Site determination and thermally assisted tunneling in homogenous nucleation

Structural Manipulation of Spin Excitations in a Molecular Junction

Single metallocene molecules act as sensitive spin detectors when decorating the probe of a scanning tunneling microscope (STM). However, the impact of the atomic-scale electrode details on the molecular spin state has remained elusive to date. Here, a nickelocene (Nc) STM junction is manipulated in an atomwise manner showing clearly the dependence of the spin excitation spectrum on the anchoring of Nc to Cu(111), a Cu monomer, and trimer. Moreover, while the spin state of the same Nc tip is a triplet with tunable spin excitation energies upon contacting the surface, it transitions to a Kondo-screened doublet on a Cu atom. Notably, the nontrivial magnetic exchange interaction of the molecular spin with the electron continuum of the substrate determines the spectral line shape of the spin excitations.

Versatile stochastic model for predictive KMC simulation of fcc metal nanostructure evolution with realistic kinetics

Stochastic lattice-gas models provide the natural framework for analysis of the surface diffusion-mediated evolution of crystalline metal nanostructures on the appropriate time scale (often 101-104 s) and length scale. Model behavior can be precisely assessed by kinetic Monte Carlo simulation, typically incorporating a rejection-free algorithm to efficiently handle the broad range of Arrhenius rates for hopping of surface atoms. The model should realistically prescribe these rates, or the associated barriers, for a diversity of local surface environments. However, commonly used generic choices for barriers fail, even qualitatively, to simultaneously describe diffusion for different low-index facets, for terrace vs step edge diffusion, etc. We introduce an alternative Unconventional Interaction-Conventional Interaction formalism to prescribe these barriers, which, even with few parameters, can realistically capture most aspects of behavior. The model is illustrated for single-component fcc metal systems, mainly for the case of Ag. It is quite versatile and can be applied to describe both the post-deposition evolution of 2D nanostructures in homoepitaxial thin films (e.g., reshaping and coalescence of 2D islands) and the post-synthesis evolution of 3D nanocrystals (e.g., reshaping of nanocrystals synthesized with various faceted non-equilibrium shapes back to 3D equilibrium Wulff shapes).

On-Surface Synthesis of Multiple Cu Atom-Bridged Organometallic Oligomers

A metal-metal bond between coordination complexes has the nature of a covalent bond in hydrocarbons. While bimetallic and trimetallic compounds usually have three-dimensional structures in solution, the high directionality and robustness of the bond can be applied for on-surface syntheses. Here, we present a systematic formation of complex organometallic oligomers on Cu(111) through sequential ring opening of 11,11,12,12-tetraphenyl-1,4,5,8-tetraazaanthraquinodimethane and bonding of phenanthroline derivatives by multiple Cu atoms. A detailed characterization with a combination of scanning tunneling microscopy and density functional theory calculations revealed the role of the Cu adatoms in both enantiomers of the chiral oligomers. Furthermore, we found sufficient strength of the bonds against sliding friction by manipulating the oligomers up to a hexamer. This finding may help to increase the variety of organometallic nanostructures on surfaces.

Precise atom manipulation through deep reinforcement learning

Atomic-scale manipulation in scanning tunneling microscopy has enabled the creation of quantum states of matter based on artificial structures and extreme miniaturization of computational circuitry based on individual atoms. The ability to autonomously arrange atomic structures with precision will enable the scaling up of nanoscale fabrication and expand the range of artificial structures hosting exotic quantum states. However, the a priori unknown manipulation parameters, the possibility of spontaneous tip apex changes, and the difficulty of modeling tip-atom interactions make it challenging to select manipulation parameters that can achieve atomic precision throughout extended operations. Here we use deep reinforcement learning (DRL) to control the real-world atom manipulation process. Several state-of-the-art reinforcement learning (RL) techniques are used jointly to boost data efficiency. The DRL agent learns to manipulate Ag adatoms on Ag(111) surfaces with optimal precision and is integrated with path planning algorithms to complete an autonomous atomic assembly system. The results demonstrate that state-of-the-art DRL can offer effective solutions to real-world challenges in nanofabrication and powerful approaches to increasingly complex scientific experiments at the atomic scale.

Molecular Diffusion and Self-Assembly: Quantifying the Influence of Substrate hcp and fcc Atomic Stacking

Molecular diffusion is a fundamental process underpinning surface-confined molecular self-assembly and synthesis. Substrate topography influences molecular assembly, alignment, and reactions with the relationship between topography and diffusion linked to the thermodynamic evolution of such processes. Here, we observe preferential adsorption sites for tetraphenylporphyrin (2H-TPP) on Au(111) and interpret nucleation and growth of molecular islands at these sites in terms of spatial variation in diffusion barrier driven by local atomic arrangements of the Au(111) surface (the 22× √3 "herringbone" reconstruction). Variable-temperature scanning tunnelling microscopy facilitates characterization of molecular diffusion, and Arrhenius analysis allows quantitative characterization of diffusion barriers within fcc and hcp regions of the surface reconstruction (where the in-plane arrangement of the surface atoms is identical but the vertical stacking differs). The higher barrier for diffusion within fcc locations underpins the ubiquitous observation of preferential island growth within fcc regions, demonstrating the relationship between substrate-structure, diffusion, and molecular self-assembly.

Multi-scale Simulation of Equilibrium Step Fluctuations on Cu(111) Surfaces

Understanding the nature of active sites is a non-trivial task, especially when the catalyst is sensitively affected by chemical reactions and environmental conditions. The challenge lies on capturing explicitly the dynamics of catalyst evolution during reactions. Despite the complexity of catalyst reconstruction, we can untangle them into several elementary processes, of which surface diffusion is of prime importance. By applying density functional theory-kinetic Monte Carlo (DFT-KMC) simulation employed with cluster expansion (CE), we investigated the microscopic mechanism of surface diffusion of Cu with defects such as steps and kinks. Based on the result, the energetics obtained from CE have shown good agreement with DFT calculations. Various diffusion events during the step fluctuations are discussed as well. Aside from the adatom attachment, the diffusion along the step edge is found to be the dominant mass transport mechanism, indicated by the lowest activation energy. We also calculated time correlation functions at 300, 400, and 500 K. However, the time exponent in the correlation function does not strictly follow the power law behavior due to the limited step length, which inhibits variation in the kink density.

Dominant contributions to the apparent activation energy in two-dimensional submonolayer growth: comparison between Cu/Ni(111) and Ni/Cu(111)

For surface-mediated processes in general, such as epitaxial growth and heterogeneous catalysis, a constant slope in the Arrhenius diagram of the rate of interest,R, against inverse temperature, logRvs 1/T, is traditionally interpreted as the existence of a bottleneck elementary reaction (or rate-determining step), whereby the constant slope (or apparent activation energy,EappR) reflects the value of the energy barrier for that elementary reaction. In this study, we expressEappRas a weighted average, where every term contains the traditional energy barrier for the corresponding elementary reaction plus an additional configurational term, while identifying each weight as the probability of executing the corresponding elementary reaction. Accordingly, the change in the leading (most probable) elementary reaction with the experimental conditions (e.g. temperature) is automatically captured and it is shown that a constant value ofEappRis possible even if control shifts from one elementary reaction to another. To aid the presentation, we consider kinetic Monte Carlo simulations of submonolayer growth of Cu on Ni(111) and Ni on Cu(111) at constant deposition flux, including a large variety of single-atom, multi-atom and complete-island diffusion events. In addition to analysing the dominant contributions to the diffusion constant of the complete adparticle system (or tracer diffusivity) and its apparent activation energy as a function of both coverage and temperature for the two heteroepitaxial systems, their surface morphologies and island densities are also compared.

Real-Space Observation of Quantum Tunneling by a Carbon Atom: Flipping Reaction of Formaldehyde on Cu(110)

We present a direct observation of carbon-atom tunneling in the flipping reaction of formaldehyde between its two mirror-reflected states on a Cu(110) surface using low-temperature scanning tunneling microscopy (STM). The flipping reaction was monitored in real time, and the reaction rate was found to be temperature independent below 10 K. This indicates that this reaction is governed by quantum mechanical tunneling, albeit involving a substantial motion of the carbon atom (∼1 Å). In addition, deuteration of the formaldehyde molecule resulted in a significant kinetic isotope effect ( R_CH2O/ R_CD2O ≈ 10). The adsorption structure, reaction pathway, and tunneling probability were examined by density functional theory calculations, which corroborate the experimental observations.

Layered Insulator/Molecule/Metal Heterostructures with Molecular Functionality through Porphyrin Intercalation

Intercalation of molecules into layered materials is actively researched in materials science, chemistry, and nanotechnology, holding promise for the synthesis of van der Waals heterostructures and encapsulated nanoreactors. However, the intercalation of organic molecules that exhibit physical or chemical functionality remains a key challenge to date. In this work, we present the synthesis of heterostructures consisting of porphines sandwiched between a Cu(111) substrate and an insulating hexagonal boron nitride ( h-BN) monolayer. We investigated the energetics of the intercalation, as well as the influence of the capping h-BN layer on the behavior of the intercalated molecules using scanning probe microscopy and density functional theory calculations. While the self-assembly of the molecules is altered upon intercalation, we show that the intrinsic functionalities, such as switching between different porphine tautomers, are preserved. Such insulator/molecule/metal structures provide opportunities to protect organic materials from deleterious effects of atmospheric environment, can be used to control chemical reactions through spatial confinement, and give access to layered materials based on the ample availability of synthesis protocols provided by organic chemistry.

Charge-State-Dependent Diffusion of Individual Gold Adatoms on Ionic Thin NaCl Films

It is known that individual metal atoms on insulating ionic films can occur in several different (meta)stable charge states, which can be reversibly switched in a controlled fashion. Here we show that the diffusion of gold adatoms on NaCl thin films depends critically on their charge state. Surprisingly, the anionic species has a lower diffusion barrier than the neutral one. Furthermore, for the former we observe that the diffusion atop a bilayer of NaCl is strongly influenced by the interface between NaCl and the underlying copper substrate. This effect disappears for a trilayer of NaCl. These observations open the prospect of controlling the diffusion properties of individual metal atoms on thin insulating films.

Two-Dimensional Ketone-Driven Metal-Organic Coordination on Cu(111)

Two-dimensional metal-organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene-4,5,9,10-tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal-organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone-metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition.

Tuning an Atomic Switch on a Surface with Electric and Magnetic Fields

Controllable switching an adatom position and its magnetization could lead to a single-atom memory. Our theoretical studies show that switching adatom between different surface sites by the quantum tunneling, discovered in several experiments, can be controlled by an external electric field. Switching a single spin by magnetic fields is found to be strongly site-dependent on a surface. This could enable to control a spin-dynamics of adatom.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively.

Adsorption geometry determination of single molecules by atomic force microscopy

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2°. The method was applied to five π-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found that the substitution of a single atom leads to strong variations of the adsorption height, as predicted by state-of-the-art density-functional theory, including van der Waals interactions with collective substrate response effects.

Formation of fe cluster superlattice in a metal-organic quantum-box network

We report on the self-assembly of Fe adatoms on a Cu(111) surface that is patterned by a metal-organic honeycomb network, formed by coordination of dicarbonitrile pentaphenyl molecules with Cu adatoms. Fe atoms landing on the metal surface are mobile and steered by the quantum confinement of the surface state electrons towards the center of the network hexagonal cavities. In cavities hosting more than one Fe, preferential interatomic distances are observed. The adatoms in each hexagon aggregate into a single cluster upon gentle annealing. These clusters are again centered in the cavities and their size is discerned by their distinct apparent heights.

Quantum tunneling enabled self-assembly of hydrogen atoms on Cu(111)

Atomic and molecular self-assembly are key phenomena that underpin many important technologies. Typically, thermally enabled diffusion allows a system to sample many areas of configurational space, and ordered assemblies evolve that optimize interactions between species. Herein we describe a system in which the diffusion is quantum tunneling in nature and report the self-assembly of H atoms on a Cu(111) surface into complex arrays based on local clustering followed by larger scale islanding of these clusters. By scanning tunneling microscope tip-induced scrambling of H atom assemblies, we are able to watch the atomic scale details of H atom self-assembly in real time. The ordered arrangements we observe are complex and very different from those formed by H on other metals that occur in much simpler geometries. We contrast the diffusion and assembly of H with D, which has a much slower tunneling rate and is not able to form the large islands observed with H over equivalent time scales. Using density functional theory, we examine the interaction of H atoms on Cu(111) by calculating the differential binding energy as a function of H coverage. At the temperature of the experiments (5 K), H(D) diffusion by quantum tunneling dominates. The quantum-tunneling-enabled H and D diffusion is studied using a semiclassically corrected transition state theory coupled with density functional theory. This system constitutes the first example of quantum-tunneling-enabled self-assembly, while simultaneously demonstrating the complex ordering of H on Cu(111), a catalytically relevant surface.

Extended pattern recognition scheme for self-learning kinetic Monte Carlo simulations

We report the development of a pattern recognition scheme that takes into account both fcc and hcp adsorption sites in performing self-learning kinetic Monte Carlo (SLKMC-II) simulations on the fcc(111) surface. In this scheme, the local environment of every under-coordinated atom in an island is uniquely identified by grouping fcc sites, hcp sites and top-layer substrate atoms around it into hexagonal rings. As the simulation progresses, all possible processes, including those such as shearing, reptation and concerted gliding, which may involve fcc-fcc, hcp-hcp and fcc-hcp moves are automatically found, and their energetics calculated on the fly. In this article we present the results of applying this new pattern recognition scheme to the self-diffusion of 9-atom islands (M(9)) on M(111), where M  =  Cu, Ag or Ni.

Vertical manipulation of native adatoms on the InAs(111)A surface

We achieved the repositioning of native In adatoms on the polar III-V semiconductor surface InAs(111)A-(2 × 2) with atomic precision in a scanning tunnelling microscope (STM) operated at 5 K. The repositioning is performed by vertical manipulation, i.e., a reversible transfer of an individual adatom between the surface and the STM tip. Surface-to-tip transfer is achieved by a stepwise vibrational excitation of the adsorbate-surface bond via inelastic electron tunnelling assisted by the tip-induced electric field. In contrast, tip-to-surface back-transfer occurs upon tip-surface point contact formation governed by short-range adhesive forces between the surface and the In atom located at the tip apex. In addition, we found that carrier transport through the point contact is not of ballistic nature but is due to electron tunnelling. The vertical manipulation scheme used here enables us to assemble nanostructures of diverse sizes and shapes with the In adatoms residing on vacancy sites of the (2 × 2)-reconstructed surface (nearest-neighbour vacancy spacing: 8.57 Å).

Influence of subsurface layers on the adsorption of large organic molecules on close-packed metal surfaces

The asymmetric molecule 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) adsorbed on Cu(111) is characterized by scanning tunneling microscopy (STM) and density functional theory (DFT) to determine the influence of subsurface atomic layers on the adsorption. In contrast to the 6-fold symmetry of the first atomic layer of close-packed surfaces, we find that the arrangement of the isolated molecules follows predominantly a 3-fold symmetry. This reduction in symmetry, where the molecule selects a specific orientation along the ⟨-211⟩ axes, reveals the contribution of lower-lying Cu layers to the molecular arrangement. Our calculations rationalize the interaction of the substrate with the molecule in terms of electrostatic screening and local relaxation phenomena.

Tunability in polyatomic molecule diffusion through tunneling versus pacing

The diffusion temperature of molecular 'walkers', molecules that are capable of moving unidirectionally across a substrate violating its symmetry, can be tuned over a wide range utilizing extension of their aromatic backbone, insertion of a second set of substrate linkers (converting bipedal into quadrupedal species), and substitution on the ring. Density functional theory simulation of the molecular dynamics identifies the motion of the quadrupedal species as pacing (as opposed to trotting or gliding). Knowledge about the diffusion mode allows us to draw conclusions on the relevance of tunneling to the surface diffusion of polyatomic organic molecules.

Atomic-scale engineering of electrodes for single-molecule contacts

The transport of charge through a conducting material depends on the intrinsic ability of the material to conduct current and on the charge injection efficiency at the contacts between the conductor and the electrodes carrying current to and from the material. According to theoretical considerations, this concept remains valid down to the limit of single-molecule junctions. Exploring this limit in experiments requires atomic-scale control of the junction geometry. Here we present a method for probing the current through a single C(60) molecule while changing, one by one, the number of atoms in the electrode that are in contact with the molecule. We show quantitatively that the contact geometry has a strong influence on the conductance. We also find a crossover from a regime in which the conductance is limited by charge injection at the contact to a regime in which the conductance is limited by scattering at the molecule. Thus, the concepts of 'good' and 'bad' contacts, commonly used in macro- and mesoscopic physics, can also be applied at the molecular scale.

Actuated transitory metal--ligand bond as tunable electromechanical switch

Electrically tunable molecules are highly attractive for the construction of molecular devices, such as switches, transistors, or machines. Here, we present a novel nanomechanical element triggered by an electrical bias as external stimulus. We demonstrate that a transitory chemical bond between a copper atom and coordinating organic molecules adsorbed on a metal surface acts as variable frequency switch, which can be actuated and probed by means of low-temperature scanning tunneling microscopy. Whereas below a threshold bias voltage the bond is permanently either formed or broken the bonding state continuously oscillates at higher voltages. The switching rate of the bistable molecular system can be widely tuned from below 1 Hz up to the kilohertz regime. The quantum yield per tunneling electron to trigger a transition between the two states varies spatially and is related to the local density of states of the bonded and nonbonded configuration.

Doping of monatomic Cu chains with single Co atoms

Close-packed Co-Cu chains of various length and composition were assembled from single Co and Cu atoms on Cu(111) by atom manipulation in a low-temperature scanning tunneling microscope. Local spectroscopy reveals significant electronic Co-Cu coupling leading to confined quantum states delocalized along the heteroatomic chain. Composite Co-Cu chains provide a model case in which the quantum state of an atomic-scale host structure can be tuned by the controlled incorporation of foreign atoms.

Quantum surface diffusion of vibrationally excited molecular dimers

We consider the thermally activated quantum diffusion of a molecular dimer in a periodic surface potential by means of a time-dependent wave packet method. We show that the potential energy surface resulting from the interplay of intradimer and dimer-surface interactions can lead to resonant states and predict high tunneling probabilities at specific, below barrier, energies that depend also on the initial vibrational state of the dimer. For soft molecular bonds, we show that the chaotic dynamical regime of classical dimers is mirrored, in the quantum case, by the tunneling induced mixing of vibrational states. The knowledge of the transmission coefficient is used to formulate an approximate description of quantum thermal diffusion by defining an effective temperature-dependent activation energy that can be compared to the classical case.

Quantum diffusion of H on Pt(111): step effects

Using a linear optical diffraction technique, we have systematically investigated the defect effects on quantum surface diffusion of hydrogen on Pt(111) surfaces. The quantum tunneling effect was clearly observed for hydrogen diffusion at low temperatures as manifested by a leveling off of the diffusion coefficient on flat surfaces. The strong influence of surface defects on the quantum diffusion is in good agreement with the creation of an inhomogeneous surface with adsorption sites of different binding energies.

Trapping and moving metal atoms with a six-leg molecule

Putting to work a molecule able to collect and carry adatoms in a controlled way on a surface is a solution for fabricating atomic structures atom by atom. Investigations have shown that the interaction of an organic molecule with the surface of a metal can induce surface reconstruction down to the atomic scale. In this way, well-defined nanostructures such as chains of adatoms, atomic trenches and metal-ligand compounds have been formed. Moreover, the progress in manipulation techniques induced by a scanning tunnelling microscope (STM) has opened up the possibility of studying artificially built molecular-metal atomic scale structures, and allowed the atom-by-atom doping of a single C(60) molecule by picking up K atoms. The present work goes a step further and combines STM manipulation techniques with the ability of a molecule to assemble an atomic nanostructure. We present a well-designed six-leg single hexa-t-butyl-hexaphenylbenzene (HB-HPB) molecule, which collects and carries up to six copper adatoms on a Cu(111) surface when manipulated with a STM tip. The 'HB-HPB-Cu atoms' complex can be further manipulated, bringing its Cu freight to a predetermined position on the surface where the metal atoms can finally be released.

Surface diffusion of Cr adatoms on Au(111) by quantum tunneling

The low-temperature surface diffusion of isolated Cr adatoms on Au(111) has been determined using nonperturbing x rays. Changes in the x-ray magnetic circular dichroism spectral line shape together with Monte Carlo calculations demonstrate that adatom nucleation proceeds via quantum tunneling diffusion rather than over-barrier hopping for temperatures <40K. The jump rates are shown to be as much as 35 orders of magnitude higher than that expected for thermal over-barrier hopping at 10 K.

Link between adatom resonances and the Cu(111) Shockley surface state

Low-temperature scanning tunneling microscopy and spectroscopy at 7 K was used to assemble and characterize native adatom islands of successive size on the Cu(111) surface. Starting from the single adatom we observe the formation of a series of quantum states which merge into the well known two-dimensional Shockley surface state in the limit of large islands. Our experiments reveal a natural physical link between this fundamental surface property and the sp(z) hybrid resonance associated with the single Cu/Cu(111) adatom.

Localization of the Cu111 surface state by single Cu adatoms

The Cu adatom-induced localization of the two-dimensional Shockley surface state at the Cu(111) surface was identified from experimental and simulated scanning tunneling microscopy spectra. The localization gives rise to a resonance located just below the surface state band edge. The adatom-induced surface state localization is discussed in terms of the existence theorem for bound states in any attractive two-dimensional potential. We also identify adatom-induced resonance states deriving from atomic orbitals in both experimental and simulated spectra.

Controlling the Dynamics of a Single Atom in Lateral Atom Manipulation

We studied the dynamics of a single cobalt (Co) atom during lateral manipulation on a copper (111) surface in a low-temperature scanning tunneling microscope. The Co binding site locations were revealed in a detailed image that resulted from lateral Co atom motion within the trapping potential of the scanning tip. Random telegraph noise, corresponding to the Co atom switching between hexagonal close-packed (hcp) and face-centered cubic (fcc) sites, was seen when the tip was used to try to position the Co atom over the higher energy hcp site. Varying the probe tip height modified the normal copper (111) potential landscape and allowed the residence time of the Co atom in these sites to be varied. At low tunneling voltages (less than approximately 5 millielectron volts), the transfer rate between sites was independent of tunneling voltage, current, and temperature. At higher voltages, the transfer rate exhibited a strong dependence on tunneling voltage, indicative of vibrational heating by inelastic electron scattering.

Quantum confinement in monatomic Cu chains on Cu(111)

The existence of one-dimensional (1D) electronic states in Cu/Cu(111) chains assembled by atomic manipulation is revealed by low-temperature scanning tunneling spectroscopy and density functional theory (DFT) calculations. Our experimental analysis of the chain-localized electron dynamics shows that the dispersion is fully described within a 1D tight-binding approach. DFT calculations confirm the confinement of unoccupied states to the chain in the relevant energy range, along with a significant extension of these states into the vacuum region.