Stereoselective Synthesis of Molecular Square and Granny Knots

The Topological Transformation of 41 Knot to 412 Link through Supramolecular Fusion

Realizing topological transformation through supramolecular fusion is particularly challenging, as the self-assembly of disparate components often results in the orthogonal assembly of building blocks into distinct structures rather than the formation of a heteroleptic architecture. This study introduces a topological transformation, transitioning from a figure-eight knot (41 knot) to a Solomon link (412 link) through a supramolecular fusion process. By employing two structurally similar amino acid ligands (L1 and L3) of varying lengths as bridge ligands, we obtained figure-eight knot 1 and a molecular tweezer-like compound 3 when individually complexed with binuclear Cp*Rh acceptor B1. Our results revealed that subtle modifications to bridge ligands can lead to dramatic changes in their structures and recognition properties. Moreover, we successfully achieved the targeted formation of a heteroleptic Solomon link 4 by blending figure-eight knot 1 and compound 3 in a 1:1 ratio without the need for templates. This procedure effortlessly converted the 41 knot into a 412 link, thus marking a significant advancement in the topological transformation. This work not only marks the construction of the first heteroleptic Solomon link comprising two distinct metallamacrocycles but also demonstrates a process of supramolecular fusion-based topological transformation involving three distinct topological structures.

Template Assisted Synthesis of Linear [5]Catenane by Post-Functionalization of Templated [2]Catenane and Using Click Reaction

Polymers with all mechanically interlocked rings, such as linear [n]catenanes, have great potential as functional materials due to possible higher degrees of freedom that may contribute to their flexibility but remain elusive. All the synthetic methods used to prepare such a polymer yield mixtures of products. In the absence of higher molecular weight linear [n]catenanes, emphasis on synthesizing low molecular weight oligomers is being pursued. Here, we have described the synthesis of a linear [5]catenane by post-functionalizing a Co(III) templated [2]catenane having a pyridine-diamide unit free for further metal ion coordination. Two molecules were synthesized with suitable threading groups: one, two terminal azide groups, and two, with two terminal alkyne groups to form two [3]pseudorotaxane utilizing Co(III) coordination. These units were then joined, forming a macrocycle, using click reaction, giving the desired metalated linear [5]catenane in 40 % yield. Removal of metal ions leads to linear [5]catenane. In addition, the formation of linear [3] and [2]catenane are also observed. All synthesized structures have been isolated by column chromatographic technique and characterized by 1H-NMR, 13C-NMR, and mass spectroscopy.

Template Assisted One-Pot Synthesis of [2], Linear [3], and Radial [4]Catenane via Click Reaction

Design and synthesis of higher order catenane are unexpectedly complex and involve precise cooperation among the precursors overcoming competing and opposing interactions. We achieved synthesis of [2], linear [3], radial [4] in a one-pot reaction by consecutive ring closing through click reactions. This synthesis gave three isolable products due to two, four, and six-click reactions between suitable coupling partners. Yields of the isolate templated-catenane decrease from lower to higher-ordered catenane (40 %, 12 %, and 4 %), probably due to the bite angle as well as the flexibility of the reacting partners. Removal of templating cobalt(III) ion leads to the formation of fully organic [2], linear [3], and radial [4]catenane. These synthesized catenanes were purified by column chromatography and characterized by 1H-NMR, 13C-NMR, and ESI-MS spectroscopy. The synthesized catenanes have free binding sites suitable for post-functionalization and may be used for the synthesis of higher-ordered catenane.

Iminopyrrole-Based Self-Assembly: A Route to Intrinsically Flexible Molecular Links and Knots

The use of 2,5-diformylpyrrole in self-assembly reactions with diamines and Zn(II)/Cd(II) salts allowed the preparation of [2]catenane, trefoil knot, and Borromean rings. The intrinsically dynamic nature of the diiminopyrrole motif rendered all of the formed assemblies intramolecularly flexible. The presence of diiminopyrrole revealed new coordination motifs and influenced the host-guest chemistry of the systems, as illustrated by hexafluorophosphate encapsulation by Borromean rings.

Knotting matters: orderly molecular entanglements

Entangling strands in a well-ordered manner can produce useful effects, from shoelaces and fishing nets to brown paper packages tied up with strings. At the nanoscale, non-crystalline polymer chains of sufficient length and flexibility randomly form tangled mixtures containing open knots of different sizes, shapes and complexity. However, discrete molecular knots of precise topology can also be obtained by controlling the number, sequence and stereochemistry of strand crossings: orderly molecular entanglements. During the last decade, substantial progress in the nascent field of molecular nanotopology has been made, with general synthetic strategies and new knotting motifs introduced, along with insights into the properties and functions of ordered tangle sequences. Conformational restrictions imparted by knotting can induce allostery, strong and selective anion binding, catalytic activity, lead to effective chiral expression across length scales, binding modes in conformations efficacious for drug delivery, and facilitate mechanical function at the molecular level. As complex molecular topologies become increasingly synthetically accessible they have the potential to play a significant role in molecular and materials design strategies. We highlight particular examples of molecular knots to illustrate why these are a few of our favourite things.

A Co-conformationally "Topologically" Chiral Catenane

Catenanes composed of two achiral rings that are oriented (Cnh symmetry) because of the sequence of atoms they contain are referred to as topologically chiral. Here, we present the synthesis of a highly enantioenriched catenane containing a related but overlooked "co-conformationally 'topologically' chiral" stereogenic unit, which arises when a bilaterally symmetric Cnv ring is desymmetrized by the position of an oriented macrocycle.

Highly selective synthesis and near-infrared photothermal conversion of metalla-Borromean ring and [2]catenane assemblies

Although the selective synthesis of complicated supramolecular architectures has seen significant progress in recent years, the exploration of the properties of these complexes remains a fascinating challenge. Herein, a series of new supramolecular topologies, metalla[2]catenanes and Borromean ring assemblies, were constructed based on appropriate Cp*Rh building blocks and two rigid alkynyl pyridine ligands (L1, L2) via coordination-driven self-assembly. Interestingly, minor differences between the two rigid alkynyl pyridine ligands with/without organic substituents led to products with dramatically different topologies. Careful structural analysis showed that π–π stacking interactions play a crucial role in stabilizing these [2]catenanes and Borromean ring assemblies, while also promoting nonradiative transitions and triggering photothermal conversion in both the solution and the solid states. These results were showcased through comparative studies of the NIR photothermal conversion efficiencies of the Borromean ring assemblies, [2]catenanes and metallarectangles, which exhibited a wide range of photothermal conversion efficiencies (12.64–72.21%). The influence of the different Cp*Rh building blocks on the NIR photothermal conversion efficiencies of their assemblies was investigated. Good photothermal conversion properties of the assemblies were also found in the solid state. This study provides a new strategy to construct valuable half-sandwich-based NIR photothermal conversion materials while also providing promising candidates for the further development of materials science.

The selective synthesis of three kinds of supermolecular topologies, molecular Borromean ring, [2]catenane and metallarectangle based on two alkynyl ligands is presented. Remarkably, the NIR photothermal conversion efficiency was found to improve as the π–π stacking increases.

Distinctive features and challenges in catenane chemistry

From being an aesthetic molecular object to a building block for the construction of molecular machines, catenanes and related mechanically interlocked molecules (MIMs) continue to attract immense interest in many research areas. Catenane chemistry is closely tied to that of rotaxanes and knots, and involves concepts like mechanical bonds, chemical topology and co-conformation that are unique to these molecules. Yet, because of their different topological structures and mechanical bond properties, there are some fundamental differences between the chemistry of catenanes and that of rotaxanes and knots although the boundary is sometimes blurred. Clearly distinguishing these differences, in aspects of bonding, structure, synthesis and properties, between catenanes and other MIMs is therefore of fundamental importance to understand their chemistry and explore the new opportunities from mechanical bonds.

Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures

By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.

Synthesis and Near-Infrared Photothermal Conversion of Discrete Supramolecular Topologies Featuring Half-Sandwich [Cp*Rh] Units

Although a large number of novel supramolecular topologies featuring half-sandwich [Cp*Rh] units have been reported, investigations into the properties of these architectures are astoundingly rare. In addition, the bidentate ligands employed to prepare these species have remained relatively homogeneous (i.e., symmetrical bis(pyri-4-dyl) ligands). To address these paucities in the field, the novel unsymmetrical ligand L2 and the rarely reported pyri-3-dyl ligand L3, all bearing aromatic phenazine groups (an N-heterocyclic analog of anthracene), were synthesized in addition to the common symmetrical pyri-4-dyl L1. [3]Catenane, [2]catenane, and Borromean rings assemblies were constructed successfully by the self-assembly of L1 with different building blocks. Afterward, ligand L2 was applied to prepare two novel molecular-tweezer-like compounds. Lastly, a twisted [2]catenane (relative to the [2]catenane constructed using L1) and a sandwiched metallarectangle were obtained using L3. π-π stacking interactions were observed to play a significant role in stabilizing these topologies, which also promoted nonradiative migration and triggered photothermal conversion in both the solution and the solid state. In the solution state, a clear rule of thumb was derived whereby the NIR photothermal conversion efficiency increased as the π-π stacking increased, and a very high photothermal conversion efficiency (35.5-62.4%) was observed. In addition, this family of half-sandwich-based assemblies also exhibited good photothermal conversion properties in the crystalline and noncrystal powder states. This research provides a novel method to synthesize excellent NIR photothermal conversion materials featuring half-sandwich [Cp*Rh] units and points to potential applications in the near future.

Piecewise-linear embeddings of knots and links with rotoinversion symmetry

This article describes the simplest members of an infinite family of knots and links that have achiral piecewise-linear embeddings in which linear segments (sticks) meet at corners. The structures described are all corner- and stick-2-transitive - the smallest possible for achiral knots.

Construction of organometallic trefoil knots and one-dimensional chains featuring half-sandwich Cp*Rh corner units and an abnormal zwitterion ligand

An abnormal flexible O-coordinated zwitterion ligand L shows self-adaptive conformation behaviour in chemical self-assembly. Two trefoil knots were obtained with C-shaped ligand L and two novel 1D chains were obtained with Z-shaped ligand L.

Effects of turn-structure on folding and entanglement in artificial molecular overhand knots

The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design.

Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.

Isogonal weavings on the sphere: knots, links, polycatenanes

Mathematical knots and links are described as piecewise linear - straight, non-intersecting sticks meeting at corners. Isogonal structures have all corners related by symmetry (`vertex'-transitive). Corner- and stick-transitive structures are termed regular. No regular knots are found. Regular links are cubic or icosahedral and a complete account of these (36 in number) is given, including optimal (thickest-stick) embeddings. Stick 2-transitive isogonal structures are again cubic and icosahedral and also encompass the infinite family of torus knots and links. The major types of these structures are identified and reported with optimal embeddings. The relevance of this work to materials chemistry and biochemistry is noted.

Tying different knots in a molecular strand

The properties of knots are exploited in a range of applications, from shoelaces to the knots used for climbing, fishing and sailing¹. Although knots are found in DNA and proteins², and form randomly in other long polymer chains^3,4, methods for tying⁵ different sorts of knots in a synthetic nanoscale strand are lacking. Molecular knots of high symmetry have previously been synthesized by using non-covalent interactions to assemble and entangle molecular chains^6-15, but in such instances the template and/or strand structure intrinsically determines topology, which means that only one type of knot is usually possible. Here we show that interspersing coordination sites for different metal ions within an artificial molecular strand enables it to be tied into multiple knots. Three topoisomers-an unknot (0₁) macrocycle, a trefoil (3₁) knot^6-15, and a three-twist (5₂) knot-were each selectively prepared from the same molecular strand by using transition-metal and lanthanide ions to guide chain folding in a manner reminiscent of the action of protein chaperones¹⁶. We find that the metal-ion-induced folding can proceed with stereoinduction: in the case of one knot, a lanthanide(III)-coordinated crossing pattern formed only with a copper(I)-coordinated crossing of particular handedness. In an unanticipated finding, metal-ion coordination was also found to translocate an entanglement from one region of a knotted molecular structure to another, resulting in an increase in writhe (topological strain) in the new knotted conformation. The knot topology affects the chemical properties of the strand: whereas the tighter 5₂ knot can bind two different metal ions simultaneously, the looser 3₁ isomer can bind only either one copper(I) ion or one lutetium(III) ion. The ability to tie nanoscale chains into different knots offers opportunities to explore the modification of the structure and properties of synthetic oligomers, polymers and supramolecules.

Lanthanide-Containing Rotaxanes, Catenanes, and Knots

The valuable luminescence, magnetic, and catalytic properties of lanthanide cations are beginning to be exploited in conjunction with structurally exotic mechanically interlocked molecules (MIMs) such as rotaxanes, catenanes and knots. This Minireview provides an account of this rapidly developing research area commencing with the use of lanthanides in extended MIM-containing frameworks. Then, attention turns to discrete lanthanide-containing pseudorotaxanes, followed by fully interlocked rotaxanes, catenanes and knots - where lanthanides have not only been incorporated into MIM architectures but have also been used to template formation of the interlocked structure. Particular focus is paid to examples where the lanthanide MIMs have been put to useful applications, in what is still a relatively youthful avenue of research in both lanthanide coordination chemistry and the chemistry of mechanically interlocked molecules.

Synthesis of a new solvent-responsive pillar[5]arene-based [1]rotaxane molecular machine

In this work, we designed a new pillar[5]arene-based molecular machine responsive to the polarity of different solvents, which can exist in an interlocked structure in CDCl₃ and CD₃OD, and can exist in an extended form in DMSO and was studied by ¹H and 2D NMR spectroscopy, HR(MS) and fluorescence spectroscopy.

Radical-Induced Hierarchical Self-Assembly Involving Supramolecular Coordination Complexes in Both Solution and Solid States

To explore a new supramolecular interaction as the main driving force to induce hierarchical self-assembly (HSA) is of great importance in supramolecular chemistry. Herein, we present a radical-induced HSA process through the construction of well-defined rhomboidal metallacycles containing triphenylamine (TPA) moieties. The light-induced radical generation of the TPA-based metallacycle has been demonstrated, which was found to subsequently drive hierarchical self-assembly of metallacycles in both solution and solid states. The morphologies of nanovesicle structures and nanospheres resulting from hierarchical self-assembly have been well-illustrated by using TEM and high-angle annular dark-field STEM (HAADF-STEM) micrographs. The mechanism of HSA is supposed to be associated with the TPA radical interaction and metallacycle stacking interaction, which has been supported by the coarse-grained molecular dynamics simulations. This study provides important information to understand the fundamental TPA radical interaction, which thus injects new energy into the hierarchical self-assembly of supramolecular coordination complexes (SCCs). More interestingly, the stability of TPA radical cations was significantly increased in these metallacycles during the hierarchical self-assembly process, thereby opening a new way to develop stable organic radical cations in the future.

Self-Sorting Assembly of Molecular Trefoil Knots of Single Handedness

We report on the stereoselective synthesis of trefoil knots of single topological handedness in up to 90% yield (over two steps) through the formation of trimeric circular helicates from ligand strands containing either imine or, unexpectedly, amide chelating units and metal ion templates of the appropriate coordination character (zinc(II) for imines; cobalt(III) for amides). The coordination stereochemistry of the octahedral metal complexes is determined by asymmetric carbon centers in the strands, ultimately translating into trefoil knots that are a single enantiomer, both physically and in terms of their fundamental topology. Both the imine-zinc and amide-cobalt systems display self-sorting behavior, with racemic ligands forming knots that individually contain only building blocks of the same chirality. The knots and the corresponding trimeric circular helicate intermediates (Zn(II)₃ complex for the imine ligands; Co(III)₃ complex for the amide ligands) were characterized by nuclear magnetic resonance spectroscopy, mass spectrometry, and X-ray crystallography. The latter confirms the trefoil knots as 84-membered macrocycles, with each of the metal ions sited at a crossing point for three regions of the strand. The stereochemistry of the octahedral coordination centers imparts alternating crossings of the same handedness within each circular helicate. The expression of chirality of the knotted molecules was probed by circular dichroism: The topological handedness of the demetalated knots was found to have a greater effect on the CD response than the Euclidean chirality of an individual chiral center.

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.