First, we compare the H-bonding between CV + and methanol obtained from 60 ps of QM/MM AIMD and from 60 ps of QUBEKit FFMD trajectories. The two amine groups of CV + are the sites of H-bonding with methanol solvent molecules (note that no H-bonding at the oxygen or nitrogen of the center ring was observed in any of the MD simulations). In both trajectories, the hydrogens of the amine groups form strong H-bonds to the oxygen of the methanol molecules that are peripheral to the chromophore. Analysis of this peripheral Hbonding shows a stable H-bond formed to all four amine hydrogens, with the identity of the H-bonding methanol molecule not changing throughout the 60 ps trajectory. The average distance of the peripheral H-bond (the distance between the amine hydrogen and the methanol oxygen), shown over time in Figure , is 1.54 ± 0.13 Å for QM/MM AIMD compared to 1.70 ± 0.17 Å for QUBEKit FFMD, indicating a stronger bond with the QM/MM model compared to the QUBEKit FF MM only model.