Towards the goal of defining a molecular charge similarity index which best quantifies the concept of molecular similarity as it relates to biological activity, the authors have evaluated a variety of definitions of the molecular charge distribution function, sigma, for use in the charge similarity index formalism. Spatially distributed nuclear charges are incorporated into electron distribution functions to approximately account for the screening of core electronic charge and to model the net effect of the total charge distribution in a manner that better reflects the inherent relation to the molecular electrostatic potential. The resulting charge similarity indices are evaluated based on their sensitivity to relative molecule displacement and their ability to meaningfully group or order a simple set of molecular structures: CH3CH2CH3, CH3OCH3 and CH3SCH3.