The RNA nucleobase uracil can suffer from photodamage when exposed to UV light, which may lead to severe biological defects. To prevent this from happening in most cases, uracil exhibits an ultrafast relaxation mechanism from the electronically excited state back to the ground state. In our theoretical work, we demonstrate how this process can be significantly influenced using shaped laser pulses. This not only sheds new light on how efficient nature is in preventing biologically momentous photodamage. We also show a way to entirely prevent photorelaxation by preparing a long-living wave packet in the excited state. This can enable new experiments dedicated to finding the photochemical pathways leading to uracil photodamage. The optimized laser pulses we present fulfill all requirements to be experimentally accessible.
The rates and outcomes of virtually all photophysical and photochemical processes are determined by conical intersections. These are regions of degeneracy between electronic states on the nuclear landscape of molecules where electrons and nuclei evolve on comparable timescales and thus become strongly coupled, enabling radiationless relaxation channels upon optical excitation. Due to their ultrafast nature and vast complexity, monitoring conical intersections experimentally is an open challenge. We present a simulation study on the ultrafast photorelaxation of uracil, based on a quantum description of the nuclei. We demonstrate an additional window into conical intersections obtained by recording the transient wavepacket coherence during this passage with an X-ray free-electron laser pulse. Two major findings are reported. First, we find that the vibronic coherence at the conical intersection lives for several hundred femtoseconds and can be measured during this entire time. Second, the time-dependent energy-splitting landscape of the participating vibrational and electronic states is directly extracted from Wigner spectrograms of the signal. These offer a physical picture of the quantum conical intersection pathways through visualizing their transient vibronic coherence distributions. The path of a nuclear wavepacket in the vicinity of the conical intersection is directly mapped by the proposed experiment.
X-ray diffraction is routinely used for structure determination of stationary molecular samples. Modern X-ray photon sources, e.g., from free-electron lasers, enable us to add temporal resolution to these scattering events, thereby providing a movie of atomic motions. We simulate and decipher the various contributions to the X-ray diffraction pattern for the femtosecond isomerization of azobenzene, a textbook photochemical process. A wealth of information is encoded besides real-time monitoring of the molecular charge density for the cis to trans isomerization. In particular, vibronic coherences emerge at the conical intersection, contributing to the total diffraction signal by mixed elastic and inelastic photon scattering. They cause distinct phase modulations in momentum space, which directly reflect the real-space phase modulation of the electronic transition density during the nonadiabatic passage. To overcome the masking by the intense elastic scattering contributions from the electronic populations in the total diffraction signal, we discuss how this information can be retrieved, e.g., by employing very hard X-rays to record large scattering momentum transfers.
UV light can induce chemical reactions in nucleic acids and thereby damage the genetic code. Like all of the five primary nucleobases, the isolated RNA base uracil exhibits ultrafast, nonradiative relaxation after photoexcitation, which helps to avoid photodamage most of the time. Nevertheless, within RNA and DNA strands, commonly occurring photolesions have been reported and are often ascribed to long-lived and delocalized excited states. Our quantum dynamical study now shows that excited-state longevity can also occur on a single nucleobase, without the need for delocalization. We include the effects of an atomistic RNA surrounding in wave packet simulations and explore the photorelaxation of uracil in its native biological environment. This reveals that steric hindrance through embedding in an RNA strand can inhibit the ultrafast relaxation mechanism of uracil, promoting excited-state longevity and potential photodamage. This process is nearly independent from the specific combination of neighboring bases.
The role of quantum-mechanical coherences in the elementary photophysics of functional optoelectronic molecular materials is currently under active study. Designing and controlling stable coherences arising from concerted vibronic dynamics in...
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