A computational study of dissociation pathways in highly ionized molecules

Sammanfattning: Proteins are one of the most important molecules in biology. The wide range of functions of different proteins is also important for medical physics. Proteins are assembled by amino acids. These amino acids are connected by peptide bonds to form a protein. The function of a protein is decided by the composition and configuration of peptides, amino acids and their peptide bonds. Successful experiments with Xray Free-electron laser has lead to progress in structural biology, however there is still a need to crystallized samples in these experiments. In this project we have investigated three amino acids. These three amino acids are included in several protein that are hard to crystallize, glycine, valine and alanine. We have investigated their separate interatomic bonds by performing density functional calculations and evaluating the susceptibility of the bonds breaking in a typical time range of Xray Free-electron laser pulses. The results shows the fast dissipation of hydrogen atoms, bond shifting within the molecules during certain ionization degrees and the dissociation of the protein backbone after 20 fs.