The microstructure of silica in basic aqueous solutions containing organic cations and prepared from monomeric precursors is reviewed and interpreted within the context of classical ideas of self-assembly of molecular aggregates. The solution properties can be understood by using the pseudo-phase separation approach coupled to the acid-base chemistry of silanol groups and the Poisson-Boltzmann equation. The silica nanoparticles frequently observed in these systems have a core-shell structure with silica in the core and the organic cations at the shell. Individual particles are observed when the forces between particles are repulsive-as is the case for small cations such as tetramethylammonium or tetrapropylammonium-and extended structures such as M41S materials are formed when the forces are attractive--as is the case for surfactants such as cetyltrimethylammonium. These ideas are useful to understand the evolution of zeolite synthesis gels from nucleation to crystal growth. Although at room temperature the silica and the organic cations are segregated, upon heating the organic cations are embedded within the particles. This transformation signals the onset of structure direction whereby the size and geometry of the organic cation induce changes in the structure of silica that may lead to zeolite nuclei.