Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated in silica slit channels filled with 1M KCl at the point of zero charge by using a hierarchical multiscale simulation methodology. Partial charges of both bulk and surface atoms from ab initio quantum calculations that take into account bond polarization and electronegativity are used in molecular dynamics (MD) simulations to obtain ion and water concentration profiles for channel widths of 1.1, 2.1, 2.75, and 4.1 nm. The interfacial electron density profiles of simulations matched well with that of recent X-ray reflectivity experiments. By simulating corresponding channels with no partial charges, it was observed that the partial charges affect the concentration profiles and transport properties such as diffusion coefficients and mobilities up to a distance of about 3 sigma(O-O) from the surface. Both in uncharged and partially charged cases, oscillations in concentration profiles of K+ and Cl- ions give rise to an electro-osmotic flow in the presence of an external electric field, indicating the presence of an electric double layer at net zero surface charge, contrary to the expectations from classical continuum theory. I-V curves in a channel-bath system using ionic mobilities from MD simulations were significantly different for channels with and without partial charges for channel widths less than 4.1 nm.