Building and Probing Small for Mechanics

The historical background of this volume “Building and Probing small for mechanics” of the Springer-Nature series “Advances in Atom and Single Molecule Machines” is presented to put in context the actual effort towards the construction of functioning molecular machinery, one molecule per one molecule or in a supramolecular assemblage. The accent is made on 3 different roots: surface science, organic chemistry and supramolecular chemistry supported by the recent progresses in nanolithography and by the quantum chemistry approaches and their semi-classical trends for mechanics in designing and interpreting the functioning of the first molecule-machines.

It is demonstrated how the mechanism of a mechanical calculator can be reduced to a 2 levels planar machinery. The initial 1790 J. Auch planar design was transformed and the mechanical parts of this new design were 3D printed reducing 1:5 the active surface occupied by the 1790 original. To avoid back-carry propagations, the ratchet springs are still metallic. In a next miniaturization step, modern metal machining techniques were used to reach a 4 mm thick planar version, 1:100 in surface of the 1790 original. This open the way to further miniaturization steps of our unique design using modern micro and nanolithography techniques.

A scanning photo-lithography process is developed to miniaturize mechanical calculators down to 40 μm in diameter for their calculating micro-gears. Our first moulding process span the dimensions from 1 mm to 60 μm for the micro-gears. Down to 100 μm, the planar calculator construction can still be based on a micro-manipulation of the moving parts under an optical microscope. Below and to reach the 10 μm, a double photo-lithography process was developed on a specific graphite/SiO₂/Si wafer for mastering surface frictions. After a baking at 120 °C, the photo-resist becomes the material constitutive of all the moving micromechanical pieces. Only the rotation micro-axles remain metallic to ensure their good anchoring to the surface. A 2-digits micro-calculator is fabricated. In base 10, the carry propagation is demonstrated.

A rapid overview on the main lithographic tools used in the top–down approach in nanotechnology including their intrinsic and extrinsic resolution is given in this chapter. Moreover, we discuss the advantages of the use of focused ion beam for very specific applications, complementary to the more standard ones. Finally, we will describe, using focused He ions, how to fabricate solid state gears at the nanoscale, in the range 200 nm down to 50 nm.

In the field of Molecular Machines, molecular gears have mainly been synthesized to be studied in solution. Then, the cogwheel subunits are restricted to be only arranged in an intramolecular manner. In the last years, the possibility to arrange a train of gears at the single molecular level and observe the propagation of a rotation motion from one molecule to its neighbor using Scanning Tunneling Microscopy (STM) opened new perspectives with the opportunity to have intermolecular arrangements on surfaces. In this chapter, we describe the research background of single molecular gears and our strategy using organometallic piano-stool complexes to anchor such gears on surfaces. Our molecules incorporate two subunits linked together through a ruthenium center acting as a ball bearing. The lower part is the anchoring tripodal ligand and the upper part the cogwheel. Various functionalities have been explored to behave as teeth, ranging from mono-dimensional phenyl rings to bi-dimensional porphyrin fragments.

Technical progress in the field of Scanning Probe Microscopy (SPM) has opened the way for the development of new surface-mounted artificial molecular machines, which can be addressed at the single molecule scale. In this context, a ruthenium-based molecular motor has been shown to undergo controlled unidirectional and reversible rotation when fueled with electrons delivered by the tip of a Scanning Tunneling Microscope. In this chapter, we report our efforts towards a deeper understanding of the mechanical properties of this molecular motor. In view of complementary force measurements to be performed at the single molecule scale using SPM techniques, the organometallic structure of the motor has been derivatized to append a long chain terminated by a hook. We detail here the design of this nano-winch architecture and the modular synthesis of a first prototype dedicated to Atomic Force Microscopy-based Single Molecule Force Spectroscopy experiments.

A reliable anchoring on the substrate is the fundamental prerequisite to investigate surface-bound molecular rotors. The choice of the anchor group is dependent on the used substrate, and the surface-molecule bond must be sufficiently strong to endure under electrical operation. Here, we give an overview of anchor groups suitable to immobilize molecules on gold and other coinage metals via chemisorption. Sulfur-, nitrogen- and oxygen-based anchors are reviewed, N-heterocyclic carbenes as well as selected examples of other carbon-based anchors are considered, and examples of anchor groups reported for surface-bound molecular rotors are given. Anchoring is discussed in terms of the surface-molecule binding mode, i.e. radical adsorption and lone pair interaction. Green’s ligand classification, Pearson’s hard/soft- acid/base (HSAB) principle as well as the concepts denticity and podality are considered. Emphasis is placed on chemical aspects, e.g. the need to protect and controllably deprotect reactive anchors such as thiols and acetylenes.

Single molecular rotors are important components for constructing bottom-up molecular mechanical machines and a window for shedding light on complex physical and chemical questions about motions of organic molecules on surfaces. Stability of each component in such a molecular construction site is a crucial prerequisite. To realize a stable stepwise rotation of a molecule by a low temperature scanning tunneling microscope (LT-STM), atomic scale axles is particularly important. An ideal atomic scale axle is expected to balance between anchoring and mobility of rotating a single molecule on a metal surface under external excitations. In this Chapter, several chemical anchoring strategies on how to pin a molecular rotor are tested and discussed. Tip-induced manipulation and motion analysis are used as tools to investigate the properties and functionality of the proposed strategies.

A molecule-gear rotating without a lateral jittering effect is constructed using a single copper adatom as a physical axle on a lead superconducting surface. The molecule-gear has a diameter of 1.2 nm with 6 tert-butyl-teeth. It is mounted on this Cu axle using the atom/molecule manipulation capability of a low temperature scanning tunneling microscope (LT-STM). Transmission of rotational motions between 2 molecule-gears, whose axles have to be exactly 1.9 nm separated, is functioning when this train of molecule-gears is completed with a molecule-handle. To manipulate the molecule-handle laterally, the first molecule-gear of the train directly entangled with the molecule-handle is step by step rotated around its Cu adatom axle. It drives the second molecule-gear mechanically engaged with the first gear to rotate like along a train of macroscopic solid-state gears. Such rotation transmission is one of the most basic function for the future construction of a complex molecular machinery.

A train of molecule gears consisting of PF₃ molecules was studied using semi-empirical ASED+ method to explore the mechanism of rotational transmission along this train. It was observed that a unidirectional rotational transmission occurs between only the first two PF₃ molecules for a PF₃ molecule train up to six molecule-gears, the four PF₃ molecules at the end of the train being used to rigidify the rotation axle of the first two PF₃. This demonstrates that in a train of molecule-gears, the rotation of each molecule is resulting from a collective action of many degrees of freedom per molecule. This collective motion is rather fragile against many others possible minimum energy trajectories which can develop on the multidimensional ground state potential energy surface of a molecule-gear train to respond to the increase of the potential energy required to rotate the first molecule-gear of the train.

The miniaturization of gears towards the nanoscale is a formidable task posing a variety of challenges to current fabrication technologies. In context, the understanding, via computer simulations, of the mechanisms mediating the transfer of rotational motion between nanoscale gears can be of great help to guide the experimental designs. Based on atomistic molecular dynamics simulations in combination with a nearly rigid-body approximation, we study the transmission of rotational motion between molecule gears and solid-state gears, respectively. For the molecule gears under continuous driving, we identify different regimes of rotational motion depending on the magnitude of the external torque. In contrast, the solid-state gears behave like ideal gears with nearly perfect transmission. Furthermore, we simulate the manipulation of the gears by a scanning-probe tip and we find that the mechanical transmission strongly depends on the center of mass distance between gears. A new regime of transmission is found for the solid-state gears.

The advent of molecular machines is placing special attention on the rotation of a single molecule. Arguably, rotations are central for the diverse movements of a machine during its working dynamics. Here, we consider molecules that are constrained by the surface and effect rotations over an axle. They are then planar molecule-rotors. The excitation of a rotation by tunneling electrons, induced for example by the tip of a scanning tunneling microscope (STM), can be quite efficient as shown by a large body of experimental evidence. These rotations are indeed excited by single tunneling electron effect and are limited by the damping of the rotation by the different degrees of freedom of the substrate. When the molecule inertia momentum is small, quantum effects become apparent and rotation becomes very efficient by the large transfer of angular momentum produced by the transferred electrons through the STM junction. For larger molecules the classical limit is rapidly attained. After several considerations on the electron-induced rotation of a single molecule, we show how to evaluate the rotational dynamics during the tunneling of electrons through a molecule-rotor.

In this chapter, we describe the effect of “static” and dynamic nanomechanical actuation at zinc porphyrin sites that are loaded with an organocatalyst. In detail, the actuation embraces several molecular events culminating in a nanometer rearrangement of a toggling arm onto the loaded zinc porphyrin site that finally entails liberation of the catalyst into solution. In this brief review we first describe the development of nanoswitches that upon toggling the switching arm turn ON/OFF catalytic processes. Then, we discuss the prospects of dynamic actuation leading to catalyst liberation in appropriately designed devices. There the catalytic activity is then correlated with the machine speed. A theoretical explanation is presented that identifies the kinetic origin of the phenomenon.

Molecular shuttles are prototypes of most complex synthetic molecular machines. In a molecular shuttle, a ring-shaped molecule or macrocycle is threaded onto a molecular axle. One of the most prominent features of these devices is that the macrocycle can shuttle reversibly between different recognition sites on the axle as a reaction to external stimuli. Molecular shuttles are currently of great interest to researchers due to their potential applications in various fields. Although kinetics and thermodynamics of these systems in bulk are well understood, the mechanistic principles of operation of molecular shuttles and their dynamics are not quantified yet. Here, we show how to use the single-molecule manipulation technique of optical tweezers to probe mechanically and perform near-equilibrium measurements on single molecular shuttles in near-physiological conditions. The method described in this chapter can be used to study the mechanical strength and the real-time operation of other artificial systems at the single-molecule level in near-physiological conditions.