Photodissociation dynamics of adenine dimer radical ions and hydrated adenine dimer ions, A þ 2 ðh 2OÞ n

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1 Available online at Chemical Physics Letters 450 (2008) Photodissociation dynamics of adenine dimer radical ions and hydrated adenine dimer ions, (n = 0 6) Sang Hwan Nam, Hye Sun Park, Seol Ryu, Jae Kyu Song *, Seung Min Park * Department of Chemistry, Kyunghee University, Seoul , Republic of Korea Received 11 July 2007; in final form 13 November 2007 Available online 19 November 2007 Abstract We studied photodissociation dynamics of adenine dimer radical ions, A þ 2, and hydrated adenine dimer ions, Aþ 2 ðh 2OÞ n (n = 1 6), at three wavelengths. The most abundant daughter ion is found to be protonated adenines, (AH) +, which implies that proton transfer is followed by dissociation in A þ 2 and Aþ 2 ðh 2OÞ n. Theoretical calculations support that the most stable structures of A þ 2 and Aþ 2 ðh 2OÞ 1 are formed by proton transfer. As cluster size of becomes larger, the intensity of A þ 2 as a daughter ion increases with the decrease in the intensity of (AH) +. Upon photoexcitation of A þ 2 by 266 nm, adenine monomer ion (A+ ) is also observed along with (AH) +, which suggests that electronically excited states of (AH) + moiety in A þ 2 promotes the hydrogen abstraction from (AH)+. Ó 2007 Elsevier B.V. All rights reserved. 1. Introduction A lot of studies on adenine have been performed to explore a remarkable stability of DNA bases against photochemical damage [1 11]. As well as their unique stability, it is also important to understand how protonated bases are produced and how protonation alters the chemical properties of bases, because proton transfer reactions play important roles in physical, chemical, and biological systems. For example, proton-transferred radicals have been suggested as a cause of mutation [12]. In this regard, adenine dimer is a prototypical system to understand the proton transfer in DNA base pairs, because the adenine dimer is structurally similar to the doubly hydrogen-bonded adenine thymine pairs. While the proton transfer in electronically excited states of DNA base pairs has been investigated extensively, relatively little is known about the proton transfer in ionic states of DNA base pairs. In addition, although protonated adenine has been studied by several groups [13 15], most of the previous works * Corresponding authors. addresses: jaeksong@khu.ac.kr (J.K. Song), smpark@khu.ac.kr (S.M. Park). focused on the monomeric properties. Therefore, the knowledge on the proton transfer reactions in ionic states of DNA base pairs will help understand the proton transfer in DNA base pairs thoroughly. Previously, we found protonated adenines along with adenine radical ions in the mass spectra obtained by photoionizations of hydrated adenine clusters [11]. Recently, protonated adenines are suggested to be produced both by proton transfer in adenine dimer ions and by hydrogen transfer in electronically excited state of neutral adenine dimers [7]. However, it is generally not easy to distinguish dynamics in the neutral states from that in the ionic states by mass spectra of ion clusters, and thus the dynamics of interest is often obscured. To gain a full understanding of photodynamics in the hydrated adenine clusters, selective studies on the ionic state dynamics are needed. In this Letter, we study how the protonated adenine is produced from the cluster ions, i.e., does hydrogen transfer or proton transfer takes place in the ionic base pairs? We observe the proton transfer in the electronic ground state of the adenine dimer ions, which is followed by dissociation upon photoexcitation. Also, we investigate the evaporation dynamics of solvents in hydrated adenine dimer ions /$ - see front matter Ó 2007 Elsevier B.V. All rights reserved. doi: /j.cplett

2 S.H. Nam et al. / Chemical Physics Letters 450 (2008) Experiments Since the details of the experimental setup have been described elsewhere [11,16], a brief overview of modification for this experiment is presented here. The hydrated adenine clusters were generated by adenine vapor at 300 C and water vapor at room temperature seeded in a He carrier gas, which co-expanded through a pulsed valve with a stagnation pressure of 1 atm. The neutral clusters were ionized by a cylindrically focused fourth harmonic output (266 nm) of a Nd:YAG laser at an excitation intensity of 50 mj/cm 2. Cluster ions were accelerated in a Wiley McLaren-type time-of-flight mass spectrometer with a flight length of 1 m, and cluster ions of interest were selected by a mass gate. The selected ions were excited by a photoexcitation pulse (532, 355, or 266 nm) in the second stage, which was consisted of four electrodes. The first electrode and the fourth electrode were grounded, while a pulsed high voltage was applied to the second electrode and the third electrode to separate daughter ions from parent ions, because the photoexcitation takes place between the second electrode and the third electrode. Although the velocities of daughter ions were the same to those of parent ions in the photoexcitation region, the daughter ions were more accelerated between the third electrode and the fourth electrode, and daughter ions could be separated from parent ions. Daughter ions as well as parent ions were detected as a function of flight time. The photoexcitation intensities of 532, 355, and 266 nm were kept as low as possible in order to reduce possible multiphoton processes. A difference mass spectrum was obtained by subtraction of the two mass distributions, which were acquired with and without the photoexcitation pulse. 3. Results and discussion 3.1. Protonated adenine in mass distributions of hydrated adenine cluster ions A typical mass distribution of hydrated adenine cluster ions obtained by the photoionization at 266 nm is presented in Fig. 1. Hydrated adenine monomer ions, A þ 1 ðh 2OÞ n, are nearly absent, while hydrated adenine dimer ions,, are clearly observed, which agrees with earlier studies [10,11]. The intensity of protonated adenine, (AH) +, is higher than that of adenine radical ion (A + ), as shown in the inset of Fig. 1. The high intensity of (AH) + implies that hydrogen transfer or proton transfer takes place either in the excited neutral states or in the ionic states [11]. Recently, the mechanism for the formation of (AH) + was carefully studied [7]. By changing the delay times and the excitation positions of two laser pulses, the electronically excited adenine dimer (A 2 ) was found to be a precursor of the AH radical by hydrogen transfer, which was ionized by additional photons. Another precursor for (AH) + was found to be the adenine dimer radical ion ða þ 2 Þ, because a decrease of Aþ 2 was observed with the Fig. 1. A mass distribution of hydrated adenine clusters obtained by multiphoton ionization at the wavelength of 266 nm. The intensities of hydrated adenine monomer ions, A þ 1 ðh 2OÞ n, are much lower than those of hydrated adenine dimer ions,. The inset shows the mass distribution of adenine ion (A + ) and protonated adenine, (AH) +. increase of (AH) + [7]. However, the photodissociation dynamics was explained without detailed mechanisms of proton transfers, mainly because it was not easy to discriminate the dynamics in the ionic states from that in the neutral states Photodissociation of adenine dimer radical ions In order to narrow down the dynamics and study the photodissociation processes in more detail, the size-selected adenine cluster ions are investigated. We note that internal energies of initial parent cluster ions are not negligible, because adenine cluster ions are produced by two photons of 266 nm (9.32 ev). For example, the internal energy of A þ 2 can be as large as 1.32 ev, because the ionization energy of A 2 is 8.00 ev [17]. Fig. 2a shows difference mass spectra upon photoexcitation of A þ 2 at 532, 355, and 266 nm, which are normalized to the depletion intensity of A þ 2. The most abundant daughter ion is (AH)+ at all wavelengths, which agrees with a previous study [7]. This indicates that the proton transfer occurs quite effectively either in the hot ground state of A þ 2 due to the internal energy or in the electronically excited state upon photoexcitation. Theoretical calculations are also carried out to understand the proton transfer in A þ 2, using the density functional theory at the level of B3LYP/6-31+G(d,p) with the GAUSSIAN 03 suite of program [18]. Stable geometries are found using analytical gradients with full geometry optimization. Charge distributions are obtained via natural bond orbital population analysis. A stable structure of A þ 2 in Fig. 3a is symmetrically planar between monomer moieties, which conforms to the most stable geometry of A 2 [19,20]. The binding energy between two moieties is calculated 1.08 ev, which is larger than the homolytic cleavage energy of neutral ones (0.77 ev) [19]. Charge is evenly delocalized

3 238 S.H. Nam et al. / Chemical Physics Letters 450 (2008) a (AH) nm A nm 266 nm Mass (amu) b 532 nm 355 nm Fig. 3. Stable geometries of adenine dimer ion, A þ 2, with the charge distributions of the moieties in parentheses. (a) Charge is evenly delocalized in symmetrically planar dimer, implying that it is denoted as a dimeric ion, (A A) +. (b) The most stable geometry is formed by the proton transfer. Charge is strongly localized in the proton-attached moiety, which suggests that A þ 2 is denoted as (AH)+ (A H) Mass (amu) 266 nm Fig. 2. (a) Difference mass spectra upon excitation of adenine dimer ion ða þ 2 Þ at 532, 355, and 266 nm, which are normalized to the depletion intensity of A þ 2. The most abundant daughter ion is (AH)+ at all wavelengths. (b) Magnified difference spectra. At 266 nm, A + is also observed with a decrease in the intensity of (AH) +. The two deconvoluted mass peaks are presented as dotted lines. in the dimer mainly due to its high symmetry, implying that it should be regarded as a dimeric ion, (A A) +, rather than an ion-solvent cluster, (A + A). Other possible dimeric ions will be stacked conformers of A þ 2. However, the stacked dimers are calculated to be less stable than the planar one in Fig. 3a, although a few stacked conformers are found as stable ones. For example, the most stable stacked dimer lies 0.5 ev above the planar one. Interestingly, a proton-transferred structure (Fig. 3b) is found to be more stable by 0.19 ev than the planar dimeric one (Fig. 3a), while a different basis set such as G(d,p) gives a similar value of 0.20 ev. The structure of the protonated moiety is quite similar to one of stable protonated adenine structures [14,15]. Charge is strongly localized in the proton-attached moiety, implying that a more stable A þ 2 is formed by proton transfer and can be denoted as (AH) + (A H). The binding energy between (AH) + and (A H) is about 1.34 ev. It is generally not easy to decide whether the proton transfer takes place in the ground state or in the excited state from fragmentation patterns only. For example, a ground state of phenol ammonia complex ion was suggested to consist of a phenol ion and an ammonia molecule (non-proton-transferred structure), because the complex ion dissociates into a phenol ion and an ammonia molecule upon photoexcitation [21,22]. However, it was concluded that a more stable state is the protontransferred structure [23]. Possibly due to proton tunneling, a proton in a phenol ion is transferred to an ammonia molecule despite the substantial activation barrier (1 ev) in the electronic ground state of the phenol ammonia complex ion. Such proton tunneling transfer has also been known in the excited state of 7-azaindole dimers even with the non-negligible activation barrier (0.5 ev) [24 26]. In fact, the activation barrier from (A A) + to (AH) + (A H), i.e., proton transfer in the ground state of A þ 2, was not easy to estimate. However, a previous study found that (AH) + was the major daughter ion of A þ 2 at the delay time of 70 ns without additional photoexcitation, when A 2 was photoionized by nm [7], which implies that the activation barrier of the proton transfer is not significant or proton tunneling occurs quite effectively in the ground state. Therefore, in our experiments, the proton transfer is suggested to take place in the ground state during the flight time (20 ls) in the field free region, because the internal energy in A þ 2 obtained in photoionization by 266 nm is not less than that in the previous study [7].

4 S.H. Nam et al. / Chemical Physics Letters 450 (2008) In the proton-transferred ground state of A þ 2, the mechanism of photodissociation is as follows: ðahþ þ ða HÞþhv!ðAHÞ þ ða HÞ!ðAHÞ þ þða HÞ A local chromophore for photoexcitation is (A H), because electronically excited states (pp * and np * state) of (AH) + lie at least 4 ev above the ground state [14], and the lowest electronically excited state of (A H) is found to be accessible by the photon energy of 532 nm in our preliminary calculation. Upon photoexcitation of (A H) moiety by 532 nm, the weak intermolecular bond in (AH) + (A H) is dissociated, which explains the appearance of (AH) + as the most abundant daughter ion. However, it is not known at this time whether the dissociation takes place in the electronically excited state or in the ground state with a lot of vibrational energy after internal conversion. Similar results in the photoexcitation at 355 nm support the proton-transferred ground state by the fact that the excitation of (A H) moiety gives rise to the appearance of (AH) + as a daughter ion. However, we cannot rule out the possibility of the proton transfer after photoexcitation, which assumes the non-proton-transferred ground state of A þ 2. The proton transfer after photoexcitation will take place by the following steps. ða AÞ þ þ hv! A A þ!ðahþ þ ða HÞ!ðAHÞ þ þða HÞ A local chromophore in (A A) + for photoexcitation is either A + or A. Although the information on excited states of A + has not been reported, a chromophore for the photoexcitation of 532 and 355 nm will be A +, because electronically excited states of A are not accessible by the photon energy of 532 and 355 nm [1,9]. Upon photoexcitation of A +, the proton transfer occurs either in the electronically excited state or in the vibrationally hot ground state after internal conversion, which is followed by the dissociation of intermolecular bonds. However, we note that these processes are suggested to have a minor contribution, because (AH) + (A H) is more stable than (A A) + in the ground state. Further experimental evidence will be discussed in the next section. Another possibility of a chromophoric state in the photoexcitation of 532 and 355 nm is a charge resonance state, because a dimeric ion, (A A) +, is found to be one of the stable structures. In the planar geometry of A þ 2, however, it is unlikely to form a charge resonance state, because the charge resonance state is usually found in the geometries of p orbital overlaps [24,27]. In addition, the charge resonance state, to our knowledge, lies 1 ev above the ground state, which suggests that the photon energy of 532 and 355 nm is not resonant with the charge resonance state. Besides, nearly identical results at 532 and 355 nm support that the charge resonance state is not accessible at least for the photoexcitation of 532 and 355 nm, because ð1þ ð2þ it is not probable for the charge resonance to be resonant both with 532 and 355 nm Adenine monomer ion as a daughter ion of adenine dimer radical ion The difference spectrum at 266 nm is not identical to those at 532 and 355 nm (Fig. 2b). With the decrease in the intensity of (AH) +, A + (m/z = 135) also appears, although the separation of two peaks is not completed due to a limited resolution. Because the electronically excited states of (AH) + are accessible by the photon energy of 266 nm [14], the daughter ions of A þ 2 at 266 nm are different. The appearance of A + suggests two possible pathways. In the first channel, the intermolecular bond in (AH) + (A H) is dissociated ahead to form (AH) +, and then hydrogen atom is abstracted to form A +. ðahþ þ ða HÞþhv!ðAHÞ þ ða HÞ!ðAHÞ þ þða HÞ! A þ þ H þða HÞ ð3þ However, this channel is highly unlikely in view of thermodynamics, because the binding energy between (AH) + and (A H) is about 1.34 ev and hydrogen abstraction from (AH) + needs as large as 4.16 ev [15]. Thus, the photon energy of 266 nm (4.66 ev) does not amount to the energy required for this channel (5.50 ev). In the other channel, upon the excitation of (AH) + moiety, the hydrogen atom transfers back to form (A A) +, and then intermolecular bond is dissociated. ðahþ þ ða HÞþhv!ðAHÞ þ ða HÞ!ðA AÞ þ! A þ þ A Because the energy state of (A A) + lies only by 0.19 ev above that of (AH) + (A H) and the cleavage energy of (A A) + is about 1.08 ev, the photon energy of 266 nm is sufficient for this channel. Certainly, this pathway is also allowed with the photon energy of 532 and 355 nm in view of thermodynamics, although the intensity of A + in the difference spectra at 532 and 355 nm is virtually negligible. In this regard, the chromophore seems to play an important role in the dissociation dynamics. In adenine neutral, the hydrogen abstraction through the repulsive potential energy surface of the electronically excited state (pr * state) is well known [6 9]. Therefore, the direct hydrogen abstraction in the electronically excited state of (AH) +, possibly such as pr * state, seems to be probable, which may not take place by excitation of (A H) moiety. It is worth noting that the photodissociation result at 266 nm also supports the proton-transferred ground state model. If (A A) + were the major species in the ground state, the photoexcitation of A by 266 nm, which is not allowed by 532 and 355 nm, could enhance the hydrogen abstraction from A through the pr * state [6 9]. Then, (AH) + would be observed by the following steps. ð4þ

5 240 S.H. Nam et al. / Chemical Physics Letters 450 (2008) ða AÞ þ þ hv! A A þ!ða HÞ ðahþ þ!ða HÞþðAHÞ þ It means that the intensity of (AH) + should increase at 266 nm compared to that at 532 and 355 nm. However, the intensity of (AH) + is reduced in the difference spectrum of 266 nm (Fig. 2b), which suggests that (A A) + is not the major species. Therefore, the wavelength dependence of the fragmentation patterns strongly supports that the proton transfer in A þ 2 takes place in the electronic ground state during the flight time possibly due to the internal energy in A þ Photodissociation dynamics of hydrated adenine dimer ions, (n = 1 6) The intensity of A þ 1 ðh 2OÞ n is quite small in Fig. 1, because intermediate electronic states of the corresponding neutrals experience an ultrafast internal conversion [1 5]. When the internal conversion to the ground state takes place, a drastic loss of water solvents by dissociation occurs either in the vibrationally excited neutral states or in the vibrationally excited ionic states [11]. However, it is possible to form A þ 1 ðh 2OÞ n by dissociation of larger hydrated cluster ions. Therefore, photodissociation study of helps explain the absence of A þ 1 ðh 2OÞ n in the mass distribution (Fig. 1). The difference mass spectra of obtained at 266 nm are presented in Fig. 4a. In small hydrated clusters, the major daughter ion is (AH) +. On the other hand, A þ 2 appears as a daughter ion from n = 4 and its intensity increases with the decrease in the intensity of (AH) +, as cluster size of parent ions becomes larger. However, any trace of A þ 1 ðh 2OÞ n or ðahþ þ ðh 2 OÞ n is not observed. In the difference mass spectra of, at first glance, (AH) + seems to be produced by detachment of the neutral clusters, (A H)(H 2 O) n, because the major daughter ion is (AH) + rather than A þ 2 in the small clusters. However, it cannot explain the appearance of A þ 2 observed in the photodissociation of larger clusters. In addition, the difference mass spectra obtained at 355 nm (Fig. 4b) shows different distributions of photofragments, which suggests a sequential evaporation of neutral solvents according to the photon energy [28 30]. Theoretical calculations are carried out for A þ 2 ðh 2OÞ 1 at the level of B3LYP/6-31+G(d,p) in order to understand photodissociation dynamics of hydrated adenine dimer ions. Fig. 5a shows an optimized geometry of A þ 2 ðh 2OÞ 1. Charge is more localized in a moiety adjacent to water, presumably because the water molecule can stabilize the charge. Another stable structure of A þ 2 ðh 2OÞ 1 is formed by proton transfer (Fig. 5b), which can be denoted as (AH) + (A H) (H 2 O). As in the case of A þ 2, the protontransferred structure of A þ 2 ðh 2OÞ 1 is more stable than the non-proton-transferred one by 0.22 ev. The stabilization energy by proton transfer in A þ 2 ðh 2OÞ 1 (0.22 ev) is larger than that in A þ 2 (0.19 ev) due to solvation effects of water. ð5þ (AH) + A + 2 (H 2 O) 6 * * * * O) 5 O) 4 O) 3 O) O) 4 O) 3 O) Mass (amu) Fig. 4. (a) Difference mass spectra of selected hydrated adenine dimer ions,, obtained by photoexcitation at 266 nm. In small hydrated clusters, the major daughter ion is (AH) +. As cluster size becomes larger, A þ 2 appears from n = 4 and its intensity increases with the decrease in the intensity of (AH) +. A trace of A þ 1 ðh 2OÞ n or (AH) + (H 2 O) n is not observed. Asterisks in the difference spectra originate from the photodissociation of daughter ions formed in the field-free flight region. For example, the asterisk in the spectrum of A þ 1 ðh 2OÞ 4 is the daughter ion of A þ 1 ðh 2OÞ 3 produced by the metastable decay of A þ 1 ðh 2OÞ 4 in the fieldfree flight region. (b) Difference mass spectra of selected hydrated adenine dimer ions,, obtained by photoexcitation at 355 nm. The binding energy between (AH) + and (A H)(H 2 O) 1 is calculated 1.38 ev, and the binding energy of the water solvent is 0.49 ev. Fig. 5c shows another proton-transferred structure of A þ 2 ðh 2OÞ 1, which is denoted as (A H) (AH) + (H 2 O). The stabilization energy by proton transfer is 0.15 ev. Therefore, the proton-transferred struc- A 2 +

6 S.H. Nam et al. / Chemical Physics Letters 450 (2008) cluster ions have a large amount of internal energies, they experiences dissociative ionization and metastable decay in the field-free region, usually ejecting neutral water molecules [30]. Therefore, internal energies of parent ions before photoexcitation may not much exceed binding energies of water solvents, which are less than 0.49 ev [31]. As a consequence, the internal energies of the photoexcited parent ions are in the range of ev upon the photoexcitation at 266 nm. Internal energy of the parent ion is dissipated via evaporation of water solvents, because it is partitioned as translational energy and internal energy of neutral fragments as well as the dissociation energy of solvents. For clusters with n 6 6, all water solvents are found to be dissociated (n = m) by the photon energy of 266 nm (Fig. 4a). Because the binding energy of a water solvent is less than 0.49 ev, a sequential evaporation of water solvents is allowed by the internal energy in the parent ions ( ev). After the evaporation of all water solvents, some internal energy can remain in the daughter ion A þ 2, which may give rise to the dissociation of the intermolecular bonds in A þ 2. A þ 2!ðAHÞ þ þða HÞ ð7þ Fig. 5. Stable geometries of singly-hydrated adenine dimer ion, A þ 2 ðh 2OÞ 1, with the charge distributions of the moieties in parentheses. (a) Charge is more localized in a moiety adjacent to water. (b) The most stable geometry is formed by the proton transfer, which is denoted as (AH) + (A H) (H 2 O). (c) Another stable structure of the proton transfer in A þ 2 ðh 2OÞ 1 is denoted as (A H) (AH) + (H 2 O). ture in Fig. 5b is more stable than that in Fig. 5c, which means that the proton transfer from the moiety of higher positive charge density (see Fig. 5a) stabilizes A þ 2 ðh 2OÞ 1 more effectively than the opposite case. The binding energy of a water solvent (0.49 ev) is much smaller than the cleavage energy of (AH) + (A H) (1.34 ev). Thus, water solvents can be considered sequentially dissociated ahead, when the evaporation proceeds statistically [28 30]. þ hm! m þ mðh 2 OÞ ð6þ The amount of total internal energies in the parent cluster ions will determine the photofragmentation patterns. However, it is not easy to estimate the internal energies of before photoexcitation, although the photon energy is well defined. After photoionization by two photons of 266 nm (9.32 ev), the internal energies of can be larger than 1 ev, because ionization energies of A 2 (H 2 O) n are less than 8.00 ev [17]. However, when the parent Interestingly, this dissociation is observed for all sizes of parent ions. However, we note that the intensity of (AH) + decreases as the cluster size of parent ions becomes larger, whereas the intensity of A þ 2 increases. The dependence of fragmentation patterns on cluster sizes and photon energies supports that the dissociation takes place statistically and sequentially. As discussed above, the binding energy of water solvents is smaller than that of (AH) + (A H) or (A A) +. Therefore, the detachment of (A H) or A from does not take place, when water solvents remain attached, which explains why (AH) + (H 2 O) n and A þ 1 ðh 2OÞ n are not observed as daughter ions in the photodissociation of. 4. Summary We found (AH) + as the most abundant daughter ion in photodissociation of (n = 0 6), which is due to the proton transfer in the ground state followed by dissociation upon photoexcitation. However, A + is also observed as a daughter ion at 266 nm, indicating that the electronically excited states of (AH) + give rise to hydrogen abstraction from (AH) +. Theoretical calculations support that the proton-transferred structures are more stable than the nonproton-transferred ones in A þ 2 and Aþ 2 ðh 2OÞ 1.A þ 1 ðh 2OÞ n and (AH) + (H 2 O) n are not observed in the difference spectra presumably due to the differences between water and adenine in binding energies to the parent ions. The intensity of (AH) + as the daughter ion decreases with the increase in the intensity of A þ 2, as cluster size of parent ions increases, which implies a sequential evaporation mechanism of neutral solvents.

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