X-ray structures of 1:1 complexes of (L)-menthol with β-cyclodextrin and permethylated β-cyclodextrin

Inclusion Complexes of Naringenin in Dimethylated and Permethylated β-Cyclodextrins: Crystal Structures and Molecular Dynamics Studies

The crystal structures of the inclusion complexes of naringenin in dimethylated and permethylated β-cyclodextrin (DM-β-CD and TM-β-CD) were determined and extensively analyzed. Naringenin is found with its 4-hydroxyphenyl residue fully immersed in the DM-β-CD cavity and its chromone group protruding from the narrow rim of the open-cone shaped host. The naringenin/DM-β-CD complex units are packed in a ‘herring bone’ fashion. In the case of naringenin/TM-β-CD, the complex units are arranged in a cage-type mode, the guest naringenin is partially encapsulated in the cavity of the closed-cone shaped host, with its chromone group laying equatorially and its 4-hydroxyphenyl protruding extensively from the wide rim of the host. Furthermore, the crystallographically-determined coordinates of both complexes were employed for Molecular Dynaimics simulations in explicit water solvent and in the absence of crystal contacts. The trajectories showed that naringenin rapidly penetrates the open narrow rim of DM-β-CD but not the closed narrow rim of TM-β-CD. Thus, in the latter case, the chromone group of naringenin is accommodated shallowly in the wide rim of the host, tethered via hydrogen bonds to the secondary methoxy groups of the host. Finally, a significantly higher binding affinity for naringenin in DM-β-CD than TM-β-CD was estimated by Molecular Mechanics/Generalized Born Surface Area calculations.

Supramolecular Recognition and Structural Elucidation of Inclusion Complexes of an Achiral Carbene Precursor in β- and Permethylated β-Cyclodextrin

[structure: see text] Inclusion of achiral carbene precursor endo-8-azibicyclo[3.2.1]octan-3-ol (1) in chiral beta-cyclodextrin (7-Cy) and tri-O-methyl-beta-cyclodextrin (TRIMEB) leads to 1:1 complexes 1@7-Cy and 1@TRIMEB, respectively. The combined methods of induced circular dichroism, NMR spectroscopy, and X-ray structure determination were employed for the first time for structural elucidation of the complexes in solution and the solid state. Significantly different orientations of 1 were observed. Compared with 1@7-Cy, 1@TRIMEB exhibits a different guest orientation and an association constant one-twentieth lower.

Structure of the inclusion complexes of heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin with indole-3-butyric acid and 2,4-dichlorophenoxyacetic acid

The crystal structures of the complexes of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin with indole-3-butyric acid and with 2,4-dichlorophenoxyacetic acid were studied by X-ray diffraction. The complexes crystallize in the monoclinic P2(1) space group. The host molecules are elliptically puckered and stacked along the a crystal axis, in a head-to-tail fashion, forming columns. One primary methoxy group of the host molecule of the complex with indole-3-butyric acid has the unusual trans-gauche conformation for permethylated CDs. All the secondary O-3-CH(3) methoxy groups, some secondary O-2-CH(3) and some primary methoxy groups pointing inwards the cavity enclose the indole or the 2,4-dichlorophenoxy moieties of the guest molecules inside the cavity, while the chains of the guests protrude between two adjacent host molecules of the columns. The mean planes of the indole and 2,4-dichlorophenoxy moieties of the guests are nearly perpendicular to the mean planes of the elliptical heptagons defined by the O-4n atoms of the hosts. The carboxyl group of the guests form hydrogen bonds with oxygen atoms of the host molecules or with the water molecules found in the space between the complexes of the same column.