By varying the metal center, organic linker, functional group and framework topology, a series of MOFs (IRMOF1, Mg-IRMOF1, Be-IRMOF1, IRMOF3-(NH2)4, IRMOF10, IRMOF13, IRMOF14) are systematically examined for CO2 storage using Monte Carlo simulations. The affinity with CO2 is enhanced by adding functional group, the constricted pore is formed by interpenetrating framework; both lead to a larger isosteric heat and Henry constant and subsequently a stronger adsorption at low pressures. The organic linker plays a critical role in tuning the free volume and accessible surface area, and largely determines CO2 adsorption at high pressures. As a combination of open framework and low density, IRMOF10 and IRMOF14 exhibit higher capacity than other MOFs and even surpass the experimentally reported highest capacity in MOF-177. The gravimetric and volumetric capacities at high pressures correlate well with the framework density, free volume, porosity and accessible surface area of MOFs. These molecular-based structure-function correlations are useful for a priori prediction of CO2 capacity and for rational screening of MOFs toward the high-efficacy CO2 storage. Using Monte Carlo and molecular dynamics simulations, separation of CO2 and CH4 mixture in three different nanomaterials, namely, silicalite, C168 schwarzite and IRMOF-1 is compared. The permselectivity based on adsorption and self-diffusivity in the mixture is marginal in IRMOF-1 and greatest in C168 schwarzite. Although IRMOF-1 has the largest storage capacity for CO2, its selectivity is not satisfactory.