Khaleel I. Assaf

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.

Halogen bonding inside a molecular container.

The synthetic macrocycle cucurbit[6]uril forms host-guest inclusion complexes with molecular dibromine and diiodine. As evidenced by their crystal structures, the encapsulated dihalogens adapt a tilted axial geometry and are held in place by two different types of halogen-bonding interactions, one with a water molecule (bond distances 2.83 Å for O···Br and 3.10 Å for O···I) and the other one with the ureido carbonyl groups of the molecular container itself (bond distances 3.33 Å for O···Br and 3.49 Å for O···I). While the former is of the conventional type, involving the lone electron pair of an oxygen donor, the latter is perpendicular, involving the π-system of the carbonyl oxygen (N-C═O···X dihedrals ca. 90°). Such perpendicular interactions resemble those observed in protein complexes of halogenated ligands. A statistical analysis of small-molecule crystal structural data, as well as quantum-chemical calculations with urea as a model (MP2/aug-cc-pVDZ-PP), demonstrates that halogen bonding with the π-system of the carbonyl oxygen can become competitive with the commonly favored lone-pair interaction whenever the carbonyl group carries electron-donating substitutents, specifically for ureas, amides, and esters, and particularly when the lone pairs are engaged in orthogonal hydrogen bonding (hX bonds). The calculations further demonstrate that the perpendicular interactions remain significantly attractive also for nonlinear distortions of the O···X-X angle to ca. 140°, the angle observed in the two reported crystal structures. The structural and theoretical data jointly support the assignment of the observed dihalogen-carbonyl contacts as genuine halogen bonds.

Water Structure Recovery in Chaotropic Anion Recognition: High-Affinity Binding of Dodecaborate Clusters to γ-Cyclodextrin†

Dodecaborate anions of the type B12X122− and B12X11Y2− (X=H, Cl, Br, I and Y=OH, SH, NH3+, NR3+) form strong (Ka up to 106 L mol−1, for B12Br122−) inclusion complexes with γ-cyclodextrin (γ-CD). The micromolar affinities reached are the highest known for this native CD. The complexation exhibits highly negative enthalpies (up to −25 kcal mol−1) and entropies (TΔS up to −18.4 kcal mol−1, both for B12I122−), which position these guests at the bottom end of the well-known enthalpy-entropy correlation for CDs. The high driving force can be traced back to a chaotropic effect, according to which chaotropic anions have an intrinsic affinity to hydrophobic cavities in aqueous solution. In line with this argument, salting-in effects revealed dodecaborates as superchaotropic dianions.

Dodecaborate-Functionalized Anchor Dyes for Cyclodextrin-Based Indicator Displacement Applications.

A new type of water-soluble anchor dyes, that is, dyes which carry an auxiliary unit for strong binding to macrocyclic host molecules, has been synthesized. It consists of 7-nitrobenzofurazan (NBD) as a dye and the dodecaborate cluster (B12H11R) as a dianionic, globular, and purely inorganic anchoring group for cyclodextrins (Ka > 10(5) M(-1)). The synthesized dodecaborate-substituted dyes show marked changes in their photophysical properties (UV-vis and fluorescence) upon complexation with cyclodextrins (β-CD and γ-CD), such that the resulting host·dye complexes (1:1 stoichiometry) present sensitive reporter pairs for indicator displacement applications.

Triple Emission from p‐Dimethylaminobenzonitrile–Cucurbit[8]uril Triggers the Elusive Excimer Emission

The intriguing dual-emission behavior of p- dimethylaminobenzonitrile (DMABN) and the identity of the associated excited states is, arguably, the most extensively investigated and also controversially discussed molecule- specific phenomenon of modern photochemistry. We have now found a new, third fluorescence band when DMABN is encapsulated within the water-soluble molecular container cucurbit[8]uril (CB8). It is centered between the previously observed emissions and assigned to the elusive excimer emission from DMABN through 1:2 CB8:DMABN complex formation. Heating of the CB8⋅(DMABN)2 complex from 0 to 100 °C results in the dissociation of the ternary complex and restoration of the dual-emission properties of the monomer. Alternatively, monomer emission can be obtained by selecting cucurbit[7]uril (CB7), a host homologue that is too small to accommodate two DMABN molecules, or by introducing ethyl instead of methyl groups at the amino terminus of the aminobenzonitrile guest.

Cucurbiturils as fluorophilic receptors

We report the formation of strong inclusion complexes between the macrocyclic host cucurbit[7]uril (CB7) and more than 20 perfluorinated compounds (PFCs) in aqueous solution. The binding constants and structures of the complexes were determined through a combination of dye displacement titrations, 19F as well as 1H NMR spectroscopy, and quantum chemical calculations. The high affinities, for example 1.2 × 107 M− 1 for perfluorohexane and 1.1 × 108 M− 1 for perfluoro(methylcylohexane), are driven, among others, by the low polarisability of the cucurbituril cavity, which favours the binding of non-polarisable guests such as PFCs. The complexation-induced chemical shifts of the 19F resonances are downfield in cases where a conformational flexibility allows the (partial) interconversion of gauche conformations (favoured in water) to anti conformations (favoured inside the cavity of CB7). Only for conformationally rigid substrates, for example SF6 and (CF3)3COH, upfield shifts prevail. These are attributed to the low polarisability of the inner cavity, similar to the upfield shifts observed for 19F resonances upon going from highly polarisable to less polarisable solvents. Cucurbituril homologues (CB5, CB6 and CB8) were also studied and, among those, evidence for the formation of inclusion complexes was observed for CB6 as host and CF4, SF6 and CF3CH2OH as guests. Besides contributing to the fundamental understanding of fluorophilic interactions, the results have implications for PFC separation and for the efficient removal of PFCs from and the sensing of PFCs in aqueous solution.

Inclusion of neutral guests by water-soluble macrocyclic hosts – a comparative thermodynamic investigation with cyclodextrins, calixarenes and cucurbiturils

Abstract The driving forces of association between three different families of macrocycles as hosts, namely cyclodextrins (α-, β-, and γ-), p-sulfonatocalix[n]arenes (n = 4–6) as well as cucurbit[n]urils (n = 6–8), and three different bicyclic azoalkane homologues as guests, namely 2,3-diazabicyclo[2.2.1]hept-2-ene (DBH), 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as well as 2,3-diazabicyclo[2.2.3]non-2-ene (DBN), were examined by means of calorimetric titrations, NMR spectroscopy and molecular dynamics simulation, all in aqueous solution. The small, spherical and uncharged guests preferably bind inside the cavities of the medium sized hosts. The inclusion complexation by β-cyclodextrin and p-sulfonatocalix[4]arene shows medium binding affinities (millimolar), while cucurbit[7]uril macrocycle shows very strong binding (micromolar). For all types of macrocycles, the complex formation is enthalpically driven (ΔH° < 0), accompanied by slightly unfavourable entropy changes (ΔS° < 0). The results are discussed in terms of the flexibility of the hosts, the hydrophobic character of their cavities and the release of high-energy water upon binding, and generalised by including two additional guests, the ketones cyclopentanone and (+)-camphor.

Investigation of isomeric flavanol structures in black tea thearubigins using ultraperformance liquid chromatography coupled to hybrid quadrupole/ion mobility/time of flight mass spectrometry

Ultra performance liquid chromatography (UPLC) when coupled to ion mobility (IMS)/orthogonal acceleration time of flight mass spectrometry is a suitable technique for analyzing complex mixtures such as the black tea thearubigins. With the aid of this advanced instrumental analysis, we were able to separate and identify different isomeric components in the complex mixture which could previously not be differentiated by a conventional high performance liquid chromatography/tandem mass spectrometry. In this study, the difference between isomeric structures theasinensins, proanthocyanidins B-type and rutin (quercetin-3O-rutinoside) were studied, and these are present abundantly in many botanical sources. The differentiation between these structures was accomplished according to their acquired mobility drift times differing from the traditional investigations in mass spectrometry, where calculation of theoretical collisional cross sections allowed assignment of the individual isomeric structures. The present work demonstrates UPLC-IMS-MS as an efficient technology for isolating and separating isobaric and isomeric structures existing in complex mixtures discriminating between them according to their characteristic fragment ions and mobility drift times. Therefore, a rational assignment of isomeric structures in many phenolic secondary metabolites based on the ion mobility data might be useful in mass spectrometry-based structure analysis in the future.

Chitin-acetate/DMSO as a supramolecular green CO2-phile

The supramolecular chemisorption of CO2 by the oligomeric chitin-acetate (CA) in DMSO as a green solvent offers a novel eco-friendly approach for CO2 capture. Since the amino groups in the sorbent material are blocked either by protonation or acetylation, the multi-armed hydroxyl based oligosaccharide captures CO2 through the formation of an organic carbonate species as confirmed by 13C NMR, in situ ATR-FTIR spectroscopy and conductivity. DFT calculations verified the formation of the CA-CO2 adduct, in which the organic carbonate group is stabilized through supramolecular ionic interaction and hydrogen bonding with the neighboring ammonium ion and hydroxyl functional group along the oligomer backbone. The use of other polar aprotic solvents (N,N-dimethylformamide (DMF), acetonitrile, and acetone) was not successful due to solubility issues.

Coulomb repulsion in short polypeptides.

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each other or the main chain.