The hydrogen storage (H-storage) capacity of alkali (Li+, Na+ and K+) and alkaline earth metal ion (Mg2+ and Ca2+) doped cubane, cyclohexane and adamantane has been investigated using Density Functional Theory (DFT) based M05-2X functional employing 6-31+G** basis set. The adsorption of number of H-2 molecules on the metal ion doped complexes depends on ionic radii and charge of the metal ions. Among the 15 complexes investigated in this study, Mg2+ ion doped cubane, cyclohexane and adamantane complexes have higher H-storage capacity when compared to other complexes. The calculated binding energy (BE) of 5H(2)@Cub-Mg2+ complex is 46.85 kcal/mol with binding energy per H-2 molecule (BE/nH(2)) of 9.37 kcal/mol. The corresponding gravimetric density of the complexes is 7.3 wt%. In the case of 4H(2)@Cyc-Mg2+ complex, the BE is 32.19 kcal/mol (BE/nH(2) is 8.05 kcal/mol with 6.9 wt % in gravimetric density). The Adm-Mg2+ complexes adsorb 4H(2) molecules with BE of 33.33 kcal/mol, the BE of per H-2 molecule is 8.33 kcal/mol. The corresponding gravimetric density of the complex is around 4.8 wt%, respectively. A new linker modified MOP-9 has been constructed based on the results and their H-storage capacity has also estimated. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.