Structural integrity of highly ionized peptides

Abstract: In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.