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The room temperature pump-probe X-ray free electron laser (XFEL) measurementsused for serial femtosecond crystallography provide remarkable informationabout the structures of the catalytic (S-state) intermediates of theoxygen-evolution reaction of photosystem II. However, mixed populations ofthese intermediates and moderate resolution limit the interpretation of thedata from current experiments. The S3 XFEL structures show extra density nearthe OEC that may correspond to a water/hydroxide molecule. However, in thelatest structure, this additional oxygen is 2.08 {\AA} from the Oe2 of D1-E189,which is closer than the sum of the van der Waals radii of the two oxygens.Here, we use Boltzmann statistics and Monte Carlo sampling to provide a modelfor the S2-to-S3 state transition, allowing structural changes and theinsertion of an additional water/hydroxide. Based on our model, water/hydroxideaddition to the oxygen-evolving complex (OEC) is not thermodynamicallyfavorable in the S2 g = 2 state, but it is in the S2 g = 4.1 redox isomer.Thus, formation of the S3 state starts by a transition from the S2 g = 2 to theS2 g = 4.1 structure. Then, electrostatic interactions support protonation ofD1-H190 and deprotonation of the Ca2+-ligated water (W3) with proton loss tothe lumen. The W3 hydroxide moves toward Mn4, completing the coordination shellof Mn4 and moving with its oxidation to Mn(IV) in the S3 state. In addition,binding additional hydroxide to Mn1 leads to a conformational change of D1-E189in the S2 g = 4.1 and S3 structures. In the S3 state in the population ofprotonated D1-E189 increases.

Thermodynamics of the S2-to-S3 State Transition of the Oxygen-Evolving Complex of Photosystem II