NDLI: π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study.

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π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Kumar, Anil Sevilla, Michael D.
Description	Author Affiliation: Kumar A ( Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States.)
Abstract	As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(â ¢), and uracil, U(N3-H)(â ¢), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(â ¢+), C(N4-H)(â ¢), adenine, A(â ¢+), A(N6-H)(â ¢), and guanine, G(â ¢+), G(N2-H)(â ¢), G(N1-H)(â ¢), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(â ¢) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
ISSN	15206106
e-ISSN	15205207
Journal	The Journal of Physical Chemistry B
Issue Number	39
Volume Number	117
Language	English
Publisher	American Chemical Society (United States)
Publisher Date	2013-10-03
Publisher Place	United States
Access Restriction	Open
Subject Keyword	DNA Chemistry RNA Adenine Analogs & Derivatives Cytosine Electrons Gases Guanine Models, Molecular Oxidation-Reduction Solvents Thymine Uracil Research Support, N.I.H., Extramural Physical chemistry
Content Type	Text
Resource Type	Article
Subject	Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry

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