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

Active template synthesis

The active template synthesis of mechanically interlocked molecular architectures exploits the dual ability of various structural elements (metals or, in the case of metal-free active template synthesis, particular arrangements of functional groups) to serve as both a template for the organisation of building blocks and as a catalyst to facilitate the formation of covalent bonds between them. This enables the entwined or threaded intermediate structure to be covalently captured under kinetic control. Unlike classical passive template synthesis, the intercomponent interactions transiently used to promote the assembly typically do not 'live on' in the interlocked product, meaning that active template synthesis can be traceless and used for constructing mechanically interlocked molecules that do not feature strong binding interactions between the components. Since its introduction in 2006, active template synthesis has been used to prepare a variety of rotaxanes, catenanes and knots. Amongst the metal-ion-mediated versions of the strategy, the copper(I)-catalysed alkyne-azide cycloaddition (CuAAC) remains the most extensively used transformation, although a broad range of other catalytic reactions and transition metals also provide effective manifolds. In metal-free active template synthesis, the recent discovery of the acceleration of the reaction of primary amines with electrophiles through the cavity of crown ethers has proved effective for forming an array of rotaxanes without recognition elements, including compact rotaxane superbases, dissipatively assembled rotaxanes and molecular pumps. This Review details the active template concept, outlines its advantages and limitations for the synthesis of interlocked molecules, and charts the diverse set of reactions that have been used with this strategy to date. The application of active template synthesis in various domains is discussed, including molecular machinery, mechanical chirality, catalysis, molecular recognition and various aspects of materials science.

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).

Foldaxane-Based Switchable [c2]Daisy Chains

Artificial molecular muscles are highly attractive in the field of molecular machinery due to their unique properties of contraction and stretching motion. However, the synthesis of molecular muscles poses formidable challenges as it is hindered by undesirable yields and poor selectivity. Herein, we present a procedure for the dynamic assembly of foldaxane-based [c2]daisy chains, wherein the hermaphroditic sequences consisting of aromatic helices and peptide rods are interlocked through inter-strand hydrogen-bonding interactions. The binding complementarity facilitates a selective and efficient assembly of [c2]daisy chain structures, inhibiting the creation of by-products. Introducing multiple recognition sites confers the system with contraction and stretching motion actuated by chemical stimuli. The rate of this muscle-like motion is calculated to be 0.8 s-1, which is 107 times faster than that of complex dissociation.

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.

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.

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.

Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics

Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.

A light-operated integrated DNA walker-origami system beyond bridge burning

Integrating rationally designed DNA molecular walkers and DNA origami platforms is a promising route towards advanced nano-robotics of diverse functions. Unleashing the full potential in this direction requires DNA walker-origami systems beyond the present simplistic bridge-burning designs for automated repeatable operation and scalable nano-robotic functions. Here we report such a DNA walker-origami system integrating an advanced light-powered DNA bipedal walker and a ∼170 nm-long rod-like DNA origami platform. This light-powered walker is fully qualified as a genuine translational molecular motor, and relies entirely on pure mechanical effects that are complicated by the origami surface but must be preserved for the walker's proper operation. This is made possible by tailor-designing the origami for optimal match with the walker to best preserve its core mechanics. A new fluorescence method is combined with site-controlled motility experiments to yield distinct and reliable signals for the walker's self-directed and processive motion despite origami-complicated fluorophore emission. The resultant integrated DNA walker-origami system provides a 'seed' system for future development of advanced light-powered DNA nano-robots (e.g., for scalable walker-automated chemical synthesis), and also truly bio-mimicking nano-muscles powered by genuine artificial translational molecular motors.

Molecular Machines and Microrobots: Nanoarchitectonics Developments and On-Water Performances

This review will focus on micromachines and microrobots, which are objects at the micro-level with similar machine functions, as well as nano-level objects such as molecular machines and nanomachines. The paper will initially review recent examples of molecular machines and microrobots that are not limited to interfaces, noting the diversity of their functions. Next, examples of molecular machines and micromachines/micro-robots functioning at the air-water interface will be discussed. The behaviors of molecular machines are influenced significantly by the specific characteristics of the air-water interface. By placing molecular machines at the air-water interface, the scientific horizon and depth of molecular machine research will increase dramatically. On the other hand, for microrobotics, more practical and advanced systems have been reported, such as the development of microrobots and microswimmers for environmental remediations and biomedical applications. The research currently being conducted on the surface of water may provide significant basic knowledge for future practical uses of molecular machines and microrobots.

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.

Nano-Hybrid Au@LCCs Systems Displaying Anti-Inflammatory Activity

Gold nanoparticles (Au NPs) have received great attention owing to their biocompatible nature, environmental, and widespread biomedical applications. Au NPs are known as capable to regulate inflammatory responses in several tissues and organs; interestingly, lower toxicity in conjunction with anti-inflammatory effects was reported to occur with Au NPs treatment. Several variables drive this benefit-risk balance, including Au NPs physicochemical properties such as their morphology, surface chemistry, and charge. In our research we prepared hybrid Au@LCC nanocolloids by the Pulsed Laser Ablation, which emerged as a suitable chemically clean technique to produce ligand-free or functionalized nanomaterials, with tight control on their properties (product purity, crystal structure selectivity, particle size distribution). Here, for the first time to our knowledge, we have investigated the bioproperties of Au@LCCs. When tested in vitro on intestinal epithelial cells exposed to TNF-α, Au@LCCs sample at the ratio of 2.6:1 showed a significantly reduced TNF gene expression and induced antioxidant heme oxygenase-1 gene expression better than the 1:1 dispersion. Although deeper investigations are needed, these findings indicate that the functionalization with LCCs allows a better interaction of Au NPs with targets involved in the cell redox status and inflammatory signaling.

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.

Vinyl sulfonyl chemistry-driven unidirectional transport of a macrocycle through a [2]rotaxane

The pH- and chemically-driven unidirectional transport of a macrocycle through a [2]rotaxane based on the vinyl sulfonyl groups is reported.

Decoded fingerprints of hyperresponsive, expanding product space: polyether cascade cyclizations as tools to elucidate supramolecular catalysis

Simple enough to be understood and complex enough to be revealing, cascade cyclizations of diepoxides are introduced as new tools to characterize supramolecular catalysis. Decoded product fingerprints are provided for a consistent set of substrate stereoisomers, and shown to report on chemo-, diastereo- and enantioselectivity, mechanism and even autocatalysis. Application of the new tool to representative supramolecular systems reveals, for instance, that pnictogen-bonding catalysis is not only best in breaking the Baldwin rules but also converts substrate diastereomers into completely different products. Within supramolecular capsules, new cyclic hemiacetals from House–Meinwald rearrangements are identified, and autocatalysis on anion–π catalysts is found to be independent of substrate stereochemistry. Decoded product fingerprints further support that the involved epoxide-opening polyether cascade cyclizations are directional, racemization-free, and interconnected, at least partially. The discovery of unique characteristics for all catalysts tested would not have been possible without decoded cascade cyclization fingerprints, thus validating the existence and significance of privileged platforms to elucidate supramolecular catalysis. Once decoded, cascade cyclization fingerprints are easily and broadly applicable, ready for use in the community.

Hyperresponsive XL product space identifies polyether cascade fingerprinting as an attractive tool to elucidate supramolecular catalysis, including pnictogen-bonding, capsule and anion–π catalysts.

Polyrotaxanes and the pump paradigm

The year 2022 marks the 30th anniversary of the first reports of polyrotaxanes in the scientific literature.

Maximizing the [c2]daisy chain to lasso ratio through competitive self-templating clipping reactions

Self-templating two-component coupling reactions allowed the isolation of two threaded products with different molecular sizes: a lasso-type [1]rotaxane and a [c2]daisy chain rotaxane. Their distribution in the final reaction mixture varies as a factor of the concentration of the reactants. Through this methodology we obtained a large 84-membered cyclic multistation [2]rotaxane.

Photochemical Energy Conversion with Artificial Molecular Machines

The exploitation of sunlight as a clean, renewable, and distributed energy source is key to facing the energetic demand of modern society in a sustainable and affordable fashion. In the past few decades, chemists have learned to make molecular machines, that is, synthetic chemical systems in which energy inputs cause controlled movements of molecular components that could be used to perform a task. A variety of artificial molecular machines operated by light have been constructed by implementing photochemical processes within appropriately designed (supra)molecular assemblies. These studies could open up new routes for the realization of nanostructured devices and materials capable to harness, convert, and store light energy.

Synergistic regulation of nonbinary molecular switches by protonation and light

We report a molecular switching ensemble whose states may be regulated in synergistic fashion by both protonation and photoirradiation. This allows hierarchical control in both a kinetic and thermodynamic sense. These pseudorotaxane-based molecular devices exploit the so-called Texas-sized molecular box (cyclo[2]-(2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene); 1⁴⁺, studied as its tetrakis-PF₆ ^- salt) as the wheel component. Anions of azobenzene-4,4'-dicarboxylic acid (2H⁺•2) or 4,4'-stilbenedicarboxylic acid (2H⁺•3) serve as the threading rod elements. The various forms of 2 and 3 (neutral, monoprotonated, and diprotonated) interact differently with 1⁴⁺, as do the photoinduced cis or trans forms of these classic photoactive guests. The net result is a multimodal molecular switch that can be regulated in synergistic fashion through protonation/deprotonation and photoirradiation. The degree of guest protonation is the dominating control factor, with light acting as a secondary regulatory stimulus. The present dual input strategy provides a complement to more traditional orthogonal stimulus-based approaches to molecular switching and allows for the creation of nonbinary stimulus-responsive functional materials.

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.

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.

A Mortise-and-Tenon Joint Inspired Mechanically Interlocked Network

Mortise-and-tenon joints have been widely used for thousands of years in wooden architectures in virtue of their artistic and functional performance. However, imitation of similar structural and mechanical design philosophy to construct mechanically adaptive materials at the molecular level is a challenge. Herein, we report a mortise-and-tenon joint inspired mechanically interlocked network (MIN), in which the [2]rotaxane crosslink not only mimics the joint in structure, but also reproduces its function in modifying mechanical properties of the MIN. Benefiting from the hierarchical energy dissipative ability along with the controllable intramolecular movement of the mechanically interlocked crosslink, the resultant MIN simultaneously exhibits notable mechanical adaptivity and structural stability in a single system, as manifested by decent stiffness, strength, toughness, and deformation recovery capacity.