Mesoporous and nanostructured zeolite-Based catalysts experience prolonged lifetimes due to increased mass transfer and reduced micropore obstruction by coke formation as compared to their bulky microporous counterparts. Diquaternary ammonium structure-Directing agents (SDAs) can be used to synthesize hierarchical MFI sheet-Like and MEL needle-Like zeolites. An explanation of the underlying molecular-Level details of the synthesis of these nanostructured zeolites is presented on the basis of non-Covalent interactions between the template and zeolite surfaces as well as silicate oligomers studied by means of classical molecular dynamics. Use was made of Si 11 and Si 33 silicate oligomers that contain structural features of the framework to be formed as originally proposed by the Leuven group. Molecular recognition is driven by a combination of strong electrostatic and weaker dispersion interactions. An analysis of the early stage of zeolite formation is necessary, as the template adsorption energies in the fully formed zeolite crystals cannot explain the preferential growth of the MFI sheets or MEL needles. Specifically, it is found that the differences in dispersion interactions between the SDA alkyl chains and the silicate oligomers are decisive in the formation of particular zeolite structures.