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Molecular design of redox-active materials with higher solubility and greater redox potential windows is instrumental in enhancing the performance of redox flow batteries Here we propose a computational procedure for a systematic evaluation of organic redox-active species by combining machine learning, quantum-mechanical, and classical density functional theory calculations. 1,517 small quinone molecules were generated from the building blocks of benzoquinone, naphthoquinone, and anthraquinone with different substituent groups. The physics-based methods were used to predict HOMO-LUMO gaps and solvation free energies that account for the redox potential differences and aqueous solubility, respectively. The high-throughput calculations were augmented with the quantitative structure-property relationship analyses and machine learning/graph network modeling to evaluate the materials’ overall behavior. The computational procedure was able to reproduce high-performance cathode electrolyte materials consistent with experimental observations and identify new electrolytes for RFBs by screening 100,000 di-substituted quinone molecules, the largest library of redox-active quinone molecules ever investigated. The efficient computational platform may facilitate a better understanding of the structure-function relationship of quinone molecules and advance the design and application of all-organic active materials for RFBs.