Electronic structure of xDNA

Journal of Physical Chemistry B

Volumn 111, Issue 30, 2007, Pages 9057-9061

  Fuentes Cabrera, Miguel ^a   Xiongce, Zhao ^a   Kent, P R C ^a   Sumpter, Bobby G ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; ELECTRONIC PROPERTIES; ELECTRONIC STRUCTURE; NUCLEOTIDES; WAVE FUNCTIONS;

ARTIFICIAL DUPLEX; BENZO-HOMOLOGATED BASES;

DNA;

EID: 34548272095     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0729056     Document Type: Article

References (47)

1. Endres, R. G.; Cox, D. L.; Singh, R. R. P. Rev. Mod. Phys. 2004, 76, 195-214.
2. (a) Tanaka, K.; Clever, G. H.; Takezawa, Y.; Yamada, Y.; Kaul, C.; Shionoya, M.; Carell, T. Nat. Nanotechnol 2006, 1, 190-194.
3. (b) Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M. Science 2003, 299, 1212-1213.
4. (c) Clever, G. H.; Carell, T. Angew. Chem., Int. Ed. 2007, 46, 250-253.
5. (d) Zhang, H. Y.; Calzolari, A.; Di Felice, R. J. Phys. Chem. B 2005, 109, 15345-15348.
6. (e) Rakitin, A.; Aich, P.; Papadopoulus, C.; Kobzar, Yu.; Vedeneev, A. S.; Lee, J. S.; Xu, J. M. Phys. Rev. Lett. 2001, 86, 3670-3673.
7. (f) Alexandre, S. S.; Soler, J. M.; Seijo, L.; Zamora, F. Phys. Rev. B 2006, 73, 205112-1, 205112-5.
8. Benner, S. A.; Sismour, A. M. Nat. Rev. 2005, 6, 533-543.
9. (a) Liu, H.; Gao, J.; Lynch, S. R.; Saito, Y. D.; Maynard, L.; Kool E. T. Science 2003, 302 868-871.
10. (b) Liu, H.; Gao, J.; Lynch, S. R.; Kool, E. T. J. Am. Chem. Soc. 2004, 126, 6900-6905.
11. (c) Liu, H.; Gao, J.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 1396-1402.
12. (d) Gao, J.; Liu, H.; Kool, E. T. Angew. Chem., Int. Ed. 2005, 44, 3118-3122.
13. (e) Liu, H.; Gao, J.; Kool, E. T. J. Org. Chem. 2005, 70, 639-647.
14. (f) Gao, J.; Liu, H.; Kool, E. T. J. Am. Chem. Soc. 2004, 126, 11826-11831.
15. (a) Lu, H.; He, K.; Kool, E. T. Angew. Chem., Int. Ed. 2004, 43, 5834-5836.
16. (b) Lee, A. H. F.; Kool, E. T. J. Org. Chem. 2005, 70, 132-140.
17. (c) Lee, A. H. F.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 3332-3338.
18. Lee, A. H. F.; Kool, E. T. J. Am. Chem. Soc. 2006, 128, 9219-9230.
19. Kim, T. W.; Delaney, J. C.; Essigmann, J. M.; Kool, E. T. Proc. Natl. Acad. Sci. 2005, 102, 15803-15808.
20. Rothemund, P. W. K. Nature 2006, 440, 297-302.
21. Huertas, O.; Blas, J. R.; Soteras, I.; Orozco, M.; Luque, F. J. J. Phys. Chem. A 2006, 110, 510-518.
22. McConnell, T. L.; Wetmore, S. D. J. Phys. Chem. B 2007, 111, 2999-3009.
23. Di Felice, R.; Calzolari, A.; Garbesi, A.; Alexandre, S. S.; Soler, J. M. J. Phys. Chem. B 2005, 109, 22301-22307.
24. (a) Fuentes-Cabrera, M.; Sumpter, B. G.; Wells, J. G J. Phys. Chem. B 2005, 109, 21135-21139.
25. (b) Huertas, O.; Poater, J.; Fuentes-Cabrera, M; Orozco, M.; Sola, M.; Luque, F. J. J. Phys. Chem. A 2006, 110, 12249-12258.
26. Fuentes-Cabrera, M.; Sumpter, B. G.; Lipkowski, P.; Wells, J. C. J. Phys. Chem. B 2006, 110, 6379-6384.
27. Case, D. A.; et al. AMBER 8.0; University of California: San Francisco, CA, 2004.
28. Jorgensen, W. L. J. Am. Chem. Soc. 1981, 103, 335.
29. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189.
30. Brünger, A. T. X-PLOR, Version 3.1. A system for X-ray crystallography and NMR; Yale University: New Haven, CT, 1992.
31. Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Grusoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comp. Phys. 1999, 151, 283-312.
32. Lu, X.-J.; Olson W. K. Nucleic Acids. Res. 2003, 31, 5108-5121.
33. de Pablo, P.; Moreno-Herrero, F.; Colchero, J.; Gómez-Herrero, J.; Herrero, P.; Baro, A. M.; Ordejón, P.; Soler, J. M.; Artacho, E. Phys. Rev. Lett. 2000, 85, 4992-4995.
34. Gervasio, F. L.; Carloni, P.; Parrinello, M. Phys. Rev. Lett. 2002, 89, 108102-1, 108102-4.
35. (a) Wang, H.; Lewis, J. P.; Sankey, O. F. Phys. Rev. Lett 2004, 93, 016401-1, 016401-4.
36. (b) Lewis, J. P.; Cheatham, T. E.; Starikov, E. B.; Wang, H.; Sankey, O. F. J. Phys. Chem. B 2003, 107, 2581-2587.
37. (a) Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
38. (b) Lee, C.; W. Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
39. For example, the 6-31G basis set led to 4612 and 4212 basis functions for xDNA and B-DNA, respectively, and adding just one set of polarization functions, e.g., 6-31G*, gives 7276 and 6232 basis functions.
40. (a) Aprà, E.; et al. NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.7; Pacific Northwest National Laboratory: Richland, WA, 2005.
41. (b) Kendall, R. A.; Aprà, E.; Bernholdt, D. E.; Bylaska, E. J.; Dupuis, M.; Fann, G. I.; Harrison, R. J.; Ju, J.; Nichols, J. A.; Nieplocha, J.; Straatsma, T. P.; Windus, T. L.; Wong, A. T. Comput. Phys. Commun. 2000, 128, 260-283.
42. (a) Kresse, G.; Hafner, J. Phys. Rev. B 1993, 37, 558.
43. (b) Kresse G.; Furthmüller, J. Comput. Mater. Sci. 1996, 6, 15.
44. (c) Kresse, G.; Furthmüller, J. Phys. Rev. B 54, 54, 11169.
45. (d) Kresse, G.; Joubert D. Phys. Rev. B 1999, 59, 1758.
46. Perdew, J. P.; Chevary, J. A.; Vosko, S. H.; Jackson, K. A.; Pederson, M. R.; Singh, D. J.; Fiolhais, C. Phys. Rev. B 1992, 46, 6671.
47. Gao, J.; Liu, H.; Kool, E. T. Angew. Chem., Int. Ed. 2005, 44, 2-5.