Nucleobase ionization potential

The effect of solvation on the IPs of nucleotides has been investigated by Le-Breton and coworkers using a combination of photoelectron spectroscopy and computational methods. They conclude that the first and second ionization potentials of the nucleotides deoxycytidine 5 -phosphate (CMP) and deoxythymidine 5 -phosphate (TMP) arise from ionization of the negatively charged phosphate group and nucleobase, respectively, both in the gas phase and in solution. The difference in the calculated first and second ionization potentials is smaller for the hydrated versus gas phase nucleosides as a consequence of the larger solvation energy for the zwit-terion formed upon ionization of the nucleobase versus the neutral radical formed upon ionization of the phosphate. The calculated adiabatic ionization potentials for the hydrated nucleobases CMP and TMP are 5.8 and 6.0 eV, respectively, considerably lower than the gas phase nucleobase ionization potentials (Table 1). 

The difference in stabilities of cation radicals located on G, GG, and GGG sequences was initially investigated by Sugiyama and Saito [14], who employed ab initio methods to calculate the gas phase ionization potentials of nucleobases stacked in B-DNA geometries. Their results indicated large differences in potential for holes on G vs GG (0.47 eV) and GGG (0.68 eV) sequences. A similar G vs GG difference was calculated by Prat et al. [62]. These values suggest that GG and GGG are, in fact, deep hole traps and they have been widely cited as evidence to that effect [54, 63]. 

Guanine is a preferential DNA target to several oxidants it shows the lowest ionization potential among the different purine and pyrimidine nucleobases and it is the only nucleic acid component that exhibits significant reactivity toward singlet oxygen ( O2) at neutral pH. ... 

Two different explanations have been advanced for the difference in trapping rates of GG and GGG. Berlin, Burin, and Ratner [54] base their explanation on the assumptions that (1) both traps are deep, i.e., -0.5 eV for GG and -0.7 eV for GGG, and (2) the ionization potential of guanine is lower than that of the other nucleobases by at least 0.4 eV. The different reactivities of the two traps were ascribed in [54] to different relaxation times of a hole in the trap. The GG units were taken to have a long relaxation time, so that a hole is likely to make a further hop before the trap closes on it, while the relaxation time of the GGG units was supposed to be relatively short, faster than the hopping time. 

Gua has the lowest reduction potential among the four nucleobases (Table 10.2), and hence it is preferentially oxidized to its radical cation (for the calculation of ionization potentials of the DNA bases see Close 2004 Crespo-Hernandez et al. 2004), and this property makes Gua and its derivatives to stick out of the other nucleobases with respect to its different free-radical chemistry. In contrast, Thy and Cyt are good electron acceptors, while the purines are only poor ones in comparison (for the calculation of electron affinities, see Richardson et al. 2004). This is of special importance in the effects caused by the absorption of ionizing radiation by DNA. 

The gas phase ionization potentials (IP) of the nucleobases have been determined by means of photoelectron spectroscopy and photoionization mass spectrometry [32]. Values for the first vertical and adiabatic ionization potentials are summarized... 

Table 1. Experimental and calculated ionization potentials (IP) and electron affinities (EA) of the nucleobases .

Base pairing of the nucleobases in duplex DNA can affect their calculated ionization potentials and electron affinities. Colson et al. [33b] reported that base pairing lowers the IP of guanine, but has little effect on the ionization of adenine in the A T base pair. The effects of base pairing on ionization potentials has been investigated by Hunter and Clark [34] using ab initio and density functional calculations. The isodesmic relations in Eqs. 1 and 2 show that A" " and G+ are stabilized by 10.2 and 17.4 kcal moC , respectively, upon base pairing. 

The identity of the radical ions formed upon steady-state radiation of DNA in low-temperature glasses has been established by means of electron paramagnetic resonance (EPR) spectroscopy [53]. EPR analysis indicates that electrons and holes are localized on a single nucleobase rather than being delocalized over several stacked bases at low temperatures. Radical ion formation is presumed to occur randomly at all four nucleosides. However, EPR studies establish that the electron holes are localized predominately on guanine, which has the lowest gas phase ionization potential and solution oxidation potential (Tables 1 and 3). Yan et al. [54]... 

Roca-Sanjuan, D., Rubio, M., Merchan, M., 8c Serrano-Andres, L. (2006). Ab initio determination of the ionization potentials of DNA and RNA nucleobases. The Journal of Chemical... 

In the direct effect of ionizing radiation on DNA, radical cations are the primary products (Chap. 12). For this reason, their reactions are of considerable interest. Obviously, photoionization (e.g., at 193 nm) and laser multi-photon excitation leads to such species (e.g., Candeias and Steenken 1992b Malone et al. 1995 Chap. 2.2). Base radical cation electron pairs have been proposed to be the first observable intermediates with a lifetime of 10 ps for Ade and four times longer for the other nucleobases (Reuther et al. 2000). Radical cations are also assumed to be intermediates in the reactions of photosensitization reactions with qui-nones, benzophenone, phthalocyanine and riboflavin (Cadet et al. 1983a Decar-roz et al. 1987 Krishna et al. 1987 Ravanat et al. 1991, 1992 Buchko et al. 1993 Douki and Cadet 1999 Ma et al. 2000). Nucleobase radical cations may be produced by electrochemical oxidation (Nishimoto et al. 1992 Hatta et al. 2001) or with strongly oxidizing radicals (for a compilation of their reduction potentials see Chap. 5.3). Rate constants are compiled in Table 10.3. 

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