Crystal structures and molecular dynamics studies of the inclusion compounds of β-citronellol in β-cyclodextrin, heptakis(2,6-di-O-methyl)-β-cyclodextrin and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin

Abstract

The crystal structures of the inclusion complexes of the β-citronellol (cl) inβ-Cyclodextrin (β-CD), heptakis(2,6-di-O-methyl)-β-Cyclodextrin (DM-β-CD) and heptakis(2,3,6-tri-O-methyl)-β-Cyclodextrin (TM-β-CD) have being investigated by X-ray crystallography. The cl/β-CD inclusion complex crystallizes in the P1space group forming dimers which are arranged along the c-axis according to the Intermediate Channel packing mode. Inside the dimeric host cavity two enantiomeric guest molecules are accommodated. The inclusion complexes of cl/DM-β-CD and cl/TM-β-CD crystallize in the P212121 space group having both 1:1 guest:host stoichiometry, the guest found always with the (−)-cl enantiomeric configuration. The guest is fully encapsulated inside the DM-β-CD host cavity whereas is partially encapsulated in the TM-β-CD which is severely puckered as in all TM-β-CD complexes and its primary side is efficiently blocked by the methoxy groups. The complex units in the case of cl/DM-β-CD pack along the crystallographic a-axis in a head-to-tail manner forming columns of herringbone mode whereas in the case of cl/TM-β-CD are arranged also head-to-tail, parallel to the b-axis, in a screw-channel mode.MD simulations based on the determined crystal structures showed that in a simulated aqueous environment the guest maintains the inclusion mode observed crystallographically in every case. MM/GBSA-calculations used for comparison of the inclusion complexes binding affinity with each other, indicated that the inclusion of β-citronellol in TM-β-CD is less favorable than in β-CD and DM-β-CD.