Ultrafast Dynamics of a Nucleobase Analogue Illuminated by a Short Intense X-ray Free Electron Laser Pulse

Understanding x-ray radiation damage is a crucial issue for both medical applications of x rays and x-ray free-electron-laser (XFEL) science aimed at molecular imaging. Decrypting the charge and fragmentation dynamics of nucleobases, the smallest units of a macro-biomolecule, contributes to a bottom-up understanding of the damage via cascades of phenomena following x-ray exposure. We investigate experimentally and by numerical simulations the ultrafast radiation damage induced on a nucleobase analogue (5-iodouracil) by an ultrashort (10 fs) high-intensity radiation pulse generated by XFEL at SPring-8 Angstrom Compact free electron Laser (SACLA). The present study elucidates a plausible underlying radiosensitizing mechanism of 5-iodouracil. This mechanism is independent of the exact composition of 5-iodouracil and thus relevant to other such radiosensitizers. Furthermore, we found that despite a rapid increase of the net molecular charge in the presence of iodine, and of the ultrafast release of hydrogen, the other atoms are almost frozen within the 10-fs duration of the exposure. This validates single-shot molecular imaging as a consistent approach, provided the radiation pulse used is brief enough.

Popular Summary

5-iodouracil (IU) is an analog for a nucleobase, a component of a large, biologically relevant molecule. While the radiosensitizing effect of IU in radiation-based cancer therapies has been known for a long time, the exact molecular mechanisms behind it (i.e., the capacity of IU to locally augment the radiation damage to tumor cells by intratumoral administration of the agent) have not been deciphered thus far. Here, we illustrate how the molecules break apart after exposure to intense x-ray free-electron laser pulses and show what ionic fragments are formed via the breakage of the molecular edifice shortly after the inner-shell ionization, thereby shedding light on the role of energetic ions in the initiation of damaging reactions.

We carry out “Coulomb explosion” ion momentum imaging experiments for IU using ultrashort (10 fs) intense (5.5 keV) x-ray free-electron laser pulses at the SACLA facility in Japan. We also employ molecular-dynamics numerical simulations, which clearly indicate that at the very early stages of the charge and nuclear dynamics following the interaction with the x-ray free-electron laser radiation, only hydrogen atoms have time to move significantly; the remaining atomic and ionic fragments do not change their position significantly. Furthermore, the bonds between the heavier atoms elongate only slightly. This result validates the methodology for single-shot diffractive imaging of biopolymers as a reliable tool. Our work additionally provides clear evidence of the local production of a “radiation soup” consisting of energetic ions whose local damage effect adds to that of the genotoxic low-energy electrons generated by electronic relaxation cascading mechanisms.

We expect that the production of the radiation soup revealed here will contribute to the general understanding of how radiosensitizers work and will inspire the design of novel radiosensitizing drugs.

Figure 1

Schematics of experimental setup and ion TOF spectrum. (a) Schematics of experimental setup. Molecular structure of 5-iodouracil is shown in the inset. (b) Yields of the 5-iodouracil ion TOF spectrum, recorded at 5.5 keV, are shown on a log scale and are plotted as a function of mass-to-charge ratio. The inset displays the full-range TOF spectrum.

Figure 2

Kinetic energy distribution (KED) of fragment ions. (a) KED of ${\mathrm{H}}^{+}$ emitted from a XFEL irradiated 5-iodouracil and detected in coincidence with iodine ions. (b) KED of ${\mathrm{O}}^{+}$, (c) KED of ${\mathrm{N}}^{+}$, and (d) KED of ${\mathrm{C}}^{+}$. Symbols are the experimental data, and lines are the result of MD simulations at $T=300\mathrm{K}$. Dotted blue lines and thin solid green lines correspond to charge buildup times $\tau =0$ and 10 fs, respectively, assuming that the charge redistribution is instantaneous. The thick red lines represent a modeling with $\tau =10\mathrm{fs}$ and $R=0.5{\mathrm{fs}}^{-1}$.

Figure 3

Distributions of normalized scalar product of momentum vectors, ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$, plotted as a function of $\cos (\theta )$. (a) ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$ for the (${\mathrm{I}}^{q+}\text{−}{\mathrm{H}}^{+}$) pair, (b) ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{N}}^{+}$), (c) ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{O}}^{+}$), and (d) ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{C}}^{+}$). Gray shadow areas indicate the angles of atoms in the neutral parent molecule. (e)–(h) ${\mathrm{SP}}_2(\mathrm{A},\mathrm{B})$ calculated with temperature, charge buildup, and charge redistribution taken into account, using the parameters $T=300\mathrm{K}$, $\tau =10\mathrm{fs}$, and $R=0.5{\mathrm{fs}}^{-1}$.

Figure 4

Distribution of normalized scalar triplet products of momentum vectors ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ plotted as a function of $\cos (\varphi )$. (a) ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{H}}^{+}\text{−}{\mathrm{H}}^{+}$), (b) ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{H}}^{+}\text{−}{\mathrm{O}}^{+}$), (c) ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{H}}^{+}\text{−}{\mathrm{N}}^{+}$), and (d) ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ for (${\mathrm{I}}^{q+}\text{−}{\mathrm{H}}^{+}\text{−}{\mathrm{C}}^{+}$). (e)–(h) ${\mathrm{SP}}_3(\mathrm{A},\mathrm{B},\mathrm{C})$ calculated with temperature, charge buildup, and charge redistribution taken into account, using the parameters $T=300\mathrm{K}$, $\tau =10\mathrm{fs}$, and $R=0.5{\mathrm{fs}}^{-1}$.

Figure 5

Time evolution of interatomic distances in 5-IU obtained by MD simulations. Upper panel: Interatomic distance of I-C (red line), O-C (sky-blue lines), H-C (dark-green line), and H-N (light-green lines) pairs. Lower panel: Interatomic distance of C-C (black lines) and C-N (orange lines) pairs.