The Energetics of Rearrangement and Water Elimination Reactions in the Radiolysis of the DNA Bases in Aqueous Solution (eaq−and·OH Attack): DFT Calculations

Naumov, Sergej; Sonntag, Clemens von

doi:10.1667/rr1081.1

Cited by 31 publications

(60 citation statements)

References 46 publications

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“…This peak cannot be definitively assigned, since we focused on dehydrogenation reactions of adenine in this work. The ring-opening reaction transients and products, as mentioned before, [40,41,[44][45][46] may present strong transitions corresponding to these shorter wavelength peaks.…”

Section: Energeticsmentioning

confidence: 54%

“…If the OH radicals add at the C 8 site, ring-opening occurs and the OD at 330 nm increases. A 2008 study by Naumov and Sonntag [46] confirmed the earlier indications that OH radicals form an adduct with adenine at the C 4 position. The adduct undergoes proton or hydrogen transfer, followed by dehydration, to form an N 6 -dehydrogenated radical.…”

mentioning

confidence: 64%

“…Hydroxyl radical typically adds to the double bonds of adenine to yield C 4 , C 5 , and C 8 radical adducts. [40,41,[44][45][46] Of these three products, the A4OH radical constitutes more than 81 % of the hydroxylated radicals generated. [41] The A4OH radical adduct is a weak oxidant.…”

mentioning

confidence: 99%

“…X-ray radiation [4,[47][48][49][50] or OH radicals [40,41] can attack the C 2 , C 8 , N 9 , N 61 , or N 62 positions directly, producing neutral radicals or ionized species. [46,51] In the realm of quantum chemistry, a plethora of highly interesting large systems have not yet been explored, including many DNA subunits. For sufficiently small species, wave function methods yield excellent results, accurate to within 1 kcal mol…”

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confidence: 99%

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Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes

Cheng

Compaan

et al. 2010

Chemistry A European J

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In order to address problems such as aging, cell death, and cancer, it is important to understand the mechanisms behind reactions causing DNA damage. One specific reaction implicated in DNA oxidative damage is hydroxyl free-radical attack on adenine (A) and other nucleic acid bases. The adenine reaction has been studied experimentally, but there are few theoretical results. In the present study, adenine dehydrogenation at various sites, and the potential-energy surfaces for these reactions, are investigated theoretically. Four reactant complexes [A···OH]* have been found, with binding energies relative to A+OH* of 32.8, 11.4, 10.7, and 10.1 kcal mol(-1). These four reactant complexes lead to six transition states, which in turn lie +4.3, -5.4, (-3.7 and +0.8), and (-2.3 and +0.8) kcal mol(-1) below A+OH*, respectively. Thus the lowest lying [A···OH]* complex faces the highest local barrier to formation of the product (A-H)*+H(2)O. Between the transition states and the products lie six product complexes. Adopting the same order as the reactant complexes, the product complexes [(A-H)···H(2)O]* lie at -10.9, -22.4, (-24.2 and -18.7), and (-20.5 and -17.5) kcal mol(-1), respectively, again relative to separated A+OH*. All six A+OH* → (A-H)*+H(2)O pathways are exothermic, by -0.3, -14.7, (-17.4 and -7.8), and (-13.7 and -7.8) kcal mol(-1), respectively. The transition state for dehydrogenation at N(6) lies at the lowest energy (-5.4 kcal mol(-1) relative to A+OH*), and thus reaction is likely to occur at this site. This theoretical prediction dovetails with the observed high reactivity of OH radicals with the NH(2) group of aromatic amines. However, the high barrier (37.1 kcal mol(-1)) for reaction at the C(8) site makes C(8) dehydrogenation unlikely. This last result is consistent with experimental observation of the imidazole ring opening upon OH radical addition to C(8). In addition, TD-DFT computed electronic transitions of the N(6) product around 420 nm confirm that this is the most likely site for hydrogen abstraction by hydroxyl radical.

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Section: Energeticsmentioning

confidence: 54%

mentioning

confidence: 64%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes

Cheng

Compaan

et al. 2010

Chemistry A European J

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“…Reviews on these calculations can be found in Refs. [8][9][10][11][12][13]. Chemical reactivity of OH species or specific processes like hydrogen abstraction on DNA bases in gas phase have been also studied [14,15].…”

Section: Introductionmentioning

confidence: 99%

Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

et al. 2014

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Abstract:We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons. PACS

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Isoguanine Formation from Adenine

Cheng

Compaan

et al. 2012

Chemistry A European J

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Several possible mechanisms underlying isoguanine formation when OH radical attacks the C2 position of adenine (A) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low‐lying A⋅⋅⋅OH reactant complexes is formed, leading to C2H2 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 N1H and O2H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.

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The Energetics of Rearrangement and Water Elimination Reactions in the Radiolysis of the DNA Bases in Aqueous Solution (e_aq⁻and^·OH Attack): DFT Calculations

Cited by 31 publications

References 46 publications

Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes

Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes

Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

Isoguanine Formation from Adenine

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