QM/MM study of the S2 to S3 transition reaction in the oxygen-evolving complex of photosystem II

Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn 4 CaO 5 cluster in photosystem II

“…Different protonation states at W2 and O5 as well as high-and low-oxidation states of the Mn ions were assumed in the constructed models (Table 1). Model 1 (W2/O5 = H 2 O/O 2− ) and model 2 (W2/O5 = OH − /O 2− ), which both have high-oxidation states, have been used in many previous DFT and QM/MM studies (10,14,16,(18)(19)(20)22), whereas model 3 (W2/O5 = OH − /H 2 O) and model 4 (W2/O5 = H 2 O/OH − ) have low-oxidation states that previous DFT calculations suggested could fit to the 1.9-and 1.95-Å structures, respectively, revealed by X-ray crystallography (12). A model of a Ca-depleted WOC with the same protonation and oxidation states as model 1 was also calculated (model 5) (Fig.…”

“…It is, thus, possible that the W3 and W4 attached to Ca 2+ are involved in proton release in water oxidation, especially during the S 2 →S 3 transition, which is inhibited by Ca 2+ depletion (53). It has also been proposed that W3 moves to Mn 4 during the S 2 →S 3 transition in the so-called oxo-oxyl mechanism (13,17,22). Thus, the carboxylate ligands bridging Mn and Ca ions may play an important role in water oxidation by tuning the reactivity of water ligands on Ca by charge shifts via their π conjugation.…”

“…High-spin states were assumed in calculations. The protonation states of W2 and O5 were assumed to be H 2 O, OH − , or O 2− following previous studies (10,(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24).…”

“…With the information of atomic coordinates from high-resolution X-ray structures of the WOC, quantum chemical calculation is now a very powerful method in investigation of the water oxidation mechanism (10,(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). Calculations using the density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) methods can be used to predict individual S-state structures and hence, the reaction scheme.…”

The MOD-QM/MM Method

“…In particular, hybrid quantum mechanics/molecular mechanics (QM/MM) methods have become available in popular software packages and are routinely applied in studies of catalytic complexes embedded in enzymatic macromolecular structures (Bakowies & Thiel, 1996; Dapprich, Komaromi, Byun, Morokuma, & Frisch, 1999; Field, Bash, & Karplus, 1990; Humbel, Sieber, & Morokuma, 1996; Luber et al, 2011; Maseras & Morokuma, 1995; Murphy, Philipp, & Friesner, 2000b; Pal et al, 2013; Philipp & Friesner, 1999; Shoji, Isobe, & Yamaguchi, 2015a; Shoji et al, 2015b; Singh & Kollman, 1986; Svensson et al, 1996; Vreven & Morokuma, 2000a, 2000b; Warshel & Levitt, 1976). QM/MM methods significantly expand the scope of quantum mechanical calculations to much larger systems by limiting the quantum mechanical description (typically based on density functional theory (DFT)) to a subsystem where chemical reactivity is localized (QM layer), while the “spectator” region is usually treated with an inexpensive model chemistry such as classical molecular mechanics force fields, or a lower level of electronic structure theory (eg, semiempirical methods).…”