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Epigenetic DNA modifications play a fundamental role in modulating gene expression and regulating cellular and developmental biological processes, thereby forming a second layer of information in DNA. The epigenetic 2′-deoxycytidine modification 5-methyl-2′-deoxycytidine, together with its enzymatic oxidation products (5-hydroxymethyl-2′-deoxycytidine, 5-formyl-2′-deoxycytidine, and 5-carboxyl-2′-deox- ycytidine), are closely related to deactivation and reactivation of DNA transcription. Here, we combine sub-30-fs transient absorption spectroscopy with high-level correlated multiconfigurational CASPT2/MM computational methods, explicitly including the solvent, to obtain a unified picture of the photophysics of deoxycytidine-derived epigenetic DNA nucleosides. We assign all the observed time constants and identify the excited state relaxation pathways, including the competition of intersystem crossing and internal conversion for 5-formyl-2′-deoxycytidine and ballistic decay to the ground state for 5-carboxy-2′-deoxycytidine. Our work contributes to shed light on the role of epigenetic derivatives in DNA photodamage as well as on their possible therapeutic use.

Studying the effects of UV and VUV radiation on non‐canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS‐CASPT2 theoretical study of the photoionisation of non‐canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2π+ , 2nO+ and 2nN+ and compare these to the corresponding electronic states in cytosine. Investigating lower‐energy decay pathways we find – unexpectedly ‐ that keto‐isocytosine+ presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol‐isocytosine+ features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine+. Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ∼1 eV) but it is nevertheless still present. We additionally compute the UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo‐processes., The photostability of isocytosine upon ionising radiation exposure is assessed theoretically in both keto and enol tautomeric forms. This non‐canonical base, which features analogous UV excited state reactivity to DNA nucleobase cytosine, unexpectedly displays sizeable energy barriers along the cationic excited state in its keto form that hamper the decay. Simulations suggest isocytosine is less photostable against photoionisation, a factor that might contribute to selecting the more resilient cytosine under prebiotic VUV radiation exposure.

Diketopyrrolopyrrole (DPP) is a pivotal functional group to tune the physicochemical properties of novel organic photoelectronic materials. Among multiple uses, DPP-thiophene derivatives forming a dimer through a vinyl linker were recently shown to quench the fluorescence observed in their isolated monomers. Here, we explain this fluorescence quenching using computational chemistry. The DPP-thiophene dimer has a low-lying doubly excited state that is not energetically accessible for the monomer. This state delays the fluorescence allowing internal conversion to occur first. We characterize the doubly excited state wavefunction by systematically changing the derivatives to tune the π-scaffold size and the acceptor and donor characters. The origin of this state's stabilization is related to the increase in the π-system and not to the charge-transfer features. This analysis delivers core conceptual information on the electronic properties of organic chromophores arranged symmetrically around a vinyl linker, opening new ways to control the balance between luminescence and internal conversion. ispartof: PHYSICAL CHEMISTRY CHEMICAL PHYSICS vol:24 issue:38 pages:23279-23288 ispartof: location:England status: published

The photochemistry of pyruvic acid has received a large attention due to its relevance to atmospheric chemistry. Pyruvic acid is produced in the troposphere from both biogenic and anthropogenic sources and is a prototypical model for the family of (Formula presented.) -dicarbonyls. What makes the photochemistry of pyruvic acid particularly interesting from a gas-phase perceptive is its expected decarboxylation upon sunlight absorption. The exact photodynamics leading to this release of CO2 remains elusive. In this work, we used a combination of excited- and ground-state ab initio molecular dynamics to unravel the possible mechanisms leading to the decarboxylation of pyruvic acid. Our calculations highlight the importance of a proton-coupled electron transfer mechanism taking place in the first excited electronic state and triggering a nonadiabatic transfer of the molecule to the ground electronic state. The decarboxylation takes place in the ground-electronic state with the concomitant formation of methylhydroxycarbene. We also calculate the photoabsorption cross-section and wavelength-dependent quantum yields for pyruvic acid, highlighting the limits of our theoretical formalism.

The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO2C2H7+ and PO2CH4+, oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO2C2H7+ and PO2CH4+. The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.

Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.

Skin photoprotection against UVA radiation is crucial, but it is hindered by the sparsity of approved commercial UVA filters. Sinapoyl malate (SM) derivatives are promising candidates for a new class of UVA filters. They have been previously identified as an efficient photoprotective sunscreen in plants due to their fast nonradiative energy dissipation. Combining experimental and computational results, in our previous letter (J. Phys. Chem. Lett. 2021, 12, 337-344) we showed that coumaryl Meldrum (CMe) and sinapoyl Meldrum (SMe) are outstanding candidates for UVA filters in sunscreen formulations. Here, we deliver a comprehensive computational characterization of the excited-state dynamics of these molecules. Using reaction pathways and excited-state dynamics simulations, we could elucidate the photodeactivation mechanism of these molecules. Upon photoexcitation, they follow a two-step logistic decay. First, an ultrafast and efficient relaxation stabilizes the excited state alongside a 90° twisting around the allylic double bond, giving rise to a minimum with a twisted intramolecular excited-state (TICT) character. From this minimum, internal conversion to the ground state occurs after overcoming a 0.2 eV barrier. Minor differences in the nonradiative decay and fluorescence of CMe and SMe are associated with an additional minimum present only in the latter. ispartof: JOURNAL OF PHYSICAL CHEMISTRY A vol:125 issue:25 pages:5499-5508 ispartof: location:United States status: published

Controlling the excited-state properties of light driven molecular machines is crucial to achieving high efficiency and directed functionality. A key challenge in achieving control lies in unravelling the complex photodynamics and especially in identifying the role played by dark states. Here we use the structure sensitivity and high time resolution of UV-pump/IR-probe spectroscopy to build a detailed and comprehensive model of the structural evolution of light driven molecular rotors. The photodynamics of these chiral overcrowded alkene derivatives are determined by two close-lying excited electronic states. The potential energy landscape of these "bright" and "dark" states gives rise to a broad excited-state electronic absorption band over the entire mid-IR range that is probed for the first time and modeled by quantum mechanical calculations. The transient IR vibrational fingerprints observed in our studies allow for an unambiguous identification of the identity of the "dark" electronic excited state from which the photon's energy is converted into motion, and thereby pave the way for tuning the quantum yield of future molecular rotors based on this structural motif.

We report an implementation of non-adiabatic coupling (NAC) forces within the equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) framework via the summed-state approach. Using illustrative examples, we compare NAC forces computed with EOM-CCSD and multi-reference (MR) wave functions (for selected cases, we also consider configuration interaction singles). In addition to the magnitude of the NAC vectors, we analyze their direction, which is important for the calculations of the rate of non-adiabatic transitions. Our benchmark set comprises three doublet radical-cations (hexatriene, cyclohexadiene, and uracil), neutral uracil, and sodium-doped ammonia clusters. When the characters of the states agree among different methods, we observe good agreement between the respective NAC vectors, both in the Franck-Condon region and away. In the cases of large discrepancies between the methods, the disagreement can be attributed to the difference in the states' character, which, in some cases, is very sensitive to electron correlation, both within single-reference and multi-reference frameworks. The numeric results confirm that the accuracy of NAC vectors depends critically on the quality of the underlying wave functions. Within their domain of applicability, EOM-CC methods provide a viable alternative to MR approaches.

The reversibly switchable fluorescent proteins Dronpa, rsFastLime, rsKame, Padron, and bsDronpa feature the same chromophore but display a 40 nm variation in absorption maxima and an only 18 nm variation in emission maxima. In the present contribution, we employ QM/MM models to investigate the mechanism of such remarkably different spectral variations, which are caused by just a few amino acid replacements. We show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed trends in absorption maxima, with only a 3.5 kcal/mol blue-shift, and in emission maxima, with an even smaller 1.5 kcal/mol blue-shift with respect to the observed quantities. In order to explain the variations across the series, we look at the chromophore's electronic structure change during absorption and emission. Such analysis indicates that a change in charge-transfer character, which is more pronounced during absorption, triggers a cascade of hydrogen-bond-network rearrangements, suggesting preparation to an isomerization event. We also show how the contribution of Arg 89 and Arg 64 residues to the chromophore conformational changes correlate with the spectral variations in absorption and emission. Furthermore, we describe how the conical intersection stability is related to the protein's photophysical properties. While for the Dronpa, rsFastLime, and rsKame triad, the stability correlates with the photoswitching speed, this does not happen for bsDronpa and Padron, suggesting a less obvious photoisomerization mechanism. ispartof: JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol:14 issue:6 pages:3163-3172 ispartof: location:United States status: published

Exciting a molecule with an ultraviolet photon often leads to bond fission, but the final outcome of the bond cleavage is typically both molecule and phase dependent. The photodissociation of an isolated gas-phase molecule can be viewed as a closed system: Energy and momentum are conserved, and the fragmentation is irreversible. The same is not true in a solution-phase photodissociation process. Solvent interactions may dissipate some of the photoexcitation energy prior to bond fission and will dissipate any excess energy partitioned into the dissociation products. Products that have no analog in the corresponding gas-phase study may arise by, for example, geminate recombination. Here, we illustrate the extent to which dynamical insights from gas-phase studies can inform our understanding of the corresponding solution-phase photochemistry and how, in the specific case of photoinduced ring-opening reactions, solution-phase studies can in some cases reveal dynamical insights more clearly than the corresponding gas-phase study.

International audience; Singlet oxygen production upon photosensitization plays a critical role in drugs based on thionucleobases. While for immunosuppressants its yield must be near zero, for phototherapeutic drugs it should be near the unity. In this work, we apply high-level quantum chemical modelling to investigate the decay of the triplet state of thionucleobases, a main determinant of the singlet oxygen yield. Working on CASPT2 optimizations of two prototypical thiothymines (2-thiothymine and 6-aza-2-thiothymine), we showed that the T-1 state is characterized by two pi pi* minima and by the intersection of T-1 with the singlet ground state. On the basis of this topography, we propose a two-step mechanistic model, which, depending on the energetic balance between the two minima, may have as a determining step either a slow transition between minima or a faster intersystem crossing to S-0. Chemical kinetics modelling, as well as simulations of the transient absorption spectra, confirmed that the two-step model can explain the experimental results available for both molecules. Moreover, through additional investigations of 2-thiocytosine and 6-thioguanine, we show that such a T-1 topography is a common theme for nucleobases. We also discuss how the triplet-state topography may be used to control the singlet oxygen yield, aiming at different medical applications.

We report a combined experimental (H (Rydberg) atom photofragment translational spectroscopy) and theoretical (ab initio electronic structure and vibronic coupling calculations) study of the effects of symmetry on the photodissociation dynamics of phenols. Ultraviolet photoexcitation to the bound S1((1)ππ*) state of many phenols leads to some O-H bond fission by tunneling through the barrier under the conical intersection (CI) between the S1 and dissociative S2((1)πσ*) potential energy surfaces in the R(O-H) stretch coordinate. Careful analysis of the total kinetic energy release spectra of the resulting products shows that the radicals formed following S1 ← S0 excitation of phenol and symmetrically substituted phenols like 4-fluorophenol all carry an odd number of quanta in vibrational mode ν(16a), whereas those deriving from asymmetrically substituted systems like 3-fluorophenol or 4-methoxyphenol do not. This contrasting behavior can be traced back to symmetry. Symmetrically substituted phenols exist in two equivalent rotamers, which interconvert by tunneling through the barrier to OH torsional motion. Their states are thus best considered in the non-rigid G4 molecular symmetry group, wherein radiationless transfer from the S1 to S2 state requires a coupling mode of a2 symmetry. Of the three a2 symmetry parent modes, the out-of-plane ring puckering mode ν(16a) shows much the largest interstate coupling constant in the vicinity of the S1/S2 CI. The nuclear motions associated with ν(16a) are orthogonal to the dissociation coordinate, and are thus retained in the radical products. Introducing asymmetry (even a non-linear substituent in the 4-position) lifts the degeneracy of the rotamers, and lowers the molecular symmetry to Cs. Many more parent motions satisfy the reduced (a'') symmetry requirement to enable S1/S2 coupling, the most effective of which is OH torsion. This motion 'disappears' on O-H bond fission; symmetry thus imposes no restriction to forming radical products with vibrational quantum number v = 0. The present work yields values for the O-H bond strengths in 3-FPhOH and 4-MeOPhOH, and recommends modest revisions to the previously reported O-H bond strengths in other asymmetrically substituted phenols like 3- and 2-methylphenol and 4-hydroxyindole.

International audience; Photochromism of the spiropyran radical cation to the corresponding merocyanine form is investigated by a combination of electrochemical oxidation, UV/vis absorption spectroscopy, spectroelectrochemistry and first-principles calculations (TD-DFT, CAS-SCF and CAS-PT2). First, we demonstrate that the ring-opening of mono-spiropyrans occurs upon one-electron oxidation and that it can be driven photochemically as well as thermally, with trapping of the merocyanine by protonation. Second, in order to explain this experimentally observed spectroelectrochemical behaviour we suggest a theoretical mechanism based on the reactivity of the two lowest electronic excited-states, which promotes effective electron transfer from the indoline (nitrogen-ring) to the pyran (oxygen-ring) moieties (and vice versa) through a conical intersection seam of degeneracy. Characterisation of the minimum energy conical intersection on this crossing revealed that it presents a rare diabatic trapping topology. The excited state molecule cannot escape from crossing the intersection seam due to the presence of only one degeneracy-lifting coordinate that efficiently channels into the formation of the merocyanine photoproduct, so giving rise to a “kitchen sink” funnel-like effect. Therefore, assuming rapid relaxation after vertical excitation to a higher electronic state, photoconversion cannot be avoided in the D1 electronic state, which rationalises the remarkably efficient visible light driven excited-state reactivity observed experimentally.

Chemical Physics, 414, ISSN:0301-0104, ISSN:1873-4421

A theoretical investigation based on DFT, TD-DFT, and CASSCF/CASPT2 methods has been carried out to elucidate the photophysics of two anilino-substituted pentacyano- and tetracyanobuta-1,3-dienes (PCBD and TCBD, respectively). These molecules exhibit exceptional electron-accepting properties, but their effective use in multicomponent systems for photoinduced electron transfer is limited because they undergo ultrafast (∼1 ps) radiationless deactivation. We show that the lowest-energy excited states of these molecules have a twisted intramolecular charge-transfer character and deactivate to the ground state through energetically accessible conical intersections (CIs). The topology of the lowest-energy CI, analyzed with a linear interpolation of the two branching-space vectors (g and h), indicates it is a sloped CI, ultimately responsible for the ultrafast deactivation of this class of compounds.

We report a theoretical study of the photoisomerization step in the operating cycle of a prototypical fluorene-based molecular rotary motor (1). The potential energy surfaces of the ground electronic state (S(0)) and the first singlet excited state (S(1)) are explored by semiempirical quantum-chemical calculations using the orthogonalization-corrected OM2 Hamiltonian in combination with a multireference configuration interaction (MRCI) treatment. The OM2/MRCI results for the So and Si minima of the relevant 1-P and 1-M isomers and for the corresponding S(0) transition state are in good agreement with higher-level calculations, both with regard to geometries and energetics. The S(1) surface is characterized at the OM2/MRCI level by locating two S(0)-S(1) minimum-energy conical intersections and nearby points on the intersection seam and by computing energy profiles for pathways toward these MECIs. Semiclassical Tully-type trajectory surface hopping (TSH) simulations with on-the-fly OM2/MRCI calculations are carried out to study the excited-state dynamics after photoexcitation to the S(1) state. Fast relaxation to the ground state is observed through the conical intersection regions, predominantly through the lowest-energy one with a strongly twisted central C=C double bond and pyramidalized central carbon atom. The excited-state lifetimes for the direct and inverse photoisomerization reactions (1.40 and 1.79 ps) and the photostationary state ratio (2.7:1) from the TSH-OM2 simulations are in good agreement with the available experimental data (ca. 1.7 ps and 3:1). Excited-state lifetimes, photostationary state ratio, and dynamical details of the TSH-OM2 simulations also agree with classical molecular dynamics simulations using a reparametrized optimized potentials for liquid simulations (OPLS) all-atom force field with ad-hoc surface hops at predefined conical intersection points. The latter approach allows for a more extensive statistical sampling.

a b s t r a c t We propose mechanisms which describe the photoinduced disruption of the intramolecular H-bond in the stable enol form of acetylacetone. The study was performed with the second-order approximate coupled cluster singles and doubles model CC2. The basis set aug-cc-pVDZ was applied. The excited-state reaction paths of the rotations around CAC, C@C and CAO bonds were investigated using both coordinate- driven (relaxed scan) and linear interpolation in internal coordinates (LIIC) approaches. We show that the 1pp⁄ excited states of the rotations around the C@C double bond relax in, a completely barrierless manner, to the ground state via S0–S1 conical intersections. This is the main relaxation channel of the excited states associated with the disruption of the strong H-bond in the enol form of acetylacetone. The CAC and CAO rotations did not show such mechanisms.

Light-driven molecular rotary motors derived from chiral overcrowded alkenes represent a broad class of compounds for which photochemical rearrangements lead to large scale motion of one part of the molecule with respect to another. It is this motion/change in molecular shape that is employed in many of their applications. A key group in this class are the molecular rotary motors that undergo unidirectional light-driven rotation about a double bond through a series of photochemical and thermal steps. In the present contribution we report a combined quantum chemical and molecular dynamics study of the mechanism of the rotational cycle of the fluorene-based molecular rotary motor 9-(2,4,7-trimethy1-2,3-dihydro-1H-inden-1-ylidene)-9H-fluorene (1). The potential energy surfaces of the ground and excited singlet states of I were calculated, and it was found that conical intersections play a central role in the mechanism of photo conversion between the stable conformer of 1 and its metastable conformer. Molecular dynamics simulations indicate that the average lifetime of the fluorene motor in the excited state is 1.40 +/- 0.10 ps when starting from the stable conformer, which increases to 1.77 +/- 0.13 ps for the reverse photoisomerization. These simulations indicate that the quantum yield of photoisomerization of the stable conformer is 0.92, whereas it is only 0.40 for the reverse photoisomerization. For the first time, a theoretical understanding of the experimentally observed photostationary state of 1 is reported that provides a detailed picture of the photoisomerization dynamics in overcrowded alkene-based molecular motor 1. The analysis of the electronic structure of the fluorene molecular motor holds considerable implications for the design of molecular motors. Importantly, the role of pyramidalization and conical intersections offer new insight into the factors that dominate the photostationary state achieved in these systems.

© 2015 AIP Publishing LLC. Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/Latransitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.

The excitation wavelength dependent photodynamics of pyrrole are investigated by nonadiabatic trajectory-surface-hopping dynamics simulations based on time dependent density functional theory (TDDFT) and the algebraic diagrammatic construction method to the second order (ADC(2)). The ADC(2) results confirm that the N-H bond dissociation occurring upon excitation at the origin of the first excited state, S-1(pi sigma*), is driven by tunnelling [Roberts et al., Faraday Discuss., 2013, 163, 95] as a barrier of DE = 1780 cm(-1) traps the population in a quasi-bound minimum. Upon excitation to S-1(pi sigma*) in the wavelength range of 236-240 nm, direct dissociation of the N-H bond takes place with a time constant of 28 fs. The computed time constant is in very good agreement with recently reported measurements. Excitation to the lowest B-2 state in the 198-202 nm range returns a time constant for N-H fission of 48 fs at the B3LYP/def2-TZVPD level, in perfect agreement with the experiment [Roberts et al. Faraday Discuss., 2013, 163, 95]. For the same wavelength range the ADC(2)/aug-cc-pVDZ decay constant is more than three times longer than the experimentally reported one. The accuracy of the B3LYP/def2-TZVPD dynamics is checked against reference complete-active-space second-order perturbation theory (CASPT2) calculations and explained in terms of correct topography of the pi pi* surface and the lack of mixing between the pi pi* and the 3p(x) Rydberg states which occurs in the ADC(2) method.

The dynamics of photoexcited 2,4-dimethylpyrrole (DMP) were studied using time-resolved velocity map imaging spectroscopy over a range of photoexcitation wavelengths (276238 nm). Two dominant H atom elimination channels were inferred from the time-resolved total kinetic energy release spectra, one which occurs with a time constant of similar to 120 fs producing H atoms with high kinetic energies centered around 50007000 cm(1) and a second channel with a time constant of similar to 3.5 ps producing H atoms with low kinetic energies centered around 25003000 cm(1). The first of these channels is attributed to direct excitation from the ground electronic state (S-0) to the dissociative 1(1)pi sigma* state (S-1) and subsequent NH bond fission, moderated by a reaction barrier in the NH stretch coordinate. In contrast to analogous measurements in pyrrole (Roberts et al. Faraday Discuss. 2013, 163, 95116), the NH dissociation times are invariant with photoexcitation wavelength, implying a relatively flatter potential in the vertical FranckCondon region of the 1(1)pi sigma* state of DMP. The origins of the second channel are less clear-cut, but given the picosecond time constant for this process, we posit that this channel is indirect and is likely a consequence of populating higher-lying electronic states [e.g., 2(1)pi sigma*(S-2)] which, following vibronic coupling into lower-lying intermediary states (namely, S-1 or S-0), leads to prompt NH bond fission.

A combination of ultrafast transient electronic absorption spectroscopy (TEAS) and transient vibrational absorption spectroscopy (TVAS) is used to investigate whether photoinduced N–H bond fission, mediated by a dissociative 1πσ(*) state, is active in aqueous adenine (Ade) at 266 and 220 nm. In order to isolate UV/visible and IR spectral signatures of the adeninyl radical (Ade[-H]), formed as a result of N–H bond fission, TEAS and TVAS are performed on Ade in D2O under basic conditions (pD = 12.5), which forms Ade[-H](-) anions via deprotonation at the N7 or N9 sites of Ade's 7H and 9H tautomers. At 220 nm we observe one-photon detachment of an electron from Ade[-H](-), which generates solvated electrons (eaq(-)) together with Ade[-H] radicals, with clear signatures in both TEAS and TVAS. Additional wavelength dependent TEAS measurements between 240–260 nm identify a threshold of 4.9 ± 0.1 eV (∼250 nm) for this photodetachment process in D2O. Analogous TEAS experiments on aqueous Ade at pD = 7.4 generate a similar photoproduct signal together with eaq(-) after excitation at 266 and 220 nm. These eaq(-) are born from ionization of Ade, together with Ade(+) cations, which are indistinguishable from Ade[-H] radicals in TEAS. Ade(+) and Ade[-H] are found to have different signatures in TVAS and we verify that the pD = 7.4 photoproduct signal observed in TEAS following 220 nm excitation is solely due to Ade(+) cations. Based on these observations, we conclude that: (i) N–H bond fission in aqueous Ade is inactive at wavelengths ≥220 nm; and (ii) if such a channel exists in aqueous solution, its threshold is strongly blue-shifted relative to the onset of the same process in gas phase 9H-Ade (≤233 nm). In addition, we extract excited state lifetimes and vibrational cooling dynamics for 9H-Ade and Ade[-H](-). In both cases, excited state lifetimes of500 fs are identified, while vibrational cooling occurs within a time frame of 4–5 ps. In contrast, 7H-Ade is confirmed to have a longer excited state lifetime of ∼5–10 ps through both TEAS and TVAS.

The proton transfer from the green fluorescent protein chromophore to a nearby water molecule is studied by means of CASSCF, CASPT2 and TDDFT calculations. A 1 πσ* electronic state is found to intersect with the photoactive 1 ππ* electronic state along the proton transfer coordinate. This state crossing constitutes a possible non-radiative deactivation pathway of the photoexcited neutral form of the chromophore. A discussion on the performance of the different levels of theory employed is also given, focusing in the ability to correctly describe the 1 πσ* electronic state.

It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G− with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S1/S0 conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G− nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G−-A and 8-oxo-G−-C base pairs are likely too short-lived to be efficient electron-transfer repair agents.

In benzophenone, intersystem crossing occurs efficiently between the S-1(n pi(star)) state and the T-1 state of dominant n pi(star) character, leading to excited triplet states after photoexcitation. The transition mechanism between S-1(n pi(star)) and T-1 is still a matter of debate, despite several experimental studies. Quantum mechanical calculations have been performed in order to assess the relative efficiencies of previously proposed mechanisms, in particular, the direct S-1 -> T-1 and indirect S-1 -> T-2(pi pi(star)) -> T-1 ones. Multiconfigurational wave function based methods are used to discuss the nature of the relevant states and also to determine minimum energy paths and conical intersections. It is found that the T-1 state has a mixed n pi(star)/pi pi(star) character and that the T-2(pi pi(star)) state acts as an intermediate state between the S-1 and T-1 states. This result is in line with recent experiments, which suggested a two-step kinetic model to populate the phosphorescent state after photoexcitation [Aloise et al., J. Phys. Chem. A, 2008, 112, 224-231].

The intrinsic photophysics of nucleobases and nucleotides following UV absorption presents a key reductionist step toward understanding the complex photodamage mechanisms occurring in DNA. The decay mechanism of adenine in particular has been the focus of intense investigation, as has how these correlate to those of its more biologically relevant nucleotide and oligonucleotides in aqueous solution. Here, we report on time-resolved photoelectron imaging of the deprotonated 3'-deoxy-adenosine-5'-monophosphate nucleotide and the adenosine di- and trinucleotides. Through a comparison of gas- and solution-phase experiments and available theoretical studies, the dynamics of the base are shown to be relatively insensitive to the surrounding environment. The decay mechanism primarily involves internal conversion from the initially populated (1)ππ* states to the ground state. The relaxation dynamics of the adenosine oligonucleotides are similar to those of the nucleobase, in contrast to the aqueous oligonucleotides, where a fraction of the ensemble forms long-lived excimer states.

A wavelength-resolved (λpump = 295, 285, 270, and 267 nm) photodissociation study of para-methylthiophenol (p-MePhSH) in ethanol solution has been performed using femtosecond transient absorption (TA) spectroscopy, and the results compared with those from studies of the corresponding photodissociation in cyclohexane solution at 270 nm. Anisotropy spectra are used to identify the electronic character of the initially populated excited state(s). S-H bond fission is found to occur via the dissociative S2(1(1)πσ*) state, which can be populated directly, or by ultrafast nonradiative transitions from the S3(2(1)ππ*) state, or by very efficient tunneling from the S1(1(1)ππ*) state, depending on the excitation wavelength, in line with conclusions from previous gas-phase studies of this same molecular photodissociation (Oliver, T. A. A.; King, G. A.; Tew, D. P.; Dixon R. N.; Ashfold, M. N. R. J. Phys. Chem. A 2012, 116, 12444). p-MePhS radicals are observed on a time scale faster than the instrument response at all wavelengths, but the available time resolution affords a rare opportunity to explore the branching between different electronic states of a product (the à and X̃ states of the p-MePhS radical in this case). The present study provides estimates of this branching in the products formed immediately after the first pass through the conical intersection (CI) between the S2 and S0 states. At 270 nm, for example, we identify a marked population inversion in the radical products, in contrast to the reported gas phase behavior. The finding that the contrast in branching ratio is largest between cyclohexane solution and the gas phase, with ethanol being intermediate, can be rationalized by recognizing the differing distributions of the S-H torsion angle (relative to the ring plane) in a room temperature solution compared with those in a jet-cooled molecular beam. The available time resolution also allows exploration of the electronic quenching of nascent à state radicals as solvent motion encourages recrossing of the S2/S0 CI. The average separation distance, , between the H + p-MePhS products arising in successful dissociation events is seen to increase with decreasing photolysis wavelength. This finding accords with the previous gas phase results, which determined that most of the excess energy following population of the dissociative S2 state (directly, or by ultrafast coupling from the S3 state) is released as product translation, and the expectation that should scale with the total kinetic energy release. The present work also confirms that geminate recombination of the H + p-MePhS products leads not just to reformation of parent p-MePhSH molecules but also to alternative adducts wherein the H atom bonds to the benzene ring. Analysis of the present data and results of high level ab initio calculations together with recent UV-IR pump-probe measurements (Murdock, D.; Harris, S. J.; Karsili, T. N. V.; Greetham, G. M.; Clark, I. P.; Towrie, M.; Orr-Ewing, A. J.; Ashfold, M. N. R. J. Phys. Chem. Lett. 2012, 3, 3715) allows identification of the likely adduct structures.

H (Rydberg) atom photofragment translational spectroscopy and ab initio electronic structure calculations are used to explore ways in which ring substituents affect the photofragmentation dynamics of gas phase pyrroles. S1 ← S0 (σ* ← π) excitation in bare pyrrole is electric dipole forbidden but gains transition probability by vibronic mixing with higher electronic states. The S1 state is dissociative with respect to N-H bond extension, and the resulting pyrrolyl radicals are formed in a limited number of (nontotally symmetric) vibrational levels (Cronin et al. Phys. Chem. Chem. Phys. 2004, 6, 5031-5041). Introducing σ-perturbing groups (e.g., an ethyl group in the 2-position or methyl groups in the 2- and 4-positions) lowers the molecular symmetry (to C(s)), renders the S1-S0 transition (weakly) allowed, and causes some reduction in N-H bond strength; the radical products are again formed in a select subset of the many possible vibrational levels but all involve in-plane (a') ring-breathing motions as expected (by Franck-Condon arguments) given the changes in equilibrium geometry upon σ* ← π excitation. The effects of π-perturbers are explored computationally only. Relative to bare pyrrole, introducing an electron donating group like methoxy (at the 3- or, particularly, the 2-position) is calculated to cause a ∼10% reduction in N-H bond strength, while CN substitution (in either position) is predicted to cause a substantial (∼3000 cm(-1)) increase in the S1-S0 energy separation but only a modest (∼2%) increase in N-H bond strength.

International audience; Here, we present some highlights of our recent study [Malhado et al. J. Phys. Chem. A 115 , 3729 (2011)] of the photoisomerization involving a conical intersection for a model protonated Schiff base (PSB) in modeled water and acetonitrile solvents, in which the inclusion of energy‐ and momentum‐transfer effects is described via a generalized Langevin equation (GLE) frictional approach and surface‐hopping dynamics. Short‐time GLE frictional effects on the model's three coordinates, the intramolecular bond length alternation, and torsional PSB coordinates and a solvent coordinate, have a number of important features. Among these are the general feature of accelerating nonadiabatic transitions to the ground electronic state and a predicted preferential higher proportion of ground‐state trans isomer, that is, a successful cis to trans photoreaction. This preference is solvent‐dependent and is enhanced in water solvent with its higher friction intensity and short time scales.

The ground- and the lowest singlet excited-state potential energy surfaces of the bis-thiaxanthylidene (3) molecular switch are investigated using a density functional method specifically designed to treat molecular systems typified by strong non-dynamic electron correlation. The results of the theoretical calculations suggest that the unique ability of substituted bis-thiaxanthylidenes to switch between three states of luminescencenon-fluorescent state, blue fluorescent state, and red fluorescent statecan be explained by specific features on the excited state potential energy surface: the potential barrier around the FranckCondon point of the anti-folded conformer and the existence of conical intersection in the vicinity of the syn-folded conformer. It is suggested that the twisted conformer, if made more stable via chemical modification, should fluoresce in the near-infrared region (gimel approximate to 740760 nm), thus offering a possibility for a four-state switching of luminescence in a single-component molecular system.

The role of the seam of intersection between the lowest (pi,pi*) and (n,pi*) excited states in the decay of electronically excited singlet thymine has been investigated with ab initio complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics on the full-dimensional CASSCF surface, with 39 degrees of freedom. The seam has a sloped-to-peaked topography, and the dynamics at the different segments of the seam have been studied by varying the initial conditions of the propagation. When the wave packet is directed to the peaked segments, part of it traverses the seam, stays on the (pi,pi*) state and heads towards decay to the ground state. In contrast to this, when the wave packet is driven to sloped seam segments it bounces back to the minimum of the (pi,pi*) state. Significant population transfer to the (n,pi*) state is observed in both cases. The results suggest that a sloped-to-peaked topography can be used to control photochemical reactivity, by driving the wave packet to different regions of the seam where a different outcome of the propagation can be expected.

The experimental ultrafast photophysics of thioxanthone in several aprotic organic solvents at room temperature is presented, measured using femtosecond transient absorption together with high-level ab initio CASPT2 calculations of the singlet- and triplet-state manifolds in the gas phase, including computed state minima and conical intersections, transition energies, oscillator strengths, and spin-orbit coupling terms. The initially populated singlet pi pi* state is shown to decay through internal conversion and intersystem crossing processes via intermediate n pi* singlet and triplet states, respectively. Two easily accessible conical intersections explain the favorable internal conversion rates and low fluorescence quantum yields in nonpolar media. The presence of a singlet-triplet crossing near the singlet pi pi* minimum and the large spin-orbit coupling terms also rationalize the high intersystem crossing rates. A phenomenological kinetic scheme is proposed that accounts for the decrease in internal conversion and intersystem crossing (i.e. the very large experimental crescendo of the fluorescence quantum yield) with the increase of solvent polarity.

The photodynamics along the main decay paths of thymine after excitation to the lowest pi,pi* state have been studied with MS-CASPT2 calculations and semiclassical CASSCF dynamics calculations including a surface hopping algorithm. The static calculations show that there are two decay paths from the Franck-Condon structure that lead to a conical intersection with the ground state. The first path goes directly to the intersection, while the second one is indirect and involves a minimum of the pi,pi* state, a small barrier, and a crossing between the pi,pi* and n,pi* states. From the static calculations, both paths have similar slopes. The dynamics calculations along the indirect path show that, after the barrier, part of the trajectories are funneled to the intersection with the ground state, where they are efficiently quenched to the ground state. The remaining trajectories populate the n,pi* state. They are also quenched to the ground state in less than 1 ps, but the static calculations show that the decay rate of the n,pi* state is largely overestimated at the CASSCF level used for the dynamics, Overall, these results suggest that both direct and indirect paths contribute to the subpicosecond decay components found experimentally. The indirect path also provides a way for fast population of the n,pi* state, which will account for the experimental picosecond decay component

We present a summary of recent advances in the understanding of the UV photophysics of the isolated DNA base adenine, emphasizing a discussion of the mechanisms behind the ultrafast relaxation following excitation to the pipi* band. Drawing on our femtosecond time-resolved photoelectron spectroscopy experiments, we discuss differences in the ultrafast relaxation of adenine and 9-methyladenine and consider the relative merits of the various proposed mechanisms.

Multireference configuration interaction (MRCI) calculations have been performed for pyrrole with the aim of providing an explanation for the experimentally observed photochemical deactivation processes. Potential energy curves and minima on the crossing seam (MXS) were determined using the analytic MRCI gradient and nonadiabatic coupling features of the COLUMBUS program system. A new deactivation mechanism based on an out-of-plane ring deformation will be presented. This mechanism directly couples the charge-transfer ^1pipi* and ground states. It may be responsible for more than 50% of the observed photofragments of pipi*-excited pyrrole. The ring-deformation mechanism should act complementary to the previously proposed NH-stretching mechanism, thus offering a more complete interpretation of the pyrrole photodynamics.

Three approximate switching algorithms for trajectory surface hopping calculations are presented using simple models to describe the dependence of the hopping probability on the nonadiabatic coupling strength. The switching algorithms are applied to the calculation of the electronic deexcitation in ethylene, methaniminium ion and trans-azobenzene. Compared with the results from the standard fewest switching algorithm (FSA), the simplest approximation based on a local diabatic representation shows some qualitative failures and overestimates the decay times severely. The other two approximate switching algorithms incorporate stochastic features and reproduce the FSA results well, with a deviation of typically 20–30% in the computed decay times. They offer a simple and efficient description of the nonadiabatic dynamics of the investigated systems.

An approach to the quantum-classical mechanics of phase space dependent operators, which has been proposed recently, is remodeled as a formalism for wave fields. Such wave fields obey a system of coupled non-linear equations that can be written by means of a suitable non-Hamiltonian bracket. As an example, the theory is applied to the relaxation dynamics of the spin-boson model. In the adiabatic limit, a good agreement with calculations performed by the operator approach is obtained. Moreover, the theory proposed in this paper can take nonadiabatic effects into account without resorting to surface-hopping approximations. Hence, the results obtained follow qualitatively those of previous surface-hopping calculations and increase by a factor of (at least) two the time length over which nonadiabatic dynamics can be propagated with small statistical errors. Moreover, it is worth to note that the dynamics of quantum-classical wave fields here proposed is a straightforward non-Hamiltonian generalization of the formalism for non-linear quantum mechanics that Weinberg introduced recently., Comment: Manuscript accepted by The Journal of Chemical Physics

In this paper we employ a CASSCF/AMBER quantum-mechanics/molecular-mechanics tool to map the intersection space (IS) of a protein. In particular, we provide evidence that the S1 excited-state potential-energy surface of the visual photoreceptor rhodopsin is spanned by an IS segment located right at the bottom of the surface. Analysis of the molecular structures of the protein chromophore (a protonated Schiff base of retinal) along IS reveals a type of geometrical deformation not observed in vacuo. Such a structure suggests that conical intersections mediating different photochemical reactions reside along the same intersection space. This conjecture is investigated by mapping the intersection space of the rhodopsin chromophore model 2-Z-hepta-2,4,6-trieniminium cation and of the conjugated hydrocarbon 3-Z-deca-1,3,5,6,7-pentaene.

Diverse ab initio and density-functional-theory methods were used to investigate geometries, energies, and electronic absorption spectra of guanidine and its protonated form, as well as their photo-deactivation processes. It was shown that the guanidine is a weakly absorbing species with the excitation spectrum consisting mostly of transitions to the Rydberg excited states and one valence n-π4 state. The lowest energy band has a maximum at ca. 6.9 eV (∼180 nm). The protonation of guanidine affects its excitation spectrum substantially. A major shift of the Rydberg states to higher energies is clearly visible and strongly absorbing transitions from the ground state to the π3-π4 and π2-π4 states appears at 7.8 eV (∼160 nm). Three low-lying conical intersections (two for guanidine and one for protonated guanidine) between the ground state and the first excited singlet state were located. They are accessible from the Franck-Condon region through amino N-H stretching and out-of-plane deformations in guanidine and protonated guanidine, respectively. The relaxation of the π3-3s Rydberg state via amino N-H bond stretching was hindered by a barrier. The nondissociated conical intersection in protonated guanidine mediates the radiationless deactivation of the compound after excitation into the π3-π4 state. This fact is detrimental for the photostability of guanidine, since its conjugate acid is stable in aqueous solution over a wide pH range and in protein environment, where guanidinium moiety in arginine is expected to be in a protonated form.

The wavelength dependences of C–Y and O–H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O–H bond fission following excitation at wavelengths λ ≲ 240 nm, on repulsive ((n/π)σ*) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ∼11 000 cm−1. For Y = I and Br, this process occurs in competition with prompt C–I and C–Br bond cleavage on another (n/π)σ* PES, but no Cl/Cl* products unambiguously attributable to one photon induced C–Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C–I bond fission is observed following excitation of 4-IPhOH at all λ ≤ 330 nm; the wavelength dependent trends in I/I* product branching ratio, kineticenergy release, and recoil anisotropy suggest that (with regard to C–I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O–H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C–Y centred (n/π)σ* potentials across the series Y = I < Br < Cl and the concomitant reduction in C–Y bond strength, cf. that of the rival O–H bond, and (ii) the much increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the risks inherent in extrapolating photochemical behaviour measured for one molecule at one wavelength to other (related) molecules and to other excitation energies.

International audience; The time evolution of electronically excited heme (iron II protoporphyrin IX, [Fe-II PP]) and its associated salt hemin (iron III protoporphyrin IX chloride, [Fe-III PP-Cl]), has been investigated for the first time in the gas phase by femtosecond pump-probe spectroscopy. The porphyrins were excited at 400 nm in the S-2 state (Soret band) and their relaxation dynamics was probed by multiphoton ionization at 800 nm. This time evolution was compared with that of the excited state of zinc protoporphyrin IX [Zn PP] whose S2 excited state likely decays to the long lived S-1 state through a conical intersection, in less than 100 fs. Instead, for [Fe-II PP] and [Fe-III PP-Cl], the key relaxation step from S-2 is interpreted as an ultrafast charge transfer from the porphyrin excited orbital pi* to a vacant d orbital on the iron atom (ligand to metal charge transfer, LMCT). This intermediate LMCT state then relaxes to the ground state within 250 fs. Through this work a new, serendipitous, preparation step was found for Fe II porphyrins, in the gas phase.

In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of 2n+O and another two of 2π+ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil+) evidence. We find that dynamic electron correlation separates the energy levels of the “3-state” conical intersection (D2/D1/D0)CI previously located with CASSCF for uracil+, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.

Light-driven reactions constitute an important class of processes in physics, chemistry, and biology. The development of accurate and efficient computational tools for the study of excited states dynamics has thus become of primary importance. Recently, we have developed a non-adiabatic ab initio molecular dynamics (AIMD) method, which combines Tully's surface hopping with TDDFT. Here, we investigate some fundamental aspects of this AIMD scheme that deal with the accuracy of TDDFT potential energy surfaces in regions of strong coupling and with the associated intensity of the non-adiabatic couplings (NACs). Of particular interest is the coupling between the ground and the first excited singlet state, which constitute a potential pitfall for all non-adiabatic AND based on TDDFT. To this end, we have investigated the excited state dynamics of protonated formaldimine (CH2NH2+) with particular emphasis on the analysis of the NAC strengths in regions of the configurational space close to surface hopping points and conical intersections. A good agreement of the structural and dynamical properties is found with respect to state averaged multiconfiguration self consistent field results. (C) 2009 Elsevier B.V. All rights reserved.