In this research, the interaction of ethyl butyryl triphenyl phosphonium chloride as an anticancer drug with a DNA which composed of twelve base pairs (Dickerson dodecamer) has been investigated. Molecular dynamic simulation of the DNA and drug in water was done for 3 ns. Two definite regions on the B-DNA, minor and major grooves, have been considered to analyze the best interaction site. Based on the calculated Gibbs free energies, it was confirmed that the interactions lead to the stabilization of the nanostructures of Dickerson model, showing an anticancer character for this compound. The chemical nature of the interactions at the minor groove of the DNA has been described by the Van der Walls and hydrogen bonds intermolecular forces.

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