The Migration of Ions Along the Axis of a Polypyrrole Helix Channel in Aqueous Solution

In order to investigate the passage of ions through a confined space, two substituted derivatives of a polypyrrole chain are considered in a helical conformation which forms a linear channel. The two species of sidechain on the 3 position of the pyrrole rings differ in their electron-withdrawing power. The system’s response to a pH change by deprotonation of pyrrole rings is discussed in terms of a quantum tunnelling of a proton between two sites at the pyrrole’s N atom. A characteristic ‘inversion time’ is calculated for the mechanism and compared for the two derivatives. In an investigation of the possibility that ions generated by the pH changes may enter the channel, molecular dynamics (MD) calculations are performed to calculate the fluctuating electrostatic potential at points along the axis for the polypyrrole chains in aqueous solution. It is found that although the atoms of the bare two polypyrrole channels derivatives generate very different time-averaged potential profiles along the axis, their polarising effect on the water molecules reorients the dipoles so as to oppose the charges from the polymer chain. It is shown that the charges on the polypyrrole helix imposes a ‘solvent structure’ on the water dipoles in the channel. The MD shows that when an electric field is applied along the channel axis the hydrated H+ is accelerated to a point half way along the channel, where further progress is inhibited; however the passage of the OH？ is unimpeded. These results are discussed in relation to the molecular confinement of the migrants through the axial electrostatic potentials and the migrant charges and structure