Structural Parameters Governing the Dynamic Combinatorial Synthesis of Catenanes in Water

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.

Dynamic covalent synthesis

Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.

Stimulus-Induced Relief of Intentionally Incorporated Frustration Drives Refolding of a Water-Soluble Biomimetic Foldamer

Frustrated, or nonoptimal, interactions have been proposed to be essential to a protein's ability to display responsive behavior such as allostery, conformational signaling, and signal transduction. However, the intentional incorporation of frustrated noncovalent interactions has not been explored as a design element in the field of dynamic foldamers. Here, we report the design, synthesis, characterization, and molecular dynamics simulations of the first dynamic water-soluble foldamer that, in response to a stimulus, exploits relief of frustration in its noncovalent network to structurally rearrange from a pleated to an intercalated columnar structure. Thus, relief of frustration provides the energetic driving force for structural rearrangement. This work represents a previously unexplored design element for the development of stimulus-responsive systems that has potential application to materials chemistry, synthetic biology, and molecular machines.

The sharp structural switch of covalent cages mediated by subtle variation of directing groups

It is considered a more formidable task to precisely control the self-assembled products containing purely covalent components, due to a lack of intrinsic templates such as transition metals to suppress entropy loss during self-assembly. Here, we attempt to tackle this challenge by using directing groups. That is, the self-assembly products of condensing a 1:2 mixture of a tetraformyl and a biamine can be precisely controlled by slightly changing the substituent groups in the aldehyde precursor. This is because different directing groups provide hydrogen bonds with different modes to the adjacent imine units, so that the building blocks are endowed with totally different conformations. Each conformation favors the formation of a specific product that is thus produced selectively, including chiral and achiral cages. These results of using a specific directing group to favor a target product pave the way for accomplishing atom economy in synthesizing purely covalent molecules without relying on toxic transition metal templates.

Coordination-Driven Tetragonal Prismatic Cage and the Investigation on Host-Guest Complexation

A coordination-driven host has been reported to encapsulate guests by noncovalent interactions. Herein, we present the design and synthesis of a new type of prism combining porphyrin and terpyridine moieties with a long cavity. The prism host can contain bisite or monosite guests through axial coordination binding of porphyrin and aromatic π interactions of terpyridine. The ligands and prismatic complexes were characterized by electrospray ionization mass spectrometry (ESI-MS), TWIM-MS, NMR spectrometry, and single-crystal X-ray diffraction analysis. The guest encapsulation was investigated through ESI-MS, NMR spectrometry, and transient absorption spectroscopy analysis. The binding constant and stability were determined by UV-Vis spectrometry and gradient tandem MS (gMS²) techniques. Based on the prism, a selectively confined condensation reaction was also performed and detected by NMR spectrometry. This study provides a new type of porphyrin- and terpyridine-based host that could be used for the detection of pyridyl- and amine-contained molecules and confined catalysis.

A cucurbit[8]uril-stabilized 3D charge transfer supramolecular polymer with a remarkable confinement effect for enhanced photocatalytic proton reduction and thioether oxidation

A water-soluble porous supramolecular polymer is assembled through a CB[8]-based 2 + 2 host–guest binding motif, which can greatly increase the efficiency of photocatalysis.

A water-soluble naphthalenediimide-containing hexacationic cage

A water-soluble cage containing three naphthalenediimide (NDI) units was synthesized in a one-pot manner without chromatographic purification, during which six irreversible C-N bonds formed simultaneously via an SN2 reaction. The cage was observed to be capable of accommodating a variety π-electron rich guests in a peripheral manner in water. However, for linear guests including I3- and I2, the cage is able to form an inclusion complex. Besides, in the solid state, the cage can absorb vapor of I2.

Structurally divergent dynamic combinatorial chemistry on racemic mixtures

Structurally Divergent Reactions on Racemic Mixtures are atypical processes in Nature. The few examples reported in the literature take place in organic solvents and are driven by the reagents’ interaction with bulky chiral catalysts. Herein, we describe a dynamic combinatorial approach to generate structural divergence from racemic building blocks. The divergence is due to a stereospecific electron-donor – electron-acceptor interaction of diastereomeric macrocycles, leading to structurally distinct pseudorotaxanes. The equilibrated dynamic combinatorial library contains, amongst various macrocycles, two different types of [2]catenanes that are non-isomeric. The formation of these [2]catenanes is due to a spontaneous stereo and structurally divergent assembly of the building blocks.

Structurally divergent reactions on racemic mixtures, which produce distinct chemical species from an enantiomeric mixture, are extremely rare in the literature. Here, the authors are able to use a dynamic combinatorial approach to yield structurally divergent, non-isomeric [2]catenanes from an enantiomeric mixture.

Dynamic Covalent Chemistry as a Facile Route to Unusual Main-Group Thiolate Assemblies and Disulfide Hoops and Cages

Dynamic Covalent Chemistry (DCC) - combining the robustness of covalent bonds with the self-correcting nature of supramolecular chemistry - facilitates the modular synthesis of complex molecular assemblies in high yields. Although numerous reactions form covalent bonds, only a small set of chemical transformations affect covalent bond formation reversibly under suitable conditions for DCC. Further progress in this area still requires the identification of dynamic motifs and greater insights into their reversibility. We have fruitfully employed DCC of both thiolate coordination to main-group elements and disulfide formation for the facile self-assembly of: (1) metal/metalloid-thiolate assemblies, and (2) purely organic cyclic and caged disulfides, thioethers, and even hydrocarbons, many of which have remained elusive by traditional stepwise synthesis yet form readily through our methods. In this Minireview, we highlight the approaches to prepare these unusual compounds and the factors inducing structural transformations or favoring the formation of certain products over others, given a set of external stimuli or reaction conditions.

Pyrroloindole-Based Dynamic Combinatorial Chemistry

We report a new class of building blocks for Dynamic Combinatorial Chemistry (DCC) based on the pyrroloindole scaffold. The attachment of l-cysteine on the α, α′ positions of the core makes the molecule suitable for disulfide exchange in aqueous dynamic combinatorial libraries (DCLs). The synthesis of the core follows a modified version of the Knoevenagel–Hemetsberger approach. The new building block (l-PI) is fluorescent (Φ = 48%) and relatively stable towards thermal and photodegradation. The chirality of the cysteine is transferred to the electron-rich pyrroloindole core. Homo- and heterochiral DCLs of l-PI with electron-deficient l- and d-naphthalenediimide (NDI) lead to similar library distributions regardless of the enantiomer used. When no salt is present, the major component is a dimer, while dimers and tetramers are obtained at increased ionic strength.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

Freeze the dynamicity: charge transfer complexation assisted control over the reaction pathway

Aqueous CT complexes of donor and acceptor molecules with reactive thiol groups were frozen and lyophilized to get alternate D–A assemblies in the solid state. Oxidation of the thiols resulted in asymmetric disulfides exclusively.

Charge transfer (CT) complexes between electron donor and acceptor molecules provide unique alternate D–A arrangements. However, these arrangements cannot be fully translated into chemo-selective organic transformations as the dynamicity of CT complexes in solution results in the co-existence of D–A assemblies and free monomers during the reaction time-scale. A conceptually new strategy to exploit CT complexes toward chemo-selective products by means of seizing the dynamicity of CT complexes is reported here. Aqueous CT complexes of donor and acceptor molecules bearing reactive thiol groups were frozen instantly and cryo-desiccated to get the alternate D–A assemblies intact in the solid state. Oxidation of reactive thiols in an oxygen rich solvent in the solid state resulted in the formation of the hetero-dimer exclusively. CT complexation and appropriate molecular arrangements are the key factors behind successful execution of this novel methodology. The strategy also paves the way to prepare unsymmetrical disulfide molecules from two dissimilar thiols.

Coordination-driven self-assembly of a molecular figure-eight knot and other topologically complex architectures

Over the past decades, molecular knots and links have captivated the chemical community due to their promising mimicry properties in molecular machines and biomolecules and are being realized with increasing frequency with small molecules. Herein, we describe how to utilize stacking interactions and hydrogen-bonding patterns to form trefoil knots, figure-eight knots and [2]catenanes. A transformation can occur between the unique trefoil knot and its isomeric boat-shaped tetranuclear macrocycle by the complementary concentration effect. Remarkably, the realization and authentication of the molecular figure-eight knot with four crossings fills the blank about 4₁ knot in knot tables. The [2]catenane topology is obtained because the selective naphthalenediimide (NDI)-based ligand, which can engender favorable aromatic donor-acceptor π interactions due to its planar, electron-deficient aromatic surface. The stacking interactions and hydrogen-bond interactions play important roles in these self-assembly processes. The advantages provide an avenue for the generation of structurally and topologically complex supramolecular architectures.

Molecular knots and links continue to fascinate synthetic chemists. Here, the authors use stacking and hydrogen-bonding interactions between a set of similar building blocks to construct several complex molecular topologies, including a figure-eight knot and a trefoil knot.

Elucidation of naphthalene diimide metallomacrocycles and catenanes by solvent dependent excimer and exciplex emission

The formation of metallocatenanes, and their disruption by aromatic solvents, is followed by excimer and exciplex emission.

Product Distribution from Precursor Bite Angle Variation in Multitopic Alkyne Metathesis: Evidence for a Putative Kinetic Bottleneck

In the dynamic synthesis of covalent organic frameworks and molecular cages, the typical synthetic approach involves heuristic methods of discovery. While this approach has yielded many remarkable products, the ability to predict the structural outcome of subjecting a multitopic precursor to dynamic covalent chemistry (DCC) remains a challenge in the field. The synthesis of covalent organic cages is a prime example of this phenomenon, where precursors designed with the intention of affording a specific product may deviate dramatically when the DCC synthesis is attempted. As such, rational design principles are needed to accelerate discovery in cage synthesis using DCC. Herein, we test the hypothesis that precursor bite angle contributes significantly to the energy landscape and product distribution in multitopic alkyne metathesis (AM). By subjecting a series of precursors with varying bite angles to AM, we experimentally demonstrate that the product distribution, and convergence toward product formation, is strongly dependent on this geometric attribute. Surprisingly, we discovered that precursors with the ideal bite angle (60°) do not afford the most efficient pathway to the product. The systematic study reported here illustrates how seemingly minor adjustments in precursor geometry greatly affect the outcome of DCC systems. This research illustrates the importance of fine-tuning precursor geometric parameters in order to successfully realize desirable targets.

Imine-based [2]catenanes in water

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

Precursor control over the self-assembly of [2]catenanes via hydrazone condensation in water

By means of hydrazone condensation, a series of homo-[2]catenanes were self-assembled in high yields in water.

Flexible Viologen Cyclophanes: Odd/Even Effects on Intramolecular Interactions

The ability of three bis-viologen cyclophanes to act as redox-triggered contractile switches is investigated. Odd/even effects in the formation of cyclic bis-viologens are circumvented by the use of a Zincke salt intermediate and a tetrathiafulvalene template to prepare a flexible cyclophane with hexyl linkers. Comparative spectro-electrochemical studies of this macrocycle with two other pentyl- or heptyl-linked cyclic bis-viologens show that the development of intramolecular interactions in aqueous solution depends on the length of the bridges. This dependence is confirmed by EPR and DFT studies of the magnetic coupling in the diradical dication species. The anti-ferromagnetic or ferromagnetic nature of the coupling depend, respectively, on the odd or even number of methylene groups in the spacer.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media

The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.

Stabilization of peptides against proteolysis through disulfide-bridged conjugation with synthetic aromatics

We developed an efficient strategy for the stabilization of peptides against proteolysis, which involves noncovalent π–π interactions between aromatic amino acid residues in peptides and synthetic electron-deficient aromatics.

Supramolecular Assemblies of Ferrocene-Hinged Naphthalenediimides: Multiple Conformational Changes in Film States

We design a new naphthalenediimide (NDI) π-system, NDI-Fc-NDI, having a ferrocene linker as a hinge unit and long alkyl chains as supramolecular assembling units. The NDI units are "directionally flexible" in concert with the pivoting motion of the ferrocene unit with a small rotational barrier. The NDI units rotate around the ferrocene unit faster than the NMR time scale in solution at room temperature. UV-vis absorption, synchrotron X-ray diffraction, and atomic force microscope studies reveal that NDI-Fc-NDI forms a fibrous supramolecular assembly in solution (methylcyclohexane and highly concentrated chloroform) and film states, wherein the NDI units are in the slipped-stack conformation. The NDI-Fc-NDI supramolecular assembly in the film state exhibits multiple phase transitions associated with conformational changes at different temperatures, which are confirmed by differential scanning calorimetry, polarized optical microscopy, and temperature-dependent X-ray diffraction. Such thermal transitions of NDI-Fc-NDI films also induce changes in the optical and electronic properties as revealed by UV-vis absorption and photoelectron yield spectroscopies, respectively. The thermal behaviors of NDI-Fc-NDI, realized by the unique molecular design, are considerably different from the reference compounds such as an NDI dimer connected with a flexible 1,4-butylene linker. These results provide us with a plausible strategy to propagate the molecular dynamics of the π-system into macroscopic properties in film states; the key factors are (i) the supramolecular alignment of molecular switching units and (ii) the directional motion of the switching units perpendicular to the supramolecular axis.

Fluorescence from an H-aggregated naphthalenediimide based peptide: photophysical and computational investigation of this rare phenomenon

Fluorescence associated with J-aggregated naphthalenediimides (NDIs) is common. However, in this study an NDI based synthetic peptide molecule is found to form a fluorescent H-aggregate in a chloroform (CHCl3)-methylcyclohexane (MCH) mixture. An attempt has been made to explain the unusual fluorescence property of this H-aggregated NDI derivative. Time correlated single photon counting (TCSPC) shows that the average lifetime of the NDI based molecule is on the order of a few nanoseconds. It is revealed from the computational study that the transition from the second exited state (S2) to the ground energy state (S0) is responsible for the fluorescence as S1 is a dark state. Such rare violation of Kasha's rule accounts for the unusual fluorescence properties of this type of NDI molecule in the H-aggregated state.

Competition-driven selection in covalent dynamic networks and implementation in organic reactional selectivity

Competition among reagents in dynamic combinatorial libraries of increased complexity leads to reactional self-sorting. This fundamental principle allowed development of selective dynamic protecting groups for controlled sequential derivatization of polyamines.

Competition among reagents in dynamic combinatorial libraries of increased complexity leads to reactional self-sorting (improved regioselectivity) in mixtures of aldehydes and oligoamines. High selectivity of a given library component is transferred to a different reacting component of low selectivity through a network of underlying equilibrating reactions which provide component exchange between all species. The selectivity of various carbonyl compounds in reactions with amines was also assessed towards the formation of defined sequences of residues along oligoamine chains. The approach was further exploited for defining selective dynamic protecting groups (DPGs), based on the reversible linkage between the substrate and the protecting group. They represent an intermediate approach between the conventional protecting groups and the protecting-group-free approach in organic synthesis. Removal of the protecting group is effected via dynamic exchange trapping by formation of a more stable product. The establishment of equilibrium eliminates the need for isolation and purification of the dynamically protected intermediate(s) and enables as well the selective sequential derivatisation of oligoamines. The DPG concept can be generalised to other reversible reactions and can thus represent a valuable alternative in the design of total synthesis of complex molecules.

Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template?

We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.

Chloride-Anion-Templated Synthesis of a Strapped-Porphyrin-Containing Catenane Host System

The synthesis, structure and anion-recognition properties of a new strapped-porphyrin-containing [2]catenane anion host system are described. The assembly of the catenane is directed by discrete chloride anion templation acting in synergy with secondary aromatic donor-acceptor and coordinative pyridine-zinc interactions. The [2]catenane incorporates a three-dimensional, hydrogen-bond-donating anion-binding pocket; solid-state structural analysis of the catenane⋅chloride complex reveals that the chloride anion is encapsulated within the catenane's interlocked binding cavity through six convergent CH⋅⋅⋅⋅Cl and NH⋅⋅⋅Cl hydrogen-bonding interactions and solution-phase (1) H NMR titration experiments demonstrate that this complementary hydrogen-bonding arrangement facilitates the selective recognition of chloride over larger halide anions in DMSO solution.

Stacking Interactions Drive Selective Self-Assembly and Self-Sorting of Pyrene-Based M(II)4L6 Architectures

Subcomponent self-assembly of two isomeric bis(3-aminophenyl)pyrenes, 2-formylpyridine and the metal ions Fe(II), Co(II), and Zn(II) led to the formation of two previously unidentified structure types: a C2-symmetric M(II)4L6 assembly with meridionally coordinated metal centers, and a C3-symmetric self-included M(II)4L6 assembly with facially coordinated metal centers. In both structures the meta linkages within the ligands facilitate π-stacking between the pyrene panels of the ligands. A C2h-symmetric M(II)2L2 box was also obtained, which was observed to selectively bind electron-deficient aromatic guests between two parallel pyrene subunits. Similar donor-acceptor interactions drove the selective self-assembly of a singular M(II)4L4L'2 architecture incorporating both a pyrene-containing diamine and an electron-deficient NDI-based diamine. This heteroleptic architecture was shown to be thermodynamically favored over the corresponding homoleptic M(II)4L6 and M(II)4L'6 complexes, which were nonetheless stable in each others' absence. By contrast, an isomeric pyrene-based diamine was observed to undergo narcissistic self-sorting in the presence of the NDI-based diamine.

Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry

We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines.

Constitutional self-selection from dynamic combinatorial libraries in aqueous solution through supramolecular interactions

We describe the predominant formation of a specific constitution arising from the combination of building blocks with different topologies through disulphide chemistry in a Dynamic Combinatorial Library (DCL). The supramolecular interactions established by a zwitterionic cysteine moiety are responsible for the self-selection of one product from all the virtual members of a large library.

Tailor-made design of J- or H-aggregated naphthalenediimide-based gels and remarkable fluorescence turn on/off behaviour depending on solvents

Design of a supramolecular chameleon that displays solvent dependent control over H/J-aggregation as well as fluorescence turn on/off behaviour depending on the proper choice of solvents.

Molecular motion of donor–acceptor catenanes in water

In this article, we use ¹H NMR spectroscopy to study the spontaneous molecular motion of donor–acceptor [2]catenanes in water.

Aromatic sulfonate anion-induced pseudorotaxanes: environmentally benign synthesis, selectivity, and structural characterization

Aromatic sulfonates allow the effective construction of anion-containing pseudorotaxanes from a tetracationic macrocycle known as the “Texas box” in organic media and under organic-free aqueous conditions.

Disulfide exchange: exposing supramolecular reactivity through dynamic covalent chemistry

A Tutorial Review of the subtle supramolecular interactions influencing the outcomes of equilibrating systems, focusing on the dynamic covalent chemistry (DCC) of disulfide exchange reactions, is presented. We discuss the topics of cation-π interactions (2.1), hydrophobic effects (2.2), hydrogen bonding interactions (2.3) aromatic donor-acceptor interactions (2.4), and metal-ligand interactions (2.5) in the context of dynamic disulfide chemistry.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Progress in the synthesis and exploitation of catenanes since the Millennium

Catenanes - molecules consisting of interlocked macrocyclic rings - have been prepared by templation strategies for some thirty years. The utilization of Cu(I) cation, aromatic donor-acceptor interactions and hydrogen bonding assisted self-assembly strategies has led to the construction of numerous examples of these aesthetically pleasing species. This review seeks to discuss key developments in the synthesis and functional application of catenanes that have occurred since the Millennium. The much expanded range of metal cation templates; the genesis and growth of anion templation, as well as the use of alternative supramolecular interactions (halogen bonding and radical templation) and thermodynamically controlled reactions to synthesize catenanes are detailed. The class of catenanes that may be described as "molecular machines" are then highlighted and to conclude, attempts to fabricate catenanes onto surfaces and into metal organic frameworks (MOFs) are discussed.