Solvent effects on charge spatial extent in DNA and implications for transfer

Physical Review Letters

Volumn 99, Issue 5, 2007, Pages

  Mantz, Yves A ^a   Gervasio, Francesco Luigi ^a   Laino, Teodoro ^a,b   Parrinello, Michele ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER; DENSITY FUNCTIONAL THEORY; MOLECULAR MECHANICS; QUANTUM THEORY; SOLVATION;

CHARGE LOCALIZATION; FINITE TEMPERATURE; SOLVATION SHELLS;

DNA;

DNA; SOLVENT; THYMINE; WATER;

CHEMICAL STRUCTURE; QUANTUM THEORY;

DNA; MODELS, MOLECULAR; QUANTUM THEORY; SOLVENTS; THYMINE; WATER;

EID: 34547652220     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.99.058104     Document Type: Article

References (38)

1. Long-Range Charge Transfer in DNA I-II: Topics in Current Chemistry, edited by, G.B. Schuster, (Springer, Heidelberg, 2004), Vol. 236-237.
2. N.C. Seeman, Nano Lett. NALEFD 1530-6984 1, 22 (2001). 10.1021/nl000182v
3. M. Di Ventra and M. Zwolak, in Encyclopedia of Nanoscience and Nanotechnology, edited by, H. Singh-Nalwa, (American Scientific Publishers, New York, 2004).
4. E.M. Boon, A.L. Livingston, N.H. Chmiel, S.S. David, and J.K. Barton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 12543 (2003). 10.1073/pnas.2035257100
5. M.R. Holman, T. Ito, and S.E. Rokita, J. Am. Chem. Soc. 129, 6 (2007). JACSAT 0002-7863 10.1021/ja0668365
6. R.G. Endres, D.L. Cox, and R.R.P. Singh, Rev. Mod. Phys. 76, 195 (2004). RMPHAT 0034-6861 10.1103/RevModPhys.76.195
7. P.T. Henderson, D. Jones, G. Hampikian, Y. Kan, and G.B. Schuster, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 96, 8353 (1999). 10.1073/pnas.96.15. 8353
8. M.E. Nùñez, D.B. Hall, and J.K. Barton, Chemistry & Biology 6, 85 (1999). CBOLE2 1074-5521 10.1016/S1074-5521(99)80005-2
9. B. Giese, J. Amaudrut, A.-K. Kohler, M. Spormann, and S. Wesserly, Nature (London) 412, 318 (2001). NATUAS 0028-0836 10.1038/35085542
10. J. Jortner, M. Bixon, T. Langenbacher, and M.E. Michel-Beyerle, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 95, 12759 (1998). 10.1073/pnas.95.22. 12759
11. M. Bixon and J. Jortner, Chem. Phys. 326, 252 (2006). CMPHC2 0301-0104 10.1016/j.chemphys.2006.01.009
12. C.-S. Liu, R. Hernandez, and G.B. Schuster, J. Am. Chem. Soc. 126, 2877 (2004). JACSAT 0002-7863 10.1021/ja0378254
13. M.A. O'Neill and J.K. Barton, J. Am. Chem. Soc. 126, 11471 (2004). JACSAT 0002-7863 10.1021/ja048956n
14. F. Shao, M.A. O'Neill, and J.K. Barton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 17914 (2004). 10.1073/pnas.0408128101
15. F. Shao, K. Augustyn, and J.K. Barton, J. Am. Chem. Soc. 127, 17445 (2005). JACSAT 0002-7863 10.1021/ja0563399
16. R.N. Barnett, C.L. Cleveland, A. Joy, U. Landman, and G.B. Schuster, Science 294, 567 (2001). SCIEAS 0036-8075 10.1126/science.1062864
17. D.M. Basko and E.M. Conwell, Phys. Rev. Lett. 88, 098102 (2002). PRLTAO 0031-9007 10.1103/PhysRevLett.88.098102
18. R.A. Marcus, J. Chem. Phys. 24, 966 (1956). JCPSA6 0021-9606 10.1063/1.1742723
19. E.M. Conwell, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 8795 (2005). 10.1073/pnas.0501406102
20. A. Hübsch, R.G. Endres, D.L. Cox, and R.R.P. Singh, Phys. Rev. Lett. 94, 178102 (2005). PRLTAO 0031-9007 10.1103/PhysRevLett.94.178102
21. J.P. Lewis, T.E. Cheatham, III, E.B. Starikov, H. Wang, and O.F. Sankey, J. Phys. Chem. B 107, 2581 (2003). JPCBFK 1520-6106 10.1021/jp026772u
22. A.A. Voityuk, J. Phys. Chem. B 109, 10793 (2005). JPCBFK 1520-6106 10.1021/jp050985c
23. Y.A. Mantz, F.L. Gervasio, T. Laino, and M. Parrinello, J. Phys. Chem. A 111, 105 (2007). JPCAFH 1089-5639 10.1021/jp063080n
24. T. Laino, F. Mohamed, A. Laio, and M. Parrinello, J. Chem. Theory Comput. 1, 1176 (2005). 1549-9618 10.1021/ct050123f
25. T. Laino, F. Mohamed, A. Laio, and M. Parrinello, J. Chem. Theory Comput. 2, 1370 (2006). 1549-9618 10.1021/ct6001169
26. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, computer code AMBER 8 (University of California, San Francisco, 2004).
27. R. Walker, computer code AMBER 8 Tutorial: DNA polyA-polyT Decamer, http://amber.scripps.edu/tutorial/polyApolyTNew/.
28. J. VandeVondele, M. Krack, F. Mohamad, M. Parrinello, T. Chassaing, and J. Hutter, Comput. Phys. Commun. 167, 103 (2005). CPHCBZ 0010-4655 10.1016/j.cpc.2004.12.014
29. J.P. Perdew and A. Zunger, Phys. Rev. B PRBMDO 0163-1829 23, 5048 (1981). 10.1103/PhysRevB.23.5048
30. J. VandeVondele and M. Sprik, Phys. Chem. Chem. Phys. 7, 1363 (2005). PPCPFQ 1463-9076 10.1039/b501603g
31. A.D. Becke, Phys. Rev. A 38, 3098 (1988). PLRAAN 1050-2947 10.1103/PhysRevA.38.3098
32. C. Lee, W. Yang, and R.G. Parr, Phys. Rev. B PRBMDO 0163-1829 37, 785 (1988). 10.1103/PhysRevB.37.785
33. J. VandeVondele and J. Hutter, J. Chem. Phys. 118, 4365 (2003). JCPSA6 0021-9606 10.1063/1.1543154
34. S. Goedecker, M. Teter, and J. Hutter, Phys. Rev. B PRBMDO 0163-1829 54, 1703 (1996). 10.1103/PhysRevB.54.1703
35. E.M. Conwell and D.M. Basko, J. Phys. Chem. B 110, 23603 (2006). JPCBFK 1520-6106 10.1021/jp064373j
36. A. Joy, A.K. Ghosh, and G.B. Schuster, J. Am. Chem. Soc. 128, 5346 (2006). JACSAT 0002-7863 10.1021/ja058758b
37. R.N. Barnett, A. Bongiorno, C.L. Cleveland, A. Joy, U. Landman, and G.B. Schuster, J. Am. Chem. Soc. 128, 10795 (2006). JACSAT 0002-7863 10.1021/ja061795y
38. W. Humphrey, A. Dalke, and K. Schulten, VMD 1.8.2, J. Mol. Graphics JMGRDV 0263-7855 14, 33 (1996). 10.1016/0263-7855(96)00018-5