Porous materials have long been a research interest due to their practical importance in traditional chemical industries such as catalysis and separation processes. The successful synthesis of porous materials requires further understanding of the fundamental physics that govern the formation of these materials. In this thesis, we apply molecular modeling methods and develop novel models to study the formation mechanism of ordered porous materials. The improved understanding provides an opportunity to rational control pore size, pore shape, surface reactivity and may lead to new design of tailor-made materials. To attain detailed structural evolution of silicate materials, an atomistic model with explicitly representation of silicon and oxygen atoms is developed. Our model is based on rigid tetrahedra (representing SiO4) occupying the sites of a body centered cubic (bcc) lattice. The model serves as the base model to study the formation of silica materials. We first carried out Monte Carlo simulations to describe the polymerization process of silica without template molecules starting from a solution of silicic acid in water at pH 2. We predicted Qn evolutions during silica polymerization and good agreement was found compared with experimental data, where Qn is the fraction of Si atoms with n bridging oxygens. The model captures the basic kinetics of silica polymerization and provides structural evolution information. Next we generalize the application of this atomic lattice model to materials with tetrahedral (T) and bridging (B) atoms and apply parallel tempering Monte Carlo methods to search for ground states. We show that the atomic lattice model can be applied to silica and related materials with a rich variety of structures including known chalcogenides, zeolite analogs, and layered materials. We find that whereas canonical Monte Carlo simulations of the model consistently produce the amorphous solids studied in our previous work, parallel tempering Monte Carlo gives rise to ordered nanoporous solids. The utility of parallel tempering highlights the existence of barriers between amorphous and crystalline phases of our model. The role of template molecules during synthesis of ordered mesoporous materials was investigated. Implemented surfactant lattice model of Larson, together with atomic tetrahedral model for silica, we successfully modeled the formation of surfactant-templated mesoporous silica (MCM-41), with explicit representation of silicic acid condensation and surfactant self-assembly. Lamellar and hexagonal mesophases form spontaneously at different synthesis conditions, consistent with published experimental observations. Under conditions where silica polymerization is negligible, reversible transformation between hexagonal and lamellar phases were observed by changing synthesis temperatures. Upon long-time simulation that allows condensation of silanol groups, the inorganic phases of mesoporous structures were found with thicker walls that are amorphous and lack of crystallinity. Compared with bulk amorphous silica, the wall-domain of mesoporous silicas are less ordered withlarger fractions of three- and four-membered rings and wider ring-size distributions. It is the first molecular simulation study of explicit representations of both silicic acid condensation and surfactant self-assembly.