Literature DB >> 12812509

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution.

Michal Hanus1, Filip Ryjácek, Martin Kabelác, Tomás Kubar, Tetyana V Bogdan, Semen A Trygubenko, Pavel Hobza.   

Abstract

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.

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Year:  2003        PMID: 12812509     DOI: 10.1021/ja034245y

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  14 in total

1.  Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

Authors:  Yongping Pan; Alexander D MacKerell
Journal:  Nucleic Acids Res       Date:  2003-12-15       Impact factor: 16.971

2.  Intriguing mass spectrometric behavior of guanosine under low energy collision-induced dissociation: H2O adduct formation and gas-phase reactions in the collision cell.

Authors:  Robin Tuytten; Filip Lemière; Walter Van Dongen; Eddy L Esmans; Erwin Witters; Wouter Herrebout; Benjamin Van Der Veken; Ed Dudley; Russell P Newton
Journal:  J Am Soc Mass Spectrom       Date:  2005-08       Impact factor: 3.109

3.  Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.

Authors:  Lukas Eberlein; Frank R Beierlein; Nico J R van Eikema Hommes; Ashish Radadiya; Jochen Heil; Steven A Benner; Timothy Clark; Stefan M Kast; Nigel G J Richards
Journal:  J Chem Theory Comput       Date:  2020-03-20       Impact factor: 6.006

4.  Theoretical model of the aqua-copper [Cu(H2O)5]+ cation interactions with guanine.

Authors:  Jaroslav V Burda; Manoj K Shukla; Jerzy Leszczynski
Journal:  J Mol Model       Date:  2005-06-01       Impact factor: 1.810

5.  Investigation of interactions of doxorubicin with purine nucleobases by molecular modeling.

Authors:  Esra Şahin Akdeniz; Cenk Selçuki
Journal:  J Mol Model       Date:  2022-02-26       Impact factor: 1.810

6.  An ab initio and AIM investigation into the hydration of 2-thioxanthine.

Authors:  Xiu-Xiang Yuan; Yan-Fang Wang; Xin Wang; Wenbo Chen; John S Fossey; Ning-Bew Wong
Journal:  Chem Cent J       Date:  2010-03-23       Impact factor: 4.215

7.  Accurate micro- and macro- gas phase basicities of hydroxyl-radical-modified pyrimidines estimated by advanced quantum chemistry methods.

Authors:  Piotr Cysewski; Katarzyna Kozłowska; Beata Szefler
Journal:  J Mol Model       Date:  2008-12-17       Impact factor: 1.810

8.  Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers.

Authors:  Andrea Alparone
Journal:  J Mol Model       Date:  2013-04-20       Impact factor: 1.810

9.  Silver- and gold-mediated nucleobase bonding.

Authors:  Paulo H Acioli; Sudha Srinivas
Journal:  J Mol Model       Date:  2014-08-10       Impact factor: 1.810

10.  Reaction electronic flux and its role in DNA intramolecular proton transfers.

Authors:  Rocío Durán; Esteban Vöhringer-Martinez; Alejandro Toro-Labbé; Bárbara Herrera
Journal:  J Mol Model       Date:  2016-06-02       Impact factor: 1.810

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