An artificial molecular machine that builds an asymmetric catalyst

Artificial Processive Catalytic Systems

Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).

Force-controlled release of small molecules with a rotaxane actuator

Force-controlled release of small molecules offers great promise for the delivery of drugs and the release of healing or reporting agents in a medical or materials context1-3. In polymer mechanochemistry, polymers are used as actuators to stretch mechanosensitive molecules (mechanophores)4. This technique has enabled the release of molecular cargo by rearrangement, as a direct5,6 or indirect7-10 consequence of bond scission in a mechanophore, or by dissociation of cage11, supramolecular12 or metal complexes13,14, and even by 'flex activation'15,16. However, the systems described so far are limited in the diversity and/or quantity of the molecules released per stretching event1,2. This is due to the difficulty in iteratively activating scissile mechanophores, as the actuating polymers will dissociate after the first activation. Physical encapsulation strategies can be used to deliver a larger cargo load, but these are often subject to non-specific (that is, non-mechanical) release3. Here we show that a rotaxane (an interlocked molecule in which a macrocycle is trapped on a stoppered axle) acts as an efficient actuator to trigger the release of cargo molecules appended to its axle. The release of up to five cargo molecules per rotaxane actuator was demonstrated in solution, by ultrasonication, and in bulk, by compression, achieving a release efficiency of up to 71% and 30%, respectively, which places this rotaxane device among the most efficient release systems achieved so far1. We also demonstrate the release of three representative functional molecules (a drug, a fluorescent tag and an organocatalyst), and we anticipate that a large variety of cargo molecules could be released with this device. This rotaxane actuator provides a versatile platform for various force-controlled release applications.

Transient control of lytic activity via a non-equilibrium chemical reaction system

The development of artificial non-equilibrium chemical reaction systems has recently attracted considerable attention as a new type of biomimetic. However, due to the lack of bioorthogonality, such reaction systems could not be linked to the regulation of any biological phenomena. Here, we have newly designed a non-equilibrium reaction system based on olefin metathesis to produce the Triton X-mimetic non-ionic amphiphile as a kinetic product. Using phospholipid vesicles encapsulating fluorescent dyes and red blood cells as cell models, we demonstrate that the developed chemical reaction system is applicable for transient control of the resulting lytic activity.

Stimuli-responsive synthetic helical polymers

Synthetic dynamic helical polymers (supramolecular and covalent) and foldamers share the helix as a structural motif. Although the materials are different, these systems also share many structural properties, such as helix induction or conformational communication mechanisms. The introduction of stimuli responsive building blocks or monomer repeating units in these materials triggers conformational or structural changes, due to the presence/absence of the external stimulus, which are transmitted to the helix resulting in different effects, such as assymetry amplification, helix inversion or even changes in the helical scaffold (elongation, J/H helical aggregates). In this review, we show through selected examples how different stimuli (e.g., temperature, solvents, cations, anions, redox, chiral additives, pH or light) can alter the helical structures of dynamic helical polymers (covalent and supramolecular) and foldamers acting on the conformational composition or molecular structure of their components, which is also transmitted to the macromolecular helical structure.

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.

Enzyme-Driven, Switchable Catalysis Based on Dynamic Self-Assembly of Peptides

Covalent regulatory systems of enzymes are widely used to modulate biological enzyme activities. Inspired by the regulation of reactive-site phosphorylation in organisms, we developed peptide-based catecholase mimetics with switchable catalytic activity and high selectivity through the co-assembly of nanofibers comprising peptides and copper ions (Cu2+ ). Through careful design and modification of the peptide backbone structure based on the change in the free energy of the system, we identified the peptide with the most effective reversible catalytic activity. Kinase/phosphatase switches were used to control the reversible transition of nanofiber formation and depolymerization, as well as to modulate the active-site microenvironment. Notably, the self-assembly and disassembly processes of nanofibers were simulated using coarse-grained molecular dynamics. Furthermore, theoretical calculations confirmed the coordination of the peptide and Cu2+ , forming a zipper-like four-ligand structure at the catalytically active center of the nanofibers. Additionally, we conducted a comprehensive analysis of the catalytic mechanism. This study opens novel avenues for designing biomimetic enzymes with ordered structures and dynamic catalytic activities.

Main Group Molecular Switches with Swivel Bifurcated to Trifurcated Hydrogen Bond Mode of Action

Artificial molecular machines have captured the full attention of the scientific community since Jean-Pierre Sauvage, Fraser Stoddart, and Ben Feringa were awarded the 2016 Nobel Prize in Chemistry. The past and current developments in molecular machinery (rotaxanes, rotors, and switches) primarily rely on organic-based compounds as molecular building blocks for their assembly and future development. In contrast, the main group chemical space has not been traditionally part of the molecular machine domain. The oxidation states and valency ranges within the p-block provide a tremendous wealth of structures with various chemical properties. Such chemical diversity─when implemented in molecular machines─could become a transformative force in the field. Within this context, we have rationally designed a series of NH-bridged acyclic dimeric cyclodiphosphazane species, [(μ-NH){PE(μ-N^tBu)₂PE(NH^tBu)}₂] (E = O and S), bis-P^V₂N₂, displaying bimodal bifurcated R²₁(8) and trifurcated R³₁(8,8) hydrogen bonding motifs. The reported species reversibly switch their topological arrangement in the presence and absence of anions. Our results underscore these species as versatile building blocks for molecular machines and switches, as well as supramolecular chemistry and crystal engineering based on cyclophosphazane frameworks.

Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions

As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

An Inbuilt Electronic Pawl Gates Orbital Information Processing and Controls the Rotation of a Double Ratchet Rotary Motor

A direct external input energy source (e.g., light, chemical reaction, redox potential, etc.) is compulsory to supply energy to rotary motors for accomplishing rotation around the axis. The stator leads the direction of rotation, and a sustainable rotation requires two mutual input energy supplies (e.g., light and heat, light and pH or metal ion, etc.); however, there are some exceptions (e.g., covalent single bond rotors and/or motors). On the contrary, our experiment suggested that double ratchet rotary motors (DRMs) can harvest power from available thermal noise, kT, for sustainable rotation around the axis. Under a scanning tunneling microscope, we have imaged live thermal noise movement as a dynamic orbital density and resolved the density diagram up to the second derivative. A second input energy can synchronize multiple rotors to afford a measurable output. Therefore, we hypothesized that rotation control in a DRM must be evolved from an orbital-level information transport channel between the two coupled rotors but was not limited to the second input energy. A DRM comprises a Brownian rotor and a power stroke rotor coupled to a -C≡C- stator, where the transport of information through coupled orbitals between the two rotors is termed the vibrational information flow chain (VIFC). We test this hypothesis by studying the DRM's density functional theory calculation and variable-temperature ¹H nuclear magnetic resonance. Additionally, we introduced inbuilt pawl-like functional moieties into a DRM to create different electronic environments by changing proton intercalation interactions, which gated information processing through the VIFC. The results show the VIFC can critically impact the motor's noise harvesting, resulting in variable rotational motions in DRMs.

A tape-reading molecular ratchet

Cells process information in a manner reminiscent of a Turing machine¹, autonomously reading data from molecular tapes and translating it into outputs^2,3. Randomly processive macrocyclic catalysts that can derivatise threaded polymers have been described^4,5, as have rotaxanes that transfer building blocks in sequence from a molecular strand to a growing oligomer^6-10. However, synthetic small-molecule machines that can read and/or write information stored on artificial molecular tapes remain elusive^11-13. Here we report on a molecular ratchet in which a crown ether (the 'reading head') is pumped from solution onto an encoded molecular strand (the 'tape') by a pulse^14,15 of chemical fuel¹⁶. Further fuel pulses transport the macrocycle through a series of compartments of the tape via an energy ratchet^14,17-22 mechanism, before releasing it back to bulk off the other end of the strand. During its directional transport, the crown ether changes conformation according to the stereochemistry of binding sites along the way. This allows the sequence of stereochemical information programmed into the tape to be read out as a string of digits in a non-destructive manner through a changing circular dichroism response. The concept is exemplified by the reading of molecular tapes with strings of balanced ternary digits ('trits'²³), -1,0,+1 and -1,0,-1. The small-molecule ratchet is a finite-state automaton: a special case²⁴ of a Turing machine that moves in one direction through a string-encoded state sequence, giving outputs dependent on the occupied machine state^25,26. It opens the way for the reading-and ultimately writing-of information using the powered directional movement of artificial nanomachines along molecular tapes.

A Light-Driven Molecular Machine Controls K+ Channel Transport and Induces Cancer Cell Apoptosis

The design of artificial ion channels with high activity, selectivity and gating function is challenging. Herein, we designed the light-driven motor molecule MC2, which provides new design criteria to overcome these challenges. MC2 forms a selective K⁺ channel through a single molecular transmembrane mechanism, and the light-driven rotary motion significantly accelerates ion transport, which endows the irradiated motor molecule with excellent cytotoxicity and cancer cell selectivity. Mechanistic studies reveal that the rotary motion of MC2 promotes K⁺ efflux, generates reactive oxygen species and eventually activates caspase-3-dependent apoptosis in cancer cells. Combined with the spatiotemporally controllable advantages of light, we believe this strategy can be exploited in the structural design and application of next-generation synthetic cation transporters for the treatment of cancer and other diseases.

Highly Sterically Hindered Peptide Bond Formation between α,α-Disubstituted α-Amino Acids and N-Alkyl Cysteines Using α,α-Disubstituted α-Amidonitrile

Peptides and proteins attract enormous attention in many fields of academia and industry. The introduction of unusual amino acids such as α,α-disubstituted α-amino acids or N-alkyl α-amino acids into normal peptide backbones is a well-utilized and useful tool for the modification of properties such as conformation, biological activity, and pharmacological profile. Despite the significant interest in sterically hindered peptides, research on peptides bearing an amide bond between an α,α-disubstituted α-amino acid and an N-alkyl α-amino acid remains underexplored because of the lack of an efficient synthetic approach. Herein, we describe a high-yielding synthetic method to access such extremely sterically hindered peptide bonds between amino acids. The reaction takes place between a peptide with an α,α-disubstituted α-amidonitrile and a second peptide bearing an N-alkyl cysteine, without a coupling reagent.

Partitional Behavior of Janus Dumbbell Microparticles in a Polyethylene Glycol (PEG)-Dextran (DEX) Aqueous Two-Phase System (ATPS)

Janus particles are known to be useful to various fields such as biomolecule-probing sensors, reaction catalysts, surfactants, and so on. They have two chemically different surfaces which possess contradictory characteristics such as polarity, hydrophobicity, etc. Here, a simple fabrication of dumbbell-shaped Janus microparticles was tested by the chemical reaction of carboxyl groups and amino groups to form amide bonds. They were distributed to the interface between polyethylene glycol (PEG)-rich phase and dextran (DEX)-rich phase, while the unreacted particles having carboxyl groups located at the top PEG-rich phase and particles having amine ligands went to the bottom DEX-rich phase of an aqueous two-phase system (ATPS). The fabrication procedures, observations, and possible applications of results are discussed.

The Mechanistic Integration and Thermodynamic Optimality of a Nanomotor

The performance of artificial nanomotors is still far behind nature-made biomolecular motors. A mechanistic disparity between the two categories exists: artificial motors often rely on a single mechanism to rectify directional motion, but biomotors integrate multiple mechanisms for better performance. This study proposes a design for a motor-track system and shows that by introducing asymmetric compound foot-track interactions, both selective foot detachment and biased foot-track binding arise from the mechanics of the system. The two mechanisms are naturally integrated to promote the motility of the motor towards being unidirectional, while each mechanism alone only achieves 50% directional fidelity at most. Based on a reported theory, the optimization of the motor is conducted via maximizing the directional fidelity. Along the optimization, the directional fidelity of the motor is raised by parameters that concentrate more energy on driving selective-foot detachment and biased binding, which in turn promotes work production due to the two energies converting to work via a load attached. However, the speed of the motor can drop significantly after the optimization because of energetic competition between speed and directional fidelity, which causes a speed-directional fidelity tradeoff. As a case study, these results test thermodynamic correlation between the performances of a motor and suggest that directional fidelity is an important quantity for motor optimization.

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.

Porous materials formed by four self-construction processes

Multiple self-construction behavior of cyclic oligoesters is described.

Macrocyclic host molecules with aromatic building blocks: the state of the art and progress

Macrocyclic host molecules play the central role in host-guest chemistry and supramolecular chemistry. The highly structural symmetry of macrocyclic host molecules can meet people's pursuit of aesthetics in molecular design, and generally means a balance of design, synthesis, properties and applications. For macrocyclic host molecules with highly symmetrical structures, building blocks, which could be described as repeat units as well, are the most fundamental elements for molecular design. The structural features and recognition ability of macrocyclic host molecules are determined by the building blocks and their connection patterns. Using different building blocks, different macrocyclic host molecules could be designed and synthesized. With decades of developments of host-guest chemistry and supramolecular chemistry, diverse macrocyclic host molecules with different building blocks have been designed and synthesized. Aromatic building blocks are a big family among the various building blocks used in constructing macrocyclic host molecules. In this feature article, the recent developments of macrocyclic host molecules with aromatic building blocks were summarized and discussed.

Post-Synthetic Macrocyclization of Rotaxane Building Blocks

Although not often encountered, cyclic interlocked molecules are appealing molecular targets because of their restrained tridimensional structure which is related to both the cyclic and interlocked shapes. Interlocked molecules such as rotaxane building blocks may be good candidates for post-synthetic intramolecular cyclization if the preservation of the mechanical bond ensures the interlocked architecture throughout the reaction. This is obviously the case if the modification does not involve the cleavage of either the macrocycle's main chain or the encircled part of the axle. However, among the post-synthetic reactions, the chemical linkage between two reactive sites belonging to embedded elements of rotaxanes still consists of an underexploited route to interlocked cyclic molecules. This Review lists the rare examples of macrocyclization through chemical connection between reactive sites belonging to a surrounding macrocycle and/or an encircled axle of interlocked rotaxanes.

Robotic end-to-end fusion of microtubules powered by kinesin

The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing the potential energy surface along the reaction coordinate, molecular machines expend energy to accelerate a reaction relative to the baseline provided by thermal motion and forces. Here, we design a nanorobotics system to accelerate end-to-end microtubule assembly by using kinesin motors and a circular confining chamber. We show that the mechanical interaction of kinesin-propelled microtubules gliding on a surface with the walls of the confining chamber results in a nonequilibrium distribution of microtubules, which increases the number of end-to-end microtubule fusion events 20-fold compared with microtubules gliding on a plane. In contrast to earlier nanorobots, where a nonequilibrium distribution was built into the initial state and drove the process, our nanorobotic system creates and actively maintains the building blocks in the concentrated state responsible for accelerated assembly through the adenosine triphosphate–fueled generation of force by kinesin-1 motor proteins. This approach can be used in the future to develop biohybrid or bioinspired nanorobots that use molecular machines to access nonequilibrium states and accelerate nanoscale assembly.

Self-Assembly of Stimuli-Responsive [2]Rotaxanes by Amidinium Exchange

Advances in supramolecular chemistry are often underpinned by the development of fundamental building blocks and methods enabling their interconversion. In this work, we report the use of an underexplored dynamic covalent reaction for the synthesis of stimuli-responsive [2]rotaxanes. The formamidinium moiety lies at the heart of these mechanically interlocked architectures, because it enables both dynamic covalent exchange and the binding of simple crown ethers. We demonstrated that the rotaxane self-assembly follows a unique reaction pathway and that the complex interplay between crown ether and thread can be controlled in a transient fashion by addition of base and fuel acid. Dynamic combinatorial libraries, when exposed to diverse nucleophiles, revealed a profound stabilizing effect of the mechanical bond as well as intriguing reactivity differences between seemingly similar [2]rotaxanes.

Boosting Photoacoustic Effect via Intramolecular Motions Amplifying Thermal-to-Acoustic Conversion Efficiency for Adaptive Image-Guided Cancer Surgery

Photoacoustic (PA) imaging emerges as a promising technique for biomedical applications. The development of new strategies to boost PA conversion without depressing other properties (e.g., fluorescence) is highly desirable for multifunctional imaging but difficult to realize. Here, we report a new phenomenon that active intramolecular motions could promote PA signal by specifically increasing thermal-to-acoustic conversion efficiency. The compound with intense intramolecular motion exhibits amplified PA signal by elevating thermal-to-acoustic conversion, and the fluorescence also increases due to aggregation-induced emission signature. The simultaneously high PA and fluorescence brightness of TPA-TQ3 NPs enable precise image-guided surgery. The preoperative fluorescence and PA imaging are capable of locating orthotopic breast tumor in a high-contrast manner, and the intraoperative fluorescence imaging delineates tiny residual tumors. This study highlights a new design guideline of intramolecular motion amplifying PA effect.

Stereodynamics of E/Z isomerization in rotaxanes through mechanical shuttling and covalent bond rotation

The mechanical bond has opened a new world for structural and dynamic stereochemistry, which is still largely underexplored and whose significance for various applications is becoming increasingly evident. We demonstrate that designed rearrangements involving both covalent and mechanical bonds can be integrated in [2]rotaxanes, leading to interesting consequences in terms of E/Z isomerization mechanisms. Two entirely distinct and concomitant stereomutations, pertaining to the same stereogenic element but involving different kinds of linkages within the molecule, are observed and are thoroughly characterized. The rate of the two processes is affected in opposite ways upon changing solvent polarity; such a phenomenon can be used to selectively modify the rate of each motion and adjust the relative contribution of the two mechanisms to the isomerization. Although the movements are not synchronized, an analysis of the intriguing fundamental implications for transition state theory, reaction pathway bifurcation, and microscopic reversibility was triggered by our experimental observations.

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Rotaxanes that display E/Z stereoisomerism depending on the ring position

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Co-existence of two different stereomutations that yield the same product

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Mutual influence and opposite solvent dependence of the two dynamic processes

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Fundamental implications for microscopic reversibility and chemical equilibrium

The concurrence and interplay of different movements of molecular components within the same structure play a key role in providing function to naturally occurring molecular machines. Despite the progress made on artificial counterparts, the construction of molecular systems, where two (or more) motions are integrated together to produce an outcome, is still in its infancy. Molecules called rotaxanes, obtained by interlocking a ring with a dumbbell-shaped axle, are an appealing yet underexplored platform for this purpose. Here, we describe rotaxanes where two coexisting and radically different processes—rotation about a covalent bond and translation of the ring along the axle—lead to the same change in the overall molecular shape. These results are significant not only to improve our fundamental understanding of the way molecular components move but also to develop sophisticated artificial nanomachines capable of transforming or transmitting motion.

Evolution of catalytic machinery: three-component nanorotor catalyzes formation of four-component catalytic machinery

The three-component nanorotor [Cu2(S)(R)]2+ (k298 = 46.0 kHz) that is a catalyst for a CuAAC reaction binds the click product at each of its copper centers thereby creating a new platform and a dynamic slider-on-deck system. Due to this sliding motion (k298 = 65.0 kHz) the zinc-porphyrin bound N-methylpyrrolidine is efficiently released into solution and catalyzes a follow-up Michael addition.

Chemically Induced Mismatch of Rings and Stations in [3]Rotaxanes

The mechanical interlocking of molecular components can lead to the appearance of novel and unconventional properties and processes, with potential relevance for applications in nanoscience, sensing, catalysis, and materials science. We describe a [3]rotaxane in which the number of recognition sites available on the axle component can be changed by acid–base inputs, encompassing cases in which this number is larger, equal to, or smaller than the number of interlocked macrocycles. These species exhibit very different properties and give rise to a unique network of acid–base reactions that leads to a fine pK_a tuning of chemically equivalent acidic sites. The rotaxane where only one station is available for two rings exhibits a rich coconformational dynamics, unveiled by an integrated experimental and computational approach. In this compound, the two crown ethers compete for the sole recognition site, but can also come together to share it, driven by the need to minimize free energy without evident inter-ring interactions.

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.

Sequence-Selective Decapeptide Synthesis by the Parallel Operation of Two Artificial Molecular Machines

We report on the preparation of a decapeptide through the parallel operation of two rotaxane-based molecular machines. The synthesis proceeds in four stages: (1) simultaneous operation of two molecular peptide synthesizers in the same reaction vessel; (2) selective residue activation of short-oligomer intermediates; (3) ligation; (4) product release. Key features of the machine design include the following: (a) selective transformation of a thioproline building block to a cysteine (once it has been incorporated into a hexapeptide intermediate by one molecular machine); (b) a macrocycle-peptide hydrazine linkage (as part of the second machine) to differentiate the intermediates and enable their directional ligation; and (c) incorporation of a Glu residue in the assembly module of one machine to enable release of the final product while simultaneously removing part of the assembly machinery from the product. The two molecular machines participate in the synthesis of a product that is beyond the capability of individual small-molecule machines, in a manner reminiscent of the ligation and post-translational modification of proteins in biology.

Functional Rotaxanes in Catalysis

Mechanically interlocked molecules (MIMs) have gained attention in the field of catalysis due to their unique molecular properties. Central to MIMs, rotaxanes are highly promising and attractive supramolecular catalysts due to their unique three-dimensional structures and the flexibility of their subcomponents. This Minireview discusses the use of rotaxanes in organocatalysis and transition-metal catalysis.

Taming the dynamics in a pharmaceutical by cocrystallization: investigating the impact of the coformer by solid-state NMR

The anti-HIV pharmaceutical efavirenz is highly dynamic in its crystalline state, and we show that these dynamics can be tamed through the introduction of a coformer.

Templated approach to well-defined, oxidatively coupled conjugated polymers

Templated oxidative polymerization affords organic soluble, oxidatively doped PEDOT-based polymers with controlled molecular weights and low dispersities (Đ ∼ 1.2) for the first time.

Synthetic platform for mono-functionalised tridentate macrocycles as key precursors of mechanically-linked macromolecular systems

Macrocycles bearing a variety of functional groups give access to a wide range of synthetic methods for further derivatisation or preparation of more complex structures such as mechanically interlocked molecules or polymeric materials.

Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms

Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.

Molecular assemblers: molecular machines performing chemical synthesis

Molecular assemblers were proposed by K. Eric Drexler in 1986, based on the ideas of R. Feynman. In his (quite lurid) book "Engines of Creation: The Coming Era of Nanotechnology" and follow-up publications Drexler proposes molecular machines capable of positioning reactive molecules with atomic precision and to build larger, more sophisticated structures via mechanosynthesis. These imaginative visions started a hot controversy. The debate culminated in a cover story of Chemical & Engineering News in 2003 (ref. 1) with the key question: "Are molecular assemblers - devices capable of positioning atoms and molecules for precisely defined reactions - possible?" with Drexler as the proponent and Nobelist Richard E. Smalley being the opponent. Smalley raised two major objections: the "fat fingers" and the "sticky fingers" problem. To grab and guide each individual atom the assembler must have many nano-fingers. Smalley argued that there is just not enough room in the nanometer-sized reaction region to accommodate all the fingers of all the manipulators necessary to have complete control of the chemistry. The sticky finger issue arises from the problem that …"the atoms of the manipulator hands will adhere to the atom that is being moved. So it will often be impossible to release the building block in precisely the right spot." Smalley concludes that the fat and the sticky finger problems are fundamental and cannot be avoided. While some of the statements of E. Drexler are bold and probably not very realistic, his ideas are inspiring and might be a good starting point to assess on how far laboratory chemistry has advanced towards real "molecular assemblers" within the last two decades.

Electrochemical Switching of a Fluorescent Molecular Rotor Embedded within a Bistable Rotaxane

We report how the nanoconfined environment, introduced by the mechanical bonds within an electrochemically switchable bistable [2]rotaxane, controls the rotation of a fluorescent molecular rotor, namely, an 8-phenyl-substituted boron dipyrromethene (BODIPY). The electrochemical switching of the bistable [2]rotaxane induces changes in the ground-state coconformation and in the corresponding excited-state properties of the BODIPY rotor. In the starting redox state, when no external potential is applied, the cyclobis(paraquat-p-phenylene) (CBPQT⁴⁺) ring component encircles the tetrathiafulvalene (TTF) unit on the dumbbell component, leaving the BODIPY rotor unhindered and exhibiting low fluorescence. Upon oxidation of the TTF unit to a TTF²⁺ dication, the CBPQT⁴⁺ ring is forced toward the molecular rotor, leading to an increased energy barrier for the excited state to rotate the rotor into the state with a high nonradiative rate constant, resulting in an overall 3.4-fold fluorescence enhancement. On the other hand, when the solvent polarity is high enough to stabilize the excited charge-transfer state between the BODIPY rotor and the CBPQT⁴⁺ ring, movement of the ring toward the BODIPY rotor produces an unexpectedly strong fluorescence signal decrease as the result of photoinduced electron transfer from the BODIPY rotor to the CBPQT⁴⁺ ring. The nanoconfinement effect introduced by mechanical bonding can effectively lead to modulation of the physicochemical properties as observed in this bistable [2]rotaxane. On account of the straightforward synthetic strategy and the facile modulation of switchable electrochromic behavior, our approach could pave the way for the development of new stimuli-responsive materials based on mechanically interlocked molecules for future electro-optical applications, such as sensors, molecular memories, and molecular logic gates.

The shuttling mechanism of foldaxanes: more than just translocation and rotation

Tailoring the structures of nanomachines to achieve specific functions is one of the major challenges in chemistry. Disentangling the different movements of nanomachines is critical to characterize their functions. Here, the motions within one kind of molecular machine, a foldaxane, composed of a foldamer with a spring-like conformation on an axle have been examined at the molecular level. With the aid of molecular dynamics simulations and enhanced sampling methods, the free-energy landscape characterizing the shuttling of the foldaxane has been drawn. The calculated free-energy barrier, amounting to 20.7 kcal mol^-1, is in good agreement with experiments. Further analysis reveals that the predominant contribution to the free-energy barrier stems from the disruption of the hydrogen bonds between the foldamer and the thread. In the absence of hydrogen bonding interactions between the terminals of the foldamer and the thread, shrinkage and swelling movements of the foldamer have been identified and investigated in detail. By deciphering the intricate mechanism of how the foldaxane shuttles, our understanding of motions within molecular machines is expected to be improved, which will, in turn, assist the construction of molecular machines with specific functions.