Molecular sensitised probe for amino acid recognition within peptide sequences.

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.

Local spectroscopy of a gate-switchable moiré quantum anomalous Hall insulator.

In recent years, correlated insulating states, unconventional superconductivity, and topologically non-trivial phases have all been observed in several moiré heterostructures. However, understanding of the physical mechanisms behind these phenomena is hampered by the lack of local electronic structure data. Here, we use scanning tunnelling microscopy and spectroscopy to demonstrate how the interplay between correlation, topology, and local atomic structure determines the behaviour of electron-doped twisted monolayer-bilayer graphene. Through gate- and magnetic field-dependent measurements, we observe local spectroscopic signatures indicating a quantum anomalous Hall insulating state with a total Chern number of ±2 at a doping level of three electrons per moiré unit cell. We show that the sign of the Chern number and associated magnetism can be electrostatically switched only over a limited range of twist angle and sample hetero-strain values. This results from a competition between the orbital magnetization of filled bulk bands and chiral edge states, which is sensitive to strain-induced distortions in the moiré superlattice.

Chiral self-organized single 2D-layers of tetramers from a functional donor-acceptor molecule by the surface template effect.

The ability to control the structural properties of molecular layers is a key for the design and preparation of organic electronic devices. While microscopic growth studies of planar, rigid and symmetric π-conjugated molecules have been performed to a larger extent, this is less the case for elongated donor-acceptor molecules with flexible functional groups, which are particularly interesting due to their high dipole moments. Prototypical molecules of this type are merocyanines (MCs), which have been widely studied for the use as efficient absorbers in organic photodetectors. For maximized light absorption and optimized electronic properties the molecular arrangement which is affected by the initial assembly of the films at the supporting substrate interface is decisive. The situation deserves special attention, when the surface nucleation leads to so far not known and bulk-unlike aggregates. Here, we report on the growth of a typical MC (HB238) on the Ag(100) surface, serving as the substrate. In the energetically preferred phase, the molecules adsorb in a face-on geometry and organize in tetramers with a circular dipole arrangement. The tetramers further self-order in large, enantiopure domains with a periodicity that is commensurate to the Ag(100) surface, likely due to a specific bonding of the thiophene and thiazol rings to the Ag surface. Using scanning tunneling microscopy (STM) in combination with low energy electron diffraction we derive the detailed structure of the tetramers. The center of the tetramer, which is most prominent in STM images, consists of four upward pointing tert-butyl groups from four molecules. It is encircled by a ring of four hydrogen bonds between terminal CN-groups and thiophene rings on neighboring molecules. In parallel, the surface interaction modifies the intramolecular dipole, which is revealed from photoemission spectroscopy. Hence, this example shows how the surface template effect leads to an unforeseen molecular organization which is considerably more complex compared to that in the bulk phases of HB238, which feature paired dipoles.

ß-Sheet Assembly Translates Conservative Single-Site Mutation into a Perturbation in Macroscopic Structure.

Transferring structural information from amino acid sequence to macroscale assembly is a challenging approach for designing protein quaternary structure. However, the pathway by which the slight variations in sequence result in a global perturbation effect on the assembled structure is unknown. Herein, we design two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and use scanning tunneling microscopy (STM) to image individual peptides in the assembled state. The submolecular resolution of STM enables us to determine the folding structure and ß-sheet supramolecular organization of peptides. QNL-His and QNL-Arg differ in their ß-strand length distribution in pleated ß-sheet association. These structural variations lead to distinguishable outcomes in their ß-sheet assembled fibrils and phase transitions. The comparison of QNL-His versus QNL-Arg structures and macroscopic properties unveils the role of assembly to amplify the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.

On-Surface Synthesis of Square-Type Porphyrin Tetramers with Central Antiaromatic Cyclooctatetraene Moiety.

The synthesis of two-dimensionally extended polycyclic heteroatomic molecules keeps attracting considerable attention. In particular, frameworks bearing planar cyclooctatetraenes (COT) moieties can display intriguing properties, including antiaromaticity. Here, we present an on-surface chemistry route to square-type porphyrin tetramers with a central COT ring, coexisting with other oligomers. This approach employing temperature-induced dehydrogenative porphyrin homocoupling in an ultrahigh vacuum environment provides access to surface-supported, unsubstituted porphyrin tetramers that are not easily achievable by conventional synthesis means. Specifically, monomeric free-base (2H-P) and Zn-metalated (Zn-P) porphines (P) were employed to form square-type free-base and Zn-functionalized tetramers on Ag(100). An atomic-level characterization by bond-resolved atomic force microscopy and scanning tunneling microscopy and spectroscopy is provided, identifying the molecular structures. Complemented by density functional theory modeling, the electronic structure is elucidated, indeed revealing antiaromaticity induced by the COT moiety. The present study thus gives access, and insights, to a porphyrin oligomer, representing both a model system for directly fused porphyrins and a potential building block for conjugated, extended two-dimensional porphyrin sheets.

Self-assembly controlled at the level of individual functional groups.

Molecular self-assembly is driven by intermolecular interactions between the functional groups on the component molecules. Small changes in molecular structure can make large differences in extended structure, and understanding this connection will lead to predictive power and control of the self-assembly process. Scanning tunneling microscopy is used to study self-assembly in two-dimensional clusters and monolayers, and the experimental approach is to study "families" of molecules where one or more functional groups is varied in a methodical way. Studied families include indole carboxylic acids, isatin derivatives (which have the indole backbone), quinaldic acid, thioethers, and fluorenone derivatives. In these systems, a variety of intermolecular interactions drive the assembly of the molecular monolayer, including hydrogen bonds, van der Waals forces, zwitterionic interactions, surface interactions, and halogen interactions.

Self-Assembled Monolayers of Molecular Conductors with Terpyridine-Metal Redox Switching Elements: A Combined AFM, STM and Electrochemical Study.

Self-assembled monolayers (SAMs) of terpyridine-based transition metal (ruthenium and osmium) complexes, anchored to gold substrate via tripodal anchoring groups, have been investigated as possible redox switching elements for molecular electronics. An electrochemical study was complemented by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) methods. STM was used for determination of the SAM conductance values, and computation of the attenuation factor ß from tunneling current-distance curves. We have shown that SAMs of Os-tripod molecules contain larger adlayer structures compared with SAMs of Ru-tripod molecules, which are characterized by a large number of almost evenly distributed small islands. Furthermore, upon cyclic voltammetric experimentation, Os-tripod films rearrange to form a smaller number of even larger islands, reminiscent of the Ostwald ripening process. Os-tripod SAMs displayed a higher surface concentration of molecules and lower conductance compared with Ru-tripod SAMs. The attenuation factor of Os-tripod films changed dramatically, upon electrochemical cycling, to a higher value. These observations are in accordance with previously reported electron transfer kinetics studies.

Correlation-driven electronic nematicity in the Dirac semimetal BaNiS2.

In BaNiS2, a Dirac nodal line band structure exists within a two-dimensional Ni square lattice system, in which significant electronic correlation effects are anticipated. Using scanning tunneling microscopy (STM), we discover signs of correlated-electron behavior, namely electronic nematicity appearing as a pair of C2-symmetry striped patterns in the local density-of-states at ∼60 meV above the Fermi energy. In observations of quasiparticle interference, as well as identifying scattering between Dirac cones, we find that the striped patterns in real space stem from a lifting of degeneracy among electron pockets at the Brillouin zone boundary. We infer a momentum-dependent energy shift with d-form factor, which we model numerically within a density wave (DW) equation framework that considers spin-fluctuation-driven nematicity. This suggests an unusual mechanism driving the nematic instability, stemming from only a small perturbation to the Fermi surface, in a system with very low density of states at the Fermi energy. The Dirac points lie at nodes of the d-form factor and are almost unaffected by it. These results highlight BaNiS2 as a unique material in which Dirac electrons and symmetry-breaking electronic correlations coexist.

Selective Activation of Aromatic C-H Bonds Catalyzed by Single Gold Atoms at Room Temperature.

Selective activation and controlled functionalization of C-H bonds in organic molecules is one of the most desirable processes in synthetic chemistry. Despite progress in heterogeneous catalysis using metal surfaces, this goal remains challenging due to the stability of C-H bonds and their ubiquity in precursor molecules, hampering regioselectivity. Here, we examine the interaction between 9,10-dicyanoanthracene (DCA) molecules and Au adatoms on a Ag(111) surface at room temperature (RT). Characterization via low-temperature scanning tunneling microscopy, spectroscopy, and noncontact atomic force microscopy, supported by theoretical calculations, revealed the formation of organometallic DCA-Au-DCA dimers, where C atoms at the ends of the anthracene moieties are bonded covalently to single Au atoms. The formation of this organometallic compound is initiated by a regioselective cleaving of C-H bonds at RT. Hybrid quantum mechanics/molecular mechanics calculations show that this regioselective C-H bond cleaving is enabled by an intermediate metal-organic complex which significantly reduces the dissociation barrier of a specific C-H bond. Harnessing the catalytic activity of single metal atoms, this regioselective on-surface C-H activation reaction at RT offers promising routes for future synthesis of functional organic and organometallic materials.

Probing the Synergistic Effects of Mg2+ on CO2 Reduction Reaction on CoPc by In Situ Electrochemical Scanning Tunneling Microscopy.

We report herein the in situ electrochemical scanning tunneling microscopy (ECSTM) study on the synergistic effect of Mg2+ in CO2 reduction reaction (CO2RR) catalyzed by cobalt phthalocyanine (CoPc). ECSTM measurement molecularly resolves the self-assembled CoPc monolayer on the Au(111) substrate. In the CO2 environment, high-contrast species are observed in the adlayer and assigned to the CO2 adsorption on CoPc. Furthermore, the contrast of the CO2-bound complex is higher in Mg2+-containing electrolytes than in Mg2+-free electrolytes, indicating the formation of the CoPc-CO2-Mg2+ complex. The surface coverage of adsorbed CO2 is positively correlated with the Mg2+ concentration as the additive in electrolytes up to a plateau of 30.8 ± 2.7% when c(Mg2+) > 30 mM. The potential step experiment indicates the higher CO2 adsorption dynamics in Mg2+-containing electrolytes than without Mg2+. The rate constants of CO2 adsorption and dissociation in different electrolytes are extracted from the data fitting of statistical results from in situ ECSTM experiments.

Mixed-Sandwich Titanium(III) Qubits on Au(111): Electron Delocalization Ruled by Molecular Packing.

Organometallic sandwich complexes are versatile molecular systems that have been recently employed for single-molecule manipulation and spin sensing experiments. Among related organometallic compounds, the mixed-sandwich S = 1/2 complex (η8-cyclooctatetraene)(η5-cyclopentadienyl)titanium, here [CpTi(cot)], has attracted interest as a spin qubit because of the long coherence time. Here the structural and chemical properties of [CpTi(cot)] on Au(111) are investigated at the monolayer level by experimental and computational methods. Scanning tunneling microscopy suggests that adsorption occurs in two molecular orientations, lying and standing, with a 3:1 ratio. XPS data evidence that a fraction of the molecules undergo partial electron transfer to gold, while our computational analysis suggests that only the standing molecules experience charge delocalization toward the surface. Such a phenomenon depends on intermolecular interactions that stabilize the molecular packing in the monolayer. This orientation-dependent molecule-surface hybridization opens exciting perspectives for selective control of the molecule-substrate spin delocalization in hybrid interfaces.

Atomic-Scale Rectification and Inelastic Electron Tunneling Spectromicroscopy.

The phenomenon of rectification describes the emergence of a DC current from the application of an oscillating voltage. Although the origin of this effect has been associated with the nonlinearity in the current-voltage I(V) relation, a rigorous understanding of the microscopic mechanisms for this phenomenon remains challenging. Here, we show the close connection between rectification and inelastic electron tunneling spectroscopy and microscopy for single molecules with a scanning tunneling microscope. While both techniques are based on nonlinear features in the I(V) curve, comprehensive line shape analyses reveal notable differences that highlight the two complementary techniques of nonlinear conductivity spectromicroscopy for probing nanoscale systems.

Towards π-wires on a semiconductor surface: Benzyne on Si(001).

Towards the goal of covalently bound molecular wires on silicon, the adsorption of benzyne on Si(001) was studied by means of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and density functional calculations (DFT). The benzyne molecule is found to adsorb preferentially via the strained triple bond on one dimer of the Si(001) surface which results in an intact π system covalently bound to the surface. With increasing coverage, the molecules primarily adsorb along the dimer rows; on stepped surfaces, these molecular wires are all oriented in the same direction.

On-surface synthesis of ethers through dehydrative coupling of hydroxymethyl substituents.

On-surface synthesis has been a subject of intensive research during the last decade. Various chemical reactions have been developed on surfaces to prepare compounds and carbon nanostructures, most of which are centered on the carbon-carbon bond formation. Despite the vast progress so far, the diversity of functional groups in organic chemistry has been far less explored in on-surface synthesis. Herein, we study the surface-assisted synthesis of ethers through the homocoupling of hydroxymethyl substituents on Ag(111). By using two hydroxymethyl substituent functionalized molecular precursors with different symmetries, we have achieved the formation of ether chains and rings. High-resolution scanning tunneling microscopy complemented with density functional theory calculations are used to support our findings and offer mechanistic insights into the reaction. This work expands the toolbox of on-surface reactions for the bottom-up fabrication of more sophisticated functional nanostructures.

Quantum Interference-Controlled Conductance Enhancement in Stacked Graphene-like Dimers.

Stacking interactions are of significant importance in the fields of chemistry, biology, and material optoelectronics because they determine the efficiency of charge transfer between molecules and their quantum states. Previous studies have proven that when two monomers are π-stacked in series to form a dimer, the electrical conductance of the dimer is significantly lower than that of the monomer. Here, we present a strong opposite case that when two anthanthrene monomers are π-stacked to form a dimer in a scanning tunneling microscopic break junction, the conductance increases by as much as 25 in comparison with a monomer, which originates from a room-temperature quantum interference. Remarkably, both theory and experiment consistently reveal that this effect can be reversed by changing the connectivity of external electrodes to the monomer core. These results demonstrate that synthetic control of connectivity to molecular cores can be combined with stacking interactions between their π systems to modify and optimize charge transfer between molecules, opening up a wide variety of potential applications ranging from organic optoelectronics and photovoltaics to nanoelectronics and single-molecule electronics.

Minor adjustments in the chemical structures of pyridine derivatives induced different co-assemblies by O-H⋯N hydrogen bonds.

The co-adsorption behaviours of aromatic carboxylic acids with various pyridine derivatives were investigated with scanning tunneling microscopy and density functional theory. Surprisingly, minor adjustments in the chemical structures of the pyridine derivatives, such as the relative position of the nitrogen atom or the lengths of the side chains on the backbone would evidently affect the intermolecular O-H⋯N hydrogen bonds and further form various co-adsorption structures.

Polymorphism and Building-Block-Resolved STM Imaging of Self-Assembled Monolayers of 4-Fluorobenzenemethanethiol on Au(111).

Self-assembled monolayers (SAMs) of 4-fluorobenzenemethanethiol (p-FBMT) on Au(111), prepared by immersion procedure (1 mM ethanolic solution; 60 °C; 18 h), were characterized by scanning tunneling microscopy (STM). The data suggest the formation of highly ordered monolayer with a commensurate structure, described by the 2 3 × 13 R 13 ∘ unit cell. The STM appearance of this cell occurs, however, in two different forms, with either well-localized individual spots or splitting of these spots in two components. These components are assigned to the tunneling through the entire molecule or sulfur docking group only. The respective spots correspond then to the terminal fluorine atom and sulfur docking group, manifesting, thus, building-block-resolving STM imaging. The accessibility of the docking group for direct tunneling is most likely related to a specific molecular organization for one of the two possible internal structures of the unit cell. The above results represent a showcase for potential of STM for imaging of upright-arranged and densely packed molecular assemblies, such as SAMs.

Structural adaptations of electrosprayed aromatic oligoamide foldamers on Ag(111).

Aromatic foldamers are promising for applications such as molecular recognition and molecular machinery. For many of these, defect free, 2D-crystaline monolayers are needed. To this end, submonolayers were prepared in ultra-high vacuum (UHV) on Ag(111) via electrospray controlled ion beam deposition (ES-CIBD). On the surface, the unfolded state is unambiguously identified by real-space single-molecule imaging using scanning tunnelling microscopy (STM) and it is found to assemble in regular structures.

Microwave-Frequency Scanning Gate Microscopy of a Si/SiGe Double Quantum Dot.

Conventional transport methods provide quantitative information on spin, orbital, and valley states in quantum dots but lack spatial resolution. Scanning tunneling microscopy, on the other hand, provides exquisite spatial resolution at the expense of speed. Working to combine the spatial resolution and energy sensitivity of scanning probe microscopy with the speed of microwave measurements, we couple a metallic tip to a Si/SiGe double quantum dot (DQD) that is integrated with a charge detector. We first demonstrate that the dc-biased tip can be used to change the occupancy of the DQD. We then apply microwaves through the tip to drive photon-assisted tunneling (PAT). We infer the DQD level diagram from the frequency and detuning dependence of the tunneling resonances. These measurements allow the resolution of ∼65 µeV excited states, an energy consistent with valley splittings in Si/SiGe. This work demonstrates the feasibility of scanning gate experiments with Si/SiGe devices.

Observing Electrocatalytic Processes via In Situ Electrochemical Scanning Tunneling Microscopy: Latest Advances.

Electrocatalysis is the foundation of many techniques currently used to address environmental and energy problems. Therefore, understanding the electrocatalytic processes is essential to guide the rational design of electrocatalysts. Scanning tunneling microscopy (STM), developed in the 1980s, remains one of the few techniques that allow surface imaging at the atomic level, making it incredibly useful in electrocatalytic research. In this review, we introduced the basic concept and latest applications of the STM technique for in situ studies of electrocatalytic processes, particularly its capability in active site identification, species adsorption/desorption analysis, surface reconstruction imaging, and electrocatalyst dissolution detection, as well as its advantages and limitations.