Sung, J.-Y.; Antill, L. M.; Cheong, J.-H.

Mitochondrial complex I is a major source of reactive oxygen species (ROS), but whether radical pair spin dynamics contribute to the regulation of ROS associated reactions remains unknown. Here we integrate cryo electron microscopy structure guided oxygen sampling with radical pair quantum dynamics to determine how the molecular architecture surrounding flavin mononucleotide (FMN) shapes modelled spin dependent radical pair reaction yields. Monte Carlo sampling revealed a broad ensemble of sterically accessible oxygen configurations, whereas spin sensitivity was concentrated within a restricted near-contact region centred at approximately 3.3, 3.4 from the FMN reference centre. This localisation was defined by the integration of structural accessibility with magnetic field and spin dephasing sensitivities and spatially overlapped with an exchange hyperfine crossover regime favourable for singlet triplet interconversion. Simulations of structural fluctuations further show that equivalent perturbations generated greater variability in singlet reaction yields within a hotspot than outside it, identifying a localized regime of enhanced structural responsiveness. These results suggest that the FMN binding pocket may act as a structure-dependent amplification layer that converts small changes in radical pair geometry into heterogeneous spin dependent reaction outcomes. Our findings establish a framework linking experimentally resolved protein architecture to radical pair spin dynamics and identify structural constraints that may shape spin-dependent ROS chemistry in mitochondrial complex I.