The interface interactions between surfactants oleic acid and oleylamine and magnetic nanoparticles are studied via molecular mechanics and dynamics. Mixtures of these two surfactants are widely advocated in the chemical synthesis of nanoparticles. However, the exact dynamic mechanism remains unclear. Here we report, for the first time, a comprehensive qualitative model showing the importance of acid-base complex formation between oleic acid and oleylamine as well as the presence of free protons in the engineering of nanoparticles of specific shapes and sizes. We show why critical parameters such as surfactant concentration may modify iron oxide nanoparticle shape and size and how this can be understood in the light of acid-base complex pair formation. We report on the influence these parameters have on both the in situ nanoparticle surface charge and zeta potential. Transmission electron microscopy (TEM), FTIR, and pH studies are used to confirm the validity of the calculated binding energies and number of acid-base pairs.