ABSTRACT A semiempirical analysis (AM1) of zwitterion and non-zwitterion structures for 3-carboxyquinoxalinyl and benzoquinoxalinyl putrescines as mono and bis derivatives was performed. Selected conformations were theoretically evaluated as DNA-complexing molecules either by intercalation or by association to minor groove, employing AMBER molecular mechanic method. Results showed that an increase in molecular planarity by adding one condensed phenyl ring in benzoquinoxaline derivatives did not produce a significant increase in stability of intercalation complexes with respect to quinoxaline derivatives. In this sense, complexes with zwitterion species resulted the less stable ones; instead, similar stability was observed for zwitterion and non zwitterion structures in minor groove association complexes.
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