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We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S2 which exhibits a sub-100-fs nonadiabatic decay to a dark state S1. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.

Multireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core-electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra.

Thionated nucleobases are obtained by replacing oxygen with sulphur atoms in the canonical nucleobases. They absorb light efficiently in the near-ultraviolet, populating singlet states which undergo intersystem crossing to the triplet manifold on an ultrashort time scale with a high quantum yield. Nonetheless there are still important open questions about the primary mechanisms responsible for this ultrafast transition. Here we track both the electronic and the vibrational ultrafast excited-state dynamics towards the triplet state for solvated 4-thiothymidine (4TT) and 4-thiouracil (4TU) with sub-30 fs broadband transient absorption spectroscopy in the ultraviolet. A global and target analysis allows us to simultaneously resolve the contributions of the different electronically and vibrationally excited states to the whole data set. Our experimental results, combined with state-of-the-art quantum mechanics/molecular mechanics simulations and Damped Oscillation Associated Spectra (DOAS) and target analysis, support that the relaxation to the triplet state is mediated by conical intersections promoted by vibrational coherences through the population of an intermediate singlet state. In addition, the analysis of the coherent vibrational dynamics reveals that, despite sharing the same relaxation mechanism and similar chemical structures, 4TT and 4TU exhibit rather different geometrical deformations, characterized by the conservation of planarity in 4TU and its partial rupture in 4TT.

High level time-dependent density functional theory (TD-DFT) computational modeling of coumarin dyes has been exploited for guiding the design of effective photocatalysts (PCs). A library of coumarins were investigated from the theoretical point of view and photophysical/electrochemical properties (absorption and emission spectra, E00, oxidation and reduction potentials) were evaluated. Comparison with literature values reported for a few candidates has been used for assessing the level of theory. On the basis of the results obtained, new strongly reducing PCs [Eox(PC.+/PC*)=−2.1 – −2.0 V vs SCE] were discovered. Through the computational study of structure-properties relationships, a number of coumarins derivatives have been synthesized and evaluated in the pinacol coupling of aldehydes as the model reaction. The new organic photoredox catalysts show experimental photophysical and electrochemical data in accordance with the ones predicted by calculation, with excited state reduction potentials surpassing those of highly reducing transition metal-based PCs. A careful investigation of their behavior as PC has revealed crucial issues that need to be taken into consideration in the general photoredox catalysis, shedding light on the use of these PC in the pinacol, as well as, in other photoredox reactions.

This work demonstrates how push-pull substitution can induce spectral tuning toward the visible range and improve the photoisomerization efficiency of azobenzene-based photoswitches, making them good candidates for technological and biological applications. The red-shifted bright ππ∗ state (S2) behaves like the lower and more productive dark nπ∗ (S1) state because less potential energy along the planar bending mode is available to reach higher energy unproductive nπ*/S0 crossing regions, which are responsible for the lower quantum yield of the parent compound. The stabilization of the bright ππ∗ state and the consequent increase in isomerization efficiency may be regulated via the strength of push-pull substituents. Finally, the torsional mechanism is recognized here as the unique productive route because structures with bending values attributable to the inversion mechanism were never detected, out of the 280 ππ∗ time-dependent density functional theory (RASPT2-validated) dynamics simulations.

Controlling the spectral tunability and isomerization activity is currently one of the hot topics in the design of photoreversible molecular switches for application in optoelectronic devices. The present work demonstrates how to manipulate the absorption of the retinal protonated Schiff base (rPSB) chromophore over the entire visible range by targeted functionalization of the retinal backbone. Moreover, a correlation between the vertical excitation energy and the profile of the potential energy surface of the bright excited state responsible for the photoreactivity of rPSB is established. This correlation was exploited to rank the functionalized rPSBs into different classes with characteristic photoisomerization activity. Eventually, the synergic effects of functionalization and of external electric fields in the range of a few MV cm−1 were applied to achieve reversable and regioselective control of the photoisomerization propensity of selected rPBS derivatives.

We theoretically monitor the photoinduced ∗ → n∗ internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ∗ and n∗ absorption features. The lowest sulfur K-edge shows strong absorption for both ∗ and n*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ∗ and an approximate timing of the conical intersection via its depletion. A spectral signature of the n∗ transition, not accessible by UV-vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. The */n∗ coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.

Ultrafast electron diffraction is a powerful technique that can resolve molecular structures with femtosecond and angstrom resolutions. We demonstrate theoretically how it can be used to monitor conical intersection dynamics in molecules. Specific contributions to the signal are identified which vanish in the absence of vibronic coherence and offer a direct window into conical intersection paths. A special focus is on hybrid scattering from nuclei and electrons, a process that is unique to electron (rather than X-ray) diffraction and monitors the strongly coupled nuclear and electronic motions in the vicinity of conical intersections. An application is made to the cis to trans isomerization of azobenzene, computed with exact quantum dynamics wavepacket propagation in a reactive two-dimensional nuclear space.

By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, we present a complete description of the primary photo-induced processes in solvated tryptophan. Our results shed new light on the role of the solvent in the relaxation dynamics of tryptophan. We unveil two consecutive coherent population transfer events involving the lowest two singlet excited states: a sub-50-fs non-adiabatic La-->Lb transfer through a conical intersection and a subsequent 220 fs reverse Lb-->La transfer due to solvent assisted adiabatic stabilization of the La state. Vibrational fingerprints in the transient absorption spectra provide compelling evidence of a vibronic coherence established between the two excited states from the earliest times after photoexcitation and lasting until the back-transfer to La is complete. The demonstration of response to the environment as a driver of coherent population dynamics among the excited states of tryptophan closes the long debate on its solvent-assisted relaxation mechanisms and extends its application as a local probe of protein dynamics to the ultrafast timescales.

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.

We demonstrate how two-photon excitation with quantum light can influence elementary photochemical events. The azobenzene trans → cis isomerization following entangled two-photon excitation is simulated using quantum nuclear wave packet dynamics. Photon entanglement modulates the nuclear wave packets by coherently controlling the transition pathways. The photochemical transition state during passage of the reactive conical intersection in azobenzene photoisomerization is strongly affected with a noticeable alteration of the product yield. Quantum entanglement thus provides a novel control knob for photochemical reactions. The distribution of the vibronic coherences during the conical intersection passage strongly depends on the shape of the initial wave packet created upon quantum light excitation. X-ray signals that can experimentally monitor this coherence are simulated.

With this work we present a protocol for the parametrization of a Linear Vibronic Coupling (LVC) Hamiltonian for quantum dynamics, using highly accurate multiconfigurational electronic structure methods such as RASPT2/RASSCF, combined with a maximum-overlap diabatization technique. Our approach is fully portable, and could be applied to many medium-size rigid molecules whose excited state dynamics requires a quantum description. We present our model and discuss the details of the electronic structure calculations needed for the parametrization, analyzing critical situations that could arise in the case of strongly interacting excited states. The protocol was applied to the simulation of the excited state dynamics of the pyrene molecule, starting from either the rst or the second bright state (S2 or S5). LVC model was benchmarked against state-of-the-art QM calculations with optimizations and energy scans, and turned out to be very accurate. The dynamics simulations, performed including all active normal coordinates with the multilayer multiconfigurational time-dependent Hartree method, show good agreement with the available experimental data, endorsing prediction of the excited state mechanism, especially for S5, whose ultrafast deactivation mechanism was not yet clearly understood.

The UVB-induced photomechanism leading the carbonyl group of a thymine nucleobase to react with the carbon-carbon double bond of a consecutive thymine nucleobase in a DNA strand to form the thymine-thymine (6-4) photodamage adduct remains poorly understood. Key questions remain unanswered, concerning both the intrinsic features of the photoreaction (such as the contribution (or not) of triplet states, the nature of the involved states and the time-scale of the photoprocess) and the role played by the non-reactive surroundings of the two reactive pyrimidine nucleobases (such as the nature of the flanked nucleobases and the flexibility of the whole DNA molecule). A small number of theoretical studies have been carried out on the title photoreaction, most of which have used reduced model systems of DNA, consequently neglecting potential key parameters for the photoreaction such as the constraints due to the double strain structure and the presence of paired and stacked nucleobases. In the present contribution the photoactivation step of the title reaction has been studied in a DNA system, and in particular for a specific DNA hairpin for which the quantum yield of photodamage formation has been recently experimentally measured. The reaction has been characterized by carrying out high-level QM/MM computations, combining the CASPT2//CASSCF approach for the study of the reactive part (i.e. the two thymine molecules) with an MM-Amber treatment of the surrounding environment. The possibility of a reaction path along both the singlet and triplet manifolds has been characterized, the nature of the reactive states has been analyzed, and the role played by the flexibility of the whole system, which in turn determines the initial accessible geometrical conformations, has been evaluated, thus substantially contributing towards the elucidation of the photoreaction mechanism. On the basis of the obtained results, it can be observed that a charge-transfer state can decay from a pro-reactive initial structure towards a region of energy degeneracy with the ground state, from which the subsequent decay along the ground state hypersurface can lead to the photoreaction.

Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.

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.

DNA owes its remarkable photostability to the ability of its building blocks – the nucleosides – to efficiently dissipate the excess electronic energy acquired upon photoexcitation with ultraviolet light. The exact mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy with broad spectral coverage and state-of-the-art quantum dynamics simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. For both nucleosides we track the wave packet motion from the Franck-Condon region to the conical intersection (CI) with to the ground state and observe a direct spectral signature of an excited-state vibrational mode leading to the CI. We find that 5mUrd exhibits an order of magnitude longer excited state lifetime with respect to Urd and assign it to the larger inertia of the methyl group involved in the ring puckering mode leading to the CI. We argue that this longer lifetime enables the activation of potentially lesion-inducing coordinates such as ring opening, elucidating the origin of the susceptibility of thymine-containing DNA strands to photodamage.

We present an overview of a methodology for the simulation of the photo-response of biological (macro)molecules, designed around a QuantumMechanics / Molecular Mechanics (QM/MM) subtractive scheme. The resulting simulation workflow, that goes from the characterization of the photo-active system to the modeling of (transient) electronic spectroscopies is implemented in the software COBRAMM, but is completely general and can be used in the framework of any specific QM/MM implementation. COBRAMMis a smart interface to existing state-of-the-art theoretical chemistry codes, combining different levels of description and different algorithms to realize tailored problem-driven computations. The power of this approach is illustrated by reviewing the studies of two fundamental problems involving biological light-sensitive molecules. First, we will consider the photodynamics of the retinalmolecule, the pigment of rhodopsin, a visual receptor protein contained in the rod cells of the retina. Retinal, with its light-induced isomerization, triggers a cascade of events leading to the production of the nerve impulse. Then, we will review some studies focusing on the interaction of DNAsystems with ultraviolet (UV) light, a problem that has become one of the benchmark for the development of nonlinear spectroscopy, because of the ultrashort excited state lifetimes that arise from very efficient radiationless excited state decayand consent self-protection of DNAagainst UV damage.

Core-excitations on different atoms are highly localized and therefore decoupled. By placing molecules in an X-ray cavity the core-transitions become coupled via the exchange of cavity photons and form delocalized hybrid light-matter excitations known as core-polaritons. We demonstrate these effects for the two inequivalent carbon atoms in 1,1-difluoroethylene. Polariton signatures in the X-ray absorption, two-photon absorption, and multidimensional four-wave mixing, signals are predicted.

We combine sub-20 fs transient absorption spectroscopy with state-of-the-art computations to study the ultrafast photoinduced dynamics of trans-azobenzene (AB). We are able to resolve the lifetime of the pi pi* state, whose decay within ca. 50 fs is correlated to the buildup of the n pi* population and to the emergence of coherences in the dynamics, to date unobserved. Nonlinear spectroscopy simulations call for the CNN in-plane bendings as the active modes in the subps photoinduced coherent dynamics out of the pi pi* state. Radiative to kinetic energy transfer into these modes drives the system to a high-energy planar n pi*/ground state conical intersection, inaccessible upon direct excitation of the lie state, that triggers an ultrafast (0.45 ps) nonproductive decay of the n pi* state and is thus responsible for the observed Kasha rule violation in UV excited trans-AB. On the other hand, cis-AB is built only after intramolecular vibrational energy redistribution and population of the NN torsional mode.

A combined theoretical/experimental study of the photoreactivity of two flavylium-derived chalcones, 2,4,4′-trihydroxychalcone and 2,4′-dihydroxychalcone, at the multiconfigurational wavefunction level of theory (CASSCF//CASPT2) in vacuo and in an implicit solvent (water, treated as a polarisable continuum) and by means of linear absorption spectroscopy is presented. The photosensitivity of flavium salts is expressed in the ability of their chalcone form to undergo a cis-trans isomerisation which has found application in logical networks. Despite a considerable amount of experimental data documenting the dependence of the isomerisation on solvent, pH and temperature, the knowledge of how chalcones process energy under various conditions at the molecular level is still scarce. On the example of 2,4,4′-trihydroxychalcone we unravel the complex excited state deactivation mechanism in vacuo involving ultrafast decay through conical intersections, formation of twisted intramolecular charge transfer species, intramolecular proton transfer and inter system crossings. Furthermore, we rationalise the observed discrepancies in the linear absorption spectra of 2,4,4′-trihydroxychalcone and 2,4′-dihydroxychalcone, thereby establishing a link between the functionalisation pattern and the observed spectral properties.

A computational protocol based on the complete and restricted active space self-consistent field (CASSCF/RASSCF) methods and their second-order perturbation theory extensions (CASPT2/RASPT2) is employed to benchmark the highly excited-state manifold of the DNA/RNA canonical purine nucleobase guanine in vacuo. Several RASPT2 schemes are tested, displaying a steady convergence of electronic transition energies and dipole moments upon active space enlargement toward the reference values. The outcome allows calibrating and optimizing computational efforts by considering cheaper and more approximate RAS schemes that could enable the characterization of the excited-state manifolds of multi-chromophoric systems, such as DNA/RNA nucleobase dimers or multimers. Simulations of two-dimensional electronic spectra show similar trends to those observed on the other purine nucleobase adenine, deviating from this and other pyrimidine nucleobases in featuring its main excited-state absorption signal, embodied by sizable double HOMO to LUMO excitation contributions, in the UV probing window.

A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm−1. The 18–24 k cm−1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.

We demonstrate the relationship between the topology (the way in which the atoms are connected), open-shell character, and singlet fission (SF) propensity in a series of diboron-doped anthracenes and phenanthrenes. The study is performed by using high-level wave-function-based quantum-chemical calculations. The results show that the molecular topology plays a crucial role for the optical properties and, respectively, for the SF propensity of the studied compounds. The topology-derived correlations between the structure and properties are interpreted in the light of the Kekule hydrocarbons concept and serve as molecular design guidelines for the discovery of new SF materials. Finally, several boron-doped polycyclic aromatic hydrocarbons are proposed as SF chromophores for organic solar cells.

In this discussion we present a methodology to describe spectral lineshape from first principles, providing insight into the solvent–solute molecular interactions in terms of static and dynamic disorder and how these shape the signals recorded experimentally in linear and nonlinear optical spectroscopies, including two-dimensional electronic spectroscopy (2DES). Two different strategies for simulating the lineshape are compared: both rely on the same evaluation of the coupling between the electronic states and the intra-molecular vibrations, while they differ in describing the influence exerted by the diverse water configurations attained along a molecular dynamics (MD) simulation. The first method accounts for such water arrangements as first order perturbations on the adenine energies computed for a single reference (gas phase) quantum calculation. The second method requires computation of the manifold of excited states explicitly at each simulation snapshot, employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. Both approaches are applied to a large number of states of the adenine singlet excited manifold (chosen because of its biological role), and compared with available experimental data. They give comparable results but the first approach is two orders of magnitude faster. We show how the various contributions (static/dynamic disorder, intra-/inter-molecular interactions) sum up to build the total broadening observed in experiments.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions. ispartof: JOURNAL OF CHEMICAL PHYSICS vol:152 issue:21 ispartof: location:United States status: published

Time-resolved X-Ray diffraction signals are simulated to monitor the ultrafast photoisomerization of azobenzene, a textbook photophysical process. Different signal contributions, with a special focus on scattering from coherences emerging at the conical intersection, are discussed.

Photoinduced processes in thiouracil derivatives have lately attracted considerable attention due to their suitability for innovative biological and pharmacological applications. Here, sub-20 fs broadband transient absorption spectroscopy in the near-UV are combined with CASPT2/MM decay path calculations to unravel the excited-state decay channels of water solvated 2-thio and 2,4-dithiouracil. These molecules feature linear absorption spectra with overlapping ππ* bands, leading to parallel decay routes which we systematically track for the first time. The results reveal that different processes lead to the triplet states population, both directly from the ππ* absorbing state and via the intermediate nπ* dark state. Moreover, the 2,4-dithiouracil decay pathways is shown to be strongly correlated either to those of 2- or 4-thiouracil, depending on the sulfur atom on which the electronic transition localizes.

Thiobases are studied by transient absorption spectroscopy employing sub-20 fs UV-pulses combined with hybrid QM(CASPT2) / MM(AMBER) computations (static and dynamic) evidencing that intersystem crossing originates from a dark intermediate state along the photoexcited relaxation pathway.

X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck-Condon point, towards the conical intersection(s).

International audience; The most relevant ‘dark’ electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck–Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump–probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.

The spectral tunability, photoisomerization efficiency and selectivity, of the native all-trans retinal protonated Shiff base (PSB) chromophore driven by a homogeneous electric field is systematically investigated. By analyzing the absorption wavelength dependence, charge distribution, and PES profiles along selected torsional angles, as well as the electronic structure, energetics, and topography of the CI seam in the presence of strong positive and negative electric fields, we recognize the existence of qualitatively/fundamentally different photophysics and photochemistry with respect to the unperturbed (i.e., absence of an electric field) chromophore. We rationalize the findings within the scope of molecular orbital theory and deliver a unified picture of the photophysics of the retinal PSB chromophore over a wide, even beyond the usually observed, spectral regime, ranging from the near-infrared to the ultraviolet absorption energies. This work has a 3-fold impact: a) it accounts for, and extends, previous theoretical studies on the subject; b) it delivers a rationale for the ES lifetimes observed in retinal proteins, both archeal and visual rhodopsins, as well as in solvent; and c) the transferability of the discovered trends on PSB mimics is demonstrated.

The photoisomerization of all‐trans retinal in channelrhodopsins triggers the opening of a cation channel in the membrane of certain green algae. The stimulus resulting from cell depolarization enables the algae to perceive and react to the present lighting conditions. This property makes channelrhodopsins especially interesting for neuroscientific applications in optogenetics. We investigate the initial photoreaction in the channelrhodopsin chimera C1C2 with a combined quantum mechanical/molecular mechanical (QM/MM) strategy. For geometry optimizations, the OM3/RHF and OM3/MRCI/Amber protocols are used. Trajectory surface hopping calculations are performed with OM3/MRCI/Amber and a statistically relevant number of molecules to obtain reaction rates and quantum yields. The utilized models include a direct hydrogen bond of the retinal Schiff base to the proposed counterions in C1C2, i. e. either toward glutamate or aspartate. Static and dynamic aspects are compared to experimental findings including time constants and spectral traces. The calculations provide a rationale for the observed short and long time components in the photokinetics of C1C2 and yield detailed insight into the photoreaction mechanisms that include bicycle pedal and hula twist motions.

We determined the complete relaxation dynamics of pyrene in ethanol from the second bright state, employing experimental and theoretical broadband heterodyne detected transient grating and two-dimensional photon echo (2DPE) spectroscopy, using pulses with duration of 6 fs and covering a spectral range spanning from 250 to 300 nm. Multiple lifetimes are assigned to conical intersections through a cascade of electronic states, eventually leading to a rapid population of the lowest long-living excited state and subsequent slow vibrational cooling. The lineshapes in the 2DPE spectra indicate that the efficiency of the population transfer depends on the kinetic energy deposited into modes required to reach a sloped conical intersection, which mediates the decay to the lowest electronic state. The presented experimental-theoretical protocol paves the way for studies on deep-ultraviolet-absorbing biochromophores ubiquitous in genomic and proteic systems.

Two-dimensional (2D) spectroscopy, originally developed for nuclear magnetic resonance, has been recently extended to the infrared and visible regimes. In this technique sequences of femtosecond light pulses are used to interrogate molecular systems and show, by a double Fourier transform, the correlation between excitation and detection frequencies. Extension to the ultraviolet (UV) regime is of great interest and promises to deliver rich structural and dynamical information on biomolecules such as DNA and proteins; however, it must overcome significant technical challenges. This review summarizes the current development status of 2DUV spectroscopy. After discussing the scientific case for the technique, we introduce its basic principles and review its experimental implementations, as well as the computational tools that have been developed to model the experiments. We conclude by giving a few application examples, which highlight the potential of 2DUV spectroscopy and motivate its further development.

4-thiouracil (4TU) is studied by transient absorption spectroscopy employing sub-20 fs UV-pulses and hybrid QM(CASPT2) / MM(AMBER) computations (static and dynamic), evidencing that, along the photoexcited relaxation pathway, intersystem crossing originates from a dark intermediate state.

Linear and nonlinear X-ray spectroscopy hold the promise to provide a complementary tool to the available ample body of terahertz to UV spectroscopic techniques, disclosing information about the electronic structure and the dynamics of a large variety of systems, spanning from transition metals to organic molecules. While experimental free electron laser facilities continue to develop, theory may take the lead in modeling and inspiring new cutting edge experiments, paving the way to their future use. As an example, the not-yet-available two-dimensional coherent X-ray spectroscopy (2DCXS), conceptually similar to 2D-NMR, is expected to provide a wealth of information about molecular structure and dynamics with an unprecedented level of detail. In the present contribution, we focus on the simulation of linear and non-linear (2DCXS) spectra of the ESCA molecule. The molecule has four inequivalent carbon K-edges and has been widely used as a benchmark for photoelectron spectroscopy. Two theoretical approaches for the computation of the system manifold of states, namely, TDDFT and RASSCF/RASPT2, are compared, and the possible signals that may appear in a 2DCXS experiment and their origin are surveyed.

When ultraviolet (UV) radiation is absorbed by DNA, the electronic energy acquired by the molecule is efficiently converted into vibrational energy on an ultrafast timescale, preventing photochemical reactions which might induce mutations or strand breaks. In those ultrafast processes, conical intersections (CIs) play a crucial role [1]. Over the past years many studies have been performed to shed light in the fate of photoexcitations in DNA, although most of them with limited (>100 fs) temporal resolution. In this work we combine transient absorption (TA) spectroscopy using sub-20 fs UV pump pulses [2, 3] and broad UV spectral coverage with TA spectroscopy simulations from first principles based on mixed quantum mechanics /molecular mechanics (QM/MM) framework at the dynamically correlated multiconfiguration wavefunction level (CASPT2) [4, 5] to study the ultrafast relaxation dynamics of pyrimidine nucleosides uridine (Urd) and 5-methyluridine (MTU)