Structures and stabilities of sugar radical nucleotides

Sarma, Rajib L.; Medhi, C.

doi:10.1016/j.theochem.2005.12.037

Cited by 4 publications

(2 citation statements)

References 34 publications

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“…Especially the free energy of the radical at the C 1 position is dramatically lower than that of the radical at the C 2 position. Our calculation results are reasonably consistent with the relative stability of the different sugar radicals that have been calculated by several other groups, − and the order is generally found to be C 1 > C 4 > C 5 > C 3 > C 2 . The lower energy levels of the sugar radicals at C 1 and C 4 positions drive the radicals at the C 2 and C 3 positions to further isomerize to the C 1 and C 4 positions respectively through a hydrogen shift.…”

Section: Resultssupporting

confidence: 91%

Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads

Li¹,

Dang

Liu³

et al. 2015

J. Org. Chem.

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Intramolecular hydrogen abstraction reactions among ketoprofen (KP) and purine nucleoside dyads have been proposed to form ketyl-sugar biradical intermediates in acetonitrile. Femtosecond transient absorption studies on KP and purine nucleoside dyads reveal that the triplet state of the KP moiety of the dyads with cisoid structure decay faster (due to an intramolecular hydrogen abstraction reaction to produce a ketyl-sugar biradical intermediate) than the triplet state of the KP moiety of the dyads with transoid structure detected in acetonitrile solvent. For the cisoid 5-KP-dG dyad, the triplet state of the KP moiety decays too fast to be observed by ns-TR(3); only the ketyl-sugar biradical intermediates are detected by ns-TR(3) in acetonitrile. For the cisoid 5-KP-dA dyad, the triplet states of the KP moiety could be observed at early nanosecond delay times, and then it quickly undergoes intramolecular hydrogen abstraction to produce a ketyl-sugar biradical intermediate. For the cisoid 5-KPGly-dA and transoid 3-KP-dA dyads, the triplet state of the KP moiety had a longer lifetime due to the long distance chain between the KP moiety and the purine nucleoside (5-KPGly-dA) and the transoid structure (3-KP-dA). The experimental and computational results suggest that the ketyl-sugar biradical intermediate is generated with a higher efficiency for the cisoid dyad. However, the transoid dyad exhibits similar photochemistry behavior as the KP molecule, and no ketyl-sugar biradical intermediate was observed in the ns-TR(3) experiments for the transoid 3-KP-dA dyad.

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Section: Resultssupporting

confidence: 91%

Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads

Li¹,

Dang

Liu³

et al. 2015

J. Org. Chem.

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“…The difference between the Gibbs free energies of the C1 0 -and C2 0 -centered radicals is found to be 8.0, 6.4, and 6.6 kcal/mol at the B3LYP/ AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels of theory in gas phase, respectively (Table III). Several previous gas phase theoretical studies [11,15,[18][19][20] have shown that the deoxyribose radicals centered at the C1 0 and C2 0 sites are most and least stable, while other gas phase theoretical studies [16,17] have shown that C4 0 -and C2 0 -centered deoxyribose radicals are most and least stable, respectively (Table III). As the molecules from which the radicals are derived and the levels of theory used are not the same [11,[15][16][17][18][19][20], a quantitative comparison of the results obtained in these studies cannot be made (Table III).…”

Section: Table IIImentioning

confidence: 94%

Hydrogen atom abstraction reactions of the sugar moiety of 2′‐deoxyguanosine with an OH radical: A quantum chemical study

Kumar

Mishra

2011

Int J of Quantum Chemistry

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Mechanisms of hydrogen atom abstraction reactions of the sugar moiety of 2 0 -deoxyguanosine with an OH radical were investigated using the B3LYP and BHandHLYP functionals of density functional theory and the second order Møller-Plesset Perturbation (MP2) theory in gas phase and aqueous media. The 6-31þG* and AUG-cc-pVDZ basis sets were used. Gibbs free barrier energies and rate constants of the reactions in aqueous media suggest that an OH radical would abstract the hydrogen atoms of the sugar moiety of 2 0 -deoxyguanosine in the following order of preference: H5 0 % H5 00 > H3 0 > H4 0 > H1 0 % H2 0 > H2 00 , the rate constant for H5 0 abstraction being 10 3 -10 5 times greater than that for H2 00 at the different levels of theory. Relative stabilities of the different deoxyribose radicals are also discussed. The most and least favored hydrogen abstraction reactions found here are in agreement with experimental observation.

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Structures, stabilities & conformational behaviors of hydrogen-atom abstractions of cytosine nucleosides: AIM & NBO analysis

Tehrani

Javan

Fattahi

et al. 2011

Computational and Theoretical Chemistry

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Structures and stabilities of sugar radical nucleotides

Cited by 4 publications

References 34 publications

Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads

Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads

Hydrogen atom abstraction reactions of the sugar moiety of 2′‐deoxyguanosine with an OH radical: A quantum chemical study

Structures, stabilities & conformational behaviors of hydrogen-atom abstractions of cytosine nucleosides: AIM & NBO analysis

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