Synthesizing interlocked molecules dynamically

As the complexity of mechanically interlocked molecular architectures increases, it is important to understand the underlying principles, such as molecular recognition and self‐assembly processes, that govern the practice of template‐directed synthesis necessary to create these particular compounds. In this review, we explain the importance of dynamic processes in the synthesis of mechanically interlocked compounds. We show how many different dynamic covalent bonds have been used in the synthesis of rotaxanes, catenanes, and other higher‐order mechanically interlocked compounds, with the goal of revealing the state of the art in dynamic covalent chemistry. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 136–154; 2009: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.20173     

Halogen‐ and Hydrogen‐Bonding Catenanes for Halide‐Anion Recognition

Halogen‐bonding (XB) interactions were exploited in the solution‐phase assembly of anion‐templated pseudorotaxanes between an isophthalamide‐containing macrocycle and bromo‐ or iodo‐functionalised pyridinium threading components. ¹H NMR spectroscopic titration investigations demonstrated that such XB interpenetrated assemblies are more stable than analogous hydrogen bonding (HB) pseudorotaxanes. The stability of the anion‐templated halogen‐bonded pseudorotaxane architectures was exploited in the preparation of new halogen‐bonding interlocked catenane species through a Grubbs’ ring‐closing metathesis (RCM) clipping methodology. The catenanes’ anion recognition properties in the competitive CDCl₃/CD₃OD 1:1 solvent mixture revealed selectivity for the heavier halides iodide and bromide over chloride and acetate.     

Solution‐Phase Dynamic Assembly of Permanently Interlocked Aryleneethynylene Cages through Alkyne Metathesis

Highly stable permanently interlocked aryleneethynylene molecular cages were synthesized from simple triyne monomers using dynamic alkyne metathesis. The interlocked complexes are predominantly formed in the reaction solution in the absence of any recognition motif and were isolated in a pure form using column chromatography. This study is the first example of the thermodynamically controlled solution‐phase synthesis of interlocked organic cages with high stability.     

Front Cover: Dynamic Covalent Chemistry for Synthesis and Co-conformational Control of Mechanically Interlocked Molecules (Eur. J. Org. Chem. 8/2023)

Mechanically interlocked molecules have found extensive applications in areas all across the physical sciences, from materials to catalysis and sensing. However, introducing mechanical bonds and entanglements at the molecular level is still a significant challenge due to the inherent restriction in entropy needed to preorganize strands before interlocking. Over the last decade, dynamic covalent chemistry has emerged as one of the most efficient methods of forming rotaxanes, catenanes and molecular knots. By using reversible bonds such as imines, disulfides and boronate esters, one can use the inherent error-correction in these linkages to form interlocked architectures with high fidelity and often in excellent yields. This review reports on recent advances in the use of dynamic covalent chemistry to make mechanically interlocked molecules, systematically surveying clipping, capping and templating approaches with dynamic bonds. Furthermore, it is also discussed how dynamic bonds can be used to control motion, co-conformational expression and catalytic activity in mechanically interlocked molecular machinery.     

Hierarchical Supramolecular Spinning of Nanofibers in a Microfluidic Channel: Tuning Nanostructures at a Dynamic Interface

One of the fundamental problems in supramolecular chemistry, as well as in material sciences, is how to control the self‐assembly of polymers on the nanometer scale and how to spontaneously organize them towards the macroscopic scale. To overcome this problem, inspired by the self‐assembly systems in nature, which feature the dynamically controlled self‐assembly of biopolymers, we have previously proposed a self‐assembly system that uses a dynamic liquid/liquid interface with dimensions in the micrometer regime, thereby allowing polymers to self‐assemble under precisely controlled nonequilibrium conditions. Herein, we further extend this system to the creation of hierarchical self‐assembled architectures of polysaccharides. A natural polysaccharide, β‐1,3‐glucan (SPG), and water were injected into opposite “legs” of microfluidic devices that had a Y‐shape junction, so that two solvents would gradually mix in the down stem, thereby causing SPG to spontaneously self‐assemble along the flow in a head‐to‐tail fashion, mainly through hydrophobic interactions. In the initial stage, several SPG nanofibers would self‐assemble at the Y‐junction owing to the shearing force, thereby creating oligomers with a three‐way junction point. This unique structure, which could not be created through conventional mixing procedures, has a divergent self‐assembly capability. The dynamic flow allows the oligomers to interact continuously with SPG nanofibers that are fed into the Y‐junction, thus amplifying the nanostructure along the flow to form SPG networks. Consequently, we were able to create stable, centimeter‐length macroscopic polysaccharide strands under the selected flow conditions, which implies that SPG nanofibers were assembled hierarchically in a supramolecular fashion in the dynamic flow. Microscopic observations, including SEM and AFM analysis, revealed the existence of clear hierarchical structures inside the obtained strand. The network structures self‐assembled to form sub‐micrometer‐sized fibers. The long fibers further entangled with each other to give stable micrometer‐sized fibers, which finally assembled to form the macroscopic strands, in which the final stabilities in the macroscopic regime were governed by that of the network structures in the nanometer regime. Thus, we have exploited this new supramolecular system to create hierarchical polymeric architectures under precisely controlled flow conditions, by combining the conventional supramolecular strategy with microfluidic science.     

Investigating the imidazolium–anion interaction through the anion-templated construction of interpenetrated and interlocked assemblies

The interaction between imidazolium cations and coordinating anions is investigated through the anion‐templated assembly of interpenetrated and interlocked structures. The orientation of the imidazolium motif with respect to anion binding, and hence the hydrogen bond donor arrangement, was varied in acyclic receptors, interpenetrated assemblies, and the first mono‐imidazolium interlocked systems. Their anion recognition properties and co‐conformations were studied by solution‐phase ¹H NMR investigations, solid‐state structures, molecular dynamics simulations, and density functional theory calculations. Our findings suggest that the imidazolium‐anion binding interaction is dominated by electrostatics with hydrogen‐bonding contributions having weak orientational dependence.     

Precision Molecular Threading/Dethreading

The general principles guiding the design of molecular machines based on interlocked structures are well known. Nonetheless, the identification of suitable molecular components for a precise tuning of the energetic parameters that determine the mechanical link is still challenging. Indeed, what are the reasons of the “all‐or‐nothing” effect, which turns a molecular “speed‐bump” into a stopper in pseudorotaxane‐based architectures? Here we investigate the threading and dethreading processes for a representative class of molecular components, based on symmetric dibenzylammonium axles and dibenzo[24]crown‐8 ether, with a joint experimental–computational strategy. From the analysis of quantitative data and an atomistic insight, we derive simple rules correlating the kinetic behaviour with the substitution pattern, and provide rational guidelines for the design of modules to be integrated in molecular switches and motors with sophisticated dynamic features.     

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures

We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double‐stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo‐DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.     

A Shape‐Persistent Quadruply Interlocked Giant Cage Catenane with Two Distinct Pores in the Solid State

Discrete interlocked three‐dimensional structures are synthetic targets that are sometimes difficult to obtain with “classical” synthetic approaches, and dynamic covalent chemistry has been shown to be a useful method to form such interlocked structures as thermodynamically stable products. Although interlocked and defined hollow structures are found in nature, for example, in some viruses, similar structures have rarely been synthesized on a molecular level. Shape‐persistent interlocked organic cage compounds with dimensions in the nanometer regime are now accessible in high yields during crystallization through the formation of 96 covalent bonds. The interlocked molecules form an unprecedented porous material with intrinsic and extrinsic pores both in the micropore and mesopore regime.     

Advances in Anion Supramolecular Chemistry: From Recognition to Chemical Applications

Since the start of this millennium, remarkable progress in the binding and sensing of anions has been taking place, driven in part by discoveries in the use of hydrogen bonding, as well as the previously under‐exploited anion–π interactions and halogen bonding. However, anion supramolecular chemistry has developed substantially beyond anion recognition, and now encompasses a diverse range of disciplines. Dramatic advance has been made in the anion‐templated synthesis of macrocycles and interlocked molecular architectures, while the study of transmembrane anion transporters has flourished from almost nothing into a rapidly maturing field of research. The supramolecular chemistry of anions has also found real practical use in a variety of applications such as catalysis, ion extraction, and the use of anions as stimuli for responsive chemical systems.     

Self‐Healing Materials from V‐ and H‐Shaped Supramolecular Architectures

Integrating self‐healing capability into supramolecular architectures is an interesting strategy, and can considerably enhance the performance and broaden the scope of applications for this important class of polymers. Herein we report the rational design of novel V‐shaped barbiturate (Ba) functionalized soft–hard–soft triblock copolymers with a reversible supramolecular healing motif (Ba) in the central part of the hard block, which undergoes autonomic repair at 30 °C. The designed synthesis also offers a suitable macromolecular building block to further self‐assemble with heterocomplementary α,ω‐Hamilton wedge (HW) functionalized polyisoprene (PI; HW‐PI‐HW), resulting in an H‐shaped supramolecular architecture with efficient self‐healing capabilities that can recover up to around 95 % of the original mechanical performance at 30 °C within 24 h.     

The Supramolecular Chemistry of Strained Carbon Nanohoops

Since 1996, a growing number of strained macrocycles, comprising only sp²‐ or sp‐hybridized carbon atoms within the ring, have become synthetically accessible, with the [n]cycloparaphenyleneacetylenes ( CPPAs ) and the [n]cycloparaphenylenes ( CPPs ) being the most prominent examples. Now that robust and relatively general synthetic routes toward a diverse range of nanohoop structures have become available, the research focus is beginning to shift towards the exploration of their properties and applications. From a supramolecular chemistry perspective, these macrocycles offer unique opportunities as a result of their near‐perfect circular shape, the unusually high degree of shape‐persistence, and the presence of both convex and concave π‐faces. In this Minireview, we give an overview on the use of strained carbon‐rich nanohoops in host–guest chemistry, the preparation of mechanically interlocked architectures, and crystal engineering.     

Heterobifunctional Rotaxanes for Asymmetric Catalysis

Heterobifunctional rotaxanes serve as efficient catalysts for the addition of malonates to Michael acceptors. We report a series of four different heterobifunctional rotaxanes, featuring an amine‐based thread and a chiral 1,1′‐binaphthyl‐phosphoric‐acid‐based macrocycle. High‐level DFT calculations provided mechanistic insights and enabled rational catalyst improvements, leading to interlocked catalysts that surpass their non‐interlocked counterparts in terms of reaction rates and stereoselectivities.     

Folding and Aggregation of Cationic Oligo(aryl‐triazole)s in Aqueous Solution

Cationic aryl triazole oligomers have been synthesized through “click chemistry”. The results show that cationic aryl triazole oligomers adopt a helical conformation in water or in a mixture of water and methanol, but prevail as a random‐coiled conformation in methanol. Importantly, circular dichroism spectroscopy and dynamic light scattering experiments revealed that cationic oligomers aggregated intermolecularly to form higher order architectures with a helical sense opposite to that of the individual helix, which eventually led to the formation of aggregates with sizes in the range 100–500 nm. The aggregation of cationic oligomers was governed by the concentration and polarity of the environment. More interestingly, cationic foldamers were able to recognize chloride and fluoride anions in aqueous solution. The recognition consequently destabilized intermolecular aggregation.     

One‐Step Formation of “Chain‐Armor”‐Stabilized DNA Nanostructures

DNA‐based self‐assembled nanostructures are widely used to position organic and inorganic objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA‐based templates that are robust against degradation at elevated temperatures, low ion concentrations, adverse pH conditions, and DNases, we built 6‐helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3′‐ends and azides on their 5′‐ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so‐called DNA catenanes. Strikingly, the structures stayed topologically intact in pure water and even after precipitation from EtOH. The structures even withstood a temperature of 95 °C when all of the 24 strands were chemically interlocked.     

Construction of Alkynylplatinum(II) Bzimpy‐Functionalized Metallacycles and Their Hierarchical Self‐Assembly Behavior in Solution Promoted by Pt⋅⋅⋅Pt and π–π Interactions

A family of new alkynylplatinum(II) 2,6‐bis(benzimidazol‐2′‐yl)pyridine (bzimpy)‐functionalized supramolecular metallacycles with different shapes and sizes have been successfully prepared by coordination‐driven self‐assembly. The obtained metallacycles showed switchable emission and a strong tendency to form intermolecular Pt???Pt and π–π stacking interactions in solution that were not displayed by their individual precursors. Further investigation revealed that the existence of the metallacyclic scaffold at the core could facilitate the formation of intermolecular Pt???Pt and π–π stacking interactions of peripheral alkynylplatinum(II) bzimpy units. Moreover, the shapes and sizes of the metallacyclic scaffold have a significant influence on the hierarchical self‐assembly behavior. Among the three metallacycles, hexagonal metallacycle A , with a relatively small size, could spontaneously self‐assemble into an aromatic guest stimuli‐responsive metallogel at room temperature without a heating–cooling process.     

Selective Monofunctionalization Enabled by Reaction‐History‐Dependent Communication in Catalytic Rotaxanes

Selective monofunctionalization of substrates with distant, yet equally reactive functional groups is difficult to achieve, as it requires the second functional group to selectively modulate its reactivity once the first functional group has reacted. We now show that mechanically interlocked catalytic rings can effectively regulate the reactivity of stoppering groups in rotaxanes over a distance of about 2 nm. Our mechanism of communication is enabled by a unique interlocked design, which effectively removes the catalytic rings from the substrates by fast dethreading as soon as the first reaction has taken place. Our method not only led to a rare example of selective monofunctionalization, but also to a “molecular if function”. Overall, the study presents a way to get distant functional groups to communicate with each other in a reaction‐history‐dependent manner by creating linkers that can ultimately perform logical operations at the molecular level.     

A Simple and Highly Effective Ligand System for the Copper(I)‐Mediated Assembly of Rotaxanes

A [2]rotaxane was produced through the assembly of a picolinaldehyde, an amine, and a bipyridine macrocycle around a Cu^I template by imine bond formation in close‐to‐quantitative yield. An analogous [3]rotaxane is obtained in excellent yield by replacing the amine with a diamine, thus showing the suitability of the system for the construction of higher order interlocked structures. The rotaxanes are formed within a few minutes simply through mixing the components in solution at room temperature and they can be isolated through removal of the solvent or precipitation.     

Self‐Assembly of Tyrosine into Controlled Supramolecular Nanostructures

In the context of designing novel amino acid nanostructures, the capacity of tyrosine alone to form well‐ordered structures under different conditions was explored. It was observed that Tyr can self‐assemble into well‐defined morphologies when deposited onto surfaces for transmission electron microscopy, atomic force microscopy, and scanning electron microscopy. The influence of various parameters that can modulate the self‐assembly process, including concentration of the amino acid, aging time, and solvent, was studied. Different supramolecular architectures, including nanoribbons, branched structures, and fern‐like arrangements were also observed.     

Interpenetrated Cage Structures

This Review covers design strategies, synthetic challenges, host–guest chemistry, and functional properties of interlocked supramolecular cages. Some dynamic covalent organic structures are discussed, as are selected examples of interpenetration in metal–organic frameworks, but the main focus is on discrete coordination architectures, that is, metal‐mediated dimers. Factors leading to interpenetration, such as geometry, flexibility and chemical makeup of the ligands, coordination environment, solvent effects, and selection of suitable counter anions and guest molecules, are discussed. In particular, banana‐shaped bis‐pyridyl ligands together with square‐planar metal cations have proven to be suitable building blocks for the construction of interpenetrated double‐cages obeying the formula [M₄L₈]. The peculiar topology of these double‐cages results in a linear arrangement of three mechanically coupled pockets. This allows for the implementation of interesting guest encapsulation effects such as allosteric binding and template‐controlled selectivity. In stimuli‐responsive systems, anionic triggers can toggle the binding of neutral guests or even induce complete structural conversions. The increasing structural and functional complexity in this class of self‐assembled hosts promises the construction of intelligent receptors, novel catalytic systems, and functional materials.