Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

Jiabo Li; Christopher J. Cramer; Donald G. Truhlar

doi:10.1016/S0301-4622(98)00228-2

Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

Jiabo Li, Christopher J. Cramer, Donald G. Truhlar

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

Abstract

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

Original language	English (US)
Pages (from-to)	147-155
Number of pages	9
Journal	Biophysical Chemistry
Volume	78
Issue number	1-2
DOIs	https://doi.org/10.1016/S0301-4622(98)00228-2
State	Published - Apr 5 1999

Bibliographical note

Funding Information:
The authors are grateful to Paul Winget for helpful discussions and assistance and to Albert J. Leo, Richard Wolfenden, and Phoebe Shih for helpful correspondence. This work was supported in part by the National Science Foundation.

Keywords

Continuum solvent
Dipole moment
Electrostatics
Free energy of solvation
Partial atomic charge
Partition coefficient
Polarizable solute

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10.1016/S0301-4622(98)00228-2

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Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory. / Li, Jiabo; Cramer, Christopher J.; Truhlar, Donald G.
In: Biophysical Chemistry, Vol. 78, No. 1-2, 05.04.1999, p. 147-155.

Research output: Contribution to journal › Article › peer-review

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abstract = "The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.",

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author = "Jiabo Li and Cramer, {Christopher J.} and Truhlar, {Donald G.}",

note = "Funding Information: The authors are grateful to Paul Winget for helpful discussions and assistance and to Albert J. Leo, Richard Wolfenden, and Phoebe Shih for helpful correspondence. This work was supported in part by the National Science Foundation.",

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AU - Li, Jiabo

AU - Cramer, Christopher J.

AU - Truhlar, Donald G.

N1 - Funding Information: The authors are grateful to Paul Winget for helpful discussions and assistance and to Albert J. Leo, Richard Wolfenden, and Phoebe Shih for helpful correspondence. This work was supported in part by the National Science Foundation.

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N2 - The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

AB - The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

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KW - Dipole moment

KW - Electrostatics

KW - Free energy of solvation

KW - Partial atomic charge

KW - Partition coefficient

KW - Polarizable solute

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Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

Abstract

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