Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment

Following the Nonadiabatic Ultrafast Dynamics of Uracil via Simulated X-ray Absorption Spectra

The nucleobase uracil exhibits high photostability due to ultrafast relaxation processes mediated by conical intersections (CoIns), where the interplay between nuclear and electron dynamics becomes crucial. In our previous study, we observed seemingly long-lived traces of electronic coherence for the relaxation process through the S2/S1 CoIn by applying our ansatz for coupled nuclear and electron dynamics in molecules (NEMol). In this work, we theoretically investigate how time-dependent transient X-ray absorption spectroscopy can be used to observe this ultrafast dynamics. Therefore, we calculated X-ray absorption spectra (XAS) for the oxygen K-edge, using a multireference protocol in combination with NEMol dynamics. Thus, we have access to both the transient XAS based on the nuclear wavepacket dynamics and the modulation of the signals caused by the electronic coherence induced by the excitation process and the presence of a CoIn seam. In both cases, we were able to qualitatively predict its influence on the resulting XAS.

Monitoring vibronic coherences and molecular aromaticity in photoexcited cyclooctatetraene with an X-ray probe: a simulation study

Understanding conical intersection (CI) dynamics and subsequent conformational changes is key for exploring and controlling photo-reactions in aromatic molecules. Monitoring of their time-resolved dynamics remains a formidable experimental challenge. In this study, we simulate the photoinduced S₃ to S₁ non-adiabatic dynamics of cyclooctatetraene (COT), involving multiple CIs with relaxation times in good agreement with experiment. We further investigate the possibility to directly probe the CI passages in COT by off-resonant X-ray Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). We find that these signals sensitively monitor key chemical features during the ultrafast dynamics. First, we distinguish two CIs by using TRUECARS signals with their appearances at different Raman shifts. Second, we demonstrate that TRXD, where X-ray photons scatter off electron densities, can resolve ultrafast changes in the aromaticity of COT. It can further distinguish between planar and non-planar geometries explored during the dynamics, as e.g. two different tetraradical-type CIs. The knowledge gained from these measurements can give unique insight into fundamental chemical properties that dynamically change during non-adiabatic passages.

Sensing ultrashort electronic coherent beating at conical intersections by single-electron pulses

SignificanceIn a theoretical study, we present an ultrafast technique for probing time-dependent molecular charge densities. An ultrafast optical pump first brings the molecule into an electronic nonstationary state. This is followed by coherent inelastic scattering of a broadband single-electron probe pulse with a variable delay T, which is detected spectrally. The technique is applied to reveal phase-sensitive background-free coherent electron beating in the conical intersection passage in uracil and reveals the otherwise elusive coherent beating of strongly coupled electrons and nuclei.

Electronic coherences in nonadiabatic molecular photophysics revealed by time-resolved photoelectron spectroscopy

Time-resolved photoelectron spectroscopy (TRPES) is a promising technique for the study of ultrafast molecular processes, such as the nonadiabatic dynamics taking place at conical intersections. Directly accessing the evolution of the coherences generated at the conical intersection should provide most valuable dynamical information. However, the signals are dominated by background contributions due to state populations, and most theoretical treatments completely neglect the role of the coherences. Here we show that distinguishable signatures of molecular coherences appear in TRPES. These can be recorded using currently available ultrashort pulses and unambiguously extracted at the postprocessing stage. The technique thus provides direct access to nonadiabatic coherence dynamics.

Conical Intersection Passages of Molecules Probed by X-ray Diffraction and Stimulated Raman Spectroscopy

Conical intersections (CoIns) play an important role in ultrafast relaxation channels. Their monitoring remains a formidable experimental challenge. We theoretically compare the probing of the S₂ → S₁ CoIn passage in 4-thiouracil by monitoring its vibronic coherences, using off-resonant X-ray-stimulated Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). The quantum nuclear wavepacket (WP) dynamics provides an accurate picture of the photoinduced dynamics. Upon photoexcitation, the WP oscillates among the Franck-Condon point, the S₂ minimum, and the CoIn with a 70 fs period. A vibronic coherence first emerges at 20 fs and can be observed until the S₂ state is fully depopulated. The distribution of the vibronic frequencies involved in the coherence is recorded by the TRUECARS spectrogram. The TRXD signal provides spatial images of electron densities associated with the CoIn. In combination, the two signals provide a complementary picture of the nonadiabatic passage, which helps in the study of the underlying photophysics in thiobases.

Selective Enhancement of Spectroscopic Features by Quantum Optimal Control

Tailored light can be used to steer atomic motions into selected quantum pathways. In optimal control theory (OCT), the target is usually expressed in terms of the molecular wave function, a quantity that is not directly observable in experiment. We present simulations using OCT that optimize the spectroscopic signal itself. By shaping the optical pump, the x-ray stimulated Raman signal, which occurs solely during the passage through conical intersections, is temporally controlled and amplified by up to 2 orders of magnitude. This enhancement can be crucial in order to bring small coherence-based signatures above the detectable threshold. Our approach is applicable to any signal that depends on the expectation value of a positive definite operator.

Monitoring molecular vibronic coherences in a bichromophoric molecule by ultrafast X-ray spectroscopy

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 organic chromophores is the key for numerous applications. Here, we present fundamental insight into the energy transfer properties of a rigid synthetic heterodimer that has been experimentally engineered to study coherences. Quantum non-adiabatic excited state simulations are used to compute X-ray Raman signals, which are able to sensitively monitor the coherence evolution. Our results verify their vibronic nature, that survives multiple conical intersection passages for several hundred femtoseconds at room temperature. Despite the contributions of highly heterogeneous evolution pathways, the coherences are unambiguously visualized by the experimentally accessible X-ray signals. They offer direct information on the dynamics of electronic and structural degrees of freedom, paving the way for detailed coherence measurements in functional organic materials.

Waveform control of molecular dynamics close to a conical intersection

Conical intersections are ubiquitous in chemical systems but, nevertheless, extraordinary points on the molecular potential energy landscape. They provide ultra-fast radiationless relaxation channels, their topography influences the product branching, and they equalize the timescales of the electron and nuclear dynamics. These properties reveal optical control possibilities in the few femtosecond regime. In this theoretical study, we aim to explore control options that rely on the carrier envelope phase of a few-cycle IR pulse. The laser interaction creates an electronic superposition just before the wave packet reaches the conical intersection. The imprinted phase information is varied by the carrier envelope phase to influence the branching ratio after the conical intersection. We test and analyze this scenario in detail for a model system and show to what extent it is possible to transfer this type of control to a realistic system like uracil.

Photoprotecting Uracil by Coupling with Lossy Nanocavities

We analyze how the photorelaxation dynamics of a molecule can be controlled by modifying its electromagnetic environment using a nanocavity mode. In particular, we consider the photorelaxation of the RNA nucleobase uracil, which is the natural mechanism to prevent photodamage. In our theoretical work, we identify the operative conditions in which strong coupling with the cavity mode can open an efficient photoprotective channel, resulting in a relaxation dynamics twice as fast as the natural one. We rely on a state-of-the-art chemically detailed molecular model and a non-Hermitian Hamiltonian propagation approach to perform full-quantum simulations of the system dissipative dynamics. By focusing on the photon decay, our analysis unveils the active role played by cavity-induced dissipative processes in modifying chemical reaction rates, in the context of molecular polaritonics. Remarkably, we find that the photorelaxation efficiency is maximized when an optimal trade-off between light-matter coupling strength and photon decay rate is satisfied. This result is in contrast with the common intuition that increasing the quality factor of nanocavities and plasmonic devices improves their performance. Finally, we use a detailed model of a metal nanoparticle to show that the speedup of the uracil relaxation could be observed via coupling with a nanosphere pseudomode, without requiring the implementation of complex nanophotonic structures.

Visualizing conical intersection passages via vibronic coherence maps generated by stimulated ultrafast X-ray Raman signals

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.

Molecular Photochemistry: Recent Developments in Theory

Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.

Cooperative Conical Intersection Dynamics of Two Pyrazine Molecules in an Optical Cavity

Hybrid light-matter states in optical cavities, known as polaritons, offer a novel means of manipulating and controlling photochemical processes. We investigate the cooperative cavity photochemistry of two pyrazine molecules undergoing conical intersection dynamics and interacting with a single cavity photon mode by exact quantum dynamics. When the cavity mode is coupled to the electronic transition between the ground and excited states, we find an enhanced polaritonic splitting and collective dark states. These features dominate the cooperative polariton dynamics and can be observed in the transient absorption spectrum.

Insight into 6-aminopenicillanic acid structure and study of the quantum mechanical calculations of the acid–base site on γ-Fe2O3@SiO2 core–shell nanocomposites and as efficient catalysts in multicomponent reactions

Magnetic 6-APA/γ-Fe₂O₃@Sio₂ nanocomposites have been developed by exploiting the potential of the acid–base bifunctional system to study the quantum mechanistic calculations.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions

We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.

Transient X-ray Absorption Spectral Fingerprints of the S1 Dark State in Uracil

Low-lying dark nπ* states play an important role in many photophysical and photochemical processes of organic chromophores. Transient X-ray absorption spectroscopy (TXAS) provides a powerful technique for probing the dynamics of valence states by exciting the electrons into high-lying core excited states. We employ multiconfigurational self-consistent field calculations to investigate the TXAS of uracil along its nonradiative photodecay pathways. An open issue is whether dark nπ* state S₁ (n is the lone pair localized on an oxygen atom) is accessible when bright ππ* state S₂ is selectively excited. Vertical core excitations were calculated along the potential energy surfaces of the three lowest states, S₀-S₂, interpolated between two minima and two minimum-energy conical intersections. Computed TXAS data from the C, N, and O K edges show distinct spectral fingerprints of the dark state in all spectral regimes. At the O 1s edge, the nπ* state has a very strong absorption at 526-527 eV, while at the C (N) 1s edge, by contrast, there is almost zero (very weak) absorption at 279-282 eV (397-398 eV). All K-edge spectra can be used to sensitively detect the dark states. Our proposed O 1s feature has already been observed in a recent TXAS experiment with thymine. Natural transition orbital analysis is used to interpret all dominant features of the three lowest-valence states along the reaction coordinate and reveal some important valence fine-structure information from the core excitation.

Observation of Ultrafast Intersystem Crossing in Thymine by Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy

We studied the photoinduced ultrafast relaxation dynamics of the nucleobase thymine using gas-phase time-resolved photoelectron spectroscopy. By employing extreme ultraviolet pulses from high harmonic generation for photoionization, we substantially extend our spectral observation window with respect to previous studies. This enables us to follow relaxation of the excited state population all the way to low-lying electronic states including the ground state. In thymine, we observe relaxation from the optically bright ¹ππ* state of thymine to a dark ¹nπ* state within 80 ± 30 fs. The ¹nπ* state relaxes further within 3.5 ± 0.3 ps to a low-lying electronic state. By comparison with quantum chemical simulations, we can unambiguously assign its spectroscopic signature to the ³ππ* state. Hence, our study draws a comprehensive picture of the relaxation mechanism of thymine including ultrafast intersystem crossing to the triplet manifold.

Photochemical pathways in nucleobases measured with an X-ray FEL

The conversion of light energy into other molecular energetic degrees of freedom is often dominated by ultrafast, non-adiabatic processes. Femtosecond spectroscopy with optical pulses has helped in shaping our understanding of crucial processes in molecular energy-conversion. The advent of new, ultrashort and bright X-ray free electron laser sources opens the possibility to use X-ray-typical element and site sensitivity for ultrafast molecular research. We present two types of spectroscopy, ultrafast Auger and ultrafast X-ray absorption spectroscopy, and discuss their sensitivity to molecular processes. While Auger spectroscopy is able to monitor bond distance changes in the vicinity of an X-ray created core hole, near-edge absorption spectroscopy can deliver high-fidelity information on non-adiabatic transitions involving lone-pair orbitals. We demonstrate these features on the example of the UV-excited nucleobase thymine, investigated at the oxygen K-edge. We find a C-O bond elongation in the Auger data in addition to ππ*/ nπ* non-adiabatic transition in X-ray near-edge absorption. We compare the results from both methods and draw a conclusive scenario of non-adiabatic molecular relaxation after UV excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

State-Dependent Fragmentation of Protonated Uracil and Uridine

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH⁺) and uridine (UrdH⁺). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Symmetry controlled excited state dynamics

Symmetry effects in internal conversion are studied by means of two isomeric cyclic tertiary aliphatic amines in a velocity map imaging (VMI) experiment on the femtosecond timescale. We conclude that lessening the symmetry of the molecule leads to loss of coherence after internal conversion between Rydberg states.

Ultrafast Photorelaxation of Uracil Embedded in an RNA Strand

Ultrafast photorelaxation of uracil can be hindered by its natural RNA environment. Multiscale quantum dynamical simulations show that the wave packet can be trapped in the photoexcited electronic state, which could potentially lead to photodamage.

Pathways to New Applications for Quantum Control

In 1998, the first successful quantum control experiment with application to a molecular framework was conducted with a shaped laser pulse, optimizing the branching ratio between different organometallic reaction channels. This work induced a vast activity in quantum control during the next 10 years, and different optimization aims were achieved in the gas phase, liquid phase, and even in biologically relevant molecules like light-harvesting complexes. Accompanying and preceding this development were important advances in theoretical quantum control simulations. They predicted several control scenarios and explained how and why quantum control experiments work. After many successful proofs of concept in molecular science, the big challenge is to expand its huge conceptual potential of directly being able to steer nuclear and/or electronic motion to more applied implementations. In this Account, based on several recent advances, we give a personal evaluation of where the field of molecular quantum control is at the moment and especially where we think promising applications can be in the near future. One of these paths leads to synthetic chemistry. The synthesis of novel pharmaceutical compounds or natural products often involves many synthetic steps, each one devouring resources and lowering the product yield. Shaped laser pulses can possibly act as photonic reagents and shorten the synthetic route toward the desired product. Chemical synthesis usually takes place in solution, and by including explicit solvent molecules in our quantum control simulations, we were able to identify their highly inhomogeneous influence on chemical reactions and how this affects potential quantum control. More important, we demonstrated for a synthetically relevant example that these complications can be overcome in theory, and laser pulses can be optimized to initiate the desired carbon-carbon bond formation. Putting this into context with the recently emerging concept of flow chemistry, which brings several practical advantages to the application of laser pulses, we want to encourage experimental groups to exploit this concept. Another path was opened by several additions to the commonly used laser pulse optimization algorithm (optimal control theory, OCT), several of which were developed in our group. The OCT algorithm as such is a purely mathematical optimization procedure, with no direct relation to experimental requirements. This means that usually the electric fields obtained out of OCT optimizations do not resemble laser pulses that can be achieved experimentally. However, the previously mentioned additions are aimed at closing the gap toward the experiment. In a recent quantum control study of our group, these algorithmic developments came to fruition. We were able to suggest a shaped laser pulse which can induce a long-living wave packet in the excited state of uracil. This might pave the way for novel experiments dedicated to investigating the formation of biological photodamage in DNA and RNA. The pulse we suggest is surprisingly simple because of the extended OCT algorithm and fulfills all criteria to be experimentally accessible.

Ultrafast Reactive Quantum Dynamics Coupled to Classical Solvent Dynamics Using an Ehrenfest Approach

The inclusion of solvent effects in the theoretical analysis of molecular processes becomes increasingly important. Currently, it is not feasible to directly include the solvent on the quantum level. We use an Ehrenfest approach to study the coupled time evolution of quantum dynamically treated solutes and classical solvents system. The classical dynamics of the solvent is coupled to the wavepacket dynamics of the solute and rotational and translational degrees of freedom of the solute are included classically. This allows quantum dynamics simulations for ultrafast processes that are decided by environment interactions without explicit separation of time scales. We show the application to the dissociation of ICN in liquid Ar as a proof of principal system and to the more applied example of uracil in water.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.