Issue 30, 2008
From the journal:

Physical Chemistry Chemical Physics

Solvation free energies of molecules. The most stable anionic tautomers of uracil

Maciej Haranczyk,*ab   Maciej Gutowskibc  and  Arieh Warshela  

* Corresponding authors

a Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, USA

b Department of Chemistry, University of Gdańsk, Gdańsk, Poland
E-mail: maharan@chem.univ.gda.pl
Fax: +48 58 523 5472

c Chemistry—School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK

Abstract

Anionic states of nucleic acid bases are suspected to play a role in the radiation damage processes of DNA. Our recent studies suggested that the excess electron attachment to the nucleic acid bases can stabilize some rare tautomers, i.e. imine–enamine tautomers and other tautomers with a proton being transferred from nitrogen sites to carbon sites (with respect to the canonical tautomer). So far, these new anionic tautomers have been characterized by the gas-phase electronic structure calculations and photoelectron spectroscopy experiments. In the current contribution we explore the effect of water solvation on the stability of the new anionic tautomers of uracil. The accurate free energies of solvation are calculated in a two step approach. The major contribution was calculated using the classical free-energy perturbation adiabatic-charging approach, where it is assumed that the solvated molecule has the charge distribution given by the polarizable continuum model. In the second step the free energy of solvation is refined by taking into account the real, average solvent charge distribution. This is done using our accelerated QM/MM simulations, where the QM energy of the solute is calculated in the mean potential averaged over many MD steps. We found that in water solution three of the recently identified anionic tautomers are 6.5–3.6 kcal mol−1 more stable than the anion of the canonical tautomer.

Graphical abstract: Solvation free energies of molecules. The most stable anionic tautomers of uracil

About
Cited by
Related
Download options Please wait...

Article information

DOI
https://doi.org/10.1039/B802300J
Article type
Paper
Submitted
12 Feb 2008
Accepted
18 Apr 2008
First published
11 Jun 2008

Phys. Chem. Chem. Phys., 2008,10, 4442-4448

Permissions

Request permissions

Solvation free energies of molecules. The most stable anionic tautomers of uracil

M. Haranczyk, M. Gutowski and A. Warshel, Phys. Chem. Chem. Phys., 2008, 10, 4442 DOI: 10.1039/B802300J

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements