Imine-based [2]catenanes in water

Odd-Even Effects Leading to Alternating Polymerization and Macrocyclization in Nitroaldol Reaction Systems

Alternating macrocyclization and polymerization was observed in dynamic nitroaldol reaction systems. The reaction of an aromatic dialdehyde reacting with linear α,ω-dinitroalkanes with even numbers of carbon atoms favored the formation of lowellane macrocycles, while the reactions involving dinitrocompounds consisted of odd numbers of carbon atoms promoted polymerization. The folding patterns of the alkyl chains played an important factor in determining the outcome of the reactions.

Selective Aliphatic Aldimine Formation and Stabilization by a Hydrophobic Capsule in Water

Imines and enamines are useful intermediates in biochemical aldol-type reactions since their acid/base characteristics are accessible near neutrality. However, the generation of aldimines in water is a challenge as the equilibrium favors the components alkyl amines and aldehydes. Here, we report the generation, recognition, and protection of aldimines accomplished by a water-soluble capsule. The capsule provides a well-defined hydrophobic cavity isolating aldimines from the medium by a dry seam of Se-N chalcogen bonds instead of a wet seam of hydrogen bonds in water. A series of diverse aldimines are formed in situ and trapped rapidly (within 45 min at mM concentrations) in D2O with more than 90% yields. The encapsulated aldimines are stable for at least one month under ambient conditions. The aliphatic aldimines are selectively formed in the capsule even though they are less stable than aromatic imines in solution. The aldimines can be released from the capsule containers by competitive guests such as adamantane.

Amide cyclodextrin that recognises monophosphate anions in harmony with water molecules

Anion recognition in water by synthetic host molecules is a popular and challenging topic. It has been considered difficult because the water molecules compete for the recognition units. In this study, we have successfully created a novel macrocycle that achieves precise recognition through multipoint hydrogen bonding in harmony with water molecules. Specifically, an N-methylpyridinium amide β-cyclodextrin (β-CD) derivative 1(OTf)7 was synthesized, whose amide groups are directly attached to each pyranose ring. The pyridinium amide CD encapsulated a monophosphate anion in water, but it did not show interactions with sulfonates or carboxylates, thus a remarkable selectivity was demonstrated. Two monophosphates with different substituents, phenyl phosphate (PhOPO3 2-) and adamantyl phosphate (AdOPO3 2-), exhibited interesting contrasting pictures in the inclusion process, which were revealed by a combination of NOESY experiments, ITC measurements, and MD simulations. PhOPO3 2- was positioned slightly "upper" (closer to the pyridinium amide side) in 17+ with the oxygen atom of the phosphate ester R-O-P involved in the hydrogen bonds with the amide N-H, and configurational entropy plays a key role in the inclusion. Meanwhile, AdOPO3 2- was positioned "lower" (closer to the methoxy rim of CD) with the terminal -PO3 2- forming hydrogen bonds with the amides, and the hydrophobic effect is a major contributing driving force of the inclusion. The molecular design presented herein to achieve the precise recognition in water and clarification of the detailed mechanisms including the hydration phenomenon greatly contribute to the development of functional molecules that work in aqueous environments.

Self-Assembly of an Unlikely Occurring Quadrangular Tube by Modulating Intramolecular Forces

One of the central focuses in self-assembly is precisely controlling the self-assembly pathway so that the target molecules can be produced exclusively. Trans-1,2-cyclohexanediamine contains two amino units that form a 60° angle when projected on a plane. This angle naturally favors the formation of triangular products in most cases when trans-1,2-cyclohexanediamine is used as a bisamino building block in the synthesis of macrocycles and tubes. Here, we synthesized a slightly bent tetraformyl precursor bearing a central dibenzothiophene moiety, whose 3,7-positions are functionalized with two m-phthalaldehyde units. We observed that combining this tetraformyl building block with trans-1,2-cyclohexanediamine yielded a quadrangular tube when the concentrations of the precursors were relatively high. Both experimental measurements and theoretical calculations indicate that the formation of this unlikely occurring quadrangular product was driven by the intramolecular C-H⋅⋅⋅π interactions between the dibenzothiophene building blocks within the tube framework. This driving force, however, was disturbed in the triangular tube, a smaller counterpart whose formation was considered previously much more thermodynamically favored. These results improved our fundamental understanding on how to create those products whose syntheses are considered difficult or impossible, by modulating the intramolecular driving forces.

Expedient Decagram-Scale Synthesis of Robust Organic Cages That Bind Sulfate Strongly and Selectively in Water

Selective anion recognition remains a key challenge in supramolecular chemistry: only a very small number of systems that can function in water are known, and these nearly always preferentially bind hydrophobic anions. In this work, we report three robust hexa-cationic cages that can be prepared on scales up to 14 g in two simple and high-yielding steps from commercially available materials. One of these cages displays unusually strong sulfate binding in water (Ka = 12,000 M-1), and demonstrates high selectivity for this anion over H2PO4-/HPO42- in DMSO/buffer mixtures. These results demonstrate that relatively large, three-dimensional supramolecular hosts can be prepared in high yields and on large scales, and can be highly potent receptors.

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.

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.

Self-Assembly via Condensation of Imine or Its N-Substituted Derivatives

ConspectusCompared to traditionally used irreversible chemical reactions, dynamic covalent chemistry (DCC) including imine formation represents a more advanced technique in the preparation of molecules with complex structures and topologies, whose syntheses require the formation of many bonds. By allowing the occurrence of error checking and self-correcting, it is likely that the target molecules with high enough thermodynamic stability could be self-assembled in high or even quantitative yield. Two questions are raised herein. First, it becomes a central problem in self-assembly that how to endow a target product with high enough thermodynamic stability so that it can be produced as the major or the only product within the self-assembly library. Second, the reversible nature of dynamic bonds jeopardizes the intrinsic stability of the products. More specifically, the imine bond which represents the mostly used dynamic covalent bond, is apt to undergo hydrolysis in the presence of water. Developing new approaches to make imine more robust and compatible with water is thus of importance. In this account, we summarized the progress made in our group in the field of self-assembly based on C═N bond formation. In organic solvent where an imine bond is relatively robust, we focus on studying how to enhance the thermodynamic stability of a target molecule by introducing intramolecular forces. These noncovalent interactions either release enthalpy to favor the formation of the target molecule or preorganize the building blocks into specific conformations that mimic the product, so that the entropy loss of the formation of the latter is thus suppressed. In water, which often leads to imine hydrolysis, we developed two strategies to enhance the water-compatibility. By taking advantage of multivalency, namely, multiple bonds are often more robust than a single bond, self-assembly via condensation of imine was performed successfully in water, a solvent that is considered as forbidden zone of imine. Another approach is to replace typical imine with its more robust and water compatible derivatives, namely, either hydrazone or oxime, whose C═N bonds are generally less electrophilic compared to typical imine. With the water-compatible dynamic bonds in hand, a variety topological nontrivial molecules such as catenanes and knots was self-assembled successfully in aqueous media, driven by hydrophobic effect. When the self-assembled molecules in the form of rings and cages were designed for supramolecular purposes, water-compatibility endows a merit that allows the hosts to take advantage of hydrophobic effect to drive host-guest recognition, enabling various tasks to be accomplished, such as separation of guest isomers with similar physical properties, recognition of highly hydrated anions, as well as stabilization of guest dimers.

Supramolecular multivalency effects enhance imine formation in aqueous medium allowing for dynamic modification of enzymatic activity

Imine formation under physiological conditions represents a challenging reaction due to the strong propensity of aldimines to be hydrolyzed. Herein we disclose the remarkable effect of supramolecular multivalency on increasing imine stability. A family of reactive aldehydes was synthesized bearing supramolecularly-active sites within their structure. The imine formation activity for such aldehydes was evaluated and compared with model aldehydes. The reaction of the best-performing species - containing two carboxylate groups-with a set of amines showed a significant decrease in imine yields as the degree of supramolecular multivalency between sidechains decreased. The reversible conjugation of amino acid derivatives and small peptides was also assayed, with excellent selectivities for the imine formation at the Nα position even in substrates containing competing sites. Preliminary results on protein bioconjugation revealed that a model enzyme could be dynamically inhibited upon reaction with the aldehyde, with its native activity being recovered by displacing the imine bonds with a suitable chemical effector (i.e., acylhydrazide).

Crystalline Nanoparticles of Water-Soluble Covalent Basket Cages (CBCs) for Encapsulation of Anticancer Drugs

We herein describe the preparation, assembly, recognition characteristics, and biocompatibility of novel covalent basket cage CBC-11, composed of four molecular baskets linked to four trivalent aromatic amines through amide groups. The cage is tetrahedral in shape and similar in size to small proteins (Mw =8637 g/mol) with a spacious nonpolar interior for accommodating multiple guests. While 24 carboxylates at the outer surface of CBC-11 render it soluble in aqueous phosphate buffer (PBS) at pH=7.0, the amphiphilic nature prompts its assembly into nanoparticles (d=250 nm, DLS). Cryo-TEM examination of nanoparticles revealed their crystalline nature with wafer-like shapes and hexagonally arranged cages. Nanoparticulate CBC-11 traps anticancer drugs irinotecan and doxorubicin, with each cage binding up to four drug molecules in a non-cooperative manner. The inclusion complexation resulted in nanoparticles growing in size and precipitating. In media containing mammalian cells (HCT 116, human colon carcinoma), the IC50 value of CBC-11 was above 100 μM. While this work presents the first example of a large covalent organic cage operating in water at the physiological pH and forming crystalline nanoparticles, it also demonstrates its biocompatibility and potential to act as a polyvalent binder of drugs for their sequestration or delivery.

Knotting matters: orderly molecular entanglements

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

A trefoil knot self-templated through imination in water

The preparation of topologically nontrivial molecules is often assisted by covalent, supramolecular or coordinative templates that provide spatial pre-organization for all components. Herein, we report a trefoil knot that can be self-assembled efficiently in water without involving additional templates. The direct condensation of three equivalents of a tetraformyl precursor and six equivalents of a chiral diamine produces successfully a [3 + 6] trefoil knot whose intrinsic handedness is dictated by the stereochemical configuration of the diamine linkers. Contrary to the conventional wisdom that imine condensation is not amenable to use in water, the multivalent cooperativity between all the imine bonds within the framework makes this trefoil knot robust in the aqueous environment. Furthermore, the presence of water is proven to be essential for the trefoil knot formation. A topologically trivial macrocycle composed of two tetraformyl and four diamino building blocks is obtained when a similar reaction is performed in organic media, indicating that hydrophobic effect is a major driving force behind the scene.

Recent trends in organic cage synthesis: push towards water-soluble organic cages

Research on organic cages has blossomed over the past few years into a mature field of study which can contribute to solving some of the challenging problems. In this review we aim to showcase the recent trends in synthesis of organic cages including a brief discussion on their use in catalysis, gas sorption, host-guest chemistry and energy transfer. Among the organic cages, water-soluble analogues are a special class of compounds which have gained renewed attention in recent times. Due to their advantage of being compatible with water, such cages have the potential of showing biomimetic activities and can find use in drug delivery and also as hosts for catalysis in aqueous medium. Hence, the synthetic strategies for the formation of water-soluble organic cages shall be discussed along with their potential applications.

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 Stimuli-Responsive [2]Rotaxanes by Amidinium Exchange

Advances in supramolecular chemistry are often underpinned by the development of fundamental building blocks and methods enabling their interconversion. In this work, we report the use of an underexplored dynamic covalent reaction for the synthesis of stimuli-responsive [2]rotaxanes. The formamidinium moiety lies at the heart of these mechanically interlocked architectures, because it enables both dynamic covalent exchange and the binding of simple crown ethers. We demonstrated that the rotaxane self-assembly follows a unique reaction pathway and that the complex interplay between crown ether and thread can be controlled in a transient fashion by addition of base and fuel acid. Dynamic combinatorial libraries, when exposed to diverse nucleophiles, revealed a profound stabilizing effect of the mechanical bond as well as intriguing reactivity differences between seemingly similar [2]rotaxanes.

Complementarity of 2,6-Dimethanolpyridine and Di(ethylene glycol) in the Complexation of Na+ Ions: Attaching Multiple Copies of [2]Catenane Branches to Isophthalaldehyde-Containing Cores

In this study we found that 2,6-dimethanolpyridine displays good complementarity toward di(ethylene glycol) for the complexation of Na⁺ ions, allowing us to use this recognition system for the efficient synthesis of hetero[2]catenanes; indeed, it allowed us to attach multiple copies of [2]catenanes to branched systems presenting multiple isophthalaldehyde units. When we attempted to form a catenane from a preformed macrocycle featuring only a single di(ethylene glycol) unit, reacting it with a di(ethylene glycol) derivative presenting two amino termini, isophthalaldehyde, and templating Na⁺ ions [i.e., with the aim of using di(ethylene glycol)·Na⁺·di(ethylene glycol) recognition to template the formation of the interlocked imino macrocycle], the yields of the hetero[2]catenane and homo[2]catenane, comprising two imino macrocyclic units, were both poor (14% and 7%, respectively). In contrast, when one or two 2,6-dimethanolpyridine units were present in the preformed macrocycles, their reactions with the same diamine, dialdehyde, and Na⁺ ions provided the hetero[2]catenanes with high selectivity and efficiency (44% and 64% yields, respectively), with minimal formation of the competing homo[2]catenane. The high complementary of the 2,6-dimethanolpyridine·Na⁺·di(ethylene glycol) ligand pair allowed us to synthesize [2]catenane dimers and trimers directly from corresponding isophthalaldehyde-presenting cores, with yields, after subsequent reduction and methylation, of 42% and 31%, respectively.

Diastereoselective Amplification of a Mechanically Chiral [2]Catenane

Achiral [2]catenanes composed of rings with inequivalent sides may adopt chiral co-conformations. Their stereochemistry depends on the relative orientation of the interlocked rings and can be controlled by sterics or an external stimulus (e.g., a chemical stimulus). Herein, we have exploited this stereodynamic property to amplify a mechanically chiral (P)-catenane upon binding to (R)-1,1'-binaphthyl 2,2'-disulfonate, with a diastereomeric excess of 85%. The chirality of the [2]catenane was ascertained in the solid state by single crystal X-ray diffraction and in solution by NMR and CD spectroscopies. This study establishes a robust basis for the development of a new synthetic approach to access enantioenriched mechanically chiral [2]catenanes.

Self-Assembly of a Purely Covalent Cage with Homochirality by Imine Formation in Water

Self-assembly of host molecules in aqueous media via metal-ligand coordination is well developed. However, the preparation of purely covalent counterparts in water has remained a formidable task. An anionic tetrahedron cage was successfully self-assembled in a [4+4] manner by condensing a trisamine and a trisformyl in water. Even although each individual imine bond is rather labile and apt to hydrolyze in water, the tetrahedron is remarkably stable or inert due to multivalence. The tetrahedral cages, as well as its neutral counterparts dissolved in organic solvent, have homochirality, namely that their four propeller-shaped trisformyl residues adopt the same rotational conformation. The cage is able to take advantage of hydrophobic effect to accommodate a variety of guest molecules in water. When a chiral guest was recognized, the formation of one enantiomer of the cage became more favored relative to the other. As a consequence, the cage could be produced in an enantioselective manner. The tetrahedron is able to maintain its chirality after removal of the chiral guest-probably on account of the cooperative occurrence of intramolecular forces that restrict the intramolecular flipping of phenyl units in the cage framework.

Gas-Phase Structural Analysis of Supramolecular Assemblies

Ion mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links.

Diverse binding of cationic guests by highly substituted [3 + 3] Schiff-base macrocycles

Schiff-base macrocycles interact with ammonium-based guests to form threaded pseudorotaxanes or unthreaded external complexes, and tautomerize in the process.

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.

A porous fluorinated organic [4+4] imine cage showing CO2 and H2 adsorption

We report the first POC, containing perfluorinated aromatic panels forming quickly and in high purity, despite low preorganization encoded in the starting materials.

Control over the macrocyclisation pathway and product topology in a copper-templated catenane synthesis

Strategies to control building block intertwining and the efficient assembly of a linear [4]catenane are presented.

Resolution of minor size differences in a family of heteroleptic coordination cages by trapped ion mobility ESI-MS

We report a complex system of heteroleptic coordination cages based on the combination of four bis-monodentate ligands whose backbones only slightly differ in shape and length. cis-[Pd2L2L'2] assemblies cleanly form after addition of PdII cations to a 1 : 1 mixture of two shape-complementary ligands, each. When three or even all four ligands are used in combination, the unambiguous discrimination of all individual species in the product mixture becomes difficult by conventional NMR spectroscopic and mass spectrometric methods. Due to steric constraints, the system is restricted to the formation of ten different coordination cages in total, two of which are isomeric. We show that high-resolution trapped ion mobility mass spectrometry (TIMS) allows the clear differentiation of all ten species. Observed size trends could be readily reproduced by the calculation of theoretical values for collisional cross sections (CCS) from geometry-optimized models.

Conjugated Polyimine Dynamers as Phase-Sensitive Membrane Probes

In this report, dynamic polyimines are introduced as multifunctional sensors of lipid bilayer phases. Under mildly acidic conditions, self-condensation of push-pull amino formyl fluorenes into polyimines occurs in solid- or liquid-ordered phases but not in liquid-disordered phases of vesicular membranes. The obtained conjugated polymers are characterized by a progressive red shift of the absorption maxima, the appearance of exciton-coupled circular dichroism (CD) bands, and fluorescence quenching. These characteristics allow multiple modes of detection of membrane phases, which are known to change under membrane tension.

Three Switchable Orthogonal Dynamic Covalent Reactions and Complex Networks Based on the Control of Dual Reactivity

Achieving complexity is central to the creation of chemical systems, inspired by natural systems. Herein we introduce a strategy of switchable orthogonal dynamic covalent chemistry (DCC) toward the regulation of complex dynamic networks. The control of dual reactivity of tautomers and resulting pathways allowed reversible covalent bonding of a large scope of primary amines, secondary amines, alcohols, and thiols with high efficiency. The selection of reaction pathways next enabled the realization of orthogonal but switchable dynamic covalent reactions (DCRs) with nucleophile pairs of amine/alcohol, alcohol/thiol, and amine/thiol by varying protonation and oxidation states. Control experiments confirmed the crucial role of dual reactivity on the stability and switchability of DCRs. The specificity toward amines, alcohols, and thiols, as well as interconversion between their corresponding assemblies, was further accomplished in one vessel, thus creating tunable communicating networks with three types of DCRs. Moreover, the switchable orthogonality combined with differential reactivity of multiple sulfonamides and nucleophiles enhanced the complexity within dynamic libraries. The generality and versatility of our approaches should facilitate their incorporation into many aspects of chemistry endeavors.

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.