Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated by using a hierarchical multiscale methodology in silica slit channels filled with l M KCl. Partial charges of both bulk and surface atoms from abinitio quantum calculations that take into account bond polarization is used in molecular dynamics simulations to obtain ion and water concentration profiles for channel widths of 1.371, 2.235 and 3.09 nm. By simulating corresponding channels with no partial charges it was observed that the partial charges affect the concentration profiles till a distance of about 0.8 nm from the surface. Both in the uncharged and charged cases, oscillations in concentration profiles of K+ and Cl- ions gives rise to an electroosmotic flow in the presence of an external electric field contrary to the expectations from continuum theory. The I-V characteristics are significantly altered by partial charges for slits less than 2.5 nm in width.