An Effective Model for Capturing the Role of Excitonic Interactions in the Wave-Packet Dynamics of DNA Nucleobases

Abstract

Investigating exciton dynamics within DNA nucleobases is essential for comprehensively understanding how inherent photostability mechanisms function at the molecular level, particularly in the context of life’s resilience to solar radiation. In this paper, we introduce a mathematical model that effectively simulates the photoexcitation and deactivation dynamics of nucleobases within an ultrafast timeframe, particularly focusing on wave-packet dynamics under conditions of strong nonadiabatic coupling. Employing the hierarchy equation of motion, we simulate two-dimensional electronic spectra (2DES) and calibrate our model by comparing it with experimentally obtained spectra. This study also explores the effects of base stacking on the photo-deactivation dynamics in DNA. Our results demonstrate that, while strong excitonic interactions between nucleobases are present, they have a minimal impact on the deactivation dynamics of the wave packet in the electronic excited states. We further observe that the longevity of electronic excited states increases with additional base stacking and pairing, a phenomenon accurately depicted by our excitonic model. This model enables a detailed examination of the wave packet’s motion on electronic excited states and its rapid transition to the ground state. Additionally, using this model, we studied base stacks in DNA hairpins to effectively capture the primary exciton dynamics at a reasonable computational scale. Overall, this work provides a valuable framework for studying exciton dynamics from single nucleobases to complex structures such as DNA hairpins.