Diffraction in low-energy electron scattering from DNA: Bridging gas-phase and solid-state theory

Physical Review A - Atomic, Molecular, and Optical Physics

Volumn 78, Issue 4, 2008, Pages

  Caron, Laurent ^a   Sanche, Léon ^a   Tonzani, Stefano ^b   Greene, Chris H ^c  

^a UNIVERSITY OF SHERBROOKE   (Canada)

^b NORTHWESTERN UNIVERSITY   (United States)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFRACTION; DNA; ELECTROMAGNETIC WAVES; ELECTRON ENERGY LOSS SPECTROSCOPY; ELECTRON SCATTERING; GAS DYNAMICS; GENES; NUCLEIC ACIDS; ORGANIC ACIDS; SCATTERING; THICK FILMS;

ENERGY ELECTRONS; GAIN INSIGHTS; GAS PHASES; SCATTERING CALCULATIONS; SINGLE MOLECULES; THIN-FILMS;

GASES;

EID: 55049127656     PISSN: 10502947     EISSN: 10941622     Source Type: Journal    
DOI: 10.1103/PhysRevA.78.042710     Document Type: Article

References (83)

1. B. Boudaïffa, P. Cloutier, D. Hunting, M. A. Huels, and L. Sanche, Science 10.1126/science.287.5458.1658 287, 1658 (2000).
2. For a review, see L. Sanche, Eur. Phys. J. D 10.1140/epjd/e2005-00206-6 35, 367 (2005).
3. V. Cobut, Y. Frongillo, J. Patau, T. Goulet, M.-J. Fraser, and J.-P. Jay-Gerin, Radiat. Phys. Chem. 10.1016/S0969-806X(97)00096-0 51, 229 (1998).
4. S. Pimblott and J. A. LaVerne, Radiat. Phys. Chem. 10.1016/j.radphyschem. 2007.02.012 76, 1244 (2007).
5. A. Bass and L. Sanche, Radiat. Environ. Biophys. 10.1007/s004110050125 37, 243 (1998), a review paper.
6. R. Barrios, P. Skurski, and J. Simons, J. Phys. Chem. B 10.1021/jp013861i 106, 7991 (2002).
7. A. M. Scheer, K. Aflatooni, G. A. Gallup, and P. D. Burrow, Phys. Rev. Lett. 10.1103/PhysRevLett.92.068102 92, 068102 (2004).
8. X. Pan, P. Cloutier, D. Hunting, and L. Sanche, Phys. Rev. Lett. 10.1103/PhysRevLett.90.208102 90, 208102 (2003).
9. A. Migus, Y. Gauduel, J. L. Martin, and A. Antonetti, Phys. Rev. Lett. 10.1103/PhysRevLett.58.1559 58, 1559 (1987).
10. C. V. Sonntag, Adv. Quantum Chem. 52, 5 (2007). 10.1016/S0065-3276(06) 52002-7
11. U. Uehara, H. Nikjoo, and D. Goodhead, Radiat. Res. 10.2307/3580095 152, 202 (1999).
12. S. Denifl, S. Ptasińska, M. Probst, J. Hrušák, P. Scheier, and T. Märk, J. Phys. Chem. A 10.1021/jp049394x 108, 6562 (2004); see citations therein.
13. S. Ptasinska, S. Denifl, S. Gohlke, P. Scheier, E. Illenberger, and T. D. Mark, Angew. Chem., Int. Ed. 10.1002/anie.200503930 45, 1893 (2006).
14. K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. 10.1021/jp980865n 102, 6205 (1998).
15. F. Martin, P. D. Burrow, Z. Cai, P. Cloutier, D. Hunting, and L. Sanche, Phys. Rev. Lett. 10.1103/PhysRevLett.93.068101 93, 068101 (2004).
16. S. Tonzani and C. H. Greene, J. Chem. Phys. 10.1063/1.1829056 122, 014111 (2005).
17. D. Bouchiha, J. D. Gorfinkiel, L. G. Caron, and L. Sanche, J. Phys. B 10.1088/0953-4075/39/4/021 39, 975 (2006).
18. A. Grandi, F. A. Gianturco, and N. Sanna, Phys. Rev. Lett. 10.1103/PhysRevLett.93.048103 93, 048103 (2004).
19. C. S. Trevisan, A. E. Orel, and T. N. Rescigno, J. Phys. B 10.1088/0953-4075/39/12/L01 39, L255 (2006).
20. C. Winstead and V. McKoy, Phys. Rev. A 10.1103/PhysRevA.73.012711 73, 012711 (2006).
21. J. Gu, Y. Xie, and H. F. Schaefer III, J. Am. Chem. Soc. 10.1021/ja0400990 127, 1053 (2005).
22. S. Kim, S. E. Wheeler, and H. F. Schaefer III, J. Chem. Phys. 10.1063/1.2197828 124, 204310 (2006).
23. C. F. Craig, W. R. Duncan, and O. V. Prezhdo, Phys. Rev. Lett. 10.1103/PhysRevLett.95.163001 95, 163001 (2005).
24. N. T. Maitra, J. Chem. Phys. 10.1063/1.2210471 125, 014110 (2006).
25. A. Wasserman, N. T. Maitra, and K. Burke, J. Chem. Phys. 10.1063/1.1877052 122, 144103 (2005).
26. J. P. Lewis, T. E. Cheatham III, E. B. Starikov, H. Wang, and O. F. Sankey, J. Phys. Chem. B 10.1021/jp026772u 107, 2581 (2003).
27. F. D. Lewis, L. Zhang, X. Liu, X. Zuo, D. M. Tiede, H. Long, and G. C. Schatz, J. Am. Chem. Soc. 10.1021/ja0539387 127, 14445 (2005).
28. L. G. Caron and L. Sanche, Phys. Rev. Lett. 10.1103/PhysRevLett.91.113201 91, 113201 (2003).
29. L. Caron and L. Sanche, Phys. Rev. A 10.1103/PhysRevA.70.032719 70, 032719 (2004).
30. L. Caron and L. Sanche, Phys. Rev. A 10.1103/PhysRevA.72.032726 72, 032726 (2005).
31. L. Caron and L. Sanche, Phys. Rev. A 10.1103/PhysRevA.73.062707 73, 062707 (2006).
32. S. Tonzani and C. H. Greene, J. Chem. Phys. 10.1063/1.2148965 124, 054312 (2006).
33. T. M. Orlando, D. Oh, Y. Chen, and A. B. Aleksandrov, J. Chem. Phys. 10.1063/1.2907722 128, 195102 (2008).
34. D. Chandler and K. Leung, Annu. Rev. Phys. Chem. 10.1146/annurev.pc.45. 100194.003013 45, 557 (1994).
35. This sequence was extracted from the ideal 36 base pairs theoretical models of DNA in the atlas of macromolecules of the Protein Explorer at http://www.umass.edu/microbio/chime/pe_beta/pe/atlas/atlas.htm.
36. M. Feig and B. M. Pettitt, Biophys. J. 75, 134 (1998).
37. S. Neidle, Nucleic Acid Structure and Recognition (Oxford University Press, New York, 2002).
38. D. Dill and J. L. Dehmer, J. Chem. Phys. 10.1063/1.1681947 61, 692 (1974).
39. J. B. Pendry, Low Energy Electron Diffraction (Academic, London, 1974).
40. G. A. Fiete and E. J. Heller, Rev. Mod. Phys. 10.1103/RevModPhys.75.933 75, 933 (2003).
41. N. F. Mott and H. S. W. Massey, The Theory of Atomic Collisions (Clarendon, Oxford, 1965), 3rd ed.
42. F. A. Gianturco and A. Jain, Phys. Rep. 10.1016/0370-1573(86)90125-0 143, 347 (1986).
43. A. Messiah, Quantum Mechanics (Wiley, New York, 1962), Appendix C.
44. T. F. O'Malley and H. S. Taylor, Phys. Rev. 10.1103/PhysRev.176.207 176, 207 (1968).
45. M. A. Morrison and L. A. Collins, Phys. Rev. A 10.1103/PhysRevA.17.918 17, 918 (1978).
46. C. Froese-Fischer, T. Brage, and P. Jonsson, Computational Atomic Structure (Insitute of Physics, Bristol, 1997).
47. S. Tonzani, Comput. Phys. Commun. 176, 146 (2007). 10.1016/j.cpc.2006.08. 006
48. S. Tonzani and C. H. Greene, J. Chem. Phys. 10.1063/1.2333455 125, 094504 (2006).
49. M. Aymar, C. H. Greene, and E. Luc-Koenig, Rev. Mod. Phys. 10.1103/RevModPhys.68.1015 68, 1015 (1996).
50. Bioengineering Institute, The University of Auckland, New Zealand, Fem/bem notes (1997), http://www.bioeng.auckland.ac.nz/cmiss/fembemnotes/ fembemnotes.pdf.
51. Scientific Computing Group, University of Basel, Pardiso, http://www.computational.unibas.ch/cs/scicomp/software/pardiso/.
52. S. Hara, J. Phys. Soc. Jpn. 10.1143/JPSJ.27.1009 27, 1009 (1969).
53. R. G. Parr and W. Yang, Density Functional Theory of Atoms and Molecules (Oxford University Press, Oxford, 1989).
54. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 10.1103/PhysRevB.37.785 37, 785 (1988).
55. R. R. Lucchese, F. A. Gianturco, and N. Sanna, Chem. Phys. Lett. 10.1016/S0009-2614(99)00422-4 305, 413 (1999).
56. F. A. Gianturco and J. A. Rodriguez-Ruiz, Phys. Rev. A 10.1103/PhysRevA.47.1075 47, 1075 (1993).
57. S. Tonzani, Ph.D. thesis, JILA and Department of Chemistry, University of Colorado, Boulder (2001).
58. L. Caron, D. Bouchiha, J. D. Gorfinkiel, and L. Sanche, Phys. Rev. A 10.1103/PhysRevA.76.032716 76, 032716 (2007).
59. D. Bouchiha, L. G. Caron, J. D. Gorfinkiel, and L. Sanche, J. Phys. B 10.1088/0953-4075/41/4/045204 41, 045204 (2008).
60. B. Segall and F. S. Ham, in Energy Bands of Solids, edited by, B. Alder, S. Fernbach and, M. Rotenberg Vol. 8 of Methods in Computational Physics (Academic, New York, 1968), p. 251.
61. G. C. Fletcher, The Electron Band Theory of Solids (North-Holland, Amsterdam, 1971).
62. D. A. Case, Annu. Rev. Phys. Chem. 10.1146/annurev.pc.33.100182.001055 33, 151 (1982).
63. C. R. Natoli, D. K. Misemer, S. Doniach, and F. W. Kutzler, Phys. Rev. A 10.1103/PhysRevA.22.1104 22, 1104 (1980).
64. A working hypothesis based on the examination of x-ray data of DNA found in the Nucleic Acid Database at http://ndbserver.rutgers.edu/ and the Protein Data Base at http://www.pdb.org/pdb/home/home.do.
65. H. Basch, D. R. Garmer, P. G. Jasien, M. Krauss, and W. J. Stevens, Chem. Phys. Lett. 10.1016/0009-2614(89)85179-6 163, 514 (1989).
66. Values obtained from the ACD/ChemSketch Freeware, version 10.00, Advanced Chemistry Development, Inc., Toronto, ON, Canada, www.acdlabs.com, 2006.
67. T. N. Olney, N. M. Cann, G. Cooper, and C. E. Brion, Chem. Phys. 10.1016/S0301-0104(97)00145-6 223, 59 (1997).
68. S. Swarts, M. Sevilla, D. Becker, C. Tokar, and K. Wheeler, Radiat. Res. 10.2307/3578034 129, 333 (1992).
69. H. Abdoul-Carime and L. Sanche, Int. J. Radiat. Biol. 10.1080/09553000110090016 78, 89 (2002).
70. Z. Cai, M.-E. Dextraze, P. Cloutier, D. Hunting, and L. Sanche, J. Chem. Phys. 10.1063/1.2141505 124, 024705 (2006).
71. X. Pan and L. Sanche, Phys. Rev. Lett. 10.1103/PhysRevLett.94.198104 94, 198104 (2005).
72. L. Sanche, Radiat. Prot. Dosim. 99, 57 (2002).
73. M. A. Huels, B. Boudaïfa, P. Cloutier, D. Hunting, and L. Sanche, J. Am. Chem. Soc. 10.1021/ja029527x 125, 4467 (2003).
74. Y. Zheng, P. Cloutier, D. Hunting, R. Wagner, and L. Sanche, J. Am. Chem. Soc. 10.1021/ja054129q 127, 16592 (2005).
75. Y. Zheng, P. Cloutier, D. J. Hunting, J. R. Wagner, and L. Sanche, J. Chem. Phys. 10.1063/1.2166364 124, 064710 (2006).
76. R. Panajotovic, F. Martin, P. Cloutier, D. J. Hunting, and L. Sanche, Radiat. Res. 10.1667/RR3521.1 165, 452 (2006).
77. J. Berdys, I. Anusiewicz, P. Skurki, and J. Simons, J. Am. Chem. Soc. 10.1021/ja049876m 126, 6441 (2004).
78. J. Berdys, P. Skurski, and J. Simons, J. Phys. Chem. B 10.1021/jp049728i 108, 5800 (2004).
79. J. Berdys, I. Anusiewicz, P. Skurski, and J. Simons, J. Phys. Chem. A 10.1021/jp035957d 108, 2999 (2004).
80. H.-A. Wagenknecht, Nat. Prod. Rep. 10.1039/b504754b 23, 973 (2006).
81. B. Giese, J. Amaudrut, A.-K. Köhler, M. Spormann, and S. Wessely, Nature 10.1038/35085542 412, 318 (2006).
82. Y. Zheng, J. R. Wagner, and L. Sanche, Phys. Rev. Lett. 10.1103/PhysRevLett.96.208101 96, 208101 (2006).
83. M. Allan, J. Electron Spectrosc. Relat. Phenom. 10.1016/0368-2048(89) 80018-0 48, 219 (1989).