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.     

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.     

Theory and method for calculating resonance Raman scattering from resonance polarizability derivatives

We present a method to calculate both normal Raman-scattering (NRS) and resonance Raman-scattering (RRS) spectra from the geometrical derivatives of the frequency-dependent polarizability. In the RRS case, the polarizability derivatives are calculated from resonance polarizabilities by including a finite lifetime of the electronic excited states using time-dependent density-functional theory. The method is a short-time approximation to the Kramers, Heisenberg, and Dirac formalism. It is similar to the simple excited-state gradient approximation method if only one electronic excited state is important, however, it is not restricted to only one electronic excited state. Since the method can be applied to both NRS and RRS, it can be used to obtain complete Raman excitation profiles. To test the method we present the results for the S2 state of uracil and the S4, S3, and S2 states of pyrene. As expected, the results are almost identical to the results obtained from the excited-state gradient approximation method. Comparing with the experimental results, we find in general quite good agreement which enables an assignment of the experimental bands to bands in the calculated spectrum. For uracil the inclusion of explicit waters in the calculations was found to be necessary to match the solution spectra. The calculated resonance enhancements are on the order of 10(4)-10(6), which is in agreement with experimental findings. For pyrene the method is also able to distinguish between the three different electronic states for which experimental data are available. The neglect of anharmonicity and solvent effects in the calculations leads to some discrepancy between theory and experiment.     

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.     

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.     

Laser spectroscopic investigation of salicylic acids hydrogen bonded with water in supersonic jets: Microsolvation effects for excited state proton dislocation

Geometric structures and excited-state proton dislocation of size-selected salicylic acid clusters (salicylic acid and 5-methoxysalicylic acid) with water were studied by using laser spectroscopic techniques. Fluorescence excitation, dispersed fluorescence, and infrared (IR) spectra of those clusters in supersonic jets were examined for both the electronic ground (S0) and first excited (S1) states. The geometric structures of the clusters were determined on the basis of the IR spectra of the OH stretch region with the help of quantum chemical calculations. The hydroxyl group of the water moiety in the clusters forms a ring involving the carboxylic group of the salicylic acid moiety. The IR spectra in S0 show that the intramolecular hydrogen bond in the salicylic acid moiety is still held upon cluster formation, but the phenolic OH stretch band intensity is remarkably weaken in the clusters. The IR spectra in the S1 state and dispersed fluorescence spectra indicated that the intramolecular excited state proton dislocation is hardly affected by the microsolvation with water, in contrast with the strong suppression of the dislocation in the self-solvation.     

Excited-state structural dynamics of 5-fluorouracil

5-Fluorouracil is an analogue of thymine and uracil, nucleobases found in DNA and RNA, respectively. The photochemistry of thymine is significant; UV-induced photoproducts of thymine in DNA lead to skin cancer and other diseases. In previous work, we have suggested that the differences in the excited-state structural dynamics of thymine and uracil arise from the methyl group in thymine acting as a mass barrier, localizing the vibrations at the photochemical active site. To further test this hypothesis, we have measured the resonance Raman spectra of 5-fluorouracil at wavelengths throughout its 267 nm absorption band. The spectra of 5-fluorouracil and thymine are very similar. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism suggests that, at most, 81% of the reorganization energy upon excitation is directed along photochemically relevant modes. This compares well with what was found for thymine, supporting the mass barrier hypothesis.     

Influence of environment on the electronic structure of Cob(III)alamins: time-resolved absorption studies of the S(1) state spectrum and dynamics

Transient absorption spectroscopy has been used to elucidate the nature of the S1 intermediate state populated following excitation of cob(III)alamin (Cbl(III)) compounds. This state is sensitive both to axial ligation and to solvent polarity. The excited-state lifetime as a function of temperature and solvent environment is used to separate the dynamic and electrostatic influence of the solvent. Two distinct types of excited states are identified, both assigned to pi3d configurations. The spectra of both types of excited states are characterized by a red absorption band (ca. 600 nm) assigned to Co 3d --> 3d or Co 3d --> corrin pi* transitions and by visible absorption bands similar to the corrin pi-->pi* transitions observed for ground state Cbl(III) compounds. The excited state observed following excitation of nonalkyl Cbl(III) compounds has an excited-state spectrum characteristic of Cbl(III) molecules with a weakened bond to the axial ligand (Type I). A similar excited-state spectrum is observed for adenosylcobalamin (AdoCbl) in water and ethylene glycol. The excited-state spectrum of methyl, ethyl, and n-propylcobalamin is characteristic of a Cbl(III) species with a sigma-donating alkyl anion ligand (Type II). This Type II excited-state spectrum is also observed for AdoCbl bound to glutamate mutase. The results are discussed in the context of theoretical calculations of Cbl(III) species reported in the literature and highlight the need for additional calculations exploring the influence of the alkyl ligand on the electronic structure of cobalamins.     

Ultrafast infrared spectroscopy of riboflavin: dynamics, electronic structure, and vibrational mode analysis

Femtosecond time-resolved infrared spectroscopy was used to study the vibrational response of riboflavin in DMSO to photoexcitation at 387 nm. Vibrational cooling in the excited electronic state is observed and characterized by a time constant of 4.0 +/- 0.1 ps. Its characteristic pattern of negative and positive IR difference signals allows the identification and determination of excited-state vibrational frequencies of riboflavin in the spectral region between 1100 and 1740 cm (-1). Density functional theory (B3LYP), Hartree-Fock (HF) and configuration interaction singles (CIS) methods were employed to calculate the vibrational spectra of the electronic ground state and the first singlet excited pipi* state as well as respective electronic energies, structural parameters, electronic dipole moments and intrinsic force constants. The harmonic frequencies of the S 1 excited state calculated by the CIS method are in satisfactory agreement with the observed band positions. There is a clear correspondence between computed ground- and excited-state vibrations. Major changes upon photoexcitation include the loss of the double bond between the C4a and N5 atoms, reflected in a downshift of related vibrations in the spectral region from 1450 to 1720 cm (-1). Furthermore, the vibrational analysis reveals intra- and intermolecular hydrogen bonding of the riboflavin chromophore.     

Excited-State Raman Spectroscopy of Inorganic Compounds

Abstract— Raman spectra of inorganic complexes in excited electronic states are discussed. A brief overview of the field of transient Raman spectroscopy and experimental considerations are presented. Two examples from the author's laboratory are used to illustrate the type of information that can be obtained. The first example, an excited-state Raman spectroscopic study of K₃[Mn(CN)₅NO], is chosen because it illustrates the connections between excited-state molecular structure and vibrational properties. The pump pulse causes a change from a linear sp-hybridized NO containing a triple bond to a bent sp²-hybridized NO containing a double bond. Both the NO stretch and normal modes involving other ligands are measured and interpreted. The second example is chosen to illustrate the vibrational consequences of photoinduced electron transfer. The Raman spectra of W(CO)₄(diimine) complexes (diimine = 2,2'-bipyridine, 4,4'-dimethyl-2,2'-bipyridine, and isopropyl-pyridine-2-carbaldehyde imine) in the lowest tungsten to diimine charge transfer excited state are discussed. The excited-state peaks are assigned to ligand ring deformation modes and to carbonyl stretching modes. The totally symmetric cis -carbonyl stretching mode in the charge transfer excited state is about 50 cm' higher in energy than that of the molecule in the ground electronic state. The increase is interpreted in terms of loss of metal-car-bonyl back-bonding in the charge transfer excited state. Finally, a summary of the field's strengths and difficulties and a brief discussion of the future perspectives are presented.     

Excited states dipole moments and polarizabilities of uracil and cytosine 5-halo derivatives

Dipole moments and polarizabilities of different excited states of uracil and cytosine 5-halo derivatives have been calculated using solvent shift methods and CNDO/S calculations. The results are discussed in relation to different solute–solvent interactions and the nature of the electronic transition.     

Evidence for an intramolecular charge transfer state in 12'-apo-beta-caroten-12'-al and 8'-apo-beta-caroten-8'-al: influence of solvent polarity and temperature

The ultrafast excited-state dynamics of two carbonyl-containing carotenoids, 12'-apo-beta-caroten-12'-al and 8'-apo-beta-caroten-8'-al, have been investigated by transient absorption spectroscopy in a systematic variation of solvent polarity and temperature. In most of the experiments, 12'-apo-beta-caroten-12'-al was excited at 430 nm and 8'-apo-beta-caroten-8'-al at 445 or 450 nm via the S0 --> S2 (11Ag- --> 11Bu+) transition. The excited-state dynamics were then probed at 860 nm for 12'-apo-beta-caroten-12'-al and at 890 or 900 nm for 8'-apo-beta-caroten-8'-al. The temporal evolution of all transient signals measured in this work can be characterized by an ultrafast decay of the S2 --> SN absorption at early times followed by the formation of a stimulated emission (SE) signal, which subsequently decays on a much slower time scale. We assign the SE signal to a low-lying electronic state of the apocarotenals with intramolecular charge-transfer character (ICT --> S0). This is the first time that the involvement of an ICT state has been detected in the excited-state dynamics of a carbonyl carotenoid in nonpolar solvents such as n-hexane or i-octane. The amplitude ratio of ICT-stimulated emission to S2 absorption was weaker in nonpolar solvents than in polar solvents. We interpret the results in terms of a kinetic model, where the S1 and ICT states are populated from S2 through an ultrafast excited-state branching reaction (tau2 < 120 fs). Delayed formation of a part of the stimulated emission is due to the transition S1 --> ICT (tau3 = 0.5-4.1 ps, depending on the solvent), which possibly involves a slower backward reaction ICT --> S1. Determinations of tau1 were carried out for a large set of solvents. Especially in 12'-apo-beta-caroten-12'-al, the final SE decay, assigned to the nonradiative relaxation ICT --> S0, was strongly dependent on solvent polarity, varying from tau1 = 200 ps in n-hexane to 6.6 ps in methanol. In the case of 8'-apo-beta-caroten-8'-al, corresponding values were 24.8 and 7.6 ps, respectively. This indicates an increasing stabilization of the ICT state with increasing solvent polarity, resulting in a decreasing ICT-S0 energy gap. Tuning the pump wavelength from the blue wing to the maximum of the S0 --> S2 absorption band resulted in no change of tau1 in acetone and methanol. Additional measurements in methanol after excitation in the red edge of the S0 --> S2 band (480-525 nm) also show an almost constant tau1 with only a 10% reduction at the largest probe wavelengths. The temperature dependence of the tau1 value of 12'-apo-beta-caroten-12'-al was well described by Arrhenius-type behavior. The extracted apparent activation energies for the ICT --> S0 transitions were in general small (on the order of a few times RT), which is in the range expected for a radiationless process.     

Effect of Solvent Polarity on Excited-State Double Proton Transfer Process of 1, 5-Dihydroxyanthraquinone

The excited-state double proton transfer (ESDPT) properties of 1, 5-dihydroxyanthraquinone (1, 5-DHAQ) in various solvents were investigated using femtosecond transient absorption spectroscopy and the DFT/TDDFT method. The steady-state fluorescence spectra in toluene, tetrahydrofuran (THF) and acetonitrile (ACN) solvents presented that the solvent polarity has an effect on the position of the ESDPT fluorescence emission peak for the 1, 5-DHAQ system. Transient absorption spectra show that the increasing polarity of the solvent accelerates the rate of excited state dynamics. Calculated potential energy curves analysis further verified the experimental results. The ESDPT barrier decreases gradually with the increase of solvent polarity from toluene, THF to ACN solvent. It is convinced that the increase of solvent polarity can promote the occurrence of the ESDPT dynamic processes for the 1, 5-DHAQ system. This work clarifies the mechanism of the influence of solvent polarity on the ESDPT process of 1, 5-DHAQ, which provides novel ideas for design and synthesis of new hydroxyanthraquinone derivatives.     

Time-dependent density functional theory study on electronically excited States of coumarin 102 chromophore in aniline solvent: reconsideration of the electronic excited-state hydrogen-bonding dynamics

The time-dependent density functional theory method was performed to investigate the electronically excited states of the hydrogen-bonded complex formed by coumarin 102 (C102) chromophore and the hydrogen-donating aniline solvent. At the same time, the electronic excited-state hydrogen-bonding dynamics for the photoexcited C102 chromophore in solution was also reconsidered. We demonstrated that the intermolecular hydrogen bond CO...H-N between C102 and aniline molecules is significantly strengthened in the electronically excited-state upon photoexcitation, since the calculated hydrogen bond energy increases from 25.96 kJ/mol in the ground state to 37.27 kJ/mol in the electronically excited state. Furthermore, the infrared spectra of the hydrogen-bonded C102-aniline complex in both the ground state and the electronically excited state were also calculated. The hydrogen bond strengthening in the electronically excited-state was confirmed for the first time by monitoring the spectral shift of the stretching vibrational mode of the hydrogen-bonded N-H group in different electronic states. Therefore, we believed that the dispute about the intermolecular hydrogen bond cleavage or strengthening in the electronically excited-state of coumarin 102 chromophore in hydrogen donating solvents has been clarified by our studies.     

Electronic structure,spectra, and mechanism of photodimerization of pyrimidine bases

Various electronic indices calculated by the CNDO /s-CI method for uracil, 5-fluorouracil, thymine, and cytosine and the Woodward-Hoffmann rule applied to the photodimerization of these molecules lead us to the following conclusions: (i) decrease of the C₅? C₆ bond order consequent to excitation is generally correlated with the photodimerization reaction for all the biological pyrimidines; (ii) excited pyrimidine molecules may be nonplanar and the excitation would be delocalized over both the molecules which photodimerize; (iii) electrostatic interactions may play a significant role in the initial stages of the photodimerization reaction; (iv) singlet precursors to the stable triplet photodimers may exist; and (v) electron density does not, in general, increase in the C₅? C₆ bond in the excited state as compared to the ground state, contradicting the proposals of some earlier workers. Hybrid population densities and σ-bond orders have been calculated for the first time for the molecules. Fluorine in 5-fluorouracil perturbs the hybrid populations as compared to those of uracil mainly in its vicinity.     

Resonance Raman spectra of uracil based on Kramers-Kronig relations using time-dependent density functional calculations and multireference perturbation theory

The use of time-dependent density functional calculations for the optimization of excited-state structures and the subsequent calculation of resonance Raman intensities within the transform-theory framework is compared to calculations of Hartree-Fock/configuration interaction singles-type (CIS). The transform theory of resonance Raman scattering is based on Kramers-Kronig relations between polarizability tensor components and the optical absorption. Stationary points for the two lowest excited singlet states of uracil are optimized and characterized by means of numerical differentiation of analytical excited-state gradients. It is shown that the effect of electron correlation leads to substantial modifications of the relative intensities. Calculations of vibrational frequencies for ground and excited states are carried out, which show that the neglect of Duschinsky mixing and the assumption of equal wave numbers for ground and excited state are not in all cases good approximations. We also compare the transform-theory resonance Raman intensities with those obtained within a simple approximation from excited-state gradients at the ground-state equilibrium position, and find that they are in qualitative agreement in the case of CIS, but show some important differences in calculations based on density functional theory. Since the results from CIS calculations are in better agreement with experiment, we also present approximate resonance Raman spectra obtained using excited-state gradients from multireference perturbation theory calculations, which confirm the CIS gradients.     

UV-vis spectra of <Emphasis Type="Italic">p</Emphasis>-benzoquinone anion radical in solution by a TD-DFT/PCM approach

Excited electronic states of the anion radical of para-benzoquinone were studied by time dependent density functional theory (TD-DFT) including bulk solvent effects by the polarizable continuum model (PCM). The computed vertical excitation energies for the first four low-lying doublet states are in good agreement with previous post-Hartree–Fock computations. Geometry optimization of excited states and inclusion of solvent effects lead to a remarkable agreement between computed adiabatic transition energies and experimental band maxima. Together with their specific interest, the results point out the reliability of TD-DFT/PCM approach for valence excitations and the need to take geometry relaxation and solvent effects into the proper account for a meaningful comparison between computed and experimental absorption spectra.     

尿嘧啶和5-氯尿嘧啶1S0→1S2跃迁动态结构的共振拉曼光谱

采用含时量子波包理论的简单模型对5-氯尿嘧啶和尿嘧啶的共振拉曼光谱开展了强度分析拟合, 获得了1(π, π*)激发态的几何结构变化动态特征. 结果表明, 尿嘧啶1S0→1S2跃迁的动态结构特征因5-位氯原子取代而改变. 5-氯尿嘧啶的动态结构特征主要沿C5=C6伸缩振动+C6H12 弯曲振动和N3H9/N1H7弯曲振动+N1C6伸缩振动反应坐标展开, 而尿嘧啶的动态结构特征主要沿嘧啶环的伸缩振动+C5H11/C6H12/N1H7弯曲振动和C4=O10伸缩振动反应坐标展开. π和π*轨道中氯原子的pz电子参与嘧啶环的p-π共轭作用导致了在1(π, π*)激发态上5-氯尿嘧啶的振动重组能更多地配分给嘧啶环的弯曲振动模式和C5=C6伸缩振动模式. 尿嘧啶在甲醇中的激发态动态结构特征与在水中的基本一致, 但波包沿C5H11/C6H12/N1H7弯曲振动+N1C6伸缩振动(υ12)和环呼吸振动(υ17)反应坐标的运动明显增强.     

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.     

Solvent effects on isomerization and spectral properties of photochromic-switching diarythene derivatives in polar and apolar solutions

The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.