A comparison of first principles density functional (DV-X alpha) electronic structure calculations for six clusters of the general form [Mo(6)Cl(8)(i)L(6)(a)](n) (n = 0, -1, -2) is presented. Substitution of different neutral and anionic axial ligands (L(a)), such as Cl-, Br-, I-, PR(3), and 4,4’-bipyridine, significantly affects calculated electronic structure and experimentally determined optical transitions of the clusters. In the extreme case, the model of two cluster units bridged by a 4,4’-bipyridine ligand predicts a band-type structure with facile charge transport between metal cores. DV-Xa results also predict a closed-shell ground state configuration and a dipole-forbidden LUMO to HOMO transition for the [(Mo6Cl8Y6a)-Y-i](2-) (Y = Cl, Br, I) clusters, which is thought to cause the unusually long-lived excited states of these species. Effects of electronic relaxation, spin-spin, and spin-orbit coupling on the symmetry and energy of the excited state are discussed. Trends in HOMO/LUMO characteristics, net atomic charges, Mulliken populations, and density of states distributions are examined. General trends in predicted absorption energies are corroborated by experimental values, but more precise values will require study of excited state geometry.