Ultrafast Nonadiabatic Fragmentation Dynamics of Doubly Charged Uracil in a Gas Phase

Abstract

A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation of doubly charged gas-phase uracil in collisions with 100 keV protons. The results are in good agreement with ion-ion coincidence measurements. Orbitals of similar energy and/or localized in similar bonds lead to very different fragmentation patterns, thus showing the importance of intramolecular chemical environment. In general, the observed fragments do not correspond to the energetically most favorable dissociation path, which is due to dynamical effects occurring in the first few femtoseconds after electron removal. High-frequency electromagnetic radiation, energetic ions, and electrons can induce chemical changes that are lethal for living systems. For this reason, such radiation sources are often used in cancer therapies, which aim at damaging the DNA of malignant cells. In this field, the use of swift highly charged ions is very promising due to their ability to deposit energy and induce cellular death in very localized areas of deep tumors (a consequence of the wellknown localization of the Bragg peak [1]). These ions can produce DNA damage either directly, through ionization and excitation [1,2], or indirectly, through chemical reactions with the species produced in the aqueous environment. The early stages of damage, which occur during the first few femtoseconds after irradiation and lead to fragmentation of the biomolecule, are far from being understood. To unravel the mechanisms at this early stage, physicists have performed numerous experiments in gas phase (see, e.g., [3][4][5]), in which swift charged ionic projectiles impinge on DNA or RNA bases, sugars, nucleosides, or even biomolecular clusters. In contrast with experiments performed in solution or directly on living systems, gas-phase experiments provide direct and precise information on single collision events. Thus they allow one to unambiguously identify fragmentation channels associated with a given biomolecule and not with the environment. Such detailed information can be achieved by combining techniques that are state of the art in gas-phase chemistry, e.g., high resolution mass spectrometry, and in collision physics, such as multicoincidence detection techniques that provide the correlation between different charged fragments as well as their relative kinetic energies and momenta.Fragmentation results from relaxation of the excess electronic energy associated with vacancies created in the different electronic shells of the molecule. Since, in these collisions, electrons can be removed from many of these shells, experiments cannot tell us how fragmentation depends (i) on the shape or energy of the molecular orbital (MO) in which the electron vacancies are created and (ii) on the intramolecular environment, i.e., on the neighboring functional groups. This information can only be obtained from ab initio molecular dynamics (MD) calculations such as those based on time-dependent density functional the...

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