Crystal structure prediction of host–guest supramolecular systems based on β-cyclodextrin dimers and trimers with luminescent probes

The method of molecular dynamics was used to model crystal structures based on dimers and trimers of β-cyclodextrin containing luminescent complexes: naphthalene stacking dimer, exhibiting excimer fluorescence, and phenanthrene–2 tert-butylbenzene heterotrimer, exhibiting room temperature phosphorescence. A novel technique was developed to construct these crystals, which consists in replacing guest molecules in the real crystalline supramolecular systems built from β-cyclodextrin dimers and trimers by a naphthalene dimer or phenanthrene–2 tert-butylbenzene complex. Due to the strength of the natural crystalline cyclodextrin framework, the obtained structures are absolutely stable and allow us to explain the observable luminescence properties of naphthalene and phenanthrene in the solid precipitates of an unknown structure. In crystals consisting of β-cyclodextrin trimers assembled into infinite nanotubes, various positions and orientations of the phenanthrene probe in the cavity of the tubes were studied, and the most promising structure for the main candidate with long-term room temperature phosphorescence was selected. Other cases, in which phenanthrene is more loosely in contact with a pair of tert-butylbenzene molecules and more freely moves within tubes, are related with shorter-term room temperature phosphorescence components. Since the packing of host β-cyclodextrin molecules plays a decisive role in the crystallization of supramolecular complexes, this technique is promising for the prediction of new crystal structures, in which embedded guest molecules have sizes suitable for host cavities, and will make obtaining many important supramolecular crystals from few experimentally measured ones possible. This method is applicable for various cyclodextrins and other cavitands, whose molecules are able to undergo dimerization or trimerization in a crystal and build a strong framework.