Three-state conical intersections in nucleic acid bases

Cytosine in Context: A Theoretical Study of Substituent Effects on the Excitation Energies of 2-Pyrimidinone Derivatives

The ultrafast radiationless decay mechanism for cytosine has been shown to be in part dependent upon high vertical excitation, while slower fluorescence displayed in some cytosine analogs is generally linked to lower vertical excitation energies. To probe how excitation energies relate to pyrimidine structure, substituent effects on the vertical excitation energies for a number of derivatives of 2-pyrimidin-(1H)-one (2P) have been calculated using multireference configuration-interaction ab initio methods. Substitutions using groups with pi electron donating, withdrawing and conjugation-extending properties at the C(4) and C(5) positions on the 2P system give predictive trends for the first three singlet excited-state energies. The S(1) pipi* energies of 2P derivatives involving C4 substitution vary linearly with the Hammett substituent parameter sigma(P)+. Cytosine is shown to have the highest bright pipi* energy of the 2P derivatives presented, with that energy being strongly dependent on the position, orientation, and geometry of the C4-amino. A simple description of the predictive energetic trends for the bright pipi* energies using frontier molecular orbital theory is presented, based on the character of the HOMO and LUMO orbitals for each derivative. The results of this study expand the current understanding of the photophysical behavior of the DNA pyrimidine bases and could be useful in the design of analogs where particular spectral properties are desired.

Quantum-Chemical Investigation of the Structures and Electronic Spectra of the Nucleic Acid Bases at the Coupled Cluster CC2 Level

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Solvent Effects on the Steady-state Absorption and Fluorescence Spectra of Uracil, Thymine and 5-Fluorouracil

We report a comparison of the steady-state absorption and fluorescence spectra of three representative uracil derivatives (uracil, thymine and 5-fluorouracil) in alcoholic solutions. The present results are compared with those from our previous experimental and computational studies of the same compounds in water and acetonitrile. The effects of solvent polarity and hydrogen bonding on the spectra are discussed in the light of theoretical predictions. This comparative analysis provides a more complete picture of the solvent effects on the absorption and fluorescence properties of pyrimidine nucleobases, with special emphasis on the mechanism of the excited state deactivation.

Photoinduced Dynamics of Hydrated Adenine Clusters

We studied the photoinduced dynamics of hydrated adenine clusters by multiphoton ionization techniques. The majority of the hydrated adenine monomers are found to experience dissociative ionization, where the adenine monomer ions are produced due to the fragmentation of the water solvents by three-photon process. Due to fast internal conversion from the electronic states reached by the first photon, the fragmentation takes place in the vibrationally excited electronic ground state and in the vibrationally excited ionic states. Thus, the abundance of the hydrated adenine monomer ion depends on the excitation photon energy, possibly because the lifetime of the intermediate states is different and an internal conversion competes with direct ionization. In addition, a significant amount of protonated adenine monomer is observed. This indicates that the proton transfer is followed by the fragmentation in the hydrated adenine clusters. The abundance of the protonated adenine monomer also depends on the excitation photon energy mainly due to the ionization efficiency of the parent species.

Radiationless decay mechanism of cytosine: an ab initio study with comparisons to the fluorescent analogue 5-methyl-2-pyrimidinone

The ultrafast radiationless decay mechanism of photoexcited cytosine has been theoretically supported by exploring the important potential energy surfaces using multireference configuration-interaction ab initio methods for the gas-phase keto-tautomer free base. At vertical excitation, the bright state is S1 (pipi*) at 5.14 eV, with S2 (nNpi*) and S3 (nOpi*) being dark states at 5.29 and 5.93 eV, respectively. Minimum energy paths connect the Franck-Condon region to a shallow minimum on the pipi* surface at 4.31 eV. Two different energetically accessible conical intersections with the ground state surface are shown to be connected to this minimum. One pathway involves N3 distorting out of plane in a sofa conformation, and the other pathway involves a dihedral twist about the C5-C6 bond. Each of these pathways from the minimum contains a low barrier of 0.14 eV, easily accessed by low vibronic levels. The path involving the N3 sofa distortion leads to a conical intersection with the ground state at 4.27 eV. The other pathway leads to an intersection with the ground state at 3.98 eV, lower than the minimum by about 0.3 eV. Comparisons with our previously reported study of the fluorescent cytosine analogue 5-methyl-2-pyrimidinone (5M2P) reveal remarkably similar conformational distortions throughout the decay pathways of both bases. The different photophysical behavior between the two molecules is attributed to energetic differences. Vertical excitation in cytosine occurs at a much higher energy initially, creating more vibrational energy than 5M2P in the Franck-Condon region, and the minimum S1 energy for 5M2P is too low to access an intersection with the ground state, causing population trapping and fluorescence. Calculations of vertical excitation energies of 5-amino-2-pyrimidinone and 2-pyrimidinone reveal that the higher excitation energy of cytosine is likely due to the presence of the amino group at the 4-position.

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.

Solvent Effect on Conical Intersections in Excited-State 9H-Adenine: Radiationless Decay Mechanism in Polar Solvent

The ground- and excited-state free energy minima and the conical intersections among these states of 9H-adenine in aqueous and acetonitrile solutions are studied theoretically to elucidate the mechanism of radiationless decay. We employ the recently proposed linear-response free energy (LRFE) to locate the energy minima and conical intersections in solution. The LRFE is calculated by using the reference interaction site model self-consistent field method. The geometry optimizations are carried out at the complete active space self-consistent field level, and the dynamic electron correlation energies are estimated by the multireference Møller-Plesset method. We find that the conical intersection between the (1)L(a) and (1)L(b) states in aqueous solution occurs at a wide area of the free energy surface, indicating a strong vibronic coupling between them. On the other hand, the (1)npi(*) state is largely blue-shifted at planar geometries in solution, which suggests that the nonadiabatic transition to this state is suppressed. The importance of the (1)pisigma(*) channel is also examined in both the gas phase and solution. Based on the free energy characteristics obtained by the calculations, we intend to explain the experimental observations that the excited state of 9H-adenine decays monoexponentially with shorter lifetimes in polar solvents than that in the gas phase.

Biradical radiationless decay channel in adenine and its derivatives

Coupled-cluster calculations of increasing accuracy (approximate doubles: CC2; doubles: EOM-CCSD; connected triples: CR-EOM-CCSD(T)) for CIS-optimized potential energy profiles of adenine and its derivatives indicate that the ultrafast internal conversion of the optically excited π π* state occurs through a state switch to a biradical state, which intersects the ground state at a lower energy. The electronic nature of the biradical state is defined by an electronic configuration in which one unpaired electron occupies a π* orbital confined to the five-membered ring. The second unpaired electron is localized very strongly on a p-type C2 atomic orbital of the six-membered ring. The biradical state minimum has a strongly puckered six-membered ring and a C2–H bond, which is twisted nearly perpendicular to the average ring plane. Consistent with the biradical-mediated internal conversion, the π π* state lifetime is extremely short in adenine and 9-methyladenine, which have barrierless crossing to the biradical state. The lifetime is slightly longer in N,N-dimethyladenine, which has a small barrier for the state switch. In 2-aminopurine the biradical state is found above the π π* state, preventing the biradical state switch and dramatically increasing the lifetime. These results, combined with an earlier work on pyrimidine bases, strongly suggest the importance of a direct decay of the doorway π π* state via a biradical state switch in the photophysics of DNA, even though the nature of the biradical state is somewhat different in purines and pyrimidines.Key words: adenine, guanine, DNA damage, radiationless decay, biradical, ab initio, coupled clusted.

Unified Model for the Ultrafast Decay of Pyrimidine Nucleobases

Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the effect of the different levels of theory on the results is carefully analyzed.

Solvent Effect on the Singlet Excited-State Lifetimes of Nucleic Acid Bases: A Computational Study of 5-Fluorouracil and Uracil in Acetonitrile and Water

The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.

Primary processes underlying the photostability of isolated DNA bases: adenine

The UV chromophores in DNA are the nucleic bases themselves, and it is their photophysics and photochemistry that govern the intrinsic photostability of DNA. Because stability is related to the conversion of dangerous electronic to less-dangerous vibrational energy, we study ultrafast electronic relaxation processes in the DNA base adenine. We excite adenine, isolated in a molecular beam, to its pipi* state and follow its relaxation dynamics using femtosecond time-resolved photoelectron spectroscopy. To discern which processes are important on which timescales, we compare adenine with 9-methyl adenine. Methylation blocks the site of the much-discussed pisigma* state that had been thought, until now, minor. Time-resolved photoelectron spectroscopy reveals that, although adenine and 9-methyl adenine show almost identical timescales for the processes involved, the decay pathways are quite different. Importantly, we confirm that in adenine at 267-nm excitation, the pisigma* state plays a major role. We discuss these results in the context of recent experimental and theoretical studies on adenine, proposing a model that accounts for all known results, and consider the relationship between these studies and electron-induced damage in DNA.

On the characterization of three state conical intersections using a group homomorphism approach: Mapping the full N−5 dimensional seam space

A method for characterizing the degeneracy preserving seam space in the vicinity of a three state conical intersection is introduced. Second order degenerate perturbation theory is used to construct an approximately diabatic Hamiltonian whose eigenenergies and eigenstates accurately describe the vicinity of the three state conical intersection in its full dimensionality. The perturbative analysis enables the large number, 6(N(int)(N(int)+1)2), of unique second order parameters needed to construct this accurate Hamiltonian to be determined from ab initio data at a limited number of nuclear configurations, with (N(int)+10) being minimal. Using the minimum energy three state conical intersection of the pyrazolyl radical (N(int) = 18), the potential of this approach is illustrated. A Hamiltonian comprised of the ten characteristic (linear) parameters and over 1440 second order parameters is constructed and used to determine the locus of the conical intersection seam as well as to describe the 18 dimensional space in the vicinity of that point of intersection. Our results demonstrate the ability of this methodology to quantitatively reproduce the ab initio potential energy surfaces near a three state conical intersection.

Solvent Effect on the Singlet Excited-state Dynamics of 5-Fluorouracil in Acetonitrile as Compared with Water

The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/pi* excited state becomes near degenerate with the bright pi/pi* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state.

On the Characterization of Three-State Conical Intersections Using a Group Homomorphism Approach: The Two-State Degeneracy Spaces

Second-order degenerate perturbation theory, in conjunction with the group homomorphism method for describing a similarity transformation, are used to characterize the subspace of two-state conical intersections contained in the branching space of a three-state conical intersection. It is shown by explicit calculation, using the lowest three-state conical intersection of (CH)3N2, that a second-order treatment yields highly accurate absolute energies, even at significant distances from the reference point of three-state intersection. The excellent agreement between the second order and ab initio results depends on the average energy component, which is computed using 5 first-order terms and 15 second-order terms. The second-order absolute energy change over the range rho = 0.0-0.3 au, where rho is the distance from the three-state conical intersection in the branching space coordinates, is approximately 6500 and 9500 cm(-1) for the E(1=2) and E(2=3) seams, respectively, with the maximum ab initio energy deviation from degeneracy of 200 cm(-1) occurring at rho = 0.3 au. The characteristic parameters gIJ and hIJ are also predicted to great accuracy, even at large rho, with the error growing to only 10-15% at rho = 0.3 au.

Ab initiostudy 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.

A femtosecond time-resolved investigation of dual fluorescence from N6,N6-dimethyladenine

The excited electronic state dynamics of N(6),N(6)-dimethyladenine (DMAde), a molecule known to emit dual fluorescence, has been studied in aqueous solution using femtosecond fluorescence up-conversion spectroscopy. Time profiles of the fluorescence of DMAde excited at lambda= 258 nm were measured at a series of wavelengths in the range 320 nm <or=lambda(fl)<or= 650 nm. At wavelengths in the near UV (lambda(fl)<or= 420 nm), the time profiles were dominated by a very short-lived decay component with a lifetime between 0.2 ps <or=tau(1)<or= 0.6 ps, depending on the detection wavelength. Two other components with lifetimes of tau(2) approximately 3.5 ps and tau(3) approximately 60 ps gave minor contributions. In the emission observed at longer wavelengths (lambda(fl)>or= 500 nm), which appeared slightly delayed compared to the UV fluorescence, the long-lived fluorescence component (tau(3)) dominated, the second component (tau(2)) disappeared. The results are consistent with the assumption that DMAde is primarily excited to a short-lived local excited (LE) electronic state that fluoresces mostly in the UV and decays rapidly, on a approximately 0.5 ps timescale, to an intramolecular charge transfer (ICT) state that emits only at longer wavelengths in the visible spectrum. The fluorescence-time profiles and transient fluorescence spectra reconstructed from the time profiles provided further information on secondary relaxation processes within and between the excited states and their non-radiative relaxation to the electronic ground state.

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

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.

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.

The Fluorescence Mechanism of 5-Methyl-2-Pyrimidinone: An Ab Initio Study of a Fluorescent Pyrimidine Analog

The photophysically important potential energy surfaces of the fluorescent pyrimidine analog 5-methyl-2-pyrimidinone have been explored using multireference configuration-interaction ab initio methods at three levels of dynamical correlation, all of which support a fluorescence mechanism. At vertical excitation S1 (dark, n(N)pi*) and S2 (bright, pipi*) are almost degenerate at 4.4 eV, with S3 (dark, n(O)pi*) at 5.1 eV. The excited system can follow the S1-S2 seam of conical intersections, accessible from the Franck-Condon region, to its minimum and then evolve from this conical intersection on the S1 (pipi*) surface to a global minimum. At lower levels of correlation, the S1 surface shows two minima separated by a barrier of up to 0.18 eV. The secondary minimum found at the lower levels of correlation becomes the global minimum with higher correlation. The S1 population at this minimum can be trapped from accessing the lowest energy S0-S1 (pipi*/gs) conical intersection by an energy gap at least 0.3-0.4 eV higher than the S1 minimum. The calculated emission energy from this minimum is 2.80 eV. Gradient pathways connecting important S1 geometries are presented, as well as other excited state conical intersections.