Benzobis(imidazolium)-cucurbit[8]uril complexes for binding and sensing aromatic compounds in aqueous solution

Quantitative SERS using the sequestration of small molecules inside precise plasmonic nanoconstructs

We show how the macrocyclic host, cucurbit[8]uril (CB[8]), creates precise subnanometer junctions between gold nanoparticles while its cavity simultaneously traps small molecules; this enables their reproducible surface-enhanced Raman spectroscopy (SERS) detection. Explicit shifts in the SERS frequencies of CB[8] on complexation with guest molecules provides a direct strategy for absolute quantification of a range of molecules down to 10(-11) M levels. This provides a new analytical paradigm for quantitative SERS of small molecules.

Synthesis and self-assembly processes of monofunctionalized cucurbit[7]uril

We present a building-block approach toward functionalized CB[7] derivatives by the condensation of methylene-bridged glycoluril hexamer 1 and glycoluril bis(cyclic ethers) 2 and 12. The CB[7] derivatives Me2CB[7] and CyCB[7] are highly soluble in water (264 mM and 181 mM, respectively). As a result of the high intrinsic solubility of Me2CB[7], it is able to solubilize the insoluble benzimidazole drug albendazole. The reaction of hexamer 1 with glycoluril derivative 12, which bears a primary alkyl chloride group, gives CB[7] derivative 18 in 16% isolated yield. Compound 18 reacts with NaN3 to yield azide-substituted CB[7] 19 in 81% yield, which subsequently undergoes click reaction with propargylammonium chloride (21) to yield CB[7] derivative 20 in 95% yield, which bears a covalently attached triazolyl ammonium group along its equator. The results of NMR spectroscopy ((1)H, variable-temperature, and DOSY) and electrospray mass spectrometry establish that 20 undergoes self-assembly to form a cyclic tetrameric assembly (204) in aqueous solution. CB[7] derivatives bearing reactive functional groups (e.g., N3, Cl) are now available for incorporation into more complex functional systems.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

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.

Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010

Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge

The computational prediction of protein-ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands--i.e., host-guest systems--represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challenge for host-guest binding affinities, through the incorporation of 11 new host-guest complexes. Ten participating research groups addressed this challenge with a variety of approaches. Statistical assessment indicates that, although most methods performed well at predicting some general trends in binding affinity, overall accuracy was not high, as all the methods suffered from either poor correlation or high RMS errors or both. There was no clear advantage in using explicit versus implicit solvent models, any particular force field, or any particular approach to conformational sampling. In a few cases, predictions using very similar energy models but different sampling and/or free-energy methods resulted in significantly different results. The protonation states of one host and some guest molecules emerged as key uncertainties beyond the choice of computational approach. The present results have implications for methods development and future blind prediction exercises.

Cucurbit[8]uril mediated donor-acceptor ternary complexes: a model system for studying charge-transfer interactions

A supramolecular self-assembly approach is described which allows for the convenient preparation of a wide range of charge-transfer (CT) donor-acceptor complexes in aqueous solutions. When one equiv of the macrocyclic host cucurbit[8]uril (CB[8]) is added to an aqueous donor and acceptor solution, a heteroternary complex forms inside the host's cavity with a well-defined face-to-face π-π-stacking geometry of the donor and acceptor. This heteroternary, CB[8]-mediated complex offers the opportunity to study the CT phenomena at low concentrations and free from complications arising from any donor-donor and acceptor-acceptor interactions as a result of the large binding affinities and the very high selectivity over the formation of these homoternary complexes. Thus, this supramolocular self-assembly strategy is a practical donor-acceptor mix-and-match approach with synthetic advantages over much more cumbersome tethering schemes. While the characteristic UV/vis features of a few CB[8] ternary systems had been described as a CT band, we present for the first time systematic evidence for the existence of CT interactions between several donor-acceptor pairs that are mediated by the host CB[8]. Correlation of the experimentally obtained CT λ(max) to computed HOMO-LUMO energies demonstrated that the CT process in the host's cavity can be described by the Mulliken model. Furthermore, the literature claim of a "CT driving force" for the formation of CB[8] ternary complexes was scrutinized and evaluated by calorimetric (ITC) and ESI-MS measurements. The findings indicated that neither in the aqueous medium nor in the "gas-phase" is CT of energetic relevance to the Gibbs free binding energy. In contrast, electrostatic considerations combined with solvation effects are much better suited to rationalize the observed trends in binding affinities. Additionally, the CT λ(max) was found to be much more red-shifted (≥75 nm) inside the CB[8] cavity than in any polar organic solvents or water, indicating a significant stabilization of the CT excited state within the host cavity, further demonstrating the unique electrostatic, polar properties of the host cavity.

Imidazole derivatives: a comprehensive survey of their recognition properties

Due to its amphoteric nature the imidazole ring can function as selective and effective anion and/or cation and even neutral organic molecules receptor system. As a result, the design of new multichannel imidazole-based receptors capable of recognizing different types of analytes is strongly demanded. This review summarizes the most recent and relevant advances in this area.

Templated synthesis of glycoluril hexamer and monofunctionalized cucurbit[6]uril derivatives

We report that the p-xylylenediammonium ion (11) acts as a template in the cucurbit[n]uril forming reaction that biases the reaction toward the production of methylene bridged glycoluril hexamer (6C) and bis-nor-seco-CB[10]. Hexamer 6C is readily available on the gram scale by a one step synthetic procedure that avoids chromatography. Hexamer 6C undergoes macrocylization with (substituted) phthalaldehydes 12, 14, 15, and 18-in 9 M H(2)SO(4) or concd HCl at room temperature to deliver monofunctionalized CB[6] derivatives 13, 16, 17, and 19-that are poised for further functionalization reactions. The kinetics of the macrocyclization reaction between hexamer and formaldehyde or phthalaldehyde depends on the presence and identity of ammonium ions as templates. p-Xylylenediammonium ion (11) which barely fits inside CB[6] sized cavities acts as a negative template which slows down transformation of 6C and paraformaldehyde into CB[6]. In contrast, 11 and hexanediammonium ion (20) act as a positive template that promotes the macrocyclization reaction between 6C and 12 to deliver (±)-21 as a key intermediate along the mechanistic pathway to CB[6] derivatives. Naphthalene-CB[6] derivative 19 which contains both fluorophore and ureidyl C═O metal-ion (e.g., Eu(3+)) binding sites forms the basis for a fluorescence turn-on assay for suitable ammonium ions (e.g., hexanediammonium ion and histamine).