Improved DFT description of intrastrand cross-link formation by inclusion of London dispersion corrections

Journal of Physical Chemistry B

Volumn 115, Issue 50, 2011, Pages 15138-15144

  Dupont, Céline ^a   Patel, Chandan ^a   Dumont, Elise ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY;

COVALENT LINKAGE; DINUCLEOTIDES; DISPERSION CORRECTION; DNA LESIONS; FUNCTIONALS; IN-SILICO SCREENING; INTRAMOLECULAR HYDROGEN BOND; REACTION PROFILE;

DISPERSIONS;

DNA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; QUANTUM THEORY;

DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; QUANTUM THEORY;

EID: 84856490940     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp209074q     Document Type: Article

References (49)

1. Bont, R. D.; van Larebeke, N. Mutagenesis 2004, 19, 169-185.
2. Scharer, O. D. Chem Bio Chem 2005, 6, 27-32.
3. Sponer, J.; Jurecka, P.; Hobza, P. J. Am. Chem. Soc. 2004, 126, 10142-10151.
4. Brown, K. L.; Basu., A. K.; Stone, M. P. Biochemistry 2009, 48, 9722-9733.
5. Wang, W.; Hellinga, H. W.; Beese, L. S. Proc. Natl. Acad. Sci. 2011, 108, 17644-17648.
6. Kanvah, S.; Joseph, J.; Schuster, G. B.; Barnett, R. N.; Ceveland, C. L.; Landman, U. Acc. Chem. Res. 2010, 43, 280-287.
7. Wiseman, H.; Halliwell, B. Biochem. J. 1996, 313, 17-29.
8. Yang, Z.; Collis, L. C.; Basu, A. K.; Zou, Y. Chem. Res. Toxicol. 2006, 18, 1339-1346.
9. Gu, C.; Zhang, Q.; Yang, Z.; Wang, Y.; Zhou, Y.; Wang, Y. Biochemistry 2006, 45, 10739-10746.
10. Their structural elucidation and screening rely on tandem mass spectrometry coupled to high-performance liquid chromatography, the sole technique with a detection threshold as low as 1:109.
11. Gates, K. S. Rev. React. Intermed. Chem. 2007, 8, 333-378.
12. Balasubramanian, B.; Pogozelski, W. K.; Tullius, T. D. Proc. Natl. Acad. Sc. 1998, 343, 9738-9743.
13. Begusova, M.; Spotheim-Maurizot, M.; Sy, D.; Michalik, V.; Charlier, M. J. Biomol. Struct. Dyn. 2001, 19, 141.
14. Xerri, B.;Morell, C.; Grand, A.; Cadet, J.; Cimino, P.; Barone, V. Org. Biomol. Chem. 2006, 4, 3986-3992.
15. Labet, V.;Morell, C.;Grand, A.; Cadet, J.; Cimino, P.; Barone, V. Org. Biomol. Chem. 2008, 6, 3300-3305.
16. Durbeej, B.; Eriksson, L. A. Photochem. Photobiol. 2003, 78, 159-167.
17. Guerra, C. F.; van der Wijst, T.; Poater, J.; Swart, M.; Bickelhaupt, F. M. Theor. Chem. Acc. 2010, 125, 245.
18. Gu, J.; Wang, J.; Leszczynski, J. Chem. Phys. Lett. 2011, 512, 108-112.
19. Morgado, C.; Vincent, M. A.; Hillier, I. H.; Shan, X. Phys. Chem. Chem. Phys. 2007, 9, 448-451.
20. Poater, J.; Swart, M.; Guerra, C. F.; Bickelhaupt, F. M. Chem. Commun. 2011, 47, 7326-7328.
21. Lin, I.-C.; Rothlisberger, U. Phys. Chem. Chem. Phys. 2008, 10, 2730-2734.
22. Burns, L. A.; Vazquez-Mayagoitia, A.; Sumpter, B. G.; Sherrill, D. C. J. Chem. Phys. 2011, 134, 084107.
23. Thanthiriwatte, K. S.; Hohenstein, E. G.; Burns, L. A.; Sherrill, D. C. J. Chem. Theory Comput. 2011, 7, 88-96.
24. Hohenstein, E. G.; Chill, S. T.; Sherrill, D. C. J. Chem. Theory Comput. 2008, 4, 1996-2000.
25. Frisch, M. J.; et al. Gaussian 09, revision B.01; Gaussian Inc.: Wallingford, CT, 2009.
26. Case, D.; et al. AMBER 11; University of California: San Francisco, CA, 2010.
27. Van Voorhis, T.; Scuseria, G. E. J. Chem. Phys. 1998, 109, 400-410.
28. Becke, A. D. J. Chem. Phys. 1996, 104, 1040-1046.
29. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157-167.
30. Grimme, S. J. Chem. Phys. 2006, 124, 034108.
31. Savin, A. In Recent Developments and Applications of Modern Density Functional Theory; Seminario, J. M., Ed.; Elsevier: Amsterdam, 1996; Chapter 9, pp 327-354.
32. Iikura, H.; Tsuneda, T.; Yanai, T.; Hirao, K. J. Chem. Phys. 2001, 115, 3540-3544.
33. Yanai, T.; Tew, D. P.; Handy, N. C. Chem. Phys. Lett. 2004, 393, 51-56.
34. Vydrov, O. A.; Scuseria, G. E. J. Chem. Phys. 2006, 125, 234109.
35. Chai, J. D.; Head-Gordon, M. J. Chem. Phys. 2008, 128, 084106.
36. Song, J. W.; Hirosawa, T.; Tsuneda, T.; Hirao, K. J. Chem. Phys. 2007, 126, 154105.
37. Grimme, S. Wiley Interdisciplinary Rev.: Comput. Mol. Sci. 2011, 1, 211-228.
38. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132, 154104.
39. Bera, P. P.; Schaefer, H. F., III. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6698-6703.
40. Garrec, J.; Patel, C.; Rothlisberger, U.; Dumont, E. submitted, 2011.
41. Loos, P.-F.; Dumont, E.; Laurent, A. D.; Assfeld, X. Chem. Phys. Lett. 2009, 475, 120-123.
42. This intramolecular hydrogen bond tends to be reinforced as a continuum model for solvation is used. It can be proposed that this correction tends to increase the partial atomic charges on the atoms implicated in this stabilizing interaction. In turn, the approaching distance d is further increased.
43. Vokacova, Z.; Budesinsky, M.; Rosenberg, I.; Schneider, B.; Sponer, J.; Sychrovsky, V. J. Phys. Chem. B 2009, 113, 1182-1191.
44. Blumberger, J.; Lamoureux, G.; Klein, M. L. J. Chem. Theor. Comput. 2007, 3, 1837-1850.
45. The deviation from the p-stacked mode constitutes a severe deficience as the offset will not a priori be constant along a series of products and in turn blurs the theoretical prediction in terms of activation energies and endothermicities.
46. Boese, A. D.; Martin, J. M. L. J. Chem. Phys. 2004, 121, 3405-3416.
47. Ceron-Carrasco, J. P.; Z-uniga, J.; Requena, A.; Perpete, E. A.; Michaux, C.; Jacquemin, D. Phys. Chem. Chem. Phys. 2011, 13, 14584-14589.
48. Hong, I. S.; Carter, K. N.; Sato, K.; Greenberg, M. M. J. Am. Chem. Soc. 2007, 129, 4089.
49. Munzel, M.; Szeibert, C.; Glas, A. F.; Globisch, D.; Carell, T. J. Am. Chem. Soc. 2011, 133, 5186-5189.