Abstract
Quantum Mechanics/Molecular Mechanics method is a robust tool in exploring enzymatic processes. Here we explore the influence of the energetic and structural properties with respect to the QM size by studying fluoroacetate dehalogenase, a metal-free enzyme that can catalyze the CF bond cleavage of a small compound fluoroacetate. By expanding the QM sizes from 14 atoms to 723 atoms, we determined the variations of energies and key structural parameters. Using M06-2X functional to calculate energies, an excellent agreement between the “by radius” strategy and “by functional group” strategy was found.
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