Recording intramolecular mechanics during the manipulation of a large molecule

Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

Bending and twisting around carbon-carbon single bonds are ubiquitous in natural and synthetic polymers. Force-induced changes were so far not measured at the single-monomer level, owing to limited ways to apply local forces. We quantified down to the submolecular level the mechanical response within individual poly-pyrenylene chains upon their detachment from a gold surface with an atomic force microscope at 5 K. Computer simulations based on a dedicated force field reproduce the experimental traces and reveal symmetry-broken bent and rotated conformations of the sliding physisorbed segment besides steric hindrance of the just lifted monomer. Our study also shows that the tip-molecule bond remains intact but remarkably soft and links force variations to complex but well-defined conformational changes.

Surface manipulation of a curved polycyclic aromatic hydrocarbon-based nano-vehicle molecule equipped with triptycene wheels

With a central curved chassis, a four-wheeled molecule-vehicle was deposited on a Au(111) surface and imaged at low temperature using a scanning tunneling microscope. The curved conformation of the chassis and the consequent moderate interactions of the four wheels with the surface were observed. The dI/dV constant current maps of the tunneling electronic resonances close to the Au(111) Fermi level were recorded to identify the potential energy entry port on the molecular skeleton to trigger and control the driving of the molecule. A lateral pushing mode of molecular manipulation and the consequent recording of the manipulation signals confirm how the wheels can step-by-step rotate while passing over the Au(111) surface native herringbone reconstructions. Switching a phenyl holding a wheel to the chassis was not observed for triggering a lateral molecular motion inelastically and without any mechanic push by the tip apex. This points out the necessity to encode the sequence of the required wheels action on the profile of the potential energy surface of the excited states to be able to drive a molecule-vehicle.

Design and Characterization of an Electrically Powered Single Molecule on Gold

The surface diffusion of individual molecules is of paramount importance in self-assembly processes and catalytic processes. However, the fundamental understanding of molecule diffusion peculiarities considering conformations and adsorption sites remain poorly known at the atomic scale. Here, we probe the 4'-(4-tolyl)-2,2':6',2″-terpyridine adsorbed on the Au(111) herringbone structure combining scanning tunneling microscopy and atomic force microscopy. Molecules are controllably translated by electrons excitations over the reconstruction, except at elbows acting as pinning centers. Experimental data supported by theoretical calculations show the formation of coordination bonds between the molecule and Au atoms of the surface. Using force spectroscopy, we quantify local variation of the surface potential and the lateral force required to move the molecule. We found an elevation of the diffusion barrier at elbows of the reconstruction of ∼100 meV compared to the rest of the surface.

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.

Solid-state SiO₂ nano-gears AFM tip manipulation on HOPG

On a native graphite surface, 15 nm-thick solid-state nanogears are nanofabricated with a 30 nm outer diameter and six teeth. The nanogears are manipulated one at a time by the tip of an atomic force microscope using the sample stage displacements for the manipulation and recording of the corresponding manipulation signals. For step heights below 3.0 nm, nanogears are manipulated up and down native graphite surface step edges. In the absence of a central shaft per nanogear, gearing between nanogears is limited to a few 1/12 turns for six teeth. When the graphite step is higher than 3 nm, a rack-and-pinion mechanism was constructed along the edge with a 90 nm nanogear pinion.

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.

Single rotating molecule-machines: nanovehicles and molecular motors

In the last decade many molecular machines with controlled molecular motions have been synthesized. In the present review chapter we will present and discuss our contribution to the field, in particular through some examples of rotating molecular machines that have been designed, synthesized, and studied in our group. After starting by explaining why it is so important to study such machines as single molecules, we will focus on two families of molecular machines, nanovehicles and molecular motors. The first members of the nanovehicle family are molecules with two triptycenes as wheels: the axle and the wheelbarrow. Then come the four-wheel nanocars. Since triptycene wheels are not very mobile on metallic surfaces, alternative wheels with a bowl-shape structure have also been synthesized and studied on surfaces. The molecular motors are built around ruthenium organometallic centers and have a piano-stool geometry with peripheric ferrocenyl groups.

STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.

High-precision imaging of an encapsulated Lindqvist ion and correlation of its structure and symmetry with quantum chemical calculations

Low-voltage aberration-corrected transmission electron microscopy (AC-TEM) of discrete Lindqvist [W(6)O(19)](2-) polyoxometalate ions inserted from an ethanolic solution of [NBu(4)](2)[W(6)O(19)] into double walled carbon nanotubes (DWNTs) allows a higher precision structural study to be performed than previously reported. W atom column separations within the constituent W(6) tungsten cage can now be visualized with sufficient clarity that reliable correlation with structural predictions from density functional theory (DFT) can be achieved. Calculations performed on [W(6)O(19)](2-) anions encapsulated in carbon nanotubes show good agreement with measured separations between pairs of W(2) atom columns imaged within equatorial WO(6) polyhedral pairs and also single W atom positions located within individual axial WO(6) octahedra. Structural data from the tilted chiral encapsulating DWNT were also determined simultaneously with the anion structural measurements, allowing the influence of the conformation of the encapsulating tubule to be included in the DFT calculation and compared against that of other candidate encapsulating nanotubes. Additional DFT calculations performed using Li(+) cations as a model for the [NBu(4)](+) counterions indicate that the latter may help to induce charge transfer between the DWNT and the [W(6)O(19)](2-) ion and this may help to constrain the motion of the ion in situ.

Motion of light adatoms and molecules on the surface of few-layer graphene

Low-voltage aberration-corrected transmission electron microscopy (TEM) is applied to investigate the feasibility of continuous electron beam cleaning of graphene and monitor the removal of residual species as present on few-layer graphene (FLG) surfaces. This combined approach allows us to detect light adatoms and evaluate their discontinuous sporadic motional behavior. Furthermore, the formation and dynamic behavior of isolated molecules on the FLG surface can be captured. The preferential source of adatoms and adsorbed molecules appeared to be carbonaceous clusters accumulated from residual solvents on the graphene surface. TEM image simulations provide potential detail on the observed molecular structures. Molecular dynamics simulations confirm the experimentally observed dynamics occurring on the energy scale imposed by the presence of the 80 kV electron beam and help elucidate the underlying mechanisms.

Single molecule logical devices

After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit.

Imaging the structure, symmetry, and surface-inhibited rotation of polyoxometalate ions on graphene oxide

Atomic-resolution imaging of discrete [γ-SiW10O36]8- lacunary Keggin ions dispersed onto monolayer graphene oxide (GO) films by low voltage aberration corrected transmission electron microscopy is described. Under low electron beam dose, individual anions remain stationary for long enough that a variety of projections can be observed and structural information extracted with ca. ± 0.03 nm precision. Unambiguous assignment of the orientation of individual ions with respect to the point symmetry elements can be determined. The C2v symmetry [γ-SiW10O36]8- ion was imaged along its 2-fold C2 axis or orthogonally with respect to one of two nonequivalent mirror planes (i.e., σv). Continued electron beam exposure of a second ion imaged orthogonal to σv causes it to translate and/or rotate in an inhibited fashion so that the ion can be viewed in different relative orientations. The inhibited surface motion of the anion, which is in response to H-bonding-type interactions, reveals an important new property for GO in that it demonstrably behaves as a chemically modified (i.e., rather than chemically neutral) surface in electron microscopy. This behavior indicates that GO has more in common with substrates used in imaging techniques such as atomic force microscopy and scanning tunneling microscopy, and this clearly sets it apart from other support films used in transmission electron microscopy.

Dynamics of molecular self-ordering in tetraphenyl porphyrin monolayers on metallic substrates

A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.

A family of electron-triggered molecular motors based on aromatic building blocks

We present our strategy to control the rotation in a molecular rotary motor and the synthesis of a family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active ferrocene groups, so that addressing the molecule with nanoelectrodes would trigger rotation. The rigidity of the structure is allowed by the use of aromatic building blocks both in the stator and in the rotor fragments.

Functional and spectroscopic measurements with scanning tunneling microscopy

Invented as a surface analytical technique capable of imaging individual atoms and molecules in real space, scanning tunneling microscopy (STM) has developed and advanced into a technique able to measure a variety of structural, functional, and spectroscopic properties and relationships at the single-molecule level. Here, we review basic STM operation and image interpretation, techniques developed to manipulate single atoms and molecules with the STM to measure functional properties of surfaces, local spectroscopies used to characterize atoms and molecules at the single-molecule level, and surface perturbations affecting surface coverage and surface reactions. Each section focuses on determining the identity and function of chemical species so as to elucidate information beyond topography with STM.

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.

Electron-triggered motions in technomimetic molecules

Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with motions triggered by electrons. The first part is devoted to our work in the field of molecular switches: after having demonstrated the possibility of controlling an intramolecular electron transfer by photoisomerisation, we are now trying to control the isomerisation, either by electrochemistry, or by embedding the photochromic compound in a self-assembled monolayer and testing the electrical conduction with a STM tip. In a second part, we present our strategy on controlling the rotation in a molecular rotary motor and the family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active groups, so that addressing the molecule with nano-electrodes would trigger rotation. The electrical control of the charge state of a molecule by a STM tip is developed in a final part.

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.

Scanning tunneling microscopy experiments on single molecular landers

Molecular landers are molecules comprising of a central rigid molecular wire maintained above a metallic surface by organic spacers, which allows specific ultrahigh vacuum-scanning tunneling microscopy experiments to be performed at the single-molecule level. The understanding of the molecule-surface interactions, intramolecular mechanics, and the possibility to perform extremely precise tip-induced manipulation permit these molecules to be brought in contact with a nanoelectrode and the resulting electronic interaction to be analyzed in well controlled conditions.

Bond breaking coupled with translation in rolling of covalently bound molecules

The response of a C60 molecule to manipulation across a surface displays a long range periodicity which corresponds to a rolling motion. A period of three or four lattice constants is observed and is accompanied by complex subharmonic structure due to molecular hops through a regular, repeating sequence of adsorption states. Combining experimental data and ab initio calculations, we show that this response corresponds to a rolling motion in which two of the four Si-C60 covalent bonds act as a pivot over which the molecule rotates while moving through one lattice constant and identify a sequence of C60 bonding configurations that accounts for the periodic structure.

Selective internal manipulation of a single molecule by scanning tunneling microscopy

We have studied the adsorption of the polyaromatic molecule 1,4"-paratriphenyldimethylacetone, which we have nicknamed Trima. The originality of this linear molecule is that it was designed and synthesized to have two functionalities. First, chemisorb itself to the surface by its two ends rather like a bridge. Second, the central part of the molecule could then be rotated by injecting electrons with the tip of the scanning tunneling microscope (STM). The length of the molecule corresponds exactly to the spacing between five dimers in a row on the Si(100)-2 x 1 surface. We found that the molecule adsorbs as expected on the clean silicon surface by using complementary STM and synchrotron radiation studies. Manipulation of individual molecules with the STM tip showed selective internal modifications that were highly voltage dependent. These manipulations were found to be compatible with an electronic excitation of the pi-pi* transition of the molecule.

Creating nanoscopic collagen matrices using atomic force microscopy

The atomic force microscope (AFM) is introduced as a biomolecular manipulation machine capable of assembling biological molecules into well-defined molecular structures. Native collagen molecules were mechanically directed into well-defined, two-dimensional templates exhibiting patterns with feature sizes ranging from a few nanometers to several hundreds of micrometers. The resulting nanostructured collagen matrices were only approximately 3-nm thick, exhibited an extreme mechanical stability, and maintained their properties over the time range of several months. Our results directly demonstrate the plasticity of biological assemblies and provide insight into the physical mechanisms by which biological structures may be organized by cells in vivo. These nanoscopic templates may serve as platforms on non-biological surfaces to direct molecular and cellular processes.

Mechanisms of reversible conformational transitions in a single molecule

The reversible interconversion between two nonplanar conformations of single Zn(II) Etioporphyrin I molecules adsorbed on a NiAl(110) surface at 13 K was induced by a scanning tunneling microscope (STM). The threshold voltage for the conformational change at negative sample bias depends linearly on the tip-sample distance, suggesting an electrostatic force mechanism. The reverse conversion involves inelastic electron tunneling via a molecular electronic resonance at 1.25 eV. In contrast with the photon-induced conformational changes, an electrically induced mechanism is realized with the STM.

The scanning tunnelling microscope as an operative tool: doing physics and chemistry with single atoms and molecules

The scanning tunnelling microscope, initially invented to image surfaces down to the atomic scale, has been further developed in the last few years to an operative tool, with which atoms and molecules can be manipulated at will at low substrate temperatures in different manners to create and investigate artificial structures, whose properties can be investigated employing spectroscopic dI/dV measurements. The tunnelling current can be used to selectively break chemical bonds, but also to induce chemical association. These possibilities give rise to startling new opportunities for physical and chemical experiments on the single atom and single molecule level. Here we provide a short overview on recent results obtained with these techniques.

Molecular assembly and self-assembly: molecular nanoscience for future technologies

In this review the emerging science of single molecules is discussed in the perspective of nanoscale molecular functions and devices. New methods for the controlled assembly of well-defined molecular nanostructures are presented: self assembly and single molecular positioning. The observation and selective modification of conformation, electronics, and molecular mechanics of individual molecules and molecular assemblies by scanning probes is demonstrated. To complement this scientific review, some of the possible consequences and visions for future developments are discussed, as far as they derive from the presented systems. The prospects of nanoscale science to stimulate technological evolution are exemplified.

STM control of chemical reaction: single-molecule synthesis

The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

MANIPULATION OF ATOMS AND MOLECULES FOR CONSTRUCTION OF NANOSYSTEMS: THE SCANNING TUNNELING MICROSCOPE AS AN OPERATIVE TOOL

Controlled manipulations with scanning tunneling microscope (STM) down to the scale of small molecules and single atoms allow to build molecular and atomic nanosystems, leading to the fascinating possibility of creating manmade structures on atomic scale. Here we present a short review on investigations based on atomic scale manipulation. Upon soft lateral manipulation of adsorbed species, in which only tip/particle forces are used, three different manipulation modes can be discerned: pushing, pulling and sliding. Even the manipulation of strongly bound native substrate atoms is possible. We demonstrate applications as local analytic and synthetic chemistry tools, with important consequences on surface structure research. Vertical manipulation of Xe and CO leads to improved imaging with functionalized tips. With CO deliberately transferred to the tip, we have also succeeded to perform vibrational spectroscopy on single molecules. Furthermore, we describe how we have reproduced a full chemical reaction with single molecules, whereby all basic steps, namely preparation of the reactants, diffusion and association, are induced with the STM tip. Here also field and electron current effects are employed. Finally, we have extended the manipulation techniques to large specially designed molecules by performing lateral manipulation in constant height and realizing the principle of a conformational molecular switch. Artificial nanoscale structures built in atom by atom fashion can serve as quantum laboratories for investigations of various physical properties.

Probing the different stages in contacting a single molecular wire

A crucial problem in molecular electronics is the control of the electronic contact between a molecule and its electrodes. As a model system, we investigated the contact between the molecular wire group of a C90H98 (Lander) molecule and the edge of a Cu(111) monatomic step. The reproducible contact and decontact of the wire was obtained by manipulating the Lander with a low temperature scanning tunneling microscope. The electronic standing wave patterns on the Cu(111) surface serve to monitor the local electronic perturbation caused by the interaction of the wire end with the step edge, giving information on the quality of the contact.