Conical intersections in thymine

The mechanisms which are responsible for the radiationless deactivation of the npi* and pipi* excited singlet states of thymine have been investigated with multireference ab initio methods (the complete-active-space self-consistent-field (CASSCF) method and second-order perturbation theory with respect to the CASSCF reference (CASPT2)) as well as with the CC2 (approximated singles and doubles coupled-cluster) method. The vertical excitation energies, the equilibrium geometries of the 1npi*and 1pipi* states, as well as their adiabatic excitation energies have been determined. Three conical intersections of the S1 and S0 energy surfaces have been located. The energy profiles of the excited states and the ground state have been calculated with the CASSCF method along straight-line reaction paths leading from the ground-state equilibrium geometry to the conical intersections. All three conical intersections are characterized by strongly out-of-plane distorted geometries. The lowest-energy conical intersection (CI1) arises from a crossing of the lowest 1pipi* state with the electronic ground state. It is found to be accessible in a barrierless manner from the minimum of the 1pipi* state, providing a direct and fast pathway for the quenching of the population of the lowest optically allowed excited states of thymine. This result explains the complete diffuseness of the absorption spectrum of thymine in supersonic jets. The lowest vibronic levels of the optically nearly dark 1npi* state are predicted to lie below CI1, explaining the experimental observation of a long-lived population of dark excited states in gas-phase thymine.     

Theoretical study toward understanding ultrafast internal conversion of excited 9H-adenine

The CASPT2/CASSCF method with the 6-311G basis set and an active space up to (14, 11) was used to explore the ultrafast internal conversion mechanism for excited 9H-adenine. Three minima, two transition states, and seven conical intersections were obtained to build up the two deactivation pathways for the internal conversion mechanism. Special efforts were made to explore the excited-state potential energy surfaces near the Franck-Condon region and determine the various barriers in the processes of deactivation. The barrier required from the 1pipi (1La) state to deactivate nonradiatively is found to be lower than that required from the 1pipi (1Lb) state. On 250 nm excitation, the 1pipi (1La) state is populated, and the transition from 1pipi (1La) to the lowest 1npi state involves very low barriers, which may account for the observed short (<50 fs) lifetime of the 1pipi excited state. The deactivation of the lowest 1npi state is required to overcome a barrier of 3.15 kcal/mol, which should be responsible for the 750 fs lifetime of the npi excited state. On 267 nm excitation, the vibrationally active 1pipi (1Lb) state is populated. Excitation at 277 nm prepares the 1pipi (1Lb) state without much excessive vibrational energy, which may be responsible for the observed >2 ps lifetime.     

Environmental photochemistry of nitro-PAHs: direct observation of ultrafast intersystem crossing in 1-nitropyrene

Femtosecond broadband transient absorption experiments of 1-nitropyrene, a nitro-polycyclic aromatic hydrocarbon of environmental concern are presented in cyclohexane and hexane solutions. The transient absorption spectra show the presence of three species that are assigned to the Franck-Condon excited lowest singlet (S1) state, the structurally relaxed S1 state, and the lowest excited triplet state. The spectral changes at early times are interpreted in terms of conformational dynamics; primarily due to an ultrafast rotation of the nitro group in the S1 state. This excited state relaxation is followed by intersystem crossing with a time constant of 7 ps. CIS/6-31G(d,p) calculations predict planarization of the nitro-aromatic torsional angle as the major nuclear relaxation coordinate, from 32.8 degrees at the HF/6-31G(d,p) level of theory in the ground state (27.46 degrees at B3LYP/6-31++G(d,p)) to 0.07 degrees in the S1 state. Vertical excitation energies at the TDDFT/6-31++G(d,p) and TDDFT/IEFPCM/6-31++G(d,p) levels of theory predict a small energy gap (<0.12 eV) between the S1(pipi*) state and the third excited triplet state T3(npi*) in the gas phase and in cyclohexane, respectively. The small energy gap suggests a large spin-orbit coupling between the S1(pipi*) and T3(npi*) states, which explains the ultrafast intersystem crossing of 1-nitropyrene in nonpolar solvents.     

A theoretical investigation of P-hydroxyphenacyl caged phototrigger compounds: how water induces the photodeprotection and subsequent rearrangement reactions

Complete active-space self-consistent field (CASSCF) calculations with a (14,11) active space and density functional theory calculations followed by Car-Parrinello molecular dynamic simulations are reported for the p-hydroxyphenacyl acetate, diethyl phosphate, and diphenyl phosphate phototrigger compounds. These calculations considered the explicit hydrogen bonding of water molecules to the phototrigger compound and help reveal the role of water in promoting the photodeprotection and subsequent rearrangement reactions for the p-hydroxyphenacyl caged phototrigger compounds experimentally observed in the presence of appreciable amounts of water but not observed in neat nonproton solvents like acetonitrile. The 267 nm excitation of the phototrigger compounds leads to an instantaneous population of the S3(1pipi*) state Franck-Condon region, which is followed by an internal conversion deactivation route to the S1(1npi*) state via a 1pipi*/1npi* vibronic coupling. The shorter lifetime of the S1(1npi*) state (approximately 1 ps) starting from the FC geometry is terminated by a fast intersystem crossing at a 3pipi*/3npi* intersection with a structure of mixed pipi*/npi* excitation in the triplet state. The deprotection reaction is triggered by a proton (or hydrogen atom) transfer assisted by water bridges and emanates from this pipi*/npi* triplet state intersection. With the departure of the leaving group, the reaction evolves into a water-mediated post-deprotection phase where the spin inversion of pQM (X, 3A) leads to a spiroketone in the ground state by a cyclization process that is followed by an attack of water to produce a 1,1'-di-hydroxyl-spiroketone. Finally, the H atom of the hydroxyl in 1,1'-di-hydroxyl-spiroketon transfers back to the p-O atom aided by water molecules to generate the p-hydroxyphenyl-acetic acid final rearrangement product.     

Charge-transfer pipi* excited state in the 7-azaindole dimer. A hybrid configuration interactions singles/time-dependent density functional theory description

The hybrid configuration interaction singles/time dependent density functional theory approach of Dreuw and Head-Gordon [Dreuw, A.; Head-Gordon, M. J. Am. Chem. Soc. 2004, 126, 4007] has been applied to study the potential energy landscape and accessibility of the charge-transfer pipi* excited state in the dimer of 7-azaindole, which has been traditionally considered a model for DNA base pairing. It is found that the charge-transfer pipi* excited state preferentially stabilizes the product of a single proton transfer. In this situation, the crossing between this state and the photoactive electronic state of the dimer is accessible. It is found that the charge-transfer pipi* excited state has a very steep potential energy profile with respect to any single proton-transfer coordinate and, in contrast, an extremely flat potential energy profile with respect to the stretch of the single proton-transfer complex. This is predicted to bring about a pair of rare fragments of the 7-azaindole dimer, physically separated and hence having very long lifetimes. This could have implications in the DNA base pairs of which the system is an analogue, in the form of replication errors.     

A three-state model for the photophysics of adenine

An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine, while for the 7H tautomer the presence of an intermediate plateau corresponding to an NH2-twisted conformation may explain the absence of ultrafast decay in 7-substituted compounds. A secondary picosecond decay is assigned to a path involving switches towards two other states, 1(pipi* Lb) and 1(npi*), ultimately leading to another conical intersection with the ground state, (gs/npi*), with a perpendicular disposition of the amino group. The topology of the hypersurfaces and the state properties explain the absence of secondary decay in 9-substituted adenines in water in terms of the higher position of the 1(npi*) state and also that the 1(pipi* Lb) state of 7H-adenine is responsible for the observed fluorescence in water. A detailed discussion comparing recent experimental and theoretical findings is given. As for other nucleobases, the predominant role of a pipi*-type state in the ultrafast deactivation of adenine is confirmed.     

A theoretical investigation of p-hydroxyphenacyl caged phototrigger compounds: an examination of the excited state photochemistry of p-hydroxyphenacyl acetate

Ab initio and density functional theory methods were employed to study the excited states and potential energy surfaces of the p-hydoxyphenacyl acetate (HPA) phototrigger compound. Complete active space (CAS) ab initio calculations predicted adiabatic electronic transition energies for the HPA-T(1)((3)npi), HPA-T(2)((3)pipi), HPA-S(1)((1)npi), HPA-T(3)((3)npi), HPA-S(2)((1)npi), HPA-S(3)((1)pipi) <-- HPA-S(0) transitions that were similar to and in agreement with those found experimentally for closely related aromatic ketones such as p-hydroxyacetophenone and results from similar calculations for other related aromatic carbonyl systems. The alpha or beta bond cleavage reactions from the S(1) excited state were both found to have relatively high barriers to reaction, and the S(1), T(1), and T(2) states are close in energy with the three S(1)((1)npi), T(1)((3)npi), and T(2)((3)pipi) surfaces intersecting at the same region. The calculations suggest that intersystem crossing (ISC) can occur very fast from the S(1) state to the nearby triplet states. This is consistent with results from ultrafast spectroscopy experiments that observe the S(1) state ISC occurs within about 1-2 ps to produce a triplet state for HPA and related pHP compounds. The alpha and beta bond cleavage reactions for the T(1) state of HPA are both predicted to have fairly high barriers and compete with one another. However, this is not completely consistent with experiments that observe the photodeprotection reactions (e.g. the beta bond cleavage) of HPA and some other pHP phototriggers in largely water containing solvents are predominant and occur very fast to release the leaving group. Comparison of the computational results with experimental results for HPA and related pHP compounds suggests that water molecules likely play an important part in changing the triplet state beta bond cleavage so that it becomes the predominant pathway and occurs very fast to give an efficient deprotection reaction. The results reported here provide new insight into the photophysics, reaction pathways, and photochemistry of the p-hydoxyphenacyl acetate and related pHP caged phototrigger compounds and also provide a benchmark for further and more sophisticated investigations in the future.     

Ab initio study on deactivation pathways of excited 9H-guanine

The complete active space with second-order perturbation theory/complete active space self-consistent-field method was used to explore the nonradiative decay mechanism for excited 9H-guanine. On the 1pipi* (1L(a)) surface we determined a conical intersection (CI), labeled (S0pipi*)(CI), between the 1pipi* (1L(a)) excited state and the ground state, and a minimum, labeled (pipi*)min. For the 1pipi* (1L(a)) state, its probable deactivation path is to undergo a spontaneous relaxation to (pipi*)min first and then decay to the ground state through (S0pipi*)(CI), during which a small activation energy is required. On the 1n(N)pi* surface a CI between the 1n(N)pi* and 1pipi* (1L(a)) states was located, which suggests that the 1n(N)pi* excited state could transform to the 1pipi* (1L(a)) excited state first and then follow the deactivation path of the 1pipi* (1L(a)) state. This CI was also possibly involved in the nonradiative decay path of the second lowest 1pipi* (1L(b)) state. On the 1n(O)pi* surface a minimum was determined. The deactivation of the 1n(O)pi* state to the ground state was estimated to be energetically unfavorable. On the 1pisigma* surface, the dissociation of the N-H bond of the six-membered ring is difficult to occur due to a significant barrier.     

Computational studies of the photophysics of hydrogen-bonded molecular systems

The role of electron- and proton-transfer processes in the photophysics of hydrogen-bonded molecular systems has been investigated with ab initio electronic-structure calculations. Adopting indole, pyridine, and ammonia as molecular building blocks, we discuss generic mechanisms of the photophysics of isolated aromatic chromophores (indole), complexes of pi systems with solvent molecules (indole-ammonia, pyridine-ammonia), hydrogen-bonded aromatic pairs (indole-pyridine), and intramolecularly hydrogen-bonded pi systems (7-(2'-pyridyl)indole). The reaction mechanisms are discussed in terms of excited-state minimum-energy paths, conical intersections, and the properties of frontier orbitals. A common feature of the photochemistry of the various systems is the electron-driven proton-transfer (EDPT) mechanism: highly polar charge-transfer states of 1pipi*, 1npi*, or 1pisigma* character drive the proton transfer, which leads, in most cases, to a conical intersection of the S1 and S0 surfaces and thus ultrafast internal conversion. In intramolecularly hydrogen-bonded aromatic systems, out-of-plane torsion is additionally needed for barrierless access to the S1-S0 conical intersection. The EDPT process plays an essential role in diverse photophysical phenomena, such as fluorescence quenching in protic solvents, the function of organic photostabilizers, and the photostability of biological molecules.     

Photoisomerization of disperse red 1 studied with transient absorption spectroscopy and quantum chemical calculations

The photoisomerization of the push-pull substituted azo dye Disperse Red 1 is studied using femtosecond time-resolved absorption spectroscopy and other spectroscopic and computational techniques. In comparison with azobenzene, the pipi* state is more stabilized by the effects of push-pull substitution than the npi* state, but the latter is probably still the lowest in energy. This conclusion is based on the kinetics, anisotropy of the excited state absorption spectrum, the spectra of the ground states, and quantum chemical calculations. The S(1)(npi*) state is formed from the initially excited pipi* state in <0.2 ps, and decays to the ground state with time constants of 0.9 ps in toluene, 0.5 ps in acetonitrile, and 1.4 ps in ethylene glycol. Thermal isomerization transforms the Z isomer produced to the more stable E isomer with time constants of 29 s (toluene), 28 ms (acetonitrile), and 2.7 ms (ethylene glycol). The pathway of photoisomerization is likely to be rotation about the N=N bond. Quantum chemical calculations indicate that along the inversion pathway ground and excited state energy surfaces remain well separated, whereas rotation leads to a region where conical intersections can occur. For the ground-state Z to E isomerization, conclusive evidence is lacking, but inversion is more probably the favored pathway in the push-pull substituted systems than in the parent azobenzene.     

Study of acyl group migration by femtosecond transient absorption spectroscopy and computational chemistry

The primary photophysical and photochemical processes in the photochemistry of 1-acetoxy-2-methoxyanthraquinone (1a) were studied using femtosecond transient absorption spectroscopy. Excitation of 1a at 270 nm results in the population of a set of highly excited singlet states. Internal conversion to the lowest singlet npi* excited state, followed by an intramolecular vibrational energy redistribution (IVR) process, proceeds with a time constant of 150 +/- 90 fs. The 1npi* excited state undergoes very fast intersystem crossing (ISC, 11 +/- 1 ps) to form the lowest triplet pipi* excited state which contains excess vibrational energy. The vibrational cooling occurs somewhat faster (4 +/- 1 ps) than ISC. The primary photochemical process, migration of acetoxy group, proceeds on the triplet potential energy surface with a time constant of 220 +/- 30 ps. The transient absorption spectra of the lowest singlet and triplet excited states of 1a, as well as the triplet excited state of the product, 9-acetoxy-2-methoxy-1,10-anthraquinone (2a), were detected. The assignments of the transient absorption spectra were supported by time-dependent DFT calculations of the UV-vis spectra of the proposed intermediates. All of the stationary points for acyl group migration on the triplet and ground state singlet potential energy surfaces were localized, and the influence of the acyl group substitution on the rate constants of the photochemical and thermal processes was analyzed.     

On the intrinsic population of the lowest triplet state of thymine

The population of the lowest triplet state of thymine after near-UV irradiation has been established, on the basis of CASPT2//CASSCF quantum chemical calculations, to take place via three distinct intersystem crossing mechanisms from the initially populated singlet bright 1pipi* state. Two singlet-triplet crossings have been found along the minimum-energy path for ultrafast decay of the singlet state at 4.8 and 4.0 eV, involving the lowest 3npi* and 3pipi* states, respectively. Large spin-orbit coupling elements predict efficient intersystem crossing processes in both cases. Another mechanism involving energy transfer from the lowest 1npi* state with much larger spin-orbit coupling terms can also be proposed. The wavelength dependence measured for the triplet quantum yield of pyrimidine nucleobases is explained by the location and accessibility of the singlet-triplet crossing regions.     

On the unusual fluorescence properties of xanthone in water

Photo-excited xanthone is known to undergo ultrafast intersystem crossing (ISC) in the 1 ps time domain. Correspondingly, its fluorescence quantum yield in most solvents is very small ( approximately 10(-4)). Surprisingly, the quantum yield in water is 100 times larger, while ISC is still rapid ( approximately 1 ps), as seen by ultrafast pump probe absorption spectroscopy. Temperature dependent steady state and time resolved fluorescence experiments point to a delayed fluorescence mechanism, where the triplet (3)npi* state primarily accessed by ISC is nearly isoenergetic with the photo-excited (1)pipi* state. The delayed fluorescence of xanthone in water decays with a time constant of 700 ps, apparently by internal conversion between the (3)npi* state and the lowest lying triplet state (3)pipi*.     

Role of electron-driven proton-transfer processes in the excited-state deactivation of the adenine-thymine base pair

Exploratory electronic structure calculations have been performed with the CC2 (simplified singles and doubles coupled-cluster) method for two conformers of the adenine (A)-thymine (T) base pair, with emphasis on excited-state proton-transfer reactions. The Watson-Crick conformer and the most stable (in the gas-phase) conformer of the A-T base pair have been considered. The equilibrium geometries of the ground state and of the lowest excited electronic states have been determined with the MP2 (second-order M?ller-Plesset) and CC2 methods, respectively. Vertical and adiabatic excitation energies, oscillator strengths, and dipole moments of the excited states are reported. Of particular relevance for the photochemistry of the A-T base pair are optically dark (1)pipi* states of charge-transfer character. Although rather high in energy at the ground-state equilibrium geometry, these states are substantially lowered in energy by the transfer of a proton, which thus neutralizes the charge separation. A remarkable difference of the energetics of the proton-transfer reaction is predicted for the two tautomers of A-T: in the Watson-Crick conformer, but not in the most stable conformer, a sequence of conical intersections connects the UV-absorbing (1)pipi* state in a barrierless manner with the electronic ground state. These conical intersections allow a very fast deactivation of the potentially reactive excited states in the Watson-Crick conformer. The results provide evidence that the specific hydrogen-bonding pattern of the Watson-Crick conformer endows this structure with a greatly enhanced photostability. This property of the Watson-Crick conformer of A-T may have been essential for the selection of this species as carrier of genetic information in early stages of the biological evolution.     

Vertical excitation energies for ribose and deoxyribose nucleosides

Vertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time-dependent density functional theory (TDDFT) method at the B3LYP/6-311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug-cc-pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest npi* and pipi* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low-energy npi* and pisigma* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low-lying excited state transitions of the binding to phosphate groups at the 5'- and 3',5'-hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de-excitation dynamics of nucleic acids are discussed.     

Time-resolved photoelectron and photoion fragmentation spectroscopy study of 9-methyladenine and its hydrates: a contribution to the understanding of the ultrafast radiationless decay of excited DNA bases

The excited state dynamics of the purine base 9-methyladenine (9Me-Ade) has been investigated by time- and energy-resolved photoelectron imaging spectroscopy and mass-selected ion spectroscopy, in both vacuum and water-cluster environments. The specific probe processes used, namely a careful monitoring of time-resolved photoelectron energy distributions and of photoion fragmentation, together with the excellent temporal resolution achieved, enable us to derive additional information on the nature of the excited states (pipi*, npi*, pisigma*, triplet) involved in the electronic relaxation of adenine. The two-step pathway we propose to account for the double exponential decay observed agrees well with recent theoretical calculations. The near-UV photophysics of 9Me-Ade is dominated by the direct excitation of the pipi* ((1)L(b)) state (lifetime of 100 fs), followed by internal conversion to the npi* state (lifetime in the ps range) via conical intersection. No evidence for the involvement of a pisigma* or a triplet state was found. 9Me-Ade-(H(2)O)(n) clusters have been studied, focusing on the fragmentation of these species after the probe process. A careful analysis of the fragments allowed us to provide evidence for a double exponential decay profile for the hydrates. The very weak second component observed, however, led us to conclude that the photophysics were very different compared with the isolated base, assigned to a competition between (i) a direct one-step decay of the initially excited state (pipi* L(a) and/or L(b), stabilised by hydration) to the ground state and (ii) a modified two-step decay scheme, qualitatively comparable to that occurring in the isolated molecule.     

Theoretical study on the singlet excited state of pterin and its deactivation pathway

The excited-state properties and related photophysical processes of the acidic and basic forms of pterin have been investigated by the density functional theory and ab initio methodologies. The solvent effects on the low-lying states have been estimated by the polarized continuum model and combined QM/MM calculations. Calculations reveal that the observed two strong absorptions arise from the strong pi --> pi* transitions to 1(pipi*L(a)) and 1(pipi*L(b)) in the acidic and basic forms of pterin. The first 1(pipi*L(a)) excited state is exclusively responsible for the experimental emission band. The vertical 1(n(N)pi*) state with a small oscillator strength, slightly higher in energy than the 1(pipi*L(a)) state, is less accessible by the direct electronic transition. The 1(n(N)pi*) state may be involved in the photophysical process of the excited pterin via the 1(pipi*L(a)/n(N)pi*) conical intersection. The radiationless decay of the excited PT to the ground state experiences a barrier of 13.8 kcal/mol for the acidic form to reach the (S(1)/S(0)) conical intersection. Such internal conversion can be enhanced with the increase in excitation energy, which will reduce the fluorescence intensity as observed experimentally.     

On the mechanism of intramolecular sensitization of photocleavage of the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group

A spectroscopic study of a variety of covalently linked thioxanthone(TX)-linker-2-(2-nitrophenyl)propoxycarbonyl(NPPOC)-substrate conjugates is presented. Herein, the TX chromophore functions as an intramolecular sensitizer to the NPPOC moiety, a photolabile protecting group used in photolithographic DNA chip synthesis. The rate of electronic energy transfer between TX and NPPOC was quantified by means of stationary fluorescence as well as nanosecond and femtosecond time-resolved laser spectroscopy. A dual mechanism of triplet-triplet energy transfer has been observed comprising a slower mechanism involving the T1(pipi*) state of TX with linker-length-dependent time constants longer than 20 ns and a fast mechanism with linker-length-dependent time constants shorter than 3 ns. Evidence is provided that the latter mechanism is due to energy transfer from the T2(npi*) state which is in fast equilibrium with the fluorescent S1(pipi*) state. In the case of direct linkage between the aromatic rings of TX and NPPOC, the spectroscopic properties are indicative of one united chromophore which, however, still shows the typical NPPOC cleavage reaction triggered by intramolecular hydrogen atom transfer to the nitro group.     

Photodissociation of uracil

We investigate the photochemistry and photodissociation dynamics of uracil by two-colour photofragment Doppler spectroscopy and by two-colour slice imaging at excitation wavelengths between 268 and 235 nm. We observe the loss of a hydrogen atom upon excitation into the pipi* state. The angular distribution indicates a statistical process, while the translational energy distribution agrees with a dissociation that takes place on the electronic ground state. The pipi* state most likely deactivates via the lower-lying npi* state. In addition there is evidence for a second pathway: direct decay of the pipi* state to the electronic ground state with subsequent dissociation. Experiments on uracil-1,3-D(2) show that there is no site selectivity in the dissociation process. No evidence was found for the direct dissociation via a pisigma* excited state that seems to be relevant in the photochemistry of adenine and many other heterocyclic molecules. Overall, the photochemistry of uracil is similar to that of thymine.