Bond breaking coupled with translation in rolling of covalently bound molecules

Assembling fullerene into nanostructures over micrometer scale with atomic precision

Assembling large organic molecules into predesigned structures for nanoscale devices is a long-standing challenge. Here, we present the atom-scale precise repositions of individual fullerene molecules and molecule transportation over the micrometer scale on a Si(111) surface via reproducible and reversible vertical manipulation by a scanning tunneling microscopy tip. A two-rod abacus consisting of ten fullerene molecules was used to perform arithmetic operations with double digits. This opens the door for the use of larger organic molecules displaying intrinsic characteristics as complex molecular devices with novel functions.

Single-Molecule Rotational Switch on a Dangling Bond Dimer Bearing

One of the key challenges in the construction of atomic-scale circuits and molecular machines is to design molecular rotors and switches by controlling the linear or rotational movement of a molecule while preserving its intrinsic electronic properties. Here, we demonstrate both the continuous rotational switching and the controlled step-by-step single switching of a trinaphthylene molecule adsorbed on a dangling bond dimer created on a hydrogen-passivated Ge(001):H surface. The molecular switch is on-surface assembled when the covalent bonds between the molecule and the dangling bond dimer are controllably broken, and the molecule is attached to the dimer by long-range van der Waals interactions. In this configuration, the molecule retains its intrinsic electronic properties, as confirmed by combined scanning tunneling microscopy/spectroscopy (STM/STS) measurements, density functional theory calculations, and advanced STM image calculations. Continuous switching of the molecule is initiated by vibronic excitations when the electrons are tunneling through the lowest unoccupied molecular orbital state of the molecule. The switching path is a combination of a sliding and rotation motion over the dangling bond dimer pivot. By carefully selecting the STM conditions, control over discrete single switching events is also achieved. Combined with the ability to create dangling bond dimers with atomic precision, the controlled rotational molecular switch is expected to be a crucial building block for more complex surface atomic-scale devices.

Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface

The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.

Measuring the mechanical properties of molecular conformers

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Manipulation of single molecules can be achieved using scanning probe microscopy but the influence of molecular conformation on this process has, until now, been unclear. Here, the authors probe two different types of porphyrin conformer on a surface and see strong differences in their mechanochemical response.

Positioning and switching phthalocyanine molecules on a Cu(100) surface at room temperature

Reversible molecular switches with molecular orientation as the information carrier have been achieved on individual phthalocyanine (H2Pc) molecules adsorbed on a Cu(100) surface at room temperature. Scanning tunneling microscopy (STM) imaging directly demonstrates that H2Pc molecules can be controlled to move along the [011] or [011̅] surface direction of the Cu(100) surface, and the orientation of H2Pc molecules can also be switched between two angles of ±28° with respect to the [011] surface direction by a lateral manipulation. Owing to the highly efficient control over the adsorption site and orientation of H2Pc adsorbed on the Cu(100) surface by lateral manipulation, a pyramidal array formed by 10 H2Pc molecules has been constructed on the Cu surface as a prototype of binary memory, and every molecule within such a molecular array can be individually and reversibly controlled by a STM tip.

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.

Switching molecular orientation of individual fullerene at room temperature

Reversible molecular switches with molecular orientation as the information carrier have been achieved on individual fullerene molecules adsorbed on Si (111) surface at room temperature. Scanning tunneling microscopy imaging directly demonstrates that the orientation of individual fullerene with an adsorption geometry of 5-6 bond is rotated by integral times as 30 degree after a pulse bias is applied between the STM tip and the molecule. Dependences of the molecular rotation probability on the voltage and the process of applied bias reveal that the rotation of a fullerene molecule takes place in two successive steps: the bonding between the fullerene and the Si surface is firstly weakened via electronic excitation and then low energy electron bombardment causes the molecule to rotate by certain degree.

Reversible switching of single tin phthalocyanine molecules on the InAs(111)A surface

Individual tin phthalocyanine (SnPc) molecules adsorbed on the InAs(111)A surface were studied by low-temperature scanning tunnelling microscopy (STM) at 5 K. Consistently with the nonplanar molecular structure, SnPc adopts two in-plane adsorption geometries with the centre Sn atom either above (SnPc(up)) or below (SnPc(down)) the molecular plane. Depending on the current and bias applied to the tunnel junction, the molecule can be reversibly switched between the two conformations, implying a controlled transfer of the Sn atom through the molecular plane. The SnPc(down) conformer is characterized by an enhanced surface bonding as compared to the SnPc(up) conformer. SnPc(up) molecules can be repositioned by the STM tip by means of lateral manipulation, whereas this is not feasible for SnPc(down) molecules. The reversible switching process thus enables one to either laterally move the molecule or anchor it to the semiconductor surface.

Selective supramolecular fullerene-porphyrin interactions and switching in surface-confined C60-Ce(TPP)2 dyads

The control of organic molecules, supramolecular complexes and donor-acceptor systems at interfaces is a key issue in the development of novel hybrid architectures for regulation of charge-carrier transport pathways in nanoelectronics or organic photovoltaics. However, at present little is known regarding the intricate features of stacked molecular nanostructures stabilized by noncovalent interactions. Here we explore at the single molecule level the geometry and electronic properties of model donor-acceptor dyads stabilized by van der Waals interactions on a single crystal Ag(111) support. Our combined scanning tunneling microscopy/spectroscopy (STM/STS) and first-principles computational modeling study reveals site-selective positioning of C(60) molecules on Ce(TPP)(2) porphyrin double-decker arrays with the fullerene centered on the π-system of the top bowl-shaped tetrapyrrole macrocycle. Three specific orientations of the C(60) cage in the van der Waals complex are identified that can be reversibly switched by STM manipulation protocols. Each configuration presents a distinct conductivity, which accounts for a tristable molecular switch and the tunability of the intradyad coupling. In addition, STS data evidence electronic decoupling of the hovering C(60) units from the metal substrate, a prerequisite for photophysical applications.

High-resolution imaging of C60 molecules using tuning-fork-based non-contact atomic force microscopy

Recent advances in non-contact atomic force microscopy (nc-AFM) have led to the possibility of achieving unprecedented resolution within molecular structures, accomplished by probing short-range repulsive interaction forces. Here we investigate C(60) molecules adsorbed on KBr(111) and Cu(111) by tuning-fork-based nc-AFM. First, measurements of C(60) deposited on KBr(001) were conducted in cryogenic conditions revealing highly resolved nc-AFM images of the self-assembly. Using constant-frequency shift mode as well as three-dimensional spectroscopic measurements, we observe that the relatively weak molecule-substrate interaction generally leads to the disruption of molecular assembled structures when the tip is probing the short-range force regime. This particular issue hindered us in resolving the chemical structure of this molecule on the KBr surface. To obtain a better anchoring of C(60) molecules, nc-AFM measurements were performed on Cu(111). Sub-molecular resolutions within the molecules was achieved which allowed a direct and unambiguous visualization of their orientations on the supporting substrate. Furthermore, three-dimensional spectroscopic measurements of simultaneous force and current have been performed above the single molecules giving information of the C(60) molecular orientation as well as its local conductivity. We further discuss the different imaging modes in nc-AFM such as constant-frequency shift nc-AFM, constant-height nc-AFM and constant-current nc-AFM as well as three-dimensional spectroscopic measurement (3D-DFS) employed to achieve such resolution at the sub-molecular scale.

Manipulation of individual water molecules on CeO2(111)

Water molecules adsorbed on the CeO(2)(111) surface are investigated by non-contact atomic force microscopy (NC-AFM) at several tip-sample temperatures ranging between 10 and 300 K. Depending on the strength of the tip-surface interaction, they appear as triangular protrusions extended over three surface oxygen atoms or as small pits at hollow sites. During NC-AFM imaging with the tip being close to the surface, occasionally the transfer of molecules between tip and surface or the tip-induced lateral displacement of water molecules to equivalent surface lattice sites is observed. We report how this situation can be exploited to produce controlled lateral manipulations. A protocol to manipulate the water molecules between pre-defined neighbouring equivalent adsorption sites of the regular lattice as well as across a surface oxygen vacancy is demonstrated.

Controlled lateral manipulation of molecules on insulating films by STM

On metallic and semiconductor surfaces functional nanostructures can be built with atomic scale precision using the tip of an atomic force microscope/scanning tunneling microscope. In contrast, controlled lateral manipulation on insulators has not been reported. The traditional pushing and pulling based manipulation methods cannot be used for molecules adsorbed on insulating films because of the unfavorable ratio between diffusion barrier and desorption energy. Here, we demonstrate that molecules adsorbed on insulating films can be laterally manipulated in a controlled way by injecting inelastically tunneling electrons at well-defined positions in a molecule. The technique was successfully applied to several different molecules.

Measuring Si-C60 chemical forces via single molecule spectroscopy

We measure the short-range chemical force between a silicon-terminated tip and individual adsorbed C(60) molecules using frequency modulation atomic force microscopy. The interaction with an adsorbed fullerene is sufficiently strong to drive significant atomic rearrangement of tip structures.

Atomic-scale mechanical properties of orientated C60 molecules revealed by noncontact atomic force microscopy

In this work, the mechanical properties of C(60) molecules adsorbed on Cu(111) are measured by tuning-fork-based noncontact atomic force microscopy (nc-AFM) and spectroscopy at cryogenic conditions. Site-specific tip-sample force variations are detected above the buckyball structure. Moreover, high-resolution images obtained by nc-AFM show the chemical structure of this molecule and describes unambiguously its orientations on the surface.

Organic structure determination using atomic-resolution scanning probe microscopy

Nature offers a huge and only partially explored variety of small molecules with potential pharmaceutical applications. Commonly used characterization methods for natural products include spectroscopic techniques such as nuclear magnetic resonance spectroscopy and mass spectrometry. In some cases, however, these techniques do not succeed in the unambiguous determination of the chemical structure of unknown compounds. To validate the usefulness of scanning probe microscopy as an adjunct to the other tools available for organic structure analysis, we used the natural product cephalandole A, which had previously been misassigned, and later corrected. Our results, corroborated by density functional theory, demonstrate that direct imaging of an organic compound with atomic-resolution force microscopy facilitates the accurate determination of its chemical structure. We anticipate that our method may be developed further towards molecular imaging with chemical sensitivity, and will become generally useful in solving certain classes of natural product structures.

Time-resolved scanning tunnelling microscopy for molecular science

Time-resolved scanning tunnelling microscopy (STM) and its application in molecular science are reviewed. STM can image individual atoms and molecules and thus is able to observe the results of molecular processes such as diffusion, desorption, configuration switching, bond-breaking and chemistry, on the atomic scale. This review will introduce time-resolved STM, its experimental limitations and implementations with particular emphasis on thermally activated and tunnelling current induced molecular processes. It will briefly examine the push towards ultrafast imaging. In general, results achieved by time-resolved STM demonstrate the necessity of both space and time resolution for fully characterizing molecular processes on the atomic scale.

Modelling components of future molecular devices

We discuss challenges involved in modelling different components of molecular devices and give several examples that demonstrate how computer modelling evolved over the last few years to become a comprehensive tool for designing molecules, predicting their adsorption and diffusion at surfaces, simulating atomic force microscopy imaging and manipulation of atoms and molecules at insulating surfaces and studying electron conduction in prototype molecular devices. We describe some of the computational techniques used for modelling adsorption, diffusion, imaging and manipulation of organic molecules at surfaces and challenges pertaining to these studies, give several examples of applications and discuss further prospects for theoretical modelling of complex organic molecules at surfaces.

Modelling the manipulation of C60 on the Si001 surface performed with NC-AFM

We present a theoretical model of manipulation of the C(60) molecule on the Si(001) surface with a non-contact atomic force microscope (NC-AFM). The model relies on the lowering of the energy barrier for the C(60) manipulation due to the interaction of the C(60) with an AFM tip and the subsequent thermal movement of the molecule over this barrier. We performed numerical simulations of these energy barriers for a series of tip positions relative to the molecule to show how the barriers change with the tip position. The values of these barriers are then used in kinetic Monte Carlo simulations to estimate the probability of the C(60) movement for different tip positions and temperatures. Virtual atomic force microscope simulations, which include the kinetic Monte Carlo treatment of the C(60) movement, are then performed to describe in real time the process of movement of the C(60) molecule during an NC-AFM scan. Our results demonstrate that manipulation of the C(60) molecule, which is covalently bound to the surface, is possible with NC-AFM, even though there is no continuous tip-molecule contact, which is known to be a necessary requirement for the C(60) manipulation with scanning tunnelling microscopy. We show that the manipulation event can be identified in real NC-AFM experiments as an abrupt change in the distance of the tip closest approach (topography), and as spikes in the frequency shift and dissipation signals.

Synthesis of single-molecule nanocars

The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new p-carborane- and ruthenium-based wheels with greater solubility in organic solvents. Although fullerene wheels must be attached in the final synthetic step, p-carborane- and ruthenium-based wheels do not inhibit organometallic coupling reactions, which allows a more convergent synthesis of molecular machines. We also prepared functional nanotrucks for the transport of atoms and molecules, as well as self-assembling nanocars and nanotrains. Although engineering challenges such as movement over long distance and non-atomically flat surfaces remain, the greatest current research challenge is imaging. The detailed study of nanocars requires complementary single molecule imaging techniques such as STM, AFM, TEM, or single-molecule fluorescence microscopy. Further developments in engineering and synthesis could lead to enzyme-like manipulation and assembly of atoms and small molecules in nonbiological environments.

Theoretical modelling of tip effects in the pushing manipulation of C(60) on the Si(001) surface

We present the results of our theoretical studies on the repulsive (pushing) manipulation of a C(60) molecule on the Si(001) surface with several scanning tunnelling microscopy tips. We show that, for silicon tips, tip-C(60) bonds are formed even with tips that do not initially have dangling bonds, and this tip-C(60) interaction drives the manipulation of the molecule. The details of the atomic structure of the tip and its position relative to the molecule do not have a significant effect on the mechanism and the sequence of adsorption configurations during the pushing manipulation of C(60) along the trough, where the trough itself provides a guiding effect. The pushing manipulation is thus a very robust process that occurs largely independently of the tip structure. On the other hand, the pushing manipulation across an Si-Si dimer row into the neighbouring trough proceeds in a more complex way, with tip deformation and detachment more likely to occur. We demonstrate the role of tip deformation and tip-molecule bond rearrangement in the continuous manipulation of the molecule. Finally, we calculate and analyse the forces acting on the tip during manipulation and identify characteristic patterns.

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Effect of C60 on solid supported lipid bilayers

We show that water-soluble fullerenes accumulate on the surface of zwitterionic and cationic supported bilayers to different extents. We propose on the basis of bilayer thicknesses, phase-transition temperatures, and fullerene movement that the water-soluble fullerenes do not penetrate into the hydrocarbon tails of supported bilayers. These findings are important to toxicity issues concerning fullerene materials and the development of decorated lipid bilayers for future drug delivery or sensor application.

A rack-and-pinion device at the molecular scale

Molecular machines, and in particular molecular motors with synthetic molecular structures and fuelled by external light, voltage or chemical conversions, have recently been reported. Most of these experiments are carried out in solution with a large ensemble of molecules and without access to one molecule at a time, a key point for future use of single molecular machines with an atomic scale precision. Therefore, to experiment on a single molecule-machine, this molecule has to be adsorbed on a surface, imaged and manipulated with the tip of a scanning tunnelling microscope (STM). A few experiments of this type have described molecular mechanisms in which a rotational movement of a single molecule is involved. However, until now, only uncontrolled rotations or indirect signatures of a rotation have been reported. In this work, we present a molecular rack-and-pinion device for which an STM tip drives a single pinion molecule at low temperature. The pinion is a 1.8-nm-diameter molecule functioning as a six-toothed wheel interlocked at the edge of a self-assembled molecular island acting as a rack. We monitor the rotation of the pinion molecule tooth by tooth along the rack by a chemical tag attached to one of its cogs.

C59Si on the Monohydride Si(100):H−(2 × 1) Surface

We propose the use of the Si atom in the experimentally observed C59Si molecule as a possible way to controllably anchor fullerene molecules on a Si surface, due to the formation of a strong bond to one of the Si surface atoms. All our results are based on ab initio total energy density functional theory, and we obtain that the binding energy is on the order of 2.1 eV, approximately 1.4 eV more stable than a C60 bonded in a similar situation. A possible route to obtain such adsorption via a (C59Si)2 dimer is examined, and we find the whole process to be exothermic by approximately 0.2 eV.

SCANNING TUNNELING MICROSCOPY MANIPULATION OF COMPLEX ORGANIC MOLECULES ON SOLID SURFACES

Organic molecules adsorbed on solid surfaces display a fascinating variety of new physical and chemical phenomena ranging from self-assembly and molecular recognition to nonlinear optical properties and current rectification. Both the fundamental interest in these systems and the promise of technological applications have motivated a strong research effort in understanding and controlling these properties. Scanning tunneling microscopy (STM) and, in particular, its ability to manipulate individual adsorbed molecules, has become a powerful tool for studying the adsorption geometry and the conformation and dynamics of single molecules and molecular aggregates. Here we review selected case studies demonstrating the enormous capabilities of STM manipulations to explore basic physiochemical properties of adsorbed molecules. In particular, we emphasize the role of STM manipulations in studying the coupling between the multiple degrees of freedom of adsorbed molecules, the phenomenon of molecular molding, and the possibility of creating and breaking individual chemical bonds in a controlled manner, i.e., the concept of single-molecule chemistry.

Recent progress on nanovehicles

Nanovehicles are a new class of molecular machines consisting of a molecular scale chassis, axles, and wheels, that can roll across solid surfaces with structurally defined directions making them of interest to synthetic chemists, surface scientists, chemical engineers, and the general car enthusiast. In this tutorial review, following a brief introduction to the development of nanomachines, our recent progress on the nanovehicle project is presented including the design, synthesis, and testing of a series of nanocars, nanotrucks, and motorized nanocars.

Directional control in thermally driven single-molecule nanocars

With the hope of directing future bottom-up fabrication through bulk external stimuli (such as electric fields) on nanometer-sized transporters, we sought to study controlled molecular motion on surfaces through the rational design of surface-capable molecular structures called nanocars. Here we show that the observed movement of the nanocars is a new type of fullerene-based wheel-like rolling motion, not stick-slip or sliding translation, due to evidence including directional preference in both direct and indirect manipulation and studies of related molecular structures.

Simple model of microscopic rolling friction

Rolling friction at a microscopic scale is studied with the help of a simple two-dimensional model. Molecular dynamics simulations show that rolling of spherical lubricant molecules exists only for concentrations lower than the concentration of a close-packed layer. At concentrations higher than a critical one due to jamming of lubricant molecules the rolling of nearest neighboring molecules is hindered. An optimal concentration exists which provides the minimum of kinetic friction. Methods for avoiding jamming and increasing the range of operation of rolling mechanism of friction are discussed.