A Doubly Kinetically-Gated Information Ratchet Autonomously Driven by Carbodiimide Hydration

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.

Kinetically controlled synthesis of rotaxane geometric isomers

Geometric isomerism in mechanically interlocked systems-which arises when the axle of a mechanically interlocked molecule is oriented, and the macrocyclic component is facially dissymmetric-can provide enhanced functionality for directional transport and polymerization catalysis. We now introduce a kinetically controlled strategy to control geometric isomerism in [2]rotaxanes. Our synthesis provides the major geometric isomer with high selectivity, broadening synthetic access to such interlocked structures. Starting from a readily accessible [2]rotaxane with a symmetrical axle, one of the two stoppers is activated selectively for stopper exchange by the substituents on the ring component. High selectivities are achieved in these reactions, based on coupling the selective formation reactions leading to the major products with inversely selective depletion reactions for the minor products. Specifically, in our reaction system, the desired (major) product forms faster in the first step, while the undesired (minor) product subsequently reacts away faster in the second step. Quantitative 1H NMR data, fit to a detailed kinetic model, demonstrates that this effect (which is conceptually closely related to minor enantiomer recycling and related processes) can significantly improve the intrinsic selectivity of the reactions. Our results serve as proof of principle for how multiple selective reaction steps can work together to enhance the stereoselectivity of synthetic processes forming complex mechanically interlocked molecules.

Kinetic Asymmetry and Directionality of Nonequilibrium Molecular Systems

Scientists have long been fascinated by the biomolecular machines in living systems that process energy and information to sustain life. The first synthetic molecular rotor capable of performing repeated 360° rotations due to a combination of photo- and thermally activated processes was reported in 1999. The progress in designing different molecular machines in the intervening years has been remarkable, with several outstanding examples appearing in the last few years. Despite the synthetic accomplishments, there remains confusion regarding the fundamental design principles by which the motions of molecules can be controlled, with significant intellectual tension between mechanical and chemical ways of thinking about and describing molecular machines. A thermodynamically consistent analysis of the kinetics of several molecular rotors and pumps shows that while light driven rotors operate by a power-stroke mechanism, kinetic asymmetry-the relative heights of energy barriers-is the sole determinant of the directionality of catalysis driven machines. Power-strokes-the relative depths of energy wells-play no role whatsoever in determining the sign of the directionality. These results, elaborated using trajectory thermodynamics and the nonequilibrium pump equality, show that kinetic asymmetry governs the response of many non-equilibrium chemical phenomena.

Stepwise Operation of a Molecular Rotary Motor Driven by an Appel Reaction

To date, only a small number of chemistries and chemical fueling strategies have been successfully used to operate artificial molecular motors. Here, we report the 360° directionally biased rotation of phenyl groups about a C-C bond, driven by a stepwise Appel reaction sequence. The motor molecule consists of a biaryl-embedded phosphine oxide and phenol, in which full rotation around the biaryl bond is blocked by the P-O oxygen atom on the rotor being too bulky to pass the oxygen atom on the stator. Treatment with SOCl2 forms a cyclic oxyphosphonium salt (removing the oxygen atom of the phosphine oxide), temporarily linking the rotor with the stator. Conformational exchange via ring flipping then allows the rotor and stator to twist back and forth past the previous limit of rotation. Subsequently, the ring opening of the tethered intermediate with a chiral alcohol occurs preferentially through a nucleophilic attack on one face. Thus, the original phosphine oxide is reformed with net directional rotation about the biaryl bond over the course of the two-step reaction sequence. Each repetition of SOCl2-chiral alcohol additions generates another directionally biased rotation. Using the same reaction sequence on a derivative of the motor molecule that forms atropisomers rather than fully rotating 360° results in enantioenrichment, suggesting that, on average, the motor molecule rotates in the "wrong" direction once every three fueling cycles. The interconversion of phosphine oxides and cyclic oxyphosphonium groups to form temporary tethers that enable a rotational barrier to be overcome directionally adds to the strategies available for generating chemically fueled kinetic asymmetry in molecular systems.

Limits on the Precision of Catenane Molecular Motors: Insights from Thermodynamics and Molecular Dynamics Simulations

Thermodynamic uncertainty relations (TURs) relate precision to the dissipation rate, yet the inequalities can be far from saturation. Indeed, in catenane molecular motor simulations, we record precision far below the TUR limit. We further show that this inefficiency can be anticipated by four physical parameters: the thermodynamic driving force, fuel decomposition rate, coupling between fuel decomposition and motor motion, and rate of undriven motor motion. The physical insights might assist in designing molecular motors in the future.

Ratcheting synthesis

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.

Switched "On" Transient Fluorescence Output from a Pulsed-Fuel Molecular Ratchet

We report the synthesis and operation of a molecular energy ratchet that transports a crown ether from solution onto a thread, along the axle, over a fluorophore, and off the other end of the thread back into bulk solution, all in response to a single pulse of a chemical fuel (CCl3CO2H). The fluorophore is a pyrene residue whose fluorescence is normally prevented by photoinduced electron transfer (PET) to a nearby N-methyltriazolium group. However, crown ether binding to the N-methyltriazolium site inhibits the PET, switching on pyrene fluorescence under UV irradiation. Each pulse of fuel results in a single ratchet cycle of transient fluorescence (encompassing threading, transport to the N-methyltriazolium site, and then dethreading), with the onset of the fluorescent time period determined by the amount of fuel in each pulse and the end-point determined by the concentration of the reagents for the disulfide exchange reaction. The system provides a potential alternative signaling approach for artificial molecular machines that read symbols from sequence-encoded molecular tapes.

Mechanochemical active ratchet

Self-propelled nanoparticles moving through liquids offer the possibility of creating advanced applications where such nanoswimmers can operate as artificial molecular-sized motors. Achieving control over the motion of nanoswimmers is a crucial aspect for their reliable functioning. While the directionality of micron-sized swimmers can be controlled with great precision, steering nano-sized active particles poses a real challenge. One of the reasons is the existence of large fluctuations of active velocity at the nanoscale. Here, we describe a mechanism that, in the presence of a ratchet potential, transforms these fluctuations into a net current of active nanoparticles. We demonstrate the effect using a generic model of self-propulsion powered by chemical reactions. The net motion along the easy direction of the ratchet potential arises from the coupling of chemical and mechanical processes and is triggered by a constant, transverse to the ratchet, force. The current magnitude sensitively depends on the amplitude and the periodicity of the ratchet potential and the strength of the transverse force. Our results highlight the importance of thermodynamically consistent modeling of chemical reactions in active matter at the nanoscale and suggest new ways of controlling dynamics in such systems.

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.

Two Squares in a Barrel: An Axially Disubstituted Conformationally Rigid Aliphatic Binding Motif for Cucurbit[6]uril

Novel binding motifs suitable for the construction of multitopic guest-based molecular devices (e.g., switches, sensors, data storage, and catalysts) are needed in supramolecular chemistry. No rigid, aliphatic binding motif that allows for axial disubstitution has been described for cucurbit[6]uril (CB6) so far. We prepared three model guests combining spiro[3.3]heptane and bicyclo[1.1.1]pentane centerpieces with imidazolium and ammonium termini. We described their binding properties toward CB6/7 and α-/β-CD using NMR, titration calorimetry, mass spectrometry, and single-crystal X-ray diffraction. We found that a bisimidazolio spiro[3.3]heptane guest forms inclusion complexes with CB6, CB7, and β-CD with respective association constants of 4.0 × 104, 1.2 × 1012, and 1.4 × 102. Due to less hindering terminal groups, the diammonio analogue forms more stable complexes with CB6 (K = 1.4 × 106) and CB7 (K = 3.8 × 1012). The bisimidazolio bicyclo[1.1.1]pentane guest forms a highly stable complex only with CB7 with a K value of 1.1 × 1011. The high selectivity of the new binding motifs implies promising potential in the construction of multitopic supramolecular components.

The Role of Chemically Innocent Polyanions in Active, Chemically Fueled Complex Coacervate Droplets

Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting because they are tightly regulated by reaction kinetics. For example, they serve as a model for membraneless organelles that are also often regulated by biochemical transformations such as post-translational modifications. They are also a great protocell model or could be used to synthesize life-they spontaneously emerge in response to reagents, compete, and decay when all nutrients have been consumed. However, the role of the unreactive building blocks, e.g., the polymeric compounds, is poorly understood. Here, we show the important role of the chemically innocent, unreactive polyanion of our chemically fueled coacervation droplets. We show that the polyanion drastically influences the resulting droplets' life cycle without influencing the chemical reaction cycle-either they are very dynamic or have a delayed dissolution. Additionally, we derive a mechanistic understanding of our observations and show how additives and rational polymer design help to create the desired coacervate emulsion life cycles.

A Doubly Dissipative System Driven by Chemical and Radiative Stimuli

The operation of a dissipative network composed of two or three different crown-ether receptors and an alkali metal cation can be temporally driven by the use (combined or not) of two orthogonal stimuli of a different nature. More specifically, irradiation with light at a proper wavelength and/or addition of an activated carboxylic acid, are used to modulate the binding capability of the above crown-ethers towards the metal ion, allowing to control over time the occupancy of the metal cation in the crown-ether moiety of a given ligand. Thus, application of either or both of the stimuli to an initially equilibrated system, where the metal cation is distributed among the crown-ether receptors depending on the different affinities, causes a programmable change in the receptor occupancies. Consequently, the system is induced to evolve to one or more out-of-equilibrium states with different distributions of the metal cation among the different receptors. When the fuel is exhausted or/and the irradiation interrupted, the system reversibly and autonomously goes back to the initial equilibrium state. Such results may contribute to the achievement of new dissipative systems that, taking advantage of multiple and orthogonal stimuli, are featured with more sophisticated operating mechanisms and time programmability.

Kinetic Barrier Diagrams to Visualize and Engineer Molecular Nonequilibrium Systems

Molecular nonequilibrium systems hold great promises for the nanotechnology of the future. Yet, their development is slowed by the absence of an informative representation. Indeed, while potential energy surfaces comprise in principle all the information, they hide the dynamic interplay of multiple reaction pathways underlying nonequilibrium systems, i.e., the degree of kinetic asymmetry. To offer an insightful visual representation of kinetic asymmetry, we extended an approach pertaining to catalytic networks, the energy span model, by focusing on system dynamics - rather than thermodynamics. Our approach encompasses both chemically and photochemically driven systems, ranging from unimolecular motors to simple self-assembly schemes. The obtained diagrams give immediate access to information needed to guide experiments, such as states' population, rate of machine operation, maximum work output, and effects of design changes. The proposed kinetic barrier diagrams offer a unifying graphical tool for disparate nonequilibrium phenomena.

Controlling the Conformation of 2-Dimethylaminobiphenyls by Transient Intramolecular Hydrogen Bonding

Temporal control of molecular motions is receiving increasing attention because it is central to the development of molecular switches and motors and nanoscopic materials with life-like properties. Inspired by previous studies, here, we report that acid 12 can be used to temporally control the conformational freedom around the C-C bond connecting the two aromatic rings of the ditopic bases 4 and 5. Consistent with NMR measurements and DFT calculations, before fuel addition, the conformational motion of the two aromatic rings of both 4 and 5 mainly consists of a large amplitude torsional oscillation spanning about 260° and passing for the anti conformation (the two nitrogen atoms at opposite sides). Immediately after the addition of 12, due to the protonation of one nitrogen and consequent formation of an N-H···N intramolecular hydrogen bond, the torsional oscillation in both 4H⁺ and 5H⁺ is not only restricted to a smaller range (about 100°) but explores the previously forbidden conformational space around the syn conformation (the two nitrogen atoms at the same side). However, the new state is an out-of-equilibrium state since decarboxylation of the conjugate base of 12 takes place and, at the end of the process, the system reverts to the more conformationally mobile state.

Dissipative Systems Driven by the Decarboxylation of Activated Carboxylic Acids

ConspectusThe achievement of artificial systems capable of being maintained in out-of-equilibrium states featuring functional properties is a main goal of current chemical research. Absorption of electromagnetic radiation or consumption of a chemical species (a "chemical fuel") are the two strategies typically employed to reach such out-of-equilibrium states, which have to persist as long as one of the above stimuli is present. For this reason such systems are often referred to as "dissipative systems". In the simplest scheme, the dissipative system is initially found in a resting, equilibrium state. The addition of a chemical fuel causes the system to shift to an out-of-equilibrium state. When the fuel is exhausted, the system reverts to the initial, equilibrium state. Thus, from a mechanistic standpoint, the dissipative system turns out to be a catalyst for the fuel consumption. It has to be noted that, although very simple, this scheme implies the chance to temporally control the dissipative system. In principle, modulating the nature and/or the amount of the chemical fuel added, one can have full control of the time spent by the system in the out-of-equilibrium state.In 2016, we found that 2-cyano-2-phenylpropanoic acid (1a), whose decarboxylation proceeds smoothly under mild basic conditions, could be used as a chemical fuel to drive the back and forth motion of a catenane-based molecular switch. The acid donates a proton to the catenane that passes from the neutral state A to the transient protonated state B. Decarboxylation of the resulting carboxylate (1acb), generates a carbanion, which, being a strong base, retakes the proton from the protonated catenane that, consequently, returns to the initial state A. The larger the amount of the added fuel, the longer the time spent by the catenane in the transient, out-of-equilibrium state. Since then, acid 1a and other activated carboxylic acids (ACAs) have been used to drive the operation of a large number of dissipative systems based on the acid-base reaction, from molecular machines to host-guest systems, from catalysts to smart materials, and so on. This Account illustrates such systems with the purpose to show the wide applicability of ACAs as chemical fuels. This generality is due to the simplicity of the idea underlying the operation principle of ACAs, which always translates into simple experimental requirements.

Autonomous Non-Equilibrium Self-Assembly and Molecular Movements Powered by Electrical Energy

The ability to exploit energy autonomously is one of the hallmarks of life. Mastering such processes in artificial nanosystems can open technological opportunities. In the last decades, light- and chemically driven autonomous systems have been developed in relation to conformational motion and self-assembly, mostly in relation to molecular motors. In contrast, despite electrical energy being an attractive energy source to power nanosystems, its autonomous harnessing has received little attention. Herein we consider an operation mode that allows the autonomous exploitation of electrical energy by a self-assembling system. Threading and dethreading motions of a pseudorotaxane take place autonomously in solution, powered by the current flowing between the electrodes of a scanning electrochemical microscope. The underlying autonomous energy ratchet mechanism drives the self-assembly steps away from equilibrium with a higher energy efficiency compared to other autonomous systems. The strategy is general and might be extended to other redox-driven systems.

Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle

Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.

Dynamic Timing Control of Molecular Photoluminescent Systems

Dynamic control of molecular photoluminescence offers chemical solutions to designing functional emissive materials. Although stimuli-switchable molecular luminescent systems are well established, how to encode these dynamic emissive systems with a "timing" feature, that is, time-dependent luminescent properties, remains challenging. This Concept aims to summarize the design principles of dynamic timing molecular photoluminescent systems by discussing the state-of-the-art of this topic and the shaping of fabrication strategies at both the molecular and supramolecular levels. An outlook and perspectives are given to outline the future opportunities and challenges in the rational design and potential applications of these smart emissive systems.

Tuning the Force, Speed, and Efficiency of an Autonomous Chemically Fueled Information Ratchet

Autonomous chemically fueled molecular machines that function through information ratchet mechanisms underpin the nonequilibrium processes that sustain life. These biomolecular motors have evolved to be well-suited to the tasks they perform. Synthetic systems that function through similar mechanisms have recently been developed, and their minimalist structures enable the influence of structural changes on machine performance to be assessed. Here, we probe the effect of changes in the fuel and barrier-forming species on the nonequilibrium operation of a carbodiimide-fueled rotaxane-based information ratchet. We examine the machine’s ability to catalyze the fuel-to-waste reaction and harness energy from it to drive directional displacement of the macrocycle. These characteristics are intrinsically linked to the speed, force, power, and efficiency of the ratchet output. We find that, just as for biomolecular motors and macroscopic machinery, optimization of one feature (such as speed) can compromise other features (such as the force that can be generated by the ratchet). Balancing speed, power, efficiency, and directionality will likely prove important when developing artificial molecular motors for particular applications.

Controlling dynamics in extended molecular frameworks

Molecular machines are essential dynamic components for fuel production, cargo delivery, information storage and processing in living systems. Scientists have demonstrated that they can design and synthesize artificial molecular machines that operate efficiently in isolation - for example, at high dilution in solution - fuelled by chemicals, electricity or light. To organize the spatial arrangement and motion of these machines within close proximity to one another in solid frameworks, such that useful macroscopic work can be performed, remains a challenge in both chemical and materials science. In this Review, we summarize the progress that has been made during the past decade in organizing dynamic molecular entities in such solid frameworks. Emerging applications of these dynamic smart materials in the contexts of molecular recognition, optoelectronics, drug delivery, photodynamic therapy and water desalination are highlighted. Finally, we review recent work on a new non-equilibrium adsorption phenomenon for which we have coined the term mechanisorption. The ability to use external energy to drive directional processes in mechanized extended frameworks augurs well for the future development of artificial molecular factories.

Recent Advances in Fuel-Driven Molecular Switches and Machines

The molecular switches and machines arena has entered a new phase in which molecular machines operate under out-of-equilibrium conditions using appropriate fuel. Unlike the equilibrium version, the dissipative off-equilibrium machines necessitate only one stimulus input to complete each cycle and decrease chemical waste. Such a modus operandi would set significant steps towards mimicking the natural machines and may offer a platform for advancing new applications by providing temporal control. This review summarises the recent progress and blueprint of autonomous fuel-driven off-equilibrium molecular switches and machines.

Transamidation-Driven Molecular Pumps

We report a new class of synthetic molecular pumps that use a stepwise information ratchet mechanism to achieve the kinetic gating required to sequester their macrocyclic substrates from bulk solution. Threading occurs as a result of active template reactions between the pump terminus amine and an acyl electrophile, whereby the bond-forming reaction is accelerated through the cavity of a crown ether. Carboxylation of the resulting amide results in displacement of the ring to the collection region of the thread. Conversion of the carbamate to a phenolic ester provides an intermediate rotaxane suitable for further pumping cycles. In this way rings can be ratcheted onto a thread from one or both ends of appropriately designed molecular pumps. Each pumping cycle results in one additional ring being added to the thread per terminus acyl group. The absence of pseudorotaxane states ensures that no dethreading of intermediates occurs during the pump operation. This facilitates the loading of different macrocycles in any chosen sequence, illustrated by the pump-mediated synthesis of a [4]rotaxane containing three different macrocycles as a single sequence isomer. A [5]rotaxane synthesized using a dual-opening transamidation pump was structurally characterized by single-crystal X-ray diffraction, revealing a series of stabilizing CH···O interactions between the crown ethers and the polyethylene glycol catchment region of the thread.

A Ribonucleotide ↔ Phosphoramidate Reaction Network Optimized by Computer-Aided Design

A growing number of out-of-equilibrium systems have been created and investigated in chemical laboratories over the past decade. One way to achieve this is to create a reaction cycle, in which the forward reaction is driven by a chemical fuel and the backward reaction follows a different pathway. Such dissipative reaction networks are still relatively rare, however, and most non-enzymatic examples are based on the carbodiimide-driven generation of carboxylic acid anhydrides. In this work, we describe a dissipative reaction network that comprises the chemically fueled formation of phosphoramidates from natural ribonucleotides (e.g., GMP or AMP) and phosphoramidate hydrolysis as a mild backward reaction. Because the individual reactions are subject to a multitude of interconnected parameters, the software-assisted tool “Design of Experiments” (DoE) was a great asset for optimizing and understanding the network. One notable insight was the stark effect of the nucleophilic catalyst 1-ethylimidazole (EtIm) on the hydrolysis rate, which is reminiscent of the action of the histidine group in phosphoramidase enzymes (e.g., HINT1). We were also able to use the reaction cycle to generate transient self-assemblies, which were characterized by dynamic light scattering (DLS), confocal microscopy (CLSM), and cryogenic transmission electron microscopy (cryo-TEM). Because these compartments are based on prebiotically plausible building blocks, our findings may have relevance for origin-of-life scenarios.

Colossal Power Extraction from Active Cyclic Brownian Information Engines

Brownian information engines can extract work from thermal fluctuations by utilizing information. To date, the studies on Brownian information engines consider the system in a thermal bath; however, many processes in nature occur in a nonequilibrium setting, such as the suspensions of self-propelled microorganisms or cellular environments called an active bath. Here, we introduce an archetypal model for a Maxwell-demon type cyclic Brownian information engine operating in a Gaussian correlated active bath capable of extracting more work than its thermal counterpart. We obtain a general integral fluctuation theorem for the active engine that includes additional mutual information gained from the active bath with a unique effective temperature. This effective description modifies the generalized second law and provides a new upper bound for the extracted work. Unlike the passive information engine operating in a thermal bath, the active information engine extracts colossal power that peaks at the finite cycle period. Our study provides fundamental insights into the design and functioning of synthetic and biological submicrometer motors in active baths under measurement and feedback control.

Pumping between phases with a pulsed-fuel molecular ratchet

The sorption of species from a solution into and onto solids underpins the sequestering of waste and pollutants, precious metal recovery, heterogeneous catalysis, analysis and separation science, and other technologies^1,2. The transfer between phases tends to proceed spontaneously in the direction of equilibrium. For example, alkyl ammonium groups mounted on silica nanoparticles are used to chemisorb cucurbituril macrocycles from solution through host-guest binding^3,4. Molecular ratchet mechanisms^5-7, in which kinetic gating^8-12 inhibits or accelerates particular steps, makes it possible to progressively drive dynamic systems^13-16 away from equilibrium^17-21. Here we report on molecular pumps²² immobilized on polymer beads^23-25 that use an energy ratchet mechanism^{5,9,19-21,26-30} to directionally transport substrates from solution onto the beads. On the addition of trichloroacetic acid (CCl₃CO₂H)^19,31-33 fuel^19,34-37, micrometre-diameter polystyrene beads functionalized³⁸ with solvent-accessible molecular pumps sequester from the solution crown ethers appended with fluorescent tags. After fuel consumption, the rings are mechanically trapped in a higher-energy, out-of-equilibrium state on the beads and cannot be removed by dilution or exhaustive washing. This differs from dissipative assembled materials^11,13-16, which require a continuous supply of energy to persist, and from conventional host-guest complexes. The addition of a second fuel pulse causes the uptake of more macrocycles, which drives the system further away from equilibrium. The second macrocycle can be labelled with a different fluorescent tag, which confers sequence information³⁹ on the absorbed structure. The polymer-bound substrates can be released back to the bulk either one compartment at a time or all at once. Non-equilibrium⁴⁰ sorption by immobilized artificial molecular machines^41-45 enables the transduction of energy from chemical fuels for the use, storage and release of energy and information.

Chemical fuels for molecular machinery

Chemical reaction networks that transform out-of-equilibrium 'fuel' to 'waste' are the engines that power the biomolecular machinery of the cell. Inspired by such systems, autonomous artificial molecular machinery is being developed that functions by catalysing the decomposition of chemical fuels, exploiting kinetic asymmetry to harness energy released from the fuel-to-waste reaction to drive non-equilibrium structures and dynamics. Different aspects of chemical fuels profoundly influence their ability to power molecular machines. Here we consider the structure and properties of the fuels that biology has evolved and compare their features with those of the rudimentary synthetic chemical fuels that have so far been used to drive autonomous non-equilibrium molecular-level dynamics. We identify desirable, but context-specific, traits for chemical fuels together with challenges and opportunities for the design and invention of new chemical fuels to power synthetic molecular machinery and other dissipative nanoscale processes.

Through the Eyes of Creators: Observing Artificial Molecular Motors

Inspired by molecular motors in biology, there has been significant progress in building artificial molecular motors, using a number of quite distinct approaches. As the constructs become more sophisticated, there is also an increasing need to directly observe the motion of artificial motors at the nanoscale and to characterize their performance. Here, we review the most used methods that tackle those tasks. We aim to help experimentalists with an overview of the available tools used for different types of synthetic motors and to choose the method most suited for the size of a motor and the desired measurements, such as the generated force or distances in the moving system. Furthermore, for many envisioned applications of synthetic motors, it will be a requirement to guide and control directed motions. We therefore also provide a perspective on how motors can be observed on structures that allow for directional guidance, such as nanowires and microchannels. Thus, this Review facilitates the future research on synthetic molecular motors, where observations at a single-motor level and a detailed characterization of motion will promote applications.

Ring-Over-Ring Deslipping From Imine-Bridged Heterorotaxanes

Ring-over-ring slippage and ring-through-ring penetration are important processes in the construction of ring-in-ring multiple interlocked architectures. We have successfully observed “ring-over-ring deslipping” on the rotaxane axle by exploiting the dynamic covalent nature of imine bonds in imine-bridged heterorotaxanes R1 and R2 with two macrocycles of different ring sizes on the axle. When the imine bridges of R1 were cleaved, a hydrolyzed hetero[4]rotaxane [4]R1′ was formed as an intermediate under dynamic equilibrium, and the larger 38-membered macrocycle M was deslipped over the 24-membered ring (24C8 or DB24C8) to dissociate into a [3]rotaxane [3]R3 and a macrocycle M. The time dependent NMR measurement and the determined thermodynamic parameters revealed that the rate-limiting step of the deslipping process was attributed to steric hindrance between two rings and reduced mobility of M due to proximity to the crown ether, which was bound to the anilinium on the axle molecule.

Generic self-stabilization mechanism for biomolecular adhesions under load

Mechanical loading generally weakens adhesive structures and eventually leads to their rupture. However, biological systems can adapt to loads by strengthening adhesions, which is essential for maintaining the integrity of tissue and whole organisms. Inspired by cellular focal adhesions, we suggest here a generic, molecular mechanism that allows adhesion systems to harness applied loads for self-stabilization through adhesion growth. The mechanism is based on conformation changes of adhesion molecules that are dynamically exchanged with a reservoir. Tangential loading drives the occupation of some states out of equilibrium, which, for thermodynamic reasons, leads to association of further molecules with the cluster. Self-stabilization robustly increases adhesion lifetimes in broad parameter ranges. Unlike for catch-bonds, bond rupture rates can increase monotonically with force. The self-stabilization principle can be realized in many ways in complex adhesion-state networks; we show how it naturally occurs in cellular adhesions involving the adaptor proteins talin and vinculin.

Cellular adhesions have the remarkable property that they adapt their stability to the applied mechanical load. Here, authors describe a generic physical mechanism that explains self-stabilization of idealized adhesion systems under shear.

Autonomous fuelled directional rotation about a covalent single bond

Biology operates through autonomous chemically fuelled molecular machinery¹, including rotary motors such as adenosine triphosphate synthase² and the bacterial flagellar motor³. Chemists have long sought to create analogous molecular structures with chemically powered, directionally rotating, components^4-17. However, synthetic motor molecules capable of autonomous 360° directional rotation about a single bond have proved elusive, with previous designs lacking either autonomous fuelling^7,10,12 or directionality⁶. Here we show that 1-phenylpyrrole 2,2'-dicarboxylic acid^18,19 (1a) is a catalysis-driven^20,21 motor that can continuously transduce energy from a chemical fuel^9,20-27 to induce repetitive 360° directional rotation of the two aromatic rings around the covalent N-C bond that connects them. On treatment of 1a with a carbodiimide^21,25-27, intramolecular anhydride formation between the rings and the anhydride's hydrolysis both occur incessantly. Both reactions are kinetically gated^28-30 causing directional bias. Accordingly, catalysis of carbodiimide hydration by the motor molecule continuously drives net directional rotation around the N-C bond. The directionality is determined by the handedness of both an additive that accelerates anhydride hydrolysis and that of the fuel, and is easily reversed additive³¹. More than 97% of fuel molecules are consumed through the chemical engine cycle²⁴ with a directional bias of up to 71:29 with a chirality-matched fuel and additive. In other words, the motor makes a 'mistake' in direction every three to four turns. The 26-atom motor molecule's simplicity augurs well for its structural optimization and the development of derivatives that can be interfaced with other components for the performance of work and tasks^32-36.

Insights from an information thermodynamics analysis of a synthetic molecular motor

Information is physical, a realization that has transformed the physics of measurement and communication. However, the flow between information, energy and mechanics in chemical systems remains largely unexplored. Here we analyse a minimalist autonomous chemically driven molecular motor in terms of information thermodynamics, a framework that quantitatively relates information to other thermodynamic parameters. The treatment reveals how directional motion is generated by free energy transfer from chemical to mechanical (conformational and/or co-conformational) processes by 'energy flow' and 'information flow'. It provides a thermodynamic level of understanding of molecular motors that is general, complements previous analyses based on kinetics and has practical implications for machine design. In line with kinetic analysis, we find that power strokes do not affect the directionality of chemically driven machines. However, we find that power strokes can modulate motor velocity, the efficiency of free energy transfer and the number of fuel molecules consumed per cycle. This may help explain the role of such (co-)conformational changes in biomachines and illustrates the interplay between energy and information in chemical systems.

Controlling catalyst activity, chemoselectivity and stereoselectivity with the mechanical bond

Mechanically interlocked molecules, such as rotaxanes and catenanes, are receiving increased attention as scaffolds for the development of new catalysts, driven by both their increasing accessibility and high-profile examples of the mechanical bond delivering desirable behaviours and properties. In this Review, we survey recent advances in the catalytic applications of mechanically interlocked molecules organized by the effect of the mechanical bond on key catalytic properties, namely, activity, chemoselectivity and stereoselectivity, and focus on how the mechanically bonded structure leads to the observed behaviour. Our aim is to inspire future investigations of mechanically interlocked catalysts, including those outside of the supramolecular community.

Carbodiimide-fueled catalytic reaction cycles to regulate supramolecular processes

Using molecular self-assembly, supramolecular chemists can create Gigadalton-structures with angstrom precision held together by non-covalent interactions. However, despite relying on the same molecular toolbox for self-assembly, these synthetic structures lack the complexity and sophistication of biological assemblies. Those assemblies are non-equilibrium structures that rely on the constant consumption of energy transduced from the hydrolysis of chemical fuels like ATP and GTP, which endows them with dynamic properties, e.g., temporal and spatial control and self-healing ability. Thus, to synthesize life-like materials, we have to find a reaction cycle that converts chemical energy to regulate self-assembly. We and others recently found that this can be done by a reaction cycle that hydrates carbodiimides. This feature article aims to provide an overview of how the energy transduced from carbodiimide hydration can alter the function of molecules and regulate molecular assemblies. The goal is to offer the reader design considerations for carbodiimide-driven reaction cycles to create a desired morphology or function of the assembly and ultimately to push chemically fueled self-assembly further towards the bottom-up synthesis of life.

A light-gated regulation of the reaction site by a cucurbit[7]uril macrocycle

On–off competitive inhibition is presented. Photoswitchable pseudorotaxane controls the rate of self-reaction and product selectivity of external reactions.

Weinreb Amide, Ketone and Amine as Potential and Competitive Secondary Molecular Stations for Dibenzo-[24]Crown-8 in [2]Rotaxane Molecular Shuttles

This paper reports the synthesis and study of new pH-sensitive DB24C8-based [2]rotaxane molecular shuttles that contain within their axle four potential sites of interaction for the DB24C8: ammonium, amine, Weinreb amide, and ketone. In the protonated state, the DB24C8 lay around the best ammonium site. After either deprotonation or deprotonation-then-carbamoylation of the ammonium, different localizations of the DB24C8 were seen, depending on both the number and nature of the secondary stations and steric restriction. Unexpectedly, the results indicated that the Weinreb amide was not a proper secondary molecular station for the DB24C8. Nevertheless, through its methoxy side chain, it slowed down the shuttling of the macrocycle along the threaded axle, thereby partitioning the [2]rotaxane into two translational isomers on the NMR timescale. The ketone was successfully used as a secondary molecular station, and its weak affinity for the DB24C8 was similar to that of a secondary amine.

Chemical engines: driving systems away from equilibrium through catalyst reaction cycles

Biological systems exhibit a range of complex functions at the micro- and nanoscales under non-equilibrium conditions (for example, transportation and motility, temporal control, information processing and so on). Chemists also employ out-of-equilibrium systems, for example in kinetic selection during catalysis, self-replication, dissipative self-assembly and synthetic molecular machinery, and in the form of chemical oscillators. Key to non-equilibrium behaviour are the mechanisms through which systems are able to extract energy from the chemical reactants ('fuel') that drive such processes. In this Perspective we relate different examples of such powering mechanisms using a common conceptual framework. We discuss how reaction cycles can be coupled to other dynamic processes through positive (acceleration) or negative (inhibition) catalysis to provide the thermodynamic impetus for diverse non-equilibrium behaviour, in effect acting as a 'chemical engine'. We explore the way in which the energy released from reaction cycles is harnessed through kinetic selection in a series of what have sometimes been considered somewhat disparate fields (systems chemistry, molecular machinery, dissipative assembly and chemical oscillators), highlight common mechanistic principles and the potential for the synchronization of chemical reaction cycles, and identify future challenges for the invention and application of non-equilibrium systems. Explicit recognition of the use of fuelling reactions to power structural change in catalysts may stimulate the investigation of known catalytic cycles as potential elements for chemical engines, a currently unexplored area of catalysis research.

Substituent Effects on Transient, Carbodiimide-Induced Geometry Changes in Diphenic Acids

Nucleotide-induced conformational changes in motor proteins are key to many important cell functions. Inspired by this biological behavior, we report a simple chemically fueled system that exhibits carbodiimide-induced geometry changes. Bridging via transient anhydride formation leads to a significant reduction of the twist about the biaryl bond of substituted diphenic acids, giving a simple molecular clamp. The kinetics are well-described by a simple mechanism, allowing structure-property effects to be determined. The kinetic parameters can be used to derive important characteristics of the system such as the efficiencies (anhydride yields), maximum anhydride concentrations, and overall lifetimes. Transient diphenic anhydrides tolerate steric hindrance ortho to the biaryl bond but are significantly affected by electronic effects, with electron-deficient substituents giving lower yields, peak conversions, and lifetimes. The results provide useful guidelines for the design of functional systems incorporating diphenic acid units.

A catalysis-driven artificial molecular pump

All biological pumps are autonomous catalysts; they maintain the out-of-equilibrium conditions of the cell by harnessing the energy released from their catalytic decomposition of a chemical fuel^1-3. A number of artificial molecular pumps have been reported to date⁴, but they are all either fuelled by light^5-10 or require repetitive sequential additions of reagents or varying of an electric potential during each cycle to operate^11-16. Here we describe an autonomous chemically fuelled information ratchet^17-20 that in the presence of fuel continuously pumps crown ether macrocycles from bulk solution onto a molecular axle without the need for further intervention. The mechanism uses the position of a crown ether on an axle both to promote barrier attachment behind it upon threading and to suppress subsequent barrier removal until the ring has migrated to a catchment region. Tuning the dynamics of both processes^20,21 enables the molecular machine^22-25 to pump macrocycles continuously from their lowest energy state in bulk solution to a higher energy state on the axle. The ratchet action is experimentally demonstrated by the progressive pumping of up to three macrocycles onto the axle from bulk solution under conditions where barrier formation and removal occur continuously. The out-of-equilibrium [n]rotaxanes (characterized with n up to 4) are maintained for as long as unreacted fuel is present, after which the rings slowly de-thread. The use of catalysis to drive artificial molecular pumps opens up new opportunities, insights and research directions at the interface of catalysis and molecular machinery.

Molecular Pumps and Motors

Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.