Zeolites represent a major cornerstone of today’s energy industry as the most-used petrochemical catalyst by weight in the world. Constituted by tetrahedra of T-atoms including Si, Al, Ge and Ti, zeolites form a huge family of nano-porous crystalline materials which also provide reliable candidates for novel, energy related applications such as efficient separations, hydrogen-purifying/storing and conversions from biomass to biofuel. However, the formation mechanism of zeolite is still not clear, as synthesis processes are complicated by requirements including structure directing agents (SDAs), hydroxide or fluoride medium, and experimental conditions like temperature. Attempts for designing new zeolite structures still fall in the trial-error loop. The application of fluoride method in zeolite synthesis has yielded many high-silica, defect-free zeolites with entirely new framework structures. However, knowledge of roles played by fluoride is still limited. 2 hypotheses have been proposed in previous studies that fluoride can play the charge directing role for composite building units (CBUs) like double-4-rings (D4Rs) and balance positive charges introduced by organic structure directing agents (OSDA). Our work here tested and supported these 2 hypotheses and further applied them to study key structures in zeolite processing and formation. Density functional theory (DFT) simulations with periodic boundary conditions have been widely applied in studying properties and structures of zeolites. Raman spectroscopy has been applied as a powerful tool for probing medium-range structures in a variety of materials including disordered silica and zeolites and can provide additional information of zeolites to other techniques including X-ray diffraction (XRD) and nuclear magnetic resonance (NMR). Collaborating with experimentalists, we constructed models closely representing experimental systems and our calculated results based on periodic DFT simulations have good agreement with experiments in terms of Raman spectroscopy and NMR chemical shifts.