University of Extremadura, Badajoz
21 December 2004
In the last decades, computational chemistry has become a highly important tool for the study of the properties of matter. Condensed phase systems—especially in liquid phase—present, however, a series of features that make it necessary to develop specific methods and to introduce additional approximations, besides those usually employed for gas phase systems. This thesis focuses on one of these methods, called asep/md (Averaged Solvent Electrostatic Potential from Molecular Dynamics) and developed by our research group.
The asep/md method has been enhanced to allow the optimization of molecular structures in solution, for which it is needed to have available the free energy derivatives with respect to the nuclear coordinates. As a complementary work, a method for the calculation of free energy differences has been established and the validity of the mean field approximation has been verified quantitatively. A computer program implementing the theoretical development has been created as well.
Some practical applications have also been performed. The mean field approximation validity has been tested with simple systems, such as liquid alcohols and aqueous solutions of carbonyl compounds. The right behavior of the geometry optimization method has been checked with simple molecules too: water, methanol and formamide. A more detailed study has been performed on the anomeric equilibruim of a monosaccharide, D-xylopyranose, and on an SN2 reaction, the Menshutkin reaction between NH3 and CH3Cl. Finally, the dynamics of the isomerization of triazene (N3H3) in water has been studied with a combined application of asep/md and a traditional qm/mm method.
- Dissertation in pdf format:
tesis.pdf [4.3 MiB] (in Spanish)
- Slide presentation in pdf format:
presentacion.pdf [4.0 MiB] (in Spanish)
- Movies for the presentation in avi (DivX 4) format:
tray-040.avi [1.5 MiB], tray-520.avi [1.6 MiB]
- fortran 90 code
for the asep/md
program, compressed in zip format:
asep-md.zip [42.8 KiB]
- All data in an iso
image for a cute cd:
tesis.iso [12.0 MiB]