Complexation of N-methyl-4-(p-methyl benzoyl)-pyridinium methyl cation and its neutral analogue by cucurbit[7]uril and β-cyclodextrin: a computational study

In this work, molecular dynamics (MD) simulations have been conducted to study the inclusion complexes between cucurbit7]uril (CB7) and β-cyclodextrin (β-CD) with N-methyl-4-(p-methyl benzoyl)-pyridinium methyl cation, and N-methyl-4-(p-methyl benzoyl)-pyridine in aqueous solutions to gain detailed information about the dynamics and mechanism of the inclusion complexes. The obtained MD trajectories were used to estimate the binding free energy of the studied complexes using the molecular mechanics/Poisson Bolzmann surface area (MM–PBSA) method. Results indicate preference of CB7 to bind to the cationic guest more than the neutral guest, whereas β-CD exhibits more or less the same affinity to complex with either species. Furthermore it was interesting to note that β-CD forms more stable complexes with both guests than CB7. Average structure of each complex and the distances between the center of masses of the guest and the host were also discussed.