  The room temperature pump-probe X-ray free electron laser (XFEL) measurements
used for serial femtosecond crystallography provide remarkable information
about the structures of the catalytic (S-state) intermediates of the
oxygen-evolution reaction of photosystem II. However, mixed populations of
these intermediates and moderate resolution limit the interpretation of the
data from current experiments. The S3 XFEL structures show extra density near
the OEC that may correspond to a water/hydroxide molecule. However, in the
latest 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 model
for the S2-to-S3 state transition, allowing structural changes and the
insertion of an additional water/hydroxide. Based on our model, water/hydroxide
addition to the oxygen-evolving complex (OEC) is not thermodynamically
favorable 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 the
S2 g = 4.1 structure. Then, electrostatic interactions support protonation of
D1-H190 and deprotonation of the Ca2+-ligated water (W3) with proton loss to
the lumen. The W3 hydroxide moves toward Mn4, completing the coordination shell
of 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-E189
in the S2 g = 4.1 and S3 structures. In the S3 state in the population of
protonated D1-E189 increases.
