Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics.
Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.
Markwick
Phineus R L
PR
Institut de Biologie Structurale J.-P. Ebel, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France. phineus.markwick@ibs.fr
Doltsinis
Nikos L
NL
Schlitter
Jürgen
J
D001482:Base Composition; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000528:radiation effects*; D004249:DNA Damage; D004307:Dose-Response Relationship, Radiation; D004735:Energy Transfer / Q000528:radiation effects; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000528:radiation effects; D017785:Photons; D011829:Radiation Dosage
D004247:DNA