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Deprotonation of Guanine Radical Cation G Mediated by the Protonated Water Cluster

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Deprotonation of Guanine Radical Cation G Mediated by the Protonated Water Cluster pubs.acs.org/JPCA Article Deprotonation of Guanine Radical Cation G•+ Mediated by the Protonated Water Cluster Xianwang Zhang, Jialong Jie,* Di Song,* and Hongmei Su Cite This: J. Phys. Chem. A 2020, 124, 6076−6083 Read Online ACCESS Metrics & More Article Recommendations *sı Supporting Information ABSTRACT: Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H2O-PCM, 4H2O-PCM, fi 5H2O-PCM, and 7H2O-PCM models are used to calculate deprotonation potential energy pro le, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G•+. ■ INTRODUCTION undergo rapid proton transfer, competing with hole transfer Proton transfer through hydrogen bonds attracts continuous along DNA or leading to oxazolone via further reaction of its − • 12−24 interests and massive research efforts, because of the product, guanine radical G( H) . As shown in Scheme 1, •+ − − significance in most essential chemical and biological G has two sites, N1 H(pKa = 3.9) and N2 H(pKa = 4.7), 1−10 − processes. Many theoretical and experimental investiga- to lose a proton. According to the pKa values, the N1 H site is tions show that molecular mechanism behind proton transfer suggested to be favored over the N2−Hsite.Pulse − 12,17 18 probably involves protonated water clusters.1 7 Two important radiolysis and ESR experiments showed that only + − • structures of protonated water clusters, H (H2O)4 with a G(N1 H) were observed in the aqueous phase after proton + 1 central hydronium core (H3O ) bound to three waters and transfer at pH = 7.0. Density functional theory (DFT) Downloaded via BEIJING NORMAL UNIV on September 25, 2020 at 08:35:17 (UTC). + fl H (H2O)2 possessing a proton uctuating between two calculations including seven water molecules as the hydration waters,2 are proposed to explain anomalously high proton shell also provided a theoretical support that G(N1−H)• is See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles. mobility of liquid water.3 Unlike other ions, the transport of more stable than G(N2−H)• by 13.6 kJ/mol.18 Therefore, the protons in aqueous solution does not require the net diffusion proton transfer of G•+ in free nucleobase is thought to occur at of ionic species but instead is driven by a periodic series of the N1−H site. + + isomerizations between H (H2O)4 and H (H2O)2, where the It is noticeable that in different DNA structures, mechanisms 3,6,10 charge is transferred along the hydrogen bond. Even for of proton transfer of G•+ are different. In the DNA duplex, a proton transfer across biomembranes such as bacteriorhodop- facile proton transfer from N1 of G•+ to N3 of hydrogen- ff sin, which a ects biological functions of protein assemblies, the bonded cytosine (C) within the G:C base pair was proposed suggested mechanism also emphasizes the participations of 12,16,21,22,25,26 (Scheme 1), since the pKa (4.3) of N3- protonated water clusters based on time-resolved Fourier •+ 18 protonated cytosine is higher than that of G . Both transient transform infrared spectroscopy (trFTIR) and in situ H2 O/ 16 11 H2 O exchange FTIR measurements. Interestingly, proton transfer is also a universal phenomenon Received: April 27, 2020 in chemical reactions of DNA molecules, the mechanism of Revised: June 24, 2020 which continues to be an active research theme because of the Published: June 25, 2020 connection with charge transport and oxidation damage of DNA. Following one-electron oxidation of DNA, for example, the instantaneously generated guanine radical cation (G•+) can © 2020 American Chemical Society https://dx.doi.org/10.1021/acs.jpca.0c03748 6076 J. Phys. Chem. A 2020, 124, 6076−6083 The Journal of Physical Chemistry A pubs.acs.org/JPCA Article Scheme 1. (a) Proton Transfer (PT) Reaction in a One- activation energy of deprotonation was determined. To Electron Oxidized G:C Base Pair and (b) Deprotonation provide further mechanistic insights, potential energy profiles from N1 and N2 Site of Guanine Radical Cation, of deprotonation were calculated under solvation models Respectively incorporating explicit waters and the polarized continuum model (PCM), which provide energy barriers matching the experimental value and thus suggest a deprotonation process assisted by protonated water cluster. The deprotonation mechanism of G•+ in free base after one-electron oxidation is clarified, revealing the crucial role of protonated water cluster. These results enrich understandings for proton transfer of DNA systems, which are closely associated with hole transfer along DNA and oxidative damage of DNA. ■ MATERIALS AND METHODS Materials. 2′-Deoxyguanosine (G, Alfa Aesar), sodium persulfate (Na2S2O8, Sigma-Aldrich), and sodium phosphate buffer (50 mM, Beijing Solarbio Science & Technology) were used as purchased. Ultrapure water obtained by Millipore fi ltration was used as solvent. The sample of G and Na2S2O8 (ca. 0.215 g) was dissolved in 3 mL of sodium phosphate ff bu er (50 mM, pH 7.0) in H2O. Laser Flash Photolysis. Nanosecond time-resolved transient absorption spectra were measured using a flash photolysis setup Edinburgh LP920 spectrometer (Edinburgh Instruments Ltd.) combined with a Nd:YAG laser (Spectra- Physics Lab 170, Newport Corp.).30,31 Each measurement was absorption spectra and kinetics measurements further con- performed in a 1 cm path length quartz cuvette that was put in firmed this intrabase proton transfer route.17,21,27 An earlier the Oxford Instruments OptistatDN Cryostat and cooled to a DFT study on isolated G•+:C base pair in the gas phase certain temperature. The sample was excited by using a 355 predicted that the interbase proton transfer is unfavorable as nm laser pulse (1 Hz; 20 mJ/pulse; full width at half- the product G(N1−H)•:C(+H)+ is 5.9 kJ/mol less stable than maximum, ≈ 7 ns). The analyzing light was from a 450 W the reactant G•+:C, conflicting with experimental results.16 pulsed xenon lamp. A monochromator equipped with a Upon incorporation of 11 water molecules around the G•+:C, photomultiplier for collecting the spectral range from 300 to the B3LYP/6-31+G** calculations showed that the G(N1− 700 nm was used to analyze transient absorption spectra. The H)•:C(+H)+ becomes more stable than the G•+:C by 5.0 kJ/ signals from the photomultiplier were displayed and recorded mol, settling this controversy.22 It follows that hydration effect as a function of time on a 100 MHz (1.25 Gs/s sampling rate) plays an important role in reaction energetics, although the oscilloscope (TDS 3012C, Tektronix), and the data were intrabase proton transfer within the G•+:C base pair takes place transferred to a PC. Data were analyzed with online software of in a hydrophobic environment. the LP920 spectrophotometer and instrument response In free base, single-strand DNA and triplex DNA, G•+ function of Gaussian type was considered. The fitting quality transfers the N1− H proton to surrounding was judged by weighted residuals and reduced χ2 value. Note − waters,12 14,17,18,20,23,28 namely, deprotonation. Since the that each kinetic measurement was performed with new N1−H site of G•+ is not hydrogen-bonded with the C base sample. anymore and then has access to water, it is intriguing to Computational Methods. The geometries were fully investigate the role of water cluster or protonated water cluster optimized using the M06-2X density functional in connection in the process of proton transfer of G•+. However, the with the 6-31++G** basis set and the polarized continuum deprotonation mechanism of G•+ has not been addressed model. M06-2X developed by Truhlar and Zhao is a hybrid properly. In a theoretical investigation on mechanisms of meta functional having 54% Hartree−Fock exchange con- peroxynitrite oxidation of guanine,29 B3LYP calculations tribution.32,33 Due to the large exchange−correlation, this involving one water molecule presented a free energy profile functional is a better choice than other functions, for example, of G•+ deprotonation, in which the transition state was located, B3LYP, which is severely influenced by the self-interaction with an energy of 65.8 kJ/mol above the reactants. error.34 The M06-2X functional has been shown to well Unfortunately, there is hitherto no reported experimental describe noncovalent interactions; thus, it is very suitable for activation energy to be compared with. Assuming the energy studying a number of chemical problems, including radicals − barrier is 65.8 kJ/mol, deprotonation should take place on the and hydrated molecule ions.32,35 37 For example, Johnson et time scale of milliseconds, which is obviously in disagreement al. used the M06-2X functional with the 6-31++G** basis set × 7 −1 • − with the nanoseconds (1.8 10 s ) rates observed in to obtain vibration spectra of [Py (H2O)n=3−5] radical anions experiments.17 and the potential energy curve for proton transfer in • − In this context, we performed a joint theoretical and [Py (H2O)3] , revealing the important role of proton-assisted experimental investigation on deprotonation of G•+ derived charge accommodation in electron capture by a heterocyclic from one-electron oxidation of free G base.
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