Theoretical study of structure and properties of a molecular reactor based on the urea-linked β-cyclodextrin dimer

In the present work, semiempirical and hybrid QM/QM′ methods are applied to investigate the structure and properties of a cyclodextrin based molecular reactor, named N,N′-bis(6A-deoxy-β-cyclodextrin-6A-yl)urea (β-CD2ur). In addition to the conformational analysis for the free host, inclusion compounds involving some reactive species participating in the indirubin formation are analyzed and the results discussed on the basis of the templating effect. The outcomes showed two main forms of cyclodextrin dimer in the equilibrium (C1 and C2), differing on the conformation around the urea bridge group. Both conformers presented suitable arrangement to accommodate the reactive species favoring the indirubin isomer formation. The analysis of the complexation processes suggests distinct modes of inclusion for indigo and indirubin isomers, with the latter leading to more favorable processes, therefore establishing some molecular basis for the templating effect.