Template synthesis of molecular knots

Securing a Supramolecular Architecture by Tying a Stopper Knot

We report on a rotaxane-like architecture secured by the in situ tying of an overhand knot in the tris(2,6-pyridyldicarboxamide) region of the axle through complexation with a lanthanide ion (Lu3+ ). The increase in steric bulk caused by the knotting locks a crown ether onto the thread. Removal of the lutetium ion unties the knot, and when the axle binding site for the ring is deactivated, the macrocycle spontaneously dethreads. When the binding interaction is switched on again, the crown ether rethreads over the 10 nm length of the untangled strand. The overhand knot can be retied, relocking the threaded structure, by once again adding lutetium ions.

Discovering privileged topologies of molecular knots with self-assembling models

Despite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.

Synthesis of a Chiral [2]Rotaxane: Induction of a Helical Structure through Double Threading

A helically chiral [2]rotaxane featuring two ammonium ion recognition sites in the dumbbell-like component and a calix-bis-crown ether as the macrocyclic component was synthesized, but with no chirality in either individual component. The enantiomeric nature of the isomers, separated through chiral HPLC, was apparent in their CD spectra, which were mirror images for all wavelengths.

Nematic colloidal knots in topological environments

The role of environment in shaping material properties is of great significance, but less is known about how non-trivial topology of the environment couples to material states, which can be of non-trivial topology themselves. In this paper, we demonstrate the role of the topology of the environment on the formation of complex nematic fields and defect structures, specifically in the system of nematic colloidal knots. The topological environments around knotted colloidal particles are suggested to exist as spherical surface-patterned nematic cavities imposing radial, uniform or hyperbolic nematic profiles. We show that topologically different nematic environments significantly affect and create differences in the colloidal field structure created within the environment, such as the location, profile and number of topological defects. Specifically, we demonstrate that topological environments in combination with knotted colloidal particles of non-trivial topology lead to the formation of diverse nematic knotted and linked fields. These fields are different adaptations of the knotted shape of the colloidal particles, creating knots and links of topological defects as well as escaped-core defect-like solitonic structures. These are observed in chiral nematic media but here are stabilised in achiral nematic media as a result of the distinct shape of the knotted colloidal particle, with a double helix segment and nematic environmental patterns. More generally, this paper is a contribution towards understanding the role of environment, especially its topology, on the response and defect formation in elastic fields, such as in nematic liquid crystal colloids.

Hierarchical Assembly of an Interlocked M8 L16 Container

The self-assembly of eight PdII cations and sixteen phenanthrene-derived bridging ligands with 60° bite angles yielded a novel M8 L16 metallosupramolecular architecture composed of two interlocked D4h -symmetric barrel-shaped containers. Mass spectrometry, NMR spectroscopy, and X-ray analysis revealed this self-assembled structure to be a very large "Hopf link" catenane featuring channel-like cavities, which are occupied by NO3- anions. The importance of the anions as catenation templates became imminent when we observed the nitrate-triggered structural rearrangement of a mixture of M3 L6 and M4 L8 assemblies formed in the presence of BF4- anions into the same interlocked molecule. Furthermore, the densely packed structure of the M8 L16 catenane was exploited in the preparation of a hexyloxy-functionalized analogue, which further self-assembled into vesicle-like aggregates in a reversible manner.

Electronic and electrochemical properties of grid-type metal ion complexes (Fe+2 and Co2+) with a pyridine-pyrimidine-pyridine based bis(hydrazone)

Se reporta la síntesis de nuevos complejos metálicos de Co2+ y Fe2+ tipo rejilla que contienen como ligando orgánico una doble hidrazona altamente soluble en solventes orgánicos. Los datos obtenidos de resonancia magnética nuclear (RMN 1H), espectroscopía infrarroja con transformada de Fourier (FT-IR) y análisis elemental indican que los complejos adoptaron una estructura de tipo rejilla. Las propiedades electrónicas de las metalo-rejillas fueron analizadas a través de espectroscopía UV-Vis en cloroformo, metanol y diclorometano. Adicionalmente, se realizaron medidas de voltamperometría cíclica y voltametría de onda cuadrada en DMF. Los complejos exhibieron dos procesos de oxidación atribuidos al ligando orgánico y a varios eventos reductivos que comprometían al ligando y a los centros metálicos, por tanto, la interacción entre la naturaleza del ion metálico y la estructura del ligando fue analizada en detalle. Estos resultados representan un avance en la química de metalo-rejillas no solo por los escasos reportes de propiedades electroquímicas encontrados en la literatura, sino también por el diseño de nuevos ligandos hidrazónicos de alta solubilidad y fácil preparación.

Chiral macrocyclic terpyridine complexes

Interlinking of two terpyridine ligands results in mononuclear chiral metal complexes (Fe and Ru) which were separated into their enantiomers.

The syntheses of novel chiral M(ii) bis(terpyridine) cage complexes Fe(L1)₂-c and Ru(L1)₂-c are described. The extraordinary design of the precursors Fe(L1)₂ and Ru(L1)₂ allows perfect preorganization for the final closing step. Due to the rigidity of the spacers between the two terpyridine moieties, the two isolated enantiomers barely racemize at room temperature in solution. The stable and axially chiral bis(terpyridine) Fe(ii) and Ru(ii) complexes were fully characterized by NMR-spectroscopy, UV-Vis spectroscopy, electrochemical measurements, high resolution mass spectrometry, circular dichroism measurements, and X-ray structural analysis.

Molecular Trefoil Knot from a Trimeric Circular Helicate

We report the two-step synthesis of a molecular trefoil knot in 90% overall yield through the self-assembly of a 12-component trimeric circular zinc helicate followed by ring closing metathesis of six pendant alkene chains. Both the trimeric circular helicate intermediate and the resulting trefoil knot were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography.

Metal ions in the synthesis of interlocked molecules and materials

The use of metal ions to template the synthesis of catenanes by Sauvage and co-workers was a pivotal moment in the development of the field of interlocked molecules. In this Review Article we shall examine the different roles metal-ligand interactions play in modern syntheses of interlocked molecules and materials, with a particular focus on seminal contributions and the advantages and disadvantages of employing metal ligand interactions.

Biological and related applications of pillar[n]arenes

Pillar[n]arenes are a new class of synthetic supramolecular macrocycles streamlined by their particular pillar-shaped architecture which consists of an electron-rich cavity and two fine-tuneable rims. The ease and diversity of the functionalization of the two rims open possibilities for the design of new architectures, topological isomers, and scaffolds. Significantly, this emerging class of macrocyclic receptors offers a unique platform for biological purposes. This review article covers the most recent contributions from the pillar[n]arene field in terms of artificial membrane transport systems, controlled drug delivery systems, biomedical imaging, biosensors, cell adhesion, fluorescent sensing, and pesticide detection based on host-guest interactions. The review also uniquely describes the properties of sub-units that make pillar[n]arenes suitable for biological applications and it provides a detailed outline for the design of new innovative pillar-like structures with specific properties to open up a new avenue for pillar[n]arene chemistry.

Integrative Self-Sorting: One-Pot Synthesis of a Hetero[4]rotaxane from a Daisy-Chain-Containing Hetero[4]pseudorotaxane

The structural complexity of mechanically interlocked molecules are very attractive to chemists owing to the challenges they present. In this article, novel mechanically interlocked molecules with a daisy-chain-containing hetero[4]rotaxane motif were efficiently synthesized. In addition, a novel integrative self-sorting strategy is demonstrated, involving an ABB-type (A for host, dibenzo-24-crown-8 (DB24C8), and B for guest, ammonium salt sites) monomer and a macrocycle host, benzo-21-crown-7 (B21C7), in which the assembled species in hydrogen-bonding-supported solvent only includes a novel daisy-chain-containing hetero[4]pseudorotaxane. The found self-sorting process involves the integrative recognition between B21C7 macrocycles and carefully designed components simultaneously containing two types of secondary ammonium ions and a host molecule, DB24C8 crown ether. The self-sorting strategy is integrative to undertake self-recognition behavior to form one single species of pseudorotaxane compared with the previous report. This self-sorting system can be used for the efficient one-pot synthesis of a daisy-chain-containing hetero[4]rotaxane in a good yield. The structure of hetero[4]rotaxane was confirmed by ¹ H NMR spectroscopy and high-resolution electrospray ionization (HR-ESI) mass spectrometry.

Knots modify the coil-stretch transition in linear DNA polymers

We perform single-molecule DNA experiments to investigate the relaxation dynamics of knotted polymers and examine the steady-state behavior of knotted polymers in elongational fields. The occurrence of a knot reduces the relaxation time of a molecule and leads to a shift in the molecule's coil-stretch transition to larger strain rates. We measure chain extension and extension fluctuations as a function of strain rate for unknotted and knotted molecules. The curves for knotted molecules can be collapsed onto the unknotted curves by defining an effective Weissenberg number based on the measured knotted relaxation time in the low extension regime, or a relaxation time based on Rouse/Zimm scaling theories in the high extension regime. Because a knot reduces a molecule's relaxation time, we observe that knot untying near the coil-stretch transition can result in dramatic changes in the molecule's conformation. For example, a knotted molecule at a given strain rate can experience a stretch-coil transition, followed by a coil-stretch transition, after the knot partially or fully unties.

Imine-based [2]catenanes in water

We report the efficient condensation of imine-based macrocycles from dialdehyde A and aliphatic diamines B n in pure water. Within the libraries, we identified a family of homologous amphiphilic [2]catenanes, whose self-assembly is primarily driven by the hydrophobic effect. The length and odd-even character of the diamine alkyl linker dictate both the yield and the conformation of the [2]catenanes, whose particular thermodynamic stability further shifts the overall equilibrium in favour of imine condensation. These findings highlight the role played by solvophobic effects in the self-assembly of complex architectures.

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.

Covalent post-assembly modification in metallosupramolecular chemistry

This review examines the growing variety of covalent reactions used to achieve the post-assembly modification of self-assembled metallosupramolecular complexes.

Understanding coordination equilibria in solution and gel-phase [2]rotaxanes

An active-metal template approach has been use to synthesise solution and surface bound addressable [2]rotaxanes giving unique insights into thermodynamic equilibria in interlocked structures.

From monomeric complexes to double-stranded helicates constructed around trans-TiO4N2 motifs with intramolecular inter-ligand hydrogen-bonding interactions

Monomeric and double-stranded helicates are built from trans-TiO₄N₂ motifs. Intramolecular hydrogen bonds govern the framework of these species. The strength of these interactions has been investigated.

Selective CO2 Capture and High Proton Conductivity of a Functional Star-of-David Catenane Metal-Organic Framework

Network structures based on Star-of-David catenanes with multiple superior functionalities have been so far elusive, although numerous topologically interesting networks are synthesized. Here, a metal-organic framework featuring fused Star-of-David catenanes is reported. Two triangular metallacycles with opposite handedness are triply intertwined forming a Star-of-David catenane. Each catenane fuses with its six neighbors to generate a porous twofold intercatenated gyroid framework. The compound possesses exceptional stability and exhibits multiple functionalities including highly selective CO₂ capture, high proton conductivity, and coexistence of slow magnetic relaxation and long-range ordering.

Molecular Knots

The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small-molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding, and catalytic activity. As the number and complexity of accessible molecular knot topologies increases, it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we give an overview of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry and molecular structure.

Surface-Assembled Mechanically Interlocked Architectures

Since the advent of supramolecular chemistry, there has been keen interest in the synthesis of interlocked molecules, given their unique potential to act as receptors, molecular machines and even motors. Despite advances in the complexity of molecular machines that can be synthesised and operated in solution, reports of the operation or even attachment of complex supramolecular systems on solid surfaces are less common. Synthetic challenges and a lack of adequate characterisation techniques to monitor the thermodynamic and kinetic influences governing assembly at the solution-surface interface has slowed progress in this area of research. This Review looks at the developments in the field of covalently assembled interlocked architectures on gold, silica and polymer surfaces, highlighting the differences observed between solution and surface assembly of these unique structures.

Reversible mechanical protection: building a 3D "suit" around a T-shaped benzimidazole axle

The T-shaped benzimidazolium/crown ether recognition motif was used to prepare suit[1]anes. These novel mechanically interlocked molecules (MIMs) were fully characterized by 1H and 13C NMR spectroscopy, single-crystal X-ray diffraction, UV-vis absorption and fluorescence spectroscopy. By conversion to a suit[1]ane, a simple benzimidazole was shown to be protected from deprotonation by strong base. Moreover, it was demonstrated that this unique three-dimensional encapsulation can be made reversible, thus introducing the concept of "reversible mechanical protection"; a protecting methodology that may have potential applications in synthetic organic chemistry and the design of molecular machinery.

Tight Embrace in a Molecular Knot with Eight Crossings

When it takes eight to tango: Since the synthesis of the simplest of all knots, the trefoil knot, in 1989, the formation of more complex knots has remained extremely challenging. The synthesis of the most complex molecular knot made to date, the 8₁₉ , by Leigh and co-workers thus represents a major step towards building topologically complex architectures.

Direct Self-Assembly of a 2D and 3D Star of David

Two- and three-dimensional metallosupramolecules shaped like a Star of David were synthesized by the self-assembly of a tetratopic pyridyl ligand with a 180° diplatinum(II) motif and Pd^II ions, respectively. In contrast to other strategies, such as template-directed synthesis and stepwise self-assembly, this design enables the formation of 2D and 3D structures in one step and high yield. The structures were characterized by both one-dimensional (¹ H, ¹³ C, ³¹ P) and two-dimensional (COSY, NOESY, DOSY) NMR spectroscopy, ESI-MS, ion-mobility mass spectrometry (IM-MS), AFM, and TEM. The stabilities of the 2D and 3D structures were measured and compared by gradient tandem mass spectrometry (gMS² ). The high stability of the 3D Star of David was correlated to its high density of coordination sites (DOCS).

Synthesizing topological structures containing RNA

Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA-DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure. By using a constructed ssRNA knot as a highly sensitive topological probe, we find that Escherichia coli DNA topoisomerase I has low RNA topoisomerase activity and that the R173A point mutation abolishes the unknotting activity for ssRNA, but not for ssDNA. Furthermore, we discover the topological inhibition of reverse transcription (RT) and obtain different RT-PCR patterns for an ssRNA knot and circle of the same sequence.

PdII2L4-type coordination cages up to three nanometers in size

The utilization of large ligands in coordination-based self-assembly represents an attractive strategy for the construction of supramolecular assemblies more than two nanometers in size. However, the implementation of this strategy is hampered by the fact that the preparation of such ligands often requires substantial synthetic effort. Herein, we describe a simple one-step protocol, which allows large bipyridyl ligands with a bent shape to be synthesized from easily accessible and/or commercially available starting materials. The ligands were used to construct PdII2L4-type coordination cages of unprecedented size. Furthermore, we provide evidence that these cages may be stabilized by close intramolecular packing of lipophilic ligand side chains. Packing effects of this kind are frequently encountered in protein assemblies, but they are seldom used as a design element in metallasupramolecular chemistry.

Halogen bonded Borromean networks by design: topology invariance and metric tuning in a library of multi-component systems

A library of supramolecular anionic networks showing Borromean interpenetration has been prepared by self-assembly of crypt-222, several metal or ammonium halides, and five bis-homologous α,ω-diiodoperfluoroalkanes. Halogen bonding has driven the formation of these anionic networks. Borromean entanglement has been obtained starting from all the four used cations, all the three used anions, but only two of the five used diiodoperfluoroalkanes. As the change of the diiodoperfluoroalkane, the cation, or the anion has a different relative effect on the metrics and bondings of the self-assembled systems, it can be generalized that bonding, namely energetic, features play here a less influential role than metric features in determining the topology of the prepared tetra-component cocrystals. This conclusion may hold true for other multi-component systems and may function as a general heuristic principle when pursuing the preparation of multi-component systems having the same topology but different composition.