Nonadiabatic Dynamics of Uracil in Aqueous Solution from QM/MM in Periodic Boundary Conditions Combined with Mixed-Reference Spin-Flip TDDFT.

Abstract

Understanding the excited-state dynamics of nucleobases in aqueous environments is essential for elucidating the mechanisms underlying DNA and RNA photostability. While puckered uracil structures have been theoretically predicted and observed in the gas phase following UV excitation, their behavior in solution remains largely unexplored. Here, we investigate the ultrafast photodynamics of uracil in water using a newly developed nonadiabatic surface-hopping QM/MM approach combined with MRSF-TDDFT, explicitly accounting for solvent effects using periodic boundary conditions. Our simulations characterize the dominant pathways and time scales of internal conversion, showing that twisted conformations previously predicted in the gas phase also emerge in solution. By comparing gas-phase and solution dynamics, we show how water modulates the population of puckered conformers and influences radiationless decay pathways. The simulations further suggest that trajectories reaching the conical intersection region in solution preferentially evolve toward planar or half-boat conformations in the ground state. These findings provide molecular-level insight into nucleobase photodynamics in the condensed phase and demonstrate the potential of the present framework for simulating excited-state dynamics in complex biological environments.