Fig. 3.

Phosphodiester cleavage reaction: potential of mean force (PMF) profile, transition state structure, and ELF isosurface. (a) The PMF profile for the phosphodiester cleavage reaction is shown. The reaction coordinate ξ is defined as: ξ = (r_O*–P − r_P–OP′). Here, r_O*–P and r_P–OP′ are the distances between the electrophilic P atom, O* is the oxygen atom of the nucleophilic hydroxide, and OP′ is the displaced oxygen atom of the substrate. (b) Displayed is the calculated transition state structure for ξ = 0 along with an ELF isosurface at contour level 0.82. (c) ELF contour profile drawn through the plane of the Zn1, Zn2, and OP′ atoms is shown.