Figure 4. The proposed molecular mechanism for epimerization
reaction catalyzed by NocTE. The direct deprotonation path and
re-protonation path Path1 were colored in pink and green. The
abbreviations R, TS, IM and P represented the reactant, transition
state, intermediate and product.
To shed light on the detailed mechanism of this special epimerization,
QM/MM calculations were performed using the cluster model on the basis
of three structure replicas from the dominant cluster of MD simulations.
Geometry optimizations, TS search and IRC calculations were carried out
at the ONIOM (M062X/6-31G*: Amber) level. Then single point energies
were calculated with larger basis set 6-311+G** and SMD solvation model
to obtain more accurate energy profile. The free energy profile and
important TS structures from the representative replica were displayed
in Figure 5. Other minimum structures and two replicas were provided in
Figure S8, Table S4 and Table S5.