Unidirectional adsorbate motion on a high-symmetry surface: "walking" molecules can stay the course

Single-molecular diffusivity and long jumps of large organic molecules: CoPc on Ag(100)

Energy dissipation and the transfer rate of adsorbed molecules do not only determine the rates of chemical reactions but are also a key factor that often dictates the growth of organic thin films. Here, we present a study of the surface dynamical motion of cobalt phthalocyanine (CoPc) on Ag(100) in reciprocal space based on the helium spin-echo technique in comparison with previous scanning tunnelling microscopy studies. It is found that the activation energy for lateral diffusion changes from 150 meV at 45-50 K to ≈100 meV at 250-350 K, and that the process goes from exclusively single jumps at low temperatures to predominantly long jumps at high temperatures. We thus illustrate that while the general diffusion mechanism remains similar, upon comparing the diffusion process over widely divergent time scales, indeed different jump distributions and a decrease of the effective diffusion barrier are found. Hence a precise molecular-level understanding of dynamical processes and thin film formation requires following the dynamics over the entire temperature scale relevant to the process. Furthermore, we determine the diffusion coefficient and the atomic-scale friction of CoPc and establish that the molecular motion on Ag(100) corresponds to a low friction scenario as a consequence of the additional molecular degrees of freedom.

Control of long-distance motion of single molecules on a surface

Spatial control over molecular movement is typically limited because motion at the atomic scale follows stochastic processes. We used scanning tunneling microscopy to bring single molecules into a stable orientation of high translational mobility where they moved along precisely defined tracks. Single dibromoterfluorene molecules moved over large distances of 150 nanometers with extremely high spatial precision of 0.1 angstrom across a silver (111) surface. The electrostatic nature of the effect enabled the selective application of repulsive and attractive forces to send or receive single molecules. The high control allows us to precisely move an individual and specific molecular entity between two separate probes, opening avenues for velocity measurements and thus energy dissipation studies of single molecules in real time during diffusion and collision.

A proposed simulation method for directed self-assembly of nanographene

A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.e. molecule functionalization) at fixed reaction temperature and initial molecule concentrations is explored. Directed self-assembly of nanographene from functionalized tetrabenzanthracene and benzene is studied with regions in the activation energy phase-space showing length-to-width ratio tunability. The degree of defects and reaction reproducibility in the simulations is also determined, with the rate of functionalized benzene addition providing additional control of the dimension and quality of the nanographene. Comparison of the reaction energetics to available density functional theory data suggests the synthesis may be experimentally tenable using aryl-halide cross-coupling and noble metal surface-assisted catalysis. With full access to the intermediate reaction network and with dynamic coupling to density functional theory-informed tight-binding simulation, the method is proposed as a computationally efficient means towards detailed simulation-driven design of new nanographene systems.

Light-Induced Translation of Motorized Molecules on a Surface

Molecular machines are a key component in the vision of molecular nanotechnology and have the potential to transport molecular species and cargo on surfaces. The motion of such machines should be triggered remotely, ultimately allowing a large number of molecules to be propelled by a single source, with light being an attractive stimulus. Here, we report upon the photoinduced translation of molecular machines across a surface by characterizing single molecules before and after illumination. Illumination of molecules containing a motor unit results in an enhancement in the diffusion of the molecules. The effect vanishes if an incompatible photon energy is used or if the motor unit is removed from the molecule, revealing that the enhanced motion is due to the presence of the wavelength-sensitive motor in each molecule.

Cytoskeletal motor-driven active self-assembly in in vitro systems

Molecular motor-driven self-assembly has been an active area of soft matter research for the past decade. Because molecular motors transform chemical energy into mechanical work, systems which employ molecular motors to drive self-assembly processes are able to overcome kinetic and thermodynamic limits on assembly time, size, complexity, and structure. Here, we review the progress in elucidating and demonstrating the rules and capabilities of motor-driven active self-assembly. We focus on the types of structures created and the degree of control realized over these structures, and discuss the next steps necessary to achieve the full potential of this assembly mode which complements robotic manipulation and passive self-assembly.

Selective and reversible self-assembly of C60fullerene on a 9,10-bis(S-acetylthiomethyl)anthracene modified gold surface

Synthesized di-S-acetyl anthracene derivative deposited on gold surface allows for selective multi-cycle capture of C₆₀fullerene by reversible forming well-ordered monolayers of C₆₀fullerene–anthracene adduct according to Diels–Alder reaction.

Complex Surface Diffusion Mechanisms of Cobalt Phthalocyanine Molecules on Ag(100)

We used time-lapsed scanning tunneling microscopy between 43 and 50 K and density functional theory (DFT) to explore the basic surface diffusion steps of cobalt phthalocyanine (CoPc) molecules on the Ag(100) surface. We show that the CoPc molecules translate and rotate on the surface in the same temperature range. Both processes are associated with similar activation energies; however, the translation is more frequently observed. Our DFT calculations provide the activation energies for the translation of the CoPc molecule between the nearest hollow sites and the rotation at both the hollow and the bridge sites. The activation energies are only consistent with the experimental findings, if the surface diffusion mechanism involves a combined translational and rotational molecular motion. Additionally, two channels of motion are identified: the first provides only a channel for translation, while the second provides a channel for both the translation and the rotation. The existence of the two channels explains a higher rate for the translation determined in experiment.

Jump rates for surface diffusion of large molecules from first principles

We apply a recently developed stochastic model for the surface diffusion of large molecules to calculate jump rates for 9,10-dithioanthracene on a Cu(111) surface. The necessary input parameters for the stochastic model are calculated from first principles using density functional theory (DFT). We find that the inclusion of van der Waals corrections to the DFT energies is critical to obtain good agreement with experimental results for the adsorption geometry and energy barrier for diffusion. The predictions for jump rates in our model are in excellent agreement with measured values and show a marked improvement over transition state theory (TST). We find that the jump rate prefactor is reduced by an order of magnitude from the TST estimate due to frictional damping resulting from energy exchange with surface phonons, as well as a rotational mode of the diffusing molecule.

Continuous observation of the stochastic motion of an individual small-molecule walker

Motion--whether it the ability to change shape, rotate or translate--is an important potential asset for functional nanostructures. For translational motion, a variety of DNA-based and small-molecule walkers have been created, but observing the translational motion of individual molecules in real time remains a significant challenge. Here, we show that the movement of a small-molecule walker along a five-foothold track can be monitored continuously within a protein nanoreactor. The walker is an organoarsenic(III) molecule with exchangeable thiol ligands, and the track a line of cysteine residues 6 Å apart within an α-haemolysin protein pore that acts as the nanoreactor. Changes in the flow of ionic current through the pore reflect the individual steps of a single walker, which require the making and breaking of As-S bonds, and occur in aqueous solution at neutral pH and room temperature. The walker moves considerably faster (∼0.7 s per step) than previous walkers based on covalent chemistry and is weakly processive (6 ± 1 steps per outing). It shows weak net directional movement, which can be described by a thermodynamic sink arising from the different environments of the cysteines that constitute the track.

Stochastic models for surface diffusion of molecules

We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

Studying the dynamic behaviour of porphyrins as prototype functional molecules by scanning tunnelling microscopy close to room temperature

Scanning tunnelling microscopy of the dynamics of functional molecules (porphyrins) close to room temperature enables a detailed determination of the thermodynamic potentials including entropic contributions of the underlying processes.

One-dimensional random walk of a synthetic small molecule toward a thermodynamic sink

We report on the spontaneous intramolecular migration of α-methylene-4-nitrostyrene from amine group to amine group along oligoethyleneimine tracks up to eight repeat units in length (number of amine footholds, n = 3, 5, 9). Each track consists of n - 1 aliphatic secondary amine footholds plus a naphthylmethylamine group foothold situated at one end of the track. Under basic conditions the α-methylene-4-nitrostyrene unit undergoes a series of reversible intramolecular Michael-retro-Michael reactions between adjacent amine groups that move it up and down the track. For n = 3 and 5 it is possible to monitor the population of every positional isomer on the track by (1)H NMR spectroscopy. On the longest track (n = 9) the fraction of walkers on each end-foothold can be quantified with respect to those on the inner footholds. In all cases the naphthylmethylamine foothold acts as a thermodynamic sink with the steady-state distribution significantly biased in favor of the walker at that site. The dynamics of the walker migration is well described by the random walk of a Brownian particle in one dimension.

Surface-enhanced Raman trajectories on a nano-dumbbell: transition from field to charge transfer plasmons as the spheres fuse

By taking advantage of the tensor nature of surface-enhanced Raman scattering (SERS), we track trajectories of the linker molecule and a CO molecule chemisorbed at the hot spot of a nano-dumbbell consisting of dibenzyldithio-linked silver nanospheres. The linear Stark shift of CO serves as an absolute gauge of the local field, while the polyatomic spectra characterize the vector components of the local field. We identify surface-enhanced Raman optical activity due to a transient asperity in the nanojunction in an otherwise uneventful SERS trajectory. During fusion of the spheres, we observe sequential evolution of the enhanced spectra from dipole-coupled Raman to quadrupole- and magnetic dipole-coupled Raman, followed by a transition from line spectra to band spectra, and the full reversal of the sequence. From the spectrum of CO, the sequence can be understood to track the evolution of the junction plasmon resonance from dipolar to quadrupolar to charge transfer as a function of intersphere separation, which evolves at a speed of ∼1 Å/min. The crossover to the conduction limit is marked by the transition of line spectra to Stark-broadened and shifted band spectra. As the junction closes on CO, the local field reaches 1 V/Å, limited to a current of 1 electron per vibrational cycle passing through the molecule, with associated Raman enhancement factor via the charge transfer plasmon resonance of 10(12). The local field identifies that a sharp protrusion is responsible for room-temperature chemisorption of CO on silver. The asymmetric phototunneling junction, Ag-CO-Ag, driven by the frequency-tunable charge transfer plasmon of the dumbbell antenna, combines the design elements of an ideal rectifying photocollector.

Molecular shape and the energetics of chemisorption: from simple to complex energy landscapes

We enumerate all local minima of the energy landscape for model rigid adsorbates characterized by three or four equivalent binding sites (e.g., thiol groups) on a close-packed (111) surface of a face-centered-cubic crystal. We show that the number of energy minima increases linearly with molecular size with a rate of increase that depends on the degree of registry between the molecule shape and the surface structure. The sparseness of energy minima and the large variations in the center-of-mass positions of these minima vs molecular size for molecules that are incommensurate with the surface suggests a strong coupling in these molecules between surface mobility and shape or size fluctuations resulting from molecular vibrations. We also find that the variation in the binding energy with respect to molecular size decreases more rapidly with molecular size for molecules with a higher degree of registry with the surface. This indicates that surface adsorption should be better able to distinguish molecules by size if the molecules are incommensurate with the surface.

Hierarchically organized bimolecular ladder network exhibiting guided one-dimensional diffusion

The assembly and dynamics of a hierarchical, bimolecular network of sexiphenyl dicarbonitrile and N,N'-diphenyl oxalic amide molecules on the Ag(111) surface are studied by scanning tunneling microscopy at controlled temperature. The network formation is governed by a two-step protocol involving hierarchic interactions, including a novel carbonitrile-oxalic amide bonding motif. For temperatures exceeding ~70 K, more weakly bound sexiphenyl dicarbonitrile molecules carry out one-dimensional diffusion guided by the more stable substructure of the network held together by the carbonitrile-oxalic amide bonding motif. A theoretical investigation at the ab initio level confirms the different binding energies of the two coupling motifs and rationalizes the network formation and the diffusion pathway.

Molecular self-assembly at solid surfaces

Self-assembly, the process by which objects initially distributed at random arrange into well-defined patterns exclusively due to their local mutual interactions without external intervention, is generally accepted to be the most promising method for large-scale fabrication of functional nanostructures. In particular, the ordering of molecular building-blocks deposited at solid surfaces is relevant for the performance of many organic electronic and optoelectronic devices, such as organic field-effect transistors (OFETs), organic light-emitting diodes (OLEDs) or photovoltaic solar cells. However, the fundamental knowledge on the nature and strength of the intermolecular and molecule-substrate interactions that govern the ordering of molecular adsorbates is, in many cases, rather scarce. In most cases, the structure and morphology of the organic-metal interface is not known and it is just assumed to be the same as in the bulk, thereby implicitly neglecting the role of the surface on the assembly. However, this approximation is usually not correct, and the evidence gathered over the last decades points towards an active role of the surface in the assembly, leading to self-assembled structures that only in a few occasions can be understood by considering just intermolecular interactions in solid or gas phases. In this work we review several examples from our recent research demonstrating the apparently endless variety of ways in which the surface might affect the assembly of organic adsorbates.

Molecular symmetry governs surface diffusion

In chemistry and physics symmetry principles are all important, for example, leading to the selection rules governing optical transitions. We have investigated the influence of the molecular symmetry on the surface potential landscape of molecules in the limit of weak molecule-substrate binding. For this purpose, the induced lateral motion of Cu(II)-tetraazaphthalocyanine molecules, for which four symmetry distinct isomers exist, on NaCl(100) was studied by scanning tunneling microscopy. This nonthermal diffusion induced by inelastic excitations is found to be qualitatively different for all four symmetry distinct isomers, demonstrating that symmetry governs the surface potential landscape.

Coalescence of 3-phenyl-propynenitrile on Cu(111) into interlocking pinwheel chains

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition.

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.

Adsorption configuration effects on the surface diffusion of large organic molecules: the case of Violet Lander

Violet Lander (C(108)H(104)) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.

Observation of all the intermediate steps of a chemical reaction on an oxide surface by scanning tunneling microscopy

By means of high-resolution scanning tunneling microscopy (STM), we have revealed unprecedented details about the intermediate steps for a surface-catalyzed reaction. Specifically, we studied the oxidation of H adatoms by O(2) molecules on the rutile TiO(2)(110) surface. O(2) adsorbs and successively reacts with the H adatoms, resulting in the formation of water species. Using time-lapsed STM imaging, we have unraveled the individual reaction intermediates of HO(2), H(2)O(2), and H(3)O(2) stoichiometry and the final reaction product-pairs of water molecules, [H(2)O](2). Because of their different appearance and mobility, these four species are discernible in the time-lapsed STM images. The interpretation of the STM results is corroborated by density functional theory calculations. The presented experimental and theoretical results are discussed with respect to previous reports where other reaction mechanisms have been put forward.

Dimerization boosts one-dimensional mobility of conformationally adapted porphyrins on a hexagonal surface atomic lattice

We employed temperature-controlled fast-scanning tunneling microscopy to monitor the diffusion of tetrapyridylporphyrin molecules on the Cu(111) surface. The data reveal unidirectional thermal migration of conformationally adapted monomers in the 300-360 K temperature range. Surprisingly equally oriented molecules spontaneously form dimers that feature a drastically increased one-dimensional diffusivity. The analysis of the bonding and mobility characteristics indicates that this boost is driven by a collective transport mechanism of a metallosupramolecular complex.

Surface diffusive motion in a periodic and asymmetric potential

9,10-Dithioanthracene adsorbed on Cu(111) diffuses exclusively along the high-symmetry axis of the molecule-substrate system. Further reduction of the symmetry of the system by asymmetric methylation does not reduce the symmetry of the motion although it has a substantial effect on the diffusion rate (100-fold reduction) and renders the diffusion barrier asymmetric. This is in contrast to the behavior expected of a classical particle, and it provides a direct single-molecule-scale vista on the validity of The Principle of Microscopic Reversibility first formulated by Tolman in 1924, which despite its fundamental role has attracted little visualization.

Dynamic interfaces in an organic thin film

Low-dimensional boundaries between phases and domains in organic thin films are important in charge transport and recombination. Here, fluctuations of interfacial boundaries in an organic thin film, acridine-9-carboxylic acid on Ag(111), have been visualized in real time and measured quantitatively using scanning tunneling microscopy. The boundaries fluctuate via molecular exchange with exchange time constants of 10-30 ms at room temperature, with length-mode fluctuations that should yield characteristic f(-1/2) signatures for frequencies less than approximately 100 Hz. Although acridine-9-carboxylic acid has highly anisotropic intermolecular interactions, it forms islands that are compact in shape with crystallographically distinct boundaries that have essentially identical thermodynamic and kinetic properties. The physical basis of the modified symmetry is shown to arise from significantly different substrate interactions induced by alternating orientations of successive molecules in the condensed phase. Incorporating this additional set of interactions in a lattice-gas model leads to effective multicomponent behavior, as in the Blume-Emery-Griffiths model, and can straightforwardly reproduce the experimentally observed isotropic behavior. The general multicomponent description allows the domain shapes and boundary fluctuations to be tuned from isotropic to highly anisotropic in terms of the balance between intermolecular interactions and molecule-substrate interactions.

Defect induced asymmetric pit formation on hydroxyapatite

Defect sites on bone minerals play a critical role in bone remodeling processes. We investigated single crystal hydroxyapatite (100) surfaces bearing crystal defects under acidic dissolution conditions using real-time in situ atomic force microscopy. At defect sites, surface structure-dependent asymmetric hexagonal etch pits were formed, which dominated the overall dissolution rate. Meanwhile, dissolution from the flat terraces proceeded by stochastic formation of flat bottom etch pits. The resulting pit shapes were intrinsically dictated by the HAP crystal structure. Computational modeling also predicted different step energies associated with different facets of the asymmetric etch pits. Our microscopic observations of HAP dissolution are significant for understanding the effects of local surface structure on the bone mineral remodeling process and provide useful insights for the design of novel therapies for treating osteoporosis and dental caries.

Molecular architectonic on metal surfaces

The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.