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The final step involved a nucleophilic substitution of the 2-chloro group by piperazine at high temperatures.
The piperazine end of the molecule extends partially into the GC region of the DNA.
The interaction energy between the piperazine and the DNA does not alter significantly during the structural changes, suggesting entropy as the driving force for the transitions.
Thus, the piperazine ring rotates while the rest of the molecule stays in the starting x-ray conformation during the simulation.
Fluphenazine is a piperazine phenothiazine that is structurally similar to perphenazine and prochlorperazine.
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