Ab initio molecular orbital calculations of DNA bases and their radical ions in various protonation states: evidence for proton transfer in GC base pair radical anions

Colson, Anny‐Odile; Besler, Brent; Close, David M.; Sevilla, Michael D.

doi:10.1021/j100181a028

Cited by 180 publications

(148 citation statements)

References 5 publications

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“…Such proton transfer reactions in DNA either slow or stop the charge transfer process in DNA. 58,61,[161][162][163] As already discussed in Sections 1.2.2 and 1.4, the proton transfer reactions will depend on the pK a of the DNA bases. While the pK a of the guanine radical cation is near 4, the pK a of adenine radical cation (A .…”

Section: Nature Of Hole Delocalization In Adenine Stacks: the Dimer Rmentioning

confidence: 94%

Theoretical Modeling of Radiation‐Induced DNA Damage

Kumar

Sevilla

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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Section: Nature Of Hole Delocalization In Adenine Stacks: the Dimer Rmentioning

confidence: 94%

Theoretical Modeling of Radiation‐Induced DNA Damage

Kumar

Sevilla

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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“…GB are given in Table VI, together with previously available theoretical 3,19 and the most recent experimental values. 13 Results show that the NLSD PA order is the same as that proposed by a mass spectrometric experimentation 13 in the framework of the kinetic method.…”

Section: Proton Affinities and Gas Phase Basicitiesmentioning

confidence: 99%

“…For thymine and cytosine the calculations were also performed with the more extended 6-31G basis set. 19 To our knowledge, the PA values obtained by the high-level ab initio-corw Ž . related method MP4r6-311 qqG d,p rrMP2r6-Ž .x 31G d are available only for cytosine and guanine.…”

mentioning

confidence: 99%

Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Russo

Toscano

Grand³

et al. 1998

J. Comput. Chem.

127

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Gradient‐corrected density functional computations with triple‐zeta‐type basis sets were performed to determine the preferred protonation site and the absolute gas‐phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero‐point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998

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“…5 A study of guanine derivatives in aqueous solution using pulse radiolytic techniques concluded that oneelectron oxidized guanine deprotonated at N1 under those conditions. 6 As well, an early HF / ab initio set of calculations concluded that the N1-deprotonated structure is more stable than the amino-deprotonated version, 7 while more recent DFT and molecular dynamics calculations led to the opposite conclusion. 8 For the case of one-electron-oxidized guanine within DNA, where it is paired with cytosine, computational results are similarly ambivalent regarding whether or not deprotonation occurs at all: Hutter and Clark concluded that transfer of a proton from N1 of guanine to N3 of cytosine is unfavorable by ca.…”

Section: Introductionmentioning

confidence: 99%

Structure of Radicals from X-irradiated Guanine Derivatives: An Experimental and Computational Study of Sodium Guanosine Dihydrate Single Crystals

Jayatilaka

Nelson

2007

J. Phys. Chem. B

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In sodium guanosine dihydrate single crystals, the guanine moiety is deprotonated at N1 due to growth from high-pH (>12) solutions. EPR and ENDOR study of crystals x-irradiated at 10 K detected evidence for three radical forms. Radical R1,characterized by two proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the N1-deprotonated guanine unit. R1 exhibited an unusually distorted structure leading to net positive isotropic components of the hydrogen couplings. Radical R2, characterized by one proton and one nitrogen hyperfine coupling was identified as the primary electron loss product. This product is equivalent to that of deprotonation at N1 by the guanine cation and represents the first ENDOR characterization of that product. Radical R3, characterized by a single hydrogen hyperfine coupling, was identified as the product of net dehydrogenation at C1 of the ribose moiety. The identification of radicals R1-R3 was supported by DFT calculations on several possible structures using the B3LYP/ 6-311G(2df,p)//6-31G(d,p) approach. Radical R4, detected after warming the crystals to room temperature, was identified as the well-known product of net hydrogenation of C8 of the (N1-deprotonated) guanine component. Radical R1, evidently formed by protonation of the primary electron addition product, was present as roughly 60% of the total radicals detected at 10 K. Radical R2 was present as roughly 27% of the total yield, and the concentration of R3 contributed the remaining 13%. R3 is evidently the product of oneelectron oxidation followed by deprotonation; thus, the balance of oxidation and reduction products is approximately equal within experimental uncertainty.

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Ab initio molecular orbital calculations of DNA bases and their radical ions in various protonation states: evidence for proton transfer in GC base pair radical anions

Cited by 180 publications

References 5 publications

Theoretical Modeling of Radiation‐Induced DNA Damage

Theoretical Modeling of Radiation‐Induced DNA Damage

Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Structure of Radicals from X-irradiated Guanine Derivatives: An Experimental and Computational Study of Sodium Guanosine Dihydrate Single Crystals

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