Sliding-Ring Catenanes

Advancements and strategic approaches in catenane synthesis

Catenanes, a distinctive category of mechanically interlocked molecules composed of intertwined macrocycles, have undergone significant advancements since their initial stages characterized by inefficient statistical synthesis methods. Through the aid of molecular recognition processes and principles of self-assembly, a diverse array of catenanes with intricate structures can now be readily accessed utilizing template-directed synthetic protocols. The rapid evolution and emergence of this field have catalyzed the design and construction of artificial molecular switches and machines, leading to the development of increasingly integrated functional systems and materials. This review endeavors to explore the pivotal advancements in catenane synthesis from its inception, offering a comprehensive discussion of the synthetic methodologies employed in recent years. By elucidating the progress made in synthetic approaches to catenanes, our aim is to provide a clearer understanding of the future challenges in further advancing catenane chemistry from a synthetic perspective.

Topological Analysis and Structural Determination of 3D Covalent Organic Frameworks

3D covalent organic frameworks (3D COFs) constitute a new type of crystalline materials that consist of a range of porous structures with numerous applications in the fields of adsorption, separation, and catalysis. However, because of the complexity of the three-periodic net structure, it is desirable to develop a thorough structural comprehension, along with a means to precisely determine the actual structure. Indeed, such advancements would considerably contribute to the rational design and application of 3D COFs. In this review, the reported topologies of 3D COFs are introduced and categorized according to the configurations of their building blocks, and a comprehensive overview of diffraction-based structural determination methods is provided. The current challenges and future prospects for these materials will also be discussed.

Precision syntheses of molecular necklaces based on coordination interactions

Molecular necklaces (MNs) are mechanically interlocked molecules that have attracted considerable attention due to their delicate structures and potential applications, such as in the syntheses of polymeric materials and DNA cleavage. However, complex and lengthy synthetic routes have limited development of further applications. Owing to their dynamic reversibility, strong bond energy and high orientation, coordination interactions were employed to synthesize MNs. In this review, progress in the coordination-based MNs has been summarized, with emphasis on design strategies and potential applications based on coordination interactions.

Radical Pairing Interactions and Donor-Acceptor Interactions in Cyclobis(paraquat-p-phenylene) Inclusion Complexes

Understanding molecular interactions in mechanically interlocked molecules (MIMs) is challenging because they can be either donor-acceptor interactions or radical pairing interactions, depending on the charge states and multiplicities in the different components of the MIMs. In this work, for the first time, the interactions between cyclobis(paraquat-p-phenylene) (abbreviated as CBPQTⁿ⁺ (n = 0-4)) and a series of recognition units (RUs) were investigated using the energy decomposition analysis approach (EDA). These RUs include bipyridinium radical cation (BIPY^•+), naphthalene-1,8:4,5-bis(dicarboximide) radical anion (NDI^•-), their oxidized states (BIPY²⁺ and NDI), neutral electron-rich tetrathiafulvalene (TTF) and neutral bis-dithiazolyl radical (BTA^•). The results of generalized Kohn-Sham energy decomposition analysis (GKS-EDA) reveal that for the CBPQTⁿ⁺···RU interactions, correlation/dispersion terms always have large contributions, while electrostatic and desolvation terms are sensitive to the variation in charge states in CBPQTⁿ⁺ and RU. For all the CBPQTⁿ⁺···RU interactions, desolvation terms always tend to overcome the repulsive electrostatic interactions between the CBPQT cation and RU cation. Electrostatic interaction is important when RU has the negative charge. Moreover, the different physical origins of donor-acceptor interactions and radical pairing interactions are compared and discussed. Compared to donor-acceptor interactions, in radical pairing interactions, the polarization term is always small, while the correlation/dispersion term is important. With regard to donor-acceptor interactions, in some cases, polarization terms could be quite large due to the electron transfer between the CBPQT ring and RU, which responds to the large geometrical relaxation of the whole systems.

Thermally Controlled Exciplex Fluorescence in a Dynamic Homo[2]catenane

Motion-induced change in emission (MICE) is a phenomenon that can be employed to develop various types of probes, including temperature and viscosity sensors. Although MICE, arising from the conformational motion in particular compounds, has been studied extensively, this phenomenon has not been investigated in depth in mechanically interlocked molecules (MIMs) undergoing coconformational changes. Herein, we report the investigation of a thermoresponsive dynamic homo[2]catenane incorporating pyrene units and displaying relative circumrotational motions of its cyclophanes as evidenced by variable-temperature ¹H NMR spectroscopy and supported by its visualization through molecular dynamics simulations and quantum mechanics calculations. The relative coconformational motions induce a significant change in the fluorescence emission of the homo[2]catenane upon changes in temperature compared with its component cyclophanes. This variation in the exciplex emission of the homo[2]catenane is reversible as demonstrated by four complete cooling and heating cycles. This research opens up possibilities of using the coconformational changes in MIMs-based chromophores for probing fluctuations in temperature which could lead to applications in biomedicine or materials science.

Rigidity and Flexibility in Rotaxanes and Their Relatives; On Being Stubborn and Easy-Going

Rotaxanes are an emerging class of molecules composed of two building blocks: macrocycles and threads. Rotaxanes, and their pseudorotaxane and polyrotaxane relatives, serve as prototypes for molecular-level switches and machines and as components in materials like elastic polymers and 3D printing inks. The rigidity and flexibility of these molecules is a characteristic feature of their design. However, the mechanical properties of the assembled rotaxane and its components are rarely examined directly, and the translation of these properties from molecules to bulk materials is understudied. In this Review, we consider the mechanical properties of rotaxanes by making use of concepts borrowed from physical organic chemistry. Rigid molecules have fewer accessible conformations with higher energy barriers while flexible molecules have more accessible conformations and lower energy barriers. The macrocycles and threads become rigidified when threaded together as rotaxanes in which the formation of intermolecular interactions and increased steric contacts collectively reduce the conformational space and raise barriers. Conversely, rotational and translational isomerism in rotaxanes adds novel modes of flexibility. We find that rigidification in rotaxanes is almost universal, but novel degrees of flexibility can be introduced. Both have roles to play in the function of rotaxanes.

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.

Self-Assembly of [3]Catenane and [4]Catenane Based on Neutral Organometallic Scaffolds

Transition metal-mediated templating and self-assembly have shown great potential to construct mechanically interlocked molecules. Herein, we describe the formation of the bimetallic [3]catenane and [4]catenane based on neutral organometallic scaffolds via the orthogonality of platinum-to-oxygen coordination-driven self-assembly and copper(I) template-directed strategy of a [2]pseudorotaxane. The structures of these bimetallic [3]catenane and [4]catenane were characterized by multinuclear NMR {¹H and ³¹P} spectroscopy, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS), and PM6 semiempirical molecular orbital theoretical calculations. In addition, single-crystal X-ray analyses of the [3]catenane revealed two asymmetric [2]pseudorotaxane units inside the metallacycle. It was discovered that tubular structures were formed through the stacking of individual [3]catenane molecules driven by the strong π-π interactions.

On-the-Fly Training of Atomistic Potentials for Flexible and Mechanically Interlocked Molecules

Mechanically interlocked molecules have gained significant attention because of their unique ability to perform well-defined motions originating from their entanglement, which is important for the design of artificial molecular machines. Atomistic simulations based on force fields (FFs) provide detailed insights into such architectures at the molecular level enabling one to predict the resulting functionalities. However, the development of reliable FFs is still challenging and time-consuming, in particular for highly dynamic and interlocked structures such as rotaxanes, which exhibit a large number of different conformers. In the present work, we present an on-the-fly training (OTFT) algorithm. By a guided and nonguided phase space sampling, relevant reference data are automatically and continuously generated and included for the on-the-fly parametrization of the FF based on a population swapping genetic algorithm (psGA). The OTFT approach provides a fast and automated FF parametrization scheme and tackles problems caused by missing phase space information or the need for big data. We demonstrate the high accuracy of the developed FF for flexible molecules with respect to equilibrium and out-of-equilibrium properties. Finally, by applying the ab initio parametrized FF, molecular dynamic simulations were performed up to experimentally relevant time scales (ca. 1 μs) enabling capture in detail of the structural evaluation and mapping out of the free-energy topology. The on-the-fly training approach thus provides a strong foundation toward automated FF developments and large-scale investigations of phenomena in and out of thermal equilibrium.

Naphthobox: a selective molecular box for planar aromatic cations

A molecular box with an electron-rich cavity, namely naphthobox, was contructed and showed selective binding to planar aromatic cations.

Discovery of an all-donor aromatic [2]catenane

We report herein the first all-donor aromatic [2]catenane formed through dynamic combinatorial chemistry, using single component libraries. The building block is a benzo[1,2-b:4,5-b′]dithiophene derivative, a π-donor molecule, with cysteine appendages that allow for disulfide exchange. The hydrophobic effect plays an essential role in the formation of the all-donor [2]catenane. The design of the building block allows the formation of a quasi-fused pentacyclic core, which enhances the stacking interactions between the cores. The [2]catenane has chiro-optical and fluorescent properties, being also the first known DCC-disulphide-based interlocked molecule to be fluorescent.

An all-donor [2]catenane has been synthesised via dynamic combinatorial chemistry. It features stacked benzodithiophenes which are quasi-pentacyclic through hydrogen bonding.

Point-of-Use Rapid Detection of SARS-CoV-2: Nanotechnology-Enabled Solutions for the COVID-19 Pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in contact. Detection based on non-contact optical techniques is very helpful in managing the spread of the virus, and to aid in the disinfection of surfaces. Nanomaterial-based methods are proven suitable for rapid detection. Given the immense need for science led innovative solutions, this manuscript critically reviews recent literature to specifically illustrate nano-engineered effective and rapid solutions. In addition, all the different techniques are critically analyzed, compared, and contrasted to identify the most promising methods. Moreover, promising research ideas for high accuracy of detection in trace concentrations, via color change and light-sensitive nanostructures, to assist fingerprint techniques (to identify the virus at the contact surface of the gas and solid phase) are also presented.

Electrochemical Switching of a Fluorescent Molecular Rotor Embedded within a Bistable Rotaxane

We report how the nanoconfined environment, introduced by the mechanical bonds within an electrochemically switchable bistable [2]rotaxane, controls the rotation of a fluorescent molecular rotor, namely, an 8-phenyl-substituted boron dipyrromethene (BODIPY). The electrochemical switching of the bistable [2]rotaxane induces changes in the ground-state coconformation and in the corresponding excited-state properties of the BODIPY rotor. In the starting redox state, when no external potential is applied, the cyclobis(paraquat-p-phenylene) (CBPQT⁴⁺) ring component encircles the tetrathiafulvalene (TTF) unit on the dumbbell component, leaving the BODIPY rotor unhindered and exhibiting low fluorescence. Upon oxidation of the TTF unit to a TTF²⁺ dication, the CBPQT⁴⁺ ring is forced toward the molecular rotor, leading to an increased energy barrier for the excited state to rotate the rotor into the state with a high nonradiative rate constant, resulting in an overall 3.4-fold fluorescence enhancement. On the other hand, when the solvent polarity is high enough to stabilize the excited charge-transfer state between the BODIPY rotor and the CBPQT⁴⁺ ring, movement of the ring toward the BODIPY rotor produces an unexpectedly strong fluorescence signal decrease as the result of photoinduced electron transfer from the BODIPY rotor to the CBPQT⁴⁺ ring. The nanoconfinement effect introduced by mechanical bonding can effectively lead to modulation of the physicochemical properties as observed in this bistable [2]rotaxane. On account of the straightforward synthetic strategy and the facile modulation of switchable electrochromic behavior, our approach could pave the way for the development of new stimuli-responsive materials based on mechanically interlocked molecules for future electro-optical applications, such as sensors, molecular memories, and molecular logic gates.

A hydrogen-bonded polymer constructed from mechanically interlocked, suit[1]ane monomers

A T-shaped 2,4,7-substituted benzimidazolium “axle” with two ester functionalities and a 24-membered crown ether “wheel” with appendages containing terminal olefin groups were threaded — axle through wheel — to form a [2]pseudorotaxane. Grubbs’ ring-closing metathesis (RCM) was then used to form a third loop and create a bicyclic cage that fully encapsulates the axle and permanently interlocks the two molecular components creating a suit[1]ane. There are no bulky groups on the axle to prevent unthreading, but the axle is trapped due to the cage-like nature of the newly created polyether host. After hydrolysis of the esters groups to carboxylic acids, this novel mechanically interlocked molecule (MIM) polymerizes in the solid state. The structure of the resulting supramolecular polymer was determined by single-crystal X-ray diffraction and contains linear one-dimensional tapes of suit[1]ane monomers linked by intermolecular hydrogen bonding between the carboxylic acid groups.

Can aromaticity be a kinetic trap? Example of mechanically interlocked aromatic [2-5]catenanes built from cyclo[18]carbon

Aromaticity serves as a kinetic trap for mechanically interlocked cyclo[18]carbon rings.

Sliding Crosslinked Thermoresponsive Materials: Polypseudorotaxanes Made of Poly(N-Isopropylacrylamide) and Acrylamide-γ-Cyclodextrin

Novel polypseudorotaxanes (PPR) based on poly(N-isopropylacrylamide) (PNIPAAm) and acrylamide-γ-cyclodextrin (AγCD) are successfully synthesized. AγCD gives rise to sliding crosslinking systems and influences the thermoresponsive and swelling behavior of PNIPAAm hydrogels. Namely, their lower critical solution temperature (LCST) can be tuned up to 38°C, thus making the resulting materials of great interest in biomedical applications. Also, AγCD influences the thermal and mechanical properties of hydrogels, by affecting the T g and E modulus values.

Neighboring Component Effect in a Tri-stable [2]Rotaxane

The redox properties of cyclobis(paraquat- p-phenylene)cyclophane (CBPQT⁴⁺) render it a uniquely variable source of recognition in the context of mechanically interlocked molecules, through aromatic donor-acceptor interactions in its fully oxidized state (CPBQT⁴⁺) and radical-pairing interactions in its partially reduced state (CBPQT^2(•+)). Although it is expected that the fully reduced neutral state (CBPQT⁽⁰⁾) might behave as a π-donating recognition unit, resulting in a dramatic change in its binding properties when compared with the other two redox states, its role in rotaxanes has not yet been investigated. To address this challenge, we report herein the synthesis of a tri-stable [2]rotaxane in which a CBPQT⁴⁺ ring is mechanically interlocked with a dumbbell component containing five recognition sites-(i) a bipyridinium radical cation (BIPY^(•+)) located centrally along the axis of the dumbbell, straddled by (ii) two tetrafluorophenylene units linked to (iii) two triazole rings. In addition to the selective recognition between (iv) the CBPQT⁴⁺ ring and the triazole units, and (v) the CBPQT^2(•+) ring and the reduced BIPY^(•+) unit in the dumbbell component, investigations in solution have now confirmed the presence of additional non-covalent bonding interactions between the CBPQT⁽⁰⁾ ring, acting as a donor in its neutral state, and the two tetrafluorophenylene acceptors in the dumbbell component. The unveiling of this piece of molecular recognition in a [2]rotaxane is reminiscent of the existence in much simpler, covalently linked, organic molecules of neighboring group participation (anchimeric assistance giving way to transannular interactions) in small-, medium-, and large-membered rings.

Cyclic and Lasso Peptides: Sequence Determination, Topology Analysis, and Rotaxane Formation

A broadly applicable chemical cleavage methodology to facilitate MS/MS sequencing was developed for macrocyclic and lasso peptides, which hold promise as exciting new therapeutics. Existing methods such as Edman degradation, CNBr cleavage, and enzymatic digestion are either limited in scope or completely fail in cleavage of constrained nonribosomal peptides. Importantly, the new method was utilized for synthesizing a unique peptide-based rotaxane (both cyclic and threaded) from the lasso peptide, benenodin-1 ΔC5.

Synthesis of Structurally Diverse Emissive Molecular Rotors with Four-Component Ugi Stators

The use of the multicomponent Ugi reaction to rapidly prepare a library of dumbbell-like molecular rotors is highlighted here. The synthetic strategy consisted of the atom-economic access to 15 bulky and structurally diverse iodinated stators, which were cross-coupled to the 1,4-diethynylphenylene rotator. From those experiments, up to six rotors 1a-c and 1l-n were obtained, with yields ranging from 35 to 69% per coupled C-C bond. In addition to the framework diversity, five of these compounds showed aggregate-enhanced emission properties thanks to their conjugated 1,4-bis(phenylethynyl)benzene cores, a property that rises by increasing the water fraction (f_w) in their THF solutions. The results highlight the significance of the diversity-oriented synthesis of rapid access to new molecular fluorescent rotors.

Introducing Stable Radicals into Molecular Machines

Ever since their discovery, stable organic radicals have received considerable attention from chemists because of their unique optical, electronic, and magnetic properties. Currently, one of the most appealing challenges for the chemical community is to develop sophisticated artificial molecular machines that can do work by consuming external energy, after the manner of motor proteins. In this context, radical-pairing interactions are important in addressing the challenge: they not only provide supramolecular assistance in the synthesis of molecular machines but also open the door to developing multifunctional systems relying on the various properties of the radical species. In this Outlook, by taking the radical cationic state of 1,1'-dialkyl-4,4'-bipyridinium (BIPY^•+) as an example, we highlight our research on the art and science of introducing radical-pairing interactions into functional systems, from prototypical molecular switches to complex molecular machines, followed by a discussion of the (i) limitations of the current systems and (ii) future research directions for designing BIPY^•+-based molecular machines with useful functions.

Supramolecular polymer hydrogels induced by host-guest interactions with di-[cyclobis(paraquat-p-phenylene)] cross-linkers: from molecular complexation to viscoelastic properties

Supramolecular polymer networks have been designed on the basis of a π-electron donor/acceptor complex: naphthalene (N)/cyclobis(paraquat-p-phenylene) (CBPQT⁴⁺ = B). For this purpose, a copolymer of N,N-dimethylacrylamide P(DMA-N1), lightly decorated with 1 mol% of naphthalene pendant groups, has been studied in semi-dilute un-entangled solution in the presence of di-CBPQT⁴⁺ (BB) crosslinker type molecules. While calorimetric experiments demonstrate the quantitative binding between N and B groups up to 60 °C, the introduction of BB crosslinkers into the polymer solution gives rise to gel formation above the overlap concentration. From a comprehensive investigation of viscoelastic properties, performed at different concentrations, host/guest stoichiometric ratios and temperatures, the supramolecular hydrogels are shown to follow a Maxwellian behavior with a strong correlation of the plateau modulus and the relaxation time with the effective amount of interchain cross-linkers and their dissociation dynamics, respectively. The calculation of the dissociation rate constant of the supramolecular complex, by extrapolation of the relaxation time of the network back to the beginning of the gel regime, is discussed in the framework of theoretical and experimental works on associating polymers.

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.

The first water-soluble pillar[5]arene dimer: synthesis and construction of a reversible fluorescent supramolecular polymer network in water

The first water-soluble pillar[5]arene dimer was successfully designed and synthesized. It can complex with carboxylate anion functionalized tetraphenyl ethylene to form a reversible fluorescent supramolecular polymer network in water.

Self-Assembly of Catenanes from Lasso Peptides

Lasso peptides exist naturally in a threaded state as [1]rotaxanes, and we reasoned that lasso peptides cleaved in their loop region could serve as building blocks for catenanes. Mutagenesis of the lasso peptide microcin J25 (MccJ25) with two cysteine residues followed by cleavage of the peptide with trypsin led to a [2]rotaxane structure that self-assembled into a [3]catenane and [4]catenanes at room temperature in aqueous solution. The [3]catenane represents the smallest ring size of a catenane composed solely of polypeptide segments. The NMR structure of the [3]catenane was determined, suggesting that burial of hydrophobic residues may be a driving force for assembly of the catenane structure.