Molecular dynamics of nor-Seco-cucurbit[10]uril complexes

Abstract

Molecular dynamics simulations were carried out to investigate the structure and dynamics of the 1:1 and 1:2 inclusion complexes formed by nor-Seco-cucurbit[10]uril (ns-CB[10]) with 1-adamantanmethylammonium in water. Two and three orientational isomers were considered for 1:1 and 1:2 complexes, respectively. These isomers are identified by the orientation/position of the ammonium group in the guest relative to the flexible and rigid carbonyl portals of the ns-CB[10] host. Results demonstrate that the inclusion of one guest molecule within one cavity in the host induces similar conformational changes in both the occupied and empty cavities. The average structure for each complex shows that the guest molecule is shifted closer to the side that lacks the CH2-bridge in the host, and that the ammonium group of the guest interacts with the oxygens of the host’s portals via ion–dipole interactions with the hydrophobic part of the guest molecule resides in the cavity of the host. Furthermore, the 1:1 complexes are found to interconvert over the time of the simulation. This observation is not found for 1:2 complexes. Finally, MM–PBSA calculations show that 1:2 complexes are significantly more stable than their 1:1 counterparts while two orientations of the 1:2 complexes are more stable than the third.