally, the amplitude and tilt are determined by fitting the simulation output to the data with oscillation.

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

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

Quantifying the evolution of atomic interaction of a complex surface with a functionalized atomic force microscopy tip

Terminating the tip of an atomic force microscope with a CO molecule allows data to be acquired with a well-known and inert apex. Previous studies have shown conflicting results regarding the electrostatic interaction, indicating in some cases that the negative charge at the apex of the CO dominates, whereas in other cases the positive charge at the end of the metal tip dominates. To clarify this, we investigated [Formula: see text](111). [Formula: see text] is an ionic crystal and the (111) surface does not possess charge inversion symmetry. Far from the surface, the interaction is dominated by electrostatics via the negative charge at the apex. Closer to the surface, Pauli repulsion and CO bending dominate, which leads to an unexpected appearance of the complex 3-atom unit cell. We compare simulated data in which the electrostatics are modeled by point particles versus a charge density calculated by DFT. We also compare modeling Pauli repulsion via individual Lennard-Jones potentials versus a total charge density overlap. In doing so, we determine forcefield parameters useful for future investigations of biochemical processes.

Strumming a Single Chemical Bond

Atomic force microscopy and scanning tunneling microscopy can image the internal structure of molecules adsorbed on surfaces. One reliable method is to terminate the tip with a nonreactive adsorbate, often a single CO molecule, and to collect data at a close distance where Pauli repulsion plays a strong role. Lateral force microscopy, in which the tip oscillates laterally, probes similar interactions but has the unique ability to pull the CO over a chemical bond, load it as a torsional spring, and release it as it snaps over with each oscillation cycle. This produces measurable energy dissipation. The dissipation has a characteristic decay length in the vertical direction of 4 pm, which is 13 times smaller than the decay length in typical STM or AFM experiments.

Amplitude Dependence of Resonance Frequency and its Consequences for Scanning Probe Microscopy

With recent advances in scanning probe microscopy (SPM), it is now routine to determine the atomic structure of surfaces and molecules while quantifying the local tip-sample interaction potentials. Such quantitative experiments using noncontact frequency modulation atomic force microscopy is based on the accurate measurement of the resonance frequency shift due to the tip-sample interaction. Here, we experimentally show that the resonance frequency of oscillating probes used for SPM experiments change systematically as a function of oscillation amplitude under typical operating conditions. This change in resonance frequency is not due to tip-sample interactions, but rather due to the cantilever strain or geometric effects and thus the resonance frequency is a function of the oscillation amplitude. Our numerical calculations demonstrate that the amplitude dependence of the resonance frequency is an additional yet overlooked systematic error source that can result in nonnegligible errors in measured interaction potentials and forces. Our experimental results and complementary numerical calculations reveal that the frequency shift due to this amplitude dependence needs to be corrected even for experiments with active oscillation amplitude control to be able to quantify the tip-sample interaction potentials and forces with milli-electron volt and pico-Newton resolutions.

Chemical bond formation showing a transition from physisorption to chemisorption

Surface molecules can transition from physisorption through weak van der Waals forces to a strongly bound chemisorption state by overcoming an energy barrier. We show that a carbon monoxide (CO) molecule adsorbed to the tip of an atomic force microscope enables a controlled observation of bond formation, including its potential transition from physisorption to chemisorption. During imaging of copper (Cu) and iron (Fe) adatoms on a Cu(111) surface, the CO was not chemically inert but transited through a physisorbed local energy minimum into a chemisorbed global minimum, and an energy barrier was seen for the Fe adatom. Density functional theory reveals that the transition occurs through a hybridization of the electronic states of the CO molecule mainly with s-, p _z -, and d _z ²-type states of the Fe and Cu adatoms, leading to chemical bonding.

An sp-hybridized molecular carbon allotrope, cyclo[18]carbon

Carbon allotropes built from rings of two-coordinate atoms, known as cyclo[n]carbons, have fascinated chemists for many years, but until now they could not be isolated or structurally characterized because of their high reactivity. We generated cyclo[18]carbon (C18) using atom manipulation on bilayer NaCl on Cu(111) at 5 kelvin by eliminating carbon monoxide from a cyclocarbon oxide molecule, C24O6. Characterization of cyclo[18]carbon by high-resolution atomic force microscopy revealed a polyynic structure with defined positions of alternating triple and single bonds. The high reactivity of cyclocarbon and cyclocarbon oxides allows covalent coupling between molecules to be induced by atom manipulation, opening an avenue for the synthesis of other carbon allotropes and carbon-rich materials from the coalescence of cyclocarbon molecules.

Discrimination of Bond Order in Organic Molecules Using Noncontact Atomic Force Microscopy

Noncontact atomic force microscopy (nc-AFM) with a CO-functionalized tip can image submolecular structures through high-resolution images with the possibility of discriminating bond order. We employ real-space pseudopotential calculations to simulate nc-AFM images of molecules containing double (dibenzo(cd,n)naphtho(3,2,1,8-pqra)perylene (DBNP), hexabenzo(bc,ef,hi,kl,no,qr)coronene (HBC)) and triple (1,2-bis[2-(2-ethynylphenyl)ethynyl]-benzene (BEEB), 6-phenylhexa-1,3,5-triynylbenzene (PHTB)) bonds. We find (1) triple bonds can be unambiguously distinguished from other interatomic interactions based on a characteristic image and (2) the degree of double bond character can be directly determined from the image. We propose that large lateral forces acting on the tip may induce specific image distortions in the cases of DBNP and BEEB.

The qPlus sensor, a powerful core for the atomic force microscope

Atomic force microscopy (AFM) was introduced in 1986 and has since made its way into surface science, nanoscience, chemistry, biology, and material science as an imaging and manipulating tool with a rising number of applications. AFM can be employed in ambient and liquid environments as well as in vacuum and at low and ultralow temperatures. The technique is an offspring of scanning tunneling microscopy (STM), where the tunneling tip of the STM is replaced by using a force sensor with an attached tip. Measuring the tiny chemical forces that act between the tip and the sample is more difficult than measuring the tunneling current in STM. Therefore, even 30 years after the introduction of AFM, progress in instrumentation is substantial. Here, we focus on the core of the AFM, the force sensor with its tip and detection mechanism. Initially, force sensors were mainly micro-machined silicon cantilevers, mainly using optical methods to detect their deflection. The qPlus sensor, originally based on a quartz tuning fork and now custom built from quartz, is self-sensing by utilizing the piezoelectricity of quartz. The qPlus sensor allows us to perform STM and AFM in parallel, and the spatial resolution of its AFM channel has reached the subatomic level, exceeding the resolution of STM. Frequency modulation AFM (FM-AFM), where the frequency of an oscillating cantilever is altered by the gradient of the force that acts between the tip and the sample, has emerged over the years as the method that provides atomic and subatomic spatial resolution as well as force spectroscopy with sub-piconewton sensitivity. FM-AFM is precise; because of all physical observables, time and frequency can be measured by far with the greatest accuracy. By design, FM-AFM clearly separates conservative and dissipative interactions where conservative forces induce a frequency shift and dissipative interactions alter the power needed to maintain a constant oscillation amplitude of the cantilever. As it operates in a noncontact mode, it enables simultaneous AFM and STM measurements. The frequency stability of quartz and the small oscillation amplitudes that are possible with stiff quartz sensors optimize the signal to noise ratio. Here, we discuss the operating principles, the assembly of qPlus sensors, amplifiers, limiting factors, and applications. Applications encompass unprecedented subatomic spatial resolution, the measurement of forces that act in atomic manipulation, imaging and spectroscopy of spin-dependent forces, and atomic resolution of organic molecules, graphite, graphene, and oxides.

Friction and Adhesion of Different Structural Defects of Graphene

Graphene structural defects, namely edges, step-edges, and wrinkles, are susceptible to severe mechanical deformation and stresses under tribo-mechanical operations. Applied forces may cause deformation by folding, buckling, bending, and tearing of these defective sites of graphene, which lead to a remarkable decline in normal and friction load bearing capacity. In this work, we experimentally quantified the maximum sustainable normal and friction forces, corresponding to the damage thresholds of the different investigated defects as well as their pull-out (adhesion) forces. Horizontal wrinkles (with respect to the basal plane, i.e., folded) sustained the highest normal load, up to 317 nN, during sliding, whereas for vertical (i.e., standing) wrinkles, step-edges, and edges, the load bearing capacities are up to 113, 74, and 63 nN, respectively. The related deformation mechanisms were also experimentally investigated by varying the normal load up to the initiation of the damage from the defects and extended with the numerical results from molecular dynamics and finite element method simulations.

CO-tip manipulation using repulsive interactions

Understanding the interactions between a tip apex and a target atom or molecule is crucial for the manipulation of individual molecules with precise control by using scanning tunnelling microscopy (STM) and atomic force microscopy. Herein, we demonstrate the manipulation of target CO molecules on a Cu(111) substrate using a CO-functionalized W tip with atomic-scale accuracy. All experiments were performed in a home-built ultra-high vacuum STM system at 5 K. The CO-tip was fabricated by picking up a single CO molecule from a Cu(111) surface. In contrast to a metal tip, repulsive interactions occur between the CO-tip and the target CO molecule. This repulsive interaction promises perfect lateral hopping without any vertical hopping. Hopping events were directly monitored as sudden current drops in the simultaneously measured I-z curves. A larger barrier height between the CO-tip and the target CO (∼9.5 eV) was found from the slope of the I-z curve, which decreases the electron tunnelling probability between the tip and sample. Therefore, electron-driven manipulation cannot be a major trigger for the CO-CO repulsive manipulation. The CO-tip is able to manipulate only the target CO molecule, even when another CO molecule was located ∼0.5 nm away. Statistical measurements revealed that the nearest neighbour atop site is the energetically stable position after hopping. However, if the CO target has another CO molecule in a neighbouring position (denoted as a 'pair'), the target CO hops more than twice as far. This means that the CO-tip experiences a larger repulsive interaction from the pair. These observations of CO-tip manipulation are useful for the design of two-dimensional artificial molecular networks as well as for developing a better understanding of catalytic oxidation processes.

Interatomic force laws that evade dynamic measurement

Measurement of the force between two atoms is performed routinely with the atomic force microscope. The shape of this interatomic force law is now found to directly regulate this capability: rapidly varying interatomic force laws, which are common in nature, can corrupt their own measurement.

Torque-Induced Change in Configuration of a Single NO Molecule on Cu(110)

We demonstrated that a nitric oxide (NO) molecule on Cu(110) acts as an "ON-OFF-ON toggle switch" that can be turned on and off by repulsive force and electron injection, respectively. On the surface, NO molecules exist in three configurations: flat along the [001] direction (ON), upright (OFF), and flat along [001[over ¯]] (ON). An NO-functionalized tip, which was characterized by scanning tunneling microscopy and inelastic electron tunneling spectroscopy, can convert an upright NO adsorbate into a flat-lying NO. Atomic force microscopy and a simulation of the interactions between the NO molecules reveal that a repulsive force not aligned with the N-O bond provides the torque that detrudes the NO toggle; i.e., the upright NO adsorbate is tilted away from the tip. Therefore, the NO adsorbate behaves as a nonvolatile sensor for the detection of locally applied repulsive torque.

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.

A standing molecule as a single-electron field emitter

Scanning probe microscopy makes it possible to image and spectroscopically characterize nanoscale objects, and to manipulate^1-3 and excite^4-8 them; even time-resolved experiments are now routinely achieved^9,10. This combination of capabilities has enabled proof-of-principle demonstrations of nanoscale devices, including logic operations based on molecular cascades ¹¹ , a single-atom transistor ¹² , a single-atom magnetic memory cell ¹³ and a kilobyte atomic memory ¹⁴ . However, a key challenge is fabricating device structures that can overcome their attraction to the underlying surface and thus protrude from the two-dimensional flatlands of the surface. Here we demonstrate the fabrication of such a structure: we use the tip of a scanning probe microscope to lift a large planar aromatic molecule (3,4,9,10-perylenetetracarboxylic-dianhydride) into an upright, standing geometry on a pedestal of two metal (silver) adatoms. This atypical and surprisingly stable upright orientation of the single molecule, which under all known circumstances adsorbs flat on metals^15,16, enables the system to function as a coherent single-electron field emitter. We anticipate that other metastable adsorbate configurations might also be accessible, thereby opening up the third dimension for the design of functional nanostructures on surfaces.

Characterization of Frictional Properties of Single-Layer Molybdenum-Disulfide Film Based on a Coupling of Tip Radius and Tip⁻Sample Distance by Molecular-Dynamics Simulations

Lateral-force microscopy is a powerful tool to study the frictional properties of two-dimensional materials. However, few works distinctly reveal the correlation between the tip radius with the tip⁻sample distance and the frictional properties of the two-dimensional (2D) materials. We performed molecular-dynamics simulations to study the atomic-scale friction of a typical two-dimensional single-layer molybdenum disulfide (SLMoS₂). The effects of tip radius and tip⁻sample distance on the frictional properties were analyzed and discussed. The frictional force⁻sliding-distance curves show typical stick⁻slip behaviors, and the periodicity can be used to characterize the lattice constants of SLMoS₂. Sub-nanoscale stick-slip movements occur in one-lattice sliding periods along with only the armchair (AC) direction and only when the tip radius is smaller than 3 Å with 1.47 Å tip-sample distance. At the same tip⁻sample distance, a smaller tip can provide a more detailed characterization and higher-precision frictional properties of SLMoS₂. A larger tip is capable of providing comparative frictional properties of SLMoS₂ at a proper vertical tip⁻sample distance, compared with the small tip.

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.

Anomalous Potential-Dependent Friction on Au(111) Measured by AFM

We present an exploratory study of the tribological properties between an AFM probe and a Au(111) surface in an aqueous environment while subjected to applied surface potentials. Using a three-electrode setup, the electrical potential and interfacial electric field on a Au(111) working electrode are controlled. Lateral force microscopy is used to measure the friction forces between the AFM probe and the Au surface. As the AFM probe approaches the surface, normal forces are also measured to gain insight into the interfacial forces. When a positive potential is applied to the Au surface, the friction is found to rise sharply at a critical potential and level off at a relatively high value. However, when a negative potential is applied, the friction forces are low, even lower compared to the open circuit potential case. These changes in friction, by a factor of approximately 35, as a function of the applied potential are found to be reversible over multiple cycles. We attribute the origin of the high friction at positive potentials to the formation of a highly confined, ordered icelike water layer at the Au/electrolyte interface that results in effective hydrogen bonding with the AFM probe. At negative potentials, the icelike water layer is disrupted, resulting in the water molecules acting as boundary lubricants and providing low friction. Such friction experiments can provide valuable insight into the structure and properties of water at charged surfaces under various conditions and can potentially impact a variety of technologies relying on molecular-level friction such as MEMs.

Unveiled electric profiles within hydrogen bonds suggest DNA base pairs with similar bond strengths

Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond resolution to support a characterization of single bond forces attending to its electrical origin. This fundamental issue has eluded a physical description so far. Our method is applied to describe hydrogen bonds (HB) in DNA base pairs. Numerical results reveal that base pairs in DNA could be equivalent considering HB strength contributions, which challenges previous interpretations of thermodynamic properties of DNA based on the assumption that Adenine/Thymine pairs are weaker than Guanine/Cytosine pairs due to the sole difference in the number of HB. Thus, our methodology provides solid foundations to support the development of extended models intended to go deeper into the molecular mechanisms of DNA functioning.

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.

Competing Annulene and Radialene Structures in a Single Anti-Aromatic Molecule Studied by High-Resolution Atomic Force Microscopy

According to Hückel theory, an anti-aromatic molecule possessing (4n)π-electrons becomes unstable. Although the stabilization has been demonstrated by radialene-type structures-fusing aromatic rings to anti-aromatic rings-in solution, such molecules have never been studied at a single molecular level. Here, we synthesize a cyclobutadiene derivative, dibenzo[b,h]biphenylene, by an on-surface intramolecular reaction. With a combination of high-resolution atomic force microscopy and density functional theory calculations, we found that a radialene structure significantly reduces the anti-aromaticity of the cyclobutadiene core, extracting π-electrons, while the small four-membered cyclic structure keeps a high density of the total charge.

Non-contact lateral force microscopy

The goal of atomic force microscopy (AFM) is to measure the short-range forces that act between the tip and the surface. The signal recorded, however, includes long-range forces that are often an unwanted background. Lateral force microscopy (LFM) is a branch of AFM in which a component of force perpendicular to the surface normal is measured. If we consider the interaction between tip and sample in terms of forces, which have both direction and magnitude, then we can make a very simple yet profound observation: over a flat surface, long-range forces that do not yield topographic contrast have no lateral component. Short-range interactions, on the other hand, do. Although contact-mode is the most common LFM technique, true non-contact AFM techniques can be applied to perform LFM without the tip depressing upon the sample. Non-contact lateral force microscopy (nc-LFM) is therefore ideal to study short-range forces of interest. One of the first applications of nc-LFM was the study of non-contact friction. A similar setup is used in magnetic resonance force microscopy to detect spin flipping. More recently, nc-LFM has been used as a true microscopy technique to systems unsuitable for normal force microscopy.

Unconventional Behavior of Friction at the Nanoscale beyond Amontons' Law

By means of a many-body van der Waals (vdW)-corrected density functional theory approach, the atomic-scale friction of a prototypical tip-substrate system consisting of an Si tip and a graphene substrate is studied. In a loading-sliding process, the tip-substrate distance is found to be essential for nanofrictional behavior, through determining the competition between vdW contributions and electronic contributions. As the tip approaches the substrate, this competition results in a smooth transition of normal forces from attraction to repulsion, and the friction coefficient in turn undergoes a sign change from negative to positive with possible giant magnitude and strong anisotropy. The loading-sliding process does not introduce any chemical modification of the underlying system. These findings reveal the boundary of validity of Amontons' law, unify negative and giant friction coefficients, rationalize the experimentally observed anisotropy of nanofriction, and are universal when vdW interactions are crucial, all of which are helpful to establish a comprehensive picture of nanofriction.

Potential energy-driven spin manipulation via a controllable hydrogen ligand

Spin-bearing molecules can be stabilized on surfaces and in junctions with desirable properties, such as a net spin that can be adjusted by external stimuli. Using scanning probes, initial and final spin states can be deduced from topographic or spectroscopic data, but how the system transitions between these states is largely unknown. We address this question by manipulating the total spin of magnetic cobalt hydride complexes on a corrugated boron nitride surface with a hydrogen-functionalized scanning probe tip by simultaneously tracking force and conductance. When the additional hydrogen ligand is brought close to the cobalt monohydride, switching between a correlated S = 1/2 Kondo state, where host electrons screen the magnetic moment, and an S = 1 state with magnetocrystalline anisotropy is observed. We show that the total spin changes when the system is transferred onto a new potential energy surface that is defined by the position of the hydrogen in the junction. These results show how and why chemically functionalized tips are an effective tool to manipulate adatoms and molecules and a promising new method to selectively tune spin systems.

Probing Intermolecular Coupled Vibrations between Two Molecules

Intermolecular interactions can induce energy shifts and coupling of molecular vibrations. However, the detection of intermolecular coupled vibrations has not been reported at the single molecule level. Here we detected an intermolecular coupled vibration between two CO molecules, one on the surface and another on the tip within the gap of a subkelvin scanning tunneling microscope, and analyzed the results by density functional calculations. We attribute the evolution of the energy and intensity of this coupled vibration as a function of tip-sample distance to the tilting and orbital alignment of the two CO molecules.

Tomography of a Probe Potential Using Atomic Sensors on Graphene

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Orthotropic Piezoelectricity in 2D Nanocellulose

The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V-1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

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.

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

How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.

The chemical properties of molecules are largely determined by the distribution of charge across them. Here, the authors demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with sub-molecular resolution.