Hydration energy of Adenine, Guanine, Cytosine and Thymine : Monte Carlo simulation

Document Type : Research Paper

Authors

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Abstract

The hydration of biomolecules is vitally important in molecular biology, so in this paper the
solvation energy and radial distribution function of DNA bases have been calculated by the
Monte Carlo simulation.The geometries of isolated Adenine, Guanine, Cytosine, and Thymine
have been optimized using 6-31+G(d,p) basis function sets. These geometries then will be used in
the Monte Carlo calculation of the DNA bases in water.We have used TIP3 model for water and
OPLS for nucleic acid bases. The computed solvation energy have Good agreement with the other
computational data Radial distribution function of O and N atoms of Adenine, Guanine, Cytosine,
and Thymine which have been computed and the results have been compared with other available
data observed for these molecules. The Monte Carlo simulation also has been performed by the
CHARMM39, 40 program in the same conditions and the results of two procedures have been
compared.