Citation: ZHANG Wen-Ying, MA Jing, YUAN Shuai, SHU Kun-Xian, DOU Yu-Sheng. A Semiclassical Dynamics Simulation on Charge Transfer and Radiationless Deactivation Excited State of π-Stacked Adenine-Thymine System[J]. Acta Physico-Chimica Sinica, ;2012, 28(07): 1676-1682. doi: 10.3866/PKU.WHXB201205041 shu

A Semiclassical Dynamics Simulation on Charge Transfer and Radiationless Deactivation Excited State of π-Stacked Adenine-Thymine System

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

Received Date: 24 February 2012
Available Online: 4 May 2012
Fund Project: 国家自然科学基金(21073242) (21073242) 重庆市自然科学基金(cstc2011jjA00009) (cstc2011jjA00009)重庆市教委科学技术项目(KJ120516)资助 (KJ120516)

A semiclassical electronic radiation ion dynamics (SERID) simulation was used to study the photophysical deactivation of π-stacked adenine and thymine. A laser was only applied to the thymine molecule during the simulations. The results showed that an (A⁺T^-)^* type exciplex was formed between excited thymine and unexcited adenine as a consequence of charge transfer. When the intermolecular distance was less than 0.300 nm, the stacked system was recovered to electronic neutrality by charge recombination because of the orbital delocalization effect. When the torsion angle of the C4'－C5' bond of the adenine molecule reached its maximum, the exciplex decayed to its ground state via an avoided crossing. The deactivation channel of the exciplex was found to be dependent on the intermolecular distance and deformation of the adenine molecule. It was difficult for the adenine molecule to under strong twist required for deactivation because of the steric hindrance encountered by the C4' and C5' atoms. Consequently, the lifetime of the A-T exciplex was clearly longer than that of the T-T exciplex.
- DNA base,
- Stacked effect,
- Exciplex,
- Charge transfer,
- Radiationless deactivation
1. [1]
  
  (1) Beukers, R.; Eker, A. P. M.; Lohman, P. H. M. DNA Repair2008, 7, 530. doi: 10.1016/j.dnarep.2007.11.010
2. [2]
  (2) Cadet, J.; Sage, E.; Douki, T. Mutat. Res. 2005, 571, 3. doi: 10.1016/j.mrfmmm.2004.09.012
3. [3]
  (3) Melnikova, V. O.; Ananthaswamy, H. N. Mutat. Res. 2005, 571,91. doi: 10.1016/j.mrfmmm.2004.11.015
4. [4]
  (4) Mouret, S.; Baudouin, C.; Charveron, M.; Favier, A.; Cadet, J.;Douki, T. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 13765. doi: 10.1073/pnas.0604213103
5. [5]
  (5) Pecourt, J. M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001,123, 10370. doi: 10.1021/ja0161453
6. [6]
  (6) Sobolewski, A. L.; Domcke,W.; Hattig, C. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 17903. doi: 10.1073/pnas.0504087102
7. [7]
  (7) Crespo-Hernández, C. E.; Kohler, B. J. Phys. Chem. B 2004,108, 11182. doi: 10.1021/jp0496046
8. [8]
  (8) Crespo-Hernández, C. E.; Cohen, B.; Kohler, B. Nature 2005,436, 1141. doi: 10.1038/nature03933
9. [9]
  (9) Kwok,W. M.; Ma, C. S.; Phillips, D. L. J. Am. Chem. Soc.2006, 128, 11894. doi: 10.1021/ja0622002
10. [10]
  (10) Takaya, T.; Su, C.; de La Harpe, K.; Crespo-Hernández, C. E.;Kohler, B. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 10285. doi: 10.1073/pnas.0802079105
11. [11]
  (11) Ullrich, S.; Schultz, T.; Zgierski, M. Z.; Stolow, A. Phys. Chem. Chem. Phys. 2004, 6, 2796.
12. [12]
  (12) Ullrich, S.; Schultz, T.; Zgierski, M. Z.; Stolow, A. J. Am. Chem. Soc. 2004, 126, 2262. doi: 10.1021/ja030532q
13. [13]
  (13) Eisinger, J.; Guéron, M.; Schulman, R. G.; Yamane, T. Proc. Natl. Acad. Sci. U. S. A. 1966, 55, 1015. doi: 10.1073/pnas.55.5.1015
14. [14]
  (14) Birks, J. B. Nature 1967, 214, 1187. doi: 10.1038/2141187a0
15. [15]
  (15) Middleton, C. T.; de La Harpe, K.; Su, C.; Law, Y. K.; Crespo-Hernández, C. E.; Kohler, B. Annu. Rev. Phys. Chem. 2009, 60,217. doi: 10.1146/annurev.physchem.59.032607.093719
16. [16]
  (16) Santoro, F.; Barone, V.; Improta, R. J. Am. Chem. Soc. 2009,131, 15232. doi: 10.1021/ja904777h
17. [17]
  (17) Markovitsi, D.; Gustavsson, T.; Talbot, F. Photochem. Photobiol. Sci. 2007, 6, 717. doi: 10.1039/b705674e
18. [18]
  (18) Conti, I.; Altoe, P.; Stenta, M.; Garavelli, M.; Orlandi, G. Phys. Chem. Chem. Phys. 2010, 12, 5016.
19. [19]
  (19) Kohler, B. J. Phys. Chem. Lett. 2010, 1, 2047. doi: 10.1021/jz100491x
20. [20]
  (20) Shukla, M. K.; Leszczynski, J. J. Biomol. Struct. Dyn. 2007, 25,93.
21. [21]
  (21) Kwok,W. M.; Ma, C.; Phillips, D. L. J. Phys. Chem. B 2009,113, 11527. doi: 10.1021/jp906265c
22. [22]
  (22) Onidas, D.; Gustavsson, T.; Lazzarotto, E.; Markovitsi, D. Phys. Chem. Chem. Phys. 2007, 9, 5143.
23. [23]
  (23) Schwalb, N. K.; Temps, F. Science 2008, 322, 243. doi: 10.1126/science.1161651
24. [24]
  (24) Davies, R. J. H.; Malone, J. F.; Gan, Y.; Cardin, C. J.; Lee, M. P.H.; Neidle, S. Nucleic Acids Res. 2007, 35, 1048. doi: 10.1093/nar/gkl1101
25. [25]
  (25) Dou, Y.; Torralva, B. R.; Allen, R. E. Chem. Phys. Lett. 2004,392, 352. doi: 10.1016/j.cplett.2004.05.087
26. [26]
  (26) Dou, Y.; Torralva, B. R.; Allen, R. E. J. Mod. Optics. 2003, 50,2615.
27. [27]
  (27) Boykin, T. B.; Bowen, R. C.; Klimeck, G. Phys. Rev. B 2001,63, 245314. doi: 10.1103/PhysRevB.63.245314
28. [28]
  (28) Haugk, M.; Elsner, J.; Frauenheim, T.; Seifert, G.; Sternberg,M. Phys. Status Solidi B 2000, 217, 473. doi: 10.1002/(SICI)1521-3951(200001)217:1<473::AID-PSSB473>3.0.CO;2-N
29. [29]
  (29) Frauenheim, T.; Seifert, G.; Elstner, M.; Niehaus, T. A.; Köhler,C.; Amkreutz, M.; Sternberg, M.; Hajnal, Z.; Carlo, D. A.;Suhai, S. J. Phys: Condens. Matter 2002, 14, 3015. doi: 10.1088/0953-8984/14/11/313
30. [30]
  (30) Wanko, M.; Garavelli, M.; Bernardi, F.; Niehaus, T. A.;Frauenheim, T.; Elstner, M. J. Chem. Phys. 2004, 120, 1674.doi: 10.1063/1.1635798
31. [31]
  (31) Zheng, G.; Lundberg, M.; Jakowski, J.; Vreven, T.; Frisch, M.J.; Morokuma, K. Int. J. Quantum Chem. 2009, 109, 1841. doi: 10.1002/qua.22002
32. [32]
  (32) Yuan, S.; Dou, Y. S.;Wu,W. F.; Hu, Y.; Zhao, J. S. J. Phys. Chem. A 2008, 112, 13326.
33. [33]
  (33) Yuan, S.;Wu,W. F.; Dou, Y. S.; Zhao, J. S. Chin. Chem. Lett.2008, 19, 1379. doi: 10.1016/j.cclet.2008.07.007
34. [34]
  (34) Dou, Y. S.; Hu, Y.; Yuan, S.;Wu,W. F.; Tang, H. Mol. Phys.2009, 107, 181. doi: 10.1080/00268970902769497
35. [35]
  (35) Yuan, S.;Wang, D.; Bai, M. Z.;Wei, Z. L.; Meng, P.; Dou, Y. S.Journal of Chongqing Univerisity and Telecommunications (Natural Science Edition) 2009, 21, 821. [袁帅, 王丹,白明泽, 魏照林, 蒙平, 豆育升. 重庆邮电大学学报(自然科学版), 2009, 21, 821.]
36. [36]
  (36) Yuan, S.;Wu,W. F.;Wen, Z. L.; Shu, K. X.; Tang, H.; Dou, Y.S.; Lo, G. Mol. Phys. 2010, 108, 3431. doi: 10.1080/00268976.2010.520755
37. [37]
  (37) Lei, Y. B.; Yuan, S.; Dou, Y. S.;Wang, Y. B.;Wen, Z. Y. J. Phys. Chem. A 2008, 112, 8497. doi: 10.1021/jp802483b
38. [38]
  (38) Shu, K. X.; Ma, J.; Yuan, S.; Dou, Y. S. Journal of Chongqing Univerisity and Telecommunications (Natural Science Edition)2011, 23, 780. [舒坤贤, 马静, 袁帅, 豆育升. 重庆邮电大学学报(自然科学版), 2011, 23, 780.]
39. [39]
  (39) Zhang,W. Y.; Yuan, S.; Li, A. Y.; Dou, Y. S.; Zhao, J. S.; Fang,W. H. J. Phys. Chem. C 2010, 114, 5594. doi: 10.1021/jp907290f
40. [40]
  (40) Dou, Y. S.; Xiong, S. S.;Wu,W. F.; Yuan, S.; Tang, H.J. Photochem. Photobiol. B 2010, 101, 31. doi: 10.1016/j.jphotobiol.2010.06.008
41. [41]
  (41) Zhang,W. Y.; Yuan, S.;Wang, Z. J.; Qi, Z. M.; Zhao, J. S.; Dou,Y. S.; Lo, G. Chem. Phys. Lett. 2011, 506, 303. doi: 10.1016/j.cplett.2011.03.024
42. [42]
  (42) Yuan, S.; Zhang,W. Y.; Li, A. Y.; Zhu, Y. M.; Dou, Y. S. Acta Phys. -Chim. Sin. 2011, 27, 825. [袁帅, 张文英, 李安阳,朱义敏, 豆育升. 物理化学学报, 2011, 27, 825.] doi: 10.3866/pku.WHXB20110337
43. [43]
  (43) Dou, Y. S.; Li,W.; Yuan, S.; Zhang,W. Y.; Li, A. Y.; Shu, K. X.;Tang, H. Acta Phys. -Chim. Sin. 2011, 27, 2559. [豆育升,李伟, 袁帅, 张文英, 李安阳, 舒坤贤, 唐红. 物理化学学报, 2011, 27, 2559.] doi: 10.3866/pku.WHXB20111115
44. [44]
  (44) Yuan, S.; Zhang,W. Y.; Liu, L. H.; Dou, Y. S.; Fang,W. H.; Lo,G. V. J. Phys. Chem. A 2011, 115, 13291. doi: 10.1021/jp207550a
45. [45]
  (45) Rehm, D.;Weller, A. Isr. J. Chem. 1970, 8, 259.
46. [46]
  (46) Liu, Q.; Liu, Z. L. Chin. J. Org. Chem. 2009, 29, 380. [刘强,刘中立. 有机化学, 2009, 29, 380.]
47. [47]
  (47) Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem.1996, 100, 5541. doi: 10.1021/jp951507c
48. [48]
  (48) Devoe, H.; Tinoco, I. J. Mol. Biol. 1962, 4, 500. doi: 10.1016/S0022-2836(62)80105-3
49. [49]
  (49) Zhang, L. B.; Bu, Y. X. J. Phys. Chem. B 2008, 112, 10723. doi: 10.1021/jp802556a
50. [50]
  (50) Zhang, L. B.; Li, H. F.; Li, J. L.; Chen, X. H.; Bu, Y. X.J. Comput. Chem. 2009, 31, 825.
51. [51]
  (51) Zhang,W. Y. Semiclassical Simulation for Deaactivation ofStacked DNA Bases. Ph.D. Dissertation, Northwest University,Xi'an, 2011. [张文英. DNA堆积碱基激发态失活的半经典动力学模拟[D]. 西安: 西北大学, 2011.]
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