Sequence recognition and self-sorting of a dipeptide by cucurbit[6]uril and cucurbit[7]uril

Cucurbit[7]uril forms very strong complex with zwitterionic dipeptide Phe-Gly with affinity exceeding 10(7) M(-1) and effectively recognizes peptide sequence of Phe-Gly over Gly-Phe as well as Tyr-Gly over Gly-Tyr and Trp-Gly over Gly-Trp with relative affinities of 23 000, 18 000 and 2000, respectively.     

Supramolecular assembly of Hoechst-33258 with cucurbit[7]uril macrocycle

Molecular assemblies of potential guest molecules through non-covalent host-guest interactions have found immense use in many applied areas. In this study supramolecular interaction of a biologically important dye Hoechst-33258 (H33258) has been investigated in aqueous solutions at different pHs, in the presence of a macrocyclic host, namely, cucurbit[7]uril (CB7). The pH dependent emission behaviour of H33258 is inherently connected with its protolytic equilibria which allow the dye in different geometrical conformations. This pH dependent structural orientation is greatly affected by the complexation with CB7. The significant structural changes in the monocationic H33258 brought out by CB7 at pH 7 have been documented in the fluorescence emission and lifetime data, which are comparatively less affected in case of the dicationic form, which is prominent in dye solutions at pH 4.5. The strong ion-dipole interactions provided by the carbonyl portals of the CB7 host adequately stabilize the CB7-H33258 complex, both in 1:1 and 2:1 stoichiometries at both the pH conditions. The Job's plot method, fluorescence anisotropy, NMR measurements and geometry optimization calculations confirm the stoichiometric arrangement and are found to be tunable with the addition of metal ions. The non-covalently stabilized assembly brings out large enhancement in the fluorescence emission due to the unique structural orientation attained by H33258, which reduces the non-radiative relaxation pathways. Comparison of the spectral data of the dye at different pH conditions in the absence and presence of CB7 proposes a large upward pK(a) shift due to CB7 encapsulation, thus providing a handy tool to modulate the photophysical characteristics of the guest molecules.     

Binding modes of cucurbit[6]uril and cucurbit[7]uril with a series of bis-pyridinium compounds

Binding behaviors of cucurbit[6]uril (CB[6]) and cucurbit[7]uril (CB[7]) with a series of bis-pyridinium compounds N, N’-hexamethylenebis(1-alkyl-4-carbamoyl pyridinium bromide) (HBPB-n) (alkyl chain length, n = 6, 8 and 10) guests were investigated using ¹H-NMR, ESI–MS and single crystal X-ray diffraction methods. The results show that CB[6] and CB[7] can form [2]pseudorotaxanes with HBPB-n easily. When increasing the length of tail alkyl chain, the binding site of CB[6] at guest molecules changed from the tail to the middle part, while CB[7] remained located over the tail chain. As CB[6] and CB[7] were added in HBPB-8 aqueous solution, a [3]pseudorotaxane was formed by the inclusion of the internal middle site in CB[6] and the tail chain in CB[7].     

Recognition of glycine by cucurbit[5]uril and cucurbit[6]uril: A comparative study of exo- and endo-binding

Recognition features of glycine (Gly) with cucurbit[5]uril (Q[5]) and cucurbit[6]uril (Q[6]) both in aqueous solution and solid state were investigated by ¹H NMR spectroscopy and X-ray crystallography. ¹H NMR data indicate that the Gly is located outside of the portals of the Q[5], exhibiting exo binding with the Q[5]. In the case of the Q[6], the Gly shows endo binding or a dual binding mode (endo and exo binding) with the host, which depends on the amount of the host in the aqueous solution. X-ray crystallography clearly display that the Gly forms 2:1 exclusion complex with the Q[5], and 2:1 inclusion complex with the Q[6]. Interestingly, hydrogen bondings between the encapsulated Gly molecules in the Q[6] were observed.     

Theoretical study on the protonation of cucurbit[6]uril

Abstract  

The most probable structures of the cucurbit[6]uril·H₃O⁺ and cucurbit[6]uril·(H₃O⁺)₂ cationic complex species have been derived by quantum mechanical DFT calculations. In these two complexes, each of the H₃O⁺ ions is bound by three strong linear hydrogen bonds to three carbonyl oxygen atoms of the parent macrocycle.     

A hemicyanine and cucurbit[n]uril inclusion complex: competitive guest binding of cucurbit[7]uril and cucurbit[8]uril

The interaction between the hemicyanine indole derivative H and the cucubit[n]urils Q[7] and Q[8] has been studied using ¹H NMR and UV spectroscopy as well as by fluorescence experiments. Competitive studies on the inclusion of H by Q[7] and Q[8] have also been conducted, and reveal that on changing the size of the Q[n] cavity, the binding behaviour can be very different.     

Binding modes of cucurbit[6]uril and cucurbit[7]uril with a tetracationic bis(viologen) guest

Binding behaviors of two cucurbit[n]urils (CB[n]) hosts with the [CH3bpy(CH2)6bpyCH3]4+ (bpy = 4,4'-bipyridinium) guest were investigated by 1H NMR and MALDI-TOF-MS experiments. While the CB[6] and CB[7] form [2]pseudorotaxanes with the host located over the hexamethylene chain of the guest, only the CB[7] forms a [3]pseudorotaxane with both host molecules residing over the bipyridinium groups. The initial CB[7] host vacates the inclusion of the hexamethylene chain as a result of the electrostatic and steric repulsions that would arise in simultaneous binding of adjacent aliphatic and aromatic portions of the guest.     

Interaction between cucurbit[6]uril and bispyridinecarboxamide

The interaction between cucurbit[6]uril and N,N′-(m-bispyridinecarboxamide)-1,n-alkane (m = 2, 3, 4; n = 4, 6, 8) has been investigated by ¹H-NMR, ESI-MS and single crystal X-ray diffraction method. The results show that cucurbit[6]uril can form pseudorotaxanes with N,N′-(m-bispyridinecarboxamide)-1,6-hexane (m = 2, 3, 4) easily. When the alkyl chain length increases (n = 8), the binding mode is identical, but the binding ability of the host towards guest decreases. In both two cases cucurbit[6]uril shows no selectivity towards positional isomers. However, in the case of n = 4, the binding mode is different, having relations with positional substitution of the guest. Only N,N′-(m-bispyridinecarboxamide)-1,4-butane (m = 2) can form pseudorotaxane with cucurbit[6]uril, while the other two (m = 3, m = 4) form external complex with cucurbit[6]uril. The possible reason for the difference has been discussed.     

Molecular-recognition properties of a water-soluble cucurbit[6]uril analogue

The molecular-recognition properties of the cucurbit[6]uril analogue (1) in aqueous buffer (sodium acetate, 50 mM, pH 4.74, 25 degrees C) toward a variety of guests including alkanediamines (6-12), aromatics (14-32), amino acids (33-36), and nucleobases (37-42) were studied by fluorescence spectroscopy. For the alkanediamines studied (H2N(CH)nNH2, n = 6, 7, 8, 9, 10, 11, 12), the association constants increase as the length of the alkane (n) is increased. Host 1 is capable of forming strong complexes with guests containing aromatic rings with association constants (Ka) ranging from 10(2) to 10(6) M(-1) as a result of the favorable pi-pi interactions that occur between host 1 and the aromatic rings of the guest when bound in the cavity of 1. Biologically relevant guests such as amino acids and nucleobases are also bound in the cavity of 1 with Ka values ranging from 10(3) to 10(6) M(-1). Consequently, cucurbit[6]uril analogue 1 functions as a versatile fluorescent sensor for the presence of a wide range of chemically and biologically important substances in aqueous solution including nitroaromatics, neurotransmitters, amino acids, and nucleobases.     

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.     

Ion binding to cucurbit[6]uril: structure and dynamics

Molecular dynamics simulations are used to study the microscopic structure and dynamics of cations bound to cucurbit[6]uril (CB[6]) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183 M for the salts and 0.0184 M for CB[6]. The cations bind only to CB[6] carbonyl oxygens. They are never found inside the CB[6] cavity. Complexes with Na(+) and K(+) mostly involve one cation, whereas with Ca(2+) single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. When bound to CB[6], sodium and potassium cations jump mainly between nearest or second-nearest neighbors. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB[6] oxygen. A few water molecules (zero to four) can occupy the CB[6] cavity, which is limited by the CB[6] oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cation activity as "lids" over the CB[6] portal cannot, however, be identified. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells.     

Daisy chain assembly formed from a cucurbit[6]uril derivative

The building block synthesis of a derivative of CB[6] that bears a reactive propargyloxy group and its functionalization by click chemistry to yield 1 which contains a covalently attached isobutylammonium group is presented. Compound 1 undergoes self-assembly to yield a cyclic [c2] daisy chain assembly (1(2)) in water. The behavior of 1(2) in response to various stimuli (e.g., guests and CB[n] receptors) is described.     

Elucidating the mechanism of binding of chromate to cucurbit[6]uril: a DFT study

We report the binding of chromate, a toxic heavy metal ion to the macrocyclic host molecule, cucurbituril using density functional theory. Due to the anionic nature of the guest molecule and the portals of the host molecule, we propose that the binding mechanism should be assisted by cations. The calculated barrier for chromate binding to cucurbituril is found to be?~17?kcal?mol^?1. The large barrier can be attributed to portal opening of the host molecule, electrostatic repulsion between the guest molecule and the portals of the host molecule and the solvent re-organization around guest molecule.     

Synthesis and binding behaviors of monomethyl cucurbit[6]uril

By reacting 3a-methylglycoluril and glycoluril with paraformaldehyde, monomethyl cucurbit[6]uril was synthesized in 14% yield. The new host molecule forms stable inclusion complexes with diamine and hexylaminocarbazole derivatives.     

Supramolecular capsules of cucurbit[6]uril and controlled release

Supramolecular capsules of THF and acid molecules inside cucurbit[6]uril have been prepared via [C₂mim]Br route. The 1:1 ratio of host–guest complexes have been characterized by ¹H NMR, thermal gravimetric analysis and elemental analysis in solution and in solid state. Two types of release have been observed in NaCl aqueous solution, including partial release of THF due to stronger binding and complete release of acid molecules (C₃–C₆) due to weaker binding.     

pH-responsive movement of cucurbit[7]uril in a diblock polypseudorotaxane containing dimethyl beta-cyclodextrin and cucurbit[7]uril

[Structure: see text] A polypseudorotaxane consisting of cucurbit[7]uril (CB[7])/N,N'-(3-phenylenebis(methylene)dipropargylamine (PMPA), [2]pseudorotaxane, and 2,6-O-dimethyl beta-cyclodextrin (DM-beta-CD)/alpha,omega-bisazidopropylene glycol 400 [2]pseudorotaxane was synthesized using the "click" reaction. The polypseudorotaxane structure was maintained in aqueous solution over a wide range of pH values with the DM-beta-CD units contributing to increased solubilization of the polypseudorotaxane without dethreading. The pH-responsive movement of the CB[7] units in the polypseudorotaxane was also observed.     

Complexation behavior of cucurbit[6]uril with short polypeptides

The binding properties of cucurbit[6]uril towards various peptides have been investigated in acidic aqueous solution. Stability constants and thermodynamic values of the complex formation between following peptides: glycyl-l-alanine, l-leucyl-l-valine, glycyl-l-asparagine, l-leucyl-l-phenylalanine, l-leucyl-l-tryptophan, glycyl-l-histidine, l-glutathione reduced (γ-l-glutamyl-l-cysteinyl-glycine, GSH), and dl-leucyl-glycyl-dl-phenylalanine) with cucurbit[6]uril in aqueous formic acid (50%, v/v) have been calculated from calorimetric titrations. From these results it can be seen that the peptides form exclusion complexes with cucurbit[6]uril. Due to the polar peptide bond they are not included within the hydrophobic cavity of cucurbit[6]uril. The complex formation is favoured by entropic contributions. The release of water molecules from the polar amino groups of the peptides and the carbonyl groups of cucurbituril are responsible.     

Monofunctionalised cucurbit[6]uril synthesis using imidazolium host-guest complexation

Monohydroxylated cucurbit[6]uril was prepared for the first time through the controlled oxidation of CB[6] in the presence of a tailor-made bisimidazolium guest, as verified by (1)H NMR, ESI-MS and X-ray crystallography. Further chemical modification of monohydroxylated CB[6] was also readily achieved.     

Molecular switch based on a cucurbit[6]uril containing bistable [3]rotaxane

A bistable CB6-based [3]rotaxane with two recognition sites has been prepared very efficiently in a high yield synthesis through CB6 catalyzed 1,3-dipolar cycloaddition; this rotaxane behaves as a reversible molecular switch and exhibits conformational changes caused by the movement of rings under base, acid and heat stimuli from one location to the other.