Probing Conformational Changes of Ubiquitin by Host–Guest Chemistry Using Electrospray Ionization Mass Spectrometry

We report mechanistic studies of structural changes of ubiquitin (Ub) by host–guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916–7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys₆ or Lys₁₁ in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host–guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys₄₈ and Lys₆₃ in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys₁₁. The complexation prohibits salt bridge formation between Lys₁₁ and Glu₃₄ and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host–guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.      

Complexation of ferrocene derivatives by the cucurbit[7]uril host: a comparative study of the cucurbituril and cyclodextrin host families

The formation of inclusion complexes between cucurbit[7]uril (CB[7]) and ferrocene and its derivatives has been investigated. The X-ray crystal structure of the 1:1 inclusion complex between ferrocene and CB[7] revealed that the guest molecule resides in the host cavity with two different orientations. Inclusion of a set of five water-soluble ferrocene derivatives in CB[7] was investigated by 1H NMR spectroscopy and calorimetric and voltammetric techniques. Our data indicate that all neutral and cationic guests form highly stable inclusion complexes with CB[7], with binding constants in the 10(9)-10(10) M(-)(1) and 10(12)-10(13) M(-1) ranges, respectively. However, the anionic ferrocenecarboxylate, the only negatively charged guest among those surveyed, was not bound by CB[7] at all. These results are in sharp contrast to the known binding behavior of the same guests to beta-cyclodextrin (beta-CD), since all the guests form stable inclusion complexes with beta-CD, with binding constants in the range 10(3)-10(4) M(-1). The electrostatic surface potentials of CB[6], CB[7], and CB[8] and their size-equivalent CDs were calculated and compared. The CD portals and cavities exhibit low surface potential values, whereas the regions around the carbonyl oxygens in CBs are significantly negative, which explains the strong affinity of CBs for positively charged guests and also provides a rationalization for the rejection of anionic guests. Taken together, our data suggest that cucurbiturils may form very stable complexes. However, the host-guest interactions are very sensitive to some structural features, such as a negatively charged carboxylate group attached to the ferrocene residue, which may completely disrupt the stability of the complexes.     

Cucurbit[7]uril host-guest complexes of the histamine H2-receptor antagonist ranitidine

The macrocyclic host cucurbit[7]uril forms very stable complexes with the diprotonated (K(CB[7])(1) = 1.8 x 10(8) dm(3) mol(-1)), monoprotonated (K(CB[7])(2) = 1.0 x 10(7) dm(3) mol(-1)), and neutral (K(CB[7])(3) = 1.2 x 10(3) dm(3) mol(-1)) forms of the histamine H(2)-receptor antagonist ranitidine in aqueous solution. The complexation behaviour was investigated using (1)H NMR and UV-visible spectroscopy as a function of pH and the pK(a) values of the guest were observed to increase (DeltapK(a1) = 1.5 and DeltapK(a2) = 1.6) upon host-guest complex formation. The energy-minimized structures of the host-guest complexes with the cationic guests were determined and provide agreement with the NMR results indicating the location of the CB[7] over the central portion of the guest. The inclusion of the monoprotonated form of ranitidine slows the normally rapid (E)-(Z) exchange process and generates a preference for the (Z) isomer. The formation of the CB[7] host-guest complex greatly increases the thermal stability of ranitidine in acidic aqueous solution at 50 degrees C, but has no effect on its photochemical reactivity.     

Bromination of N-phenyloxypropyl-N'-ethyl-4,4'-bipyridium in cucurbit[8]uril molecular reactor

CB[n](n=6-8) is a family of synthetic macrocyclic host molecules composed of n glycoluril units, which can be employed as molecular reactor. N-phenyloxypropyl-N'-ethyl-4,4'-bipyridium (1) was designed to form a host-guest inclusion complex with CB[n](n=6-8), subsequently, the bromination reaction of 1 and its corresponding inclusion complexes was investigated in this work. In the case of 1/CB[8], the folded including mode is quite helpful to acquire 1-bormination product completely through intramolecular charge transfer (ICT), and CB[8] can provide a safe bromination environment for 1.     

Blurring the Lines between Host and Guest: A Chimeric Receptor Derived from Cucurbituril and Triptycene

We report the synthesis and X‐ray crystal structure of a cucurbituril–triptycene chimeric receptor ( 1 ). Host 1 binds to guests typical of CB[6]–CB[8], but also binds to larger guests such as blue box ( 20 ) and the Fujita square ( 22 ). Intriguingly, the geometries of the 1 ? 20 and 1 ? 22 complexes blur the lines between host and guest in that both components fulfill both roles within each complex. The fluorescence output of 1 is fully quenched by the formation of complexes with pyridinium‐derived guests.     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

The cucurbit[n]uril family: prime components for self-sorting systems

We determined the values of Ka for a wide range of host-guest complexes of cucurbit[n]uril (CB[n]), where n = 6-8, using 1H NMR competition experiments referenced to absolute binding constants measured by UV/vis titration. We find that the larger homologues--CB[7] and CB[8]--individually maintain the size, shape, and functional group selectivity that typifies the recognition behavior of CB[6]. The cavity of CB[7] is found to effectively host trimethylsilyl groups. Remarkably, the values of Ka for the interaction of CB[7] with adamantane derivatives 22-24 exceeds 10(12) M(-1)! The high levels of selectivity observed for each CB[n] individually is also observed for the CB[n] family collectively. That is, the selectivities of CB[6], CB[7], and CB[8] toward a common guest can be remarkably large. For example, guests 1, 3, and 11 prefer CB[8] relative to CB[7] by factors greater than 10(7), 10(6), and 3000, respectively. Conversely, guests 23 and 24 prefer CB[7] relative to CB[8] by factors greater than 5100 and 990, respectively. The high levels of selectivity observed individually and collectively for the CB[n] family renders them prime components for the preparation of functional biomimetic self-sorting systems.     

Theoretical insights into the formation, structure, and electronic properties of anticancer oxaliplatin drug and cucurbit[n]urils n = 5 to 8

Geometries, formation and electronic properties of cucurbit[n]uril-oxaliplatin n = 5–8, host-guest complexes are investigated with DFT calculations. The formation of inclusion complexes of CB[n]-oxaliplatin are facile in CB[n] n = 6–8. In the complex, the cyclohexyl group is found to be deep inside the cavity, with the formation of a hydrogen bonding between the portal oxygen atoms and the amine nitrogen of the oxaliplatin guest. NBO analysis shows the transfer of charge from the metal center to the CB[7] unit and the existence of hydrogen bonding between the oxygen portal and amine nitrogen. The HOMO orbital is localized on the carboxylate group and the LUMO orbital are localized on the cucurbituril unit in CB[7]-oxaliplatin complex. The strength of the interaction determined here reflects the ability of CB[n] to act as a host for suitably oxaliplatin guests, even in aqueous solution.     

A study of binding interactions between terpyridine derivatives and cucurbit[10]uril

The binding interactions of a series of 2,2′:6′,2″-terpyridine (TPY) derivatives and their metal complexes with cucurbit[10]uril (CB[10]) were investigated by ¹H NMR, UV/Vis, emission spectroscopy, and ESI mass spectrometry. ¹H NMR titrations revealed CB[10] could encapsulate methylated TPY (MTPY), and the binding ratio between guest MTPY and host was 1:1 and 2:1 via ESI-MS characterization. For the transition metal complexes composed of Fe(II) or Ru(II) or Rh(III) and TPY derivatives, the octahedral TPY?metal?TPY core can be included in the cavity of CB[10]. Three binding modes (1:1, 1:2 and 1:3) have been detected for the binding of the metal?MPTY complexes with CB[10] by ESI-MS.     

Group 1 coordination chains and hexagonal networks of host cyclotriveratrylene with halogenated monocarbaborane anions

Halogenated carbaborane ions [CB(11)H(6)X(6)](-) in which X=Cl or Br have been combined with the host molecule cyclotriveratrylene (CTV) and Group 1 metal cations to give crystalline materials. The complexes [Na(ctv)(H(2)O)(CB(11)H(6)X(6))](CF(3)CH(2)OH) feature chiral Na-CTV coordination chains with complexation of the [CB(11)H(6)X(6)](-) ion by the Na(+) ion, together with the CTV molecular cavity. The coordination chains are hydrogen bonded together to give a puckered two-dimensional hexagonal grid structure. [K(ctv)(CB(11)H(6)Cl(6))(CF(3)CH(2)OH)(0.5)] is essentially isostructural. Complexes [Rb(ctv)(CB(11)H(6)Br(6))(H(2)O)] and [Cs(ctv)(CB(11)H(6)X(6))(CH(3)CN)] are coordination polymers with related distorted hexagonal grid structures. Use of N,N'-dimethylformamide (DMF) as a solvent results in an entirely different type of assembly, with [Na(2)(dmf)(4)(H(2)O)(2)(ctv)][(dmf)(0.5)(ctv)][CB(11)H(6)Br(6)](2) showing unusual [Na-mu-(dmf)-Na] bridges, and once again forming a distorted hexagonal coordination polymer.     

Determination of the purity of cucurbit[n]uril (n = 7, 8) host samples

The formation of highly stable inclusion complexes in aqueous solution between the organometallic cobaltocenium cation (Cob(+)) and the hosts cucurbit[7]uril (CB7) and cucurbit[8]uril (CB8) was used to develop a simple method, based on UV-vis titrations, to assay the purity of samples of these two hosts. The equilibrium association constant (K) of the Cob(+)@CB7 complex had been previously reported by our group as 5.7 × 10(9) M(-1) at 25 °C in 50 mM sodium acetate medium. In this work, we determine a K value of 1.9 × 10(8) M(-1) at 25 °C in the same medium for the Cob(+)@CB8 complex. The high stability of these complexes and their decreased molar absorptivity coefficients (at 261 nm), compared to that for free Cob(+), lead to straightforward titration plots when graphing absorbance versus concentration of added CB7 (or CB8) host, at constant Cob(+) concentration.     

Isolated supramolecular [Ru(bpy)3]-viologen-[Ru(bpy)3] complexes with trapped CB[7,8] and photoinduced electron-transfer study in nonaqueous solution

The synthesis of two supramolecular diruthenium complexes, 1 ?CB[7] and 1 ?CB[8] (CB[n]=cucurbit[n]uril), which contain the respective host CB[7] and CB[8], were synthesized and isolated. In the case of host CB[8], the desired supramolecular complex was obtained by utilizing dihydroxynapthalene as a template during the synthesis. The ¹H NMR spectra, electrochemistry, and photochemistry of these supramolecular complexes were performed in nonaqueous solution. The results show that both CB[7,8] hosts mainly bind to the linker part in solution in acetonitrile. This binding also lowers the oxidation potential of the ruthenium metal center and hinders the quenching effect by the viologen moiety. It has also been shown that external methylviologen can be included into 1 ?CB[8]. Analysis with NMR spectroscopy, electrochemistry, and photochemistry clearly shows a viologen radical dimer formation between the bound viologen and free methylviologen, thereby showing that the unique abilities of the CB[8] host can be utilized even in nonaqueous solution.     

Inclusion compounds of cucurbit[<Emphasis Type="Italic">n</Emphasis>]urils with metal complexes

A new class of supramolecular compounds—inclusion compounds of metal complexes encapsulated in organic macrocyclic cavitands cucurbit[n]urils (CB[n], C_6n H_6n N_4n O_2n , n = 7−10)—has been surveyed. A unique combination of a rather rigid hydrophobic intramolecular cavity and negatively charged portals favors the formation of stable host-guest compounds. Basic methods of synthesis of inclusion compounds of CB[n] with metal complexes have been reported, and the structures of the resulting products isolated as crystals and characterized by X-ray crystallography have been considered. The effect of encapsulation on the geometric and spectral characteristics of the complexes and their redox properties has been traced. It has been shown that encapsulation in CB[n] can lead to a change in the reactivity of the complexes in thermolysis and isomerization and aquation reactions. Encapsulation of biologically active metal complexes in CB[n] is a promising strategy for designing new-generation prolonged-action pharmaceuticals.     

Synthesis and solid-state study of supramolecular host-guest assemblies: Bis[6-O,6-O'-(1,2:3,4-diisopropylidene-alpha-D-galactopyranosyl)thiophosphoryl] dichalcogenides

A complementary approach for studying structural details of complex solid materials formed by symmetrical and unsymmetrical dichalcogenides, which employs both X-ray diffraction (XRD) and solid-state NMR (SS NMR), is presented. The new diagnostic technique allows reversible crystallographic space group change and very subtle distortion of host geometry to be followed during guest migration in the crystal lattice. Bis[6-O,6-O'-(1,2:3,4-diisopropylidene-alpha-D-galactopyranosyl)]thiophosphoryl selenenyl sulfide, a representative of wheel-and-axle host (WAAH) molecules, can be synthesized in the solid state by grinding and gentle heating of disulfide 1 and diselenide 2. Full characterization of disulfide 1 in the solid phase has been reported (J. Org. Chem. 1995, 60, 2549). In the current work, the synthesis and both XRD and SS NMR studies of the isostructural diselenide substrate 2 are presented. A (31)P cross polarization magic angle spinning experiment is employed to follow the progress of synthesis of selenenyl sulfide 3 in the solid state. It is concluded that selenenyl sulfide exists in equilibrium with disulfide and diselenide in a 1:1:1 ratio in both the liquid and the powdered solid. A mixture of isostructural dichalcogenides crystallized from different solvents form three-component host-guest inclusion complexes with columnar architecture. In the host-guest complex of diselenide 2 with toluene (space group C2), columns of host molecules are in parallel orientations along all the axes, whereas in the structures of diselenide 2 with propan-2-ol and propan-1-ol (space group P3 2), the columns of host molecules lay along the 3-fold symmetry axis. Thermal processes effecting structural changes in the host lattice and the kinetics of reversible guest molecule diffusion were investigated using SS NMR spectroscopy. Finally, the Se/S scrambling phenomenon and limitations in the X-ray structure refinement of organic compounds containing selenium and sulfur in chains are discussed.     

Non-covalent interactions of coumarin dyes with cucurbit[7]uril macrocycle: modulation of ICT to TICT state conversion

Non-covalent interaction of coumarin laser dyes, namely coumarin-1 (C1), coumarin-481 (C481) and coumarin-6H (C6H), with a versatile macrocyclic host molecule cucurbit[7]uril (CB7), has been investigated in aqueous solution using photophysical methods. Steady-state and time-resolved fluorescence studies illustrate significant enhancements/modifications in the fluorescence yields, lifetimes and spectral features of C1, C481 and C6H on interaction with CB7, and are assigned to 1 : 1 complex formation between the dyes and the CB7 host. The complex formation is mainly driven by charge-dipole interaction, as evident from the binding constant values (K ~ 10(4)-10(5) M(-1)). The large changes in the excited state behaviour of C1 and C481 as compared to C6H in the presence of CB7 indicate that CB7 binds C1 and C481 through the encapsulation of the 7-N,N'-diethylamino group of the dyes and the structural rigidity imposed by this interaction dramatically alters the excited state properties of the dyes by preventing the conversion of their emissive intramolecular charge transfer (ICT) state to the non-radiative twisted intramolecular charge transfer (TICT) state. The present results direct towards the probable supramolecular approach using water soluble macrocyclic CB7, in the development of aqueous dye laser systems in the blue-green region.     

Dynamic Interfacial Adhesion through Cucurbit[n]uril Molecular Recognition

Supramolecular building blocks, such as cucurbit[n]uril (CB[n])‐based host–guest complexes, have been extensively studied at the nano‐ and microscale as adhesion promoters. Herein, we exploit a new class of CB[n]‐threaded highly branched polyrotaxanes (HBP‐CB[n]) as aqueous adhesives to macroscopically bond two wet surfaces, including biological tissue, through the formation of CB[8] heteroternary complexes. The dynamic nature of these complexes gives rise to adhesion with remarkable toughness, displaying recovery and reversible adhesion upon mechanical failure at the interface. Incorporation of functional guests, such as azobenzene moieties, allows for stimuli‐activated on‐demand adhesion/de‐adhesion. Macroscopic interfacial adhesion through dynamic host–guest molecular recognition represents an innovative strategy for designing the next generation of functional interfaces, biomedical devices, tissue adhesives, and wound dressings.     

Electron Density Shift in Imidazolium Derivatives upon Complexation with Cucurbit[6]uril

In this study, we have investigated the supramolecular interaction between series of 1‐alkyl‐3‐methylimidazolium guests with variable alkyl substituent lengths and cucurbit[6]uril (CB6) in the solution and the solid state. Correct interpretation of ¹H NMR spectra was a key issue for determining the binding modes of the complexes in solution. Unusual chemical shifts of some protons in the ¹H NMR spectra were explained by the polarization of the imidazolium aromatic ring upon the complexation with the host. The formation of 1:1 complex between 1‐ethyl‐3‐methylimidazolium and CB6 is in disagreement with previously reported findings describing an inclusion of two guest molecules in the CB6 cavity.     

Orientation of pyrylium guests in cucurbituril hosts

According to recent reports, supramolecular complexes of the pyrylium cation with cucurbit[x]urils (CB[x], x = 7, 8) show promising photoluminescence suitable for electroluminescent devices. In turn, photoluminescence seems to be related to the stereochemistry of the complexes; however, that has been controversial. Here, we report that in H(2)O, 2,6-disubsituted-4-phenyl pyryliums (Pylm) form dimers quantitatively (equilibrium constants >10(4) M(-1)), but they enter as such only in the larger CB[8]. In terms of orientation, (1)H NMR shows that Me-Pylm, Ph-Pylm, and t-Bu-Pylm insert their 4-phenyl groups in either the CB[7] or CB[8] cavity. The orientation of iPr-Pylm in the iPr-Pylm@CB[7] complex is similar. Experimental conclusions are supported by DFT calculations using the M062X functional and the 6-31G(d) basis set. In the case of (iPr-Pylm)(2)@CB[8], (1)H NMR of both the guest and the host indicates that both guests might enter CB[8] from the same side with their iPr groups in the cavity, but DFT calculations leave room for ambiguity. In addition to the size and hydrophobicity of the 2,6-substituents of the guests, as well as the size and flexibility of the hosts, theory reveals the importance of explicit solvation (H(2)O) and finite temperature effects (particularly for (1)H NMR shielding calculations) in the determination of the stereochemistry of those complexes.     

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.     

Size selective supramolecular cages from aryl-bisimidazolium derivatives and cucurbit[8]uril

A series of bisimidazolium salts were synthesized as novel guests for the macrocyclic host molecule cucurbit[8]uril (CB[8]). These bisimidazolium-CB[8] binary complexes exhibited a unique cage structure with the imidazolium rings acting as lids, leading to a size-dependent binding selectivity by altering the hydrophobic linker between the two imidazolium moieties. This new class of CB[8] complexes was also capable of binding small solvent molecules, including acetone, acetonitrile, diethyl ether, and tetrahydrofuran (THF) in an aqueous environment.