Solvation Free Energies of the Nucleic Acid Bases

by: JL Miller, PA Kollman

J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8587-8594.

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DOI, American Chem. Soc. Publications

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Abstract

Abstract: We present free energy perturbation calculations on the solvation free energies of the N-methylated nucleic acid bases adenine, guanine, cytosine, thymine, and uracil. This work demonstrates the importance of using thermodynamic cycles, a careful study of convergence, and the use of both single and dual perturbation topologies. We find that the calculated solvation free energies of 9-methyladenine and 1-methylthymine are close to available experimental data. Additionally, we predict the solvation free energies for 9-methylguanine, 1-methylcytosine, and 1-methyluracil. The topologies used in these perturbations can be directly applied to free energy studies of higher order nucleic acid structures.

@article{citeulike:2943699, abstract = {Abstract: We present free energy perturbation calculations on the solvation free energies of the N-methylated nucleic acid bases adenine, guanine, cytosine, thymine, and uracil. This work demonstrates the importance of using thermodynamic cycles, a careful study of convergence, and the use of both single and dual perturbation topologies. We find that the calculated solvation free energies of 9-methyladenine and 1-methylthymine are close to available experimental data. Additionally, we predict the solvation free energies for 9-methylguanine, 1-methylcytosine, and 1-methyluracil. The topologies used in these perturbations can be directly applied to free energy studies of higher order nucleic acid structures.}, address = {Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California 94143}, author = {Miller, J. L. and Kollman, P. A. }, citeulike-article-id = {2943699}, doi = {10.1021/jp9605358}, journal = {J. Phys. Chem.}, keywords = {molecular\_simulation, nucleic\_acids, solvation}, month = {May}, number = {20}, pages = {8587--8594}, posted-at = {2008-06-30 12:15:23}, priority = {0}, title = {Solvation Free Energies of the Nucleic Acid Bases}, url = {http://dx.doi.org/10.1021/jp9605358}, volume = {100}, year = {1996} }

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TY - JOUR ID - citeulike:2943699 L3 - citeulike-article-id:2943699 TI - Solvation Free Energies of the Nucleic Acid Bases JF - J. Phys. Chem. VL - 100 IS - 20 SP - 8587 EP - 8594 AD - Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California 94143 N2 - Abstract: We present free energy perturbation calculations on the solvation free energies of the N-methylated nucleic acid bases adenine, guanine, cytosine, thymine, and uracil. This work demonstrates the importance of using thermodynamic cycles, a careful study of convergence, and the use of both single and dual perturbation topologies. We find that the calculated solvation free energies of 9-methyladenine and 1-methylthymine are close to available experimental data. Additionally, we predict the solvation free energies for 9-methylguanine, 1-methylcytosine, and 1-methyluracil. The topologies used in these perturbations can be directly applied to free energy studies of higher order nucleic acid structures. KW - molecular_simulation KW - nucleic_acids KW - solvation AU - Miller, JL AU - Kollman, PA PY - 1996/05/16/ UR - http://dx.doi.org/10.1021/jp9605358 ER -

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