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.

Control over Dethreading Kinetics Allows Evaluating the Entropy Stored in an Interlocked Molecular Machine Out-of-Equilibrium.

The operation of nanomachines is fundamentally different from that of their macroscopic counterparts. In particular, the role of solvent is critical yet rarely associated with machine functionality. Here, we study a minimal model of one of the most advanced molecular machines to gain control of its operation by engineering components and the employed solvent. Operation kinetics were changed over more than four orders of magnitude and could be modulated by solvent. Leveraging solvent properties, it was possible to monitor the relaxation of the molecular machine towards equilibrium and measure the heat exchanged in the process. Our work expands the capabilities of acid-base powered molecular machines, confirming experimentally that such systems have a dominant entropy content.

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.

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.

Transfer of Axial Chirality to the Nanoscale Endows Carbon Nanodots with Circularly Polarized Luminescence.

We report the synthesis, purification and characterization of chiral carbon nanodots starting from atropoisomeric precursors. The obtained atropoisomeric carbon nanodots are soluble in organic solvents and have good thermal stability, which are desirable features for technological applications. The synthetic protocol is robust, as it supports a number of variations in terms of molecular doping agents. Remarkably, the combination of axially chiral precursors and 1,4-benzoquinone as doping agent results in green-emissive carbon dots displaying circularly polarized luminescence. Dissymmetry factors of |3.5|×10-4 are obtained in solution, without the need of any additional element of chirality. Introducing axial chirality expands the strategies available to tailor the properties of carbon nanodots, paving the way for carbon nanoparticles that combine good processability in organic solvents with engineered advanced chiroptical properties.

Nuclear Magnetic Resonance Reveals Molecular Species in Carbon Nanodot Samples Disclosing Flaws.

Carbon nanodots are currently one of the hot topics in the nanomaterials world, due to their accessible synthesis and promising features. However, the purification of these materials is still a critical aspect, especially for syntheses involving molecular precursors. Indeed, the presence of unreacted species or small organic molecules formed during solvothermal treatments can affect the properties of the synthesized nanomaterials. To illustrate the extreme importance of this issue, we present two case studies in which insufficient purification results in misleading conclusions regarding the chiral and fluorescent properties of the investigated materials. Key to identify molecular species is the use of nuclear magnetic resonance, which proves to be an effective tool. Our work highlights the need to include nuclear magnetic resonance as a standard characterization technique for carbon-based nanomaterials, to minimize the risk of observing properties that arise from molecular species, rather than the target carbon nanodots.

Disulfide-Linked Allosteric Modulators for Multi-cycle Kinetic Control of DNA-Based Nanodevices.

Nature employs sulfur switches, that is, redox-active disulfides, to kinetically control biological pathways in a highly efficient and reversible way. Inspired by this mechanism, we describe herein a DNA-based synthetic nanodevice that acts as a sulfur switch and can be temporally controlled though redox regulation. To do this, we rationally designed disulfide DNA strands (modulators) that hybridize to a ligand-binding DNA nanodevice and act as redox-active allosteric regulators inducing the nanodevice to release or load its ligand. Upon reduction, the allosteric modulator spontaneously de-hybridizes from the nanodevice and, as a result, its effect is transient. The system is reversible and has an unprecedented high tolerance to waste products and displays transient behavior for over 40 cycles without significant loss of efficiency. Kinetic control of DNA-based ligand-binding nanodevices through purely chemical reactions paves the way for temporal regulation of more complex chemical pathways.

Individual-Molecule Perspective Analysis of Chemical Reaction Networks: The Case of a Light-Driven Supramolecular Pump.

The first study in which stochastic simulations of a two-component molecular machine are performed in the mass-action regime is presented. This system is an autonomous molecular pump consisting of a photoactive axle that creates a directed flow of rings through it by exploiting light energy away from equilibrium. The investigation demonstrates that the pump can operate in two regimes, both experimentally accessible, in which light-driven steps can be rate-determining or not. The number of photons exploited by an individual molecular pump, as well as the precision of cycling and the overall efficiency, critically rely on the operating regime of the machine. This approach provides useful information not only to guide the chemical design of a self-assembling molecular device with desired features, but also to elucidate the effect of the environment on its performance, thus facilitating its experimental investigation.

Fuel-Responsive Allosteric DNA-Based Aptamers for the Transient Release of ATP and Cocaine.

We show herein that allostery offers a key strategy for the design of out-of-equilibrium systems by engineering allosteric DNA-based nanodevices for the transient loading and release of small organic molecules. To demonstrate the generality of our approach, we used two model DNA-based aptamers that bind ATP and cocaine through a target-induced conformational change. We re-engineered these aptamers so that their affinity towards their specific target is controlled by a DNA sequence acting as an allosteric inhibitor. The use of an enzyme that specifically cleaves the inhibitor only when it is bound to the aptamer generates a transient allosteric control that leads to the release of ATP or cocaine from the aptamers. Our approach confirms that the programmability and predictability of nucleic acids make synthetic DNA/RNA the perfect candidate material to re-engineer synthetic receptors that can undergo chemical fuel-triggered release of small-molecule cargoes and to rationally design non-equilibrium systems.

Substrate-Induced Self-Assembly of Cooperative Catalysts.

Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.

Energy consumption in chemical fuel-driven self-assembly.

Nature extensively exploits high-energy transient self-assembly structures that are able to perform work through a dissipative process. Often, self-assembly relies on the use of molecules as fuel that is consumed to drive thermodynamically unfavourable reactions away from equilibrium. Implementing this kind of non-equilibrium self-assembly process in synthetic systems is bound to profoundly impact the fields of chemistry, materials science and synthetic biology, leading to innovative dissipative structures able to convert and store chemical energy. Yet, despite increasing efforts, the basic principles underlying chemical fuel-driven dissipative self-assembly are often overlooked, generating confusion around the meaning and definition of scientific terms, which does not favour progress in the field. The scope of this Perspective is to bring closer together current experimental approaches and conceptual frameworks. From our analysis it also emerges that chemically fuelled dissipative processes may have played a crucial role in evolutionary processes.

Electrochemically Triggered Co-Conformational Switching in a [2]catenane Comprising a Non-Symmetric Calix[6]arene Wheel and a Two-Station Oriented Macrocycle.

Catenanes with desymmetrized ring components can undergo co-conformational rearrangements upon external stimulation and can form the basis for the development of molecular rotary motors. We describe the design, synthesis and properties of a [2]catenane consisting of a macrocycle-the 'track' ring-endowed with two distinct recognition sites (a bipyridinium and an ammonium) for a calix[6]arene-the 'shuttle' ring. By exploiting the ability of the calixarene to thread appropriate non-symmetric axles with directional selectivity, we assembled an oriented pseudorotaxane and converted it into the corresponding oriented catenane by intramolecular ring closing metathesis. Cyclic voltammetric experiments indicate that the calixarene wheel initially surrounds the bipyridinium site, moves away from it when it is reduced, and returns in the original position upon reoxidation. A comparison with appropriate model compounds shows that the presence of the ammonium station is necessary for the calixarene to leave the reduced bipyridinium site.

Redox-Switchable Calix[6]arene-Based Isomeric Rotaxanes.

Operating molecular machines are based on switchable systems whose components can be set in motion in a controllable fashion. The presence of nonsymmetrical elements is a mandatory requirement to obtain and demonstrate the unidirectionality of motion. Calixarene-based macrocycles have proved to be very efficient hosts in the design of oriented rotaxanes and of pseudorotaxanes with strict control over the direction of complexation. A series of two-station rotaxanes based on bipyridinium-ammonium axles was synthesized and characterized. A recently reported supramolecularly assisted strategy for the synthesis of different orientational isomers was exploited, and the ammonium unit was identified as a proper secondary station for the calixarene. Displacement of the macrocycle was triggered by electrochemical reduction of the bipyridinium primary station, and it was shown that the shuttling is influenced both by the length of the chain of the axle component and by the position of the secondary station with respect to the calixarene rims.

Dissipative Synthetic DNA-Based Receptors for the Transient Loading and Release of Molecular Cargo.

Supramolecular chemistry is moving into a direction in which the composition of a chemical equilibrium is no longer determined by thermodynamics but by the efficiency with which kinetic states can be populated by energy consuming processes. Herein, we show that DNA is ideally suited for programming chemically fueled dissipative self-assembly processes. Advantages of the DNA-based systems presented in this study include a perfect control over the activation site for the chemical fuel in terms of selectivity and affinity, highly selective fuel consumption that occurs exclusively in the activated complex, and a high tolerance for the presence of waste products. Finally, it is shown that chemical fuels can be used to selectively activate different functions in a system of higher complexity embedded with multiple response pathways.

Synthesis of Densely Packaged, Ultrasmall Pt02 Clusters within a Thioether-Functionalized MOF: Catalytic Activity in Industrial Reactions at Low Temperature.

The gram-scale synthesis, stabilization, and characterization of well-defined ultrasmall subnanometric catalytic clusters on solids is a challenge. The chemical synthesis and X-ray snapshots of Pt02 clusters, homogenously distributed and densely packaged within the channels of a metal-organic framework, is presented. This hybrid material catalyzes efficiently, and even more importantly from an economic and environmental viewpoint, at low temperature (25 to 140 °C), energetically costly industrial reactions in the gas phase such as HCN production, CO2 methanation, and alkene hydrogenations. These results open the way for the design of precisely defined catalytically active ultrasmall metal clusters in solids for technically easier, cheaper, and dramatically less-dangerous industrial reactions.

Substrate-Induced Self-Assembly of Cooperative Catalysts.

Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.

Remote electrochemical modulation of pKa in a rotaxane by co-conformational allostery.

Allosteric control, one of Nature's most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pKa of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pKa to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron- and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.

Efficient active-template synthesis of calix[6]arene-based oriented pseudorotaxanes and rotaxanes.

A substrate can modify its chemical features, including a change of its reactivity, as a consequence of non-covalent interactions upon inclusion within a molecular host. Since the rise of supramolecular chemistry, this phenomenon has stimulated the ingenuity of scientists to emulate the function of enzymes by designing supramolecular systems in which the energetics and selectivity of reactions can be manipulated through programmed host-guest interactions and/or steric confinement. In this paper we investigate how the engulfment of a positively charged pyridinium-based guest inside the π-rich cavity of a tris-(N-phenylureido)calix[6]arene host affects its reactivity towards a SN2 reaction. We found that the alkylation of complexed substrates leads to the formation of pseudorotaxanes and rotaxanes with faster kinetics and higher yields with respect to the standard procedures exploited so far. More importantly, the strategy described here expands the range of efficient synthetic routes for the formation of mechanically interlocked species with a strict control of the mutual orientation of their non-symmetric molecular components.

Covalent capture of oriented calix[6]arene rotaxanes by a metal-free active template approach.

We describe the active template effect of a calix[6]arene host towards the alkylation of a complexed pyridylpyridinium guest. The acceleration of the reaction within the cavity is significant and rim-selective, enabling the efficient preparation of rotaxanes with full control of the mutual orientation of their nonsymmetric components.

Plugging a Bipyridinium Axle into Multichromophoric Calix[6]arene Wheels Bearing Naphthyl Units at Different Rims.

Tris-(N-phenylureido)-calix[6]arene derivatives are heteroditopic non-symmetric molecular hosts that can form pseudorotaxane complexes with 4,4'-bipyridinium-type guests. Owing to the unique structural features and recognition properties of the calix[6]arene wheel, these systems are of interest for the design and synthesis of novel molecular devices and machines. We envisaged that the incorporation of photoactive units in the calixarene skeleton could lead to the development of systems the working modes of which can be governed and monitored by means of light-activated processes. Here, we report on the synthesis, structural characterization, and spectroscopic, photophysical, and electrochemical investigation of two calix[6]arene wheels decorated with three naphthyl groups anchored to either the upper or lower rim of the phenylureido calixarene platform. We found that the naphthyl units interact mutually and with the calixarene skeleton in a different fashion in the two compounds, which thus exhibit a markedly distinct photophysical behavior. For both hosts, the inclusion of a 4,4'-bipyridinium guest activates energy- and/or electron-transfer processes that lead to non-trivial luminescence changes.