Constrictive Binding Research Articles

How the water-soluble hemicarcerand incarcerates guests at room temperature decoded with modular simulations

Molecular dynamics simulations of hemicarcerands and related variants allow the study of constrictive binding and offer insight into the rules of molecular complexation, but are limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how Octacid4 encapsulates guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that in aqueous molecular dynamics simulations at 298 K apo Octacid4 adopts two clusters of conformations one of which has an equatorial portal open but the guest-bound Octacid4 adopts one cluster of conformations with all portals closed. These results explain how Octacid4 incarcerates guests at room temperature and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.

Deconvoluting the Role of Charge in a Supramolecular Catalyst.

We have demonstrated that the microenvironment of a highly anionic supramolecular catalyst can mimic the active sites of enzymes and impart rate accelerations of a million-fold or more. However, these microenvironments can be challenging to study, especially in the context of understanding which specific features of the catalyst are responsible for its high performance. We report here the development of an experimental mechanistic probe consisting of two isostructural catalysts. When examined in parallel transformations, the behavior of these catalysts provides insight relevant to the importance of anionic host charge on reactivity. These two catalysts exhibit similar host-substrate interactions, but feature a significant difference in overall anionic charge (12- and 8-). Within these systems, we compare the effect of constrictive binding in a net neutral aza-Cope rearrangement. We then demonstrate how the magnitude of anionic host charge has an exceptional influence on the reaction rates for a Nazarov cyclization, evidenced by an impressive 680-fold change in reaction rate as a consequence of a 33% reduction in catalyst charge.

Enabling New Modes of Reactivity via Constrictive Binding in a Supramolecular-Assembly-Catalyzed Aza-Prins Cyclization.

Supramolecular assembly 1 catalyzes a bimolecular aza-Prins cyclization featuring an unexpected transannular 1,5-hydride transfer. This reaction pathway, which is promoted by constrictive binding within the supramolecular cavity of 1, is kinetically disfavored in the absence of 1, as evidenced by the orthogonal reactivity observed in bulk solution. Mechanistic investigation through kinetic analysis and isotopic labeling studies indicates that the rate-limiting step of the transformation is the encapsulation of a transient iminium ion and supports the proposed 1,5-hydride transfer mechanism. This represents a rare example of such an extreme divergence of product selectivity observed within a catalytic metal-ligand supramolecular enzyme mimic.

ChemInform Abstract: Building on Cram′s Legacy: Stimulated Gating in Hemicarcerands

AbstractReview: 44 refs.

Building on Cram's legacy: stimulated gating in hemicarcerands.

ConspectusDonald Cram’s pioneering Nobel Prize-winning work on host–guest molecules led eventually to his creation of the field of container molecules. Cram defined two types of container molecules: carcerands and hemicarcerands. Host–guest complexes of carcerands, called carceplexes, are formed during their synthesis; once a carceplex is formed, the trapped guest cannot exit without breaking covalent bonds. Cram defined a quantity called constrictive binding, arising from the mechanical force that prevents guest escape. The constrictive binding in carceplexes is high. In contrast, hemicarcerands have low constrictive binding and are able to release the incarcerated guests at elevated temperatures without breaking covalent bonds. We have designed molecules that can switch from carcerand to hemicarcerand through a change in structure that we call gating.The original discovery of gating in container molecules involved our computational studies of a Cram hemicarceplex that was observed to release a guest upon heating. We found that the side portals of this hemicarceplex have multiple thermally accessible conformations. An eight-membered ring that is part of a portal changes from a “chair” to a “boat” structure, leading to the enlargement of the side portal and the release of the guest. This type of gating is analogous to phenomena often observed with peptide loops in enzymes. We refer to this phenomenon as thermally controlled gating.We have also designed and synthesized redox and photochemically controlled gated hemicarceplexes. Gates are built onto host molecules so that the opening or closing of such gates is stimulated by reducing or oxidizing conditions, or by ultraviolet irradiation. In both cases, the appropriate stimuli can produce a carceplex (closed gates) or hemicarceplex (open gates). A hemicarceplex with closed gates behaves like a carceplex, due to its very high constrictive binding energy. When the gates are opened, constrictive binding is dramatically lowered, and guest entrance and exit become facile. This stimulated switching between open and closed states controls access of the guest to the binding site. The experimental and computational investigations of gated hemicarcerands and several potential applications of gated hemicarceplexes are described in this Account.

Kinetics and Thermodynamics of Berberine Inclusion in Cucurbit[7]uril

The kinetics and thermodynamics of berberine inclusion in cucurbit[7]uril was studied by stopped-flow method, fluorescence titrations, and isothermal calorimetry in neat water. The ~500-fold fluorescence intensity enhancement upon encapsulation was exploited to monitor the complex formation in real time at various temperatures. The increase in the fluorescence intensity could be fitted well by assuming a simple 1:1 binding equilibrium without any intermediate formation. For the rate constants of association and dissociation, (1.9 ± 0.1) × 10(7) M(-1) s(-1) and (0.81 ± 0.08) s(-1) were found at 298 K, respectively. The ingression into the cavity of CB7 had 32 ± 2 kJ mol(-1) activation enthalpy, implying a constrictive binding, whereas 69 ± 2 kJ mol(-1) was obtained for the activation enthalpy of the egression. Substantial structural change had to occur when berberine passed through the tight carbonyl-rimmed portal of the macrocycle to reach the transition state. An enthalpy-driven complexation took place with a slight entropy gain.

Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM

Recruitment of the Legionella pneumophila effector DrrA to the Legionella-containing vacuole, where it activates and AMPylates Rab1, is mediated by a P4M domain that binds phosphatidylinositol 4-phosphate [PI(4)P] with high affinity and specificity. Despite the importance of PI(4)P in Golgi trafficking and its manipulation by pathogens, the structural bases for PI(4)P-dependent membrane recruitment remain poorly defined. Here, we determined the crystal structure of a DrrA fragment including the P4M domain in complex with dibutyl PI(4)P and investigated the determinants of phosphoinositide recognition and membrane targeting. Headgroup recognition involves an elaborate network of direct and water-mediated interactions with basic and polar residues in the context of a deep, constrictive binding pocket. An adjacent hydrophobic helical element packs against the acyl chains and inserts robustly into PI(4)P-containing monolayers. The structural, biochemical, and biophysical data reported here support a detailed structural mechanism for PI(4)P-dependent membrane targeting by DrrA.

Chemistry inside molecular containers in the gas phase

Inner-phase chemical reactions of guest molecules encapsulated in a macromolecular cavity give fundamental insight into the relative stabilization of transition states by the surrounding walls of the host, thereby modelling the situation of substrates in enzymatic binding pockets. Although in solution several examples of inner-phase reactions are known, the use of cucurbiturils as macrocyclic hosts and bicyclic azoalkanes as guests has now enabled a systematic mass spectrometric investigation of inner-phase reactions in the gas phase, where typically the supply of thermal energy results in dissociation of the supramolecular host-guest assembly. The results reveal a sensitive interplay in which attractive and repulsive van der Waals interactions between the differently sized hosts and guests need to be balanced with a constrictive binding to allow thermally activated chemical reactions to compete with dissociation. The results are important for the understanding of supramolecular reactivity and have implications for catalysis.

The Entrapment of Chiral Guests with Gated Baskets: Can a Kinetic Discrimination of Enantiomers Be Governed through Gating?

The capacity of gated hosts for controlling a kinetic discrimination between stereoisomers is yet to be understood. To conduct corresponding studies, however, one needs to develop chiral, but modular and gated hosts. Accordingly, we used computational (RI-BP86/TZVP//RI-BP86/SV(P)) and experimental (NMR/CD/UV/Vis spectroscopy) methods to examine the transfer of chirality in gated baskets. We found that placing stereocenters of the same kind at the rim (R(1) =CH3, so-called bottom) and/or top amide positions (R(2) =sec-butyl) would direct the helical arrangement of the gates into a P or M propeller-like orientation. With the assistance of (1)H NMR spectroscopy, we quantified the intrinsic (thermodynamic) and constrictive (kinetic) binding affinities of (R)- and (S)-1,2-dibromopropane 5 toward baskets (S3b/P)-2, (S3t/M)-3, and (S3bt/P)-4. Interestingly, each basket has a low ( ≤1.3 kcal mol(-1)), but comparable (de<10%) affinity for entrapping enantiomeric (R/S)-5. In terms of the kinetics, basket (S3b/P)-2, with a set of S stereocenters at the bottom and P arrangement of the gates, would capture (R)-5 at a faster rate (kin(R)/kin(S) =2.0±0.2). Basket (S3t/M)-3, with a set of S centers at the top and M arrangement of the gates, however, trapped (S)-5 at a faster rate (kin(R)/kin(S) =0.30±0.05). In light of these findings, basket (S3bt/P)-4, with a set of S stereocenters installed at both top and bottom sites along with a P disposition of the gates, was found to have a lower ability to differentiate between enantiomeric (R/S)-5 (kin(R)/kin(S) =0.8). Evidently, the two sets of stereocenters in this "hybrid" host acted concurrently, each with the opposite effect on the entrapment kinetics. Gated baskets are hereby established to be a prototype for quantifying the kinetic discrimination of enantiomers through gating and elucidating the electronic/steric effects on the process.

Gated container molecules

Donald J. Cram, the great UCLA chemist, received the Nobel Prize for his discoveries about host-guest complexes [1]. Both theoretical and experimental studies have been conducted about the nature and strength of interactions between the host and guest molecules. The concepts of constrictive binding (the activation energy of the binding process) and intrinsic binding (the free energy difference between the complex and the free host and guest molecules) were introduced to characterize different binding properties (Figure 1) [2].

Self‐Assembled Molecular Reaction Vessels Reloaded

Enzyme-like catalysis of Nazarov cyclizations has been achieved by encapsulation of pentadienols into a metallosupramolecular capsule. Constrictive binding of the substrate and functional-group activation give rise to a tremendous rate acceleration of up to a factor of 2.1×106, thus, pushing the efficiency of self-assembled molecular capsules as catalysts to a new level.

Guest recognition of a tetrapyridinohemicarcerand through hydrogen bonding and constrictive binding interactions

Abstract Tetrapyridinohemicarcerand 2 having four hydrogen-bonding acceptors of inward-directing pyridyl units was synthesized and their binding properties for a variety of organic guest molecules have been investigated. Tetrapyridinohemicarcerand 2 formed kinetically stable complexes with various sulfonic acids via intermolecular –SO 3 H–pyridyl hydrogen bonding and constrictive binding interactions in C 2 D 2 Cl 4 at 25 °C. But carboxylic acids or alcohols cannot be a stable guest at the same conditions. Tetrapyridinohemicarcerand 2 also binds various disubstituted benzenes. Especially 1,4-diiodobenzene forms stable hemicarceplex 1,4-diiodobenzene@ 2 , which seems to be stabilized by constrictive binding as well as by –C–H⋯I interactions between dioxymethylene of 2 and iodo group of guest.

Enzymelike Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

The water-soluble, self-assembled, tetrahedral assembly K(12)Ga(4)L(6) (L = 1,5-biscatecholamidenaphthalene) catalyzes the Nazarov cyclization of 1,3-pentadienols with extremely high levels of efficiency. The catalyzed reaction proceeds over a million times faster than the background reaction, an increase comparable to those observed in some enzymatic systems. This catalysis operates under aqueous conditions at mild temperatures and pH, and the reaction is halted by the addition of an appropriate inhibitor. This unprecedented rate enhancement is attributed to both the stabilization of protonated reaction intermediates and the effect of constrictive binding on the bound guest.

Isotope Effects as Probe ofConstrictiveandIntrinsicBinding in Hemicarceplexes

Kinetic isotope effects (KIE) of hemicarceplex dissociation for naphthalene and p-xylene hemicarceplexes with partially and fully deuterated guests have been measured. The KIEs are consistent with the absence of steric effects in the transition states of hemicarceplex dissociation, which supports an earlier interpretation of constrictive binding energy in hemicarceplexes as being primarily controlled by different forms of gating.

Reversible Guest Exchange Mechanisms in Supramolecular Host—Guest Assemblies

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Reversible guest exchange mechanisms in supramolecular host–guest assemblies

Synthetic chemists have provided a wide array of supramolecular assemblies able to encapsulate guest molecules. The scope of this tutorial review focuses on supramolecular host molecules capable of reversibly encapsulating polyatomic guests. Much work has been done to determine the mechanism of guest encapsulation and guest release. This review covers common methods of monitoring and characterizing guest exchange such as NMR, UV-VIS, mass spectrometry, electrochemistry, and calorimetry and also presents representative examples of guest exchange mechanisms. The guest exchange mechanisms of hemicarcerands, cucurbiturils, hydrogen-bonded assemblies, and metal-ligand assemblies are discussed. Special attention is given to systems which exhibit constrictive binding, a motif common in supramolecular guest exchange systems.

The Cucurbit[n]uril Family

AbstractFor Abstract see ChemInform Abstract in Full Text.

The Cucurbit[n]uril Family

In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed "cucurbituril" by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants--the pumpkin. In the intervening years, the fundamental binding properties of CB[6]-high affinity, highly selective, and constrictive binding interactions--have been delineated by the pioneering work of the research groups of Mock, Kim, and Buschmann, and has led to their applications in waste-water remediation, as artificial enzymes, and as molecular switches. More recently, the cucurbit[n]uril family has grown to include homologues (CB[5]-CB[10]), derivatives, congeners, and analogues whose sizes span and exceed the range available with the alpha-, beta-, and gamma-cyclodextrins. Their shapes, solubility, and chemical functionality may now be tailored by synthetic chemistry to play a central role in molecular recognition, self-assembly, and nanotechnology. This Review focuses on the synthesis, recognition properties, and applications of these unique macrocycles.

Mechanism of Host−Guest Complexation by Cucurbituril

The factors affecting host-guest complexation between the molecular container compound cucurbit[6]uril (CB6) and various guests in aqueous solution are studied, and a detailed complexation mechanism in the presence of cations is derived. The formation of the supramolecular complex is studied in detail for cyclohexylmethylammonium ion as guest. The kinetics and thermodynamics of complexation is monitored by NMR as a function of temperature, salt concentration, and cation size. The binding constants and the ingression rate constants decrease with increasing salt concentration and cation-binding constant, in agreement with a competitive binding of the ammonium site of the guest and the metal cation with the ureido carbonyl portals of CB6. Studies as a function of guest size indicate that the effective container volume of the CB6 cavity is approximately 105 A(3). It is suggested that larger guests are excluded for two reasons: a high activation barrier for ingression imposed by the tight CB6 portals and a destabilization of the complex due to steric repulsion inside. For example, in the case of the nearly spherical azoalkane homologues 2,3-diazabicyclo[2.2.1]hept-2-ene (DBH, volume ca. 96 A(3)) and 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO, volume ca. 110 A(3)), the former forms the CB6 complex promptly with a sizable binding constant (1300 M(-1)), while the latter does not form a complex even after several months at optimized complexation conditions. Molecular mechanics calculations are performed for several CB6/guest complexes. A qualitative agreement is found between experimental and calculated activation energies for ingression as a function of both guest size and state of protonation. The potential role of constrictive binding by CB6 is discussed.

Molecular engineering. Part 5.1 Tuning the constrictive binding of container host by the atomic order of portal pillars

Two D4h container hosts 12 and 13 with 4(CH2–O–bridge–O–CH2) portal pillars were obtained in good yields by stepwise synthetic routes and showed complementary complexation behaviors to their analogues with (O–CH2–bridge-CH2–O)4 portal pillars. 1H NMR spectral chemical shifts of host’s inward-turned OCH2O protons were sensitive to guest change. The stability orders of hemicarceplexes were 12–p-(CH3CH2)2C6H4 > 12–p-(CH3O)2C6H4 12–o-(CH3O)2C6H4 > 12–m-(CH3O)2C6H4 and 13–CH3COCH2CH3 > 13–CH3COCH2CH(CH3)2 > 13–CH3CON(CH3)2 > 13–CH3COOCH2CH3 > 13–CH3CH2CON(CH3)2 in terms of the activation energy barrier for decomplexation. Large solvent effects on the activation energy for decomplexation of hemicarceplexes were observed.