Guest Binding Research Articles

Interplay of Stereochemistry and Charge Governs Guest Binding in Flexible ZnII4L4 Cages.

Here, we report the synthesis of a family of chiral ZnII4L4 tetrahedral cages by subcomponent self-assembly. These cages contain a flexible trialdehyde subcomponent that allows them to adopt stereochemically distinct configurations. The incorporation of enantiopure 1-phenylethylamine produced Δ4 and Λ4 enantiopure cages, in contrast to the racemates that resulted from the incorporation of achiral 4-methoxyaniline. The stereochemistry of these ZnII4L4 tetrahedra was characterized by X-ray crystallography and chiroptical spectroscopy. Upon binding the enantiopure natural product podocarpic acid, the ZnII stereocenters of the enantiopure Δ4-ZnII4L4 cage retained their Δ handedness. In contrast, the metal stereocenters of the enantiomeric Λ4-ZnII4L4 cage underwent inversion to a Δ configuration upon encapsulation of the same guest. Insights gained about the stereochemical communication between host and guest enabled the design of a process for acid/base-responsive guest uptake and release, which could be followed by chiroptical spectroscopy.

Structural Deformations in Cucurbit[n]urils: Analysis, Host-Guest Dependence, and Automated Ellipticity Measurements Using ElliptiCB[n

Cucurbit[n]urils (CB[n]s) are cyclic macrocycles with rich host-guest chemistry. In many cases, guest binding in CB[n]s results in host structural deformations. Unfortunately, measuring such deformations remains a major challenge, with only a handful of manual estimations reported in the literature. To address this challenge, we have developed the public program ElliptiCB[n], which is available on GitHub, that provides a robust and automated method for measuring the elliptical deformations in CB[n] hosts. We outline the development and validation of this approach, apply ElliptiCB[n] to measure the ellipticity of the 1113 available CB[n] structures from the Cambridge Structural Database (CSD), and directly investigate the structural deformations of CB[5], CB[6], CB[7], CB[8], and CB[10] hosts. We also report the general landscape of accessible CB[n] elliptical deformations and compare ellipticity distributions across CB[n] hosts and host-guest complexes. We found that in almost all cases guest binding significantly impacts the distribution of host ellipticity distributions and that these distributions are dissimilar across host-guest complexes of differently sized CB[n]s. We anticipate that this work will provide a useful approach for understanding of the flexibility of CB[n] hosts and will also enable future measurement and standardization of ellipticity measurements of CB[n]s.

Modulating the guest binding ability within mixed-coordination geometry [Pd(μ-L)4RuCl2]2+ and [Pd(μ-L)4Pt]4+ cage architectures.

Heterobimetallic cages built from Pd and either octahedral Ru or square-planar Pt moieties and bridged by ligands with H bonding-accepting or -donating properties are reported. They showed stimulus-responsive dis- and reassembly, while guest binding was found to be dependent on the complementary properties of the guest to the host in terms of charge, size and H bonding properties.

Guest binding is governed by multiple stimuli in low-symmetry metal-organic cages containing bis-pyridyl(imine) vertices

Guest binding is governed by multiple stimuli in low-symmetry metal-organic cages containing bis-pyridyl(imine) vertices

Structural and antibacterial assessment of two distinct dihydroxy biphenyls encapsulated with β-cyclodextrin supramolecular complex

β-Cyclodextrin plays a vital role in biological application because it can enhance the stability and solubility of the guest molecules in the supramolecular inclusion complexes. Moreover, the β-Cyclodextrin inclusion complex has control-releasing behavior and lower toxicity than bare guest molecules. To improve the solubility and stability properties of two structurally different fluorescent guest molecules, namely 2,2′-dihydroxy biphenyl and 3,3′-dihydroxy biphenyls, they involve the β-Cyclodextrin inclusion complex process. Optical measurements clearly described the efficient binding through the changes in the absorbance and emission intensities of guest molecules in the presence of β-Cyclodextrin. The Job's plot from absorbance measurements reveals the 1:1 stochiometric ratio of binding of guests and the β-Cyclodextrin host. The FT-IR spectra of the solid complex show the characteristic stretching and bending vibrations from both the guests and the host molecule. The 1HNMR spectra of the inclusion complex promote downfield shifting of guest molecule protons upon binding with the β-Cyclodextrin host. The solid complex prepared using the solution method exhibits superior antibacterial activity against both gram-positive and gram-negative bacteria compared to the kneading and physical mixing methods.

Neutral guest binding by meso‑3,5-bis(trifluoromethyl)phenyl two-wall calix[4]pyrrole: N-oxide recognition features and unique acetonitrile binding mode

Two-wall calix[4]pyrroles bearing two aryl substituents at diametrically opposed meso-positions have been well explored toward the recognition and sensing of anionic substrates. However, their ability to form stable complexes with neutral guests remains underexplored. Herein, we report the heterocyclic N-oxides (such as pyridine N-oxide (PNO), 4-methylpyridine N-oxide (MPNO), and 4-phenylpyridine N-oxide (PPNO)) binding features of meso-3,5-bis(trifluoromethyl)phenyl two-wall calix[4]pyrrole 1. Single crystal X-ray diffraction analysis of the PNO complex of 1 revealed the formation of two types of closely resembled 1/1 complexes within the same crystal, wherein the calix[4]pyrrole core adopted a cone-like conformation and the PNO was bound to the cleft delineated by two aromatic walls adopting pseudo-edge-to-face (PETF) geometry. MPNO formed only one type of 1/1 complex with receptor 1 having PETF geometry in the solid state. Solution phase interaction of 1 with PNO, MPNO, and PPNO was investigated by 1H NMR spectroscopic titrations carried out in CD3CN. On the other hand, X-ray diffraction analysis of single crystals of 1, grown from CH3CN solution, unveiled the formation of a 1/2 host-acetonitrile solvate containing an unstable arrangement of CH3CN dimer displaying a unique CH3CN coordination mode in the solid state. Furthermore, a unique 1D supramolecular chain of CH3CN was stabilized within the narrow channel in the crystal lattice of 1•(CH3CN)2.

Fabrication of Azacrown Ether‐Embedded Covalent Organic Frameworks for Enhanced Cathode Performance in Aqueous Ni−Zn Batteries

AbstractCrown ethers (CEs), known for their exceptional host–guest complexation, offer potential as linkers in covalent organic frameworks (COFs) for enhanced performance in catalysis and host–guest binding. However, their highly flexible conformation and low symmetry limit the diversity of CE‐derived COFs. Here, we introduce a novel C3‐symmetrical azacrown ether (ACE) building block, tris(pyrido)[18]crown‐6 (TPy18C6), for COF fabrication (ACE‐COF‐1 and ACE‐COF‐2) via reticular synthesis. This approach enables precise integration of CEs into COFs, enhancing Ni2+ ion immobilization while maintaining crystallinity. The resulting Ni2+‐doped COFs (Ni@ACE‐COF‐1 and Ni@ACE‐COF‐2) exhibit high discharge capacity (up to 1.27 mAh ⋅ cm−2 at 8 mA ⋅ cm−2) and exceptional cycling stability (>1000 cycles) as cathode materials in aqueous alkaline nickel‐zinc batteries. This study serves as an exemplar of the seamless integration of macrocyclic chemistry and reticular chemistry, laying the groundwork for extending the macrocyclic‐synthon driven strategy to a diverse array of COF building blocks, ultimately yielding advanced materials tailored for specific applications.

Multipocket Cage Enables the Binding of High-Order Bulky and Drug Guests Uncovered by MS Methodology.

Achieving high guest loading and multiguest-binding capacity holds crucial significance for advancement in separation, catalysis, and drug delivery with synthetic receptors; however, it remains a challenging bottleneck in characterization of high-stoichiometry guest-binding events. Herein, we describe a large-sized coordination cage (MOC-70-Zn8Pd6) possessing 12 peripheral pockets capable of accommodating multiple guests and a high-resolution electrospray ionization mass spectrometry (HR-ESI-MS)-based method to understand the solution host-guest chemistry. A diverse range of bulky guests, varying from drug molecules to rigid fullerenes as well as flexible host molecules of crown ethers and calixarenes, could be loaded into open pockets with high capacities. Notably, these hollow cage pockets provide multisites to capture different guests, showing heteroguest coloading behavior to capture binary, ternary, or even quaternary guests. Moreover, a pair of commercially applied drugs for the combination therapy of chronic lymphocytic leukemia (CLL) has been tested, highlighting its potential in multidrug delivery for combined treatment.

A Benchmark Test of High-Throughput Atomistic Modeling for Octa-Acid Host–Guest Complexes

Years of massive applications of high-throughput atomistic modeling tools such as molecular docking and end-point free energy calculations in the drug industry and academic exploration have made them indispensable parts of hierarchical screening. While the similarities between host–guest and protein–ligand complexes lead to the direct extension of techniques for protein–ligand screening to host–guest systems, the practical performance of these hit identification tools remains unclear in host-–-guest binding. Recent reports on specific host–guest complexes suggest that the experience on the accuracy ladder accumulated from protein–ligand cases could be invalid in host–guest complexes, which makes it an urgent need to perform a systematic benchmark to secure solid numerical supports and guidance of practical setups. Concerning molecular docking, there still lacks a comprehensive benchmark considering popular docking programs. As for end-point reranking, quantitative and rigorous free energy estimation via end-point formulism requires establishing statistically meaningful measurements of uncertainties due to finite sampling, which is neglected or underestimated by a significant portion in almost all main-stream applications. Further, a face-to-face comparison between different screening tools is required for the design of a hierarchical workflow. To fill the above-mentioned critical gaps, in this work, using a dataset containing tens of host–guest complexes involving basket-like macromolecular hosts from the octa acid family, we extensively benchmark seven academic docking protocols and perform post-docking end-point rescoring with twenty protocols. The resulting comprehensive benchmark provides conclusive pictures of the practical value of docking and end-point screening in OA host–guest binding.

Carboxylated pillar[5]arene cavity accommodates organic cations in the host-guest complexes

The electron-rich cavity of carboxylated pillar[5]arene efficiently encapsulates cationic guest molecules within supramolecular assemblies. In this study we provide evidence of the host-guest complexation between carboxylated pillar[5]arene and benzamidine, a competitive inhibitor of serine proteases. We show the unexpected inclusion of the polar amidinium functionality within the central cavity of the macrocyclic host sustained by N+-H···π and cation···π interactions. In addition to the in-cavity complexation, simultaneous external binding of bipyridinium guests with varying stoichiometries has been observed. The interesting aspect is the inclusion of a hydrogen bonded pair of 1,2-bis(4-pyridyl)ethylene guests into pillar[5]arene cavity. Additional insights into inclusion characteristics are provided by NMR and ion mobility mass spectrometry (IM-MS) studies, offering information for the solution/gas phase and enabling a comprehensive description of the complexation process across different phases. This work expands the portfolio of cationic guest molecules capable of being encapsulated by carboxylated pillar[5]arene, showing new promises and directions for their inclusion and self-assembly behavior.

Virtual screening of cucurbituril host-guest complexes: Large-scale benchmark of end-point protocols under MM and QM Hamiltonians

The similarity of protein–ligand and host–guest complexes leads to the direct extension of end-point free energy techniques to virtual screening of the latter. Despite the massive application of end-point calculations in modelling and predictions of host–guest binding, it still lacks a large-scale benchmark test with sufficient sizes, sampling length and diverse coverages of chemical spaces to get rid of many disturbing factors and provide an unbiased statistical perspective of practical performance and value of end-point screening. Cucurbiturils as one of the main-stream macrocycles are quite popular in pharmaceutical research and industrial applications as drug reservoirs and carriers. In this work, we gather a large dataset of ∼150 host–guest complexes involving cucurbiturils with varying numbers of repeating units, extensively sample the conformational space in physical end states with both the single- and three-trajectory protocols, and extract the affinity estimates with a variety of MM and QM/GBSA Hamiltonians with implicit solvents. The diversity of chemical compositions, the quality of configurational sampling, and the comprehensiveness of parameter combinations are unprecedently high, enabling us to deduce conclusive pictures of the end-point performance in host–guest binding. Unlike previous reports on improved performance due to the incorporation of the QM treatment, shifting to QM/GBSA treatments deteriorates both the reproduction of absolute affinities and the prediction of affinity ranks in our large-scale end-point benchmark, regardless of the employed sampling protocol (i.e., single- and three-trajectory realization). Overall, in the end-point screening of cucurbituril host–guest complexes, we recommend sticking to the original MM/GBSA Hamiltonians in both sampling and free energy estimation. The best/recommended selection with high accuracy and robustness among all end-point protocols benchmarked in this work is the three-trajectory GAFF + GBOBC-I regime, which achieves top performances for both the reproduction of absolute affinities and ranking different host–guest pairs. Docking estimates with seven main-stream protocols have been observed as a promising tool for host–guest binding, but their ranking powers in the current large host–guest dataset does not surpass end-point tools, validating the value of post-docking end-point screening.

Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures.

Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by "hydrogen bond enhanced halogen bonds" (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. This research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.

Probing noncovalent binding, spectroscopic characteristics and antiproliferative behavior of inclusion complex between quinoline and para-sulfonatothiacalix[4]arene

The inclusion complex between bowl-shaped para-sulfonatothiacalix[4]arene (TSCX4) macrocycle and quinoline has been studied with a unison of UV–visible, infra-red, flourescence emission and 1H nuclear magnetic resonance (NMR) and 2D nuclear overhauser effect spectroscopy (NOESY), high resolution mass spectrometry (HRMS) experiments. Both 1H NMR titration and HRMS experiments point to 1:1 stoichiometry for the water soluble Q⊂TSCX4 complex. The electronic structure of the inclusion complex obtained from density functional theory (DFT) showed a partial encapsulation of quinoline guest, which is held within the host cavity by C–H---π, π---π and hydrogen bonding interactions. The fluorescence emission spectra upon complexation display marginal blue shift of the 411 nm band in TSCX4. Moreover, the binding constant (7.1 × 103 M−1) determined from fluoresence emission experiments underline the effective host–guest binding in the complex, which was corroborated through frequency up-shift (‘blue shift’) of characteristic Ar-OH (3433 cm−1) and SO3- vibrations (1141 cm−1 and 1037 cm−1) in the measured infrared spectra of TSCX4. The antiproliferative activitities of the Q⊂TSCX4 complex against HeLA, MDA-MB-231and N2a cells are presented. The Q⊂TSCX4 complex has been shown to be efficient against N2a (neuroblastoma) cell line.

A micro-fabricated potentiometric platform with application in a COVID-19 drug quantification and the determination of its binding affinity to a supramolecular host

Recent applications in host–guest chemistry include advanced sensing technologies, drug formulations, and drug delivery. Quantification of host–guest binding constants is significant to the continued optimization of their use. Binding constants offer valuable information about the stability and affinity of the formedcomplex that is essential to both drug formulations and delivery. In this study a novel green, portable, disposable, and cost-efficient microfabricated potentiometric sensor is introduced and successfully applied to determine the concentration of remdesivir (RMD), a COVID-19 drug, and its binding affinity to the supramolecular host sulfobutylether-β-cyclodextrin (SBEβCD) as a compatible solubilizing agent; to overcome the low water solubility of RMD which presents a significant challenge in its intravenous administration. The sensor incorporates multi-walled carbon nanotubes to improve stability and detection limits. To reduce interference effects and enhance the selectivity of the sensor for RMD, 4-tert-butyl-calix[8]arene was employed as an ionophore. A Nernstian potentiometric response for RMD over a concentration range of 1.0 × 10−3 to 1.0 × 10−6 M with a slope of 58.2 ± 0.9 mV decade−1 and a detection limit of 0.23 µM were achieved. The binding constant of the RMD-SBEβCD complex was determined to be 9.76 × 103 M−1. The proposed sensor was shown to be effective for drug quantification and measurements of binding affinities, providing valuable insights into the physicochemical properties of target drugs.

Coordination cages integrated into swelling poly(ionic liquid)s for guest encapsulation and separation

Coordination cages have been widely reported to bind a variety of guests, which are useful for chemical separation. Although the use of cages in the solid state benefits the recycling, the flexibility, dynamicity, and metal-ligand bond reversibility of solid-state cages are poor, preventing efficient guest encapsulation. Here we report a type of coordination cage-integrated solid materials that can be swelled into gel in water. The material is prepared through incorporation of an anionic FeII4L6 cage as the counterion of a cationic poly(ionic liquid) (MOC@PIL). The immobilized cages within MOC@PILs have been found to greatly affect the swelling ability of MOC@PILs and thus the mechanical properties. Importantly, upon swelling, the uptake of water provides an ideal microenvironment within the gels for the immobilized cages to dynamically move and flex that leads to excellent solution-level guest binding performances. This concept has enabled the use of MOC@PILs as efficient adsorbents for the removal of pollutants from water and for the purification of toluene and cyclohexane. Importantly, MOC@PILs can be regenerated through a deswelling strategy along with the recycling of the extracted guests.

Cage-To-Cage Transformations in Self-Assembled Coordination Cages Using "Acid/Base" or "Guest Binding-Induced Strain" as Stimuli.

Controlling supramolecular systems between different functional forms by utilizing acids/bases as stimuli is a formidable challenge, especially where labile coordination bonds are involved. A pair of acid/base responsive, interconvertible 1,5-enedione/pyrylium based Pd2L4-type cages are prepared that exhibit differential guest binding abilities towards disulfonates of varied sizes. A three-state switch has been achieved, where (i) a weakly coordinating base induced cage-to-cage transformation in the first step, (ii) a strongly coordinating base triggered cage disassembly as the second step, and (iii) the third step shows acid(strong) promoted generation of initial cage, thereby completing the cycle. To our surprise, binding of a specific disulfonate guest facilitated cage-to-cage transformations by inducing strain on the cage assembly thereby opening the labile pyrylium rings of the cage. Through a competitive guest binding study, we demonstrated the superior guest binding capability of the octacationic pyrylium-based cage over a similar-sized tetracationic cage. These results provide a reliable approach to reversibly modulate the guest binding properties of acid/base-responsive self-assembled coordination cages.

Cage‐To‐Cage Transformations in Self‐Assembled Coordination Cages Using “Acid/Base” or “Guest Binding‐Induced Strain” as Stimuli

AbstractControlling supramolecular systems between different functional forms by utilizing acids/bases as stimuli is a formidable challenge, especially where labile coordination bonds are involved. A pair of acid/base responsive, interconvertible 1,5‐enedione/pyrylium based Pd2L4‐type cages are prepared that exhibit differential guest binding abilities towards disulfonates of varied sizes. A three‐state switch has been achieved, where (i) a weakly coordinating base induced cage‐to‐cage transformation in the first step, (ii) a strongly coordinating base triggered cage disassembly as the second step, and (iii) the third step shows acid(strong) promoted generation of initial cage, thereby completing the cycle. To our surprise, binding of a specific disulfonate guest facilitated cage‐to‐cage transformations by inducing strain on the cage assembly thereby opening the labile pyrylium rings of the cage. Through a competitive guest binding study, we demonstrated the superior guest binding capability of the octacationic pyrylium‐based cage over a similar‐sized tetracationic cage. These results provide a reliable approach to reversibly modulate the guest binding properties of acid/base‐responsive self‐assembled coordination cages.

Recognition site modifiable tetrapodal receptor and the effect of alkane chains on monosaccharide recognition

Traditional molecular recognition studies usually focus on obtaining strong host–guest interactions, which may lead to the neglect of important tendencies caused by other factors. Moreover, most receptors typically fix their recognition sites in the backbone of the receptor, resulting in great synthetic challenges for varying recognition functional groups. In this contribution, we developed a new class of tetrapodal receptors. The terminal functional groups of the receptor can be varied by simple chemistry. Through 1H NMR titration experiments and binding constant analysis, the influence of the size and shape of alkane chains on monosaccharide recognition was investigated. The introduction of ester functional groups allows the access of moderate binding affinity to unveil otherwise masked contribution of dispersion force in saccharide recognition. These results also imply that stronger forces may not always be beneficial for host–guest binding while functional groups with a particular shape may favor the discrimination of isomers through steric hindrance effect. Thereby, these tetrapodal receptors and their analogues provide an ideal platform for comparing the effects of various functional groups on molecular recognition.

Cycloglycolurils: Hybrid Glycoluril-Cyclobenzil Macrocycles.

Two novel glycoluril macrocycles have been synthesized from cyclotetrabenzil and cyclotribenzoin precursors using solvent-free condensations with urea. The crystal structure of the cyclotetra(p-phenylene)glycoluril macrocycle shows a twisted ring conformation, while that of the cyclotri(m-phenylene)glycoluril hybrid exhibits a distinct tubular supramolecular packing. These structures establish a potentially broad new class of macrocycles with intriguing guest binding properties owing to their available N-H motifs.

Inclusion Complexes between β-Cyclodextrin and Gaseous Substances—N2O, CO2, HCN, NO2, SO2, CH4 and CH3CH2CH3: Role of the Host’s Cavity Hydration

The thermodynamic aspects of the process of inclusion complex formation between β-cyclodextrin (acting as a host) and gaseous substances (guests; N2O, CO2, NO2, SO2, HCN, CH4, CH3CH2CH3) are studied by employing well-calibrated and tested density functional theory (DFT) calculations. This study sheds new light on the intimate mechanism of the β-cyclodextrin/gas complex formation and answers several intriguing questions: how the polarity and size of the guest molecule influence the complexation thermodynamics; which process of encapsulation by the host macrocycle is more advantageous—insertion to the central cavity without hydration water displacement or guest binding accompanied by a displacement of water molecule(s); what the major factors governing the formation of the complex between β-cyclodextrin and gaseous substances are. The special role that the cluster of water molecules inside the host’s internal cavity plays in the encapsulation process is emphasized.