Discovery of an Interlocked and Interwoven Molecular Topology in Nanocarbons via Dynamic C-C Bond Formation

Topologically complex carbon nanostructures are an exciting but largely unexplored class of materials due to their challenging synthesis. Previous methods are low yielding because they rely on irreversible Csp2-Csp2 bond formation, which necessitates complex templating strategies to enforce entanglement. Here, reversible zirconocene coupling of alkynes is developed as a new method to access complex molecular topologies, where dynamic C-C bond formation facilitates entanglement under thermodynamic control, allowing the use of simple precursors without the need for preassembly. This strategy enables the scalable, high-yield synthesis of three topologically distinct nanocarbons, including the serendipitous discovery of a structure containing a new topological motif that was not previously identified or realized synthetically. This motif, consisting of an unusual combination of interlocking and interweaving, was recognized to be generalizable to a new topological class of molecules, introduced here as perplexanes.

Computational discovery and systematic analysis of protein entangling motifs in nature: from algorithm to database

Nontrivial protein topology has the potential to revolutionize protein engineering by enabling the manipulation of proteins' stability and dynamics. However, the rarity of topological proteins in nature poses a challenge for their design, synthesis and application, primarily due to the limited number of available entangling motifs as synthetic templates. Discovering these motifs is particularly difficult, as entanglement is a subtle structural feature that is not readily discernible from protein sequences. In this study, we developed a streamlined workflow enabling efficient and accurate identification of structurally reliable and applicable entangling motifs from protein sequences. Through this workflow, we automatically curated a database of 1115 entangling protein motifs from over 100 thousand sequences in the UniProt Knowledgebase. In our database, 73.3% of C2 entangling motifs and 80.1% of C3 entangling motifs exhibited low structural similarity to known protein structures. The entangled structures in the database were categorized into different groups and their functional and biological significance were analyzed. The results were summarized in an online database accessible through a user-friendly web platform, providing researchers with an expanded toolbox of entangling motifs. This resource is poised to significantly advance the field of protein topology engineering and inspire new research directions in protein design and application.

Metal Coordination-Induced Structural Regulation of Twisted Cucurbit[14]uril-Based Supramolecular Assemblies for Mercury Ions Detection on Smart Platform

The high selectivity and reversibility of metal coordination enable precise modulation of the structural morphology of supramolecular assemblies, which is essential for the development and intelligent application of functionalized materials. In this study, sheet-like supramolecular assemblies (Pyr-O@tQ[14]) constructed by twisted cucurbit[14]urils (tQ[14]) and pyrene derivatives (Pyr-O) through host-guest interactions, which exhibit excellent optical properties, achieves highly sensitive detection of Hg2+ by fluorescence quenching, with a limit of detection of 0.177 μM. A novel smart platform, compatible with smartphones, is developed to enhance the detection efficiency and practicality for practical applications. From a microscopic structural perspective, adjusting the concentration of Hg2+ can change the structural morphology of Pyr-O@tQ[14] from lamellar to square and finally to spherical, demonstrating the dynamic control of the assembly structure in response to environmental stimuli. This study not only presents a novel and efficient intelligent quantitative sensing platform for Hg2+ detection but also highlights the unique advantages of tQ[14] in constructing supramolecular assemblies with tunable, responsive structures, opening new avenues for the design and synthesis of advanced smart materials.

Activity-driven polymer knotting for macromolecular topology engineering

Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here, we unexpectedly find that knots can be efficiently generated in active polymer systems. When one end of an actively reptative polymer is anchored, it undergoes continual self-knotting as a result of intermittent giant conformation fluctuations and the outward reptative motion. Once a knot is formed, it migrates to the anchoring point due to a nonequilibrium ratchet effect. Moreover, when the active polymer is grafted on a passive polymer, it can function as a self-propelling soft needle to either transfer its own knots or directly braid knots on the passive polymer. We further show that these active needles can create intermolecular bridging knots between two passive polymers. Our finding highlights the nonequilibrium effects in modifying the dynamic pathways of polymer systems, which have potential applications in macromolecular topology engineering.

Solvent- and Concentration-Induced Topological Transformation of a Ruthenium(II)-Based Trigonal Prism to a Triply Interlocked [2] Catenane

Synthesis of interlocked supramolecular cages has been a growing field of interest due to their structural diversity. Herein, we report the template-free synthesis of a Ru(II) triply interlocked [2] catenane using coordination-driven self-assembly. The self-assembly of a triazine-based tripyridyl donor L (2,4,6-tris(5-(pyridin-4-yl)thiophen-3-yl)-1,3,5-triazine) with a dinuclear Ru(II) acceptor M (Ru2(dhnq)(η6-p-cymene)2)(CF3SO3)2) yielded two distinct structures depending on the solvent and concentration. In methanol, a triply interlocked metalla [2] catenane (MC2) was formed, whereas in nitromethane, a non-interlocked cage (MC1) was obtained. The non-interlocked cage MC1 was gradually converted to MC2 in nitromethane by the increase in the concentration of cage MC1 from 0.5 to 9 mM. The interlocked cage (MC2) was stable after formation and was unaffected by the change in concentration. Notably, the free cage (MC1) exhibited host-guest interactions with polycyclic aromatic aldehydes, stabilizing the non-interlocked structure even at higher concentrations. In contrast, the triply interlocked [2] catenane (MC2) remains stable due to self-penetration and does not encapsulate guest molecules. This work showcases the stimuli-induced irreversible structural transformation of a triangular prismatic cage to its triply interlocked [2] catenane by employing metal-ligand coordination chemistry.

Exploring the Impact of Ring Mobility on the Macroscopic Properties of Doubly Threaded Slide-Ring Gel Networks

The integration of mechanically interlocked molecules (MIMs) into polymeric materials has led to the development of mechanically interlocked polymers (MIPs). One class of MIPs that have gained attention in recent years are slide-ring gels (SRGs), which are generally accessed by crosslinking rings on a main-chain polyrotaxane. The mobility of the interlocked crosslinking moieties along the polymer backbone imparts enhanced properties onto these networks. An alternative synthetic approach to SRGs is to use a doubly threaded ring as the crosslinking moiety, yielding doubly threaded slide-ring gel networks (dt-SRGs). In this study, a photo-curable ligand-containing thread was used to assemble a series of metal-templated pseudo[3]rotaxane crosslinkers that allow access to polymer networks that contain doubly threaded interlocked rings. The physicochemical and mechanical properties of these dt-SRGs with varying size of the ring crosslinking moieties were investigated and compared to an entangled gel (EG) prepared by polymerizing the metal complex of the photo-curable ligand-containing thread, and a corresponding covalent gel (CG). Relative to the EG and CG, the dt-SRGs exhibit enhanced swelling behavior, viscoelastic properties, and stress relaxation characteristics. In addition, the macroscopic properties of dt-SRGs could be altered by "locking" ring mobility in the structure through remetalation, highlighting the impact of the mobility of the crosslinks.

Phosphorescent metallaknots of Au(I)-bis(acetylide) strands directed by Cu(I) π-coordination

Knots containing metal atoms as part of their continuous strand backbone are termed as metallaknots. While several metallaknots have been synthesized through one-pot self-assembly, the designed synthesis of metallaknots by controlling the arrangement of entanglements and strands connectivity remains unexplored. Here, we report the synthesis of metallaknots composed with Au(I)-bis(acetylide) linkages and templated by Cu(I) ions. Varying the ratio of the building blocks results in the switchable formation of two trefoil knots with different stoichiometries and symmetries (C2 or D3) and an entangled metalla-complex. While the entangled complex formed serendipitously, the strand ends can be subsequently linked through coordinative closure to generate a 41 metallaknot in a highly designable fashion. The comparable structural characteristics of resulting metalla-complexes allow us to probe the correlations between their topologies and photophysical properties, showing the backbone rigidity of knots endows complexes with excellent phosphorescent properties. This strategy, in conjunction with the coordinative closure approach, provides a straightforward route for the formation of highly phosphorescent metallaknots that were previously challenging to access.

Cinquefoil Knot Possessing Dynamic and Tunable Metal Coordination

While the majority of knots are made from the metal-template approach, the use of entangled, constrained knotted loops to modulate the coordination of the metal ions remains inadequately elucidated. Here, we report on the coordination chemistry of a 140-atom-long cinquefoil knotted strand comprising five tridentate and five bidentate chelating vacancies. The knotted loop is prepared through the self-assembly of asymmetric "3 + 2" dentate ligands with copper(II) ions that favor five-coordination geometry. The formation of the copper(II) pentameric helicate is confirmed by X-ray crystallography, while the corresponding copper(II) knot is characterized by XPS and LR-/HR ESI-MS. Upon removal of the original template, the knotted ligand facilitates zinc(II) ions, which typically form four- or six-coordination geometries, resulting in the formation of an otherwise inaccessible zinc(II) metallic knot with coordinatively unsaturated metal centers. The coordination numbers and geometries of the zinc(II) cations are undoubtedly determined by X-ray crystallography. Despite the kinetically labile nature and high reversibility of the zinc(II) complex preventing the detection of 5-to-6 coordination equilibrium in solution, the effects on metal-ion coordination induced by knotting hold promise for fine-tuning the coordination of metal complexes.

Folding a Molecular Strand into a Trefoil Knot of Single Handedness with Co(II)/Co(III) Chaperones

We report the synthesis of a right-handed (Δ-stereochemistry of strand crossings) trefoil knot from a single molecular strand containing three pyrazine-2,5-dicarboxamide units adjacent to point-chiral centers and six pyridine moieties. The oligomeric ligand strand folds into an overhand (open-trefoil) knot through the assistance of coordinatively dynamic Co(II) "chaperones" that drive the formation of a three-metal-ion circular helicate. The entangled structure is kinetically locked by oxidation to Co(III) and covalently captured by ring-closing olefin metathesis to generate a trefoil knot of single topological handedness. The stereochemistry of the strand crossings in the metal-coordinated overhand knot is governed by the stereochemistry of the point-chiral carbon centers in the ligand strand. The overhand and trefoil knots were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography. Removal of the metal ions from the knot, followed by hydrogenation of the alkene, yielded the wholly organic trefoil knot. The metal-free knot and parent ligand were investigated by circular dichroism (CD) spectroscopy. The CD spectra indicate that the topological stereochemistry of the knot has a greater effect on the asymmetry of the chromophore environment than do the point-chiral centers of the strand.

Triply Interlocked [2]catenanes: Rational Synthesis, Reversible Conversion Studies and Unprecedented Application in Photothermal Responsive Elastomer

Triply interlocked [2]catenane complexes featuring two identical, mechanically interlocked units are extraordinarily rare chemical compounds, whose properties and applications remain open to detailed studies. Herein, we introduce the rational design of a new ligand precursor, L1, suitable for the synthesis of six triply interlocked [2]catenanes by coordination-driven self-assembly. The interlocked compounds can be reversibly converted into the corresponding simple triangular prism metallacage by addition of H2O or DMF solvents to their CH3OH solutions, thereby demonstrating the importance of π⋅⋅⋅π stacking and hydrogen bonding interactions in the formation of triply interlocked [2]catenanes. Moreover, extensive studies have been conducted to assess the remarkable photothermal conversion performance. Complex 6 a, exhibiting outstanding photothermal conversion performance (conversion efficiency in solution : 31.82 %), is used to prepare novel photoresponsive elastomer in combination with thermally activated liquid crystal elastomer. The resultant material displays robust response to near-infrared (NIR) laser and the capability of completely reforming the shape and reversible actuation, paving the way for the application of half-sandwich organometallic units in photo-responsive smart materials.

Giant Expanded Porous Metallo-Hexagons

Molecular self-assembly is a widely recognized approach for fabricating biomimetic functional nanostructures. Here, we report the synthesis of two giant hollow coronoid-like supramolecular hexagons, H1 and H2. These hexagons feature large cavities, showcasing unique inner and outer hexagons fixed by specific connectivities for enhanced stability and high metal center density. H1 exhibits properties that can be transformed through the thermodynamic conversion of the metallopolymer formed by L1 and L2. With an edge length of 6.8 nm, H2 is one of the largest hexagons reported to date. 1D and 2D NMR, TEM, ESI-MS, and TWIM-MS experiments provided conclusive evidence for the composition and structure of the assembled hexagons. This work demonstrates the feasibility of constructing giant supramolecular architectures with precise control over their size and shape, opening up new possibilities for the design and synthesis of sophisticated supramolecules and nonbiological materials.

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.

Self-assembly of the smallest and tightest molecular trefoil knot

Molecular knots, whose synthesis presents many challenges, can play important roles in protein structure and function as well as in useful molecular materials, whose properties depend on the size of the knotted structure. Here we report the synthesis by self-assembly of molecular trefoil metallaknot with formula [Au6{1,2-C6H4(OCH2CC)2}3{Ph2P(CH2)4PPh2}3], Au6, from three units of each of the components 1,2-C6H4(OCH2CCAu)2 and Ph2P(CH2)4PPh2. Structure determination by X-ray diffraction revealed that the chiral trefoil knot contains only 54 atoms in the backbone, so that Au6 is the smallest and tightest molecular trefoil knot known to date.

Biasing the Formation of Solution-Unstable Intermediates in Coordination Self-Assembly by Mechanochemistry

Due to the reversible nature of coordination bonds and solvation effect, coordination self-assembly pathways are often difficult to elucidate experimentally in solution, as intermediates and products are in constant equilibration. The present study shows that some of these transient and high-energy self-assembly intermediates can be accessed by means of ball-milling approaches. Among them, highly aqueous-unstable Pd3 L11 and Pd6 L14 open-cage intermediates of the framed Fujita Pd6 L14 cage and Pd2 L22 , Pd3 L21 and Pd4 L22 intermediates of Mukherjee Pd6 L24 capsule are successfully trapped in solid-state, where Pd=tmedaPd2+ , L1=2,4,6-tris(4-pyridyl)-1,3,5-triazine and L2=1,3,5-tris(1-imidazolyl)benzene). Their structures are assigned by a combination of solution-based characterization tools such as standard NMR spectroscopy, DOSY NMR, ESI-MS and X-ray diffraction. Collectively, these results highlight the opportunity of using mechanochemistry to access unique chemical space with vastly different reactivity compared to conventional solution-based supramolecular self-assembly reactions.

Knot Formation on DNA Pushed Inside Chiral Nanochannels

We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.

Constructing Ultrastable Metallo-Cages via In Situ Deprotonation/Oxidation of Dynamic Supramolecular Assemblies

Coordination-driven self-assembly enables the spontaneous construction of metallo-supramolecules with high precision, facilitated by dynamic and reversible metal-ligand interactions. The dynamic nature of coordination, however, results in structural lability in many metallo-supramolecular assembly systems. Consequently, it remains a formidable challenge to achieve self-assembly reversibility and structural stability simultaneously in metallo-supramolecular systems. To tackle this issue, herein, we incorporate an acid-/base-responsive tridentate ligand into multitopic building blocks to precisely construct a series of metallo-supramolecular cages through coordination-driven self-assembly. These dynamic cagelike assemblies can be transformed to their static states through mild in situ deprotonation/oxidation, leading to ultrastable skeletons that can withstand high temperatures, metal ion chelators, and strong acid/base conditions. This in situ transformation provides a reliable and powerful approach to manipulate the kinetic features and stability of metallo-supramolecules and allows for modulation of encapsulation and release behaviors of metallo-cages when utilizing nanoscale quantum dots (QDs) as guest molecules.

[2,2] Paracyclophanes-based double helicates for constructing artificial light-harvesting systems and white LED device

The construction of efficient artificial light-harvesting systems (ALHSs) is of vital importance in utilizing solar energy. Herein, we report the non-covalent syntheses of double helicates PCP-TPy1/2 and Rp,Rp-PCP-TPy1/2 by metal-coordination interaction and their applications in ALHSs and white light-emitting diode (LED) device. All double helicates exhibit significant aggregation-induced emission in tetrahydrofuran/water (1:9, v/v) solvent. The aggregated double helicates can be used to construct one-step or sequential ALHSs with fluorescent dyes Eosin Y (EsY) and Nile red (NiR) with the energy transfer efficiency up to 89.3%. Impressively, the PMMA film of PCP-TPy1 shows white-light emission when doped 0.075% NiR, the solid of double helicates (Rp,Rp-) PCP-TPy2 can be used as the additive of a blue LED bulb to achieve white-light emission. In this work, we provided a general method for the preparation of novel double helicates and explored their applications in ALHSs and fluorescent materials, which will promote future construction and application of helicates as emissive devices.

Metallo-Supramolecular Hexagonal Wreath with Four Switchable States Based on a pH-Responsive Tridentate Ligand

In biological systems, many biomacromolecules (e.g., heme proteins) are capable of switching their states reversibly in response to external stimuli, endowing these natural architectures with a high level of diversity and functionality. Although tremendous efforts have been made to advance the complexity of artificial supramolecules, it remains a challenge to construct metallo-supramolecular systems that can carry out reversible interconversion among multiple states. Here, a pH-responsive tridentate ligand, 2,6-di(1H-imidazole-2-yl)pyridine (H₂DAP), is incorporated into the multitopic building block for precise construction of giant metallo-supramolecular hexagonal wreaths with three metal ions, i.e., Fe(II), Co(II), and Ni(II), through coordination-driven self-assembly. In particular, a Co-linked wreath enables in situ reversible interconversion among four states in response to pH and oxidant/reductant with highly efficient conversion without losing structural integrity. During the state interconversion cycles, the physical properties of the assembled constructs are finely tuned, including the charge states of the backbone, valency of metal ions, and paramagnetic/diamagnetic features of complexes. Such discrete wreath structures with a charge-switchable backbone further facilitate layer-by-layer assembly of metallo-supramolecules on the substrate.

Platinum(II)-Metallaclip-Based Theranostics for Cell Imaging and Synergetic Chemotherapy-Photodynamic Therapy

Supramolecular coordination complexes formed by coordination-induced assembly not only avoid the loss of activity of precursors but also provide an efficient way for controlled release, which can be further used in various fields of biology such as drug delivery, cell imaging, and tumor treatment. In this work, a Pt^II metallaclip (4) was prepared from 4-[4-(1,2,2-triphenylvinyl)phenyl]pyridine (1), 5,10,15-triphenyl-20-(pyridin-4-yl)porphyrin (2), 90^o Pt, and glycol-chain-modified isophthalic acid (3) in an acetone/water mixture through the "coordination-driven self-assembly" method. ³¹P and ¹H NMR spectroscopy and high-resolution mass spectrometry were used to characterize the obtained metallaclip 4. 4 can self-assemble into fluorescent nanostructures in aqueous solution because of the tetraphenylethylene unit and its amphiphilic nature. Importantly, the fluorescent nanoparticles not only can be employed for cell imaging but also can generate singlet oxygen (¹O₂) under 660 nm laser irradiation and the release of Pt drug in the tumor issue for cancer therapy. The work may provide a new way for scientists to construct functional biomaterials with multiple applications via molecular self-assembly.

The Story of the Little Blue Box: A Tribute to Siegfried Hünig

The tetracationic cyclophane, cyclobis(paraquat-p-phenylene), also known as the little blue box, constitutes a modular receptor that has facilitated the discovery of many host-guest complexes and mechanically interlocked molecules during the past 35 years. Its versatility in binding small π-donors in its tetracationic state, as well as forming trisradical tricationic complexes with viologen radical cations in its doubly reduced bisradical dicationic state, renders it valuable for the construction of various stimuli-responsive materials. Since the first reports in 1988, the little blue box has been featured in over 500 publications in the literature. All this research activity would not have been possible without the seminal contributions carried out by Siegfried Hünig, who not only pioneered the syntheses of viologen-containing cyclophanes, but also revealed their rich redox chemistry in addition to their ability to undergo intramolecular π-dimerization. This Review describes how his pioneering research led to the design and synthesis of the little blue box, and how this redox-active host evolved into the key component of molecular shuttles, switches, and machines.

Aggregation-Induced Emission Metallocuboctahedra for White Light Devices

Materials for organic light-emitting devices which exhibit superior emission properties in both the solution and solid states with a high fluorescence quantum yield have been extensively sought after. Herein, two metallocages, S1 and S2, were constructed, and both showed typical aggregation-induced emission (AIE) features with intense yellow fluorescence. By adding blue-emissive 9,10-dimethylanthracene, pure white light emission can be produced in the solution of S1 and S2. Furthermore, due to the remarkable AIE feature and good fluorescence quantum yield in the solid state, metallocages are highly emissive in the solid state and can be utilized to coat blue LED bulbs or integrate with blue-emitting chips to obtain white light. This study advances the usage of metallocages as practical solid-state fluorescent materials and provides a fresh perspective on highly emissive AIE materials.

Density-tunable pathway complexity in a minimalistic self-assembly model

An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.

Crystallization- and Metal-Driven Selection of Discrete Macrocycles/Cages and Their Metallosupramolecular Polymers from Dynamic Systemic Networks

Reversible imine- and metal-coordination reactions are dynamic enough to produce complex libraries of macrocycles, cages, and supramolecular polymers in solution, from which amplification effects have been identified in solution or during crystallization in response to ligand- and metal-driven selection modes. Crystallization-driven selection can lead to the amplification of unexpected metallosupramolecular architectures. The addition of Ag+ triggered the change of the optimal components, so that the crystallization process showed different ligand preferences than in solution. The most packed constituents are amplified in the solid state, taking into account the optimal coordination of metal ions together with non-specific non-covalent interactions between the macrocycle packed in dimers or trimers in the solid state.

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.

Topological digestion drives time-varying rheology of entangled DNA fluids

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalise using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.

Altering the binding affinities of tetraruthenocycles for polycyclic aromatic hydrocarbons by post-assembly modification

We developed a strategy for manipulating the binding strength of polycyclic aromatic hydrocarbons (PAHs) via covalent post-assembly modification (PAM) of tetranuclear ruthenium macrocycles containing s-tetrazine ligands. The macrocycles act as efficient receptors for various PAHs. Inverse electron demand Diels-Alder (IEDDA) reaction of the macrocycles was applied to reduce the binding ability significantly.

High capacity topological coding based on nested vortex knots and links

Optical knots and links have attracted great attention because of their exotic topological characteristics. Recent investigations have shown that the information encoding based on optical knots could possess robust features against external perturbations. However, as a superior coding scheme, it is also necessary to achieve a high capacity, which is hard to be fulfilled by existing knot-carriers owing to the limit number of associated topological invariants. Thus, how to realize the knot-based information coding with a high capacity is a key problem to be solved. Here, we create a type of nested vortex knot, and show that it can be used to fulfill the robust information coding with a high capacity assisted by a large number of intrinsic topological invariants. In experiments, we design and fabricate metasurface holograms to generate light fields sustaining different kinds of nested vortex links. Furthermore, we verify the feasibility of the high-capacity coding scheme based on those topological optical knots. Our work opens another way to realize the robust and high-capacity optical coding, which may have useful impacts on the field of information transfer and storage.

Robust and high capacity optical coding will be at the base of future developments of information transfer and storage. Here the authors develop a topological all-optical coding scheme, which possesses good stability and a high capacity, using nested vortex knots and links.

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.

Mechanochemical Access to a Short-Lived Cyclic Dimer Pd2 L2 : An Elusive Kinetic Species En Route to Molecular Triangle Pd3 L3 and Molecular Square Pd4 L4

Pd-based molecular square Pd₄ L₄ and triangle Pd₃ L₃ represent the molecular ancestors of metal-coordination polyhedra that have been an integral part of the field for the last 30 years. Conventional solution-based reactions between cis-protected Pd ions and 2,2'-bipyridine exclusively give Pd₄ L₄ and/or Pd₃ L₃ as the sole products. We herein show that, under solvent-free mechanochemical conditions, the self-assembly energy landscape can be thermodynamically manipulated to form an elusive cyclic dimer Pd₂ L₂ for the first time. In the absence of solvent, Pd₂ L₂ is indefinitely stable in the solid-state, but converts rapidly to its thermodynamic products Pd₃ L₃ and Pd₄ L₄ in solution, confirming Pd₂ L₂ as a short-lived kinetic species in the solution-based self-assembly process. Our results highlight how mechanochemistry grants access to a vastly different chemical space than available under conventional solution conditions. This provides a unique opportunity to isolate elusive species in self-assembly processes that are too reactive to both "see" and "capture".

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.

Tetratopic Terpyridine Building Unit as a Precursor to Wheel-Like Metallo-Supramolecules

In an effort to construct molecules with distinct shapes and functions, the design and synthesis of multitopic ligands are often able to play an important role. Here, we report the synthesis of a novel tetratopic organic ligand LA, which can be viewed as a bis-tenon with successive angular orientations in space. The particular ligand has been treated with different tailored metal-organic ligands to afford new members of the molecular wheel family (multi-rhomboidal-shaped wheel and bis-trapezium-shaped wheel) that show enhanced stability. Two-dimensional (2D) diffusion nuclear magnetic resonance (NMR) spectroscopy (DOSY), electrospray ionization (ESI) mass spectrometry, traveling wave ion mobility (TWIM), and gradient tandem mass spectrometry (gMS₂) experiments, as well as molecular modeling, have been employed to provide structural information and differentiate the isomeric separation process. In addition, considering that LA has rotational properties, it is expected to open the door to functional supramolecules and stimuli-responsive materials.

Vernier template synthesis of molecular knots

Molecular knots are often prepared using metal helicates to cross the strands. We found that coordinatively mismatching oligodentate ligands and metal ions provides a more effective way to synthesize larger knots using Vernier templating. Strands composed of different numbers of tridentate 2,6-pyridinedicarboxamide groups fold around nine-coordinate lanthanide (III) ions to generate strand-entangled complexes with the lowest common multiple of coordination sites for the ligand strands and metal ions. Ring-closing olefin metathesis then completes the knots. A 3:2 (ditopic strand:metal) Vernier assembly produces +3₁#+3₁ and -3₁#-3₁ granny knots. Vernier complexes of 3:4 (tetratopic strand:metal) stoichiometry selectively form a 378-atom-long trefoil-of-trefoils triskelion knot with 12 alternating strand crossings or, by using opposing stereochemistry at the terminus of the strand, an inverted-core triskelion knot with six alternating and six nonalternating strand crossings.

Molecular weaving

Historically, the interlacing of strands at the molecular level has mainly been limited to coordination polymers and DNA. Despite being proposed on a number of occasions, the direct, bottom-up assembly of molecular building blocks into woven organic polymers remained an aspirational, but elusive, target for several decades. However, recent successes in two-dimensional and three-dimensional molecular-level weaving now offer new opportunities and research directions at the interface of polymer science and molecular nanotopology. This Perspective provides an overview of the features and potential of the periodic nanoscale weaving of polymer chains, distinguishing it from randomly entangled polymer networks and rigid crystalline frameworks. We review the background and experimental progress so far, and conclude by considering the potential of molecular weaving and outline some of the current and future challenges in this emerging field.

Design and Self-Assembly of Macrocycles with Metals at the Corners Based on Dissymmetric Terpyridine Ligands

Terpyridine-based discrete supramolecular architectures with metal ions in the corners have rarely been reported. Herein, we report two dissymmetric terpyridyl ligands LA and LB decorated at the 5-position and 4-position of terpyridine respectively. The complexes constructed by the self-assembly of LA and LB with Zn(II) exhibit hand-circle-like structures. Moreover, all Zn(II) are successfully fixed in the corners. A series of dimeric to hexameric macrocycles is obtained by head-to-tail connections with changing concentration. This work will pave the way for preparation of more elaborate self-assembled structures based on dissymetric ligands.

Preparation of tricationic tris(pyridylpalladium(II)) metallacyclophane as an anion receptor

A tricationic tris(pyridylpalladium(II)) metallacyclophane was prepared from 3,5-dibromopyridine by a successive treatment with tetrakis(triphenylphosphine)palladium(0), diphosphine, and silver salt. Single-crystal X-ray diffraction analysis revealed that the metallacyclophane incorporated one of three counter anions into its hole-shaped cavity to form multidentate C-H⋯anion interactions. Solution-phase ¹H NMR experiments in DMSO-d₆ indicated that the metallacyclophane exhibited selective binding behavior toward nitrate, tetrafluoroborate, p-toluenesulfonate, perchlorate, and hydrogen sulfate ions, whereas the hexafluoroantimonate ion exhibited only weak interaction toward the metallacyclophane. This anion recognition behavior was further demonstrated by an extraction experiment of water-soluble sulfonate dyes.

Hierarchical self-assembly into chiral nanostructures

One basic principle regulating self-assembly is associated with the asymmetry of constituent building blocks or packing models. Using asymmetry to manipulate molecular-level devices and hierarchical functional materials is a promising topic in materials sciences and supramolecular chemistry. Here, exemplified by recent major achievements in chiral hierarchical self-assembly, we show how chirality may be utilized in the design, construction and evolution of highly ordered and complex chiral nanostructures. We focus on how unique functions can be developed by the exploitation of chiral nanostructures instead of single basic units. Our perspective on the future prospects of chiral nanostructures via the hierarchical self-assembly strategy is also discussed.

A Hydrogen-Bonded Ravel Assembled by Anion Coordination

Anion-coordination-driven assembly (ACDA) is showing increasing power in the construction of anionic supramolecular architectures. Herein, by expanding the anion centers from oxoanion (phosphate or sulfate) to organic tris-carboxylates, an Archimedean solid (truncated tetrahedron) and a highly entangled, double-walled tetrahedron featuring a ravel topology have been assembled with tris-bis(urea) ligands. The results demonstrate the promising ability of tris-carboxylates as new anion coordination centers in constructing novel topologies with increasing complexity and diversity compared to phosphate or sulfate ions on account of the modifiable size and easy functionalization character of these organic anions.

Topological and physical links in soft matter systems

Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.

Metal-Peptide Nonafoil Knots and Decafoil Supercoils

Despite the frequent occurrence of knotted frameworks in protein structures, the latent potential of peptide strands to form entangled structures is rarely discussed in peptide chemistry. Here we report the construction of highly entangled molecular topologies from Ag(I) ions and tripeptide ligands. The efficient entanglement of metal-peptide strands and the wide scope for design of the amino acid side chains in these ligands enabled the construction of metal-peptide 9₁ torus knots and 10₁² torus links. Moreover, steric control of the peptide side chain induced ring opening and twisting of the torus framework, which resulted in an infinite toroidal supercoil nanostructure.

Designing narcissistic self-sorting terpyridine moieties with high coordination selectivity for complex metallo-supramolecules

Coordination-driven self-assembly is a powerful approach for the construction of metallosupramolecules, but designing coordination moieties that can drive the self-assembly with high selectivity and specificity remains a challenge. Here we report two ortho-modified terpyridine ligands that form head-to-tail coordination complexes with Zn(II). Both complexes show narcissistic self-sorting behaviour. In addition, starting from these ligands, we obtain two sterically congested multitopic ligands and use them to construct more complex metallo-supramolecules hexagons. Because of the non-coaxial structural restrictions in the rotation of terpyridine moieties, these hexagonal macrocycles can hierarchically self-assemble into giant cyclic nanostructures via edge-to-edge stacking, rather than face-to-face stacking. Our design of dissymmetrical coordination moieties from congested coordination pairs show remarkable self-assembly selectivity and specificity.

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.