Primary Effects of X-ray and Photo-Absorption Induced Excitations in Biomolecules

Abstract

To see whether single molecule scattering experiments can yield atomic resolution structures of biomolecules, it is necessary to understand the physics underlying the radiation damage processes induced by the X-ray radiation. The first part of this work is concerned with the electron dynamics during the Auger decay as part of the radiation damage processes in single molecule scattering experiments. To test if Hartree-Fock theory suffices to describe auto-ionization processes like the Auger decay, we simulated the electron dynamics in a one-dimensional model system and a beryllium atom after instantaneous core-shell ionization using time-dependent Hartree-Fock theory. The simulations employed both numerical grids as well as B-splines. In a model system containing six particles the initially created core-hole is refilled during the electron dynamics. But no clear emission of a particle into the continuum occurred. During the electron dynamics in a beryllium atom, however, neither a refilling of the initially created core-hole nor the emission of a particle was observed. As two different, flexible basis sets were used it is likely to be the limitation of Hartree-Fock theory causing the absence of the Auger process in the simulations. In addition, we used the approach described above to simulate the electron dynamics after instantaneous valence-shell ionization in two small organic molecules. The electron dynamics exhibit a diffusion-like behavior of the valence hole. These dynamics, however, do not reproduce the charge migration dynamics predicted by correlated ab-initio methods. To compare different hopping algorithms and to validate previous simulation results, excited state molecular dynamics simulations of the photo-isomerization dynamics of a small retinal model and the photo-active yellow protein were per- formed in the second part of this thesis. In the retinal model small differences in the excited state lifetimes and quantum yields are observed among the different hop- ping algorithms. The simulations of the photo-active yellow protein chromophore yield a photo-isomerization pathway that agrees with the isomerization pathway previously predicted. There is, however, a large difference in the excited state life- times among the hopping algorithms. Additionally, the excited state molecular dynamics simulations are used to study the molecular dynamics induced excita- tion energy transfer in a small bi-chromophoric molecule. The molecular dynamics simulations together with ab-initio calculations indicate that molecular dynamics on different nonadiabatically coupled potential energy surfaces can explain the ex- citation energy transfer from one chromophore to another. This offers a different explanation of excitation energy transfer processes in small molecules compared to Förster and Dexter theory.