Molecular modelling methods, including Simulated Annealing/Energy Minimization, Molecular Dynamics and Density Functional Theory are used to probe the nano-structures and aggregation mechanisms involved in the nucleation of two classes of inorganic material: microporous silicas and the II/VI semiconductor, ZnS. Simulations reveal a new structural chemistry for nano-particulate ZnS and provide insight into the pre-nucleation mechanisms of both classes of material. Studies of the silica systems emphasize the importance of including the effects of solvation and pH.