Comparison between Mandelate Racemase mechanism structures

All the structures found by the micro-iterative method correspond to the same chemical step found with the coordinate scan method described in section 2.3. However, we have been able to locate another intermediate for the mechanism III in mandelate substrate. The energetic profile would be as figure 3.5.

Figure 3.5: New energy profile for mechanism III for the racemization of mandelate substrate after the refinement.

So in this new case the mechanism III turns out to be a symmetric mechanism step. The central TS is the configuration inversion S$\to$R, and the two intermediates are due to a weak stabilization of the carbanion with the conjugate acid. These shallow minima have few chemical meaning and they probably due to a recognized failure of PM3 semiempirical Hamiltonian. In conclusion, they will not be included in the following discussion and then the mechanism III for mandelate will be considered practically as a one-step mechanism.