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 (nD=1.10±0.12) are extremely low, close to the gas phase. The calculated molecular quadrupole moments of CBs are extremely large (Θzz=−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/Å3=68+62(n−5)+12.5(n−5)2, affording representative cavity volumes of 68 Å3 for CB5, 142 Å3 for CB6, 242 Å3 for CB7, and 367 Å3 for CB8. The volume of the 2 bond dipole regions is comparably smaller, amounting, for example, to 2×35 Å3 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.

Hydrocarbons are no longer afraid of water when they are reversibly encapsulated by cucurbituril (see picture). The pumpkin‐shaped molecular container displays a high affinity and selectivity towards neutral molecules in salt‐free aqueous solutions. A supramolecular sensing ensemble, composed of cucurbit[6]uril and an anchored indicator dye, is introduced as a highly sensitive fluorescence‐based online detection tool for gas binding in solution.

The host-guest complexation of hydrocarbons (22 guest molecules) with cucurbit[7]uril (CB7) was investigated in aqueous solution. Association constants were determined by using the indicator displacement strategy, which allows binding constant determinations also for poorly water-soluble (hydrophobic) guests. The binding constants (103–109 M−1) increased with the size of the hydrocarbon, pointing to the hydrophobic effect and dispersion interactions as driving forces. Besides potential applications for the sensing and separation of hydrocarbons, the measured affinities provide unique benchmark data for the binding of neutral guest molecules. Consequently, a computational blind challenge, the HYDROPHOBE challenge, was conducted in order to allow a comparison with state-of-the-art computational methods for predicting host-guest affinity constants. In total, 5 computational data sets were submitted, which allowed the comparison of experimental binding constants with those predicted by coupled-cluster theory (DLPNO-CCSD(T)), dispersion-corrected density functional theory (DFT), and explicit solvent molecular dynamics (MD) simulations parameterized with two different force field combinations from the AMBER simulation package. All submissions were capable of predicting the general binding trend, with a slightly better correlation for the MD compared to the quantum-chemical (QM) data sets (R2MD = 0.80 vs R2QM = 0.66, average values for the submitted data sets). On the other hand, QM calculations showed better predictions for the absolute values of the binding affinities as reflected by the mean signed errors (4.3 kcal mol−1 for MD vs 1.8 kcal mol−1 for QM). When searching for sources of uncertainty in predicting the host-guest affinities, the experimentally known hydration energies of the investigated hydrocarbons could be employed, which provided a distinct advantage of the HYDROPHOBE challenge. The comparison with the employed solvation models (explicit solvent for MD and COSMO-RS for QM) confirmed a good correlation for both methods, but revealed a rather constant offset of the COSMO data, by ca. +2 kcal mol−1, which was traced back to a required reference-state correction in the QM submissions (2.38 kcal mol−1). Introduction of the reference-state correction improved the predictive power of the QM methods, particularly for small hydrocarbons up to C5. The correlations of both QM and MD submissions also exposed specific outliers, which could be due to peculiarities of the investigated guests, for example, different degrees of conformational changes upon complexation, such as helical structures of the longer n-alkyl chains within the cavity. The latter was confirmed by 2D NMR experiments and both the MD as well as QM calculations.

The demand for practical and convenient enzyme assays for histone lysine methyltransferases (HKMTs) emerges along with the rapid development of this young class of enzymes. A supramolecular reporter pair composed of p-sulfonatocalix[4]arene (CX4) and the fluorescent dye lucigenin (LCG) has been used to monitor enzymatic trimethylation of lysine residues in peptide substrates. The assay affords a switch-ON fluorescence response and operates in a continuous, real-time, and label-free fashion. The underlying working principle relies on the higher affinity of the macrocycle towards the trimethylated product of the enzymatic reaction as compared to the substrate, which allows the assay to be carried out in the product-selective mode. The final product incorporates a trimethylammonium moiety, a known high-affinity binding motif for CX4. Two substrates corresponding to the H3 N-terminal tail, namely, S2 (RTKQTARKSTGGKAP) and S6 (QTARKSTGGS), were selected as model compounds for methylation with the Neurospora crassa Dim-5 enzyme and investigated by the newly developed supramolecular tandem HKMTs assay. Only the longer substrate S2 underwent methylation in solution. The potential of the assay for inhibitor screening was demonstrated by means of inhibition studies with 1,10-phenanthroline to afford an inhibition constant of (70±20) μM.

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A supramolecular tandem assay for direct continuous monitoring of nucleotide triphosphate-dependent enzymes such as potato apyrase is described. The underlying principle of the assay relies on the use of anion-receptor macrocycles in combination with fluorescent dyes as reporter pairs. A combinatorial approach was used to identify two complementary reporter pairs, i.e. an amino-gamma-cyclodextrin with 2-anilinonaphtalene-6-sulfonate (ANS) as dye (fluorescence enhancement factor of 17 upon complexation) and a polycationic cyclophane with 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS) as dye (fluorescence decrease by a factor of more than 2000), which allow the kinetic monitoring of potato apyrase activity at different ATP concentration ranges (microM and mM) with different types of photophysical responses (switch-ON and switch-OFF). Competitive fluorescence titrations revealed a differential binding of ATP (strongest competitor) versus ADP and AMP, which constitutes the prerequisite for monitoring enzymatic conversions (dephosphorylation or phosphorylation) involving nucleotides. The assay was tested for different enzyme and substrate concentrations and exploited for the screening of activating additives, namely divalent transition metal ions (Ni(2+), Mg(2+), Mn(2+), and Ca(2+)). The transferability of the assay could be demonstrated by monitoring the dephosphorylation of other nucleotide triphosphates (GTP, TTP, and CTP).

The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.

The inclusion of small hydrocarbons into molecular container compounds in solution has received considerable attention. [1][2][3][4][5][6][7][8][9] It allows for a puristic understanding of the solvophobic driving force for the formation of discrete host-guest complexes [10] and has additional potential for gas storage, uptake, and separation, thus complementing solid-state applications of porous materials [11,12] or surface-immobilized macrocycles. [13] Studies on the precipitation of complexes between the smallest alkanes with a-cyclodextrin date back to the 1950s. [14] Subsequently, synthetic hosts such as cryptophanes, [1] self-assembling capsules, [2][3][4][5] and hemicarcerands [6,7] have been investigated for their potential to entrap small hydrocarbons. Herein, we describe a highly sensitive fluorescence-based method for the quantification of volatile hydrocarbons binding with cucurbituril. We observe exceptionally strong, highly selective, and reversible binding in aqueous solution.Cucurbit[n]urils (CBn) are water-soluble, highly symmetric pumpkin-shaped synthetic macrocycles, [15,16] and their unique supramolecular chemistry is presently unfolding. [17,18] They are well-established to bind organic ammonium ions through a combination of hydrophobic interactions inside the nonpolar inner cavity and ion-dipole interactions with the carbonyl portals. While a CB5 derivative has been reported to bind very small guests such as methane and acetylene, [12, 19] the homologue which holds most promise for hydrocarbon binding is CB6, [20] the original cucurbituril, which possesses an intermediary size to allow inclusion of guests with up to seven heavy atoms into its inner cavity. [18,21] Unfortunately, CB6 has an intrinsically low water solubility of about 30 mm, which complicates the determination of actual binding constants. [21,22] In particular, it prevents 1 H NMR titrations, which have been routinely employed in all previous studies on solution-phase gas binding by molecular containers. [1][2][3][4][5][6][7][8][9] The binding of xenon with CB6 has been studied by 129 Xe NMR spectroscopy in the presence of 0.2 m Na 2 SO 4 , [23] where the solubility is increased (but where also the binding strength suffers). Alternatively, an alkylated CB6 derivative with higher water solubility has been employed, which was also investigated by isothermal titration calorimetry, to afford a binding constant of 3400 m À1 with xenon. [24] The binding constants, which we report herein for several simple hydrocarbons, are much larger than those observed for xenon, and, in fact, the largest ones reported for neutral guests with CB6. [18] In several cases, they exceed those previously observed for any molecular container. [1][2][3][4][5][6][7][8][9] In the quest for a convenient method to monitor volatile hydrocarbon binding to CB6, we selected an indicator displacement strategy [25] based on our recently developed anchor dye approach. [26] In detail, compound 1 possesses a putrescine anchor for strong binding with CB6, [27] and a ...