This investigation reports the molecular properties of metal (M = Mg, Sc, Cu, Zn) doped-fluorinated phthalocyanines (M-FPcs) and their ability to separate and capture CO2 in the presence of H2O using DFT studies. The structural investigations of M-FPcs show that Sc-FPc alone is non-planar while other M-FPcs exhibit a planar geometry. The HOMO-LUMO gap shows that Sc-FPc is least stable and hence more reactive. The DOS plot shows the influence of 3d-orbitals of Sc, Cu and Zn on F-Pc. On interacting M-FPcs with CO2 and H2O, it can be seen that the interaction of H2O is greater than CO2. The trend of CO2 interaction is as follows: Sc > Mg > Zn > Cu. Furthermore, Gibbs free energy for the Sc-FPc + CO2 system shows that the interaction is spontaneous and feasible while for Mg, Cu and Zn FPc the interaction is non-spontaneous. However, H2O spontaneously interacts with all the metal FPcs and destabilizes the systems except for Sc-FPc in which H2O interaction stabilizes the molecule. The calculated adsorption capacity (n) value shows that all the metal-phthalocyanine systems have higher adsorption capacity for CO2 than for H2O. Interestingly, the adsorption of CO2 on Sc-FPc differs by an order of 10(8) with respect to H2O. Furthermore, the adsorption capacity is low for systems having metals with high van der Waals radii. Conclusively, the Sc-FPc is the best-suited material for CO2 separation and capture in the presence and absence of water molecules, respectively.