In this section the need to use the second derivatives direct algorithm to refine the location of transition state structures obtained in enzymatic systems will be analyzed. The 25 approximate QM/MM transition state structures previously found by means of a reaction coordinate approach for the three mechanisms of racemization of the mandelate and propargylglycolate by Mandelate Racemase enzyme have been refined using the micro-iterative method.
We want to show that the refinement of transition state structures is especially useful to assure that a structure, found as the highest potential energy point on a profile depicted by a particular reaction coordinate, lies in the correct quadratic region. This is more important in those steps of the enzymatic process where the selected reaction coordinate may not reflect quite accurately the geometrical changes taking place in the active site.
The point now is how precise the location of the transition state structures has to be to produce a reliable reaction path. Is the location of the transition state structure as the maximum energy point along an energy profile built up as a function of a conveniently chosen reaction coordinate sufficient or after that the transition state structures have to be refined? The purpose of this section is to use the different reaction channels we have previously found[1] for the racemization of mandelate and propargylglycolate by Mandelate Racemase enzyme to shed some light to that question.
Furthermore, we advance that an accurate exploration of the PES is a useful preliminary task
for free energy computations. As we will see, the choice of a geometrical reaction coordinate for a PMF calculation
cannot be evident without the previous knowledge of the PES.