Dynamics of molecules translocating through carbon nanotubes as nanofluidic channels

We present a molecular dynamics simulation of molecules translocating through carbon nanotubes in vacuo and in aqueous environment for applications in engineered nanofluidic channels. The molecules studied include both rigid and semi-flexible molecules. We show that in the absence of water solvation, the van der Waals interaction between the molecule and the nanotube wall can induce a rapid spontaneous encapsulation of the molecule inside the nanotube channel. The encapsulation process is strongly impeded for nanotubes dissolved in water due to the competition between the van der Waals, hydrophobic and hydrogen bonding interactions in the nanotube/water/molecule complex. Water adsorption inside the nanotube channel plays an important role in determining the dynamics of the spontaneous insertion process.