Molecular machines from individuals to swarms.

A molecular machine can be defined as an assembly of a discrete number of molecular components (that is, a supramolecular structure) designed to perform a function through the mechanical movements of its components, which occur under appropriate external stimulation. Hence, molecular machines contain a motor part, that is a device capable of converting energy into mechanical work. Molecular motors and machines operate via nuclear rearrangements and, like their macroscopic counterparts, are characterized by the kind of energy input supplied to make them work, the manner in which their operation can be monitored, the possibility to repeat the operation at will, i.e., establishing a cyclic process, the time scale needed to complete a cycle of operation, and the performed function. Owing to the progress made in several branches of Chemistry, and to the better understanding of the operation mechanisms of molecular machines of the biological world, it has become possible to design and construct simple prototypes of artificial molecular motors and machines. The extension of the concept of machine to the molecular level is of great interest not only for basic research, but also for the growth of nanoscience and the development of nanotechnology. We will illustrate some basic features and design principles of molecular machines, and we will describe a few recent examples of artificial systems, based on rotaxanes, catenanes and related species, taken from our own research. Open image in new window

The concept of a "power stroke"-a free-energy releasing conformational change-appears in almost every textbook that deals with the molecular details of muscle, the flagellar rotor, and many other biomolecular machines. Here, it is shown by using the constraints of microscopic reversibility that the power stroke model is incorrect as an explanation of how chemical energy is used by a molecular machine to do mechanical work. Instead, chemically driven molecular machines operating under thermodynamic constraints imposed by the reactant and product concentrations in the bulk function as information ratchets in which the directionality and stopping torque or stopping force are controlled entirely by the gating of the chemical reaction that provides the fuel for the machine. The gating of the chemical free energy occurs through chemical state dependent conformational changes of the molecular machine that, in turn, are capable of generating directional mechanical motions. In strong contrast to this general conclusion for molecular machines driven by catalysis of a chemical reaction, a power stroke may be (and often is) an essential component for a molecular machine driven by external modulation of pH or redox potential or by light. This difference between optical and chemical driving properties arises from the fundamental symmetry difference between the physics of optical processes, governed by the Bose-Einstein relations, and the constraints of microscopic reversibility for thermally activated processes.

The extension of the concept of machine to the molecular level is of great interest for thegrowth of nanoscience and the development of nanotechnology. A molecular machine can bedefined as an assembly of a discrete number of molecular components (that is, asupramolecular structure) designed to perform a function through the mechanicalmovements of its components, which occur under appropriate external stimulation. Hence,molecular machines contain a motor part, that is a device capable of converting energy intomechanical work. Molecular motors and machines operate via nuclear rearrangementsand, like their macroscopic counterparts, are characterized by the kind of energyinput supplied to make them work, the manner in which their operation can bemonitored, the possibility to repeat the operation at will, i.e., establishing a cyclicprocess, the timescale needed to complete a cycle of operation, and the performedfunction. Owing to the progresses made in several branches of chemistry, and tothe better understanding of the operation mechanisms of molecular machinesof the biological world, it has become possible to design and construct simpleprototypes of artificial molecular motors and machines. Some examples basedon rotaxanes, catenanes, and related interlocked molecules will be described.

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Proteins at Interfaces: Conformational Behavior and Wear

A Track-Based Molecular Synthesizer that Builds a Single-Sequence Oligomer through Iterative Carbon-Carbon Bond Formation

Keywords: Jean-Pierre Sauvage, Sir J. Eraser Stoddart, Bernard L. Feringa, 2016, Nobel Prize, molecular machines Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa share the 2016 Nobel Prize Chemistry (1), awarded jointly to them for the design and synthesis of molecular machines. A molecular machine, or nanomachine, is any discrete number of molecular components that produce quasi-mechanical movements (output) response to specific stimuli (input). (2) This was demonstrated (3) 1983, when Jean-Paul Sauvage managed to synthesise a catenane (Figure 1), which is formed by linking together two ring-shaped molecules by a mechanical bond, a recently coined term to describe the connection between the macrocycles of a catenane. In order that the molecular machine can perform a specific task, its components must be able to move relation to one another, as is the case the two interlocked rings the catenane. It was Fraser Stoddart, who 1991 synthesised a rotaxane (4), which has a molecular axle threaded through a molecular ring (Figure 2a,b), and demonstrated that the ring could move up and down the axle, leading to such devices as a molecular elevator, a molecular muscle and a molecule-based computer chip. In 1999, Bernard Feringa managed to demonstrate a molecular motor (5), which the rotor blade spins continually the same direction. Using a molecular motor, he managed to rotate a glass cylinder that was 10,000 times bigger than the motor itself. concept of a has emerged, a version of which was developed at Rice University by the research group of James Tour (6), and consisted of a molecule with an H-shaped 'chassis' with fullerene groups attached at the four comers to act as wheels (Figure 3). However, the original device did not have a molecular motor, and so might not be regarded as an actual Feringa and his co-workers have synthesised a molecule with four motorized wheels, which they deposited onto a copper surface and used electrons from a scanning tunnelling microscope (STM) to provide sufficient energy that they could drive some of the molecules a specific direction, similar fashion to steering a car. As a result of inelastic electron tunnelling, conformational changes are induced the rotors which propels the molecule over the surface. Since it is possible to change, individually, the direction of the rotary motion the motor units, either random or preferentially linear trajectories can be attained the self-propelling molecular 'four-wheel' device. It is believed that it might be possible to produce more sophisticated molecular cars, which a more complete control of the direction of motion can be achieved. (7) Jean-Francois Morin et al. (8) are working on a nanocar of the future, fitted with carborane wheels and a light powered helicene molecular motor. However, although a unidirectional rotation was observed the motor solution, it has not yet proved possible to drive it on a surface by means of light-energy. A nanocar race event, initially scheduled October 2016 and described as The First Ever Race of Molecule-Cars, has been postponed (9) in order to give enough time the teams to prepare and the microscope to be optimized. This postponement is essential to make the event a true > challenge. As yet, the real future molecular machines is unknown and probably unknowable, but we may note the following, taken from the 2016 Nobel Prize Chemistry website (10). …

Progress of mankind has always been related to the development and construction of new machines. In the last decades, science and technology have been involved in a race to increase the capacity of novel machines as well as in a progressive miniaturization of their parts. Further efforts to design and construct machines at the nanometer scale will lead to new and exciting applications in medicine, energy and materials. However, until now every attempt to build artificial systems at the molecular level with complex functions pales beside the Nature’s molecular machines at work. Myosin and kinesin enzymes responsible of muscle contraction, ATP synthase and cellular transport are all examples of Nature’s ability to provide living systems with complex machinery whose structures and detailed mechanisms we are just starting to unveil. Thus, by learning from Nature, we will be able to make use of the excellent properties refined by slow evolution. When we mimic Nature, we try to duplicate some of the features found in biological systems using synthetic analogues. Taking natural molecular machines as a starting point, we will try to design, synthesize and explore biomimetic artificial machines. Located at the interface between biology, physics and chemistry, the task of mimicking Nature’s results will need combined efforts from different disciplines and the use of every possible tool from theoretical calculations to advanced synthetic chemistry and structural characterization. In this chapter we will briefly review some of the better-known natural molecular machines as an inspiration for the design of biomimetic artificial machines. Specifically, the structure and function of the retinal molecular machine will be discussed. Taking the Nature’s work as a starting point, we will specify some of the requirements to build efficient molecular machines, such as controlling the motion at the molecular level and the energy supply. We will use these concepts to design a set of retinal-based biomimetic chemical switches. Comparison between the synthetic and biological structures allows to gather a better understanding of both systems together with some suggestions for further improvements. Some practical applications will also be presented together with an outlook for the near future.

Periodic pattern mining from spatio-temporal trajectory data

Spatial and temporal aspects in visual interaction

The design of artificial molecular machines often takes inspiration from macroscopic machines. However, the parallels between the two systems are often only superficial, because most molecular machines are governed by quantum processes. Previously, rotary molecular motors powered by light and chemical energy have been developed. In electrically driven motors, tunnelling electrons from the tip of a scanning tunnelling microscope have been used to drive the rotation of a simple rotor in a single direction and to move a four-wheeled molecule across a surface. Here, we show that a stand-alone molecular motor adsorbed on a gold surface can be made to rotate in a clockwise or anticlockwise direction by selective inelastic electron tunnelling through different subunits of the motor. Our motor is composed of a tripodal stator for vertical positioning, a five-arm rotor for controlled rotations, and a ruthenium atomic ball bearing connecting the static and rotational parts. The directional rotation arises from sawtooth-like rotational potentials, which are solely determined by the internal molecular structure and are independent of the surface adsorption site.

Quantum chemical ab initio calculations along with full geometry optimizations of Disperse Orange 3 (DO3), molecule in the ground state of the trans and cis conformations and carbazole (Cz), phenylenediamine molecules were performed applying the method of density functional theory (DFT). The obtained geometry of the ground state was used as initial one for the performed calculation with the optimization in the first excited state. The excited state has been investigated applying ab initio configuration interaction single-excitation molecular. Three variable light induced molecular machine was designed based on results of the obtained internal molecular motions during excitation of the DO3 molecule and the full geometry optimization was performed applying Hartree-Fock method for this device. The ZINDO method was applied performing the spectra calculations of the isolated photoactive molecules and the supermolecule- device. Several molecular logical machines are designed.

In literature, the effectiveness of haptics for motor learning is controversially discussed. Haptics is believed to be effective for motor learning in general; however, different types of haptic control enhance different movement aspects. Thus, in dependence on the movement aspects of interest, one type of haptic control may be effective whereas another one is not. Therefore, in the current work, it was investigated if and how different types of haptic controllers affect learning of spatial and temporal movement aspects. In particular, haptic controllers that enforce active participation of the participants were expected to improve spatial aspects. Only haptic controllers that provide feedback about the task's velocity profile were expected to improve temporal aspects. In a study on learning a complex trunk-arm rowing task, the effect of training with four different types of haptic control was investigated: position control, path control, adaptive path control, and reactive path control. A fifth group (control) trained with visual concurrent augmented feedback. As hypothesized, the position controller was most effective for learning of temporal movement aspects, while the path controller was most effective in teaching spatial movement aspects of the rowing task. Visual feedback was also effective for learning temporal and spatial movement aspects.

Natural molecular machines have inspired the development of artificial molecular machines, which have the potential to revolutionize several areas of technology. Artificial molecular machines commonly employ molecular switches, molecular motors, and molecular shuttles as fundamental building blocks. The observation of artificial molecular machines constructed by these building blocks can be highly challenging due to their small sizes and intricate behaviors. The use of modern instrumentation and advanced observational techniques plays a crucial role in the observation and characterization of molecular machines. Furthermore, a well-designed molecular structure is also a critical factor in making molecular machines more observable. This review summarizes the common methods from diverse perspectives used to observe molecular machines and emphasizes the significance of comprehending their behaviors in the design of superior artificial molecular machines.

The design and control of functional molecular machines and devices is one of the fascinating and challenging research targets in molecular science (Feringa et al., 2000; Kinbara & Aida, 2005; Kay et al., 2007). They were originally inspired from biological machines such as ATP synthases (Boyer, 1993; Abrahams et al., 1994) and myosin and kinesin (Julicher et al., 1997). They now include various kinds of artificial molecular machines such as transmitters, shuttles, nanocars and logic gates (Balzani et al., 2008), which can be driven by external forces at the molecular level. Some of them are not simply sizeddown versions of macroscopic machines and are controlled at the quantum level (Roncaglia & Tsironis, 1998). Lasers are energy sources over a wide range of wave lengths from mid-infrared to ultraviolet, which make it possible to drive various sizes of molecular machines without any direct contact. Lasers are expected to play an important role as a source of external forces for controlling molecular machines because lasers have various controlling-parameters such as central frequencies, pulse shapes, photon polarizations and time differences between two pulses (Assion et al., 1998; Gouliemakis et al., 2004). Based on coherent control theory (Kosloff et al. 1989; Shi & Rabitz, 1990; Shapiro & Brumer, 2000), laser pulses can be designed to produce the maximum desired target with minimum laser energy (Assion et al., 1998; Rice & Zhao, 2000; Gordon & Fujimura, 2002; Bandrauk et al., 2002). Molecular machines can be controlled through coherent interactions between lasers and molecules at a quantum level (Hoki et al., 2003). The procedures are sometimes called “quantum ignition” for driving molecular motors (Fujimura et al., 2004). The time evolution is obtained by solving the time-dependent Schrodinger equation or the Liouville equation (Sugawara & Fujimura, 1994; Ohtsuki et al., 1999; Hoki et al., 2001). Application of coherent control theory enables extraction of key factors for driving molecular motors with a unidirectional motion, though we have to wait for further experimental progress to carry out coherent control experiments on artificial molecular machines. In this chapter, we present fundamental principles for unidirectional motions of chiral molecular motors driven by linearly polarized laser pulses having no photon helicity.