Citation: HUA Shu-Gui, JIN Hao, OUYANG Yong-Zhong. Contribution of Non-Covalent Interactions to the Gas-Phase Stability of the Double-Helix of B-DNA: A Density Functional Theory Study with GEBF Approach[J]. Acta Physico-Chimica Sinica, ;2015, 31(7): 1309-1314. doi: 10.3866/PKU.WHXB201505111 shu

Contribution of Non-Covalent Interactions to the Gas-Phase Stability of the Double-Helix of B-DNA: A Density Functional Theory Study with GEBF Approach

1.
1 College of Life Science and Chemistry, Jiangsu Key Laboratory of Biological Functional Molecules, Jiangsu Second Normal University, Nanjing 210013, P. R. China;
2 Software College, Nanchang Key Laboratory for Gas Phase Molecular Science, East China Institute of Technology, Nanchang 330013, P. R. China

Received Date: 16 March 2015
Available Online: 11 May 2015
Fund Project: 江苏省自然科学基金(BK20130748) (BK20130748) 江苏省高校自然科学研究项目(13KJB150012) (13KJB150012) 江西省自然科学基金(20142BAB213010) (20142BAB213010)国家自然科学基金(21405013)资助项目 (21405013)

We employed the generalized energy-based fragmentation (GEBF) approach to investigate the gas-phase structures of B-DNA double-helices up to 10 base pairs at several theoretical levels. By comparing the results obtained using the M06-2X functional and other methods (including the B3LYP, B3LYP-vdW, and TPSS functionals), we found that the absence of stacking interactions could lead to the enlargement of the vertical distance between adjacent bases. The magnitude of this enlargement of the vertical distance quickly decreases as the length of the double-helix increases. The gas-phase stabilization of the double-helical structure of B-DNA is a cooperative effect, in which hydrogen bonding plays a more important role than stacking interaction does up to 10 base pairs.
- Base pair,
- Hydrogen bond,
- Generalized energy-based fragmentation approach,
- π-π stacking interaction
1. [1]
  
  (1) Šponer, J.; Riley, K. E.; Hobza, P. Phys. Chem. Chem. Phys. 2008, 10, 2595. doi: 10.1039/b719370j
2. [2]
  (2) Gil, A.; Branchadell, V.; Bertran, J.; Oliva, A. J. Phys. Chem. B 2009, 113, 4907. doi: 10.1021/jp809737c
3. [3]
  (3) Banáš, P.; Mládek, A.; Otyepka, M.; Zgarbová, M.; Jure?ka, P.; Svozil, D.; Lankaš, F.; Šponer, J. J. Chem. Theory Comput. 2012, 8, 2448. doi: 10.1021/ct3001238
4. [4]
  (4) Sedlák, R.; Jure?ka, P.; Hobza, P. J. Chem. Phys. 2007, 127, 075104. doi: 10.1063/1.2759207
5. [5]
  (5) Pitoňák, M.; Neogrády, P.; Hobza, P. Phys. Chem. Chem. Phys. 2010, 12, 1369. doi: 10.1039/B919354E
6. [6]
  (6) Riley, K. E.; Pionak, M.; Jurecka, P.; Hobza, P. Chem. Rev. 2010, 110, 5023. doi: 10.1021/cr1000173
7. [7]
  (7) Zhang, Y.; Ma, N.; Wang, W. J. Theor. Comput. Chem. 2012, 11, 1165. doi: 10.1142/S0219633612500770
8. [8]
  (8) Jones, G. J.; Robertazzi, A.; Platts, J. A. J. Phys. Chem. B 2013, 117, 3315. doi: 10.1021/jp400345s
9. [9]
  (9) Wilson, K. A.; Kellie, J. L.; Wetmore, S. D. Nucleic Acids Res. 2014, 42, 6726. doi: 10.1093/nar/gku269
10. [10]
  (10) Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. J. Chem. Phys. 2001, 114, 5149. doi: 10.1063/1.1329889
11. [11]
  (11) ?erný, J.; Kabelá?, M.; Hobza, P. J. Am. Chem. Soc. 2008, 130, 16055. doi: 10.1021/ja805428q
12. [12]
  (12) Cooper, V. R.; Thonhauser, T.; Langreth, D. C. J. Chem. Phys. 2008, 128, 204102. doi: 10.1063/1.2924133
13. [13]
  (13) Cooper, V. R.; Thonhauser, T.; Puzder, A.; Schröder, E.; Lundqvist, B. I.; Langreth, D. C. J. Am. Chem. Soc. 2008, 130, 1305.
14. [14]
  (14) Šponer, J.; Mládek, A.; Špa?ková, N.; Cang, X.; Cheatham, T.; Grimme, S. J. Am. Chem. Soc. 2013, 135, 9785. doi: 10.1021/ja402525c
15. [15]
  (15) Barone, G.; Guerra, C.; Bickelhaupt, F. ChemistryOpen 2013, 2, 186. doi: 10.1002/open.v2.5/6
16. [16]
  (16) Grunenberg, J.; Barone, G.; Spinello, A. J. Chem. Theory Comput. 2014, 10, 2901. doi: 10.1021/ct500329f
17. [17]
  (17) Hesselmann, A.; Jansen, G.; Schütz, M. J. Am. Chem. Soc. 2006, 128, 11730. doi: 10.1021/ja0633363
18. [18]
  (18) Fiethen, A.; Jansen, G.; Hesselmann, A.; Schütz, M. J. Am. Chem. Soc. 2008, 130, 1802. doi: 10.1021/ja076781m
19. [19]
  (19) Koby?ecka, M.; Leszczynski, J.; Rak, J. J. Chem. Phys. 2009, 131, 085103. doi: 10.1063/1.3204939
20. [20]
  (20) Churchill, C. D. M.; Wetmore, S. D. J. Phys. Chem. B 2009, 113, 16046. doi: 10.1021/jp907887y
21. [21]
  (21) Svozil, D.; Hobza, P.; Šponer, J. J. Phys. Chem. B 2010, 114, 1191.
22. [22]
  (22) Sharma, P.; Lait, L. A.; Wetmore, S. D. Phys. Chem. Chem. Phys. 2013, 15, 2435. doi: 10.1039/c2cp43910g
23. [23]
  (23) Sharma, P.; Lait, L. A.; Wetmore, S. D. Phys. Chem. Chem. Phys. 2013, 15, 15538. doi: 10.1039/c3cp52656a
24. [24]
  (24) Šponer, J.; Florián, J.; Ng, H. L.; Šponer, J. E.; Špacková, N. Nucleic Acids Research 2000, 28, 4893. doi: 10.1093/nar/28.24.4893
25. [25]
  (25) Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D. Nucleic Acids Research 2006, 34, 564. doi: 10.1093/nar/gkj454
26. [26]
  (26) Vijayaraghavan, R.; Iz rodin, A.; Ganesh, V.; Surianarayanan, M.; MacFarlane, D. R. Angew. Chem. Int. Edit. 2010, 49, 1631. doi: 10.1002/anie.200906610
27. [27]
  (27) Li, W.; Li, S.; Jiang, Y. J. Phys. Chem. A 2007, 111, 2193. doi: 10.1021/jp067721q
28. [28]
  (28) Deev, V.; Collins, M. A. J. Chem. Phys. 2005, 122, 154102. doi: 10.1063/1.1879792
29. [29]
  (29) Collins, M. A.; Deev, V. J. Chem. Phys. 2006, 125, 104104. doi: 10.1063/1.2347710
30. [30]
  (30) Addicoat, M. A.; Collins, M. A. J. Chem. Phys. 2009, 131, 104103. doi: 10.1063/1.3222639
31. [31]
  (31) Ganesh, V.; Dongare, R. K.; Balanarayan, P.; Gadre, S. R. J. Chem. Phys. 2006, 125, 104109. doi: 10.1063/1.2339019
32. [32]
  (32) Deshmukh, M. M.; Gadre, S. R. J. Phys. Chem. A 2009, 113, 7927.
33. [33]
  (33) Ahalkar, A. P.; Katouda, M.; Gadre, S. R.; Nagase, S. J. Comput. Chem. 2010, 31, 2405.
34. [34]
  (34) Bettens, R. P. A.; Lee, A. M. J. Phys. Chem. A 2006, 110, 8777.
35. [35]
  (35) Hua, W.; Fang, T.; Li, W.; Yu, J.; Li, S. J. Phys. Chem. A 2008, 112, 10864. doi: 10.1021/jp8026385
36. [36]
  (36) Dong, H.; Hua, S.; Li, S. J. Phys. Chem. A 2009, 113, 1335. doi: 10.1021/jp8071525
37. [37]
  (37) Hua, S.; Hua, W.; Li, S. J. Phys. Chem. A 2010, 114, 8126.
38. [38]
  (38) Li, W. J. Chem. Phys. 2013, 138, 9.
39. [39]
  (39) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 09, Revision A.01; Gaussian Inc.:Wallingford, CT, 2009.
40. [40]
  (40) Li, S.; Li, W.; Fang, T.; Ma, J.; Hua, W.; Hua, S.; Jiang, Y. Low- Scaling Quantum Chemistry (LSQC), Version 2.2; Nanjing University: Nanjing, 2012.
41. [41]
  (41) http://www.rcsb.org/.
42. [42]
  (42) Wu, Q.; Yang, W. T. J. Chem. Phys. 2002, 116, 515. doi: 10.1063/1.1424928
43. [43]
  (43) Rapacioli, M.; Spiegelman, F.; Talbi, D.; Mineva, T.; ursot, A.; Heine, T.; Seifert, G. J. Chem. Phys. 2009, 130, 244304. doi: 10.1063/1.3152882
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