Figure 3.

The initial (dashed lines) and final (solid lines) strings from the three sets of simulations with Mg²⁺ bound at the catalytic site: A (green, initial path is a concerted mechanism), B (purple, initial path is sequential with a proton transferred intermediate), and C (red, initial path is sequential with a phosphorane intermediate). The three initial paths are depicted in Figure 1, but the final paths all correspond qualitatively to pathway A in Figure 1. The strings are projected in the space of the collective coordinates (r1 – r2) and (r3 – r4), corresponding to the proton transfer reaction to the O5′ and the oxygen–phosphorus bond breaking/forming, respectively. The strings from sets A and C have converged to a similar path. The string from set B is still evolving, as described in the text, but is already close to the converged strings from A and C.