The cage effect of electron beam irradiation damage in cryo-electron microscopy

Electron beam irradiation can cause damage to biological and organic samples, as determined via transmission electron microscopy (TEM). Cryo-electron microscopy (cryo-EM) significantly reduces such damage by quickly freezing the environmental water around organic molecules. However, there are multiple hypotheses about the mechanism of cryo-protection in cryo-EM. A lower temperature can cause less molecular dissociation in the first stage, or frozen water can have a “cage” effect by preventing the dissociated fragments from flying away. In this work, we used real-time time-dependent density functional theory (rt-TDDFT-MD) molecular dynamic simulations to study the related dynamics. We used our newly developed natural orbital branching (NOB) algorithm to describe the molecular dissociation process after the molecule is ionized. We found that despite the difference in surrounding water molecules at different temperatures, the initial dissociation process is similar. On the other hand, the dissociated fragments will fly away at room temperature, while they will remain in the same cage when frozen water is used. Our results provide direct support for the cage effect mechanism.