Zeolites are fascinating and versatile materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange, and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities for maximizing their application performance. This review article intends to summarize the published reports on the applications of molecular simulation in adsorption, separation and diffusion. The theoretical aspects, adsorption thermodynamics, adsorption isotherm were comprehensively studied in relation to the adsorption applications and how the adsorbates' characteristics influence the adsorption. This review comprehensively discusses the theoretical and computational aspects of diffusion of pure components, long chain hydrocarbons or mixture diffusion, including the molecular dynamics simulations and kinetic Monte Carlo. Furthermore, the cation-zeolite-adsorbate interactions are thoroughly examined so as to elucidate the role of cations in zeolites applications and how the cation exchange influences structural dynamics and properties of zeolites. This study also focuses on the role of cations in gas/liquid adsorption and separations. (C) 2017 Elsevier Inc. All rights reserved.