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This research mainly focuses on the computational modeling of 2D- Metal and Covalent Organic Frameworks using Quantum Mechanics, Monte-Carlo, hybrid QM/MM, and Molecular Dynamics simulations to investigate their gas adsorption, and thermal properties. In this work, the interlayer slipping effect and the nature of metals on gas adsorption in 2D-Phthalocyanine MOFs have been systematically studied. It is found that the binding strengths and adsorption capacities of MOFs are drastically increased upon shifting the top layers to the energetically stable offsets. For example, the NO adsorption capacity of the slipped-AA structure is approximately 0.69 times higher than the perfect stacked (eclipsed) geometry. The nature of metal (at nodal position) has a remarkable effect on the adsorption properties of eclipsed-AA structures, however, this effect is almost negligible in slipped-AA structures. For example, the NO adsorption capacity difference between Ni and Cu in eclipsed-AA is nearly 100 mg/g, however, it is reduced to 2 mg/g in slipped-AA structures (at 298 K and 75 bar). The thermal conductivity (k) of BBO COFs over a wide range of temperatures (800-300 K) is investigated using Non-Equilibrium Molecular Dynamics simulations. The k values of BBO-COFs are as high as 0.326 W/mK at 300 K, depending on the size of the unit cell. Hybrid QM/MM simulations for modeling bulk enzymes on 2D TpAzo-COF are systematically investigated, indicating the porous site of COF is an energetically suitable site for binding. The 2D TpSMe-DPP COF to serve as a scaffold for mercury adsorption is demonstrated and found that the thioether and imine functional groups facilitate the soft metal binding. Lastly, the transition state searches for the bis-imine and benzimidazole formations are demonstrated to synthesize the 1D-COFs with suitable SBUs. The COF formation with a small benzaldehyde unit is adequate, whereas, the complexity is increase upon increasing the size of SBUs.