High fidelity kinetic self-sorting in multi-component systems based on guests with multiple binding epitopes

Guest-induced narcissistic self-sorting in water via imine formation

Two anionic tetrahedral cages were self-assembled as the only observable products in weakly basic water via imine condensation. The success of the high-yielding formation of the cages in water relies on (i) multivalency enhancing the stability of the imine bond and affording these cages water compatibility and (ii) a guest template with a complementary size and geometry that provides a hydrophobic driving force by occupying the corresponding cage cavity. When all four precursors, namely two trisaldehydes and two trisamines, were combined in water, narcissistic self-sorting occurred when both guest templates were present. In organic media where the hydrophobic effect is absent, narcissistic self-sorting did not occur in the analogous cage systems, confirming the importance of guest templates.

Direct Detection of Hydrogen Bonds in Supramolecular Systems Using 1H-15N Heteronuclear Multiple Quantum Coherence Spectroscopy

Hydrogen-bonded supramolecular systems are usually characterized in solution through analysis of NMR data such as complexation-induced shifts and nuclear Overhauser effects (nOe). Routine direct detection of hydrogen bonding particularly in multicomponent mixtures, even with the aid of 2D NMR experiments for full assignment, is more challenging. We describe an elementary rapid ¹H-¹⁵N HMQC NMR experiment which addresses these challenges without the need for complex pulse sequences. Under readily accessible conditions (243/263 K, 50 mM solutions) and natural ¹⁵N abundance, unambiguous assignment of ¹⁵N resonances facilitates direct detection of intra- and intermolecular hydrogen bonds in mechanically interlocked structures and quadruply hydrogen-bonded dimers─of dialkylaminoureidopyrimidinones, ureidopyrimidinones, and diamidonaphthyridines─in single or multicomponent mixtures to establish tautomeric configuration, conformation, and, to resolve self-sorted speciation.

The Contributions of Supramolecular Kinetics to Dynamics of Supramolecular Polymers

Supramolecular polymers exhibit well-controlled dynamics with fascinating capacity for remodeling, self-healing, and stimuli-responsiveness. Supramolecular kinetics of non-covalent bonds is a dominant control handle among the relevant factors to tailor dynamics of supramolecular polymers. This Review focuses on elucidating how supramolecular kinetics dictates the polymer dynamics in supramolecular polymer systems. The ways to tailor supramolecular kinetics are firstly examined as prerequisites for structure-activity study of supramolecular polymers. We next discuss the role of supramolecular kinetics in supramolecular polymers under different polymer architectures by the combination of both of theoretical and experimental studies. Finally, we conclude by discussing the existing challenges and opportunities in the current studies.

Self-Sorting Governed by Chelate Cooperativity

Self-sorting phenomena are the basis of manifold relevant (bio)chemical processes where a set of molecules is able to interact with no interference from other sets and are ruled by a number of codes that are programmed in molecular structures. In this work, we study, the relevance of chelate cooperativity as a code for achieving high self-sorting fidelities. In particular, we establish qualitative and quantitative relationships between the cooperativity of a cyclic system and the self-sorting fidelity when combined with other molecules that share identical geometry and/or binding interactions. We demonstrate that only systems displaying sufficiently strong chelate cooperativity can achieve quantitative narcissistic self-sorting fidelities either by dictating the distribution of cyclic species in complex mixtures or by ruling the competition between the intra- and intermolecular versions of a noncovalent interaction.

Supramolecular complexation with kinetic stabilization: cucurbit[6]uril encapsulated doxorubicin-based prodrugs for pH-responsive controlled release

Kinetically-stabilized host–guest complexation for the construction of a pH-responsive drug delivery system.

Kinetically controlled narcissistic self-sorting of Pd(II)-linked self-assemblies from structurally similar tritopic ligands

Although many examples of self-sorting have been reported, self-sorting of structurally similar building blocks is potentially difficult. Herein, we present the narcissistic self-sorted state from two kinds of structurally similar...

Photoresponsive Binding Dynamics in High-Affinity Cucurbit[8]uril-Dithienylethene Host-Guest Complexes

The use of external stimuli to control the binding kinetics in supramolecular systems is of critical importance for the development of advanced molecular machines and devices. In this work, a study focused on the kinetics of a water-soluble host-guest system based on cucurbit[8]uril and two dithienylethene (DTE) photoswitches is reported. It is shown that for the DTE guest comprising two anionic sulfonate side arms appended to pyridinium moieties, the formation/dissociation of the pseudorotaxane structures is slowed down by more than 100000-fold with respect to its bipyridinium analogue. The decrease in ingression rate leads to the emergence of a competitive metastable product with the open DTE isomer that has an important influence in the overall binding kinetics. Moreover, the host-guest dissociation kinetics is demonstrated to be approximately 100-fold slower for the closed DTE isomer (t_1/2 =107 h vs. t_1/2 =1.2 h for the open isomer) allowing control over the dissociation rate with light.

Nonlinear Dependence on Na+ Ions for the Binding Dynamics of Cucurbit[6]uril with the trans-1-Methyl-4-(4-hydroxystyryl)pyridinium Cation

The binding dynamics of the trans-1-methyl-4-(4-hydroxystyryl)pyridinium cation (HSP⁺) to cucurbit[6]uril (CB[6]) in the presence of Na⁺ cations were studied to establish the effect of the relative concentrations of the system's components (HSP⁺, CB[6], and Na⁺) on these dynamics. The formation of the HSP⁺@CB[6] complex was temporally uncoupled from the photoisomerization of trans-HSP⁺, while a nonlinear effect of the Na⁺ cation concentration on the HSP⁺@CB[6] dynamics was observed. This nonlinearity is a consequence of Na⁺ having the opposite effect on the association and dissociation rate constants for the HSP⁺@CB[6] complex, creating a conceptual framework for using such nonlinearities to control multistep reactions in cucurbit[n]uril chemistry.

Kinetics and Mechanism of Cation-Induced Guest Release from Cucurbit[7]uril

The release of two organic guests from cucurbit[7]uril (CB7) was selectively monitored by the stopped‐flow method in aqueous solutions of inorganic salts to reveal the mechanistic picture in detail. Two contrasting mechanisms were identified: The symmetric dicationic 2,7‐dimethyldiazapyrenium shows a cation‐independent complex dissociation mechanism coupled to deceleration of the ingression in the presence of alkali and alkaline earth cations (Mⁿ⁺) due to competitive formation of CB7–Mⁿ⁺ complexes. A much richer, unprecedented kinetic behaviour was observed for the ingression and egression of the monocationic and non‐symmetric berberine (B⁺). The formation of ternary complex B⁺–CB7–Mⁿ⁺ was unambiguously revealed. A difference of more than two orders of magnitude was found in the equilibrium constants of Mⁿ⁺ binding to B⁺–CB7 inclusion complex. Large cations, such as K⁺ and Ba²⁺, also promoted B⁺ expulsion from the ternary complex in a bimolecular process. This study reveals a previously hidden mechanistic picture and motivates systematic kinetic investigations of other host–guest systems.

A pH-Switchable Triple Hydrogen-Bonding Motif

A stimuli responsive linear hydrogen bonding motif, capable of in situ protonation and deprotonation, has been investigated. The interactions of the responsive hydrogen bonding motif with complementary partners were examined through a series of 1H NMR experiments, revealing that the recognition preference of the responsive hydrogen bonding motif in a mixture can be switched between two states.

A Cucurbit[8]uril 2:2 Complex with a Negative pKa Shift

A viologen derivative carrying a benzimidazole group (V-P-I ²⁺ ; viologen-phenylene-imidazole V-P-I) can be dimerized in water using cucurbit[8]uril (CB[8]) in the form of a 2:2 complex resulting in a negative shift of the guest pK_a , by more than 1 pH unit, contrasting with the positive pK_a shift usually observed for CB-based complexes. Whereas 2:2 complex protonation is unclear by NMR, silver cations have been used for probing the accessibility of the imidazole groups of the 2:2 complexes. The protonation capacity of the buried imidazole groups is reduced, suggesting that CB[8] could trigger proton release upon 2:2 complex formation. The addition of CB[8] to a solution containing V-P- I³⁺ indeed released protons as monitored by pH-metry and visualized by a coloured indicator. This property was used to induce a host/guest swapping, accompanied by a proton transfer, between V-P-I ³⁺ ⋅CB[7] and a CB[8] complex of 1-methyl-4-(4-pyridyl)pyridinium. The origin of this negative pK_a shift is proposed to stand in an ideal charge state, and in the position of the two pH-responsive fragments inside the two CB[8] which, alike residues engulfed in proteins, favour the deprotonated form of the guest molecules. Such proton release triggered by a recognition event is reminiscent of several biological processes and may open new avenues toward bioinspired enzyme mimics catalyzing proton transfer or chemical reactions.

Self-complementary and narcissistic self-sorting of bis-acridinium tweezers

A molecular tweezer incorporating two acridinium moieties linked by a 1,3-dipyridylbenzene spacer was synthesized in three steps. The formation of its self-complementary dimer in water was demonstrated as a result of π-π stacking and hydrophobic interactions. Moreover, a 1 : 1 mixture of this bis-acridinium tweezer with one built on a 2,6-diphenylpyridyl spacer evidenced its narcissistic self-sorting behaviour in water.

Rational design and implementation of a cucurbit[8]uril-based indicator-displacement assay for application in blood serum

In this study, we report the first supramolecular indicator displacement assay (IDA) based on cucurbit[n]uril (CBn) host and a [2.2]paracyclophane derivative as indicator that is operational in blood serum.

In this study, we report the first supramolecular indicator-displacement assay (IDA) based on cucurbit[n]uril (CBn) hosts that is operational in blood serum. Rational design principles for host–guest chemosensing in competitively binding media were derived through detailed mathematical simulations. It was shown that currently known CBn-based chemosensing ensembles are not suited for use in highly competitive matrices such as blood serum. Conversely, the simulations indicated that a combination of cucurbit[8]uril (CB8) and an ultra-high affinity dye would be a promising IDA reporter pair for the detection of Alzheimer's drug memantine in blood serum. Therefore, a novel class of [2.2]paracyclophane-derived indicator dyes for the host CB8 was developed that possesses one of the highest host–guest affinities (K_a > 10¹² M^–1 in water) known in supramolecular host–guest chemistry, and which provides a large Stokes shift (up to 200 nm). The novel IDA was then tested for the detection of memantine in blood serum in a physiologically relevant sub- to low micromolar concentration range.

Change of the kinetics of inclusion in cucurbit[7]uril upon hydrogenation and methylation of palmatine

The negative activation entropy of tetrahydropalmatine inclusion makes the entry into cucurbit[7]uril significantly slower than in the case of dehydrocorydaline.

Guest-length driven high fidelity self-sorting in supramolecular capsule formation of calix[5]arenes in water

Only homocapsules 1⊃NC8N⊂1 and 2⊃NC10N⊂2 are selectively formed out of ten potentially different products.

A supramolecular five-component relay switch that exposes the mechanistic competition of dissociative versus associative binding to cucurbiturils by ratiometric fluorescence monitoring

A putrescine derivative of aminomethyladamantane is established as a ditopic guest with two mutually exclusive binding sites for cucurbit[6]uril and cucurbit[7]uril.

Acyclic Cucurbit[n]uril-type Receptors: Preparation, Molecular Recognition Properties and Biological Applications

This article traces the development of acyclic cucurbit[n]uril-type receptors with a focus on work from the Isaacs group. First, we describe the synthesis of methylene bridged glycoluril dimers capped with aromatic sidewalls which allowed us to probe the interconversion of the S- and C-shaped dimers which is a fundamental step in CB[n] formation. The C-shaped compounds were found to undergo discrete self-assembly (dimerization) in both water and organic solvents which lead us to investigate multicomponent self-sorting systems. We supressed the self-association of 8 by electrostatic repulsion in the putative dimer which allowed expression of its innate molecular recognition properties toward methylene blue and related planar cationic dyes. Longer glycoluril oligomers (trimer - hexamer, acyclic decamer) were prepared by starving the CB[n]-forming reaction of formaldehyde. The longer oligomers (e.g. 15 and 16) bind to alkylammonium ions in water ≈ 100-fold weaker than macrocyclic CB[n] highlighting the high preorganization of the acyclic but polycyclic framework. We prepared a wide variety of acyclic CB[n] compounds (wall variants, solubilizing group variants, linker variants) based on glycoluril trimer and tetramer. In particular, 26 and 27 have been shown to possess a wide variety of chemically and biologically interesting functions. For example, 26 was used to formulate the insoluble drug Albendazole and treat mice bearing SK-OV-3 xenograft tumors. Compound 27 binds tightly to the neuromuscular blocking agents rocuronium, vecuronium, and cisatracurium and acts as an in vivo reversal agent for these compounds in anesthetized rats. Container 27 was also found to modulate the hyperlocomotive effect of rats that had been treated with methamphetamine. Finally, 38 has been used as a cross reactive component of sensor arrays that are capable of classifying and quantifying cancer related nitroamines and a range of over the counter drugs. Overall, the work demonstrates that acyclic CB[n]-type compounds are nicely pre-organized and therefore retain the essential aspects of the recognition properties of macrocyclic CB[n] but allow for more straightforward tailoring of structure and solubility that enables a variety of chemically and biologically important applications.

Substituent effect on the dynamics of the inclusion complex formation between protoberberine alkaloids and cucurbit[7]uril

The dynamics and activation parameters of alkaloid entry into and exit from cucurbit[7]uril significantly depend on the substitution pattern.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.

Decoupled Associative and Dissociative Processes in Strong yet Highly Dynamic Host-Guest Complexes

Kinetics and thermodynamics in supramolecular systems are intimately linked, yet both are independently important for application in sensing assays and stimuli-responsive switching/self-healing of materials. Host-guest interactions are of particular interest in many water-based materials, sensing, and drug delivery applications. Herein we investigate the binding dynamics of a variety of electron-rich aromatic moieties forming hetero-ternary complexes with the macrocycle cucurbit[8]uril (CB[8]) and an auxiliary guest, dimethyl viologen, with high selectivity and equilibrium binding constants (K_eq up to 10¹⁴ M^-2). Using stopped-flow spectrofluorimetry, association rate constants were observed to approach the diffusion limit and were found to be insensitive to the structure of the guest. Conversely, the dissociation rate constants of the ternary complexes varied dramatically with the guest structure and were correlated with the thermodynamic binding selectivity. Hence differing molecular features were found to contribute to the associative and dissociative processes, mimicking naturally occurring reactions and giving rise to a decoupling of these kinetic parameters. Moreover, we demonstrate the ability to exploit these phenomena and selectively perturb the associative process with external stimuli (e.g., viscosity and pressure). Significantly, these complexes exhibit increased binding equilibria with increasing pressure, with important implications for the application of the CB[8] ternary complex for the formation of hydrogels, as these gels exhibit unprecedented pressure-insensitive rheological properties. A high degree of flexibility therefore exists in the design of host-guest systems with tunable kinetic and thermodynamic parameters for tailor-made applications across a broad range of fields.

An easy gene assembling strategy for light-promoted transfection by combining host-guest interaction of cucurbit[7]uril and gold nanoparticles

Cucurbit[7]uril (CB[7]), a representative member of the host family cucurbit[n]uril, can host-guest interact with many guest molecules such as adamantane, viologen and naphthalene derivatives. This host-guest interaction provides an easy strategy in gene vector assembling. Furthermore, CB[7] can self-assemble on gold nanospheres (AuNSs). Herein, the combination of CB[7] and AuNSs provides both advantages of host-guest interaction and photo-thermal effect of AuNSs. In this study, polyethyleneimine (PEI) and polyethylene glycol (PEG) were separately interacted with CB[7] via host-guest interaction. Then by assembling on AuNSs, PEI and PEG were combined together to condense DNA into polyplexes as well as enhance circulation stability of the polyplexes. These gene vectors were found to have high cellular uptake efficiency and low cytotoxicity. Furthermore, the well distributed AuNSs in the polyplexes could transform light into heat under light exposure because of the photo-thermal effect. This was found to effectively promote the entry of gene into cytoplasm and highly enhanced gene transfection efficiency.

Anion-capped metallohost allows extremely slow guest uptake and on-demand acceleration of guest exchange

The switching of molecular recognition selectivity is important for tuning molecular functions based on host–guest binding. While the switching processes in artificial functional molecules are usually driven by changes of the thermodynamic stabilities, non-equilibrium phenomena also play an important role in biological systems. Thus, here we designed a host–guest system utilizing a non-equilibrium kinetically trapped state for on-demand and time-programmable control of molecular functions. We synthesized a bis(saloph) macrocyclic cobalt(III) metallohost 1(OTf)₂, which has anion caps at both sides of the cation-binding site. The anion caps effectively retard the guest uptake/release so that we can easily make a non-equilibrium kinetically trapped state. Indeed, we can obtain a long-lived kinetically trapped state {[1·K]³⁺+La³⁺} prior to the formation of the thermodynamically more stable state {[1·La]⁵⁺+K⁺}. The guest exchange to the more stable state from this kinetically trapped state is significantly accelerated by exchange of TfO⁻ anion caps by AcO⁻ in an on-demand manner.

Host—guest assemblies can exploit stimuli-responsive guest binding and release for molecular recognition, but are typically governed by thermodynamics alone. Here, the authors design macrocycles with removable and exchangeable anion caps, allowing for the kinetic trapping and on-demand exchange of guest ions.

Five-Component Self-Assembly of Cucurbituril-Based Hetero-pseudorotaxanes

[5]Pseudorotaxanes can be obtained by self-sorting using heteroditopic guests and various cucurbituril homologues as hosts. The assembly and chemically induced disassembly of the pseudorotaxanes can be monitored by measuring the fluorescence of the anthracene guest in solution. Mass spectral evidence for the supramolecular assemblies is obtained in the gas phase. The disassembly in the gas phase can be achieved by collision-induced dissociation leading to the corresponding [2]- and [3]pseudorotaxanes.

Contrasting pK a Shifts in Cucurbit[7]uril Host-Guest Complexes Governed by an Interplay of Hydrophobic Effects and Electrostatic Interactions

Cucurbit[7]uril inclusion complexes with guests bearing dimethylamino groups show the expected upward pK a shifts, whereas their diethylamino counterparts display a decrease in pK a due to the preferential stabilization of the unprotonated form. These results identify the diethylamino group as the substituent of choice to avoid receptor-assisted protonation of guest molecules and present new evidence for the role of the hydrophobic effect as a driving force in cucurbituril complexation.

Kinetics of the reversible inclusion of flavopereirine in cucurbit[7]uril

The temperature dependence of the formation and dissociation kinetics of the flavopereirine–cucurbit[7]uril complex is revealed.

pH-Driven self-sorting in a four component host–guest system

A four component host–guest system was found to self-sort only under equimolar and acidic conditions.

Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform

Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by ¹H or ¹³C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

Coevolution and ratiometric behaviour in metal cation-driven dynamic covalent systems

Coevolution can be defined as the correlated changes of structurally and/or functionally connected entities. Dynamic Covalent Libraries (DCLs) have been used to demonstrate coevolution and ratiometric behaviour on a molecular level using dynamic covalent molecules such as imines and hydrazones.

Dynamic Covalent Libraries (DCLs) have been used to demonstrate coevolution behaviour on a molecular level using dynamic covalent molecules such as imines and hydrazones. Two systems are presented: the first system is based on a dialdehyde and two diamines in combination with Zn(ii) and Hg(ii) to form a 2 × 2 Constitutional Dynamic Network (CDN) of four complexes of macrocyclic bis-imines. Whereas the two metal ions, when reacted separately form a complex with each macrocycle with low selectivity, when applied together, each cation yields selectively a complex with one of the two macrocycles. Thus, the simultaneous application of both cations, where one might have expected the formation of four different complexes, results in the synergistic evolution (co-evolution) towards a simpler, more selective outcome under agonist amplification. The second system of 4 components, 2 amines and 2 aldehydes displays metalloselection together with a correlated evolution in distribution on complexation of Zn(ii) and Cu(i) with the dynamic ligand constituents and exhibits a dynamic ratiometry process related to the antagonistic behaviour of a pair of ligand constituents.

Kinetically controlled simplification of a multiresponsive [10 × 10] dynamic imine library

Kinetically controlled self-sorting processes in complex synthetic mixtures represent an important model for behaviours of biological networks, which operate far from equilibrium and without interference among simultaneous metabolic pathways. However, most of the previously reported kinetic self-sorting protocols dealt with small dynamic libraries and a single external stimulus. Here, we report the iterative simplification of a large imine dynamic combinatorial library (DCL) constructed from 10 aldehydes and 10 anilines, under the sequential influence of an oxidant, an adsorbent, and an increase in temperature. Six components of this initial DCL are mechanically isolated and amplified at least three-fold relative to their equilibrium distributions at the outset of the sorting process.

A Kinetic Self-Sorting Approach to Heterocircuit [3]Rotaxanes

In this proof-of-concept study, an active-template coupling is used to demonstrate a novel kinetic self-sorting process. This process iteratively increases the yield of the target heterocircuit [3]rotaxane product at the expense of other threaded species.

Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes

The self-assembly of two regioisomeric hydrogen-bonding naphthalenes was studied in mixed states in different polarity solvents. The regioisomers co-assemble to form heteromeric rosettes in chloroform. Upon injecting this solution into methylcyclohexane the heteromeric rosettes kinetically form amorphous aggregates, which over time differentiate into thermodynamically stable distinct nanostructures through self-sorting.