The aqueous redox flow battery is a promising technology for large-scale low cost energy storage. The rich possibilities for the tailoring of organic molecules and the possibility to discover active materials of lower cost and decreased environmental impact continue to drive research and development of organic compounds suitable for redox flow battery applications. In this work, we focus on the characterization of aromatic molecules with 1,4-diaza groups for flow battery applications. We examine the influence of electron-withdrawing and electron-donating substituents and the effect of the relative position of the substituent(s) on the molecule. We found that electron-withdrawing substituents increased the potential, while electron-donating decreased it, in agreement with expectations. The number of carboxy-groups on the pyrazinic ring was found to have a strong impact on the heterogeneous electron transfer kinetics, with the slowest kinetics observed for pyrazine-2,3,5,6-tetracarboxylic acid. The stability of quinoxaline was investigated by cyclic voltammetry and in a flow cell configuration. Substitution at the 2,3-positions in quinoxaline was found to decrease the capacity fade rate significantly. Furthermore, we demonstrated how molecular aggregation reduces the effective number of electrons involved in the redox process for quinoxalines. This translates to a significant reduction of the achievable volumetric capacity at higher concentrations, yielding values significantly lower than the theoretical capacity. Finally, we demonstrate that such capacity-limiting molecular aggregation may be reduced by introducing flexible side chains with bulky charged groups in order to increase electrostatic repulsion and steric hindrance.