Theoretical study on the fragmentation dynamics of L-Alanine2+

X-rays are used with both diagnostic and therapeutic (cancer treatment) objectives. The time scale of the fragmentations of biomolecules that may occur after being radiated with X-rays is around 1 to 100 fs. These values are so small that one cannot establish the mechanism of these processes by experimental studies. So, another approach is needed and molecular dynamics (MD) simulations have shown to be successful for this purpose. Co-workers from an experimental group in Turku University have recently performed experiments with X-radiation to ionize the L-alanine. This ionization step leads to fragments which time of flights (ToFs) are recorded in a PEPIPICO (photo- electron photo-ion photo-ion coincidence map). In the present work, we tackle the study of fragmentation of L-alanine2+ in gas phase. We begin with the theoretical study on the energy barriers for different fragmentation channels. Then, using Car-Parrinello MD (CP MD) we study the thermal dissociation. In this method we assume that the Born-Oppenheimer approximation is valid. It means that we work under adiabatic conditions. Finally, for processes in excited states we resort to the use of time dependent density functional theory molecular dynamics (TD-DFT MD). Here we prepare an initial doubly charged state by removing two electrons from a particular inner Kohn- Sham orbital of the neutral molecule. The system evolves according to the Ehrenfest MD approximation. The mean-field potential energy surface (PES) which drives nuclear dynamics is computed at the TD-DFT level, propagating time-dependent Kohn-Sham orbitals. Nuclear forces are computed using the Hellmann-Feynman theorem. DFT calculations at the BLYP/6-311++G(d,p) level of theory show that the fragmentations of doubly charged L-Alanine on C-C bonds have energy barriers and the dissociation leads to two singly charged fragments. From our CP MD simulations, we found that the critical temperature for the thermal fragmentation of L-alanine is 1900 K. Two fragmentation channels are distinguished depending on the temperature used for the simulations: below 11254 K the fragmentation leads to two singly charged fragments: COOH and CH3CH(NH2) with masses 45/44 respectively. Above 11254 K, two singly charged fragments are produced: COOH, H2CCH2 which masses are 45/28 and a neutral fragment, NH2 (mass 16). Both fragmentation channels are supported by experimental PEPIPICO results. TD-DFT MD simulations give other interesting results that are not found using the CP MD in ground state. H3C· CH(NH2)COOH bond breaks leading to a CH3 fragment observed in PEPIPICO map. Continuing this simulation we expect further dissociation as supported by this mentioned PEPIPICO path