Guest Binding Research Articles

Hydrostatic‐Pressure‐Controlled Molecular Recognition: A Steroid Sensing Case Using Modified Cyclodextrin

AbstractDansyl‐modified cyclodextrin (CD) demonstrates molecular recognition behavior under high pressure as revealed by means of hydrostatic‐pressure UV/Vis, circular dichroism, and fluorescence spectroscopies, as well as fluorescence lifetime measurements. The dansyl branch, originally included into the CD cavity, was gradually excluded with increasing pressure, and then reached to lie on the primary rim. The CD sector rule can be used to explain the pressure‐dependent pre‐equilibration of ‘naphthyl‐in’ and ‘naphthyl‐out’ complexes. These in‐out conformers play pivotal roles in guest binding under high pressure. The supramolecular complexation of cholic acid, i. e., ursodeoxycholic or chenodeoxycholic acid, with the modified CD was also suppressed upon hydrostatic pressurization due to both positive reaction volumes (ΔV>0). The present work provides a useful strategy for designing a pressure‐responsive chemical sensor based on modified CD.

Porous Metal-Organic Polyhedra: Morphology, Porosity, and Guest Binding.

Designing porous materials which can selectively adsorb CO2 or CH4 is an important environmental and industrial goal which requires an understanding of the host–guest interactions involved at the atomic scale. Metal–organic polyhedra (MOPs) showing permanent porosity upon desolvation are rarely observed. We report a family of MOPs (Cu-1a, Cu-1b, Cu-2), which derive their permanent porosity from cavities between packed cages rather than from within the polyhedra. Thus, for Cu-1a, the void fraction outside the cages totals 56% with only 2% within. The relative stabilities of these MOP structures are rationalized by considering their weak nondirectional packing interactions using Hirshfeld surface analyses. The exceptional stability of Cu-1a enables a detailed structural investigation into the adsorption of CO2 and CH4 using in situ X-ray and neutron diffraction, coupled with DFT calculations. The primary binding sites for adsorbed CO2 and CH4 in Cu-1a are found to be the open metal sites and pockets defined by the faces of phenyl rings. More importantly, the structural analysis of a hydrated sample of Cu-1a reveals a strong hydrogen bond between the adsorbed CO2 molecule and the Cu(II)-bound water molecule, shedding light on previous empirical and theoretical observations that partial hydration of metal−organic framework (MOF) materials containing open metal sites increases their uptake of CO2. The results of the crystallographic study on MOP–gas binding have been rationalized using DFT calculations, yielding individual binding energies for the various pore environments of Cu-1a.

SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.

The prediction of host-guest binding affinities with computational modelling is still a challenging task. In the 7th statistical assessment of the modeling of proteins and ligands (SAMPL) challenge, a new host named TrimerTrip was synthesized and the thermodynamic parameters of 16 structurally diverse guests binding to the host were characterized. In the TrimerTrip-guest challenge, only structures of the host and the guests are provided, which indicates that the predictions of both the binding poses and the binding affinities are under assessment. In this work, starting from the binding poses obtained from our previous enhanced sampling simulations in the configurational space, we perform extensive alchemical and end-point free energy calculations to calculate the host-guest binding affinities retrospectively. The alchemical predictions with two widely accepted charge schemes (i.e. AM1-BCC and RESP) are in good agreement with the experimental reference, while the end-point estimates perform poorly in reproducing the experimental binding affinities. Aside from the absolute value of the binding affinity, the rank of binding free energies is also crucial in drug design. Surprisingly, the end-point MM/PBSA method seems very powerful in reproducing the experimental rank of binding affinities. Although the length of our simulations is long and the intermediate spacing is dense, the convergence behavior is not very good, which may arise from the flexibility of the host molecule. Enhanced sampling techniques in the configurational space may be required to obtain fully converged sampling. Further, as the length of sampling in alchemical free energy calculations already achieves several hundred ns, performing direct simulations of the binding/unbinding event in the physical space could be more useful and insightful. More details about the binding pathway and mechanism could be obtained in this way. The nonequilibrium method could also be a nice choice if one insists to use the alchemical method, as the intermediate sampling is avoided to some extent.

Feet‐to‐Feet‐Connected Multitopic Resorcinarene Macrocycles

AbstractThe past three decades have witnessed extraordinary advances in the preparation of macrocycles from a resorcinarene platform. Bridging two or more resorcinarene units through multipoint connections produces multitopic resorcinarene‐based hosts. The unique properties arising from multivalency offer diverse applications, such as molecular flasks, molecular machines, and supramolecular polymers. The face‐to‐face connection of two or more resorcinarenes results in a convergent, expanded guest binding space in which many large guests can be accommodated. In contrast, the feet‐to‐feet connection provides an extroverted, ditopic feature that can lead to different applications. Herein, we highlight the synthesis of extroverted, multitopic resorcinarene macrocycles and discuss their fascinating functions, such as molecular recognition, allosteric guest binding, and supramolecular polymerization.

Functional Ionic Liquid Crystals.

Ionic liquid crystals have emerged as a new class of functional soft materials in the last two decades, and they exhibit synergistic characteristics of ionic liquids and liquid crystals such as macroscopic orientability, miscibility with various species, phase stability, nanostructural tunability, and polar nanochannel formation. Owing to these characteristics, the structures, properties, and functions of ionic liquid crystals have been a hot topic in materials chemistry, finding various applications including host frameworks for guest binding, separation membranes, ion-/proton-conducting membranes, reaction media, and optoelectronic materials. Although several excellent review articles of ionic liquid crystals have been published recently, they mainly focused on the fundamental aspects, structures, and specific properties of ionic liquid crystals, while these applications of ionic liquid crystals have not yet been discussed at one time. The aim of this feature article is to provide an overview of the applications of ionic liquid crystals in a comprehensive manner.

Feeding a Molecular Squid: A Pliable Nanocarbon Receptor for Electron-Poor Aromatics

A hybrid nanocarbon receptor consisting of a calix[4]arene and a bent oligophenylene loop (“molecular squid”), was obtained in an efficient, scalable synthesis. The system contains an electron-rich cavity with an adaptable shape, which can serve as a host for electron deficient guests, such as diquat, 10-methylacridinium, and anthraquinone. The new receptor forms inclusion complexes in the solid state and in solution, showing a dependence of the observed binding strength on the shape of the guest species and its charge. The interaction with the methylacridinium cation in solution was interpreted in terms of a 2:1 binding model, with K11 = 5.92(7) × 103 M–1. The solid receptor is porous to gases and vapors, yielding an uptake of ca. 4 mmol/g for methanol at 293 K. In solution, the receptor shows cyan fluorescence (λmaxem = 485 nm, ΦF = 33%), which is partly quenched upon binding of guests. Methylacridinium and anthraquinone adducts show red-shifted emission in the solid state, attributable to the charge-transfer character of these inclusion complexes.

Balancing Ligand Flexibility versus Rigidity for the Stepwise Self-Assembly of M12 L24 via M6 L12 Metal-Organic Cages.

Non-covalent interactions are important for directing protein folding across multiple intermediates and can even provide access to multiple stable structures with different properties and functions. Herein, we describe an approach for mimicking this behavior in the self-assembly of metal-organic cages. Two ligands, the bend angles of which are controlled by non-covalent interactions and one ligand lacking the above-mentioned interactions, were synthesized and used for self-assembly with Pd2+ . As these weak interactions are easily broken, the bend angles have a controlled flexibility giving access to M2 (L1)4 , M6 (L2)12 , and M12 (L2)24 cages. By controlling the self-assembly conditions this process can be directed in a stepwise fashion. Additionally, the multiple endohedral hydrogen-bonding sites on the ligand were found to play a role in the binding and discrimination of neutral guests.

Structural Elucidation of the Mechanism of Molecular Recognition in Chiral Crystalline Sponges.

To gain insight into chiral recognition in porous materials we have prepared a family of fourth generation chiral metal–organic frameworks (MOFs) that have rigid frameworks and adaptable (flexible) pores. The previously reported parent material, [Co2(S‐mandelate)2(4,4′‐bipyridine)3](NO3)2, CMOM‐1S, is a modular MOF; five new variants in which counterions (BF4 −, CMOM‐2S) or mandelate ligands are substituted (2‐Cl, CMOM‐11R; 3‐Cl, CMOM‐21R; 4‐Cl, CMOM‐31R; 4‐CH3, CMOM‐41R) and the existing CF3SO3 − variant CMOM‐3S are studied herein. Fine‐tuning of pore size, shape, and chemistry afforded a series of distinct host–guest binding sites with variable chiral separation properties with respect to three structural isomers of phenylpropanol. Structural analysis of the resulting crystalline sponge phases revealed that host–guest interactions, guest–guest interactions, and pore adaptability collectively determine chiral discrimination.

SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations

Host-guest binding remains a major challenge in modern computational modelling. The newest 7th statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and calculate the binding affinities in all three host-guest binding cases of the 6th SAMPL challenge. In this work, we report a retrospective study on the TrimerTrip host-guest systems by employing the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The calculated binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations. Note that as the work is performed after the close of the SAMPL7 challenge, we do not participate in the challenge and the results are not formally submitted to the SAMPL7 challenge.

Structural Elucidation of the Mechanism of Molecular Recognition in Chiral Crystalline Sponges

AbstractTo gain insight into chiral recognition in porous materials we have prepared a family of fourth generation chiral metal–organic frameworks (MOFs) that have rigid frameworks and adaptable (flexible) pores. The previously reported parent material, [Co2(S‐mandelate)2(4,4′‐bipyridine)3](NO3)2, CMOM‐1S, is a modular MOF; five new variants in which counterions (BF4−, CMOM‐2S) or mandelate ligands are substituted (2‐Cl, CMOM‐11R; 3‐Cl, CMOM‐21R; 4‐Cl, CMOM‐31R; 4‐CH3, CMOM‐41R) and the existing CF3SO3− variant CMOM‐3S are studied herein. Fine‐tuning of pore size, shape, and chemistry afforded a series of distinct host–guest binding sites with variable chiral separation properties with respect to three structural isomers of phenylpropanol. Structural analysis of the resulting crystalline sponge phases revealed that host–guest interactions, guest–guest interactions, and pore adaptability collectively determine chiral discrimination.

A Robust Double-walled Knotted Cage Revealed Guest Binding through Adaptive Portal Expansion

Mechanically interlocked host frameworks are expected to show dynamic guest inclusion/release without disruption of their inherent structures. Here, we synthesized a double-walled knotted cage from a kinetically inert Pt(II) block, which has a robust but semiflexible backbone to give an expansible cavity with expansible portals. The Pt cage showed great kinetic stability toward base, acid, and nucleophiles. Comparisons of the kinetics with a Pd(II) analog strongly supported the portal expansion mechanism for the guest inclusion in the double-walled cages.

Control of Guest Inclusion and Chiral Recognition Ability of 6-O-Modified β-Cyclodextrins in Organic Solvents by Aromatic Substituents at the 2-O Position.

The host-guest chemistry and applications of cyclodextrins in aqueous media is well established. However, a comprehensive study in organic solvents is lacking. Here, we report the design and synthesis of 6-O-tert-butyldimethylsilylated β-cyclodextrin (TBDMS-β-CD) bearing various aromatic substitutions at the 2-O position and their inclusion complex formation with aromatic guests in nonpolar organic solvents. Compared to the parent TBDMS-β-CD, these derivatives exhibit at least a 10-fold increase in inclusion ability toward pyrene through cooperative guest binding with the CD cavity and the aromatic substituents at the 2-O position. The type of the aromatic substituent largely affects the chiral recognition ability of TBDMS-β-CD toward 1-(1-naphthyl)ethylamine in cyclohexane. A TBDMS-β-CD derivative with a p-tolyl substituent has a remarkable chiral selectivity for the (S)-1-(1-naphthyl)ethylamine over the corresponding (R)-isomer (KS /KR =4.1±0.5), whereas a TBDMS-β-CD derivative with a 2-picolyl substituent shows the inverse chiral selectivity (KR /KS =8.7±0.6).

Substitution effects on the binding interactions of redox-active arylazothioformamide ligands and copper(I) salts

ABSTRACT The straightforward synthesis of redox-active arylazothioformamide (ATF) ligands allows for electronic diversity as to measure the weak-binding interactions of transition metal salts in supramolecular coordination complexes. A small library of para-substituted ATFs was created with varied electronic components to evaluate how electron-donating and electron-withdrawing groups alter binding association constants. Following full characterisation, including single-crystal X-ray diffraction, UV-Vis titration studies were performed using copper(I) salts to assess the Host:Guest binding. Simultaneously, substitutions were evaluated computationally by modelling the Gibbs’ Free Energy change of the rotational barriers from ligand crystal structures to the predicted metal coordinating species and the various complexes. The multi-model association calculations and experimental measurements interplay to help limit error propagations and reliably predict the more accurate binding models. Through a thorough investigation it was found that experimentally, each ligand supports a 2:1 binding model yet may employ unique binding mechanisms to achieve that model.

Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics.

Calculations of ligand binding free energies and kinetic rates are important for drug design. However, such tasks have proven challenging in computational chemistry and biophysics. To address this challenge, we have developed a new computational method, ligand Gaussian accelerated molecular dynamics (LiGaMD), which selectively boosts the ligand nonbonded interaction potential energy based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique. Another boost potential could be applied to the remaining potential energy of the entire system in a dual-boost algorithm (LiGaMD_Dual) to facilitate ligand binding. LiGaMD has been demonstrated on host-guest and protein-ligand binding model systems. Repetitive guest binding and unbinding in the β-cyclodextrin host were observed in hundreds-of-nanosecond LiGaMD_Dual simulations. The calculated guest binding free energies agreed excellently with experimental data with <1.0 kcal/mol errors. Compared with converged microsecond-time scale conventional molecular dynamics simulations, the sampling errors of LiGaMD_Dual simulations were also <1.0 kcal/mol. Accelerations of ligand kinetic rate constants in LiGaMD simulations were properly estimated using Kramers' rate theory. Furthermore, LiGaMD allowed us to capture repetitive dissociation and binding of the benzamidine inhibitor in trypsin within 1 μs simulations. The calculated ligand binding free energy and kinetic rate constants compared well with the experimental data. In summary, LiGaMD provides a powerful enhanced sampling approach for characterizing ligand binding thermodynamics and kinetics simultaneously, which is expected to facilitate computer-aided drug design.

Kinetics and Thermodynamics of Binding between Zwitterionic Viologen Guests and the Cucurbit[7]uril Host.

The host-guest binding interactions between a series of zwitterionic, symmetric viologens, and the cucurbit[7]uril host were investigated using NMR and UV-vis spectroscopic techniques. The nature of the viologen side arms had strong effects on the kinetics of association and dissociation and weaker, more uniform influence on the thermodynamic stability of the final 1:1 inclusion complexes, which can also be characterized as pseudorotaxanes.

Zwitterionic Ru(III) Complexes: Stability of Metal-Ligand Bond and Host-Guest Binding with Cucurbit[7]uril.

A wide range of ruthenium-based coordination compounds have been reported to possess potential as metallodrugs with anticancer or antimetastatic activity. In this work, we synthesized a set of new zwitterionic Ru(III) compounds bearing ligands derived from N-alkyl (R) systems based on pyridine, 4,4'-bipyridine, or 1,4-diazabicyclo[2.2.2]octane (DABCO). The effects of the ligand(s) and their environment on the coordination stability have been investigated. Whereas the [DABCO-R]+ ligand is shown to be easily split out of a negative [RuCl4]- core, positively charged R-pyridine and R-bipyridine ligands form somewhat more stable Ru(III) complexes and can be used as supramolecular anchors for binding with macrocycles. Therefore, supramolecular host-guest assemblies between the stable zwitterionic Ru(III) guests and the cucurbit[7]uril host were investigated and characterized in detail by using NMR spectroscopy and single-crystal X-ray diffraction. Paramagnetic 1H NMR experiments supplemented by relativistic DFT calculations of the structure and hyperfine NMR shifts were performed to determine the host-guest binding modes in solution. In contrast to the intramolecular hyperfine shifts, dominated by the through-bond Fermi-contact mechanism, supramolecular hyperfine shifts were shown to depend on the "through-space" spin-dipole contributions with structural trends being satisfactorily reproduced by a simple point-dipole approximation.

Does the degree of substitution on the cyclodextrin hosts impact their affinity towards guest binding?

Although cyclodextrins have been extensively utilized in various branches of supramolecular chemistry due to their numerous attractive attributes, however, to achieve even advanced applications, they often need structural modification through substitutions of suitable functional groups at their rims. A systematic investigation on how the degree of substitution on the cyclodextrin rims affects the binding affinity for a given guest molecule has however rarely been reported, especially from the perspective of photophysical studies. Herein, we report the non-covalent interaction of a styryl based dye, LDS-798, with three different sulfobutylether beta cyclodextrin (SBEnβCD) derivatives bearing varying degrees of substitution (n), using ground state absorption, steady-state emission, excited-state lifetime and time-resolved fluorescence anisotropy measurements. The dye-host binding constant values indicate that the strength of the interaction between LDS-798 and SBEnβCD derivatives follows an increasing trend with an increasing number of tethered sulfobutylether substituents on the cyclodextrin rims, which is attributed to the gradual increase of the electrostatic interaction between the negatively charged sulfobutylether groups and the positively charged LDS-798. Excited state lifetime measurements and ionic strength dependent studies on the dye-SBEnβCD complexes further support the increased affinity between the dye and the host in the supramolecular complexes, with an increasing number of sulfobutylether substituents on the βCD rims. The obtained results suggest that the molecular recognition of LDS-798 with SBEnβCD derivatives can be tuned very effectively by varying the number of sulfobutylether substituents on the cyclodextrin rims. Considering that SBE7βCD is one of the FDA approved agents for drug formulations, the obtained results with other SBEnβCD hosts may be useful in designing selective drug delivery applications, drug formulations, and effective fluorescence on-off switches.

High-Performance n -Hexane Purification by Nonporous Adaptive Crystals of Leaning Pillar[6]arene

The production of high-purity n-hexane under mild conditions is of great significance in both the petrochemical industry and synthetic chemistry. Here, we report an easy-to-operate and energy-effic...

Amorphous High-Surface-Area Aluminum Hydroxide-Bicarbonates for Highly Efficient Methyl Orange Removal from Water.

Amorphous high-surface-area aluminum hydroxide-bicarbonates were synthesized starting from AlCl3, base, and bicarbonate in water. Composites with a chemical formulas of [Al13O4(μ-OH)24(H2O)6.5(OH)5.5](HCO3)1.5 (I-NaOH) and [Al13O4(μ-OH)24(H2O)6(OH)6](HCO3) (I-NH3) were obtained by the use of NaOH/NaHCO3 and NH3/NH4HCO3 as base/bicarbonate, respectively. The surface area of the composites was highly dependent on the pH level of the synthetic solution, and composites with high surface areas (ca. 200 m2 g-1) were obtained around pH 7-8. Pore-size distributions determined from the N2 adsorption isotherms showed that I-NH3 and I-NaOH possess mainly large (pore radius rp > 3 nm) and small (rp < 3 nm) pores, respectively, despite similar surface areas. While SEM images showed that both I-NH3 and I-NaOH were aggregates of nanoparticles, the particles were more fused in I-NaOH, which is in line with the existence of small pores and the use of a stronger base (NaOH), which would facilitate the dehydration condensation reaction. The composites were applied as adsorbents to remove methyl orange (MO) from water. The time course of MO adsorption was readily fitted with a pseudo-second-order model, and over 90% MO removal was attained within 10 min with I-NH3, while I-NaOH showed much less MO removal (26%). The MO adsorption isotherm of I-NH3 was reproduced with a Langmuir model with an adsorption capacity of 154 mg g-1. Notably, the aluminum hydroxide-bicarbonates could not absorb methylene blue, which is a cationic dye, while anions (MO and PO43-) were readily absorbed. Solid-state 27Al MAS NMR spectra showed that the concentration of 5-coordinated aluminum species, which may serve as guest binding sites, was higher for I-NH3. These results show that electrostatic interaction between anionic MO and coordinatively unsaturated 5-coordinated cationic aluminum species and the large external surface area of I-NH3 contribute to the highly efficient MO adsorption.

Pressure Induced Wetting and Dewetting of the Nonpolar Pocket of Deep-Cavity Cavitands in Water.

Hydrophobic interactions drive the binding of nonpolar ligands to the oily pockets of proteins and supramolecular species in aqueous solution. As such, the wetting of host pockets is expected to play a critical role in determining the thermodynamics of guest binding. Here we use molecular simulations to examine the impact of pressure on the wetting and dewetting of the nonpolar pockets of a series of deep-cavity cavitands in water. The portals to the cavitand pockets are functionalized with both nonpolar (methyl) and polar (hydroxyl) groups oriented pointing either upward or inward toward the pocket. We find wetting of the pocket is favored by the hydroxyl groups and dewetting is favored by the methyl groups. The distribution of waters in the pocket is found to exhibit a two-state-like equilibrium between wet and dry states with a free energy barrier between the two states. Moreover, we demonstrate that the pocket hydration of the cavitands can be collapsed onto a unified adsorption isotherm by assuming the effective pressures within each cavitand pocket differ by a shift pressure that depends on the chemical identity and number of functional groups placed about the portal. These observations support the development of a two-state capillary evaporation model that accurately describes the equilibrium between states and naturally gives rise to the effective shift pressures observed from simulation. This work demonstrates that the hydration of host pockets can be tuned following simple design rules that in turn are expected to impact the thermodynamics of guest complexation.