Molecular structure-directing agents (SDAs) have been widely used to synthesize crystalline and nanoporous zeolites that exhibit a wide range of technologically important adsorption, ion-exchange, and/or catalytic reaction properties. In particular, organic species are typically used under alkaline conditions to prepare crystalline silicate, aluminosilicate, or other crystalline frameworks. The resulting structures depend on the molecular composition and architecture of the SDA species used and their interactions with the crystallizing inorganic framework. By varying the properties of the SDA (size, charge distribution, polarity, hydrophilicity, etc.), a wide variety of frameworks have been synthesized, although the specific molecular interactions that govern the formation of different structures are still not well understood. Here, we report results that establish important SDA-framework interactions of two closely related imidazole derivatives, N,N',2-trimethylimidazolium hydroxide and N,N'-diisopropylimidazolium hydroxide, that yield two very different zeolite structures (ITW and MTT respectively), when synthesized in the presence of similar synthesis solutions containing fluoride species. Even though the starting synthesis solutions for both zeolite structures are nearly identical in composition and hydrothermal treatment conditions, very different ITW or MTT zeolite structures are formed, indicating that framework selectivity is governed by the molecular interactions among the SDA molecules, silicate framework, and fluoride anions. Powerful one- and two-dimensional (2D) solid-state ²⁹Si{¹⁹F), ²⁹Si{¹³C}, and ²⁹Si{¹H} HETeronuclear CORrelation (HETCOR) NMR measurements provide detailed and unambiguous information on the molecular interactions among the organic SDA and inorganic framework moieties of these complicated multicomponent systems. In addition, J-coupling-mediated double-quantum-filtered (DQF) ²⁹Si-²⁹Si NMR correlation experiments establish the connectivities among different ²⁹Si tetrahedral sites in the siliceous zeolite frameworks. In combination, these powerful 2D NMR methods provide new means for characterizing local interactions among structure-directing organic species and their different zeolite framework structures, which can consequently be elucidated in unprecedented detail. The results provide new insights on the molecular interactions that are ultimately responsible for imparting structural selectivity in zeolite syntheses.