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Theoretical methods used in this thesis:
Statistical Mechanics

The statistical mechanics can be used to transform our detailed information at microscopic level obtained during the simulation to thermodynamic magnitudes [16,190,191].

There are many macroscopic properties that can be calculated from computer simulation of molecular systems e.g. heat capacity, radial distribution functions or non-equilibrium properties such as diffusion coefficients. However, here we will only give a short perspective to the free energy calculations. Reaction free energy (Helmholtz or Gibbs functions) is the magnitude that describes the spontaneity of thermic processes in NVT and NPT ensembles, respectively, that is, the tendency of molecular systems to associate and/or react. In addition, under the framework of Transition State theory, it will describe the kinetics of such process.


Xavier Prat Resina 2004-09-09