Post-doc (2004-2005)

In January 2004, being awarded with an EMBO (European Molecular Biology Organization) postdoctoral fellowship, I joint the group of Prof. Pavel Hobza  (currently retired).

During my two years of EMBO post-doc I have tried to diversify my scientific projects:

  • In my first paper as a post-doc and tutoring a student (I. Dabkowska, the first author of the paper), I applied my previous experience in ab initio calculations to the study of nucleic acid base pairs. This work, published in the J. Phys. Chem. A journal has been already cited many times in the last years.
  • Secondly, I have been working in the analysis of the nature of the intermolecular interaction in model systems of hydrated peptides (Valdés et al. Chem. Phys. 2006, 331, 96) in collaboration with the group of Prof. S. Galembeck (University of Sao Paolo, Brazil).
  • Finally, I have been responsible to start and develop a new line of research in the group of Prof. Hobza concerning the theoretical study of isolated peptides containing aromatic side chains, which has constituted the main research of my post-doctoral stay. This project has been carried out in collaboration with Dr. M. Mons (Francis Perrin Laboratory, CNES, France) and Dr. de Vries (University of Santa Barbara, California, USA) whom have significantly contributed to the improvement of the experimental techniques currently used for the study of biomolecules in the gas phase. My research on this topic has included different studies. Among them I would like to point out the first one, published in Chem. Eur. J. and classified as VIP paper, where we reviewed the methodologies employed in the study of isolated small peptides and we suggested a robust and rigorous strategy of calculation applicable to the study of any isolated small peptide. The relevance of this work in the field of biomolecules in the gas phase is also reflected in the fact that it has been many times cited and I have been invited to present it in the Gordon Research Conference in biomolecules in the gas phase (Maine, USA, 2005), in the MIBII (Prague, 2005) and in different seminars of various Spanish universities [Department of Physical and Inorganic Chemistry (University of Valladolid) and Department of Biology and Molecular Biology (University of Barcelona)]. Further, I have studied other peptides where the experimental results were not conclusive enough and where the theoretical contribution became essential for their better understanding. This is for instance the case of WG and WGG peptides, which geometrical structure has been reported for the first time (Valdés et al. J. Phys. Chem. B  2006, 110, 6385). The quality of this publication is reflected in the number of citations received.

The research carried out during my EMBO post-doc has favorably contributed to obtain information that will help to elucidate the reasons that determine the molecular structure of peptides (crucial in their biological function). Additionally, we have carried out an exhaustive and detailed study on the role played by the dispersion forces in the stability of isolated peptides containing aromatic side chains. I would like to mention here that Prof. Pavel Hobza is one of the world wide experts in the field of weak interactions, which he has mostly studied during his fruitful scientific career in molecular complexes and now also in isolated systems. I would also like to point out that some of these projects have been part of the Ph. D. Thesis of Dr. David Reha, whom I have been supervising since my arrival to Prague until his Ph. D. defense.

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