We report that two molecular building blocks differ only by two protons, yet they form totally different nanostructures. The protonated one self-organized into hollow nanospheres (~200 nm), whereas the one without the protons self-assembled into rectangular plates. Consequently, the geometrically defined nanoassemblies exhibit radically different properties. As self-assembly directing units, protons impart ion-pairing and hydrogen-bonding probabilities. The plate-forming nanosystem fluoresces weakly, probably due to energy transfer among chromophores (Φ < 0.2), but the nanospheres emit strong yellow fluorescence (Φ ≈ 0.58-0.85).