Low-temperature UHV scanning tunneling microscope double sample holder for in situ exchangeable clean room processed samples

A generalization of the double sample holder (DSH) concept is presented for an ultra-high vacuum (UHV) low-temperature (LT) multi-probe scanning tunneling microscope (STM). In UHV, the DSH is carrying, side-by-side, a reference metal sample [Au(111) single crystal for STM tip apex preparation] and an ancillary stand-alone small sample holder (for samples originating from a clean room) that can be mounted in situ in/out of the DSH plate. STM tip navigation on both sample surfaces is performed using a UHV scanning electron microscope positioned above the STM stage. For demonstration, clean room nanofabricated graphene nano-gears (diameter down to 25 nm) on a sapphire sample are characterized using STM. The STM tip apices are cleaned on the atomically precise and UHV cleaned Au(111) reference sample surface. Using our new DSH plate and in situ STM tip apex re-preparation on the reference metallic sample, we demonstrate how a clean room originating sample can be imaged at the atomic resolution using our LT-UHV 4-STM.

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.

Single-Molecule Bioelectronic Sensors with AI-Aided Data Analysis: Convergence and Challenges

Single-molecule bioelectronic sensing, a groundbreaking domain in biological research, has revolutionized our understanding of molecules by revealing deep insights into fundamental biological processes. The advent of emergent technologies, such as nanogapped electrodes and nanopores, has greatly enhanced this field, providing exceptional sensitivity, resolution, and integration capabilities. However, challenges persist, such as complex data sets with high noise levels and stochastic molecular dynamics. Artificial intelligence (AI) has stepped in to address these issues with its powerful data processing capabilities. AI algorithms effectively extract meaningful features, detect subtle changes, improve signal-to-noise ratios, and uncover hidden patterns in massive data. This review explores the synergy between AI and single-molecule bioelectronic sensing, focusing on how AI enhances signal processing and data analysis to boost accuracy and reliability. We also discuss current limitations and future directions for integrating AI, highlighting its potential to advance biological research and technological innovation.

Impact of Single-Melamine Tautomerization on the Excitation of Molecular Vibrations in Inelastic Electron Tunneling Spectroscopy

Vibrational quanta of melamine and its tautomer are analyzed at the single-molecule level on Cu(100) with inelastic electron tunneling spectroscopy. The on-surface tautomerization gives rise to markedly different low-energy vibrational spectra of the isomers, as evidenced by a shift in mode energies and a variation in inelastic cross sections. Spatially resolved spectroscopy reveals the maximum signal strength on an orbital nodal plane, excluding resonant inelastic tunneling as the mechanism underlying the quantum excitations. Decreasing the probe-molecule separation down to the formation of a chemical bond between the melamine amino group and the Cu apex atom of the tip leads to a quenched vibrational spectrum with different excitation energies. Density functional and electron transport calculations reproduce the experimental findings and show that the shift in the quantum energies applies to internal molecular bending modes. The simulations moreover suggest that the bond formation represents an efficient manner of tautomerizing the molecule.

Atomically Precise Manufacturing of Silicon Electronics

Atomically precise manufacturing (APM) is a key technique that involves the direct control of atoms in order to manufacture products or components of products. It has been developed most successfully using scanning probe methods and has received particular attention for developing atom scale electronics with a focus on silicon-based systems. This review captures the development of silicon atom-based electronics and is divided into several sections that will cover characterization and atom manipulation of silicon surfaces with scanning tunneling microscopy and atomic force microscopy, development of silicon dangling bonds as atomic quantum dots, creation of atom scale devices, and the wiring and packaging of those circuits. The review will also cover the advance of silicon dangling bond logic design and the progress of silicon quantum atomic designer (SiQAD) simulators. Finally, an outlook of APM and silicon atom electronics will be provided.

The Case for a Defect Genome Initiative

The Materials Genome Initiative (MGI) has streamlined the materials discovery effort by leveraging generic traits of materials, with focus largely on perfect solids. Defects such as impurities and perturbations, however, drive many attractive functional properties of materials. The rich tapestry of charge, spin, and bonding states hosted by defects are not accessible to elements and perfect crystals, and defects can thus be viewed as another class of "elements" that lie beyond the periodic table. Accordingly, a Defect Genome Initiative (DGI) to accelerate functional defect discovery for energy, quantum information, and other applications is proposed. First, major advances made under the MGI are highlighted, followed by a delineation of pathways for accelerating the discovery and design of functional defects under the DGI. Near-term goals for the DGI are suggested. The construction of open defect platforms and design of data-driven functional defects, along with approaches for fabrication and characterization of defects, are discussed. The associated challenges and opportunities are considered and recent advances towards controlled introduction of functional defects at the atomic scale are reviewed. It is hoped this perspective will spur a community-wide interest in undertaking a DGI effort in recognition of the importance of defects in enabling unique functionalities in materials.

Light- and Chemical-Doping-Induced Magnetic Behavior of Eu Molecular Systems

Variable temperature electron paramagnetic resonance (VT-EPR) was used to investigate the role of the environment and oxidation states of several coordinated Eu compounds. We find that while Eu(III) chelating complexes are diamagnetic, simple chemical reduction results in the formation of paramagnetic species. In agreement with the distorted D3h symmetry of Eu molecular complexes investigated in this study, the EPR spectrum of reduced complexes showed axially symmetric signals (g⊥ = 2.001 and g∥ = 1.994) that were successfully simulated with two Eu isotopes with nuclear spin 5/2 (151Eu and 153Eu with 48% and 52% natural abundance, respectively) and nuclear g-factors 151Eu/153Eu = 2.27. Illumination of water-soluble complex Eu(dipic)3 at 4 K led to the ligand-to-metal charge transfer (LMCT) that resulted in the formation of Eu(II) in a rhombic environment (gx = 2.006, gy = 1.995, gz = 1.988). The existence of LMCT affects the luminescence of Eu(dipic)3, and pre-reduction of the complex to Eu(II)(dipic)3 reversibly reduces red luminescence with the appearance of a weak CT blue luminescence. Furthermore, encapsulation of a large portion of the dipic ligand with Cucurbit[7]uril, a pumpkin-shaped macrocycle, inhibited ligand-to-metal charge transfer, preventing the formation of Eu(II) upon illumination.

Enhancement of Graphene Phonon Excitation by a Chemically Engineered Molecular Resonance

The abstraction of pyrrolic hydrogen from a single phthalocyanine on graphene turns the molecule into a sensitive probe for graphene phonons. The inelastic electron transport measured with a scanning tunneling microscope across the molecular adsorbate and graphene becomes strongly enhanced for a graphene out-of-plane acoustic phonon mode. Supporting density functional and transport calculations elucidate the underlying physical mechanism. A molecular orbital resonance close to the Fermi energy controls the inelastic current while specific phonon modes of graphene are magnified due to their coupling to symmetry-equivalent vibrational quanta of the molecule.

Design and Manipulation of a Minimalistic Hydrocarbon Nanocar on Au(111)

Nanocars are carbon-based single-molecules with a precise design that facilitates their atomic-scale control on a surface. The rational design of these molecules is important in atomic and molecular-scale manipulation to advance the development of molecular machines, as well as for a better understanding of self-assembly, diffusion and desorption processes. Here, we introduce the molecular design and construction of a collection of minimalistic nanocars. They feature an anthracene chassis and four benzene derivatives as wheels. After sublimation and adsorption on an Au(111) surface, we show controlled and fast manipulation of the nanocars along the surface using the tip of a scanning tunneling microscope (STM). The mechanism behind the successful displacement is the induced dipole created over the nanocar by the STM tip. We utilized carbon monoxide functionalized tips both to avoid decomposition and accidentally picking the nanocars up during the manipulation. This strategy allowed thousands of maneuvers to successfully win the Nanocar Race II championship.

Nanoscale Electrically Driven Light Source Based on Hybrid Semiconductor/Metal Nanoantenna

A micro- or nanosized electrically controlled source of optical radiation is one of the key elements in optoelectronic systems. The phenomenon of light emission via inelastic tunneling (LEIT) of electrons through potential barriers or junctions opens up new possibilities for development of such sources. In this work, we present a simple approach for fabrication of nanoscale electrically driven light sources based on LEIT. We employ STM lithography to locally modify the surface of a Si/Au film stack via heating, which is enabled by a high-density tunnel current. Using the proposed technique, hybrid Si/Au nanoantennas with a minimum diameter of 60 nm were formed. Studying both electronic and optical properties of the obtained nanoantennas, we confirm that the resulting structures can efficiently emit photons in the visible range because of inelastic scattering of electrons. The proposed approach allows for fabrication of nanosized hybrid nanoantennas and studying their properties using STM.

Effect of lubricants on the rotational transmission between solid-state gears

Lubricants are widely used in macroscopic mechanical systems to reduce friction and wear. However, on the microscopic scale, it is not clear to what extent lubricants are beneficial. Therefore, in this study, we consider two diamond solid-state gears at the nanoscale immersed in different lubricant molecules and perform classical MD simulations to investigate the rotational transmission of motion. We find that lubricants can help to synchronize the rotational transmission between gears regardless of the molecular species and the center-of-mass distance. Moreover, the influence of the angular velocity of the driving gear is investigated and shown to be related to the bond formation process between gears.

Topographic signatures and manipulations of Fe atoms, CO molecules and NaCl islands on superconducting Pb(111)

Topological superconductivity emerging in one- or two-dimensional hybrid materials is predicted as a key ingredient for quantum computing. However, not only the design of complex heterostructures is primordial for future applications but also the characterization of their electronic and structural properties at the atomic scale using the most advanced scanning probe microscopy techniques with functionalized tips. We report on the topographic signatures observed by scanning tunneling microscopy (STM) of carbon monoxide (CO) molecules, iron (Fe) atoms and sodium chloride (NaCl) islands deposited on superconducting Pb(111). For the CO adsorption a comparison with the Pb(110) substrate is demonstrated. We show a general propensity of these adsorbates to diffuse at low temperature under gentle scanning conditions. Our findings provide new insights into high-resolution probe microscopy imaging with terminated tips, decoupling atoms and molecules by NaCl islands or tip-induced lateral manipulation of iron atoms on top of the prototypical Pb(111) superconducting surface.

One-Dimensional Lateral Force Anisotropy at the Atomic Scale in Sliding Single Molecules on a Surface

Using a q+ atomic force microscopy at low temperature, a sexiphenyl molecule is slid across an atomically flat Ag(111) surface along the direction parallel to its molecular axis and sideways to the axis. Despite identical contact area and underlying surface geometry, the lateral force required to move the molecule in the direction parallel to its molecular axis is found to be about half of that required to move it sideways. The origin of the lateral force anisotropy observed here is traced to the one-dimensional shape of the molecule, which is further confirmed by molecular dynamics simulations. We also demonstrate that scanning tunneling microscopy can be used to determine the comparative lateral force qualitatively. The observed one-dimensional lateral force anisotropy may have important implications in atomic scale frictional phenomena on materials surfaces.

Comparative study of adsorptions, reactions and electronic properties of U atoms on Cu(111), Ag(111), Au(111) and Ru(0001) surfaces

The mysterious properties of individual U atoms on transition metal surfaces play indispensable parts in supplementing our understanding of uranium-transition metal systems, which are important subjects for both nuclear energy applications and fundamental scientific studies. By using scanning tunneling microscopy and density functional theory calculations, the adsorptions, reactions and electronic properties of individual U atoms on Cu(111), Ag(111), Au(111) and Ru(0001) surfaces were comparatively studied for the first time in this work. Upon the deposition of a small amount of U onto Cu(111) or Ag(111) at 8 K, individual U atoms show relatively high activity and can either be adsorbed on intact substrate surfaces or induce various surface vacancies surrounded by clusters of substrate atoms. By contrast, the majority of U atoms tend to dispersedly adsorb on intact surfaces of Au(111) and Ru(0001) rather than producing surface vacancies at the same temperature. In all cases, Kondo resonance manifested as asymmetric dip feature around Fermi energy is only observed in the differential tunneling conductance spectra of single U adatoms on Ag(111).

Optical scanning tunneling microscopy based chemical imaging and spectroscopy

Through coupling optical processes with the scanning tunneling microscope (STM), single-molecule chemistry and physics have been investigated at the ultimate spatial and temporal limit. Electrons and photons can be used to drive interactions and reactions in chemical systems and simultaneously probe their characteristics and consequences. In this review we introduce and review methods to couple optical imaging and spectroscopy with scanning tunneling microscopy. The integration of the STM and optical spectroscopy provides new insights into individual molecular adsorbates, surface-supported molecular assemblies, and two-dimensional materials with subnanoscale resolution, enabling the fundamental study of chemistry at the spatial and temporal limit. The inelastic scattering of photons by molecules and materials, that results in unique and sensitive vibrational fingerprints, will be considered with tip-enhanced Raman spectroscopy. STM-induced luminescence examines the intrinsic luminescence of organic adsorbates and their energy transfer and charge transfer processes with their surroundings. We also provide a survey of recent efforts to probe the dynamics of optical excitation at the molecular level with scanning tunneling microscopy in the context of light-induced photophysical and photochemical transformations.

Temperature-Dependent Tip-Induced Motion of Ga Adatom on GaAs (110) Surface

The temperature-dependent tip-induced-motion of a Ga adatom on a GaAs (110) surface is experimentally demonstrated using scanning tunneling microscopy (STM). The surface adsorption energy profile obtained by first-principle electronic structure calculations reveals that the origin of the Ga motion observed at 78 K is attributable to the tip-induced Ga adatom hopping between the most stable potential minima among the three local minima, whereas that observed at 4.2 K is attributable to the tip-induced hopping and sliding motions through the next stable minima as well as the most stable minima. Furthermore, it is shown that a slight progressive modification of the adatom motion observed only at 4.2 K resulting from repeated STM line scans is consistent with the overall picture taking account of the heating of the adatom owing to the tip current.

Kondo-free mirages in elliptical quantum corrals

The quantum mirage effect is a fascinating phenomenon in fundamental physics. Landmark experiments on quantum mirages reveal atomic-scale transport of information with potential to remotely probe atoms or molecules with minimal perturbation. Previous experimental investigations are Kondo-effect based; the quantum mirages appear only near the Fermi energy. This strongly limits the exploration of the mechanism and potential application. Here we demonstrate a Kondo-free quantum mirage that operates in a wide energy range beyond Fermi energy. Together with an analytical model, our systematic investigations identify that the quantum mirage is the result of quantum interference of the onsite electronic states with those scattered by the adatom at the focus of elliptical quantum corrals, where two kinds of scattering paths are of critical importance. Moreover, we also demonstrate the manipulation of quantum mirages with pseudo basic logic operations, such as NOT, FANOUT and OR gates.

The quantum mirage effect is a fascinating phenomenon but in general the underlying mechanism is unclear. Here, by building elliptical quantum corrals of adatoms on a metal surface, the authors establish the mechanism of Kondo-free mirages and utilize it to build atomic-scale logic gates.

Recent Progress with In Situ Characterization of Interfacial Structures under a Solid-Gas Atmosphere by HP-STM and AP-XPS

: Surface science is an interdisciplinary field involving various subjects such as physics, chemistry, materials, biology and so on, and it plays an increasingly momentous role in both fundamental research and industrial applications. Despite the encouraging progress in characterizing surface/interface nanostructures with atomic and orbital precision under ultra-high-vacuum (UHV) conditions, investigating in situ reactions/processes occurring at the surface/interface under operando conditions becomes a crucial challenge in the field of surface catalysis and surface electrochemistry. Promoted by such pressing demands, high-pressure scanning tunneling microscopy (HP-STM) and ambient pressure X-ray photoelectron spectroscopy (AP-XPS), for example, have been designed to conduct measurements under operando conditions on the basis of conventional scanning tunneling microscopy (STM) and photoemission spectroscopy, which are proving to become powerful techniques to study various heterogeneous catalytic reactions on the surface. This report reviews the development of HP-STM and AP-XPS facilities and the application of HP-STM and AP-XPS on fine investigations of heterogeneous catalytic reactions via evolutions of both surface morphology and electronic structures, including dehydrogenation, CO oxidation on metal-based substrates, and so on. In the end, a perspective is also given regarding the combination of in situ X-ray photoelectron spectroscopy (XPS) and STM towards the identification of the structure-performance relationship.

Imaging and Dynamics of Water Hexamer Confined in Nanopores

Epitaxial two-dimensional (2D) nanostructures with regular patterns show great promise as templates for adsorbate confinement. Prospectively, employing 2D semiconductors with reduced density of states leads to a long excited-state lifetime that allows us to directly image the dynamics of the adsorbate. We show that epitaxial blue phosphorene (blueP) on Au(111) provides such a platform to trap water molecules in the periodic nanopores without formation of strong bonds. The trapped water aggregate is tentatively assigned to a hexamer based on our scanning tunneling microscopy studies and first-principles calculations. Real-space observation of conformational switching of the hexamer induced by inelastic electrons is achieved by using low-temperature scanning tunneling microscopy with molecular resolution. We found a localized interfacial charge rearrangement between the water hexamer and P atoms underneath that is responsible for the reversible desorption and adsorption of water molecules by changing the sample bias polarity from positive to negative, offering a promising strategy for engineering the electronic properties of blueP.

Role of Valence Band States and Plasmonic Enhancement in Electron-Transfer-Induced Transformation of Nitrothiophenol

Hot-electron-induced reactions are more and more recognized as a critical and ubiquitous reaction in heterogeneous catalysis. However, the kinetics of these reactions is still poorly understood, which is also due to the complexity of plasmonic nanostructures. We determined the reaction rates of the hot-electron-mediated reaction of 4-nitrothiophenol (NTP) on gold nanoparticles (AuNPs) using fractal kinetics as a function of the laser wavelength and compared them with the plasmonic enhancement of the system. The reaction rates can be only partially explained by the plasmonic response of the NPs. Hence, synchrotron X-ray photoelectron spectroscopy (XPS) measurements of isolated NTP-capped AuNP clusters have been performed for the first time. In this way, it was possible to determine the work function and the accessible valence band states of the NP systems. The results show that besides the plasmonic enhancement, the reaction rates are strongly influenced by the local density of the available electronic states of the system.

Reversible gas-solid reaction in an electronically-stimulated palladium nanogap

We investigated a nanogap between a pair of palladium electrode tips with gas (nitrogen, hydrogen, and oxygen) and a biasing voltage using in situ atomic resolution environmental transmission electron microscopy (ETEM). We found an unexpected gas-solid (nitrogen-palladium) reaction that occurs on the surface of the positive electrode tip. A palladium nitride compound was synthesized with gaseous nitrogen at low pressure at room temperature. The nitridation of palladium was previously reported and predicted to occur only under high pressure and at high temperature. The reaction in ETEM apparatus was reversible with the change in the magnitude of an electric field in the nanogap. Additionally, the asymmetrical surface dynamics on the pair of electrode tips in gas (nitrogen, hydrogen, and oxygen) were revealed by ETEM observation. It is likely that the electrons in the gap induce the reversible reaction. This study has opened a new route toward creating nanoscale materials because the creation, stabilization, and annihilation of the material in a nanogap can be controlled electrically and electronically on demand for various applications.

First-Principle Prediction on STM Tip Manipulation of Ti Adatom on Two-Dimensional Monolayer YBr3

Scanning tunneling microscopy (STM) is an important tool in surface science on atomic scale characterization and manipulation. In this work, Ti adatom manipulation is theoretically simulated by using a tungsten tip (W-tip) in STM based on first-principle calculations. The results demonstrate the possibility of inserting Ti adatoms into the atomic pores of monolayer YBr₃, which is thermodynamically stable at room temperature. In this process, the energy barriers of vertical and lateral movements of Ti are 0.38 eV and 0.64 eV, respectively, and the Ti atoms are stably placed within YBr₃ by >1.2 eV binding energy. These theoretical predictions provide an insight that it is experimentally promising to manipulate Ti adatom and form artificially designed 2D magnetic materials.

Dynamical modeling of manipulation process in Trolling-Mode AFM

Dynamical lumped modeling of Trolling-mode AFM in manipulation of bio-samples is presented. The combination of high accuracy and compatibility with physiological conditions makes AFM a unique tool for studying biological materials in liquid medium. However, AFM microcantilever suffers from severe sensitivity degradation and noise intensification while operating in liquid; the large hydrodynamic drag between the cantilever and the surrounding liquid overwhelms the tip-sample interaction forces that are important in controlling the process. Therefore, an appropriate nanoneedle should be long enough to keep the cantilever out of liquid medium and short enough to be able to transmit the required force to push nanoparticle. Nonetheless, a long nanoneedle may deflect under the pushing force; therefore, its bending deflection should be accounted for in governing equations. Moreover, analytical and finite element stress analysis of nanoneedle and cantilever is performed to assure about their selected material and geometry. JKR theory is utilized to model contact mechanics between the needle/surface and the particle. Drag and meniscus forces are used to model the liquid media. Governing equations are solved using ODE45 and the system behavior is simulated. Critical conditions of sliding including critical time and force are obtained and changes of pushing force, needle deflection and indentation depths are illustrated. Also, effects of velocity variations are observed. Then, different heights for nanoneedle are tested and an appropriate one is selected for our purpose (to keep the needle out of liquid and transmit the force appropriately). The simulation is repeated for various biological particles and their behaviors are studied. At the end, the present simulation is validated through comparing the results with a previous work. This comparison shows that the simulation is reliable for the intended purpose.

Role of π-Radicals in the Spin Connectivity of Clusters and Networks of Tb Double-Decker Single Molecule Magnets

When single molecule magnets (SMMs) self-assemble into 2D networks on a surface, they interact via the π-electrons of their ligands. This interaction is relevant to the quantum entanglement between molecular qubits, a key issue in quantum computing. Here, we examine the role played by the unpaired radical electron in the top ligand of Tb double-decker SMMs by comparing the spectroscopic features of isolated and 2D assembled entities on surfaces. High-resolution scanning tunneling microscopy (STM) is used to evidence experimentally the Kondo resonance of the unpaired radical spins in clusters and islands and its quenching due to up-pairing at orbital overlaps. The presence or the absence of the Kondo feature in the dI/dV maps turns out to be a good measure of the lateral interaction between molecules in 2D networks. In a 2D cluster of molecules, the π-orbital lobes that are linked through the orbital overlap show paired-up electron wave function (one singly occupied molecular orbital (SOMO) with spin-up and the other with spin-down) and therefore do not experience the Kondo resonance in the experiment. As a result, small clusters built by STM-assisted manipulation of molecules show alternating Kondo features of quantum mechanical origin, from the monomer to the dimer and the trimer. On the other hand, when the TbPc₂ molecular clusters grow larger and form extended domains, a geometric rearrangement occurs, leading to the quenching of the Kondo signal on one lobe out of two. The even distribution of overlapping (SOMO) lobes on the perimeter of the molecule is induced by the square symmetry of the semi-infinite lattice and clearly distinguishes the lattice from the clusters.

Simultaneous and coordinated rotational switching of all molecular rotors in a network

A range of artificial molecular systems has been created that can exhibit controlled linear and rotational motion. In the further development of such systems, a key step is the addition of communication between molecules in a network. Here, we show that a two-dimensional array of dipolar molecular rotors can undergo simultaneous rotational switching when applying an electric field from the tip of a scanning tunnelling microscope. Several hundred rotors made from porphyrin-based double-decker complexes can be simultaneously rotated when in a hexagonal rotor network on a Cu(111) surface by applying biases above 1 V at 80 K. The phenomenon is observed only in a hexagonal rotor network due to the degeneracy of the ground-state dipole rotational energy barrier of the system. Defects are essential to increase electric torque on the rotor network and to stabilize the switched rotor domains. At low biases and low initial rotator angles, slight reorientations of individual rotors can occur, resulting in the rotator arms pointing in different directions. Analysis reveals that the rotator arm directions are not random, but are coordinated to minimize energy via crosstalk among the rotors through dipolar interactions.

The butterfly - a well-defined constant-current topography pattern on Si(001):H and Ge(001):H resulting from current-induced defect fluctuations

Dangling bond (DB) arrays on Si(001):H and Ge(001):H surfaces can be patterned with atomic precision and they exhibit complex and rich physics making them interesting from both technological and fundamental perspectives. But their complex behavior often makes scanning tunneling microscopy (STM) images difficult to interpret and simulate. Recently it was shown that low-temperature imaging of unoccupied states of an unpassivated dimer on Ge(001):H results in a symmetric butterfly-like STM pattern, despite the fact that the equilibrium dimer configuration is expected to be a bistable, buckled geometry. Here, based on a thorough characterization of the low-bias switching events on Ge(001):H, we propose a new imaging model featuring a dynamical two-state rate equation. On both Si(001):H and Ge(001):H, this model allows us to reproduce the features of the observed symmetric empty-state images which strongly corroborates the idea that the patterns arise due to fast switching events and provides an insight into the relationship between the tunneling current and switching rates. We envision that our new imaging model can be applied to simulate other bistable systems where fluctuations arise from transiently charged electronic states.

Spectroscopic Line Shapes of Vibrational Quanta in the Presence of Molecular Resonances

Line shapes of molecular vibrational quanta in inelastic electron tunneling spectroscopy may indicate the strength of electron-vibration coupling, the hybridization of the molecule with its environment, and the degree of vibrational damping by electron-hole pair excitation. Bare as well as C60-terminated Pb tips of a scanning tunneling microscope and clean as well as C60-covered Pb(111) surfaces were used in low-temperature experiments. Depending on the overlap of orbital and vibrational spectral ranges different spectroscopic line shapes of molecular vibrational quanta were observed. The energy range covered by the molecular resonance was altered by modifying the adsorption configuration of the molecule terminating the tip apex. Concomitantly, the line shapes of different vibrational modes were affected. The reported observations represent an experimental proof to theoretical predictions on the contribution from resonant processes to inelastic electron tunneling.

Diels-Alder attachment of a planar organic molecule to a dangling bond dimer on a hydrogenated semiconductor surface

Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local "on-surface" chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels-Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties.

Controllable dissociations of PH3 molecules on Si(001)

We demonstrate for the first time to our knowledge that controllable dissociation of PH3 adsorption products PHx (x = 2, 1) can be realized by STM (scanning tunneling microscope) manipulation techniques at room temperature. Five dissociative products and their geometric structures are identified via combining STM experiments and first-principle calculations and simulations. In total we realize nine kinds of controllable dissociations by applying a voltage pulse among the PH3-related structures on Si(001). The dissociation rates of the five most common reactions are measured by the I-t spectrum method as a function of voltage. The suddenly increased dissociation rate at 3.3 V indicates a transition from multivibrational excitation to single-step excitation induced by inelastic tunneling electrons. Our studies prove that selectively breaking the chemical bonds of a single molecule on semiconductor surface by STM manipulation technique is feasible.

Resolving the complex structure of molecular networks

The arrangement of molecules in molecular networks determines their physical and chemical properties. Addressing this fundamental issue requires proper structural characterization tools. Due to an overlap, interdigitation, tilting or stacking of molecules revealing the structure of the networks is challenging. Tebi et al (2015 Nanotechnology 27 025704) developed a clever approach that enables accessing the arrangement of individual molecules in complex chemical networks. The proposed method utilizes imaging and manipulation with scanning tunneling microscopy.

Interaction of a conjugated polyaromatic molecule with a single dangling bond quantum dot on a hydrogenated semiconductor

Controlling the strength of the coupling between organic molecules and single atoms provides a powerful tool for tuning electronic properties of single-molecule devices. Here, using scanning tunneling microscopy and spectroscopy (STM/STS) supported by theoretical modeling, we study the interaction of a planar organic molecule (trinaphthylene) with a hydrogen-passivated Ge(001):H substrate and a single dangling bond quantum dot on that surface. The electronic structure of the molecule adsorbed on the hydrogen-passivated surface is similar to the gas phase structure and the measurements show that HOMO and LUMO states contribute to the STM filled and empty state images, respectively. Furthermore, we show that the electronic properties are not significantly affected when the molecule is attached to the single dangling bond, which is in contrast with the strong interaction of the molecule with a dangling bond dimer. Our results show that the dangling bond quantum dots could stabilize organic molecules on a hydrogenated semiconductor without affecting their originally designed gas phase electronic properties. Together with the ability to laterally manipulate the molecules on the surface, this will be advantageous in the construction of single-molecule devices, where the coupling and positioning of the molecules on the substrate could be tuned by a proper design of the surface quantum dot arrays, comprising both single and dimerized dangling bonds.

Organic Covalent Patterning of Nanostructured Graphene with Selectivity at the Atomic Level

Organic covalent functionalization of graphene with long-range periodicity is highly desirable-it is anticipated to provide control over its electronic, optical, or magnetic properties-and remarkably challenging. In this work we describe a method for the covalent modification of graphene with strict spatial periodicity at the nanometer scale. The periodic landscape is provided by a single monolayer of graphene grown on Ru(0001) that presents a moiré pattern due to the mismatch between the carbon and ruthenium hexagonal lattices. The moiré contains periodically arranged areas where the graphene-ruthenium interaction is enhanced and shows higher chemical reactivity. This phenomenon is demonstrated by the attachment of cyanomethyl radicals (CH2CN(•)) produced by homolytic breaking of acetonitrile (CH3CN), which is shown to present a nearly complete selectivity (>98%) binding covalently to graphene on specific atomic sites. This method can be extended to other organic nitriles, paving the way for the attachment of functional molecules.

Realization of a quantum Hamiltonian Boolean logic gate on the Si(001):H surface

The design and construction of the first prototypical QHC (Quantum Hamiltonian Computing) atomic scale Boolean logic gate is reported using scanning tunnelling microscope (STM) tip-induced atom manipulation on an Si(001):H surface. The NOR/OR gate truth table was confirmed by dI/dU STS (Scanning Tunnelling Spectroscopy) tracking how the surface states of the QHC quantum circuit on the Si(001):H surface are shifted according to the input logical status.

Atomically crafted spin lattices as model systems for quantum magnetism

Low-dimensional quantum magnetism presents a seemingly unlimited source of rich, intriguing physics. Yet, because realistic experimental representations are difficult to come by, the field remains predominantly theoretical. In recent years, artificial spin structures built through manipulation of magnetic atoms in a scanning tunnelling microscope have developed into a promising testing ground for experimental verification of theoretical models. Here, we present an overview of available tools and discuss recent achievements as well as future avenues. Moreover, we show new observations on magnetic switching in a bistable bit that can be used to extrapolate information on the magnetisation of the microscope tip.

Atom-by-atom assembly

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to 'see' individual atoms by means of imaging, but is also a tool that is used to 'touch' and 'take' the atoms, or to 'hear' their movements. Therefore, the STM can be considered as the 'eyes', 'hands' and 'ears' of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed.

Manipulating photon emission efficiency with local electronic states in a tunneling gap

We demonstrate manipulation of photon emission efficiency in a tunneling gap by tuning the rates of elastic and inelastic electron tunneling processes with local electronic states. The artificial local electronic states are created by a scanning tunneling microscope tip on a CuN nanoisland grown on a Cu(100) surface at cryogenic temperature. These local electronic states can either enhance or suppress the excitation of tip-induced surface plasmon modes at specific bias voltages, and thus the induced photon emission rates. A theoretical model quantitatively analyzing inelastic and elastic tunneling processes associated with characteristic electronic states shows good agreement with experiments. We also show that tip-induced photon emission measurement can be used for probing the electronic states in the tunneling gap.

Three-dimensional manipulation with scanning near-field optical nanotweezers

Recent advances in nanotechnologies have prompted the need for tools to accurately and non-invasively manipulate individual nano-objects. Among the possible strategies, optical forces have been predicted to provide researchers with nano-optical tweezers capable of trapping a specimen and moving it in three dimensions. In practice, however, the combination of weak optical forces and photothermal issues has thus far prevented their experimental realization. Here, we demonstrate the first three-dimensional optical manipulation of single 50 nm dielectric objects with near-field nanotweezers. The nano-optical trap is built by engineering a bowtie plasmonic aperture at the extremity of a tapered metal-coated optical fibre. Both the trapping operation and monitoring are performed through the optical fibre, making these nanotweezers totally autonomous and free of bulky optical elements. The achieved trapping performances allow for the trapped specimen to be moved over tens of micrometres over a period of several minutes with very low in-trap intensities. This non-invasive approach is foreseen to open new horizons in nanosciences by offering an unprecedented level of control of nanosized objects, including heat-sensitive biospecimens.

Controlled manipulation of gadolinium-coordinated supramolecules by low-temperature scanning tunneling microscopy

Coordination bonding between para-quarterphenyl-dicarbonitrile linkers and gadolinium on Ag(111) has been exploited to construct pentameric mononuclear supramolecules, consisting of a rare-earth center surrounded by five molecular linkers. By employing a scanning tunneling microscope tip, a manipulation protocol was developed to position individual pentamers on the surface. In addition, the tip was used to extract and replace individual linkers yielding tetrameric, pentameric, nonameric, and dodecameric metallosupramolecular arrangements. These results open new avenues toward advanced nanofabrication methods and rare-earth nanochemistry by combining the versatility of metal-ligand interactions and atomistic manipulation capabilities.

Formation of nickel–carbon heterofullerenes under electron irradiation

Transformation of a graphene flake with an attached nickel cluster to new metal–carbon nanoobjects under electron irradiation is simulated.

Observation and manipulation of hexa-adamantyl-hexa-benzocoronene molecules by low temperature scanning tunneling microscopy

Observation and manipulation of Ad₆HBC molecules by STM (image of a dimer created by molecular manipulation).

The manipulation of C60 in molecular arrays with an STM tip in regimes below the decomposition threshold

The ability of scanning tunneling microscopy to manipulate selected C(60) molecules within close packed C(60) arrays on a (Au,In)/Si(111) surface has been examined for mild conditions below the decomposition threshold. It has been found that knockout of the chosen C(60) molecule (i.e., vacancy formation) and shifting of the C(60) molecule to the neighboring vacant site (if available) can be conducted for wide ranges of bias voltages (from -1.5 to +0.5 V), characteristic manipulation currents (from 0.02 to 100 nA) and powers (from 2 × 10(-8) to 0.1 μW). This result implies that the manipulation is not associated with the electrical effects but rather has a purely mechanical origin. The main requirement for successful C(60) knockout has been found to be to ensure a proper 'impact parameter' (deviation from central impact on the C(60) sphere by the tip apex), which should be less than ~1.5 Å. A certain difference has been detected for the manipulation of C(60) in extended molecular arrays and molecular islands of a limited size. While it is possible to manipulate a single C(60) molecule in an array, in the case of a C(60) island it appears difficult to manipulate a given fullerene without affecting the other ones constituting the island.

Controlled clockwise and anticlockwise rotational switching of a molecular motor

The design of artificial molecular machines often takes inspiration from macroscopic machines. However, the parallels between the two systems are often only superficial, because most molecular machines are governed by quantum processes. Previously, rotary molecular motors powered by light and chemical energy have been developed. In electrically driven motors, tunnelling electrons from the tip of a scanning tunnelling microscope have been used to drive the rotation of a simple rotor in a single direction and to move a four-wheeled molecule across a surface. Here, we show that a stand-alone molecular motor adsorbed on a gold surface can be made to rotate in a clockwise or anticlockwise direction by selective inelastic electron tunnelling through different subunits of the motor. Our motor is composed of a tripodal stator for vertical positioning, a five-arm rotor for controlled rotations, and a ruthenium atomic ball bearing connecting the static and rotational parts. The directional rotation arises from sawtooth-like rotational potentials, which are solely determined by the internal molecular structure and are independent of the surface adsorption site.

Molecular Kondo chain

An important development in recent synthesis strategies is the formation of electronically coupled one and two-dimensional organic systems for potential applications in nanoscale molecule-based devices. Here, we assemble one-dimensional spin chains by covalently linking basic molecular building blocks on a Au(111) surface. Their structural properties are studied by scanning tunneling microscopy and the Kondo effect of the basic molecular blocks inside the chains is probed by scanning tunneling spectroscopy. Tunneling spectroscopic images reveal the existence of separate Kondo regions within the chains while density functional theory calculations unveil antiferromagnetic coupling between the spin centers.