Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: evidence for the observation of three rare tautomers

In light of a recently published study on the IR spectroscopy of guanine in He droplets (Choi, M. Y.; Miller, R. E. J. Am. Chem. Soc. 2006, 128, 7320), the present letter proposes a new interpretation of the resonant two-photon ionization (R2PI) experiments on gas phase guanine, which is supported by quantum chemistry calculations. Whereas He droplet experiments detect the most stable forms, only one of these forms is observed (very marginally) in the R2PI spectrum, which is actually dominated by three less stable "rare" tautomers, whose stabilities lie in the 3-7 kcal/mol range. The absence of the most stable forms in the R2PI spectrum suggests that a tautomer-dependent ultrafast relaxation process takes place in the excited state of these stable tautomers. The present reinterpretation modifies qualitatively the picture of the excited state of guanine tautomers and should contribute to the understanding of the deactivation mechanisms taking place in the excited state of DNA bases.     

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase,in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.     

Imino tautomers of gas-phase guanine from mid-infrared laser spectroscopy

We reinvestigated the assignment of the three major guanine conformers detected via resonance enhanced two-photon ionization (R2PI) in supersonic expansions and present IR/UV double resonance spectra in the spectral region between 1500 and 1800 cm(-1). Comparison with B3LYP/TZVPP and RI-MP2/cc-pVQZ calculations shows that both conformers B and C are 7H-keto tautomers with an imine group in the 2-position. They differ only in the local conformation of the imine group but are otherwise identical. Conformer A is an amino-enol form with the OH group in the trans position.     

Stabilization of NH tautomers of quinolines by osmium and ruthenium

Complexes OsH2Cl2(PiPr3)2 and RuH2Cl2(PiPr3)2 promote the tautomerization of quinoline and 8-methylquinoline to NH tautomers, which lie about 44 kcal.mol-1 above the usual CH tautomers. The NH tautomers are stabilized by coordination to the metal center and by means of a Cl...HN interaction. As a consequence, the six-coordinate elongated dihydrogen complexes OsCl2{kappa-C2-(HNC9H5R)}(eta2-H2)(PiPr3)2, the five-coordinate derivatives RuCl2{kappa-C2-(HNC9H5R)}(PiPr3)2, and the six-coordinate dihydrogen compounds RuCl2{kappa-C2-(HNC9H5R)}(eta2-H2)(PiPr3)2 (R = H, Me) have been isolated and characterized.     

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.     

To what extent can methyl derivatives be regarded as stabilized tautomers of xanthine?

Taking xanthine (Xan) as an example, validity of an approach to experimental investigations of nucleotide bases' tautomeric equilibrium, based on the use of methyl derivatives corresponding to their prototropic tautomers, was studied by (1)H NMR in dimethylsulfoxide (DMSO) and by quantum chemical calculations at the B3LYP/6-311++G(d,p) level of theory. From (1)H NMR spectra of m(7)Xan, m(9)Xan, Xan and m(3)Xan conclusion was made that the N7H tautomeric forms of the last two compounds dominate in solution, which was supported by quantum chemical data. Calculated relative energies of the N9H tautomers of Xan and m(3)Xan (8.74 and 9.57 kcal/mol, accordingly) are rather close to the m(9)Xan one (9.11 kcal/mol). Nonspecific influence of DMSO modelled by the COSMO algorithm therewith reduces these values by approximately 2-3 kcal/mol. The data obtained imply that methyl derivatives are rather good models of high-energy tautomers of nucleotide bases, if their relative energies are not less than a few kcal/mol.     

Electronic transitions of guanine tautomers, their stacked dimers, trimers and sodium complexes

Planar and nonplanar geometries of the keto-N9H and keto-N7H tautomers of the guanine base of DNA as well as the hydrogen bonded complexes of these species with three water molecules each were optimized using the density functional theory at the B3LYP/6-31G** level. Geometries of the isolated bases were also optimized using the ab initio approach at the MP2/6-31G** level. The isolated keto-N9H and keto-N7H tautomers as well as their hydrogen bonded complexes with three water molecules each were solvated in bulk water employing the polarized continuum model (PCM) of the self-consistent reaction field theory (SCRF). Stacked dimers and trimers of both the tautomers of guanine were generated by placing the planar forms of the species at a fixed distance of 3.5 A from the neighboring one and rotating one molecule with respect to the other by 110 degrees for the keto-N9H form and 90 degrees for the keto-N7H form which corresponded to total energy minima at the B3LYP/6-31G** level. Geometry optimization for the cation of the monomer of guanine was performed at the same level of theory, and its solvation in bulk water was treated using the PCM model of the SCRF theory. The geometries of complexes of the two tautomers of guanine with a Na+ ion each were optimized at the B3LYP/6-31G** level, and the Na+ ion is predicted to bind with the keto-N9H tautomer preferentially. While the complex of the keto-N7H form of guanine with three water molecules in gas phase is slightly more stable than the corresponding complex of the keto-N9H form of guanine, the reverse is true in bulk water. Stacking interactions enhance the relative stability of the keto-N9H tautomer over that of the keto-N7H tautomer, suggesting that in bulk solutions, the former would be dominant. Electronic spectra of the isolated tautomers of guanine, those of their complexes with three water molecules each, the (keto-n9h and keto-n7h) cation of guanine, the complexes of the tautomers with a Na+ ion each, the stacked dimers and trimers of the two tautomers were calculated using configuration interaction involving single electron excitations (CIS). The relative absorption intensities of the two tautomers of guanine near 275 and 248 nm in the monomer, dimer, and trimer are predicated to be in the opposite order. Thus the absorption intensity oscillation observed using a guanine aqueous solution can be explained in terms of oscillation of relative populations of the two tautomers of the molecule. The 248 nm absorption peak would be appreciably red-shifted on formation of the cation of guanine. Binding of the Na+ ion with the two tautomers of guanine reduces intensities of their transitions appreciably and also it causes large red-shifts in the same.     

Effect of the H-bonding on aromaticity of purine tautomers

Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F(-) and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (-14.12 and -10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to -14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N(-)···HF type are stronger by ~10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N(-)···HF energies in pyrrole and imidazole are -32.28 and -30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability.     

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.     

黄嘌呤及其互变异构体的密度泛函理论研究

嘌呤碱及其衍生物在生物系统中起重要作用。对人具有兴奋和利尿作用的茶碱和咖啡碱就是黄嘌呤的甲基衍生物。黄嘌呤存在多种互变异构体,从理论计算的角度研究这些互变异构体的几何结构、电子结构及相对稳定性,进一步研究溶剂对其结构和性质的影响是有意义旧。密度泛函理论方法既考虑了电子相关,又较其它CI（组态相互作用）或MPn（n级微扰）方法节省机时。其计算结果较好,被广泛应用于研究各种化合物。本文采用密度泛函B3LYP／6—311G方法对14种黄嘌呤可能的互变异构体（见图1）,分别在气相和水相中进行几何构型全自由度优化和能量计算,讨论了异构体的相对稳定性,水的溶剂化作用对异构体的能量、几何构型、电荷分布和偶极矩的影响,探讨了溶剂极性对异构体的能量和偶极矩的影响。     

Photofragmentation in selected tautomers of protonated adenine

The photofragmentation by UV excitation of selectively prepared 1(+) and 3(+) tautomers of protonated adenine is studied after excitation at a 266 and 263 nm wavelengths with two different experimental set-ups located in Seoul and Orsay. While the production of 1(+) tautomers with an electrospray ion source is now well accepted, calculations were used to ascribe the preparation of 3(+) tautomers from cold adenine dimers. The fragmentation patterns are rather similar for both tautomers, suggesting similar mechanisms as a statistical fragmentation in the ground electronic state after internal conversion.     

Solvation free energies of molecules. The most stable anionic tautomers of uracil

Anionic states of nucleic acid bases are suspected to play a role in the radiation damage processes of DNA. Our recent studies suggested that the excess electron attachment to the nucleic acid bases can stabilize some rare tautomers, i.e. imine-enamine tautomers and other tautomers with a proton being transferred from nitrogen sites to carbon sites (with respect to the canonical tautomer). So far, these new anionic tautomers have been characterized by the gas-phase electronic structure calculations and photoelectron spectroscopy experiments. In the current contribution we explore the effect of water solvation on the stability of the new anionic tautomers of uracil. The accurate free energies of solvation are calculated in a two step approach. The major contribution was calculated using the classical free-energy perturbation adiabatic-charging approach, where it is assumed that the solvated molecule has the charge distribution given by the polarizable continuum model. In the second step the free energy of solvation is refined by taking into account the real, average solvent charge distribution. This is done using our accelerated QM/MM simulations, where the QM energy of the solute is calculated in the mean potential averaged over many MD steps. We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer.     

A semiempirical and ab initio MO study of the tautomers ofN-unsubstituted pyrazolones [hydroxy pyrazoles]

Semiempirical (MNDOC, MINDO/3, AM1, and MNDO) and ab initio (STO-3G and 4-31G basis sets) calculations on the relative stabilities, structures, and dipole moments of the 8 theoretically possible tautomeric forms of pyrazolone are reported. It is shown that MNDO + CI and MINDO/3 predict that 5-hydroxy pyrazole, 3-hydroxy pyrazole, and 2-pyrazolin-5-on are the most stable. These results correspond to the known experimental data. Of all used quantum chemical methods, the MINDO/3 results for the dipole moments of the investigated tautomers are in best agreement with the known experimental data. The electronic excitation energies were calculated using the CNDO/S-CI method. The results are in good agreement with the experimental UV spectra.     

On isomers and tautomers of Nitro-1-deazapurine: A DFT study

The 1-deazapurine molecules substituted by the NO₂ group at three different positions of the six-membered ring were subject of computational study performed at the B3LYP/cc-pVTZ level. For each substitution three tautomers were considered. The N3H tautomers are relatively instable in the gas and water phases which is due to significant decrease in aromaticity of the N3H forms. In the gas phase, the equilibria between the N7H and N9H tautomers are determined by a competition of the repulsive and attractive intermolecular interaction of different moieties of Nitro-1-deazapurine. The close neighborhood of the two tertiary N atoms and attractive close neighborhood of the tertiary N atom and the NH group result in preference of the N9H tautomer over the N7H one by ca. 3.5 kcal/mol. By comparing energy of different forms and proposed isodesmic reaction we showed that the Gibbs free energy of the attractive interaction between the NO₂ and HN groups is equal to ca. 1.0 kcal/mol, whereas the repulsive interaction between the NO₂ group and the tertiary N atom of the imidazole is equal to ca. 6.4 kcal/mol. It was shown also that the increase in dipole moment in the water media is the crucial effect influencing the N7H/N9H tautomeric equilibria of Nitro-1-deazapurines. For the three isomers dissolved in water, the two tautomers, N7H and N9H, are predicted to be observed and the former should dominate slightly for the 2-Nitro isomer whereas the latter for the 6-Nitro and 1-Nitro isomers. The NBO analysis showed that the NO₂ group withdraws 0.3 e of the σ-electrons from the pyridine ring of 1-deazapurine and has no influence on the σ-electrons of the imidazole ring. The NBO analysis shows also that the ratio between number of π-electrons which are withdrawed from imidazole vs. pyridine ring is characteristic for position of the substitution. The isodesmic reaction used revealed also that the NO₂ group destabilizes the N3H-1-deazapurine system, whereas it stabilizes the N7H- and N9H-1-deazapurine systems.     

2,6-二巯基嘌呤互变异构体热力学稳定性的密度泛函理论研究

利用密度泛函(DFT)B3LYP/6-311G(d,p)方法,水相计算采用自洽反应场(SCRF)中的Onsager模型,对气相和水相中可能存在的13种2,6-二巯基嘌呤互变异构体进行了全优化,并计算了各异构体的热力学参数、偶极矩及原子净电荷。计算结果表明,不论是气相还是水相,二硫酮DTP(1,3,7)是最稳定的异构体。溶剂化效应使各异构体的稳定性均增强,偶极矩大者其稳定性显著增大。溶剂化吉布斯自由能与异构体在两相中偶极矩之差存在相关性。二硫酮DTP(1,3,7)在水相中与致癌物BPDE进行亲核取代反应时,二硫酮DTP(1,3,7)中的S10原子优先进攻亲电试剂BPDE.     

Excited-state ab initio calculations and multidimensional Franck-Condon simulations on guanine

The guanine enol and keto N7H and N9H tautomers have been optimized at the CASSCF/cc-pVDZ levels of theory. Except for the enol N7H tautomer, CASSCF predicts distorted nonplanar S1 state geometries. Among the vibronic simulations carried out with the optimized structures only the enol N7H tautomer qualitatively mirrors the appearance of the experimental R2PI spectrum. Refined symmetry-adapted cluster configuration interaction (SACCI) geometries of the enol N7H tautomer produce simulations in good agreement with experiment and support the assignment of the first vibronic band and associated vibronic features of the R2PI spectrum to this tautomer. The sharp spectral features and the fact that Franck-Condon simulations based on the harmonic approximation allow for a faithful reproduction of the spectral signature associated with the enol N7H tautomer indicate that within the simulated energy window the S1 potential energy surface of this isomer is fairly harmonic and free from conical intersections involved in the S1 state lifetime-shortening relaxation processes of other DNA bases and possibly the remaining tautomers of guanine.     

Hydration effect on the stability of the keto-enol tautomers of 5-hydroxy-6-methyluracil

The structure and energies of six tautomeric forms of 5-hydroxy-6-methyluracil (OMU) and their 1:n (n = 1−4) complexes with water were determined by the density functional theory (PBE/3z) method. The stability series of the tautomers and changes in it depending on the number of water molecules in the nearest environment of the tautomer were found. The effect of the water solvent was also included using the continuum (B3LYP/6-311+G(2d,p), COSMO) model. Both complex formation and medium effects significantly influenced the stability series of the tautomers. Although the decrease in the energy of the diketo form on hydration was smaller than for the enol states, diketo tautomer a remained the most stable form of OMU in solution. Inclusion of hydration in calculations suggests that the energies of three enol tautomers b–d were equalized (ΔH ≈ 5.5 kJ/mol). This should be taken into account for the conditions that facilitate the keto-enol tautomerism of OMU.     

6-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平下,对14种气相和水相中可能存在的6-硫代黄嘌呤异构体进行了几何构型的全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能。Onsager反应场溶剂模型用于水相的计算.计算结果表明,6-硫代黄嘌呤在气相中和水相中主要以硫酮的形式存在.在气相和水相中,硫酮-N7(H)均比硫酮-N9(H)更稳定.计算结果同已有实验结果一致.6-硫代黄嘌呤异构化的熵效应小,对互变异构平衡几乎没有显著的影响,而焓变对互变异构产生了主要的影响.较详细地讨论了水溶剂化作用对异构体的能量、几何结构、电荷分布和偶极矩的影响.     

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.     

An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.