Portal Effects on the Stability of Cucurbituril Complexes

This work is concerned with the properties of cucurbit[n]uril (CBn) host portals. The carbonyl oxygens lining each of the cavity openings on these hosts give rise to a rim of negative charge density, which often has strong effects on guest binding processes. The negative effect that carboxylates exert on guest binding to cucurbit[7]uril (CB7) is described in detail, as well as the fact that the protonation state of terminal −COO⁻/COOH groups can be utilized to control CB7 shuttling on suitably designed pseudorotaxanes. Carboxylates can also slow down the kinetics of CB7 complex formation and dissociation. Finally, the electrostatic properties of the portals are useful -with suitable molecular design- to develop strong cooperativity effects, resulting from attractive side-by-side interactions, on the assembly of multi-component supramolecular complexes.     

Inorganic-organic hybrid molecular architectures of cyanometalate host and organic guest systems: specific behavior of the guests

Molecular architectures built of inorganic cyanometalate building blocks provide variegated host structures with several organic guest molecules. The strategies to derive novel structures are presented briefly. The formation of a charge-transfer (CT) complex as the guest inside the cavity and the photochemistry of the CT complexes are discussed. The chemical pressure that the guest experiences inside the cavity is also discussed based on the vibrational spectroscopic results.     

Ultrastable Host–Guest Complexes and Their Applications

This review describes monovalent synthetic receptor–ligand (or host–guest) pairs with extremely high binding affinity, comparable to that of the biotin–avidin pair, and their applications. Cucurbit[7]uril (CB[7]), a member of the host family cucurbit[n]uril (CB[n], n=5–8, 10), forms ultrastable host–guest complexes with ferrocene-, adamantane- or bicyclo[2.2.2]octane-based molecules having ammonium groups properly positioned to interact with the carbonyl oxygens at the portals of CB[7]. The extremely high affinity is achieved by a large enthalpic gain arising from the near perfect size/shape complementarity between the rigid CB cavity and the rigid core of the guest molecules, with the critical assistance of the positive entropy change due to the extensive dehydration of the host and guest. The high stability of the complexes allowed us and others to explore several biological applications such as immobilization of biomolecules on a solid surface, protein isolation, triggering intracellular events, and regulating enzymatic activities. These complexes with their exceptional affinity, chemical robustness, simple preparation, biocompatibility, and easy handling may replace the biotin–(strept)avidin system in diverse areas of research, including affinity chromatography, high throughput biochemical assays, imaging, and sensor technologies.     

Mixed Crystals as Host-Guest Systems for Probing Molecular Interactions

A method is described for probing interactions between molecules at the surfaces of growing crystals. For this purpose, mixed crystals have been treated as unique host-guest systems where the guest molecules are occluded into the host crystal through stereospecific interactions occurring at the different growing surfaces of the host. Owing to the process of molecular recognition at such surfaces, the adsorption and occlusion of the guest molecules takes place at specific sites, resulting in a reduction in symmetry of the mixed crystal compared to the pure host. The concept of reduction in symmetry is general, and has been instrumental for probing subtle molecular interactions at the surfaces of growing crystals, for the transformation of centrosymmetric single crystals into crystals with polar arrangement, and for “absolute” asymmetric synthesis inside centrosymmetric crystals.     

State transition of macroscopic supramolecular hydrogel by the host-guest coverage effect

In this work, a hydrophobic guest monomer containing adamant end-group was synthesized and introduced into the acrylamide hydrogel system to prepare macroscopic guest hydrogel. The swelling, transparency, and mechanical properties of the guest hydrogels can be significantly changed by soaking the guest hydrogel into hydrophilic cyclodextrin solution because the hydrophobic guest groups were recognized and covered by the hydrophilic host molecules. In addition, the surface lubrication property could be adjusted by changing the proportion of acrylamide and adamantane monomers in the hydrogel system. More importantly, cyclodextrin can bind with adamantane through host-guest interactions, enabling the adjustment of the hydrophilicity/hydrophobicity properties of the hydrogel system. By controlling the assembly time, the hydrogel with different lubrication behaviors can be obtained. The controllable surface friction that this specific binding of host-guest interaction has broad application prospects in intelligent device, bionic lubrication and other fields.     

Polymerization of styrene in γ-cyclodextrin channels: Lightly rotaxanated polystyrenes with altered stereosequences

Modeling of polystyrene (PS) with various stereosequences in γ-cyclodextrin (γ-CD) channels has been conducted and it was found that only isotactic PS stereoisomers can fit into the γ-CD cavity. Thus, based on the modeling of stereoisomeric polystyrenes in narrow γ-CD channels, it was suggested that PSs with unusual microstructures might be produced via constrained polymerization of styrene monomer in its γ-CD-IC crystals. The in situ polymerization of styrene inside the narrow channels of its γ-CD-IC crystals suspended in aqueous media was performed. Alternatively, the solid-state polymerization of styrene/γ-CD-IC has also been conducted by exposure to γ-radiation. It was found that most host γ-CD molecules slip off during polymerization and the channel structure was not preserved. Consequently, much of the guest styrene monomer polymerizes outside of the host γ-CD channels, where the constrained environment is absent. Yet, a lightly rotaxanated structure has been obtained, where some threaded γ-CD molecules ∼15 wt% (∼1 γ-CD per 70 PS repeat units) are permanently entrapped along the PS chains after polymerization. ¹³C NMR spectra of PSs synthesized from styrene/γ-CD-IC and homogeneously in toluene show some differences, which are presumably due to variations in the stereosequences of PSs obtained from the partially constrained polymerization of styrene/γ-CD-IC.     

Oxidation Catalysis by Rationally Designed Artificial Metalloenzymes

The principle of enzyme mimics has been raised to its pinnacle by the design of hybrids made from inorganic complexes embedded into biomolecules. The present review focuses on the design of artificial metalloenzymes for oxidation reactions by oxygen transfer reactions, with a special focus on proteins anchoring inorganic complexes or metal ions via supramolecular interactions. Such reactions are of great interest for the organic synthesis of building blocks. In the first part, following an overview of the different design of artificial enzymes, the review presents contributions to the rational design of efficient hybrid biocatalysts via supramolecular host/guest approaches, based on the nature of the inorganic complex and the nature of the protein, with special attention to the substrate binding. In the second part, the original purpose of artificial metalloenzymes has been twisted to enable the observation of transient intermediates, to decipher metal-based oxidation mechanisms. The host protein crystals have been used as crystalline molecular-scale vessels, within which inorganic catalytic reactions have been followed, thanks to X-ray crystallography. These hybrids should be an alternative to enzymes for sustainable chemistry.     

Deep Inside Cucurbiturils: Physical Properties and Volumes of their Inner Cavity Determine the Hydrophobic Driving Force for Host–Guest Complexation

Cucurbit[n]urils (CBn) bind guest molecules through a combination of electrostatic interactions with the carbonyl rims and hydrophobic interactions with the inner cavity. Investigations with solvatochromic probes in CB7 reveal that the polarity of the cavity resembles that of alcohols (e.g., n-octanol), while its polarizability (P=0.12) and apparent refractive index (n_D=1.10±0.12) are extremely low, close to the gas phase. The calculated molecular quadrupole moments of CBs are extremely large (Θ_zz=−120 to −340 Buckingham). A survey of reported binding constants of neutral guests and hydrophobic residues that form 1 : 1 inclusion complexes with CB6, reveals a preferential inclusion of C3–C5 residues in its cavity. The largest guests which show non-negligible binding contain 7 heavy atoms (excluding hydrogen). For CB7, the strongest binding is observed for guests with adamantyl (10 heavy atoms) and ferrocenyl groups (11 heavy atoms), while the largest guests known to be complexed are carborane and the adduct of two pyridine derivatives (12 heavy atoms). The evaluation of different volumes shows that the most meaningful cavity, namely that responsible for binding of hydrophobic residues, is confined by the planes through the oxygen carbonyls. The volume of this inner cavity follows the formula V/ų=68+62(n−5)+12.5(n−5)², affording representative cavity volumes of 68 ų for CB5, 142 ų for CB6, 242 ų for CB7, and 367 ų for CB8. The volume of the 2 bond dipole regions is comparably smaller, amounting, for example, to 2×35 ų for CB6. The analysis of packing coefficients for representative sets of known guests with clearly defined hydrophobic binding motifs reveals average values of 47 % for CB5, 58 % for CB6, 52 % for CB7, and 53 % for CB8, which are well in line with the preferred packing (“55 % solution”, see S. Mecozzi, J. Rebek, Chem. Eur. J. 1998 , 4, 1016–1022) in related supramolecular host–guest assemblies. The driving force for binding of hydrophobic guests and residues by CBs is interpreted in terms of the unimportance of dispersion interactions (owing to the low polarizability of their cavity) and the dominance of classical and nonclassical hydrophobic effects related to the removal of very-high-energy water molecules (2 for CB5, 4 for CB6, 8 for CB7, and 12 for CB8) from the cavity.     

Inclusion complexation of (11-ferrocenylundecyl)trimethylammonium bromide by β-cyclodextrin and its effects on electrochemical behavior of the surfactant

This report describes the influence of β-cyclodextrin complexation on thermodynamic and kinetic parameters of the electrode reaction of (11-ferrocenylundecyl)trimethylammonium bromide in aqueous media. The host attracted the reduced form having a less positive charge more strongly than the corresponding oxidized one. Thus, a hydrophobic interaction between the non-polar host cavity and the ferrocene moiety plays an important role in the inclusion complexation. Fast-scan voltammetric behavior of the amphiphilic ion suggested that inclusion-ejection processes practically attain equilibrium in the scan-rate range below 10 V s⁻¹, because of their fast rates. The relation between the peak current and peak potential leads to the conclusion that the enveloped guest exchanges no electrons directly with an electrode. The mean diffusion coefficient of the surfactant can be written as a linear combination of the contributions from a free monomolecular, a micelle-forming, and a host-bound surfactant. Since the binding affinity of the ferrocene moiety for the host cavity is much stronger than the aggregation force between the amphiphilic molecules in aqueous media, the host disrupts the micelles by incorporating the surfactant molecule into its cavity.     

Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments

Resistance to the antibiotic tetracycline (Tc) is regulated by its binding as a Tc:Mg2+ complex to the Tet Repressor protein (TetR). Tc:TetR recognition is a complex problem, with the protein and ligand each having several possible conformations and protonation states, which are difficult to elucidate by experiment alone. We used a combination of free-energy simulations and crystallographic analysis to investigate the electrostatic interactions between protein and ligand and the possible role of induced fit in Tc binding. Tc in solution was described quantum mechanically, while Tc:TetR interactions were described by a recent, high-quality molecular-mechanics model. The orientations of the amide and imidazole groups were determined experimentally by a careful analysis of Debye-Waller factors in alternate crystallographic models. The agreement with experiment for these orientations suggested that the simulations and their more detailed, thermodynamic predictions were reliable. We found that the ligand prefers an extended, zwitterionic state both in solution and in complexation with the protein. Tc is thus preorganized for binding, while the protein combines lock-and-key behavior for regions close to the ligand's amide, enolate, and ammonium groups, with an induced fit for regions close to the Mg2+ ion. These insights and the modeling techniques employed should be of interest for engineering improved TetR ligands and improved TetR proteins for gene regulation, as well as for drug design.     

A novel electroneutral anion host based on organoboron betaines

Host-guest binding of anions in organic solvents may find attractive applications in ion sensing and transport, if the host can extract the negatively charged guest species from its solvation sphere. The most powerful means to dismantle the anionic guest from solvent molecules that is required for selective binding is to provide positive charges in the host compound. They have to be counterbalanced by negatively charged subsites in order to conserve electroneutrality, but must avoid collapse into ion pairing with the cationic sites. According to this concept the cage compound 3 was constructed by attachment of anionic tetraphenylborate moieties to the parent macrotricyclic amine 1 . The betainic product 3 was shown to be soluble in water-immiscible dipolar organic solvents like propylene carbonate and formed inclusion complexes with chloride and bromide in the gas phase as well as in solution.     

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.     

Stereochemical Discrimination at Organic Crystal Surfaces 2: The Effect of the Molecular Structure and Conformation of Dipeptides Additives on the Morphology of Glyclyglycine Crystals

The centrosymmetric monoclinic crystals of glycyl-glycine were grown in the presence of three dipeptides (racemic and resolved Gly-Ala, Ala-Gly and Gly-Leu); the presence of each yielded a different morphology. It was found by a combined theoretical and experimental study that the conformation of the guest molecule is determined by the highly stereospecific intermolecular interactions between adsorbed additive and the molecules of particular surface layers of the growing crystals. Theoretical calculations predicted the preferred conformation of the leucine side chain of Gly-Leu consistent with the change in morphology. Occluded racemic Gly-Leu segregates along the b axis of the single crystals of Gly-Gly.     

Polymer Inclusion Compounds: Model Systems for Ordered Bulk Polymer Phases and Starting Materials for Fabricating Polymer–Polymer Molecular Composites

Several small molecules can be cocrystallized with polymers to form inclusion compounds (ICs). Urea, perhydrotriphenylene and the cyclodextrins are examples, and serve to form the host crystalline lattice containing the guest polymer chains in their ICs. The guest polymer chains are confined to narrow, cylindrical channels created by the host, small-molecule lattice, where the polymers are highly extended as a consequence of being squeezed, and are separated from neighbouring polymer chains by the IC channel walls composed exclusively of the small-molecule lattice. The net result is a unique solid-state environment for polymers residing in IC channels, which can be utilized as model systems for ordered, bulk polymer phases. Comparison of the behaviour of polymer chains isolated and extended in IC crystals with the behaviour observed for ordered, bulk phases of polymers is beginning to permit an assessment of contributions made by the inherent, single chain and the cooperative, interchain interactions to the properties of ordered, bulk polymers. It is also possible to release and coalesce polymers from their IC crystals in a manner which leads to their consolidation with a chain-extended morphology. Embedding polymer IC crystals into a carrier polymer, followed by in situ release and coalescence of the included polymers from their IC crystals, offers a means to obtain polymer–polymer composites with unique morphologies. Several such polymer IC-generated composites are described and it is suggested that their unique morphologies might translate into useful, tailorable properties, as well as providing a means for addressing several questions that are fundamental to the behaviour of both phase-separated and homogeneous polymer solids. © 1997 SCI     

Y型沸石吸附噻吩的能量及结构异质性的分子模拟

采用GCMC方法计算了噻吩在全硅Y和NaY沸石上的吸附,通过变化不同的噻吩吸附量得到吸附能量的异质性,并基于主客体径向分布函数剖析了吸附能量的异质性。根据对噻吩分子与沸石之间能量的分析,噻吩分子与沸石之间的作用主要由短程的色散作用控制。NaY沸石上吸附表现出与全硅Y沸石明显不同的吸附位特征,钠离子的引入明显地增强了对噻吩的吸附作用。钠离子与噻吩之间的静电和色散作用是引起这两种不同化学组成沸石吸附热不同的重要因素。进一步对径向分布函数分析确定了NaY沸石中S—Na,CHsp2—Na之间存在独特的作用位。     

Host‐Guest Chemistry of Self‐Assembled Hemi‐Cage Systems: The Dramatic Effect of Lost Pre‐Organization

New hemi‐cage compounds with the formula Pd₂( L1 )₂( L2 )₂ ( L1 =ditopic pyridine ligand, L2 =bpy or TMEDA) have been synthesized and characterized by spectroscopic methods, X‐ray crystallography and electronic structure methods. The host‐guest chemistry of these new structures, with naphthoquinone as a guest, reveals the key role of the host shape and flexibility on competitive binding processes. The influence of counteranions, solvent and non‐covalent interactions to binding were quantified by Density Functional Theory calculations. Together, this study provides new insights into the concept of pre‐organized guest binding when applied to charged, coordination‐assembled hosts.     

New dendrimer-peptide host-guest complexes: towards dendrimers as peptide carriers

Adamantyl urea and adamantyl thiourea modified poly(propylene imine) dendrimers act as hosts for N-terminal tert-butoxycarbonyl (Boc)-protected peptides and form chloroform-soluble complexes. Investigations with NMR spectroscopy show that the peptide is bound to the dendrimer by ionic interactions between the dendrimer outer shell tertiary amines and the C-terminal carboxylic acid of the peptide, and also through host-urea to peptide-amide hydrogen bonding. The hydrogen-bonding nature of the peptide-dendrimer interactions was further confirmed by using Fourier transform IR spectroscopy, for which the NH- and CO-stretch signals of the peptide amide moieties shift towards lower wavenumbers upon complexation with the dendrimer. Spatial analysis of the complexes with NOESY spectroscopy generally shows close proximity of the N-terminal Boc group of the peptide to the peripheral adamantyl groups on the dendrimer host. The influence of side-chain motif on interactions with the host is analyzed by using seven different N-Boc-protected tripeptides as guests for the dendrimer. Downfield shifts of up to 1.3 ppm were observed for the guest amide NH-proton signals. These shifts decreased with increasing 'bulkiness' of the amino acid side chains. Despite this, the dendrimer was capable of making multiple peptide-dendrimer complexes when presented with a library of seven peptides. The different peptides were all present in the host, which did not show specific preferences, and could be released under mild acidic conditions. These results show the general nature of the peptide-dendrimer interactions in the formation of either single- or multiple-peptide-dendrimer complexes.     

Host–guest interactions in tetramethyl-cucurbit[6]uril with anti-tuberculosis drug isoniazid

A novel supramolecular host–guest complex of anti-tuberculosis drug isoniazid (INH) with symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril (TMeQ[6]) has been investigated using ¹H NMR spectroscopy methods, mass spectrometer and single-crystal X-ray diffraction analysis. The result revealed that the INH guest is located the portal of the TMeQ[6] host in both the solutions and the solid state. The driving forces for the association between the guest INH and the host TMeQ[6] are made by a balance between hydrogen bonding interactions and ion-dipole interactions.     

Diffusional and orientational dynamics of various single terylene diimide conjugates in mesoporous materials

Mesoporous silica materials are ideally suited as host–guest systems in nanoscience with applications ranging from molecular sieves, catalysts, nanosensors to drug-delivery-systems. For all these applications a thorough understanding of the interactions between the mesoporous host system and the guest molecules is vital. Here, we investigate these interactions using single molecule spectroscopy (SMS) to study the dynamics of three different terylene diimide (TDI) dyes acting as molecular probes in hexagonal and lamellar mesoporous silica films. The diffusion behaviour in the hexagonal phase is represented by the trajectories of the single molecules. These trajectories are highly structured and thus provide information about the underlying host structure, such as domain size or the presence of defects inside the host structure. The three structurally different TDI derivatives allowed studying the influence of the molecular structure of the guest on the translational diffusion behaviour in the hexagonal phase and the lamellar phase. In the lamellar phase, the differences between the three guests are quite dramatic. First, two populations of diffusing molecules – one with parallel orientation of the molecules to the lamellae and the other with perpendicular orientation – could be observed for two of the TDI derivatives. These populations differ drastically in their translational diffusion behaviour. Depending on the TDI derivative, the ratio between the two populations is different. Additionally, switching between the two populations was observed. These data provide new insights into host–guest interactions like the influence of the molecular structure of the guest molecules on their diffusional as well as on their orientational behaviour in structurally confined guest systems.     

NMR Studies on Li+, Na+ and K+ Complexes of Orthoester Cryptand o-Me2-1.1.1

Cryptands, a class of three-dimensional macrobicyclic hosts ideally suited for accommodating small guest ions, have played an important role in the early development of supramolecular chemistry. In contrast to related two-dimensional crown ethers, cryptands have so far only found limited applications, owing in large part to their relatively inefficient multistep synthesis. We have recently described a convenient one-pot, template synthesis of cryptands based on O,O,O-orthoesters acting as bridgeheads. Here we report variable-temperature, ¹H-1D EXSY and titration NMR studies on lithium, sodium, and potassium complexes of one such cryptand (o-Me₂-1.1.1). Our results indicate that lithium and sodium ions fit into the central cavity of the cryptand, resulting in a comparably high binding affinity and slow exchange with the bulk. The potassium ion binds instead in an exo fashion, resulting in relatively weak binding, associated with fast exchange kinetics. Collectively, these results indicate that orthoester cryptands such as o-Me₂-1.1.1 exhibit thermodynamic and kinetic properties in between those typically found for classical crown ethers and cryptands and that future efforts should be directed towards increasing the binding constants.