Cavity diameter and height of cyclodextrins and cucurbit[n]urils from the molecular electrostatic potential topography

Understanding the interactions of cyclodextrins (CD) and cucurbit[n]uril (CB[n]) hosts with a variety of guest molecules following their encapsulation within the cavity of these macrocycles have become increasingly important in the recent years. The electronic charge distribution and the cavity dimension are some of the key factors those govern their interactions with cations or neutral guests. In the present work the molecular electrostatic potential (MESP) topography has been utilized to obtain the 'effective' cavity diameter and height of CB[n] (n = 6-8) homologues and 8 conformers each of alpha-, beta- and gamma-CD. It has been shown that the shape of CD cavity be it cone- or barrel-like stems from the hydrogen bonding patterns within primary hydroxyl groups. The width of CB[7] is comparable to the beta-CD conformer that possesses either O6H-O-5' or intraglucose O6H-O-5 interactions. The cavity diameters of alpha- and gamma-CD are predicted to be respectively, 1.0 and 1.5 larger than CB[6] and CB[8] hosts. MESP topography reveals that the cavities of CB[n] are less hydrophilic with largely hydrophilic portals as compared to CD hosts. Cremer-Pople puckering parameters were derived for all the CD conformers and CB[n]. It has been demonstrated that the clockwise and anticlockwise hydrogen bonding patterns in the lower as well as upper rims of different CD conformers are less distorted and exhibit a little deviation from the A degrees C-3 chair conformation of alpha-d-glucopyranose constituting monomeric unit of CD.