Adsorption in porous materials plays a significant role in industrial separation processes. Here, the host-guest interaction and the pore shape influence the distribution of products. Metal-organic frameworks (MOFs) are promising materials for separation purposes as their diversity due to their building block synthesis from metal corners and organic linker gives rise to a wide range of porous structures. The selectivity differs from MOF to MOF as the size and shapes of their pores are tuneable by altering the organic linkers and thus changing the host-guest interactions in the pores. Using mainly molecular simulation techniques, this work focuses on three types of separations using MOFs. Firstly, the experimental incorporation of calix[4]arenes in MOFs as a linker to create additional adsorption sites is investigated. For a mixture of methane and hydrogen, it is shown that in the calix[4]arene-based MOFs, methane is adsorbed preferentially over hydrogen with much higher selectivities compared to other MOFs in the literature. Remarkably, it was shown that extra voids created by calix[4]arene-based linkers, were accessible to only hydrogen molecules. Secondly, the strong correlation between different pore sizes and shapes in MOFs and their capabilities to separate xylene isomers were investigated for a number of MOFs. Finally, the underlying molecular mechanism of enantioseparation behaviour in a homochiral MOF for a number of chiral diols is presented. The simulation results showed good agreement with experimental enantioselectivity values. It was observed that high enantioselectivity occurs only at high loadings and when a perfect match in terms of size and shape exists between the pore size and the adsorbates. Ultimately, the information obtained from molecular simulations will further our understanding of how network topology, pore size and shape in MOFs influence their performance as selective adsorbents for desired applications.