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

The relative free energies of the isomers formed upon N-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the N-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy N-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from N-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 N-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from N-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with Delta 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 N-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 N-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 N-chlorinated cytidine than in other N-chlorinated nucleosides.

Automated summary

The study investigates the free energy of isomers formed upon N-chlorination of DNA nucleobases using the G4(MP2) composite ab initio method. Results demonstrate that chlorine transfer from N-chlorothymine to cytosine, adenine, or guanine occurs via exergonic processes in both gas-phase and aqueous solution. The thermodynamic preference for chlorine transfer to cytidine indicates its potential deleterious effect due to the ease of nitrogen-centered radical formation.