Neutral molecular shuttle in acetonitrile dilute solution investigated by molecular dynamics and density functional theory

The oxidized form of a fully synthetic rotaxane – composed by a benzylic amide macrocycle (bam) mechanically locked onto a thread – in acetonitrile dilute solution has been investigated by classical molecular dynamics (MD) simulations and density functional theory (DFT) computations. On the basis of experimental observations, we performed MD simulations considering such a supramolecular assembly for nano-technological applications in a conformation showing the bam in electrostatic interaction with the succinamide (succ) station. At room temperature and equilibrium conditions the MD trajectory reveals that, the bam macrocycle coordinates the succ moiety by means of a cooperative hydrogen bonding network composed by four strong OCNH⋯OCNR contacts. In turn, DFT-predicted 1H NMR chemical shifts for methylene protons of the free and complexed succ in solution result in excellent agreement with the upfield shift of 1.2 ppm detected in laboratory, thus reinforcing the experimental scenario put forward in absence of any external perturbation. Also, we realize that the intrinsic flexibility of the investigated rotaxane allows the presence of folded conformations clearly exhibiting the naphthalimide end-group in interaction, through π–π interactions, with complementary aromatic moieties located within the locked macrocycle itself.