Citation: YUAN Shuai, ZHANG Wen-Ying, LI An-Yang, ZHU Yi-Min, DOU Yu-Sheng. Dynamics Simulation of a New Deactivation Pathway for Stacked Adenines[J]. Acta Physico-Chimica Sinica, ;2011, 27(04): 825-830. doi: 10.3866/PKU.WHXB20110337 shu

Dynamics Simulation of a New Deactivation Pathway for Stacked Adenines

1.
College of Bio-information, Chongqing University of Posts and Telecommunications, Chongqing 400065, P. R. China

Received Date: 8 December 2010
Available Online: 18 February 2011
Fund Project: 国家自然科学基金(20773168, 21073242) (20773168, 21073242)重庆邮电大学博士启动基金(A2009-63)资助项目 (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.
- Adenine,
- Semiclassical dynamic simulation,
- Bonded excimer,
- Deactivation
1. [1]
  
  (1) Taylor, J. S. Accounts Chem. Res. 1994, 27, 76.
2. [2]
  (2) Vink, A. A.; Roza, L. J. Photochem. Photobiol. B 2001, 65, 101.
3. [3]
  (3) Beukers, R.; Eker, A.; Lohman, P. DNA Repair 2008, 7, 530.
4. [4]
  (4) Roca-Sanjuán, D.; Olaso- nzález, G.; nzález-Ramírez, I.; Serrano-Andrés, L.; Merchán, M. J. Am. Chem. Soc. 2008, 130, 10768.
5. [5]
  (5) Crespo-Hernández, C.; Cohen, B.; Hare, P.; Kohler, B. Chem. Rev. 2004, 104, 1977.
6. [6]
  (6) Shukla, M.; Leszczynski, J. J. Biomol. Struct. Dyn. 2007, 25, 93.
7. [7]
  (7) Saigusa, H. J. Photochem.Photobiol. C 2006, 7, 197.
8. [8]
  (8) de Vries, M.; Hobza, P. Annu. Rev. Phys. Chem. 2007, 58, 585.
9. [9]
  (9) Liang, X. J.; Cui, L.; Wu, D. Y.; Tian, Z. Q. Acta Phys. -Chim. Sin. 2009, 25, 1605.
10. [10]
  [梁晓静, 崔丽, 吴德印, 田中群. 物理化学学报, 2009, 25, 1605.]
11. [11]
  (10) Weng, K. F.; Wang, H. G.; Zhu, X. M.; Zheng, X. M. Acta Phys. -Chim. Sin. 2009, 25, 1799.
12. [12]
  [翁克凤, 王惠钢, 祝新明, 郑旭明. 物理化学学报, 2009, 25, 1799.]
13. [13]
  (11) Daniels, M.; Hauswirth, W. Science 1971, 171, 675.
14. [14]
  (12) Vigny, P. Acad. Sci. Ser. D 1971, 272, 3206.
15. [15]
  (13) Pecourt, J. M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2000, 122, 9348.
16. [16]
  (14) Ismail, N.; Blancafort, L.; Olivucci, M.; Kohler, B.; Robb, M. J. Am. Chem. Soc. 2002, 124, 6818.
17. [17]
  (15) Zgierski, M. Z.; Patchkovskii, S.; Fujiwara, T.; Lim, E. C. Chem. Phys. Lett. 2007, 440, 145.
18. [18]
  (16) Serrano-Andrés, L.; Merchán, M.; Borin, A. C. Chem. Eur. J. 2006, 12, 6559.
19. [19]
  (17) Lei, Y. B.; Yuan, S.; Dou, Y. S.; Wang, Y. B.; Wen, Z. Y. J. Phys. Chem. A, 2008, 112, 8497.
20. [20]
  (18) Crespo-Hernández, C.; Kohler, B. Nature 2005, 436, 1141.
21. [21]
  (19) Middleton, T.; de La Harpe, K.; Charlene, S.; Law, Y. K.; Crespo-Hernández, C.; Kohler, B. Annu. Rev. Phys. Chem. 2009, 60, 217.
22. [22]
  (20) Wang, Y. S.; Haze, O.; Dinnocenzo, J.; Farid, S.; Farid, R.; uld, I. J. Org. Chem. 2007, 72, 6970.
23. [23]
  (21) Ben-Nun, M.; Martínez, T. J. Adv. Chem. Phys. 2002, 124, 439.
24. [24]
  (22) Bernardi, F.; Olivucci, M.; Robb, M. A. J. Am. Chem. Soc. 1992, 114, 1606.
25. [25]
  (23) Bearpark, M. J.; Bernardi, F.; Olivucci, M.; Robb, M. A. Chem. Phys. Lett. 1994, 217, 513.
26. [26]
  (24) Dou, Y. S.; Torralva, B.; Allen, R. J. Mod. Optics. 2003, 50, 2615.
27. [27]
  (25) Dou, Y. S.; Torralva, B.; Allen, R. Chem. Phys. Lett. 1998, 378, 323.
28. [28]
  (26) Graf, M.; Vogl, P. Phys. Rev. B 1995, 51, 49.
29. [29]
  (27) Dou, Y. S.; Lei, Y. B.; Wen, Z. Y.;Wang, Y. B.; Lo, G.; Allen, R. Appl. Surf. Sci. 2007, 253, 6400.
30. [30]
  (28) Dou, Y. S.; Lei, Y. B.; Li, A. Y.; Wen, Z. Y.; Torralva, B.; Lo, G.; Allen, R. J. Phys. Chem. A 2007, 111, 1133.
31. [31]
  (29) Yuan, S.; Dou, Y. S.; Wu, W. F.; Hu, Y.; Zhao, J. S. J. Phys. Chem. A 2008, 112, 13326.
32. [32]
  (30) Yuan, S.; Wu, W. F.; Dou, Y. S.; Zhao, J. S. Chin. Chem. Lett. 2008, 19, 1379.
33. [33]
  (31) Dou, Y. S.; Hu, Y.; Yuan, S.; Wu, W. F.; Tang, H. Mol. Phys. 2009, 107, 181.
34. [34]
  (32) Yuan, S.; Wu, W. F.; Wen, Z. Y.; Shu, K. X.; Tang, H.; Dou, Y. S.; Lo, G. Mol. Phys. 2010, 108, 3431.
35. [35]
  (33) Dou, Y. S.; Yuan, S.; Lo, G. V. Appl. Surf. Sci. 2007, 253, 6404.
36. [36]
  (34) Li, A. Y.; Yuan, S.; Dou, Y. S.; Wang, Y. B.; Wen, Z. Y. Chem. Phys. Lett. 2009, 478, 28.
37. [37]
  (35) Zhang, W. Y.; Yuan, S.; Li, A. Y.; Dou, Y. S.; Zhao, J. S.; Fang, W. H. J. Phys. Chem. C 2010, 114, 5594.
38. [38]
  (36) Dou, Y. S.; Xiong, S. S.; Wu, W. F.; Yuan, S.; Tang, H. J. Photochem. Photobiol. B 2010, 101, 31.
39. [39]
  (37) Perun, S.; Sobolewski, A. L.; Domcke, W. J. Am. Chem. Soc. 2005, 127, 6257.
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沈阳化工大学材料科学与工程学院沈阳 110142