Template synthesis of molecular knots

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.

Selective synthesis of iridium(iii)-derived molecular Borromean rings, [2]catenane and ring-in-ring macrocycles via coordination-driven self-assembly

Unprecedented iridium(iii) derived molecular Borromean rings, 2[catenane] and ring-in-ring metallacycles were synthesizedviacoordination driven self-assembly using an iridium(iii)-based acceptor and dipyridyl donors.

Tying a Molecular Overhand Knot of Single Handedness and Asymmetric Catalysis with the Corresponding Pseudo-D3-Symmetric Trefoil Knot

We report the stereoselective synthesis of a left-handed trefoil knot from a tris(2,6-pyridinedicarboxamide) oligomer with six chiral centers using a lanthanide(III) ion template. The oligomer folds around the lanthanide ion to form an overhand knot complex of single handedness. Subsequent joining of the overhand knot end groups by ring-closing olefin metathesis affords a single enantiomer of the trefoil knot in 90% yield. The knot topology and handedness were confirmed by NMR spectroscopy, mass spectrometry, and X-ray crystallography. The pseudo-D3-symmetric knot was employed as an asymmetric catalyst in Mukaiyama aldol reactions, generating enantioselectivities of up to 83:17 er, which are significantly higher than those obtained with a comparable unknotted ligand complex.

Face and edge directed self-assembly of Pd12 tetrahedral nano-cages and their self-sorting

Reactions of a cis-blocked Pd(ii) 90° acceptor [cis-(tmeda)Pd(NO3)2] (M) with 1,4-di(1H-tetrazol-5-yl)benzene (H2L1 ) and [1,3,5-tri(1H-tetrazol-5-yl)benzene] (H3L2 ) in 1 : 1 and 3 : 2 molar ratios respectively, yielded soft metallogels G1 and G2 [tmeda = N,N,N',N'-tetramethylethane-1,2-diamine]. Post-metalation of the gels G1 and G2 with M yielded highly water-soluble edge and face directed self-assembled Pd12 tetrahedral nano-cages T1 and T2, respectively. Such facile conversion of Pd(ii) gels to discrete tetrahedral metallocages is unprecedented. Moreover, distinct self-sorting of these two tetrahedral cages of similar sizes was observed in the self-assembly of M with a mixture of H2L1 and H3L2 in aqueous medium. The edge directed tetrahedral cage (T1) was successfully used to perform Michael reactions of a series of water insoluble nitro-olefins assisted by encapsulation into the cage in aqueous medium.

A chiral "Siamese-Twin" calix[4]pyrrole tetramer

We describe our results in the attempted template syntheses of oligomacrocycle calix[4]pyrrole dimer 4, using Hay coupling reaction conditions, tetraalkynyl calix[4]pyrrole 5 as starting material and two bipyridyl N-oxides of different length as templates. We found that the short bis-N-oxide 3 was not an efficient template for the macrocyclization reaction producing an insoluble crude reaction mixture containing exclusively oligomerization and polycondensation products. On the other hand, when we used the long bis-N-oxide 6 as template we obtained a soluble crude reaction mixture in which we did not detect the expected calix[4]pyrrole dimer 4. Instead, we isolated, in low yield, an encapsulation complex of the bis-N-oxide 6 in a partially reacted calix[4]pyrrole dimer. The major isolated species was an unprecedented calix[4]pyrrole tetramer encapsulating two molecules of 6. The complex adopted a chiral helical-like conformation in the solid state resembling the previously described so-called "Siamese-Twin porphyrins".

Assembled molecular face-rotating polyhedra to transfer chirality from two to three dimensions

In nature, protein subunits on the capsids of many icosahedral viruses form rotational patterns, and mathematicians also incorporate asymmetric patterns into faces of polyhedra. Chemists have constructed molecular polyhedra with vacant or highly symmetric faces, but very little is known about constructing polyhedra with asymmetric faces. Here we report a strategy to embellish a C_3h truxene unit with rotational patterns into the faces of an octahedron, forming chiral octahedra that exhibit the largest molar ellipticity ever reported, to the best of our knowledge. The directionalities of the facial rotations can be controlled by vertices to achieve identical rotational directionality on each face, resembling the homo-directionality of virus capsids. Investigations of the kinetics and mechanism reveal that non-covalent interaction among the faces is essential to the facial homo-directionality.

Protein subunits on the capsids of icosahedral viruses can form patterns with rotational symmetry, which are difficult to recreate in the laboratory. Here the authors report a strategy to construct 3D chiral polyhedra with rotational faces from 2D chiral truxene-based units through dynamic covalent chemistry.

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.

Cationic pillar[6]arene/ATP host-guest recognition: selectivity, inhibition of ATP hydrolysis, and application in multidrug resistance treatment

Due to the differences in the cavity size of the hosts and the charge and length of the guests, a cationic water-soluble pillar[6]arene (WP6) selectively complexes with ATP to form a stable 1 : 1 inclusion complex WP6⊃ATP. This host-guest complexation was utilized to efficiently inhibit the hydrolysis of ATP, arising from the existence of the hydrophobic cavity of WP6. A folic acid functionalized diblock copolymer (FA-PEG-b-PAA) was employed to PEGylate WP6 to endow the polyion complex (PIC) micelles with specific targeting ability, preferentially delivering WP6 to folate receptor over-expressing KB cell. This host-guest complexation was further used to block the efflux pump to transport anticancer drugs out of cells by cutting off the energy source, which enhanced the efficacy of the cancer chemotherapy of DOX·HCl towards drug resistant MCF-7/ADR cell. This supramolecular method provides an extremely distinct strategy to potentially overcome multidrug resistance (MDR).

[C-H···anion] interactions mediate the templation and anion binding properties of topologically non-trivial metal-organic structures in aqueous solutions

Two synthetic approaches-temperature variation and anion templation-allowed for the selective formation of a [2]catenane ([2]C4+ ) or a trefoil knot (TK6+ ), or for the enhanced formation of a Solomon link (SL8+ ), all from a simple set of starting materials (Zn(ii) acetate, diformylpyridine (DFP) and a diamino-2,2'-bipyridine (DAB)) in mixed aqueous solutions. The catenane formed exclusively at 90 °C in a 1 : 1 mixed solvent of D2O and MeOD. In the presence of bromide ion as template, TK6+ formed exclusively at 50 °C in the same solvent. In the solid state, TK6+ hosts two bromide ions in its central cavity by forming six Csp2 -H hydrogen bonds. In D2O, TK6+ , which was originally prepared as a trifluoroacetate (TFA) salt, was found to exchange two TFA counterions for two monovalent anions of different sizes and shapes, which lodged within the knot's central cavity. In contrast to bromide, the larger triflate anion (CF3SO3-) promoted the formation of SL8+ , which was characterized by 1H NMR spectroscopy and mass spectrometry. Two dimensional heteronuclear 19F-1H-HOSEY NMR experiments detected CH···F interactions inside the cavity of SL8+ . Thus, the product distribution of this dynamic link forming system is sensitive to temperature and the size and shape of the anion template, and one of the products, TK6+ , is capable of binding a variety of monovalent anions in D2O with high affinity (with log β2 values of 4 to 6 being typical).

Exploiting recognition-mediated assembly and reactivity in [2]rotaxane formation

A small molecular reaction network exploits recognition-mediated reactive processes in order to drive the assembly and formation of both a self-replicating linear template (thread) and a [2]rotaxane, in which the linear template is encircled by a diamide macrocycle. Complementary recognition sites, placed at strategic positions on the reactive building blocks, drive these assembly and replication processes. Template-instructed experiments show that the thread is capable of efficient self-replication and that no cross-catalytic relationships exist between the thread and the [2]rotaxane. The rate of [2]rotaxane formation is insensitive to the addition of a preformed template, however, [2]rotaxane formation does show enhanced diastereoselectivity, most likely originating from its recognition-mediated formation through a ternary reactive complex.

Dynamic covalent synthesis of aryleneethynylene cages through alkyne metathesis: dimer, tetramer, or interlocked complex?

A modular dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) and the mechanistic features were explored.

A dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) was explored. Our study on the relationship of the COP structures and the geometry of their building blocks reveals that the topology of aryleneethynylene COPs strongly depends on the size of the building blocks. A tetramer (D_2h symmetric), dimer, or interlocked complex can be formed from monomers with the same face-to-edge angle but in different sizes. As alkyne metathesis is a self-exchange reaction and non-directional, the cyclooligomerization of multi-alkyne monomers involves both intramolecular cyclization and intermolecular metathesis reaction, resulting in complicated thermodynamic process disturbed by kinetic competition. Although a tetrahedron-shaped tetramer (T_d symmetric) has comparable thermodynamic stability to a D_2h symmetric tetramer, its formation is kinetically disfavored and was not observed experimentally. Aryleneethynylene COPs consist of purely unsaturated carbon backbones and exhibit large internal cavities, which would have interesting applications in host–guest chemistry and development of porous materials.

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.

Fluorescence indicator displacement detection based on pillar[5]arene-assisted dye deprotonation

A fluorescence switch based on a pH-sensitive dye and a cationic pillar[5]arene was employed in fluorescence indicator displacement detection of phenolic contaminants.

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.

Knot theory in modern chemistry

This tutorial review provides an introduction to the mathematics of knots and topological concepts in the context of the chemical sciences.

Multicavity macrocyclic hosts

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

Anion-templated hexagonal nanotubes

Hydrogen bonding between bromide anions and a tetrahydroxytriptycene ligand was used to assemble crystalline hexagonal tubes with nanometer diameters in good yield. Use of a hexahydroxytriptycene ligand again gave hexagonal nanotubes, but containing the spontaneously-oxidised quinone-tetrahydroxy ligand. The surprisingly robust nanotubes are stable to heat, vacuum and water, and represent an unprecedented use of O-H···anion coordination to assemble complex three-dimensional structures.

Particles with changeable topology in nematic colloids

We show that nematic colloids can serve as a highly variable and controllable platform for studying inclusions with changeable topology and their effects on the surrounding ordering fields. We explore morphing of toroidal and knotted colloidal particles into effective spheres, distinctively changing their Euler characteristic and affecting the surrounding nematic field, including topological defect structures. With toroidal particles, the inner nematic defect eventually transitions from a wide loop to a point defect (a small loop). Trefoil particles become linked with two knotted defect loops, mutually forming a three component link, that upon tightening transform into a two-component particle-defect loop link. For more detailed topological analysis, Pontryagin-Thom surfaces are calculated and visualised, indicating an interesting cascade of defect rewirings caused by the shape morphing of the knotted particles.

Molecular knots in biology and chemistry

Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

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.

Controllable Coordination Self-Assembly Based on Flexible Tripodal Ligands: From Finite Metallocages to Infinite Polycatenanes Step by Step

This article describes the developments in coordination self-assembly based on flexible tripodal ligands with different metal species. Various finite metallocages such as M3 L2 , M6 L8 , M6 L4 , M4 L4 and different catenanes based on discrete metallocages constructed from flexible tripodal ligands with suitable metal species are presented here. Many M3 L2 metallocages based on ligands L(1) -L(12) and different two-coordinated metal species have been prepared, in which various Ag(I) salts and other metal species that have been protected by suitable groups, such as Zn(OAc)2 , ZnBr2 , and PdBr2 , have been used as effective acceptors. All of the M6 L8 -type metallocages are constructed from ligands L(2) or L(12) -L(20) and different four-coordinated metal species, such as various palladium(II) salts or NiCl2 , and have similar topological structures. Only a few discrete M6 L4 -type metallocages, based on ligands L(21) -L(24) , have been reported, using different strategies such as protecting groups and steric hindrance. All of the M4 L4 -type cages have similar topological structures and are constructed from ligands L(25) -L(29) with multiple donor sites. More intriguing interlocking ensembles constructed from discrete metallocages are also described here in detail, namely, three [2]catenanes based on ligands L(30) -L(32) and four polycatenanes based on ligands L(33) -L(34) .

A Solomon link through an interwoven molecular grid

A molecular Solomon link was synthesized through the assembly of an interwoven molecular grid consisting of four bis(benzimidazolepyridyl)benzthiazolo[5,4-d]thiazole ligands and four zinc(II), iron(II), or cobalt(II) cations, followed by ring-closing olefin metathesis. NMR spectroscopy, mass spectrometry, and X-ray crystallography confirmed the doubly interlocked topology, and subsequent demetalation afforded the wholly organic Solomon link. The synthesis, in which each metal ion defines the crossing point of two ligand strands, suggests that interwoven molecular grids should be useful scaffolds for the rational construction of other topologically complex structures.

An infinite chainmail of M6L6 metallacycles featuring multiple Borromean links

Borromean rings or links are topologically complex assemblies of three entangled rings where no two rings are interlinked in a chain-like catenane, yet the three rings cannot be separated. We report here a metallacycle complex whose crystalline network forms the first example of a new class of entanglement. The complex is formed from the self-assembly of CuBr2 with the cyclotriveratrylene-scaffold ligand (±)-tris(iso-nicotinoyl)cyclotriguaiacylene. Individual metallacycles are interwoven into a two-dimensional chainmail network where each metallacycle exhibits multiple Borromean-ring-like associations with its neighbours. This only occurs in the solid state, and also represents the first example of a crystalline infinite chainmail two-dimensional network. Crystals of the complex were twinned and have an unusual hollow tubular morphology that is likely to result from a localized dissolution-recrystallization process.

On Zn(II) 2,2'-bisdipyrrin circular helicates

Coordination of two 2,2'-bisdipyrrin ligands, bearing methyl ester or methylthioether peripheral groups, with Zn(II) cations leads not only to the formation of the expected linear helicates but also concomitantly to novel tri- and tetra-nuclear circular species that have been isolated and fully characterized in solution and by X-ray diffraction.

Encapsulation of xenon by a self-assembled Fe4L6 metallosupramolecular cage

We report (129)Xe NMR experiments showing that a Fe4L6 metallosupramolecular cage can encapsulate xenon in water with a binding constant of 16 M(-1). The observations pave the way for exploiting metallosupramolecular cages as economical means to extract rare gases as well as (129)Xe NMR-based bio-, pH, and temperature sensors. Xe in the Fe4L6 cage has an unusual chemical shift downfield from free Xe in water. The exchange rate between the encapsulated and free Xe was determined to be about 10 Hz, potentially allowing signal amplification via chemical exchange saturation transfer. Computational treatment showed that dynamical effects of Xe motion as well as relativistic effects have significant contributions to the chemical shift of Xe in the cage and enabled the replication of the observed linear temperature dependence of the shift.