Bipolar conductance switching of single anthradithiophene molecules

The authors acknowledge funding by the Emmy-Noether-Program of the Deutsche Forschungsgemeinschaft, the SFB 767, and the Baden-Württemberg Stiftung. R.P. and A.A. thank the Basque Departamento de Universidades e Investigacion (grant no. IT-756-13) and the Spanish Ministerio de Economia y Competitividad (grant no. FIS2013-48286-C2-8752-P) for financial support.Single molecular switches are basic device elements in organic electronics. The pentacene analogue anthradithiophene (ADT) shows a fully reversible binary switching between different adsorption conformations on a metallic surface accompanied by a charge transfer. These transitions are activated locally in single molecules in a low-temperature scanning tunneling microscope . The switching induces changes between bistable orbital structures and energy level alignment at the interface. The most stable geometry, the “off” state, which all molecules adopt upon evaporation, corresponds to a short adsorption distance at which the electronic interactions of the acene rings bend the central part of the molecule toward the surface accompanied by a significant charge transfer from the metallic surface to the ADT molecules. This leads to a shift of the lowest unoccupied molecular orbital down to the Fermi level (EF). In the “on” state the molecule has a flat geometry at a larger distance from the surface; consequently the interaction is weaker, resulting in a negligible charge transfer with an orbital structure resembling the highest occupied molecular orbital when imaged close to EF. The potential barrier between these two states can be overcome reversibly by injecting charge carriers locally into individual molecules. Voltage-controlled current traces show a hysteresis characteristic of a bipolar switching behavior. The interpretation is supported by first-principles calculations.PostprintPeer reviewe

Remotely controlled isomer selective molecular switching

Nonlocal addressing—the “remote control”—of molecular switches promises more efficient processing for information technology, where fast speed of switching is essential. The surface state of the (111) facets of noble metals, a confined two-dimensional electron gas, provides a medium that enables transport of signals over large distances and hence can be used to address an entire ensemble of molecules simultaneously with a single stimulus. In this study we employ this characteristic to trigger a conformational switch in anthradithiophene (ADT) molecules by injection of hot carriers from a scanning tunneling microscope (STM) tip into the surface state of Cu(111). The carriers propagate laterally and trigger the switch in molecules at distances as far as 100 nm from the tip location. The switching process is shown to be long-ranged, fully reversible, and isomer selective, discriminating between cis and trans diastereomers, enabling maximum control.PostprintPeer reviewe

Electric-field-driven direct desulfurization

The ability to elucidate the elementary steps of a chemical reaction at the atomic scale is important for the detailed understanding of the processes involved, which is key to uncover avenues for improved reaction paths. Here, we track the chemical pathway of an irreversible direct desulfurization reaction of tetracenothiophene adsorbed on the Cu(111) closed-packed surface at the submolecular level. Using the precise control of the tip position in a scanning tunneling microscope and the electric field applied across the tunnel junction, the two carbon–sulfur bonds of a thiophene unit are successively cleaved. Comparison of spatially mapped molecular states close to the Fermi level of the metallic substrate acquired at each reaction step with density functional theory calculations reveals the two elementary steps of this reaction mechanism. The first reaction step is activated by an electric field larger than 2 V nm–1, practically in absence of tunneling electrons, opening the thiophene ring and leading to a transient intermediate. Subsequently, at the same threshold electric field and with simultaneous injection of electrons into the molecule, the exergonic detachment of the sulfur atom is triggered. Thus, a stable molecule with a bifurcated end is obtained, which is covalently bound to the metallic surface. The sulfur atom is expelled from the vicinity of the molecule.PostprintPeer reviewe

Chiral and catalytic effects of site-specific molecular adsorption

Open access funded by Max Planck Society. The authors acknowledge the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy-EXC-2123 Quantum Frontiers - 390837967; Core program PC2-PN23080202 and the PN-III-P2-2.1-PED-2021-0378 (contract no. 575PED/2022) granted projects, financed by the Romanian Ministry of Research, Innovation and Digitalization/UEFISCDI; and the generous allocation of computer time at the computing center of Donostia International Physics Center and at the Red Española de Supercomputación (project QHS-2021-2-0019). A.A. acknowledges support from Project No. PID2019-103910GB-I00, funded by MCIN/AEI/10.13039/501100011033/ and FEDER Una manera de hacer Europa, and Project No. IT-1527-22 funded by the Basque Government.The changes of properties and preferential interactions based on subtle energetic differences are important characteristics of organic molecules, particularly for their functionalities in biological systems. Only slightly energetically favored interactions are important for the molecular adsorption and bonding to surfaces, which define their properties for further technological applications. Here, prochiral tetracenothiophene molecules are adsorbed on the Cu(111) surface. The chiral adsorption configurations are determined by Scanning Tunneling Microscopy studies and confirmed by first-principles calculations. Remarkably, the selection of the adsorption sites by chemically different moieties of the molecules is dictated by the arrangement of the atoms in the first and second surface layers. Furthermore, we have investigated the thermal effects on the direct desulfurization reaction that occurs under the catalytic activity of the Cu substrate. This reaction leads to a product that is covalently bound to the surface in chiral configurations.Publisher PDFPeer reviewe

Controlling single molecule conductance by a locally induced chemical reaction on individual thiophene units

The authors acknowledge the Emmy-Noether-Program of the Deutsche Forschungsgemeinschaft, the SFB 767, Core Program PN19-03 (contract number 21 N/08.02.2019) founded by the Romanian Ministry of Research and Innovation, Basque Departamento de Universidades e Investigación (grant no. IT-756-13), the Spanish Ministerio de Economía y Competitividad (grant no. FIS2013-48286-C2-8752-P and FIS2016-75862-P) andthe Operational Programme Research, Development and Education financed by European Structural and Investment Funds and the Czech Ministry of Education, Youth and Sports (Project No. SOLID21 CZ.02.1.01/0.0/0.0/16_019/0000760).Among the prerequisites for the progress of single‐molecule‐based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ‐induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.Publisher PDFPeer reviewe

Fast Molecular Compression by a Hyperthermal Collision Gives Bond-Selective Mechanochemistry

Using electrospray ion beam deposition, we collide the complex molecule Reichardt’s Dye (C41H30NO+) at low, hyperthermal translational energy (2 - 50 eV) with a Cu(100) surface and image the outcome at single-molecule level by scanning tunneling microscopy. We observe bond-selective reaction induced by the translational kinetic energy. The collision impulse compresses the molecule and bends specific bonds, prompting them to react selectively. This dynamics drives the system to seek thermally inaccessible reactive pathways, since the compression timescale (sub-ps) is much shorter than the thermalization timescale (ns), thereby yielding reaction products that are unobtainable thermally

Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules

The importance of organic chemistry in modern science and industry has lead to an emergence of a variety of advanced techniques for the identification of organic molecules. The most common of them are vibrational spectroscopies, diffraction techniques and nuclear magnetic resonance spectroscopy (NMR). Resolving the molecular structures with thesemethods relies on the unique responses and interactions of the ensemble of the molecules to the applied stimuli, such as electromagnetic radiation or particle beams. Another approach to the structural determination relies on the real-space investigation and is offered by microscopy techniques. One of them, scanning tunneling microscopy (STM) is capable of identification of the organic structures by imaging explicitly single molecules at the nanoscale. Further integration of non-contact atomic force microscopy (nc-AFM) with STM allows direct observation of the molecular structures with atomic resolution. This unique possibility can be utilized to study chemistry with extraordinary precision at the scale of individual molecules. In this thesis, a homebuilt combined STM/nc-AFM instrument is used to investigate three distinct organic systems, focusing on the structure elucidation and chemical reactivity of single organic molecules. The first research project concerns the structural and electronic properties of a tetracenothiophene (TCT), adsorbed on the Cu(111) surface. The TCT molecule is a pentacene derivative with a sulfur-containing thiophene group. The two pathways of an electric-field-driven desulfurization reaction of this thiophene group are demonstrated: a two-step pathway and a direct transition from the intact to the desulfurized state. The reaction is triggered by positioning the STM tip above the thiophene moiety and ramping the bias voltage. In the two-step pathway, the first step is induced only by the presence of the electric field. The second step can be induced by applying the electric field and simultaneously injecting the electrons into the system. With both high-resolution STM and nc-AFM imaging, we identify the two steps as the subsequent splitting of the two C-S bonds of the thiophene group. As a result, the two carbon atoms of the former thiophene group form covalent bonds to Cu surface atoms. After the reaction, the desulfurized molecule is anchored to the substratemechanically. The conductance measured through the molecule suspended between the tip and the sample electrodes increases by »50 % after the reaction. Due to the properties of the facile thiophene-copper bonding, it is of interest as an anchoring technique in single-molecule electronics. In the second project, the chemical reactions induced by hyperthermal collisions of Reichardt’s Dye molecules with a metal surface are investigated. Collisions with hyperthermal kinetic energies lead to a non-equilibrium process where the high energy of themolecules is dispersed in a very short time. By controlling the kinetic energy of the incident organic molecules with Electrospray Ionization-Beam Deposition (ES-IBD), we accessed new, thermally inaccessible states. We identified both thermally and kinetically created species of Reichardt’s Dye with the STM/nc-AFMimaging and compared the results. Hyperthermal deposition of Reichardt’s Dye indeed leads to the creation of new states that are inaccessible by thermal activation. This approach to reaction kinetics can be applied to different systems to yield new molecular species. In the last chapter, we test the ability of STM/nc-AFM to identify the branched structures of small carbohydrates. This class of molecules is representative of many biologically active molecules that are difficult to analyze with traditional methods such as mass spectrometry and nuclearmagnetic resonance spectroscopy. The carbohydrates can exhibit a polymerized and branched structure, often consisting of monosaccharideswith identical mass and composition. Therefore, the full identification of their structure, if possible at all, requires a series of precise experiments, significantly increasing the material consumption. Carbohydrates, as well as proteins and peptides, are often not available in required amounts. The real space approach to investigating carbohydrates, including STM and nc-AFM, may provide information about the branching aspect of carbohydrate structure at low material cost, thanks to the possibility of structural identification performed on a single organic molecule. We analyzed a model system consisting of linear pentamers and branched hexamers of mannose. The studies of these linear carbohydrates lead to the identification of single monosaccharide units on Cu(100) and Cu(111). We also identified and assigned folded structures encountered during the experiments to single and double pentamers ofmannose. Moreover, the imaging allowed us to approximately localize the branching points in the branched hexamers of mannose. This effort demonstrates the potential of using STM/nc-AFMas a complementary technique for the structural identification of carbohydrates.publishe