PNNL

Abstract

Calculations of the direct ionization potentials (DIP) of DNA nucleobases in the fully solvated DNA helix are reported. The results show an unexpected large shift of roughly 3.2-3.3 eV compared to the corresponding gas-phase IP values. The DIP shift is nearly the same for all the four DNA bases and appears to vary slowly with the stacking and H-bonding interactions of the nucleobases. We demonstrate that the large shift in the DIP of bases is due to the electric potential around the DNA resulting from the long range solvent structure created by the negative phosphate groups and positive counterions of the DNA helical structure. Thermal fluctuations in the fluid can result in DIP changes of roughly 1ev on a picosecond time scale. The model used in this work is based on a QM/MM approach in which the base (or clusters of bases) are chosen as the QM system and calculated using a high-level quantum chemistry method. The remaining DNA fragment and the species in solution are included in an exact molecular mechanics (MM) model. The expected high accuracy of the QM/MM model is defended in terms of the essentially Columbic nature of the interactions of the solvent (the MM region) with isolated base in the quantum region. For the test anion, Cl-, the QM/MM approach yields the 3.4 eV (gas-phase) to 9.3 eV (aqueous solution) shift of the ionization energy in agreement with experimental values (3.6 and 9.6 eV). The localization of the electronic excitation inside the QM region is supported by current experimental and theoretical evidence indicating that the HOMO of the nucleotide is localized on the base rather than the sugar or the phosphate backbone. Our calculations performed in the native DNA environment support this localization. The QM/MM model presented in this work provides an important simplification to the difficult problem of incorporating a detailed structural model of the physiological conditions into investigations of the electronic processes in DNA.