Modulation with acetonitrile of the dynamics of guest binding to the two distinct binding sites of cholate aggregates

Bile salt aggregates are supramolecular systems containing two different binding sites. The effect of the addition of acetonitrile on the specificity and dynamics of guest binding to the two binding sites of cholate aggregates was studied. The protection of guests included in the aggregate from interaction with ions in the aqueous phase was evaluated from quenching of the singlet and triplet excited states of guest molecules bound to the cholate aggregates. The dynamics of guest binding to the primary and secondary binding sites of the cholate aggregates were determined at increasing acetonitrile mole fractions. The structure of the aggregates was not significantly altered provided the cholate concentrations were higher than 20 mM and the acetonitrile mole fraction did not exceed 0.033 (9.1% v/v). These results show that acetonitrile can be used to modulate the solubility of guests in the aggregates and to manipulate the residence time of guests in the primary and secondary binding sites.     

Acid–Base Controllable Recognition Properties of a Highly Versatile Calix[6]crypturea

Versatile concave receptors with binding properties that can be controlled by external stimuli are rare. Herein, we report on a calix[6]crypturea ( 1 ) that features two different binding sites in close proximity, that is, a tris(2‐aminoethyl)amine (tren)‐based tris‐ureido cap that provides convergent hydrogen‐bond‐donor sites and a hydrophobic cavity suitable for the inclusion of organic guests. The binding properties of this heteroditopic receptor have been evaluated by NMR spectroscopic studies. Compound 1 behaves as a remarkably versatile host that strongly binds neutral molecules, anions, or contact ion pairs. Within each family of guests, compound 1 is able to discriminate between different guests with a high degree of selectivity. Indeed, neutral molecules that possess hydrogen‐bond donor and acceptor groups, chloride anions, and linear ammonium ions associated to F^? or Cl^? are particularly well recognized. In comparison with all the related receptors, compound 1 displays several unique features: 1) charged or neutral species are also recognized in polar or protic solvents, 2) thanks to the flexibility of the calixarene structure, induced‐fit processes allow the binding of large, biologically relevant ammonium salts such as neurotransmitters, and 3) the protonation of the basic cap leads to a positively charged receptor, 1? H⁺, which is reluctant to host anions and in which host properties are now governed by strong charge–dipole interactions with the guests. In other words, compound 1 presents an acid–base controllable tris‐ureido recognition site protected by a hydrophobic corridor that can select guests through induced‐fit processes. Thus, its versatile host properties can be allosterically controlled by protonation and selective guest‐switching processes are possible. To illustrate all these remarkable features, a sophisticated three‐pole supramolecular switch, based on the interconversion of host–guest systems displaying either charged or neutral guests, is described.     

Artificial receptors that provides a preorganized hydrophobic environment: a biomimetic approach to dopamine recognition in water

[structure: see text] The recognition of dopamine in water has been achieved with tripodal oxazoline-based artificial receptors, capable of providing a preorganized hydrophobic environment by rational design, which mimics a hydrophobic pocket predicted for a human D2 receptor. The receptors show an amphiphilic nature owing to the presence of hydrophilic sulfonate groups at the periphery of the tripodal oxazoline ligands, which seems to contribute in forming the preorganized hydrophobic environment. The artificial receptors recognized dopamine hydrochloride in water with reasonable selectivity among various organoammonium guests examined. The observed binding behavior of the receptors was explained by evoking guest inclusion in the preorganized hydrophobic pocket-like environment and not by simple ion-pairing interactions. The rationally predicted 1:1 inclusion binding mode was supported by binding studies such as with a reference receptor that cannot provide a similar binding pocket, Job and VT-NMR experiments, electrospray ionization mass analysis, and guest selectivity data. This study implies that an effective hydrophobic environment can be generated even from an acyclic, small molecular artificial receptor. Such a preorganized hydrophobic environment, as being utilized in biological systems, can be effectively used as a complementary binding force for the recognition of organoammonium guests such as dopamine hydrochloride in water.     

Effects of Side Arm Length and Structure of Para-Substituted Phenyl Derivatives on Their Binding to the Host Cyclobis(paraquat-p-phenylene)

The binding constants with the host cyclobis(paraquat-p-phenylene), 1(4+), have been determined in CH(3)CN by UV-vis spectrophotometry for a series of p-phenylene guests, symmetrically substituted with side arms of varying length and functionality. Semiempirical molecular orbital theory was employed to provide a detailed structural and energetic interpretation of the experimental binding data. In particular, the length of the side arms and the type and position of the heteroatoms on the side arms were systematically varied in order to understand the effects of external interactions on the association constants of the guests with host 1(4+). A large chelate effect involving the ethyleneoxy side arm oxygen atoms and a cooperative effect between the guest aromatic core and the side arms are significant factors which determine the binding with this host. Sequential ethyleneoxy linkages along the side arms markedly increase the binding constant with respect to a compound in which the same number of oxygens along the side arms are separated by longer aliphatic linkages. In addition, a multiplicative rather than additive effect on the binding constant is observed which demonstrates that the oxygen atoms exhibit a strong chelate effect. It was also discovered that while the side arms of these guests contribute most of the driving force for complexation, an aromatic core is necessary for the guest to reside in the cavity of the host. The binding of these guests then is dependent upon cooperation between the arms and the aromatic core. Furthermore, elongation of the central aromatic core with aliphatic side arms containing no heteroatoms leaves the association constant relatively unchanged and replacement of the oxygen atoms with sulfur markedly decreases the observed binding. These effects have been used to rationalize several observations regarding this system in the literature and may serve to improve the design of new supramolecular systems and to better understand the host/guest interaction process.     

Thermodynamic integration to predict host-guest binding affinities

An alchemical free energy method with explicit solvent molecular dynamics simulations was applied as part of the blind prediction contest SAMPL3 to calculate binding free energies for seven guests to an acyclic cucurbit-[n]uril host. The predictions included determination of protonation states for both host and guests, docking pose generation, and binding free energy calculations using thermodynamic integration. We found a root mean square error (RMSE) of 3.6 kcal mol(-1) from the reference experimental results, with an R(2) correlation of 0.51. The agreement with experiment for the largest contributor to this error, guest 6, is improved by 1.7 kcal mol(-1) when a periodicity-induced free energy correction is applied. The corrections for the other ligands were significantly smaller, and altogether the RMSE was reduced by 0.4 kcal mol(-1). We link properties of the host-guest systems during simulation to errors in the computed free energies. Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods.     

Synthesis and Binding Properties of a Tren-Capped Hexahomotrioxacalix[3]arene

The straightforward synthesis of a new hexahomotrioxacalix[3]arene-based ligand capped by a tren subunit was developed and the binding properties of the corresponding zinc complex were explored by NMR spectroscopy. Similarly to the closely related calix[6]tren-based systems, the homooxacalixarene core ensures the mononuclearity of the zinc complex and the metal center displays a labile coordination site for exogenous guests. However, very different host–guest properties were observed: i) in CDCl₃, the zinc complex strongly binds a water molecule and is reluctant to recognize other neutral guests, ii) in CD₃CN, the exo-coordination of anions prevails. Thus, in strong contrast to the calix[6]tren-based systems, the coordination of neutral guests that thread through the small rim and fill the polyaromatic cavity was not observed. This unique behaviour is likely due to the fact that the 18-membered ethereal macrocycle is too small to let a molecule threading through it. This work illustrates the key role played by the second coordination sphere in the binding properties of metal complexes.     

Highly organized spherical hosts that bind organic guests in aqueous solution with micromolar affinity: microcalorimetry studies

Two novel closed-shell hemicarcerand-like hosts with spherical cavities of 11 A diameter that are soluble in aqueous solution were constructed. The binding of xylenes, aryl ethers, polyaromatic compounds, ferrocene derivatives, and bicyclic aliphatic compounds were examined by NMR spectroscopy and microcalorimetry. NMR binding studies indicated that binding depended upon guest hydrophobicity and shape. No binding was detected for guests in which a charge must be desolvated as part of inclusion or for guests that can not fit within the cavity of the host. Three complexes 2.naphthalene, 2.p-xylene, and 2.ferrocene were isolated and found to be indefinitely stable in the solid phase and in aqueous solution. The binding constants for these complexes are estimated to be greater than 10(8) M-1. Thirteen guests were examined by microcalorimetry with binding constants ranging between 10(7) and 10(3) M-1. A comparison of results obtained here with those from previous work with beta-cyclodextrin and cyclophane hosts, along with analysis of the entropy-enthalpy compensation data, indicate that there is a higher degree of guest desolvation with this host structure than with open-shell hosts. This accounts at least partially for the increase in affinity observed with these closed-shell hosts. Replacing a hydroxy group in the host portal with a hydrogen atom does not affect the binding constant, a finding consistent with the guest residing deeply buried within the host cavity. It was observed that aromatic guests are bound with higher affinity than aliphatic ones in agreement with results that point to the importance of London dispersion forces in the association of aromatic components in face-to-edge orientations. The correlation of changes in NMR chemical shift with microcalorimetry data supports a model in which increased CH-pi interactions strengthen association between host and guest due to the dominant role of van der Waals dispersion forces. Remarkably, the binding constant for the 1,4 isomer of dimethoxybenzene is 32 times higher than for the 1,2 isomer, and even greater discrimination is observed between the xylene guests since the binding constant for p-xylene is 80 times greater than that for o-xylene. This discrimination between isomeric guests by a rigid host indicates that changes in specific hydrophobic interactions have substantial effects upon binding affinity.     

Effect of the guest size and shape on its binding dynamics with sodium cholate aggregates

The binding dynamics of the guests acenaphthene, phenanthrene, fluorene, and acenaphthenol with sodium cholate aggregates were studied using laser flash photolysis and fluorescence. The location of the guests in the bile salt aggregate is determined by the guest's hydrophobicity, where acenaphthene, phenanthrene, and fluorene bind to the primary aggregates, while acenaphthenol binds to the secondary bile salt aggregates. The residence time of the guests in the primary aggregates and the access of ionic species from the aqueous phase to the guest in the aggregate depend on the size and the shape of the guest. These results show that bile salt aggregates are adaptable supramolecular host systems.     

pH-dependent binding of guests in the cavity of a polyhedral coordination cage: reversible uptake and release of drug molecules

A range of organic molecules with acidic or basic groups exhibit strong pH-dependent binding inside the cavity of a polyhedral coordination cage. Guest binding in aqueous solution is dominated by a hydrophobic contribution which is compensated by stronger solvation when the guests become cationic (by protonation) or anionic (by deprotonation). The Parkinson''s drug 1-amino-adamantane (‘amantadine’) binds with an association constant of 10⁴ M^–1 in the neutral form (pH greater than 11), but the stability of the complex is reduced by three orders of magnitude when the guest is protonated at lower pH. Monitoring the uptake of the guests into the cage cavity was facilitated by the large upfield shift for the ¹H NMR signals of bound guests due to the paramagnetism of the host. Although the association constants are generally lower, guests of biological significance such as aspirin and nicotine show similar behaviour, with a substantial difference between neutral (strongly binding) and charged (weakly binding) forms, irrespective of the sign of the charged species. pH-dependent binding was observed for a range of guests with different functional groups (primary and tertiary amines, pyridine, imidazole and carboxylic acids), so that the pH-swing can be tuned anywhere in the range of 3.5–11. The structure of the adamantane-1-carboxylic acid complex was determined by X-ray crystallography: the oxygen atoms of the guest form CH···O hydrogen bonds with one of two equivalent pockets on the internal surface of the host. Reversible uptake and release of guests as a function of pH offers interesting possibilities in any application where controlled release of a molecule following an external stimulus is required.     

One Guest or Two? A Crystallographic and Solution Study of Guest Binding in a Cubic Coordination Cage

A crystallographic investigation of a series of host–guest complexes in which small-molecule organic guests occupy the central cavity of an approximately cubic M₈L₁₂ coordination cage has revealed some unexpected behaviour. Whilst some guests form 1:1 H⋅G complexes as we have seen before, an extensive family of bicyclic guests—including some substituted coumarins and various saturated analogues—form 1:2 H⋅G₂ complexes in the solid state, despite the fact that solution titrations are consistent with 1:1 complex formation, and the combined volume of the pair of guests significantly exceeds the Rebek 55±9 % packing for optimal guest binding, with packing coefficients of up to 87 %. Re-examination of solution titration data for guest binding in two cases showed that, although conventional fluorescence titrations are consistent with 1:1 binding model, alternative forms of analysis—Job plot and an NMR titration—at higher concentrations do provide evidence for 1:2 H⋅G₂ complex formation. The observation of guests binding in pairs in some cases opens new possibilities for altered reactivity of bound guests, and also highlights the recently articulated difficulties associated with determining stoichiometry of supramolecular complexes in solution.     

Probing Helical Hydrophobic Binding Sites in Branched Starch Polysaccharides Using NMR Spectroscopy

Branched starch polysaccharides are capable of binding multiple hydrophobic guests, but their exploitation as multivalent hosts and in functional materials is limited by their structural complexity and diversity. Linear α(1–4)‐linked glucose oligosaccharides are known to bind hydrophobic guests inside left‐handed single helices in solution and the solid state. Here, we describe the development of an amphiphilic probe that binds to linear α(1–4)‐linked glucose oligosaccharides and undergoes a conformational switch upon complexation, which gives rise to dramatic changes in the ¹H NMR spectrum of the probe. We use this probe to explore hydrophobic binding sites in the branched starch polysaccharides amylopectin and β‐limit dextrin. Diffusion‐ordered (DOSY), nuclear Overhauser effect (NOESY) and chemical shift perturbation (HSQC) NMR experiments are utilised to provide evidence that, in aqueous solution, branched polysaccharides bind hydrophobic guests in well‐defined helical binding sites, similar to those reported for complexation by linear oligosaccharides. By examining the binding affinity of the probe to systematically enzymatically degraded polysaccharides, we deduce that the binding sites for hydrophobic guests can be located on internal as well as external branches and that proximal α(1–6)‐linked branch points weaken but do not prevent complexation.     

Exploring the relation between amplification and binding in dynamic combinatorial libraries of macrocyclic synthetic receptors in water

Herein we describe an extensive study of the response of a set of closely related dynamic combinatorial libraries (DCLs) of macrocyclic receptors to the introduction of a focused range of guest molecules. We have determined the amplification of two sets of diastereomeric receptors induced by a series of neutral and cationic guests, including biologically relevant compounds such as acetylcholine and morphine. The host–guest binding affinities were investigated using isothermal titration calorimetry. The resulting dataset enabled a detailed analysis of the relationship between the amplification of selected receptors and host–guest Gibbs binding energies, giving insight into the factors affecting the design, simulation and interpretation of DCL experiments. In particular, two questions were addressed: Is amplification by a given guest selective for the best receptor? And does the best guest induce the largest amplification of a given receptor? Our experimental results and computer simulations showed that the relative levels of amplification of hosts by a guest are well‐correlated with their relative affinities, and simulations have confirmed previous observations that amplification can be selective for the best receptor when only modest amounts of guest are used. In contrast, the correlation between guest binding and the extent of amplification of a given receptor across a wide range of guests tends to be poorer, because every guest has its own unique set of affinities for competing receptors in the DCL. This implies that the results of screening a DCL for selective receptors by comparing the response of the mixture to two different guests should be interpreted with caution. DCLs are complex mixtures in which all compounds are connected through a set of equilibria. Obtaining quantitative information about all host–guest binding constants from such systems will require the explicit and simultaneous consideration of all of the main equilibria within a DCL.     

Characterization of second coordination shell ionophore–siderophore host–guest assemblies and binding selectivities in binary and complex mixtures by electrospray ionization mass spectrometry

An ESI-MS method for the determination of host–guest association constants and binding selectivities for systems of binary and complex mixtures, respectively, is presented in an effort to quantitatively study the strength of host–guest interactions, while accounting for the different ESI-MS spray efficiencies of each component. Association constants were obtained for host–guest complexes formed between a series of crown ether and linear ionophore hosts and various guests, including protonated amines, and an apo- and ferri-siderophore, ferrioxamine B.     

Thermodynamic analysis of receptors based on guanidinium/boronic acid groups for the complexation of carboxylates, alpha-hydroxycarboxylates, and diols: driving force for binding and cooperativity

The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.     

Multicavity Metallosupramolecular Architectures

Discrete metallosupramolecular systems are often macrocyclic or cage‐like architectures with an accessible internal cavity. Guest molecules can reside within these cavities and much of the interest in these systems is derived from these fascinating host–guest interactions. A range of potential applications stem from the ability of these metallosupramolecular architectures to encapsulate guests. These applications include catalysis or acting as molecular reaction flasks, the molecular scavenging of pollutants, storage of reactive species, and drug delivery. Multicavity metallosupramolecular architectures combine the ability of large hollow assemblies to bind multiple guests concurrently with the binding specificity associated with small cages. A variety of different approaches to generating separate compartments within a single metallosupramolecular assembly have emerged. These include interpenetrated cages, cages with polytopic ligands that have a long backbone, and molecules that have two or more clefts. This review examines these approaches, and highlights key contributions to the field.     

Maximizing Coordination Capsule–Guest Polar Interactions in Apolar Solvents Reveals Significant Binding

Guest encapsulation underpins the functional properties of self‐assembled capsules yet identifying systems capable of strongly binding small organic molecules in solution remains a challenge. Most coordination capsules rely on the hydrophobic effect to ensure effective solution‐phase association. In contrast, we show that using non‐interacting anions in apolar solvents can maximize favorable interactions between a cationic Pd₂L₄ host and charge‐neutral guests resulting in a dramatic increase in binding strength. With quinone‐type guests, association constants in excess of 10⁸ m ^?1 were observed, comparable to the highest previously recorded constant for a metallosupramolecular capsule. Modulation of optoelectronic properties of the guests was also observed, with encapsulation either changing or switching‐on luminescence not present in the bulk phase.     

Protein recognition by a self-assembled deep cavitand monolayer on a gold substrate

This paper details the first use of a self-folding deep cavitand on a gold surface. A sulfide-footed deep, self-folding cavitand has been synthesized, and its attachment to a cleaned gold surface studied by electrochemical and SPR methods. Complete monolayer formation is possible if the cavitand folding is templated by noncovalent binding of choline or by addition of space-filling thiols to cover any gaps in the cavitand adsorption layer. The cavitand is capable of binding trimethylammonium-tagged guests from an aqueous medium and can be deposited in 2 × 2 microarrays on the surface for characterization by SPR imaging techniques. When biotin-labeled guests are used, the cavitand:guest construct can recognize and immobilize streptavidin proteins from aqueous solution, acting as an effective supramolecular biosensor for monitoring protein recognition.     

Influence of planarity and size on guest binding with sodium cholate aggregates

Bile salt aggregates are supramolecular structures with two types of binding sites, called primary and secondary sites. The objective of this work was to explore how the nonplanarity and size of guests (biphenyl [BP], 1-1'-binaphthyl [BNP] and dibenz[b,f]oxepin [DBX]) affected their binding affinity and dynamics to sodium cholate (NaC) aggregates. Fluorescence and laser-flash photolysis experiments were performed to obtain information on the binding environment for the guests, the accessibility of quenchers to guests in the aggregate and the dissociation rate constants of the guests from the aggregates. All guests were bound to the more hydrophobic primary aggregate, showing that this site can accommodate nonplanar molecules. However, the structure of the guest affects the structure of the primary aggregates, leading to changes in the accessibility of anions to aggregate-bound guests and to changes for the guest dissociation rate constants from the aggregates.     

Molecular recognition of cyclodecapeptides to ibuprofen and naproxen enantiomers: a theoretical study

Cyclopeptide derivatives have attracted great interest in host-guest chemistry during the past decades. In this work, four cyclopeptides including one cyclodecapeptide (CDP) and three modified CDPs (M-CDP involves I-CDP, E-CDP, and H-CDP) are adopted as hosts to differentiate the four guests of the amphetamine (AP) and ibuprofen (IP) enantiomers using a proposed integrated computation protocol. The obtained results demonstrated that the guests of AP and IP enantiomers could be recognized by different cyclopeptides using the certain optimized quantum chemistry methods. Specifically, the AP or IP enantiomers might be identified by the corresponding cyclopepitdes in the five pairs of the inclusion complexes associated with the large differences of binding energies of hosts with guests, that is, the two of H-CDP/AP and H-CDP/IP by B3LYP, the two of I-CDP/IP and H-CDP/IP by CAM-B3LYP, and the other one of I-CDP/IP by M06-2X, which are mainly determined by their corresponding stable conformations, electronic properties, and favorable interactions. The intermolecular hydrogen bonds and NBO analyses of the inclusion complexes further suggest the corresponding differences of binding energies. The visual nonbonded weak interactions for the studied systems gave the reasons why the AP and IP enantiomers are identified by the corresponding cyclopeptides. Molecular dynamics simulated results further support the above conclusions. The investigation provides detailed information at a molecular level about the recognition of the two chiral drug molecules by the four cyclodecapeptides. The integrated computation protocol proposed in this work provides people a feasible way to study interaction of hosts and guests, molecular recognition, and chiral separation.     

Selective Co‐Encapsulation Inside an M6L4 Cage

There is broad interest in molecular encapsulation as such systems can be utilized to stabilize guests, facilitate reactions inside a cavity, or give rise to energy‐transfer processes in a confined space. Detailed understanding of encapsulation events is required to facilitate functional molecular encapsulation. In this contribution, it is demonstrated that Ir and Rh‐Cp‐type metal complexes can be encapsulated inside a self‐assembled M₆L₄ metallocage only in the presence of an aromatic compound as a second guest. The individual guests are not encapsulated, suggesting that only the pair of guests can fill the void of the cage. Hence, selective co‐encapsulation is observed. This principle is demonstrated by co‐encapsulation of a variety of combinations of metal complexes and aromatic guests, leading to several ternary complexes. These experiments demonstrate that the efficiency of formation of the ternary complexes depends on the individual components. Moreover, selective exchange of the components is possible, leading to formation of the most favorable complex. Besides the obvious size effect, a charge‐transfer interaction may also contribute to this effect. Charge‐transfer bands are clearly observed by UV/Vis spectrophotometry. A change in the oxidation potential of the encapsulated electron donor also leads to a shift in the charge‐transfer energy bands. As expected, metal complexes with a higher oxidation potential give rise to a higher charge‐transfer energy and a larger hypsochromic shift in the UV/Vis spectrum. These subtle energy differences may potentially be used to control the binding and reactivity of the complexes bound in a confined space.