Quantum chemical modeling of energy flow and photoprotection in photosystem II

Photosystem II (PSII) functions as a dynamic supramolecular machine in plants, balancing efficient light harvesting with photoprotection under fluctuating illumination. Its 300 pigments, arranged in antenna complexes around the reaction centers (RCs), form an extended excitonic network whose functional organization and regulation remain poorly resolved. Here, we present a comprehensive atomistic model of the PSII supercomplex C 2 S 2 M 2 , constructed using polarizable quantum mechanics/molecular mechanics (QM/MM) calculations, to elucidate excitation energy transfer under both light-harvesting and photoprotective regimes. Our results show that efficient energy funneling to the RCs is mediated by two primary energy transfer pathways, which involve the terminal emitter domains of each antenna complex and span the two PSII monomers. Finally, we demonstrate that the switch to the photoprotective regime requires the simultaneous activation of more than two quenching sites per RC.