A high-level quantum chemical study of the thermodynamics associated with chlorine transfer between N-chlorinated nucleobases

Abstract

<p>The relative free energies of the isomers formed upon <i>N</i>-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite <i>ab initio</i> method (the free energies of the <i>N</i>-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy <i>N</i>-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from <i>N</i>-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from <i>N</i>-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from <i>N</i>-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with ∆G^o values of −50.3 (cytosine), −28.0 (guanine), and −6.7 (adenine) kJ mol^–1. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from <i>N</i>-chlorothymine to the three other nucleobases: −58.4 (cytosine), −26.4 (adenine), and −18.7 (guanine) kJ mol^–1. Therefore, our calculations, whether in the gas phase or in aqueous solution, clearly indicate that chlorine transfer from any of the <i>N</i>-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in <i>N</i>-chlorinated cytidine than in other <i>N</i>-chlorinated nucleosides. </p>