A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.

This paper reports a specific reaction parameter (SRP) PM3/d model for iron that can reproduce the DFT/MM results of the hydrogen abstraction reaction from the C11 position of linoleic acid by the Soybean lipoxygenase-1 enzyme. A suite of nonlinear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic) and direction set minimization algorithms. The PM3/d-SRP Fe parameters are derived along three consecutive steps. The final parameterization step includes the effect of the whole enzyme in order to get a better quantum mechanical/molecular mechanical description.