Literature DB >> 21247073

Ionization of purine tautomers in nucleobases, nucleosides, and nucleotides: from the gas phase to the aqueous environment.

Eva Pluharrová1, Pavel Jungwirth, Stephen E Bradforth, Petr Slavícek.   

Abstract

We have simulated ionization of purine nucleic acid components in the gas phase and in a water environment. The vertical and adiabatic ionization processes were calculated at the PMP2/aug-cc-pVDZ level with the TDDFT method applied to obtain ionization from the deeper lying orbitals. The water environment was modeled via microsolvation approach and using a nonequilibrium polarizable continuum model. We have characterized a set of guanine tautomers and investigated nucleosides and nucleotides in different conformations. The results for guanine, i.e., the nucleic acid base with the lowest vertical ionization potential, were also compared to those for the other purine base, adenine. The main findings of our study are the following: (i) Guanine remains clearly the base with the lowest ionization energy even upon aqueous solvation. (ii) Water solvent has a strong effect on the ionization energetics of guanine and adenine and their derivatives; the vertical ionization potential (VIP) is lowered by about 1 eV for guanine while it is ∼1.5 eV higher in the nucleotides, overall resulting in similar VIPs for GMP(-), guanosine and guanine in water. (iii) Water efficiently screens the electrostatic interactions between nucleic acid components. Consequently, ionization in water always originates from the base unit of the nucleic acid and all the information about conformational state is lost in the ionization energetics. (iv) The energy splitting between ionization of the two least bound electrons increases upon solvation. (v) Tautomerism does not contribute to the width of the photoelectron spectra in water. (vi) The effect of specific short-range interactions with individual solvent molecules is negligible for purine bases, compared to the long-range dielectric effects of the aqueous medium.

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Year:  2011        PMID: 21247073     DOI: 10.1021/jp110388v

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  10 in total

1.  Chemical reactivity analysis of deoxyribonucleosides and deoxyribonucleoside analogues (NRTIs): a first-principles density functional approach.

Authors:  Vipin Kumar; Shyam Kishor; Lavanya M Ramaniah
Journal:  J Mol Model       Date:  2012-03-21       Impact factor: 1.810

2.  One-electron oxidation of ds(5'-GGG-3') and ds(5'-G(8OG)G-3') and the nature of hole distribution: a density functional theory (DFT) study.

Authors:  Anil Kumar; Amitava Adhikary; Michael D Sevilla; David M Close
Journal:  Phys Chem Chem Phys       Date:  2020-02-19       Impact factor: 3.676

3.  First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate.

Authors:  Debashree Ghosh; Anirban Roy; Robert Seidel; Bernd Winter; Stephen Bradforth; Anna I Krylov
Journal:  J Phys Chem B       Date:  2012-05-04       Impact factor: 2.991

4.  Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study.

Authors:  Anil Kumar; Michael D Sevilla
Journal:  J Phys Chem B       Date:  2022-02-13       Impact factor: 2.991

5.  Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations.

Authors:  Alessandro Nicola Nardi; Alessio Olivieri; Marco D'Abramo
Journal:  J Phys Chem B       Date:  2022-06-07       Impact factor: 3.466

6.  Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives.

Authors:  Noel Gardner; David Magers; Glake Hill
Journal:  J Mol Model       Date:  2013-05-31       Impact factor: 1.810

Review 7.  Structure-activity features of purines and their receptors: implications in cell physiopathology.

Authors:  Mauricio Díaz-Muñoz; Rolando Hernández-Muñoz; Armando Butanda-Ochoa
Journal:  Mol Biomed       Date:  2022-01-26

Review 8.  Theoretical Modeling of Redox Potentials of Biomolecules.

Authors:  Cheng Giuseppe Chen; Alessandro Nicola Nardi; Andrea Amadei; Marco D'Abramo
Journal:  Molecules       Date:  2022-02-05       Impact factor: 4.411

9.  Guanosine Dianions Hydrated by One to Four Water Molecules.

Authors:  Samanta Makurat; Qinqin Yuan; Jacek Czub; Lidia Chomicz-Mańka; Wenjin Cao; Xue-Bin Wang; Janusz Rak
Journal:  J Phys Chem Lett       Date:  2022-04-05       Impact factor: 6.888

10.  Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution.

Authors:  Valeria D'Annibale; Alessandro Nicola Nardi; Andrea Amadei; Marco D'Abramo
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

  10 in total

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