Exploring the Multidimensional Free Energy Surface of Phosphoester Hydrolysis with Constrained QM/MM Dynamics

The mechanism of the hydrolysis of phosphate monoesters,
a ubiquitous
biological reaction, has remained under debate. We here investigated
the hydrolysis of a nonenzymatic model system, the monomethyl phosphate
dianion, by hybrid quantum mechanical and molecular mechanical simulations.
The solvation effects were taken into account with explicit water.
Detailed free energy landscapes in two-dimensional and three-dimensional
space were resolved using the multidimensional potential of mean constraint
force, a newly developed method that was demonstrated to be powerful
for free energy calculations along multiple coordinates. As in previous
theoretical studies, the associative and dissociative pathways were
indistinguishable. Furthermore, the associative pathway was investigated
in great detail. We propose a rotation of an O–H bond in the
transition between two pentacoordinated structures, during which an
overall transition state was identified with an activation energy
of 50 kcal/mol. This is consistent with experimental data. The results
support a concerted proton transfer from the nucleophilic water to
the phosphate group, and then to the leaving group.