We present the synthesis of a series of six new glycoluril derived molecular clips and acyclic CB[n]-type molecular containers (1 – 3) that all feature SO3− solubilizing groups but differ in the number of glycoluril rings between the two terminal dialkoxyaromatic sidewalls. We report the x-ray crystal structure of 3b which shows that its dialkoxynaphthalene sidewalls actively define a hydrophobic cavity with high potential to engage in π–π interactions with insoluble aromatic guests. Compounds 1 – 3 possess very good solubility characteristics (≥ 38 mM) and undergo only very weak self-association (Ks < 92 M−1) in water. The weak self-association is attributed to unfavorable SO3−•••SO3− electrostatic interactions in the putative dimers 12 – 42. Accordingly, we created phase solubility diagrams to study their ability to act as solubilizing agents for four water insoluble drugs (PBS-1086, camptothecin, β-estradiol, and ziprasidone). We find that the containers 3a and 3b which feature three glycoluril rings between the terminal dialkoxy-o-xylylene and dialkoxynaphthalene sidewalls are less efficient solubilizing agents than 4a and 4b because of their smaller hydrophobic cavities. Containers 1 and 2 behave as molecular clip type receptors and therefore possess the ability to bind to and thereby solubilize aromatic drugs like camptothecin and ziprasidone, and PBS-1086.

Cucurbit[6]uril (CB[6]) with a substituent attached solely to one methylene bridge was prepared for the first time. The monosubstituted CB[6] undergoes self-assembly to form a cyclic tetramer in the solid state. The affinity of the monosubstituted CB[6] to a series of alkylammonium salts was measured revealing a minor effect of the substituent on the binding properties of the macrocycle.

Molecular clip 1 remains monomeric in water and engages in host•guest recognition processes with suitable guests. We report the Ka values for 32 1•guest complexes measured by 1H NMR, UV/Vis, and fluorescence titrations. The cavity of 1 is shaped by aromatic surfaces of negative electrostatic potential and therefore displays high affinity and selectivity for planar and cationic aromatic guests which distinguishes it from CB[n] receptors that prefer aliphatic over aromatic guests. Electrostatic effects play a dominant role in the recognition process whereby ion-dipole interactions may occur between ammonium ions and the C=O groups of 1, between the SO3− groups of 1 and pendant cationic groups on the guest, and within the cavity of 1 by cation-π interactions. Host 1 displays high affinity toward dicationic guests with large planar aromatic surfaces (e.g. naphthalene diimide NDI+ and perylene diimide PDI+) and cationic dyes derived from acridine (e.g. methylene blue and azure A). The critical importance of cation-π interactions was ascertained by a comparison of analogous neutral and cationic guests (e.g. methylene violet vs. methylene blue; quinoline vs. N-methylquinolinium; acridine vs. N-methylacridinium; neutral red vs. neutral red H+) whose affinities differ by up to 380-fold. We demonstrate that the high affinity of 1 toward methylene blue (Ka = 3.92 × 107 M−1; Kd = 25 nM) allows for the selective sequestration and destaining of U87 cells stained with methylene blue.