Aqueous organic redox flow batteries have many appealing properties in the application of large-scale energy storage. The large chemical tunability of organic electrolytes shows great potential to improve the performance of flow batteries. Computational studies at the quantum-mechanics level are very useful to guide experiments, but in previous studies explicit water interactions and thermodynamic effects were ignored. Here, we applied the computational electrochemistry method based on ab initio molecular dynamics to calculate redox potentials of quinones and their derivatives. The calculated results are in excellent agreement with experimental data. We mixed side chains to tune their reduction potentials, and found that solvation interactions and entropy effects play a significant role in side-chain engineering. Based on our calculations, we proposed several high-performance negative and positive electrolytes. Our first-principles study paves the way towards the development of large-scale and sustainable electrical energy storage.