  Accurate calculations of electrostatic potentials and treatment of substrate
polarizability are critical for predicting the permeation of ions inside
water-filled nanopores. The {\it ab initio} molecular dynamics method (AIMD),
based on Density Functional Theory (DFT), accounts for the polarizability of
materials, water, and solutes, and it should be the method of choice for
predicting accurate electrostatic energies of ions. In practice, DFT coupled
with the use of periodic boundary conditions in a charged system leads to large
energy shifts. Results obtained using different DFT packages may vary because
of the way pseudopotentials and long-range electrostatics are implemented.
Using maximally localized Wannier functions, we apply robust corrections that
yield relatively unambiguous ion energies in select molecular and aqueous
systems and inside carbon nanotubes. Large binding energies are predicted for
ions in metallic carbon nanotube arrays, while with consistent definitions
Na$^+$ and Cl$^-$ energies are found to exhibit asymmetries comparable with
those computed using non-polarizable water force fields.
