This study presents a comprehensive investigation of the Auger spectra of three thionated uracils using a combination of theory and experiment. Non-resonant Auger spectra measured at the K-edges of carbon, nitrogen, and oxygen, as well as at the L2,3 edge of sulfur, are reported. Even though the final decay states (valence two-hole states) are the same for all edges, the resulting Auger spectra are strikingly different, highlighting the local nature of the Auger decay. Theoretical modeling, which employed a series of approaches incorporating varying levels of correlation and different treatments of the metastable states, provides a clear interpretation of the experimental spectra. The analysis highlights the crucial role of electron correlation, evident in both the density of the decay states and the spectra constructed using channel-specific partial decay widths, as well as the importance of spin-orbit coupling in shaping the L-edge spectra of thiouracils.

The photophysics of nucleobases has been the subject of both theoretical and experimental studies over the past decades due to the challenges posed by resolving the steps of their radiationless relaxation dynamics, which cannot be described in the framework of the Born-Oppenheimer approximation (BOA). In this context, the ultrafast dynamics of 2-thiouracil has been investigated with a time-resolved NEXAFS study at the Free Electron Laser FLASH. Near Edge X-ray Absorption Fine Structure spectroscopy (NEXAFS) can be used to observe electronic transitions in ultrafast molecular relaxation. We performed time-resolved UV-pump/X-ray probe absorption measurements at the sulfur 2s (L1) and 2p (L2/3) edges. We are able to identify absorption features corresponding to the S2 (ππ*) and S1 (nπ*) electronic states. We observe a delay of 102 ± 11 fs in the population of the nπ* state with respect to the initial optical excitation and interpret the delay as the time scale for the S2 → S1 internal conversion. We furthermore identify oscillations in the absorption signal that match a similar observation in our previous X-ray photoelectron spectroscopy study on the same molecule.

We present a combined experimental and theoretical study of the vibrationally resolved valence photoelectron spectra of the complete series of thiouracils (2-thiouracil, 4-thiouracil, and 2,4-dithiouracil) for binding energies between 8 and 17 eV. The theoretical spectra were calculated using equation-of-motion coupled cluster theory for ionization potential combined with the time-independent double-harmonic adiabatic Hessian approach. For all three thiouracils, the first ionization potential is found between 8.4 and 8.7 eV, which is 1 eV lower than for the canonical nucleobase uracil. Ionization bands up to 12 eV show strong vibrational progressions and are well reproduced by the calculations. These bands are attributed to the ionization of (primarily) sulfur- and oxygen-localized valence molecular orbitals. For higher binding energies, the calculations indicate that nonadiabatic couplings are important for the interpretation of the photoelectron spectra.

The photochemistry of heterocyclic molecules plays a decisive role for processes and applications like DNA photo-protection from UV damage and organic photocatalysis. The photochemical reactivity of heterocycles is determined by the redistribution of photoenergy into electronic and nuclear degrees of freedom, initially involving ultrafast internal conversion. Most heterocycles are planar in their ground state and internal conversion requires symmetry breaking. To lower the symmetry, the molecule must undergo an out-of-plane motion, which has not yet been observed directly. Here we show using the example of 2-thiouracil, how Coulomb explosion imaging can be utilized to extract comprehensive information on this molecular deformation, linking the extracted deplanarization of the molecular geometry to the previously studied temporal evolution of its electronic properties. Particularly, the protons of the exploded molecule are well-suited messengers carrying rich information on its geometry at distinct times after electronic excitation. We expect that our new analysis approach centered on these peripheral protons can be adapted as a general concept for future time-resolved studies of complex molecules in the gas phase.

We report a study of the electronic and nuclear relaxation dynamics of the photoexcited RNA base uracil in the gas phase using time-resolved core-level photoelectron spectroscopy together with high-level calculations. The dynamics was investigated by trajectory surface hopping calculations, and the core ionization energies were calculated for geometries sampled from these. The molecule was excited by a UV laser and dynamics probed on the oxygen, nitrogen, and carbon sites by core electron spectroscopy. We find that the main de-excitation channel of the initially excited S2(ππ*) state involves internal conversion to the S1(nπ*) state with a time constant of 17 ± 4 fs, while a portion of S2(ππ*) population returns directly to the ground state by internal conversion. We find no evidence that the S1(nπ*) state decays to the ground state; instead, it decays to triplet states with a time constant of 1.6 ± 0.4 ps. Oscillations of the S1(nπ*) state O 1s intensity as a function of time correlate with those of calculated C4═O8 and C5═C6 bond lengths, which undergo a sudden expansion following the initial π → π* excitation. Our calculations support our interpretation of the data and provide detailed insight into the relaxation processes of uracil.

Thionated nucleobases have drawn considerable attention due to their role in medical treatment and biology, which triggered studies of their photophysics and photochemistry using various experimental and theoretical techniques. In particular, vacuum ultraviolet (VUV)-induced dissociative photoionization of 2-thiouracil (2-TU) has been recently studied using synchrotron radiation [Robinson et al., Molecules 2023, 28, 2354]. Here, using molecular dynamics simulations at the semiempirical OM2 level, we study the fragmentation dynamics of the cations of 2-TU and its isomer, 4-thiouracil (4-TU). Considering various VUV photon energies, we calculate energy-resolved mass spectra and breakdown diagrams for 2-TU and 4-TU. Remarkably, we find that the major fragments are different between the two compounds: 69 amu (C3NH3O+) for 2-TU and 85 amu (C3NH3S+) for 4-TU. Our simulations provide direct mechanistic insight into this observation and the fragmentation processes of thionated uracils in general.

AbstractThe fate of thymine upon excitation by ultraviolet radiation has been the subject of intense debate. Today, it is widely believed that its ultrafast excited state gas phase decay stems from a radiationless transition from the bright ππ* state to a dark nπ* state. However, conflicting theoretical predictions have made the experimental data difficult to interpret. Here we simulate the early gas phase ultrafast dynamics in thymine at the highest level of theory to date. This is made possible by performing wavepacket dynamics with a recently developed coupled cluster method. Our simulation confirms an ultrafast ππ* to nπ* transition (τ = 41 ± 14 fs). Furthermore, the predicted oxygen-edge X-ray absorption spectra agree quantitatively with experiment. We also predict an as-yet uncharacterized πσ* channel that leads to hydrogen dissociation at one of the two N-H bonds. Similar behavior has been identified in other heteroaromatic compounds, including adenine, and several authors have speculated that a similar pathway may exist in thymine. However, this was never confirmed theoretically or experimentally. This prediction calls for renewed efforts to experimentally identify or exclude the presence of this channel.

The fate of thymine upon excitation by ultraviolet radiation has been the subject of intense debate over the past three decades. Today, it is widely believed that its ultrafast excited state decay stems from a radiationless transition from the bright ${\pi}{\pi}^*$ state to a dark $n{\pi}^*$ state. However, conflicting theoretical predictions have made the experimental data difficult to interpret. Here we simulate the ultrafast dynamics in thymine at the highest level of theory to date, performing wavepacket dynamics with a new coupled cluster method. Our simulation confirms an ultrafast ${\pi}{\pi}^*$ to $n{\pi}^*$ transition (${\tau} = 41 \pm 14$ fs). Furthermore, the predicted oxygen-edge X-ray absorption spectra agree quantitatively with the experimental results. Our simulation also predicts an as-yet uncharacterized photochemical pathway: a ${\pi}{\sigma}^*$ channel that leads to hydrogen dissociation at one of the two N-H bonds in thymine. Similar behavior has been identified in other heteroaromatic compounds, including adenine, and several authors have speculated that a similar pathway may exist in thymine. However, this was never confirmed theoretically or experimentally. This prediction calls for renewed efforts to experimentally identify or exclude the presence of this channel.

Molecular photoabsorption results in an electronic excitation/ionization which couples to the rearrangement of the nuclei. The resulting intertwined change of nuclear and electronic degrees of freedom determines the conversion of photoenergy into other molecular energy forms. Nucleobases are excellent candidates for studying such dynamics, and great effort has been taken in the past to observe the electronic changes induced by the initial excitation in a time-resolved manner using ultrafast electron spectroscopy. The linked geometrical changes during nucleobase photorelaxation have so far not been observed directly in time-resolved experiments. Here, we present a study on a thionucleobase, where we extract comprehensive information on the molecular rearrangement using Coulomb explosion imaging. Our measurement links the extracted deplanarization of the molecular geometry to the previously studied temporal evolution of the electronic properties of the system. In particular, the protons of the exploded molecule are well-suited messengers carrying rich information on the molecule's geometry at distinct times after the initial electronic excitation. The combination of ultrashort laser pulses to trigger molecular dynamics, intense X-ray free-electron laser pulses for the explosion of the molecule, and multi-particle coincidence detection opens new avenues for time-resolved studies of complex molecules in the gas phase.

The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.

We present a comprehensive, combined experimental and theoretical study of the core-level photoelectron and near-edge x-ray absorption fine structure (NEXAFS) spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil at the oxygen 1s, nitrogen 1s, carbon 1s, and the sulfur 2s and 2p edges. X-ray photoelectron spectra were calculated using equation-of-motion coupled-cluster theory (EOM-CCSD), and NEXAFS spectra were calculated using algebraic diagrammatic construction and EOM-CCSD. For the main peaks at O and N 1s as well as the S 2s edge, we find a single photoline. The S 2p spectra show a spin-orbit splitting of 1.2 eV with an asymmetric vibrational line shape. We also resolve the correlation satellites of these photolines. For the carbon 1s photoelectrons, we observe a splitting on the eV scale, which we can unanimously attribute to specific sites. In the NEXAFS spectra, we see very isolated pre-edge features at the oxygen 1s edge; the nitrogen edge, however, is very complex, in contrast to the XPS findings. The C 1s edge NEXAFS spectrum shows site-specific splitting. The sulfur 2s and 2p spectra are dominated by two strong pre-edge transitions. The S 2p spectra show again the spin-orbit splitting of 1.2 eV.

The free-electron laser in Hamburg, FLASH, is the first extreme ultra-violet and soft X-ray free-electron laser (FEL) user facility and has been continuously upgraded since its start in 2005. Further major works are currently underway within the FLASH2020+ project that pioneeringly implements full repetition rate external seeding at a superconducting accelerator facility. With fully tunable undulators providing variable polarization FEL pulses, we expect FLASH to turn into the ideal spectroscopy machine for ultrafast processes within the coming years.

In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S2 state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300–400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S2 → S1 → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.

We present results from an ultrafast X-ray absorption spectroscopic study into the dynamics of gas-phase UV-photoexcited acetylacetone molecules, revealing signatures of non-adiabatic dynamics and ultrafast hydrogen transfer.

The random nature of self-amplified spontaneous emission (SASE) is a well-known challenge for x-ray core level spectroscopy at SASE free-electron lasers (FELs). Especially in time-resolved experiments that require a combination of good temporal and spectral resolution the jitter and drifts in the spectral characteristics, relative arrival time as well as power fluctuations can smear out spectral-temporal features. We present a combination of methods for the analysis of time-resolved photoelectron spectra based on power and time corrections as well as self-referencing of a strong photoelectron line. Based on sulfur 2p photoelectron spectra of 2-thiouracil taken at the SASE FEL FLASH2, we show that it is possible to correct for some of the photon energy drift and jitter even when reliable shot-to-shot photon energy data is not available. The quality of pump–probe difference spectra improves as random jumps in energy between delay points reduce significantly. The data analysis allows to identify coherent oscillations of 1 eV shift on the mean photoelectron line of 4 eV width with an error of less than 0.1 eV.

We present real-world data processing on measured electron time-of-flight data via neural networks. Specifically, the use of disentangled variational autoencoders on data from a diagnostic instrument for online wavelength monitoring at the free electron laser FLASH in Hamburg. Without a-priori knowledge the network is able to find representations of single-shot FEL spectra, which have a low signal-to-noise ratio. This reveals, in a directly human-interpretable way, crucial information about the photon properties. The central photon energy and the intensity as well as very detector-specific features are identified. The network is also capable of data cleaning, i.e. denoising, as well as the removal of artefacts. In the reconstruction, this allows for identification of signatures with very low intensity which are hardly recognisable in the raw data. In this particular case, the network enhances the quality of the diagnostic analysis at FLASH. However, this unsupervised method also has the potential to improve the analysis of other similar types of spectroscopy data.

We present a comparative study of the gas-phase UV spectra of uracil and its thionated counterparts (2-thiouracil, 4-thiouracil and 2,4-dithiouracil), closely supported by time-dependent density functional theory calculations to assign the transitions observed. We systematically discuss pure gas-phase spectra for the (thio)uracils in the range of 200-400 nm (similar to 3.2-6.4 eV), and examine the spectra of all four species with a single theoretical approach. We note that specific vibrational modelling is needed to accurately determine the spectra across the examined wavelength range, and systematically model the transitions that appear at wavelengths shorter than 250 nm. Additionally, we find in the cases of 2-thiouracil and 2,4-dithiouracil, that the gas-phase spectra deviate significantly from some previously published solution-phase spectra, especially those collected in basic environments.

We present the first investigation of excited state dynamics by resonant Auger-Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a ππ* excited state, thymine is known to undergo internal conversion to an nπ* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state π* resonances of thymine (see our previous study Wolf, et al., Nat. Commun., 2017, 8, 29). We resolve and compare the Auger-Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the nπ* state signatures the appearance of additional resonant Auger-Meitner contributions at photon energies between the nπ* state and the ground state resonances. We assign these contributions to population transfer from the nπ* state to a ππ* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited ππ* singlet state which we have not observed in our previous study.