Various MO methods with differing degrees of sophistication are shown to yield qualitatively consistent results for methyl isoalloxazins. However, with crude methods such as the HMO and ${omega}$-technique, the choice of Coulomb and resonance integralsis critical, in contrast with simpler molecular systems. The empirical value of ${omega}$=0.5 appears to be more reasonable than 1.4. Methyl groups in these flaving are best treated by the group orbital approximation. The pseudo-heteroatom approximation overestimates methyl hyperconfiguration with the Pariser-Parrpole SCR MO method. siglet ${pi}{ ightarrow}{pi}^*$ transition energies are calculated by the P-P-P method and agree reasonably with the experimental values. 2- and 4-Thioisoalloxazine analogs are also treated. Reactivity indices of the flavin molecule are presented, includeing superdelocalizability. frontier orbital and radical densities. Various aspects of the applications of these indices of the methyl groups on dipolemoments, inozation potentialsm elctron affinities, and spectra are decribed in detail.