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.     

Photoisomerization and thermal isomerization of arylazoimidazoles

Photoisomerization and thermal isomerization behaviors of an extensive series of arylazoimidazoles are investigated. Absorption spectra are characterized by a structured pipi* absorption band around 330-400 nm with a tail on the lower energy side extending to 500 nm corresponding to an npi* transition. The trans-to-cis photoisomerization occurs on excitation into these absorption bands. The quantum yields are dependent on the excitation wavelength, as observed for azobenzene derivatives, but are generally larger than those of azobenzene. The thermal cis-to-trans isomerization rates are also generally larger than that of azobenzene and are comparable to those of 4-N,N-dimethylaminoazobenzene and 4-nitroazobenzene. Arylazoimidazoles with no substituent on the imidazole nitrogen are unique in that the quantum yield for the trans-to-cis photoisomerization and the rate of thermal cis-to-trans isomerization are particularly large. It is proposed that the fast thermal isomerization is due to an involvement of self-catalyzed and protic molecule-assisted tautomerization to a hydrazone form.     

Ab initio study of a biradical radiationless decay channel of the lowest excited electronic state of cytosine and its derivatives

A theoretical model for the ultrafast S1-->S0 internal conversion of cytosine is presented, in which a state switch from the initially prepared 1pipi* state to the out-of-plane deformed excited state of biradical character controls the rate of the S1(1pipi*) decay. This mechanism successfully accounts for the dramatically longer S1 lifetimes of 5-fluorocytosine and N-acetylcytosine relative to cytosine. The replacement of the C5 hydrogen atom by a methyl group is predicted to lead to a substantial, but not dramatic, increase in the S1 lifetime, also consistent with experiment. It is this ability to correctly predict the substituent effects that distinguishes the present model from the previously proposed mechanisms.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Ab initio study of 4-monosubstituted pyrimidines in ground and excited n → π* states

Ab initio SCF and SCF -CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH₃, NH₂, OH, F, and C₂H₃ and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C₂H₃, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.     

用HAM/3法研究胞嘧啶及其甲基衍生物的光电子能谱与紫外光谱

本文用半经验SCF-MO-HAM/3方法计算了胞嘧啶和它的某些甲基衍生物的电离能、激发能和振子强度.指认了这些分子的紫外光电子能谱和紫外电子光谱.讨论了在紫外光电子能谱指认上与CNDO/S的不同之处.分析了胞嘧啶在磷酸三甲酯中可能存在的主要异构体形式.     

Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory

We present resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectra of jet-cooled 2-aminopurine (2AP) as well as Fourier transform infrared (FTIR) gas phase spectra. 2AP is a fluorescing isomer of the nucleobase adenine. The results show that there is only one tautomer of 2AP which absorbs in the wavelength range 32,300-34,500 cm(-1). The comparison with the calculated IR spectra of 9H- and 7H-2AP points to 9H-2AP as the dominating tautomer in the gas phase but the spectra are too similar to allow an unambiguous assignment to the respective tautomer. Hence, we determined vertical and adiabatic excitation energies of both tautomers employing combined density functional theory and multi-reference configuration interaction techniques. For the 0-0 band of the first 1pipi* transition of 9H-2AP we obtain a theoretical value of 32,328 cm(-1), in excellent agreement with the band origin of our R2PI spectrum at 32,371 cm(-1). The first singlet pipi* transition of the less stable 7H-2AP tautomer is predicted to be red-shifted by about 1700 cm(-1) with respect to the corresponding transition in 9H-2AP. From the absence of experimental bands in the energy region between 30,300 and 32,350 cm(-1) we conclude that 7H-2AP is not present to an appreciable extent in the molecular beam. Our calculations yield nearly equal energies for the 1npi* and 1pipi* minima of isolated 2AP, similar to the situation in adenine. The hitherto existing argument that the energetic order of states is responsible for the different spectroscopic properties of these isomers therefore does not hold. Rather, vibronic levels close to the origin of the 1pipi* transition cannot access the conical intersection between the 1pipi* and S(0) states along a puckering coordinate of the six-membered ring, in contrast to the situation in electronically excited 9H-adenine. As a consequence, a rich vibrational structure can be observed in the R2PI spectrum of 2AP whereas the spectrum of 9H-adenine breaks off at low energies.     

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.     

Detailed dynamics of the nonradiative deactivation of adenine: a semiclassical dynamics study

A realistic dynamics simulation study is reported for the ultrafast radiationless deactivation of 9H-adenine. The simulation follows two different excitations induced by two 80 fs (fwhm) laser pulses that are different in energy: one has a photon energy of 5.0 eV, and the other has a photon energy of 4.8 eV. The simulation shows that the excited molecule decays to the electronic ground state from the (1)pipi* state in both excitations but through two different radiationless pathways: in the 5.0 eV excitation, the decay channel involves the out-of-plane vibration of the amino group, whereas in the 4.8 eV excitation, the decay strongly associates with the deformation of the pyrimidine at the C 2 atom. The lifetime of the (1) npi* state determined in the simulation study is 630 fs for the 5.0 eV excitation and 1120 fs for the 4.8 eV excitation. These are consistent with the experimental values of 750 and 1000 fs. We conclude that the experimentally observed difference in the lifetime of the (1) npi* state at various excitations results from the different radiationless deactivation pathways of the excited molecule to the electronic ground state.     

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.     

TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach

A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of pisigma* type Rydberg transition was found near the lowest singlet pipi* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases.     

Photodissociation dynamics of allyl bromide at 234, 265, and 267 nm

The photodissociation dynamics of allyl bromide was investigated at 234, 265, and 267 nm. A two-dimensional photofragment ion velocity imaging technique coupled with a [2+1] resonance-enhanced multiphoton ionization scheme was utilized to obtain the angular and translational energy distributions of the nascent Br* (2P1/2) and Br (2P3/2) atoms. The Br fragments show a bimodal translational energy distribution, while the Br* fragments reveal one translational energy distribution. The vertical excited energies and the mixed electronic character of excited states were calculated at ab initio configuration interaction method. It is presumed that the high kinetic energy bromine atoms are attributed to the predissociation from 1(pipi*) or 1(pisigma*) state to the repulsive 1(nsigma*) state, and to the direct dissociation from 3(nsigma*) and 3(pisigma*) states, while the low kinetic energy bromine atoms stem from internal conversion from the lowest 3(pipi*) state to 3(pisigma*) state.     

A theoretical insight into the photophysics of psoralen

Psoralen photophysics has been studied on quantum chemistry grounds using the multiconfigurational second-order perturbation method CASPT2. Absorption and emission spectra of the system have been rationalized by computing the energies and properties of the low-lying singlet and triplet excited states. The S1 pipi* state has been determined to be responsible of the lowest absorption and fluorescence bands and to initially carry the population in the photophysical processes related to the phototherapeutic properties of psoralen derivatives. The low-lying T1 pipi* state is, on the other hand, protagonist of the phosphorescence, and its prevalent role in the reactivity of psoralen is suggested to be related to the elongation of the pyrone ring C3-C4 bond, where the spin density is distributed on both carbon atoms. Analysis of energy gaps and spin-orbit coupling elements indicates that the efficient photophysical process leading to the population of the lowest triplet state does not take place at the Franck-Condon region but along the S1 relaxation path.     

Optimum geometries and relative energies for cytosine,thymine, uracil,the imino tautomer of cytosine,the enol tautomer of thymine,and the enol tautomer of uracil by the MINDO/2 SCF MO method

A MINDO /2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, ?9.0, and ?14.2 kcal/mol for C?C*, T?T*, and U?U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO /2.     

Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine

The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.     

Temporary anion states of pyrimidine and halopyrimidines

The empty-level electronic structures of pyrimidine and its 2-chloro, 2-bromo, and 5-bromo derivatives have been studied with electron transmission spectroscopy (ETS) and dissociative electron attachment spectroscopy (DEAS) in the 0-5 eV energy range. The spectral features were assigned to the corresponding anion states with the support of theoretical calculations at the ab initio and density functional theory levels. The empty orbital energies obtained by simple Koopmans' theorem calculations, scaled with empirical equations, quantitatively reproduced the energies of vertical electron attachment to π* and σ* empty orbitals measured in the ET spectra and predicted vertical electron affinities close to zero for the three halo derivatives. The total anion currents of the halo derivatives, measured at the walls of the collision chamber as a function of the impact electron energy, presented intense maxima below 0.5 eV. The mass-selected spectra showed that, in this energy, range the total anion current is essentially due to halide fragment anions. The DEA cross sections of the bromo derivatives were found to be about six times larger than that of the chloro derivative. The absolute cross sections at incident electron energies close to zero were evaluated to be 10(-16)-10(-15) cm(2).     

Performance of TDDFT Vertical Excitation Energies of Core-Substituted Naphthalene Diimides

We have evaluated the performance of various density functionals, covering generalized gradient approximation (GGA), global hybrid (GH) and range-separated hybrid (RSH), using time dependent density functional theory (TDDFT) for computing vertical excitation energies against experimental absorption maximum (λ_max) for a set of 10 different core-substituted naphthalene diimides (cNDI) recorded in dichloromethane. The computed excitation in case of GH PBE0 is most accurate while the trend is most systematic with RSH LCY-BLYP compared to λ_max. We highlight the importance of including solvent effects for optimal agreement with the λ_max. Increasing the basis set size from TZ2P to QZ4P has a negligible influence on the computed excitation energies. Notably, RSH CAMY-B3LYP gave the least error for charge-transfer excitation. The poorest agreement with λ_max is obtained with semi-local GGA functionals. Use of the optimally-tuned RSH LCY-BLYP* is not recommended because of the high computational cost and marginal improvement in results.     

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.     

The triplet state of cytosine and its derivatives: electron impact and quantum chemical study

The excitation of the lowest electronic states and vibrational excitation of cytosine (C) have been studied using electron energy loss spectroscopy (EELS, 0-100 eV) with angular analysis. The singlet states have been found to be in good agreement with UV-VIS absorption results on sublimed films, slightly blueshifted by about 0.1 eV. The EEL spectra recorded at residual energy below 2 eV show clear shoulders at energy losses of 3.50 and 4.25 eV (+/-0.1 eV). They are assigned to the lowest triplet electronic states of cytosine. Energies and molecular structures of the lowest-lying triplet state of C and its methylated and halogenated 5-X-C, 6-X-C, and 5-X, 6-X-C substituted derivatives (X=CH3, F, Cl, and Br) have been studied using quantum chemical calculations with both molecular orbital and density functional methods, in conjunction with the 6-311++G(d,p), 6-311++G(3df,2p), and aug-cc-pVTZ basis sets. The triplet-singlet energy gap obtained using coupled-cluster theory [CCSD(T)] and density functional theory (DFT) methods agrees well with those derived from EELS study. The first C's vertical triplet state is located at 3.6 eV, in good agreement with experiment. The weak band observed at 4.25 eV is tentatively assigned to the second C's vertical triplet excitation. For the substituted cytosines considered, the vertical triplet state is consistently centered at 3.0-3.2 eV above the corresponding singlet ground state but about 1.0 eV below the first excited singlet state. Geometrical relaxation involving out-of-plane distortions of hydrogen atoms leads to a stabilization of 0.6-1.0 eV in favor of the equilibrium triplet. The lowest-lying adiabatic triplet states are located at 2.3-3.0 eV. Halogen substitution at both C(5) and C(6) positions tends to reduce the triplet-singlet separations whereas methylation tends to enlarge it. The vibrational modes of triplet cytosine and the ionization energies of substituted derivatives were also evaluated.