Singlet Excited-State Behavior of Uracil and Thymine in Aqueous Solution: A Combined Experimental and Computational Study of 11 Uracil Derivatives

A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives

The role of N1-substitution in controlling the deactivation processes in photoexcited cytosine derivatives has been explored using picosecond time-resolved IR spectroscopy. The simplest N1-substituted derivative, 1-methylcytosine, exhibits relaxation dynamics similar to the cytosine nucleobase and distinct from the biologically relevant nucleotide and nucleoside analogues, which have longer-lived excited-state intermediates. It is suggested that this is the case because the sugar group either facilitates access to the long-lived (1)n(O)π* state or retards its crossover to the ground state.

Primary photochemistry of nitrated aromatic compounds: excited-state dynamics and NO· dissociation from 9-nitroanthracene

We report results of femtosecond-resolved ex-periments which elucidate the time scale for the primary photoinduced events in the model nitroaromatic compound 9-nitroanthracene. Through time-resolved fluorescence measurements, we observed the ultrafast decay of the initially excited singlet state, and through transient absorption experiments, we observed the spectral evolution associated with the formation of the relaxed phosphorescent T(1) state. Additionally, we have detected for the first time the accumulation of the anthryloxy radical which results from the nitro-group rearrangement and NO(•) dissociation from photoexcited 9-nitroanthracene, a photochemical channel which occurs in parallel with the formation of the phosphorescent state. The spectral evolution in this molecule is highly complex since both channels take place in similar time ranges of up to a few picoseconds. Despite this complexity, our experiments provide the general time scales in which the primary products are formed. In addition, we include calculations at the time-dependent density functional level of theory which distinguish the molecular orbitals responsible for the n-π* character of the "receiver" vibronic triplet states that couple with the first singlet state and promote the ultrafast transfer of population between the two manifolds. Comparisons with the isoelectronic compounds anthracene-9-carboxylic acid and its conjugated base, which are highly fluorescent, show that in these two compounds the near-isoenergeticity of the S(1) with an appropriate "receiver" triplet state is disrupted, providing support to the idea that a specific energy coincidence is important for the ultrafast population of the triplet manifold, prevalent in polycyclic nitrated aromatic compounds.

Comparison of the non-radiative decay mechanisms of 4-pyrimidinone and uracil: an ab initio study

We performed a comparative theoretical study of the relaxation mechanisms of the excited states of uracil and 4-pyrimidinone with the CASSCF, CASPT2, and CC2 ab initio methods. The calculated vertical excitation energies agree with the experimental UV absorption maxima of the two compounds. Three low-lying conical intersections between the S(0) and S(1) states (one for uracil, two for 4-pyrimidinone) are established. They are accessible from the Franck-Condon region of the 1pipi* state through out-of-plane deformations related to C=C (for uracil) or C=N (for 4-pyrimidinone) torsions of the heterocyclic ring. These conical intersections mediate the radiationless deactivation of the compounds after excitation of the lowest 1pipi* state. The relaxation of the 1pipi* state of 4-pyrimidinone via C=C twisting is hindered by a barrier. The relaxed scan of the C=N double-bond twisting of 4-pyrimidinone indicates that the formation of the Dewar form may represent a photochemical channel in 4-pyrimidinone. This fact is detrimental for the photostability of 4-pyrimidinone, since the Dewar form is separated by a high potential-energy barrier from the canonical form of 4-pyrimidinone on the ground-state potential-energy surface, which prevents a thermal back-reaction. The investigation of the vertical excitation energies and the reaction paths shows that 4-pyrimidinone is less photostable than uracil.

Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy

The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.

Photodissociation dynamics of thiophenol-d1: the nature of excited electronic states along the S-D bond dissociation coordinate

The S-D bond dissociation dynamics of thiophenol-d1 (C6H5SD) pumped at 266, 243, and 224 nm are examined using the velocity map ion imaging technique. At both 266 and 243 nm, distinct peaks associated with X and A states of the phenylthiyl radical (C6H5S*) are observed in the D+ image at high and low kinetic energy regions, respectively. The partitioning of the available energy into the vibrational energy of the phenylthiyl radical is found to be enhanced much more strongly at 266 nm compared to that at 243 nm. This indicates that the pipi* electronic excitation at 266 nm is accompanied by significant vibrational excitation. Given the relatively large anisotropy parameter of -0.6, the S-D dissociation at 266 nm is prompt and should involve the efficient coupling to the upper-lying n(pi)sigma* repulsive potential energy surface. The optical excitation of thiophenol at 224 nm is tentatively assigned to the pisigma* transition, which leads to the fast dissociation on the repulsive potential energy surface along the S-D coordinate. The nature of the electronic transitions associated with UV absorption bands is investigated with high-level ab initio calculations. Excitations to different electronic states of thiophenol result in unique branching ratios and vibrational excitations for the fragment of the phenylthiyl radical in the two lowest electronic states.

Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case

A simple vibronic model aimed at investigating the interplay between bright excitonic states and dark charge-transfer (CT) states in stacked adenine (Ade) nucleobases is presented. Two orbitals (the HOMO and the LUMO) for each Ade site have been included in the electronic Hamiltonian, whose parameters have been fitted to reproduce the main features of the absorption spectra of two stacked 9-methyladenine (9Me-A) molecules, computed in aqueous solution at the PCM/TD-PBE0 level. Three modes for each adenine unit have been included in the Hamiltonian, to describe the main structural changes among the different excited state minima of the adenine stacked dimer, as described at the TD-DFT level. The developed vibronic Hamiltonian (four electronic states and six nuclear coordinates) has been adopted to perform quantum dynamical calculations of a photoexcited Ade stacked dimer, utilizing the multiconfigurational time-dependent Hartree method. The obtained results indicate that the transfer between the bright excitonic state and the CT state is fast and effective.

Benign decay vs. photolysis in the photophysics and photochemistry of 5-bromouracil. A computational study

The excited state potential energy surface of 5-bromouracil has been studied with ab initio CASPT2//CASSCF calculations to rationalize the competition between the benign decay and the photolysis found experimentally. The surface is characterized by an extended region of degeneracy between S(1) and S(0). The access to this region has been studied with minimum energy path calculations from the FC structure, the seam of intersection has been mapped in detail, and the decay paths from different regions of the seam have been characterized. There are two decay paths with low barriers that are limiting cases for the actual decay dynamics. The first path involves the bromine elimination and leads to a region of near degeneracy between the ground and excited states, and the second one leads back to the reactant through a conical intersection between the two states. The conical intersection for benign decay is part of a seam that lies along the C(5)-Br stretching coordinate, and decay at the region of the seam with a stretched C(5)-Br bond leads to photolysis. Thus, the reactivity depends on the point of the seam at which decay to the ground state takes place. The low experimental photolysis quantum yield suggests that the energetically favored decay is the one that regenerates the reactant, while the low barriers computed to access the region of decay are in agreement with the measured picosecond excited state lifetime.

Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations

Guanosine monophosphate (GMP) in aqueous solutions has been studied with femtosecond broad-band transient absorption spectroscopy and by quantum-mechanical calculations. The sample was excited at 267 or 287 nm and probed between 270 and 1000 nm with 100 fs resolution, for various pH values between 2 and 7. At pH 2, when the guanine ring is ground-state protonated (GMPH(+)), we observe isosbestic behavior indicating state-to-state relaxation. The relaxation is biexponential, tau(1) = 0.4 ps, tau(2) = 2.2 ps, and followed by slower internal conversion with tau(3) = 167 ps. For nonprotonated GMP in the pH range 7-4, we find biexponential decay in the region 400-900 nm (tau(1) = 0.22 ps, tau(2) = 0.9 ps), whereas, between 270 and 400 nm, the behavior is triexponential with one growing, tau(1) = 0.25 ps, and two decaying, tau(2) = 1.0 ps, tau(3) = 2.5 ps, components. The excited-state evolution is interpreted with the help of quantum-chemical calculations, performed at the time-dependent PBE0 level accounting for bulk solvent effects and specific solvation. The computed dynamics involves L(a) and L(b) bright excited states, whereas the n(0)pi* and pisigma* dark excited states play a minor role. Independent of the pH, the photoinduced evolution involves ultrafast L(b)-->L(a) conversion (tau(ba) << 100 fs) and exhibits the presence of a wide planar plateau on L(a). For neutral GMP a barrierless path connects this region to a conical intersection (CI) with the ground state, giving an account of the ultrafast decay of this species. For protonated GMPH(+) the system evolves into a stable minimum L(a min) characterized by out-of-plane displacement of NH and CH groups, which explains the longer (167 ps) fluorescence lifetime.

Thymine dimerization in DNA model systems: cyclobutane photolesion is predominantly formed via the singlet channel

UV-induced formation of cylcobutane pyrimidine dimers (CPD) in all thymine DNA models have been studied by femtosecond IR spectroscopy. CPDs are shown to form within approximately 1 ps during the decay of the initially excited (1)pi pi * state. The quantum yields phi(D)(ps) determined after the (1)pi pi * decay equal the final yield phi(D)(cw). This gives evidence for a predominance of the singlet channel in CPD formation.

DNA excited-state dynamics: from single bases to the double helix

Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.

Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: on-the-fly surface-hopping study with semiempirical methods

The photoinduced relaxation dynamics of pyrimidine nucleobases (uracil, thymine, and cytosine) was studied using the surface-hopping approach at the semiempirical OM2/MRCI level of theory. The relevant potential energy surfaces were characterized by performing geometry optimizations of the energy minima of the lowest electronic states and of the most important conical intersections and by computing excitation energies at each configuration. Surface-hopping molecular dynamics simulations were performed to describe the nonadiabatic dynamics after excitation into the optically active state. In each of the molecules, the two lowest excited singlet states are involved in the dynamics, and there are competing relaxation paths. The dynamics is dominated by a two-step relaxation mechanism in uracil and thymine, while the direct decay to the ground state is most important in cytosine. For all three molecules, the simulations yield ultrafast S(2)-S(1) deexcitation within 50 fs and internal conversion to the ground state in less than 1 ps, consistent with recent experimental results from time-resolved photoelectron spectroscopy.

Absorption spectrum of A-T DNA unraveled by quantum mechanical calculations in solution on the (dA)2 x (dT)2 tetramer

The absorption spectrum of A-T DNA is computed for the first time in aqueous solution by means of quantum mechanical calculations performed on realistic models, thereby accounting for both stacking and base pairing interactions and including solvent effects through the polarizable continuum model. The computed and experimental spectra are in close agreement. Our analysis allows the identification of all the electronic transitions hidden in the broad absorption spectrum of A-T DNA, thus determining their most relevant properties and providing an explanation for the most significant experimental features, such as the small blue shift of the band maximum and the appearance of a shoulder on the red wing of the absorption band. The lowest-energy dark excited state corresponds to a charge-transfer state between two stacked adenine bases.