In this paper the need to use a second derivatives direct algorithm to refine the location of transition state structures obtained in enzymatic systems has been 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 mandelate and propargylglycolate by mandelate racemase enzyme have been refined using a modified micro-iterative optimization method developed in this work. 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.
Bibliographical noteFunding Information:
We are grateful for financial support from the Spanish ‘Ministerio de Ciencia y Tecnologı́a’ and the ‘Fondo Europeo de Desarrollo Regional’ through project No. BQU2002-00301, and the use of the computational facilities of the CESCA.
- Mandelate racemase reaction mechanisms
- Micro-iterative method
- Quantum mechanical/molecular mechanical transition state structures
- Reaction coordinate approach
- Second derivatives direct optimization method