Catenanes: fifty years of molecular links

Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement

How to direct the self-assembly of simple templates toward constructs with complex shape and topology is still an open problem. Recent advancements have made it possible to self-assemble various types of knotted constructs, but targeting general multicomponent topologies, that is, links and catenanes, has proved much harder. Here, we study how the yield and complexity of self-assembled links depends on both intrinsic and extrinsic system properties and, particularly, template shape and spatial confinement. We show that slit confinement does not necessarily suppress linking but can rather enhance it significantly thanks to entropic effects. We also found that only a limited set of binary links are recurrent for different template shapes. These privileged topologies include all those experimentally realized so far plus a few additional ones, such as the 7₇² and 7₈² links that, hence, ought to be ideal candidates for broadening the current class of constructs with addressable topology.

Stereocontrolled Synthesis of β-Lactams within [2]Rotaxanes: Showcasing the Chemical Consequences of the Mechanical Bond

The intramolecular cyclization of N-benzylfumaramide [2]rotaxanes is described. The mechanical bond of these substrates activates this transformation to proceed in high yields and in a regio- and diastereoselective manner, giving interlocked 3,4-disubstituted trans-azetidin-2-ones. This activation effect markedly differs from the more common shielding protection of threaded functions by the macrocycle, in this case promoting an unusual and disfavored 4-exo-trig ring closure. Kinetic and synthetic studies allowed us to delineate an advantageous approach toward β-lactams based on a two-step, one-pot protocol: an intramolecular ring closure followed by a thermally induced dethreading step. The advantages of carrying out this cyclization in the confined space of a benzylic amide macrocycle are attributed to its anchimeric assistance.

Creating complex molecular topologies by configuring DNA four-way junctions

The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

Directional Molecular Transportation Based on a Catalytic Stopper-Leaving Rotaxane System

Ratchet mechanism has proved to be a key principle in designing molecular motors and machines that exploit random thermal fluctuations for directional motion with energy input. To integrate ratchet mechanism into artificial systems, precise molecular design is a prerequisite to control the pathway of relative motion between their subcomponents, which is still a formidable challenge. Herein, we report a straightforward method to control the transportation barrier of a macrocycle by selectively detaching one of the two stoppers using a novel DBU-catalyzed stopper-leaving reaction in a rotaxane system. The macrocycle was first allowed to thread onto a semidumbbell axle from the open end and subsequently thermodynamically captured into a nonsymmetrical rotaxane. Then, it was driven energetically uphill until it reached a kinetically trapped state by destroying its interaction with ammonium site, and was finally quantitatively released from the other end when the corresponding stopper barrier was removed. Although the directional transportation at the present system was achieved by discrete chemical reactions for the sake of higher transportation efficiency, it represents a new molecular transportation model by the strategy of using stopper-leavable rotaxane.

Catenation and encapsulation induce distinct reconstitutions within a dynamic library of mixed-ligand Zn4L6 cages

Two new Zn4L6 cages composed of diamine subcomponents containing either naphthalene diimide (NDI) or porphyrin moieties are described. Their structural differences allow these cages to exhibit distinct interactions with different chemical stimuli, yielding different supramolecular products. The electron-poor NDI subunits of the first cage were observed to thread through electron-rich aromatic crown-ether macrocycles, forming mechanically-interlocked species up to a [3]catenane, whereas the porphyrin ligands of the second cage interacted favourably with C70, causing it to be bound as a guest. When mixed, the two cages were observed to form a dynamic combinatorial library (DCL) of seven constitutionally distinct mixed-ligand Zn4L6 cages. The DCL was observed to reconstitute in opposing ways when treated with either the crown ether or C70: the electron-rich macrocycle templated the formation of heteroleptic catenanes, whereas C70 caused the DCL to self-sort into homoleptic structures.

A bifunctional chiral [2]catenane based on 1,1'-binaphthyl-phosphates

A novel [2]catenane was synthesised by ring-closing metathesis from a Ca-bisphosphate template. The resulting interlocked structure features two chiral 1,1'-binaphthyl-phosphates, leading to a bifunctional catenane structure. Initial binding studies point at the applicability of such mechanically interlocked bisphosphates as artificial receptors for dicationic guest molecules.

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples.

Topoisomerase-Based Preparation and AFM Imaging of Multi-Interlocked Circular DNA

Multi-interlocked circular DNA structures have been in high demand for fabricating complicated functional DNA architectures and nanodevices such as molecular switches, shuttles, and motors. Even though various innovative methods have been developed in the past, creation of multi-interlocked circular DNA structures with defined numbers of DNA molecules and linking patterns is still a challenging task nowadays. Here, we propose a top-down decatenation of kinetoplast DNA as a new approach for creating multi-interlocked circular DNA structures. Through optimizing the amount and reaction time of topoisomerase II, we synthesized completely mutually interlocked tricircular, tetra-circular, and oligo-circular DNA structures, which have not yet been acquirable through any other existing synthetic means. The catenation structures of multiple circular DNA were further verified through atomic force microscopic analysis of the backbone overlapping patterns and the circumference. It accordingly is our expectation that the top-down enzymatic approaches could offer a highly interlocked network with defined numbers of circular DNA with simple protocols, and could consequently be beneficial to the design and fabrication of sophisticated functional molecules and nanodevices in the areas of supramolecular chemistry, DNA nanotechnology, and material science.

Facile syntheses of [3]-, [4]- and [6]catenanes templated by orthogonal supramolecular interactions

A branched [6]catenane was synthesised under aqueous conditions in high yield using orthogonal supramolecular interactions as a template.

A water soluble [6]catenane consisting of two interlocking [3]catenanes was synthesised in 91% yield using readily accessible precursors. The new strategy features the simultaneous use of orthogonal Cu⁺–phenanthroline and CB[6]–ammonium interactions for preorganising the precursors and the efficient CB[6]-catalysed azide–alkyne cycloaddition as bond forming reactions for ring closing, resulting in high structural complexity and fidelity of the products without compromising interlocking efficiency. A related [4]catenane with three different types of macrocycles was also obtained in good yield.

One-pot synthesis of a [c2]daisy-chain-containing hetero[4]rotaxane via a self-sorting strategy

The construction and efficient synthesis of hetero[n]rotaxanes with high structural complexity are always attractive challenges. Herein, we demonstrate a facile one-pot preparation of a hetero[4]rotaxane, by employing a self-sorting strategy, which contains an interpenetrated dibenzo-24-crown-8 (DB24C8) based [c2]daisy chain structure and is ended with a benzo-21-crown-7 (B21C7) based rotaxane at each side. The key to the design involved encoding the selective threading using a steric hindrance-related "language", where highly selective self-assemblies occurred in a three-component self-sorting process, which included the threading of a benzylalkylammonium into a B21C7 and interpenetrated dimerized formation of a DB24C8 based [c2]daisy chain simultaneously; the precise pre-assembled system resulted in the efficient synthesis of hetero[4]rotaxane with a high-level of structural complexity under the "CuAAC" reaction.

Supramolecular transformations within discrete coordination-driven supramolecular architectures

In this review, a comprehensive summary of supramolecular transformations within discrete coordination-driven supramolecular architectures, including helices, metallacycles, metallacages, etc., is presented.

An acid/base responsive side-chain polyrotaxane system with a fluorescent signal

A side-chain polyrotaxane system can generate a remarkable fluorescent signal change in response to acid/base stimuli.

Conformations of large macrocycles and ring-in-ring complexes

A kinetically directed, stepwise approach towards molecular Borromean links enabled the isolation and structural characterization of synthetic intermediates along the way.

Towards the molecular Borromean link with three unequal rings: double-threaded ruthenium(ii) ring-in-ring complexes

Synthesis of double-threaded ruthenium(ii) ring-in-ring complexes and the Borromean link with three unequal rings detected by mass spectrometry.

Supramolecular main-chain polycatenanes formed by orthogonal metal ion coordination and pillar[5]arene-based host–guest interaction

A novel supramolecular main-chain polycatenane was constructed by coordination-driven self-assembly, host–guest interaction and supramolecular polymerization.

Multicavity macrocyclic hosts

Multicavity macrocyclic hosts are host molecules comprising more than one macrocyclic guest binding components connected through multipoint linkages.

Synthesis of linear [5]catenanes via olefin metathesis dimerization of pseudorotaxanes composed of a [2]catenane and a secondary ammonium salt

[5]Catenanes were synthesized by olefin metathesis dimerization.

Guest-dependent directional complexation based on triptycene derived oxacalixarene: formation of oriented rotaxanes

Structural changes in the guest cause inversion of the dominant threading direction in triptycene derived oxacalixarene with different semi-cavities.

The manipulation of supramolecular devices to carry out sophisticated and programmed tasks is bound up with the spatial allocation of their components, especially the threading direction of the guest, which controls the host–guest orientation in the device. However, insights are needed to probe more possibilities for steering the threading direction. We have developed a new system consisting of a three-dimensional nonsymmetric oxacalixarene (H) with a fixed comformation and (bi)pyridinium salts (G1–G3), in which we found that based on the intrinsic discrepancies between the two semi-cavities of H, the electron densities of the axles greatly affect the threading direction. This was unequivocally demonstrated by NMR spectra and single crystal structures. With elaborate design, unidirectional threading was achieved, resulting in an oriented rotaxane. Therefore, we describe a new approach in which the threading direction and final orientation may be finely controlled by adjustment of the structure of the guest.

Homochiral [2]Catenane and Bis[2]catenane from Alleno-Acetylenic Helicates - A Highly Selective Narcissistic Self-Sorting Process

Homochiral strands of alternating alleno-acetylenes and phenanthroline ligands (P)-1 and (P2)-2, as well as their corresponding enantiomers, selectively assemble with the addition of silver(I) salt to yield dinuclear and trinuclear double helicates, respectively. Upon increasing the solvent polarity, the dinuclear and trinuclear helicates interlock to form a [2]catenane and bis[2]catenane, bearing 14 chirality elements, respectively. The solid-state structure of the [2]catenane reveals a nearly perfect fit of the interlocked strands, and the ECD spectra show a significant amplification of the chiroptical properties upon catenation, indicating stabilization of the helical secondary structure. Highly selective narcissistic self-sorting was demonstrated for a racemic mixture consisting of both short and long alleno-acetylenic strands, highlighting their potential for the preparation of linear catenanes of higher order.

Lanthanide Template Synthesis of Trefoil Knots of Single Handedness

We report on the assembly of 2,6-pyridinedicarboxamide ligands (1) with point chirality about lanthanide metal ion (Ln(3+)) templates, in which the helical chirality of the resulting entwined 3:1 ligand:metal complexes is covalently captured by ring-closing olefin metathesis to form topologically chiral molecular trefoil knots of single handedness. The ligands do not self-sort (racemic ligands form a near-statistical mixture of homoleptic and heteroleptic lanthanide complexes), but the use of only (R,R)-1 leads solely to a trefoil knot of Λ-handedness, whereas (S,S)-1 forms the Δ-trefoil knot with complete stereoselectivity. The knots and their isomeric unknot macrocycles were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography and the expression of the chirality that results from the topology of the knots studied by circular dichroism.