Molecular identification via molecular fingerprint extraction from atomic force microscopy images.

Non-Contact Atomic Force Microscopy with CO-functionalized metal tips (referred to as HR-AFM) provides access to the internal structure of individual molecules adsorbed on a surface with totally unprecedented resolution. Previous works have shown that deep learning (DL) models can retrieve the chemical and structural information encoded in a 3D stack of constant-height HR-AFM images, leading to molecular identification. In this work, we overcome their limitations by using a well-established description of the molecular structure in terms of topological fingerprints, the 1024-bit Extended Connectivity Chemical Fingerprints of radius 2 (ECFP4), that were developed for substructure and similarity searching.

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

Understanding how carbon dioxide (CO) behaves and interacts with surfaces is paramount for the development of sensors and materials to attempt CO 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 CO 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 CO islands, both confined between the PDI-Au chains as well as free-standing on the surface and reveal a chiral arrangement of CO molecules in a windmill-like structure that encloses a standing-up CO molecule and other foreign species existing at the surface.

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.

Efficacy and Safety of Adjuvant Radiotherapy in Re-excised Soft-tissue Sarcoma After Unplanned Resection.

Introduction: The objective of this study was to evaluate the efficacy and safety of adjuvant radiotherapy (aRT) in patients with soft-tissue sarcoma (STS) re-excised after unplanned tumor resection (UPR).

Materials And Methods: From 2000 to 2015, we retrospectively evaluated patients with STS of limb or trunk who underwent post-UPR re-excision in our expert center and received or not aRT.

Results: Median follow-up was 121 months (IQR 94-165).

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.

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.

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.

Long-Term Outcomes After Linac Radiosurgery for Benign Meningiomas.

Aims: Although several studies on outcomes following stereotactic radiosurgery (SRS) for benign meningiomas have been reported, Linac-based SRS outcomes have not been as widely evaluated. The aim of this retrospective institutional single-centre study was to determine long-term outcomes of Linac-based SRS for benign intracranial meningiomas.

Materials And Methods: From July 1996 to May 2011, 60 patients with 69 benign meningiomas were included.

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.

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.

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.

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

MoS monolayer samples were synthesized on a SiO/Si wafer and transferred to Ir(111) for nano-scale characterization. The samples were extensively characterized during every step of the transfer process, and MoS on the final substrate was examined down to the atomic level by scanning tunneling microscopy (STM). The procedures conducted yielded high-quality monolayer MoS of milimeter-scale size with an average defect density of 2 × 10 cm.

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.

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.

Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy.

We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomic-scale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt(111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions.

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).

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.

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.

Tug-of-war between corrugation and binding energy: revealing the formation of multiple moiré patterns on a strongly interacting graphene-metal system.

The formation of multidomain epitaxial graphene on Rh(111) under ultra-high vacuum (UHV) conditions has been characterized by scanning tunnelling microscopy (STM) measurements and density functional theory (DFT) calculations. At variance with the accepted view for strongly interacting graphene-metal systems, we clearly demonstrate the formation of different rotational domains leading to multiple moiré structures with a wide distribution of surface periodicities. Experiments reveal a correlation between the STM apparent corrugation and the lattice parameter of the moiré unit cell, with corrugations of just 30-40 pm for the smallest moirés.

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.

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.

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.

Point defects on graphene on metals.

Understanding the coupling of graphene with its local environment is critical to be able to integrate it in tomorrow's electronic devices. Here we show how the presence of a metallic substrate affects the properties of an atomically tailored graphene layer. We have deliberately introduced single carbon vacancies on a graphene monolayer grown on a Pt(111) surface and investigated its impact in the electronic, structural, and magnetic properties of the graphene layer.

'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.