Acta Phys. -Chim. Sin. ›› 2011, Vol. 27 ›› Issue (04): 825-830.doi: 10.3866/PKU.WHXB20110337


Dynamics Simulation of a New Deactivation Pathway for Stacked Adenines

YUAN Shuai, ZHANG Wen-Ying, LI An-Yang, ZHU Yi-Min, DOU Yu-Sheng   

  1. College of Bio-information, Chongqing University of Posts and Telecommunications, Chongqing 400065, P. R. China
  • Received:2010-12-08 Revised:2011-01-10 Published:2011-03-29
  • Contact: DOU Yu-Sheng
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (20773168, 21073242) and Research Fund of Chongqing University of Posts and Telecommunications, China (A2009-63).


A semiclassical dynamics simulation study was undertaken to investigate the deactivation of the lowest excited state of π-stacked adenines, as induced by a laser pulse. Only one of the adenines was subjected to a laser pulse in this simulation. The simulation results show that the interaction between the excited adenines (A) and their unexcited neighbors (A′) increases significantly, followed by a shortening of the intermolecular distance. The interbases interaction leads to a new deactivated pathway in which atom C2 in molecule A and atom C2′ in molecule A′ are link to each other and form a “bonded excimer” intermediate. The lifetime of the “bonded excimer” intermediate is about 390 fs. The deformation of the pyrimidine ring at the C2 atom and the displacement of the H2′ atom away from the pyrimidine ring play a significant role in the deactivation process of the “bonded excimer” intermediate. After deactivation, the C2-C2′ dissociates and the released bond energy converts to molecular kinetic energy. Both adenine molecules return to the planar geometries of their ground states.

Key words: Adenine, Semiclassical dynamic simulation, Bonded excimer, Deactivation