A Kinetic Self-Sorting Approach to Heterocircuit [3]Rotaxanes

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.

Concise and Efficient Synthesis of Sequentially Isomeric Hetero[3]rotaxanes

Stereoisomerism, stemming from the spatial orientation of components in molecular structures, plays a decisive role in nature. While the unconventional bonding found in mechanically interlocked molecules gives rise to unique expressions of stereochemistry, the exploration of their stereoisomers is still in its infancy. Sequence isomerism, characterized by variations in the ordering of mechanically interlocked components in catenanes and rotaxanes, mirrors the sequence variations found in biological macromolecules. Herein, we report the use of artificial molecular pumps for the precise and simple production of sequentially isomeric hetero[3]rotaxanes. Utilizing redox-driven pumping cassettes with different rings, we have synthesized two hetero[3]rotaxane isomers in high isolated yields from two [2]rotaxanes. This research represents a significant advance in sequential molecular assembly, paving the way for the development of sophisticated, functionalized, mechanically interlocked materials.

In Vivo Self-Sorting of Peptides via In Situ Assembly Evolution

Despite significant progress achieved in artificial self-sorting in solution, operating self-sorting in the body remains a considerable challenge. Here, we report an in vivo self-sorting peptide system via an in situ assembly evolution for combined cancer therapy. The peptide E3C16-SS-EIY consists of two disulfide-connected segments, E3C16SH and SHEIY, capable of independent assembly into twisted or flat nanoribbons. While E3C16-SS-EIY assembles into nanorods, exposure to glutathione (GSH) leads to the conversion of the peptide into E3C16SH and SHEIY, thus promoting in situ evolution from the nanorods into self-sorted nanoribbons. Furthermore, incorporation of two ligand moieties targeting antiapoptotic protein XIAP and organellar endoplasmic reticulum (ER) into the self-sorted nanoribbons allows for simultaneous inhibition of XIAP and accumulation surrounding ER. This leads to the cytotoxicity toward the cancer cells with elevated GSH levels, through activating caspase-dependent apoptosis and inducing ER dysfunction. In vivo self-sorting of E3C16-SS-EIY decorated with ligand moieties is thoroughly validated by tissue studies. Tumor-bearing mouse experiments confirm the therapeutic efficacy of the self-sorted assemblies for inhibiting tumor growth, with excellent biosafety. Our findings demonstrate an efficient approach to develop in vivo self-sorting systems and thereby facilitating in situ formulation of biomedical agents.

Kinetic Control of Complexity in Multiple Dynamic Libraries

Multiple dynamic libraries of compounds are generated when more than one reversible reaction comes into play. Commonly, two or more orthogonal reversible reactions are used, leading to non-communicating dynamic libraries which share no building blocks. Only a few examples of communicating libraries have been reported, and in all those cases, building blocks are reversibly exchanged from one library to the other, constituting an antiparallel dynamic covalent system. Herein we report that communication between two different dynamic libraries through an irreversible process is also possible. Indeed, alkyl amines cancel the dynamic regime on the nucleophilic substitution of tetrazines, generating kinetically inert compounds. Interestingly, such amine can be part of another dynamic library, an imine-amine exchange. Thus, both libraries are interconnected with each other by an irreversible process which leads to kinetically inert structures that contain parts from both libraries, causing a collapse of the complexity. Additionally, a latent irreversible intercommunication could be developed. In such a way, a stable molecular system with specific host-guest and fluorescence properties, could be irreversibly transformed when the right stimulus was applied, triggering the cancellation of the original supramolecular and luminescent properties and the emergence of new ones.

Facial Selectivity in Mechanical Bond Formation: Axially Chiral Enantiomers and Geometric Isomers from a Simple Prochiral Macrocycle

In 1971, Schill recognized that a prochiral macrocycle encircling an oriented axle led to geometric isomerism in rotaxanes. More recently, we identified an overlooked chiral stereogenic unit in rotaxanes that arises when a prochiral macrocycle encircles a prochiral axle. Here, we show that both stereogenic units can be accessed using equivalent strategies, with a single weak stereodifferentiating interaction sufficient for moderate to excellent stereoselectivity. Using this understanding, we demonstrated the first direct enantioselective (70% ee) synthesis of a mechanically axially chiral rotaxane.

Sequence-sorted redox-switchable hetero[3]rotaxanes

Programming the sequence of functional units in redox-switchable hetero[3]rotaxanes is achieved by integrative self-sorting for a library of five crown ethers.

Precision synthesis of linear oligorotaxanes and polyrotaxanes achieving well-defined positions and numbers of cyclic components on the axle

Interest in macromolecules has increased because of their functional properties, which can be tuned using precise organic synthetic methods. For example, desired functions have been imparted by controlling the nanoscale structures of such macromolecules. In particular, compounds with interlocked structures, including rotaxanes, have attracted attention because of their unique supramolecular structures. In such supramolecular structures, the mobility and freedom of the macrocycles are restricted by an axle and dependent on those of other macrocycles, which imparts unique functions to these threaded structures. Recently, methods for the ultrafine engineering and synthesis, as well as functions, of "defined" rotaxane structures that are not statistically dispersed on the axle (i.e., control over the number and position of cyclic molecules) have been reported. Various synthetic strategies allow access to such well-defined linear oligo- and polyrotaxanes, including [1]rotaxanes and [n]rotaxanes (mostly n > 3). These state-of-the-art synthetic methods have resulted in unique functions of these oligo-and polyrotaxane materials. Herein, we review the effective synthetic protocols and functions of precisely constructed one-dimensional oligomers and polymers bearing defined threaded structures, and discuss the latest reports and trends.

π-Stacking Stopper-Macrocycle Stabilized Dynamically Interlocked [2]Rotaxanes

The synthesis of mechanically interlocked molecules is valuable due to their unique topologies. With π-stacking intercomponent interaction, e.g., phenanthroline and anthracene, novel [2]rotaxanes have been synthesized by dynamic imine clipping reaction. Their X-ray crystal structures indicate the π-stackings between the anthracene moiety (stopper) on the thread and the (hetero)aromatic rings at the macrocycle of the rotaxanes. Moreover, the length of glycol chains affects the extra π-stacking intercomponent interactions between the phenyl groups and the dimethoxy phenyl groups on the thread. Dynamic combinatorial library has shown at best 84% distribution of anthracene-threaded phenanthroline-based rotaxane, coinciding with the crystallography in that the additional π-stacking intercomponent interactions could increase the thermodynamic stability and selectivity of the rotaxanes.

Activity-Based Protein Profiling (ABPP) of Oxidoreductases

Over the last two decades, activity-based protein profiling (ABPP) has been established as a tremendously useful proteomic tool for measuring the activity of proteins in their cellular context, annotating the function of uncharacterized proteins, and investigating the target profile of small-molecule inhibitors. Unlike hydrolases and other enzyme classes, which exhibit a characteristic nucleophilic residue, oxidoreductases have received much less attention in ABPP. In this minireview, the state of the art of ABPP of oxidoreductases is described and the scope and limitations of the existing approaches are discussed. It is noted that several ABPP probes have been described for various oxidases, but none so far for a reductase, which gives rise to opportunities for future research.

Synthetic strategies towards mechanically interlocked oligomers and polymers

Mechanically interlocked molecules have fascinated chemists for decades. Initially a tantalising synthetic challenge, interlocked molecules have continued to capture the imagination for their aesthetics and, increasingly, for their potential as molecular machines and use in materials applications. Whilst preliminary statistical attempts to prepare these molecules were exceedingly inefficient, a raft of template-directed strategies have now been realised, providing a vast toolbox from which chemists can access interlocked structures in excellent yields. For many envisaged applications it is desirable to move away from small, discrete interlocked molecules and turn to oligomers and polymers instead, either due to the need for multiple mechanical bonds within the desired material, or to exploit an extended scaffold for the organisation and arrangement of individual mechanically interlocked units. In this tutorial-style review we outline the synthetic strategies that have been employed for the synthesis of mechanically interlocked oligomers and polymers, including oligo-/polymerisation of (pseudo)interlocked precursors, metal-organic self-assembly, the use of orthogonal template motifs, iterative approaches and grafting onto polymer backbones.

Rotaxane PtII-complexes: mechanical bonding for chemically robust luminophores and stimuli responsive behaviour

We report an approach to rotaxanes in which the metal ion of a cyclometallated Pt^II luminophore is embedded in the space created by the mechanical bond. Our results show that the interlocked ligand environment stabilises a normally labile Pt^II–triazole bond against displacement by competing ligands and that the crowded environment of the mechanical bond retards oxidation of the Pt^II centre, without perturbing the photophysical properties of the complex. When an additional pyridyl binding site is included in the axle, the luminescence of the Pt^II centre is quenched, an effect that can be selectively reversed by the binding of Ag^I. Our results suggest that readily available interlocked metal-based phosphors can be designed to be stimuli responsive and have advantages as stabilised triplet harvesting dopants for device applications.

We report an approach to interlocked Pt^II luminophores in which the mechanical bond stabilises the coordination environment of the embedded metal ion.

Recent advances in higher order rotaxane architectures

Despite dramatic advances in the template-directed synthesis of archetypal [2]rotaxanes, higher order rotaxanes with multiple molecular components (rings or dumbbells) are relatively daunting subjects owing to their synthetic challenges. With unique interlocked architectures, higher order rotaxanes have found applications in artificial molecular machines. In this feature article, we will focus on the recent advances in higher order rotaxanes with well-defined structures. Different types of rotaxane architectures will be described, and their synthetic approaches will be highlighted. Moreover, the stimuli-responsive molecular motion with increasing complexity in these diverse architectures will also be discussed.

Controlling the selective synthesis of [2]- and [3]rotaxanes by intermolecular steric hindrance between the macrocyclic hosts

Two hydrogen-bonded azo-macrocycles with little disparity of the side chains in steric hindrance exhibited a substantial difference in complexation (slow/fast exchange) towards bipyridinium. Inspired by this finding, these macrocycles were applied to efficiently and selectively construct [2]- and [3]rotaxanes through one-pot synthesis. The origin of the selectivity in this novel approach was elucidated by comparing single crystal structures, DFT calculations and stepwise synthesis.

Probing the Dynamics of the Imine-Based Pentafoil Knot and Pentameric Circular Helicate Assembly

We investigate the self-assembly dynamics of an imine-based pentafoil knot and related pentameric circular helicates, each derived from a common bis(formylpyridine)bipyridyl building block, iron(II) chloride, and either monoamines or a diamine. The mixing of circular helicates derived from different amines led to the complete exchange of the N-alkyl residues on the periphery of the metallo-supramolecular scaffolds over 4 days in DMSO at 60 °C. Under similar conditions, deuterium-labeled and nonlabeled building blocks showed full dialdehyde building block exchange over 13 days for open circular helicates but was much slower for the analogous closed-loop pentafoil knot (>60 days). Although both knots and open circular helicates self-assemble under thermodynamic control given sufficiently long reaction times, this is significantly longer than the time taken to afford the maximum product yield (2 days). Highly effective error correction occurs during the synthesis of imine-based pentafoil molecular knots and pentameric circular helicates despite, in practice, the systems not operating under full thermodynamic control.

Homo and heteroassembly of amide-based [2]rotaxanes using α,α′-dimethyl-p-xylylenediamines

The selective formation of [2]rotaxanes affords two out of seven possible interlocked isomers thanks to a marked conformational preference.

Heterorotaxanes

Heterorotaxanes, in which at least two types of macrocycles were introduced as the wheel components in rotaxanes, have attracted more and more attention during the past few decades owing to their unique structural features and intriguing properties. The coexistence of varied macrocycles endows the resultant heterorotaxanes not only versatile shuttling and switching behaviors but also great potential for the construction of functional rotaxane systems for applications. In this feature article, a survey of the successful synthesis of heterorotaxanes will be provided based on the various strategies towards the synthesis of heterorotaxanes, i.e. orthogonal binding approach, self-sorting approach, cooperative capture approach, active metal template approach, etc.

Stereoselective Synthesis of Mechanically Planar Chiral Rotaxanes

Chiral interlocked molecules in which the mechanical bond provides the sole stereogenic unit are typically produced with no control over the mechanical stereochemistry. Here we report a stereoselective approach to mechanically planar chiral rotaxanes in up to 98:2 d.r. using a readily available α-amino acid-derived azide. Symmetrization of the covalent stereocenter yields a rotaxane in which the mechanical bond provides the only stereogenic element.

Chirality in rotaxanes and catenanes

Although chiral mechanically interlocked molecules (MIMs) have been synthesised and studied, enantiopure examples are relatively under-represented in the pantheon of reported catenanes and rotaxanes and the underlying chirality of the system is often even overlooked. This is changing with the advent of new applications of MIMs in catalysis, sensing and materials and the appearance of new methods to access unusual stereogenic units unique to the mechanical bond. Here we discuss the different stereogenic units that have been investigated in catenanes and rotaxanes, examples of their application, methods for assigning absolute stereochemistry and provide a perspective on future developments.

A Fluorescent Ditopic Rotaxane Ion-Pair Host

We report a rotaxane based on a simple urea motif that binds Cl- selectively as a separated ion pair with H+ and reports the anion binding event through a fluorescence switch-on response. The host selectively binds Cl- over more basic anions, which deprotonate the framework, and less basic anions, which bind more weakly. The mechanical bond also imparts size selectivity to the ditopic host.

Chelating Rotaxane Ligands as Fluorescent Sensors for Metal Ions

Although metal-ion-binding interlocked molecules have been under intense investigation for over three decades, their application as scaffolds for the development of sensors for metal ions remains underexplored. In this work, we demonstrate the potential of simple rotaxanes as metal-ion-responsive ligand scaffolds through the development of a proof-of-concept selective sensor for Zn2+ .

Ring-through-ring molecular shuttling in a saturated [3]rotaxane

Mechanically interlocked molecules such as rotaxanes and catenanes comprise two or more components whose motion relative to each other can be controlled. A [2]rotaxane molecular shuttle, for example, consists of an axle bearing two recognition sites and a single macrocyclic wheel that can undergo a to-and-fro motion along the axle-shuttling between the recognition sites. The ability of mechanically interlocked molecules to undergo this type of large-amplitude change is the core mechanism behind almost every interlocked molecular switch or machine, including sophisticated mechanical systems such as a molecular elevator and a peptide synthesizer. Here, as a way to expand the scope of dynamics possible at the molecular level, we have developed a molecular shuttling mechanism involving the exchange of rings between two recognition sites in a saturated [3]rotaxane (one with no empty recognition sites). This was accomplished by passing a smaller ring through a larger one, thus achieving ring-through-ring molecular shuttling.

Efficient Multicomponent Active Template Synthesis of Catenanes

We describe a simple and high yielding active template synthesis of [2]catenanes. In addition to mechanical bond formation using a single premacrocycle bearing an azide and alkyne moiety, our method is also suitable for the co-macrocyclization of readily available bis-alkyne and bis-azide comonomers and even short alkyne/azide components which oligomerize prior to mechanical bond formation.

A high-speed network of nanoswitches for on/off control of catalysis

Copper(i) ion translocation is the key for fast and reliable communication between networked devices in the catalytic machinery.

Properties and emerging applications of mechanically interlocked ligands

Mechanically interlocked molecules have a long and rich history as ligands thanks to the key role coordination chemistry has played in the development of high yielding passive template syntheses of rotaxanes and catenanes. In this Feature Article, we highlight the effect of the mechanical bond on the properties of metal ions bound within the sterically hindered environment of the macrocycle cavity, and discuss the emerging applications of interlocked ligands in catalysis, sensing and supramolecular materials.

Porphyrinoid rotaxanes: building a mechanical picket fence

Building on recent progress in the synthesis of functional porphyrins for a range of applications using the Cu-mediated azide-alkyne cycloaddition (CuAAC) reaction, we describe the active template CuAAC synthesis of interlocked triazole functionalised porphyrinoids in excellent yield. By synthesising interlocked analogues of previously studied porphyrin-corrole conjugates, we demonstrate that this approach gives access to rotaxanes in which the detailed electronic properties of the axle component are unchanged but whose steric properties are transformed by the mechanical "picket fence" provided by the threaded rings. Our results suggest that interlocked functionalised porphyrins, readily available using the AT-CuAAC approach, are sterically hindered scaffolds for the development of new catalysts and materials.

One-pot synthesis of hetero[6]rotaxane bearing three different kinds of macrocycle through a self-sorting process

A hetero[6]rotaxane bearing three different kinds of macrocycle is designed and successfully synthesized through a one-pot “click” reaction by employing a facile and efficient integrative self-sorting principle.

In this article, a six-component self-sorting process that involves three types of crown ether macrocycle and three types of cation guest molecule was carefully and thoroughly investigated. The six components include three kinds of crown ether, namely bis(p-phenylene-34-crown-10) (BPP34C10), dibenzo-24-crown-8 (DB24C8) and benzo-21-crown-7 (B21C7), and their corresponding cation guest molecules, namely a 4,4′-bipyridine dication (BPY²⁺) and dibenzylammonium (DBA) and benzylalkylammonium (BAA) ions, respectively. Based on this well-established highly selective six-component self-sorting process, a hetero[6]rotaxane bearing three different kinds of crown ether macrocycle was designed and successfully synthesized through a facile and efficient one-pot “click” stoppering strategy. Such work is proposed to be a significant advance in the construction of mechanically interlocked molecules with high structural complexity, as well as a good supplement in the areas of multi-component self-sorting and noncovalent self-assembly.

Stepwise, Protecting Group Free Synthesis of [4]Rotaxanes

Despite significant advances in the last three decades towards high yielding syntheses of rotaxanes, the preparation of systems constructed from more than two components remains a challenge. Herein we build upon our previous report of an active template copper-catalyzed azide-alkyne cycloaddition (CuAAC) rotaxane synthesis with a diyne in which, following the formation of the first mechanical bond, the steric bulk of the macrocycle tempers the reactivity of the second alkyne unit. We have now extended this approach to the use of 1,3,5-triethynylbenzene in order to successively prepare [2]-, [3]- and [4]rotaxanes without the need for protecting group chemistry. Whilst the first two iterations proceeded in good yield, the steric shielding that affords this selectivity also significantly reduces the efficacy of the active template (AT)-CuAAC reaction of the third alkyne towards the preparation of [4]rotaxanes, resulting in severely diminished yields.

Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform

Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by ¹H or ¹³C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes

Examples of using two-dimensional shape-persistent macrocycles, i.e. those having noncollapsible and geometrically well-defined skeletons, for constructing mechanically interlocked molecules are scarce, which contrasts the many applications of these macrocycles in molecular recognition and functional self-assembly. Herein, we report the crucial role played by macrocyclic shape-persistency in enhancing multipoint recognition for the highly efficient template-directed synthesis of rotaxanes. Cyclo[6]aramides, with a near-planar conformation, are found to act as powerful hosts that bind bipyridinium salts with high affinities. This unique recognition module, composed of two macrocyclic molecules with one bipyridinium ion thread through the cavity, is observed both in the solid state and in solution, with unusually high binding constants ranging from ∼10¹³ M^-2 to ∼10¹⁵ M^-2 in acetone. The high efficacy of this recognition motif is embodied by the formation of compact [3]rotaxanes in excellent yields based on either a "click-capping" (91%) or "facile one-pot" (85%) approach, underscoring the great advantage of using H-bonded aromatic amide macrocycles for the highly efficient template-directed synthesis of mechanically interlocked structures. Furthermore, three cyclo[6]aramides bearing different peripheral chains 1-3 demonstrate high specificity in the synthesis of a [3]rotaxane from 1 and 2, and a [2]rotaxane from 3via a "facile one-pot" approach, in each case as the only isolated product. Analysis of the crystal structure of the [3]rotaxane reveals a highly compact binding mode that would be difficult to access using other macrocycles with a flexible backbone. Leveraging this unique recognition motif, resulting from the shape-persistency of these oligoamide macrocycles, in the template-directed synthesis of compact rotaxanes may open up new opportunities for the development of higher order interlocked molecules and artificial molecular machines.