Orbital and Skeletal Structure of a Single Molecule on a Metal Surface Unveiled by Scanning Tunneling Microscopy

Control of Andreev Reflection via a Single-Molecule Orbital

Charge transport across a single-molecule junction fabricated from a normal-metal tip, a phthalocyanine, and a conventional superconductor in a scanning tunneling microscope is explored as a function of the gradually closed vacuum gap. The phthalocyanine (2H-Pc) molecule and its pyrrolic-hydrogen-abstracted derivative (Pc) exhibit vastly different behavior. Andreev reflection across the 2H-Pc contact exhibits a temporary enhancement that diminishes again with increasing conductance. In contrast, the single-Pc junction lacks Andreev reflection in the same conductance range. Spectroscopies and supporting nonequilibrium Green's function calculations highlight the importance of a molecular orbital close to the Fermi energy for Andreev reflection.

Chemical Activation of a Single Melamine Molecule via Isomerization Followed by Metalation with a Copper Atom

Scanning probe methods have very successfully been used for inducing on-surface reactions and imaging with high resolution the reaction partners at the single-molecule level. However, the entire sequence of chemically activating an educt, identifying its reactive site, running a chemical reaction, and quantifying the involved forces and energies has been missing to date. Here, the organic molecule melamine adsorbed on Cu(100) serves as a single-molecule model system for activation via tautomerization and subsequent metalation with a single Cu atom. An atomic force microscope with a CO-decorated tip probes the most reactive intramolecular site of the tautomer, while a Cu-terminated tip transfers a single Cu atom to this site. Following the interaction between the mutually approached reaction partners up to the verge of chemical-bond formation enables access to the force and energy involved in the single-molecule metalation process. Total-energy calculations from density functional theory support the experimental findings and illustrate the structure of the reactants.

Distance and Voltage Dependence of Orbital Density Imaging Using a CO-Functionalized Tip in Scanning Tunneling Microscopy

The appearance of frontier molecular ion resonances measured with scanning tunneling microscopy (STM)─often referred to as orbital density images─of single molecules was investigated using a CO-functionalized tip in dependence on bias voltage and tip-sample distance. As model systems, we studied pentacene and naphthalocyanine on bilayer NaCl on Cu(111). Absolute tip-sample distances were determined by means of atomic force microscopy (AFM). STM imaging revealed a transition from predominant p- to s-wave tip contrast upon increasing the tip-sample distance, but the contrast showed only small changes as a function of voltage. The distance-dependent contrast change is explained with the steeper decay of the tunneling matrix element for tunneling between two p-wave centers, compared to tunneling between two s-wave centers. In simulations with a fixed ratio of s- to p-wave tip states, we can reproduce the experimental data including the distance-dependent transition from predominant p- to s-wave tunneling contribution.

Automated Structure Discovery for Scanning Tunneling Microscopy

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