Jump to main content
Jump to site search

Issue 23, 2011
Previous Article Next Article

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

Author affiliations

Abstract

We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and π–π stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform–water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4–1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.

Graphical abstract: The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

Back to tab navigation

Supplementary files

Article information


Submitted
05 Dec 2010
Accepted
21 Mar 2011
First published
12 May 2011

Phys. Chem. Chem. Phys., 2011,13, 10908-10922
Article type
Paper

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry

R. F. Ribeiro, A. V. Marenich, C. J. Cramer and D. G. Truhlar, Phys. Chem. Chem. Phys., 2011, 13, 10908
DOI: 10.1039/C0CP02784G

Social activity

Search articles by author

Spotlight

Advertisements