Radiation Induced Dissociation Pathways and Charge Redistribution in X-ray Free-Electron Laser Imaging

Historically, structure determination of nano-crystals, proteins and macromolecules required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. The development of the x-ray free-electron laser (XFEL) has opened the door for high resolution single particle imaging using x-rays, as the extreme intensity ensures that enough diffraction statistics is collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event.
In this study, we use first-principles based methods to study the effect of radiation induced ionization of seven amino-acids. We benchmark a hierarchy of methods, considering theory on the level of Born-Oppenheimer molecular dynamics as well as non-adiabatic molecular dynamics. In addition, we study the impact on our results of how the ionization process is approximated. In order to estimate the effects of radiation damage on structural recovery, we study dissociation pathways, fragmentation statistics and charge redistribution.