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.

Atomic-scale defects and electronic properties of a transferred synthesized MoS2 monolayer.

MoS2 monolayer samples were synthesized on a SiO2/Si wafer and transferred to Ir(111) for nano-scale characterization. The samples were extensively characterized during every step of the transfer process, and MoS2 on the final substrate was examined down to the atomic level by scanning tunneling microscopy (STM). The procedures conducted yielded high-quality monolayer MoS2 of milimeter-scale size with an average defect density of 2 × 1013 cm-2. The lift-off from the growth substrate was followed by a release of the tensile strain, visible in a widening of the optical band gap measured by photoluminescence. Subsequent transfer to the Ir(111) surface led to a strong drop of this optical signal but without further shifts of characteristic peaks. The electronic band gap was measured by scanning tunneling spectroscopy (STS), revealing n-doping and lateral nano-scale variations. The combined use of STM imaging and density functional theory (DFT) calculations allows us to identify the most recurring point-like defects as S vacancies.

Substrate-induced enhancement of the chemical reactivity in metal-supported graphene.

Graphene is commonly regarded as an inert material. However, it is well known that the presence of defects or substitutional hetero-atoms confers graphene promising catalytic properties. In this work, we use first-principles calculations to show that it is also possible to enhance the chemical reactivity of a graphene layer by simply growing it on an appropriate substrate. Our comprehensive study demonstrates that, in strongly interacting substrates like Rh(111), graphene adopts highly rippled structures that exhibit areas with distinctive chemical behaviors. According to the local coupling with the substrate, we find areas with markedly different adsorption, dissociation and diffusion pathways for both molecular and atomic oxygen, including a significant change in the nature of the adsorbed molecular and dissociated states, and a dramatic reduction (∼60%) of the O2 dissociation energy barrier with respect to free-standing graphene. Our results show that the graphene-metal interaction represents an additional and powerful handle to tailor the graphene chemical properties with potential applications to nano patterning, graphene functionalization and sensing devices.

Unveiling the atomistic mechanisms for oxygen intercalation in a strongly interacting graphene-metal interface.

The atomistic mechanisms involved in the oxygen (O) intercalation in the strongly interacting graphene (G) on Rh(111) system are characterized in a comprehensive experimental and theoretical study, combining scanning tunneling microscopy and density functional theory (DFT) calculations. Experimental evidence points out that the G areas located just above the metallic steps of the substrate are the active sites for initializing the intercalation process when some micro-etching points appear after molecular oxygen gas exposure. These regions are responsible for both the dissociation of the oxygen molecules and the subsequent penetration to the G-metal interface. Unlike in other species, the DFT calculations exclude single-point defects as additional entry paths to the interface. After penetration, the intercalation proceeds inwards due to the high mobility of atomic oxygen at the interface following mid-height paths connecting the higher areas of the rippled graphene structure. At larger coverages, the accumulation of O atoms under the high areas increases the G-metal distance in the neighboring low areas, paving the way for the O incorporation and the G detachment that leads to the final O-(2 × 1) structure. Furthermore, our results show that these mechanisms are possible only at temperatures slightly lower than those in which graphene etching takes place.

The Electric Field of CO Tips and Its Relevance for Atomic Force Microscopy.

Metal tips decorated with CO molecules have paved the way for an impressively high resolution in atomic force microscopy (AFM). Although Pauli repulsion and the associated CO tilting play a dominant role at short distances, experiments on polar and metallic systems show that electrostatic interactions are necessary to understand the complex contrast observed and its distance evolution. Attempts to describe those interactions in terms of a single electrostatic dipole replacing the tip have led to contradictory statements about its nature and strength. Here, we solve this puzzle with a comprehensive experimental and theoretical characterization of the AFM contrast on Cl vacancies. Our model, based on density functional theory (DFT) calculations, reproduces the complex evolution of the contrast between both the Na cation and Cl anion sites, and the positively charged vacancy as a function of tip height, and highlights the key contribution of electrostatic interactions for tip-sample distances larger than 500 pm. For smaller separations, Pauli repulsion and the associated CO tilting start to dominate the contrast. The electrostatic field of the CO-metal tip can be represented by the superposition of the fields from the metal tip and the CO molecule. The long-range behavior is defined by the metal tip that contributes the field of a dipole with its positive pole at the apex. At short-range, the CO exhibits an opposite field that prevails. The interplay of these fields, with opposite sign and rather different spatial extension, is crucial to describe the contrast evolution as a function of the tip height.

Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot.

We assemble bistable silicon quantum dots consisting of four buckled atoms (Si4-QD) using atom manipulation. We demonstrate two competing atom switching mechanisms, downward switching induced by tunneling current of scanning tunneling microscopy (STM) and opposite upward switching induced by atomic force of atomic force microscopy (AFM). Simultaneous application of competing current and force allows us to tune switching direction continuously. Assembly of the few-atom Si-QDs and controlling their states using versatile combined AFM/STM will contribute to further miniaturization of nanodevices.

Quantum degeneracy in atomic point contacts revealed by chemical force and conductance.

Quantum degeneracy is an important concept in quantum mechanics with large implications to many processes in condensed matter. Here, we show the consequences of electron energy level degeneracy on the conductance and the chemical force between two bodies at the atomic scale. We propose a novel way in which a scanning probe microscope can detect the presence of degenerate states in atomic-sized contacts even at room temperature. The tunneling conductance G and chemical binding force F between two bodies both tend to decay exponentially with distance in a certain distance range, usually maintaining direct proportionality G∝F. However, we show that a square relation G∝F2 arises as a consequence of quantum degeneracy between the interacting frontier states of the scanning tip and a surface atom. We demonstrate this phenomenon on the Si(111)-(7×7) surface reconstruction where the Si adatom possesses a strongly localized dangling-bond state at the Fermi level.

Chemical identification of individual surface atoms by atomic force microscopy.

Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules and of the electronic properties of magnetic impurity atoms, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution, by detecting and precisely measuring the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible.

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.

Forces and currents in carbon nanostructures: are we imaging atoms?

First-principles calculations show that the rich variety of image patterns found in carbon nanostructures with the atomic force and scanning tunneling microscopes can be rationalized in terms of the chemical reactivity of the tip and the distance range explored in the experiments. For weakly reactive tips, the Pauli repulsion dominates the atomic contrast and force maxima are expected on low electronic density positions as the hollow site. With reactive tips, the interaction is strong enough to change locally the hybridization of the carbon atoms, making it possible to observe atomic resolution in both the attractive and the repulsive regime although with inverted contrast. Regarding STM images, we show that in the near-contact regime, due to current saturation, bright spots correspond to hollow positions instead of atomic sites, providing an explanation for the most common hexagonal pattern found in the experiments.

'Sub-atomic' resolution of non-contact atomic force microscope images induced by a heterogeneous tip structure: a density functional theory study.

A Si adatom on a Si(111)-(7 × 7) reconstructed surface is a typical atomic feature that can rather easily be imaged by a non-contact atomic force microscope (nc-AFM) and can be thus used to test the atomic resolution of the microscope. Based on our first principles density functional theory (DFT) calculations, we demonstrate that the structure of the termination of the AFM tip plays a decisive role in determining the appearance of the adatom image. We show how the AFM image changes depending on the tip-surface distance and the composition of the atomic apex at the end of the tip. We also demonstrate that contaminated tips may give rise to image patterns displaying so-called 'sub-atomic' features even in the attractive force regime.

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.

Surface-controlled reversal of the selectivity of halogen bonds.

Intermolecular halogen bonds are ideally suited for designing new molecular assemblies because of their strong directionality and the possibility of tuning the interactions by using different types of halogens or molecular moieties. Due to these unique properties of the halogen bonds, numerous areas of application have recently been identified and are still emerging. Here, we present an approach for controlling the 2D self-assembly process of organic molecules by adsorption to reactive vs. inert metal surfaces. Therewith, the order of halogen bond strengths that is known from gas phase or liquids can be reversed. Our approach relies on adjusting the molecular charge distribution, i.e., the σ-hole, by molecule-substrate interactions. The polarizability of the halogen and the reactiveness of the metal substrate are serving as control parameters. Our results establish the surface as a control knob for tuning molecular assemblies by reversing the selectivity of bonding sites, which is interesting for future applications.

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

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

High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: the case of graphene-metal interfaces.

Over many years, computational simulations based on density functional theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy. For this task we use a localised basis set with the Conquest code, both in their primitive, pseudo-atomic orbital form, and using a recent multi-site approach. This multi-site scheme allows us to maintain accuracy while saving computational time and memory requirements, even in our exemplar complex system of graphene grown on Rh(1 1 1) with and without intercalated atomic oxygen. This system offers a rich scenario that will serve as a benchmark, demonstrating that highly accurate simulations in cells with over 3000 atoms are feasible with modest computational resources.

Purely substitutional nitrogen on graphene/Pt(111) unveiled by STM and first principles calculations.

Nitrogen doping of graphene can be an efficient way of tuning its pristine electronic properties. Several techniques have been used to introduce nitrogen atoms on graphene layers. The main problem in most of them is the formation of a variety of C-N species that produce different electronic and structural changes on the 2D layer. Here we report on a method to obtain purely substitutional nitrogen on graphene on Pt(111) surfaces. A detailed experimental study performed in situ, under ultra-high vacuum conditions with scanning tunneling microscopy (STM), low energy electron diffraction (LEED) and Auger electron spectroscopy (AES) of the different steps on the preparation of the sample, has allowed us to gain insight into the optimal parameters for this growth method, that combines ion bombardment and annealing. This experimental work is complemented by first-principles calculations and STM simulations that provide the variation of the projected density of states due to both the metallic substrate and the nitrogen atoms. These calculations enlighten the experimental findings and prove that the species found are graphitic nitrogen. This easy and effective technique leads to the possibility of playing with the amount of dopants and the metallic substrate to obtain the desired doping of the graphene layer.

Graphene Tunable Transparency to Tunneling Electrons: A Direct Tool To Measure the Local Coupling.

The local interaction between graphene and a host substrate strongly determines the actual properties of the graphene layer. Here we show that scanning tunneling microscopy (STM) can selectively help to visualize either the graphene layer or the substrate underneath, or even both at the same time, providing a comprehensive picture of this coupling with atomic precision and high energy resolution. We demonstrate this for graphene on Cu(111). Our spectroscopic data show that, in the vicinity of the Fermi level, graphene π bands are well preserved presenting a small n-doping induced by Cu(111) surface state electrons. Such results are corroborated by Angle-Resolved Photoemission Spectra (ARPES) and Density Functional Theory with van der Waals (DFT + vdW) calculations. Graphene tunable transparency also allows the investigation of the interaction between the substrate and foreign species (such as atomic H or C vacancies) on the graphene layer. Our calculations explain graphene tunable transparency in terms of the rather different decay lengths of the graphene Dirac π states and the metal surface state, suggesting that it should apply to a good number of graphene/substrate systems.

Sublattice localized electronic states in atomically resolved graphene-Pt(111) edge-boundaries.

Understanding the connection of graphene with metal surfaces is a necessary step for developing atomically precise graphene-based technology. Combining high-resolution STM experiments and DFT calculations, we have unambiguously unveiled the atomic structure of the boundary between a graphene zigzag edge and a Pt(111) step. The graphene edges minimize their strain by inducing a 3-fold edge-reconstruction on the metal side. We show the existence of an unoccupied electronic state that is mostly localized on the C-edge atoms of one particular graphene sublattice, which could have implications in the design of graphene based devices.

Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy.

The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7 × 7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems.

Tip-induced reduction of the resonant tunneling current on semiconductor surfaces.

We report scanning tunneling microscope measurements showing a substantial decrease of the current, almost to zero, on the Si(111)-(7x7) reconstruction in the near-to-contact region under low bias conditions. First principles simulations for the tip-sample interaction and transport calculations show that this effect is driven by the substantial local modification of the atomic and electronic structure of the surface. The chemical reactivity of the adatom dangling bond states that dominate the electronic density of states close to the Fermi level and their spatial localization result in a strong modification of the electronic current.