Photochemical and photophysical reaction dynamics of chemical and biological systems

Abstract

In this thesis we present a set of theoretical methodologies focused on photophysical and photochemical phenomena, which were implemented and subsequently applied to a collection of chemical and biological relevant systems. The developments and applications are divided in four sections which are: energy transfer, dynamical studies of photoreactivity in biological systems, photochemical response to external forces and finally dynamical behaviour of molecular devices. In the energy transfer section it is tackle the problem of finding which molecular coordinates modulates more efficiently the triplet energy transfer process (i.e. the triplet energy transfer reaction coordinate), together with a dynamical approach to the energy transfer at constant temperature. The photochemical dynamics section firstly deals with the static and dynamical characterization of a minimal molecular model to study the phenomena of chemiluminescence and bioluminescence. Then the preliminary results of the simulations of fluorescence in the IrisFP are shown. Subsequently the photodynamical response to external forces section contains a discussion on the effect of external forces in the reactivity of molecular systems, as well as change of spectroscopic properties. Finally it is considered the design and operation of molecular motors control by light irradiation, where molecular simulations are used as a characterization tool of their properties. Additionally, it was developed a set of programs focused on modularity, parallelism and readability, aiming to perform the numerical simulations described in this thesis.