Addendum: Solvation Energies of Butylparaben, Benzo[a]pyrene diol epoxide, Perfluorooctanesulfonic acid, and DEHP in Complex with DNA Bases

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

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Faculty Opinions recommendation of Single base interrogation by a fluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1116761.572836 ◽

2008 ◽

Author(s):

Scott Silverman

Keyword(s):

Fluorescence Spectroscopy ◽

Dna Bases ◽

Single Base

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Oxidized DNA Bases in Breast Cancer

10.21236/ada413879 ◽

2002 ◽

Author(s):

Mehul Desai ◽

Krystyna Frenkel

Keyword(s):

Breast Cancer ◽

Dna Bases

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Ion solvation by dipolar aprotic solvents. An ab initio study

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19870006 ◽

1987 ◽

Vol 52 (1) ◽

pp. 6-13 ◽

Cited By ~ 2

Author(s):

Petr Kyselka ◽

Zdeněk Havlas ◽

Ivo Sláma

Keyword(s):

Ab Initio ◽

Geometry Optimization ◽

Molecular Structures ◽

Dimethyl Sulphoxide ◽

Ion Solvation ◽

Interaction Energies ◽

Ab Initio Study ◽

Solvation Energies ◽

Dipolar Aprotic Solvents ◽

Complete Geometry Optimization

The paper deals with the solvation of Li+, Be2+, Na+, Mg2+, and Al3+ ions in dimethyl sulphoxide, dimethylformamide, acetonitrile, and water. The ab initio quantum chemical method was used to calculate the solvation energies, molecular structures, and charge distributions for the complexes water···ion, acetonitrile···ion, dimethyl sulphoxide···ion, and dimethylformamide···ion. The interaction energies were corrected for the superposition error. Complete geometry optimization was performed for the complex water···ion. Some generalizations are made on the basis of the results obtained.

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