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

Subject Areas : Journal of Physical & Theoretical Chemistry

S. Ketabi ¹ , M. Hashemian Zadeh ² , A. Amiri ³

1 - Not mentioned
2 - Not mentioned
3 - Not mentioned

Received: 2015-04-24 Accepted : 2015-04-24 Published : 2004-08-01

Keywords:

Abstract :

The hydration of biomolecules is vitally important in molecular biology, so in this paper thesolvation energy and radial distribution function of DNA bases have been calculated by theMonte Carlo simulation.The geometries of isolated Adenine, Guanine, Cytosine, and Thyminehave been optimized using 6-31+G(d,p) basis function sets. These geometries then will be used inthe Monte Carlo calculation of the DNA bases in water.We have used TIP3 model for water andOPLS for nucleic acid bases. The computed solvation energy have Good agreement with the othercomputational 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 availabledata observed for these molecules. The Monte Carlo simulation also has been performed by theCHARMM39, 40 program in the same conditions and the results of two procedures have beencompared.

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