Two azo functionalized Zn(II)-based MOFs, {[Zn(SDB)(3,3'-L)0.5]·xG}n, IITKGP-13A, and {[Zn2(SDB)2(4,4'-L)]·xG}n, IITKGP-13B (IITKGP stands for Indian Institute of Technology Kharagpur), have been constructed through the self-assembly of isomeric N,N'-donor spacers (3,3'-L = 3,3'-azobispyridine and 4,4'-L = 4,4'-azobispyridine) with organic ligand 4,4'-sulfonyldibenzoic acid (SDBH2) and Zn(NO3)2·6H2O (G represents disordered solvent molecules). Single-crystal X-ray diffraction studies reveal the 2D structure with sql topology for both MOFs. However, the subtle change in positions of coordinating N atoms of spacers makes IITKGP-13A noninterpenetrated, while IITKGP-13B bears a 2-fold interpenetrated structure. IITKGP-13A exhibits higher uptake of CO2 over CH4 and N2 with high IAST selectivities for mixed CO2/CH4 (50:50, biogas) and CO2/N2 (15:85, flue gas) gas systems. In contrast, IITKGP-13B takes up very low amount of CO2 gas (0.4 mmol g-1) compared to IITKGP-13A (1.65 mmol g-1) at 295 K. Density functional theory (DFT)-based electronic structure calculations have been performed to explain the origin of the large differences in CO2 uptake capacity between the two MOFs at the atomistic level. The results show that the value of the change in enthalpy (ΔH) at 298 K temperature and 1 bar pressure for the CO2 adsorption is more negative in IITKGP-13A as compared to that in IITKGP-13B, thus indicating that CO2 molecules are more favored to get adsorbed in IITKGP-13A than in IITKGP-13B. The computed values for the Gibbs' free energy change (ΔG) for the CO2 adsorption are positive for both of the MOFs, but a higher value is observed for the IITKGP-13B. The noncovalent types of interactions are the main contribution toward the attractive energies between the host MOF frameworks and guest CO2 molecules, which has been studied with the help of energy decomposition analysis (EDA).