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.     

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.     

Nonradiative deactivation mechanisms of uracil, thymine, and 5-fluorouracil: a comparative ab initio study

The mechanisms of the ultrafast nonradiative deactivation of uracil and its substituted derivatives thymine (5-methyluracil) and 5-fluorouracil after absorption of UV light are explored and compared by means of ab initio multistate (MS) CASPT2 calculations. The MS-CASPT2 method is applied for the calculation of potential energy profiles, especially for the geometry optimization in the electronically excited state, with the aim of an accurate prediction of deactivation pathways. The resulting energy curves of each molecule exhibit that the conical intersection between the (1)ππ* and ground states is accessible via small energy barriers from the minimum in the (1)ππ* state as well as from that in the (1)nπ* state. The barrier of 5-fluorouracil in the (1)ππ* state is calculated to be definitely higher than those of uracil and thymine, which is consistent with experiments and suggests that the elongation of the excited-state lifetime of uracil by fluorine substitution is significantly contributed from intrinsic electronic effect of the molecule. However, no evidence of the experimentally observed longer excited-state lifetime of thymine than uracil is found in the presently calculated MS-CASPT2 potential energy curves in the (1)ππ* and (1)nπ* states, implying nonnegligible contribution of other factors such as solvation effect and substituent mass to the photoinduced dynamics of uracil derivatives.     

Assessing solvent effects on the singlet excited state lifetime of uracil derivatives: A femtosecond fluorescence upconversion study in alcohols and D2O

The excited state lifetimes of uracil, thymine and 5-fluorouracil have been measured using femtosecond UV fluorescence upconversion in various protic and aprotic polar solvents. The fastest decays are observed in acetonitrile and the slowest in aqueous solution while those observed in alcohols are intermediate. No direct correlation with macroscopic solvent parameters such as polarity or viscosity is found, but hydrogen bonding is one key factor affecting the fluorescence decay. It is proposed that the solvent modulates the relative energy of two close-lying electronically excited states, the bright ππ^* and the dark nπ^* states. This relative energy gap controls the non-radiative relaxation of the ππ^* state through a conical intersection close to the Franck–Condon region competing with the ultrafast internal conversion to the ground state. In addition, an inverse isotope effect is observed in D₂O where the decays are faster than in H₂O.     

Nonadiabatic dynamics of uracil: population split among different decay mechanisms

Nonadiabatic dynamics simulations performed at the state-averaged CASSCF method are reported for uracil. Supporting calculations on stationary points and minima on the crossing seams have been performed at the MR-CISD and CASPT2 levels. The dominant mechanism is characterized by relaxation into the S(2) minimum of ππ* character followed by the relaxation to the S(1) minimum of nπ* character. This mechanism contributes to the slower relaxation with a decay constant larger than 1.5 ps, in good agreement with the long time constants experimentally observed. A minor fraction of trajectories decay to the ground state with a time constant of about 0.7 ps, which should be compared to the experimentally observed short constant. The major part of trajectories decaying with this time constant follows the ππ* channel and hops to the ground state via an ethylenic conical intersection. A contribution of the relaxation proceeding via a ring-opening conical intersection was also observed. The existence of these two latter channels together with a reduced long time constant is responsible for a significantly shorter lifetime of uracil compared to that of thymine.     

The influence of microhydration on the ionization energy thresholds of uracil and thymine

In the present study the ionization energy thresholds (IET's) of uracil and thymine have been calculated (with the B3LYP, PMP2, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with one to three water molecules placed in the first hydration shell. Then (B3LYP) polarizable continuum model (PCM) calculations were performed with one to three waters of the hydration shell included. Calculations show there is a distinct effect of microhydration on uracil and thymine. For uracil, one added water results in a decrease in the IET of about 0.15 eV. The second and third water molecules cause a further decrease by about 0.07 eV each. For thymine, the first water molecule is seen to decrease the IET by about 0.1 eV, while the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with one to three waters of hydration are smaller than the experimental values determined by Kim et al. (Kim, S. K.; Lee, W.; Herschbach, D. R. J. Phys. Chem. 1996, 100, 7933). Preliminary results presented here indicate that the experimental results may involve keto-enol tautomers of thymine. The results of placing the microhydrated structures of uracil and thymine in a PCM cavity was seen to make very little difference in the IET when compared to the IET of ordinary uracil or thymine in a PCM cavity. The implications are that accurate calculations of the IET's of uracil and thymine can be obtained by simply considering long-range solvation effects.     

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.     

Excited-State Dynamics of Thienoguanosine,an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^thG) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^thG exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto–amino tautomers. We herein investigate the photophysics of ^thG in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5–20.5 and 7–13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^thG, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.     

Fluorescent and phosphorescent pyrimidine labels : α-Diketone derivatives of uracil and thymine

The syntheses of 1-(3,4-dioxopentyl)uracil (V), 1-(2,3-dioxobutyl)uracil (XIIa), 1-(2,3-dioxobutyl)-3-methyluracil (XIIb) and 1-(2,3-dioxobutyl)thymine (XIIc) are described. These are the first compounds to be prepared which have α-diketone functions attached to biologically important pyrimidines. Preparation of the dioxopentyluracil was by oximation of 1-(4-oxopentyl)uracil, and of the dioxobutyl compounds was by alkylation of the appropriate pyrimidine with the dimethoxy ketal of bromobiacetyl, followed by hydrolysis under special conditions. The characteristics of the absorption and emission spectra in various solvents are presented and discussed. Dioxopentyl uracil exhibits both phosphorescence and fluorescence at room temperature; the dioxobutyl pyrimidines are fluorescent but non-phosphorescent under the same conditions. The fluorescence quantum yields of all four compounds are about 0.2%, similar to those of biacetyl or 2,3-pentanedione.     

6-甲基-4-羟基嘧啶单体及二聚体激发态质子转移异构化反应及光谱的理论研究

采用ab initio HF理论的组态相关CIS方法和连续溶剂模型PCM, 分别在6-311+G*和6-31G水平上研究了6-甲基-4-羟基嘧啶单体及二聚体激发态质子转移的异构化反应; 对其反应势能面的研究发现, 单体基态和激发态的异构化反应一起可以形成四能级的分子电子体系, 而二聚体的却不能, 由此解释了单体和二聚体的紫外吸收光谱和荧光发射光谱均对应于酮式构型的原因. 利用混合含时密度泛函TD/MPW1PW91理论方法在溶剂存在下计算了标题物质的紫外吸收光谱和荧光发射光谱.     

Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine

The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multicomponent decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S2 electronic state is responsible for the first step that occurs on a femtosecond time scale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S2/S1 conical intersection is responsible for the picosecond decay.     

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.     

Ultrafast intersystem crossing in 1-nitronaphthalene. An experimental and computational study

Previous studies have established that the major pathway for the first singlet excited state of 1-nitronaphthalene is intersystem crossing to the triplet manifold. In this contribution we present determinations of the decay of the S1 state of this compound in several solvents to establish the time scale of the multiplicity change as a function of the polarity and hydrogen-bonding ability of the solvent environment. The measurements were made with the femtosecond frequency up-conversion technique to follow the weak spontaneous molecular emission which precedes triplet formation. Our results show that in all environments the S1 lifetime is 100 fs or less, making 1-nitronaphthalene the organic compound with the fastest multiplicity change ever measured. We also show that the bathochromic shifts observed for the first absorption band imply changes in the relative energies of the singlet and triplet manifolds, which in turn manifest in a 2-fold increase of the fluorescence lifetime in cyclohexane compared with the polar solvents. Additionally, we performed excited-state calculations at the TD-DFT/ PBE0/6-311++G(d,p) level of theory with the PCM model for solvation. The TD-DFT theory identifies the presence of upper triplet states which can act as receiver states in this highly efficient photophysical pathway. Together, the experimental and theoretical results show that the dynamics of the S1 state in 1-nitronaphthalene represent an extreme manifestation of El-Sayed's rules due to a partial (n-pi*) character in the receiver triplets which are nearly isoenergetic with S1, determining a change in the molecular spin state within 100 fs.     

Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study

The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.     

Polymerization of cyclic derivatives of uracil and thymine

Cyclic derivatives of uracil and thymine were synthesized from their corresponding 1-(2′-chloroethyl) derivatives by dehydrochlorination. These compounds were found to undergo a variety of reactions, giving many valuable derivatives of uracil and thymine. The cyclic derivatives, as monomers, were polymerized with a cationic initiator by a unique ring-opening process. The polymerization proceeded by ring opening with isomerization of the pyrimidine ring to give a polymer in which pyrimidine rings were connected with ethylene between N-1 and N-3 or O-4 in the pyrimidine ring. The structure of these polymers was determined by nuclear magnetic resonance (NMR), ultraviolet (UV), infrared (IR), and mass spectra. The structure was affected by polymerization temperature.     

Excited-state behavior of ortho-phenylenes

The excited-state properties of unsubstituted ortho-phenylene oligomers have been studied using TD-DFT. Calculations of vertical transitions at the helical ground-state geometries are in good qualitative agreement with the experimental UV-vis spectra. In the excited state, the spring-like compounds compress; for the longer oligomers, this compression is localized at one end of the oligomer. This behavior explains the unusual experimentally observed hypsochromic shifts in fluorescence spectra with increasing oligomer length.     

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.     

Radiationless transition rates of thymine and uracil in neutral aqueous solution at 300°K

Recent experiments in low-intensity fluorescence spectrometry, flash photolysis and continuous photolysis at 300°K in an aqueous medium have provided data for uracil and thymine from which all the pertinent phenomenological characteristics (Φ_fl^0′, Φ_isc^0′, Φ′_chem) of the 0′ level can be evaluated. It is necessary to postulate considerable internal conversion ¹S → ⁰S with τ_ic ≈ 1–2 × 10⁻¹² sec, this process correlating with the dielectric relaxation time of water.     

Solvent effects on electron-driven proton-transfer processes: adenine-thymine base pairs

Time-Dependent Density Functional Theory (TD-DFT) computations, with M05-2X and PBE0 functionals, have been employed for a detailed study of the Electron-Driven Proton-Transfer (PT) processes in an Adenine-Thymine Watson-Crick Base Pair in the gas phase and in solution, with the bulk solvent described by the polarizable continuum model. In the gas phase, TD-DFT computations predict that the Adenine → Thymine Charge Transfer (CT) excited state undergoes a barrierless PT reaction, in agreement with CC2 computations (S. Perun, A. Sobolewski, W. Domcke, J. Phys. Chem. A, 2006, 110, 9031.). The good agreement between the TD-DFT approach and CC2 results validates the former for the studies of excited state properties, excited state proton transfer reaction, and deactivation mechanisms in the DNA base pairs. Next, it is shown that inclusion of solvent effects significantly influences the possibility of both barrier-less excited state proton transfer and radiation-less deactivation through conical intersection with the ground state, affecting the energy of the CT excited state in the Franck-Condon region, the energy barrier associated to the PT process and the energy gap with the ground electronic state. These findings clearly indicate that environmental effects, with a special attention to proper treatment of dynamical solvation effects, have to be included for reliable computational analysis of photophysical and photochemical processes occurring in condensed phases.     

2-pyridone: The role of out-of-plane vibrations on the S1<-->S0 spectra and S1 state reactivity

The S(1)<-->S(0) vibronic spectra of supersonic jet-cooled 2-pyridone [pyridin-2-one (2PY)] and its N-H deuterated isotopomer (d-2PY) have been recorded by two-color resonant two-photon ionization, laser-induced fluorescence and emission, and fluorescence depletion spectroscopies. By combining these methods, the B origin of 2PY at 0(0) (0)+98 cm(-1) and the bands at +218 and +252 cm(-1) are identified as overtones of the S(1) state out-of-plane vibrations nu(1) (') and nu(2) ('), as are the analogous bands of d-2PY. Anharmonic double-minimum potentials are derived for the respective out-of-plane coordinates that predict further nu(1) (') and nu(2) (') overtones and combinations, reproducing approximately 80% of the vibronic bands up to 600 cm(-1) above the 0(0) (0) band. The fluorescence spectra excited at the electronic origins and the nu(1) (') and nu(2) (') out-of-plane overtone levels confirm these assignments. The S(1) nonplanar minima and S(1)<--S(0) out-of-plane progressions are in agreement with the determination of nonplanar vibrationally averaged geometries for the 0(0) (0) and 0(0) (0)+98 cm(-1) upper states by Held et al. [J. Chem. Phys. 95, 8732 (1991)]. The fluorescence lifetimes of the S(1) state vibrations show strong mode dependence: Those of the out-of-plane levels decrease rapidly above 200 cm(-1) excess vibrational energy, while the in-plane vibrations nu(5) ('), nu(8) ('), and nu(9) (') have longer lifetimes, although they are above or interspersed with the "dark" out-of-plane states. This is interpreted in terms of an S(1) (') state reaction with a low barrier towards a conical intersection with a prefulvenic geometry. Out-of-plane vibrational states can directly surmount this barrier, whereas in-plane vibrations are much less efficient in this respect. Analysis of the fluorescence spectra allows to identify nine in-plane S(0) (') state fundamentals, overtones of the S(0) state nu(1) (") and nu(2) (") out-of-plane vibrations, and >30 other overtones and combination bands. The B3LYP6-311++G(d,p) calculated anharmonic wave numbers are in very good agreement with the observed fundamentals, overtones, and combinations, with a deviation Delta(rms)=1.3%.