Raman spectroscopic study of the tautomeric composition of adenine in water

An experimental and theoretical study of the tautomeric composition of adenine (Ade) in water using Raman spectroscopy is reported. Experimental resonance Raman spectra of adenine at excitation wavelengths of 200, 218, and 266 nm were compared with quantum-mechanical calculations of N(9)H- and N(7)H-adenine tautomers and their cations. Both theoretical and experimental studies of nonresonance Raman spectra (457 nm excitation) of adenine were also performed for comparison. A satisfactory agreement of the calculated results with the experimental data was obtained. The Raman spectra are interpreted, and the basic regularities of the Raman intensity distribution are explained. On the basis of the analysis performed, the tautomeric composition of adenine in water is revealed. It is shown that the Ade-N(9),N(1)H(+) cation is the predominant form and that some neutral forms of Ade-N(9)H and Ade-N(7)H tautomers exist in water at pH 3.     

The electronic spectrum of protonated adenine: theory and experiment

In this work we present the results of a combined experimental and theoretical study concerned with the question how a proton changes the electronic spectrum and dynamics of adenine. In the experimental part, isolated adenine ions have been formed by electro-spray ionisation, stored, mass-selected and cooled in a Paul trap and dissociated by resonant photoexcitation with ns UV laser pulses. The S(0)-S1 spectrum of protonated adenine recorded by fragment ion detection lies in a similar energy range as the first pipi* transition of neutral 9H-adenine. It shows a flat onset with a broad substructure, indicating a large S(0)-S1 geometry shift and an ultra-short lifetime. In the theoretical part, relative energies of the ground and the excited states of the most important tautomers have been calculated by means of a combined density functional theory and multi-reference configuration interaction approach. Protonation at the nitrogen in position 1 of the neutral 9H-adenine tautomer yields the most stable protonated adenine species, 1H-9H-A+. The 3H-7H-A+ and the 3H-9H-A+ tautomers, formed by protonation of 7H- and 9H-adenine in 3-position, are higher in energy by 162 cm(-1) and 688 cm(-1), respectively. Other tautomers lie at considerably higher energies. Calculated vertical absorption spectra are reported for all investigated tautomers whereas geometry optimisations of excited states have been carried out only for the most interesting ones. The S1 state energies and geometries are found to depend on the protonation site. The theoretical data match best with the experimental onset of the spectrum for the 1H-9H-A+ tautomer although we cannot definitely exclude contributions to the experimental spectrum from the 3H-7H-A+ tautomer at higher energies. The vertical S(0)--> S1 excitation energy is similar to the one in neutral 9H-adenine. As for the neutral adenine, we find a conical intersection of the S1 of protonated adenine with the ground state in an out-of-plane coordinate but at lower energies and accessible without barrier.     

Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism

The DNA base adenine and four monomethylated adenines were studied in solution at room temperature by femtosecond pump-probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S(1) state) populated by a UV pump pulse. In H(2)O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 +/- 0.03 ps and 8.8 +/- 1.2 ps. In contrast, signals from monomethylated adenines decay monoexponentially. The S(1) lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (tau = 4.23 +/- 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H(2)O at room temperature to be 22 +/- 4% (estimated standard deviation). To understand how the environment affects nonradiative decay, we performed the first solvent-dependent study of nucleobase dynamics on the ultrafast time scale. In acetonitrile, both lowest energy tautomers of adenine are present in roughly similar proportions as in water. The lifetimes of the 9-substituted adenines depend somewhat more sensitively on the solvent than those of the 7-substituted adenines. Transient signals for adenine in H(2)O and D(2)O are identical. These solvent effects strongly suggest that excited-state tautomerization is not an important nonradiative decay pathway. Instead, the data are most consistent with electronic energy relaxation due to state crossings between the optically prepared (1)pipi* state and one or more (1)npi* states and the electronic ground state. The pattern of lifetimes measured for the monomethylated adenines suggests a special role for the (1)npi* state associated with the N7 electron lone pair.     

Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase

Gas-phase metal affinities of DNA and RNA bases for the Na(+) and K(+) ions were determined at density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of nucleic acid bases and the alkali ions on the different binding sites, were considered. Structural features of the sodium and potassium complexes were found to be similar except in some uracil and thymine compounds in which the tendency of potassium ion toward monocoordination appeared evident. B3LYP bond energies for both metal ions were in agreement with the available experimental results in the cases of uracil and thymine for which the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base. For adenine, although the interaction of the ions with the most stable free tautomer generated the least stable molecular complex, the best agreement with experiment was found in just this case. For the remaining cytosine and guanine bases, our calculations indicated that the metal ion affinity value closest to experiment should be determined taking into account the role played by the different tautomers of the free bases with similar energy and all the possible complexes obtained by them.     

Photoinduced dynamics of hydrated adenine clusters

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

Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules

KeV atomic particles traversing biological matter are subject to charge exchange and screening effects which dynamically change this particle's effective charge. The understanding of the collision cascade along the track thus requires a detailed knowledge of the interaction dynamics of radiobiologically relevant molecules, such as DNA building blocks or water, not only with ionic but also with neutral species. We have studied collisions of keV H(+), He(+), and C(+) ions and H(0), He(0), and C(0) atoms with the DNA base adenine by means of high resolution time-of-flight spectrometry. For H(0) and H(+) we find qualitatively very similar fragmentation patterns, while for carbon, strong differences are observed when comparing C(0) and C(+) impact. For collisions with He(0) and He(+) projectiles, a pronounced delayed fragmentation channel is observed, which has not been reported before.     

Photofragmentation of closo-carboranes part 1: Energetics of decomposition

The ionic fragmentation following B 1s and C 1s excitation of three isomeric carborane cage compounds [closo-dicarbadodecaboranes: orthocarborane (1,2-C2B10H12), metacarborane (1,7-C2B10H12), and paracarborane (1,12-C2B10H12)] is compared with the energetics of decomposition. The fragmentation yields for all three molecules are quite similar. Thermodynamic cycles are constructed for neutral and ionic species in an attempt to systemically characterize single-ion closo-carborane creation and fragmentation processes. Lower energy decomposition processes are favored. Among the ionic species, the photon-induced decomposition is dominated by BH+ and BH2(+) fragment loss. Changes in ion yield associated with core to bound excitations are observed.     

Transitions to high tautomeric states can be induced in adenine by interactions with carboxylate and sodium ions: DFT calculation data

Twelve triple complexes of nine adenine tautomers with carboxylate ion of acetic acid CH₃COO⁻ and sodium ion Na⁺ of the CH₃COO⁻:Ade:Na⁺ type were studied by the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) quantum chemical method. It was established that three rare adenine tautomers generate more stable complexes than the ground state one. The B3LYP/6-311++G(d,p) full optimization was applied to four most stable triple complexes in order to refine on their stability order. To evaluate contributions of each ligands for stabilization of these complexes, calculations of energies and dipole moments of respective binary complexes of the CH₃COO⁻:Ade and Ade:Na⁺ types were performed at the B3LYP/6-31++G(d,p) level of theory. At the same level, there were computed energies and dipole moments of isolated tautomers. Two of them, first calculated in this work, appeared to be zwitter-ions. Highly cooperative interplay of interactions of both ligands with adenine tautomers was observed in triple complexes. Preferable sites of coordination of Na⁺ with tautomers were ascertained. Biological importance of the results obtained is discussed.     

Fragmentation of protonated dipeptides containing arginine. Effect of activation method

The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.     

Gas phase ion chemistry of charged silver(I) adenine ions via multistage mass spectrometry experiments and DFT calculations

Electrospray ionization (ESI) of solutions containing adenine and AgNO(3) yields polymeric [Ad(x)+ Ag(y)-zH]((y-z)+) species. Density functional theory (DFT) calculations have been used to examine potential structures for several of the smaller ions while multistage mass spectrometry experiments have been used to probe their unimolecular reactivity (via collision-induced dissociation (CID)) and bimolecular reactivity (via ion-molecule reactions with the neutral reagents acetonitrile, methanol, butylamine and pyridine). DFT calculations of neutral adenine tautomers and their silver ion adducts provide insights into the binding modes of adenine. We find that the most stable [Ad + Ag](+) ion does not correspond to the most stable neutral adenine tautomer, consistent with previous studies that have shown that transition metal ions can stabilize rare tautomeric forms of nucleobases. Both the charge and the stoichiometry of the [Ad(x)+ Ag(y)-zH]((y-z)+) complexes play pivotal roles in directing the types of fragmentation and ion-molecule reactions observed. Thus, [Ad(2)+ Ag(2)](2+) is observed to dissociate to [Ad + Ag](+) and to react with butylamine via proton transfer, while [Ad(2)+ Ag(2)- H](+) fragments via loss of neutral adenine to form the [Ad + Ag(2)- H](+) ion and does not undergo proton transfer to butylamine. DFT calculations on several isomeric [Ad(2)+ Ag(2)](2+) ions suggest that planar centrosymmetric cations, in which two adjacent silver atoms are bridged by two N7H adenine tautomers via N(3),N(9)-bidentate interactions, are the most stable. The [Ad + Ag(2)-H](+) ion adds two neutral reagents in ion-molecule reactions, consistent with the presence of two vacant coordination sites. It undergoes a silver atom loss to form the [Ad + Ag - H](+) radical cation, which in turn fragments quite differently to the even electron [Ad + Ag](+) ion. Several other pairs of radical cation/even electron adenine-silver complexes were also found to undergo different fragmentation reactions.     

Mass spectrometric identification of ring-chain tautomers of 4-cyano-3-pyrazolidones in the gas phase

Analysis of the electron impact mass spectra of a series of 4-cyano-3-pyrazolidones, which manifest ring-chain tautomerism in polar solvents, showed that these compounds also exist in the gas phase as a mixture of tautomers, which undergo characteristic fragmentation. The quantitative tautomer ratio in this series is a function of electronic and steric substituent effects. The fragmentation pathways for each of the tautomers were determined using high-resolution mass spectrometry.M. V. Lomonosov Moscow State University, 119899 Moscow. Yerevan State University, 375025 Yerevan. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp 1525–1530, November, 1995 Original article submitted November 1, 1995.     

Phase control of molecular fragmentation with a pair of femtosecond-laser pulses

We demonstrate the control of molecular fragmentation of o-xylene (C(8)H(10)) on a femtosecond time scale in two-pulse measurements with a pair of femtosecond-laser pulses. Parent and fragment-ion yields were recorded as a function of interpulse delays, i.e., different relative phases of the excitation pulses. The experiments revealed different fragmentation mechanisms in the temporal region of direct overlapping pulses and for separated pulses. For overlapping pulses all ion yields followed the excitation intensity which oscillated as a function of interpulse delay due to the change of constructive and destructive interference of the light fields. For larger delays, in particular, the oscillations of the C(+) and CH(3) (+) fragment-ion yield showed a significant deviation from each other. The results are interpreted as a manifestation of optical phase-dependent electronic excitations mapped onto the nuclear fragmentation dynamics.     

Isoguanine formation from adenine

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A?C?2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A?C?2???OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG?1 or isoG?2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20?kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(?) →isoG+H(?) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG?1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.     

Mass spectrometric fragmentation of the tautomers of 1,3-diketones. A gas chromatographic/mass spectrometric study

The diketo and ketoenol tautomers of aliphatic 1,3-diketones can be easily separated by gas chromatography. The mass spectra of tautomers of pentane-2,4-diones substituted at C(l) and C(3), separated in this way, have been obtained. The fragmentation mechanisms are discussed. The mass spectra of the tautomers are quite different, and the main fragmentation pathways can be easily linked to the structures of the (non-interconverting!) tautomeric molecular ions. Furthermore, isomers differing by the position of the substituent can also be identified by their mass spectra.     

Femtosecond time-resolved photoelectron-photoion coincidence imaging of multiphoton multichannel photodynamics in NO2

The multiphoton multichannel photodynamics of NO(2) has been studied using femtosecond time-resolved coincidence imaging. A novel photoelectron-photoion coincidence imaging machine was developed at the laboratory in Amsterdam employing velocity map imaging and "slow" charged particle extraction using additional electron and ion optics. The NO(2) photodynamics was studied using a two color pump-probe scheme with femtosecond pulses at 400 and 266 nm. The multiphoton excitation produces both NO(2) (+) parent ions and NO(+) fragment ions. Here we mainly present the time dependent photoelectron images in coincidence with NO(2) (+) or NO(+) and the (NO(+),e) photoelectron versus fragment ion kinetic energy correlations. The coincidence photoelectron spectra and the correlated energy distributions make it possible to assign the different dissociation pathways involved. Nonadiabatic dynamics between the ground state and the A (2)B(2) state after absorption of a 400 nm photon is reflected in the transient photoelectron spectrum of the NO(2) (+) parent ion. Furthermore, Rydberg states are believed to be used as "stepping" states responsible for the rather narrow and well-separated photoelectron spectra in the NO(2) (+) parent ion. Slow statistical and fast direct fragmentation of NO(2) (+) after prompt photoelectron ejection is observed leading to formation of NO(+)+O. Fragmentation from both the ground state and the electronically excited a (3)B(2) and b (3)A(2) states of NO(2) (+) is observed. At short pump probe delay times, the dominant multiphoton pathway for NO(+) formation is a 3x400 nm+1x266 nm excitation. At long delay times (>500 fs) two multiphoton pathways are observed. The dominant pathway is a 1x400 nm+2x266 nm photon excitation giving rise to very slow electrons and ions. A second pathway is a 3x400 nm photon absorption to NO(2) Rydberg states followed by dissociation toward neutral electronically and vibrationally excited NO(A (2)Sigma,v=1) fragments, ionized by one 266 nm photon absorption. As is shown in the present study, even though the pump-probe transients are rather featureless the photoelectron-photoion coincidence images show a complex time varying dynamics in NO(2). We present the potential of our novel coincidence imaging machine to unravel in unprecedented detail the various competing pathways in femtosecond time-resolved multichannel multiphoton dynamics of molecules.     

1,3-Dipolar character of 6-membered aromatic rings. XXIV—mass spectrometry of 1-aryl-3-oxidopyridinium

Evaporation of 1-aryl-3-oxidopyridiniums is sometimes accompanied by rearrangement to 3-aryloxypyridine, but not to valence bond tautomers of the starting products. The fragmentation patterns are elucidated by metastable peaks and precise mass measurements and discussed.     

A velocity map imaging study of the one and two photon dissociations of state-selected DCl+ cations

DCl(+)(X (2)Pi(32),v(+")=0) cations have been prepared by 2+1 resonance enhanced multiphoton ionization, and their subsequent fragmentation following excitation at numerous wavelengths in the range of 240-350 nm studied by velocity map imaging of the resulting Cl(+) products. This range of excitation wavelengths allows selective population of A (2)Sigma(+) state levels with all vibrational (v(+')) quantum numbers in the range 0< or =v(+')< or =15. Image analysis yields wavelength dependent branching ratios and recoil anisotropies of the various D+Cl(+) ((3)P(J), (1)D, and (1)S) product channels. Levels with 10< or =v(+')< or =15 have sufficient energy to predissociate, forming D+Cl(+)((3)P(J)) products with perpendicular recoil anisotropies-consistent with the A (2)Sigma(+)<--X (2)Pi parent excitation and subsequent fragmentation on a time scale that is fast compared with the parent rotational period. Branching into the various spin-orbit states of the Cl(+)((3)P(J)) product is found to depend sensitively upon v(+') and, in the case of the v(+')=13 level, to vary with the precise choice of excitation wavelength within the A (2)Sigma(+)<--X (2)Pi(13,0) band. Such variations have been rationalized qualitatively in terms of the differing contributions made to the overall predissociation rate of DCl(+)(A,v(+')) molecules by coupling to repulsive states of (4)Pi, (4)Sigma(-), and (2)Sigma(-) symmetries, all of which are calculated to cross the outer limb of the A (2)Sigma(+) state potential at energies close to that of the v(+')=10 level. Cl(+)((3)P(J)) fragments are detected weakly following excitation to A (2)Sigma(+) state levels with v(+')=0 or 1, Cl(+)((1)D) fragments dominate the ion yield when exciting via 2< or =v(+')< or =6 and via v(+')=9, while Cl(+)((1)S) fragments dominate the Cl(+) images obtained when exciting via levels with v(+')=7 and 8. Analysis of wavelength resolved action spectra for forming these Cl(+) ions and of the resulting Cl(+) ion images shows that (i) these ions all arise via two photon absorption processes, resonance enhanced at the one photon energy by the various A(v(+')<10) levels, (ii) the first A (2)Sigma(+)<--X (2)Pi absorption step is saturated under the conditions required to observe significant two photon dissociation, and (iii) the final absorption step from the resonance enhancing A(v(+')) level involves a parallel transition.     

The role of tautomers in the UV absorption of urocanic acid

Tautomeric effects in the UV-absorption of trans-urocanic acid in the gas phase are investigated by means of quantum chemical calculations of sixteen tautomers at different levels, followed by absorption cross section simulations. It is shown that several trans tautomers give significant contributions to the total spectrum and that cis tautomers should not contribute to the spectrum at room temperature. The spectra of tautomers protonated at the N1 site of the imidazole ring are strongly red shifted in comparison to the spectra of tautomers protonated at the N3 site. As a consequence, excitation of the first absorption band at different wavelengths produces very different tautomeric populations. This effect helps to explain specific features observed in dispersion emission spectroscopy as well as the anomalous photophysics of urocanic acid.     

Disentangling intrinsic ultrafast excited-state dynamics of cytosine tautomers

Gas-phase ultrafast excited-state dynamics of cytosine, 1-methylcytosine, and 5-fluorocytosine were investigated in molecular beams using femtosecond pump-probe photoionization spectroscopy to identify the intrinsic dynamics of the major cytosine tautomers. The results indicate that, upon photoexcitation in the first absorption band, the cytosine enol tautomer exhibits a significantly longer excited-state lifetime than its keto and imino counterparts. The initially excited states of the cytosine keto and imino tautomers decay with sub-picosecond dynamics for excitation wavelengths shorter than 300 nm, whereas that of the cytosine enol tautomer decays with time constants ranging from 3 to 45 ps for excitation between 260 and 285 nm.