The link between M41S mesoporous silicates and all-silica zeolites during the initial stages of synthesis is analyzed with small-angle scattering and conductivity experiments. The phase behavior of silica in aqueous solutions is studied for a family of quaternary ammonium hydroxides, from tetramethylammonium to dodecyltrimethylammonium. All solutions exhibit a critical aggregation concentration at a 1:1 SiO2:[OH−]initial molar ratio with solutions containing short chain compounds forming optically transparent (clear) nanoparticle suspensions, and solutions of long chain compounds phase separating into a solid and a liquid phase. The solid phase is analyzed with X-ray diffraction and thermogravimetric analysis and is found to have a hexagonal structure similar to MCM-41. Mid-sized chain length compounds form solutions containing both the phase separated solid and nanoparticles. In addition to studying phase behavior, the role of attractive hydrophobic interactions is studied using water/ethanol solutions. In ethanolic solutions, the entire family of quarternary ammonium compounds are found to form stable nanoparticle suspensions.