Licentiate seminar: Electron and ion dynamics in organic molecules: Connecting theory with experiments

Abstract

Organic molecules can be found everywhere, from macromolecular systems as building blocks or workhorses in living cells to carbon-containing compounds such as methane, abundant both in the Earth’s crust and in the atmosphere. Upon X-ray radiation, such molecules respond differently depending on their local electronic and ionic environment. Energy that is absorbed has the potential to be utilized, as demonstrated by the functionality of photovoltaic cells. However, it can also result in detrimental effects, such as the alteration of the molecular structure due to radiation-induced damage. This work focuses on small organic molecules and how we can use theoretical models and experimental data to understand ultrafast electronic processes during photoabsorption and ionization. The research employed a theoretical framework utilizing Density Functional Theory-based software to perform calculations of Near-Edge X-ray Absorption Fine Structure spectroscopy (NEXAFS) in order to investigate the electronic environment of the initial virtual molecular orbitals within the system under investigation. This method has been used in three projects: i) X-ray induced fragmentation of the amino acid dimer cystine, ii) Fragmentation study on iodine-doped nitroimidazoles, iii) Photoabsorption analysis of triphenylamine (TPA) adsorbed on gold. Born-Oppenheimer-based molecular dynamics was performed to study the integrity of atomic bonds and the dynamics of generated fragments as function of charge state. Additionally, X-ray induced molecular fragmentation has been studied experimentally by means of electrospray ionization (ESI) and an ion trap. The combined effort of theoretical calculations and experimental data show varying integrity of the disulfide bond in cystine as function of photon energy. This is an important realization due to the stabilizing effect which the sulphur-sulphur bond has in proteins. The generated fragments from irradiating across several absorption edges in nitroimidazole-based radiosensitizers was similar for all investigated edges. Furthermore, their generation of sensitization-relevant species such as NO2 continued to stay high after enhancing the photon-molecule cross-section with high-z elements. These results suggests that further improvements to the nitroimidazole system is possible and should be done. Lastly, TPA, a component used in organic solar cells showed a new feature in the pre-edge region in the NEXAFS spectrum upon adsorption to a gold surface. A number of new electronic states fill the energy gap between lowest unoccupied and highest occupied orbitals. The implications of these findings are significant for the design of molecular nanoelectronic devices that rely on donor systems that share similar characteristics.