About this Journal Submit a Manuscript Table of Contents
ISRN Physical Chemistry
Volume 2013 (2013), Article ID 146401, 10 pages
http://dx.doi.org/10.1155/2013/146401
Research Article

Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine

1Faculty of Science, King Khalid University, Abha, Saudi Arabia
2Faculty of Science, Jazan University, Jazan, Saudi Arabia
3Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
4Department of Structural Biology and Biomolecular Chemistry, Max F Perutz Laboratories, University of Vienna, 1030 Vienna, Austria

Received 17 December 2012; Accepted 6 January 2013

Academic Editors: E. B. Starikov and A. Tilocca

Copyright © 2013 Abdullah G. Al-Sehemi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We studied for the first time 16 tautomers/rotamers of diphosphocytosine by four computational methods. Some of these tautomers/rotamers are isoenergetic although they have different structures. High-level electron correlation MP2 and MP4(SDQ) ab initio methods and density functional methods employing a B3LYP and the new M06-2X functional were used to study the structure and relative stability of 16 tautomers/rotamers of diphosphocytosine. The dienol tautomers of diphosphocytosine are shown to be much more stable than the keto-enol and diketo forms. The tautomers/rotamers stability could be ranked as PC3 = PC12 < PC2 = PC11 < PC1 < PC10 < PC8 < PC9 < PC15 < PC16 < PC6~PC7 < PC13 < PC4~PC14 < PC5. This stability order was discussed in the light of stereo and electronic factors. Solvation effect has been modeled in a high dielectric solvent, water using the polarized continuum model (PCM). Consideration of the solvent causes some reordering of the relative stability of diphosphocytosine tautomers: PC3~PC12~PC2~PC11 < PC1 < PC10 < PC8 < PC9 < PC15~PC16 < PC13 < PC6~PC7~PC14 < PC4~PC5.