ROS which include free radicals (•OH, O₂•⁻) and hydrogen peroxide act as vital components in cell signaling mechanisms and oxidative stress development. At pathological levels, ROS contribute to inflammation, neurodegeneration, and cancer. The neutralization of ROS by flavonoids occurs through three mechanisms which can be quantum-chemically adjusted: (1) strong binding interactions (ΔE < −4.5 eV), (2) efficient electron transfer (small HOMO-LUMO gaps < 2.8 eV), and (3) high charge donation (>0.35 e). The research employs DFT and molecular dynamics to enhance the six flavonoid subclasses. The ROS scavenging properties of Flavonols and anthocyanidins are superior because of their conjugated π-systems (−5.1 eV ΔE), appropriate electronic gaps (2.4–2.6 eV), and catechol-assisted charge transfer (0.42–0.45 e). The placement of hydroxyl groups in space determines how radicals become stabilized through distinct structural arrangements which lead to faster •OH quenching than non-conjugated structures. The Flavone molecule achieves the lowest optimized energy value of 150.9 kJ/mol which demonstrates its superior thermodynamic stability while Flavanols (1.800 D) and Flavonols (1.758 D) exhibit the highest dipole moments that indicate better water solubility and polarity. Our predictions also include the formation of a stable adduct by combining allicin with a flavonoid. The analysis of electrophilic sulfur sites and nucleophilic oxygen sites predicts superior antioxidant and metal-chelating properties than the individual compounds.