Preface

I started the writing of this thesis not only to obtain a doctoral degree, but also to compile in a particular way all the work that I have done during all this time. The articles published during these years can only give a short overview of my research task. They may be found in the given references [1,2,3,4,5,6,7]. I decided to give my own perspective of the things I have learnt and the results I have obtained. Some sections are directly the published articles, but some other are not and contain a significative amount of unpublished data.

As you probably have already noticed, English is not my mother language. You may find lots of grammatical mistakes all along this thesis, but I thought that it was preferable to write science in bad english that many people could understand, rather than to write it in my beloved Catalan that unfortunately only few researchers in the scientific community read.

This thesis has four main chapters:

Chapter 1

In this chapter we can find an introduction not only to the methods used in the thesis, but there are also some sections devoted to some other methods. The number of strategies in theoretical chemistry is so big that a wide perspective helps to understand the choice we have done. Moreover, sometimes when a particular method has been modified it is difficult to split the theoretical framework between the standard methodology and our own contribution. This is why some redundancy can be found between the first chapter and the rest of the thesis.

Chapter 2

Here we can find an initial study of Mandelate Racemase enzymatic catalysis with QM/MM methods. An interesting insight is given to the chemistry of this enzyme. However, the complexity of the different reaction mechanisms with different substrates emphasizes the need for additional methods to study Mandelate Racemase reactivity and enzymatic catalysis in general. The work of this section has been published in reference [1].

Chapter 3

This is the main body of the thesis. In this chapter a progressive development of a method to locate stationary points in big systems is carried out. In the first section the equations for minima and transition state search are developed, implemented and tested in small systems. This part corresponds mainly to the reference [2].

The second and third sections are devoted to the development and application respectively of a micro-iterative method. Here the equations implemented in the first section are now coupled to a minimizer in order to find real transition states in enzymatic systems [3], [4].

The work of the last section 3.4 contains unpublished results. We propose, implement and test a strategy to avoid the computational problems that arise in the optimization process when dealing with very big matrices.

All this chapter would have not been possible without the collaboration of Dr. Gérald Monard and Dr. Josep Maria Bofill. I am indebted to them for their help, their time and for all the things they have taught me.

Chapter 4

This last chapter of results contains the calculation of free energy profile corresponding to the Mandelate Racemase reaction. In particular, the potential of mean force is calculated including a wide discussion about the choice of the crucial reaction coordinate according to the previous results obtained in the transition state optimization. The paper corresponding to this section is under preparation[7].

I must thank Dr. Jiali Gao for his help and hospitality during a three months stay at the University of Minnesota. I learnt there the fundamental part of the simulation techniques applied in this chapter.

Appendix

Two appendices conclude the thesis. The first is a brief exposition of several important aspects referring our daily tool, the computer. The second is a route map of the source code that my collaborators and I had to write to carry out the simulations.

This thesis has two main subjects studied explicitly, namely, the applied study of Mandelate Racemase reactivity (chapter 2 and 4) from one part, and the development of methods for optimization of structures in big systems (chapter 3) from the other.

However, both subjects are interrelated. The variety and complexity of Mandelate Racemase mechanisms studied in chapter 2 is the motivation to develop some new tools and it serves as an appropriate system to test the optimization methods of chapter 3. And the knowledge of the optimized structures is very valuable for the posterior study of Mandelate Racemase reaction by molecular dynamics in chapter 4. Therefore, despite some new tools have been developed and they can be exported to other molecular systems, I prefer to include Mandelate Racemase enzyme and its particular chemical problem as the central motivation of my investigation.

Finally I must thank to my directors Dr. Angels González and Dr. Josep Maria Lluch for their patience and the given opportunity to develop my PhD. I thank also Dr. Mireia Garcia, who has been my unofficial third supervisor during an important part of my four years work.

Xavier Prat Resina
Bellaterra, Febrer 2004