NMR solvent shifts of adenine in aqueous solution from hybrid QM/MM molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 111, Issue 19, 2007, Pages 5225-5232

  Komin, Sittipong ^a   Gossens, Christian ^b   Tavernelli, Ivano ^b   Rothlisberger, Ursula ^b   Sebastiani, Daniel ^a  

^a MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

^b EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL SHIFT; HYDROGEN BONDS; MOLECULAR DYNAMICS; QUANTUM THEORY; RESONANCE; SOLVATION;

ADENINE; ALL-ATOM FORCE FIELD; RESONANCE LINES;

NUCLEIC ACIDS;

EID: 34249788737     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp067263l     Document Type: Article

References (80)

1. Brown, S. P.; Spiess, H. W. Chem. Rev. 2001, 101, 4125.
2. Spiess, H. W. J. Polym. Sci., Part A: Poly. Chem. 2004, 42, 5031.
3. Spiess, H. W. J. Polym. Sci. A: Poly. Chem. 2004, 42, 5031.
4. Sebastiani, D. Mod. Phys. Lett. B 2003, 17, 1301.
5. Bühl, M.: Kaupp, M.; Malkina, O. L.; Malkin, V. J. Comput. Chem. 1999, 20, 91.
6. Gauss, J. Chem. Phys. Lett. 1992, 191, 614.
7. Schulz-Dobrick, M.; Metzroth, T.; Spiess, H. W.; Gauss, J.; Schnell, I. ChemPhysChem 2005, 6, 315.
8. Auer, A. A.; Gauss, J.; Staton, J. F. J. Chem. Phys. 2003, 118, 10407.
9. Jones, R. O.; Gunnarsson, O. Rev. Mod. Phys. 1989, 61, 689.
10. Martin, R. M. Electronic Structure: Basic Theory and Practical Methods; Cambridge University Press: Cambridge, New York, 2004.
11. Knowles, P.; Schütz, M.; Werner, H.-J. Ab initio methods for electron correlation in molecules. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; NIC Series; John von Neumann Institute for Computing; Jülich, Germany, 2000; Vol. 3, pp 97-179.
12. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry; Dover Publications Inc.; Mineola, New York, 1996.
13. Ochsenfeld, C.; Brown, S. P.; Schnell, I.; Gauss, J.; Spiess, H. W. J. Am. Chem. Soc. 2001, 123, 2597.
14. Mauri, F.; Pfrommer, B.; Louie, S. Phys. Rev. Lett. 1997, 79, 2340.
15. Yoon, Y.; Pfrommer, B.; Mauri F.; Louie, S. Phys. Rev. Lett. 1998, 80, 3388.
16. Schmidt, J.; Hoffmann, A.; Spiess H. W.: Sebastiani, D. J. Phys. Chem. B 2006, 110, 23204.
17. Hoffmann, A.; et al. Chem. Phys. Lett. 2004, 388, 164.
18. Sebastiani, D. ChemPhysChem 2006, 7, 164.
19. Pfrommer, B.; Mauri, F.; Louie, S. J. Am. Chem. Soc. 2000, 122, 123.
20. Sebastiani, D.; Parrinello, M. ChemPhysChem 2002, 3, 675.
21. Murakhtina, T.; Heuft, J.; Meijer, J.-E.; Sebastiani, D. ChemPhys-Chem 2006, 7, 2578.
22. Sulkowska, A.; Michnik, A. J. Mol. Struct. (THEOCHEM) 1997, 410, 27.
23. Gonnella, N. C.; et al. J. Am. Chem. Soc. 1983, 105, 2050.
24. Schindler, M. J. Am. Chem. Soc. 1988, 110, 6623.
25. Piana, S.; Sebastiani, D.; Carloni P.: Parrinello, M. J. Am. Chem. Soc. 2001, 122, 123.
26. Vidossich, P.; Piana, S.; Miani, A.; Carloni, P. J. Am. Chem. Soc. 2006, 128, 7215.
27. Sebastiani, D.; Rothlisberger, U. Advances in Density Functional Based Modelling Techniques: Recent Extensions of the Car-Parrinello Approach. Methods and Principles in Medicinal Chemistry;Mannhold, R., Kubiny, H., Folkers, G., Eds.; Wiley-VCH: Weinheim, Germany, 2003; Vol. 88.
28. Iftimie, R.; Minary P.; Tuckerman, M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6654.
29. Klein, R. A.; Mennuci, B.; Tomasi, J. J. Phys. Chem. A 2004, 108, 5851.
30. Amovilli, C.; Mennucci, B. J. Phys. Chem. B 1997, 101, 1051.
31. Klein, R. A.; Mennuci, B.; Tomasi, J. J. Phys. Chem. A 2004, 108, 5851.
32. Fattebert, J.-L.; Gygi, F. Int. J. Quantum Chem. 2003, 93, 139.
33. Gordon, M. S.; et al. J. Phys. Chem. A 2001, 105, 293.
34. Di Fiori, N.; Orendt, A.; Caputo, M. C.; Ferraro, M. B.; Facelli, J. C. Magn. Reson. Chem. 2004, 42, S41.
35. Cui, Q. J. Chem. Phys. 2002, 117, 4720.
36. Klamt, A.; Schuurmann, G. J. Chem. Soc. Perkin Trans. 1993, 2, 799.
37. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471.
38. Cui, Q.; Karplus, M. J. Chem. Phys. 2000, 112, 1133.
39. Sherwood, P. Hybrid quantum mechanics/moleculer mechanics approaches. In Modern Methods and Algorithms of Quantum Chemistry, Grotendorst, J., Ed.; NIC Series; John von Neumann Institute for Computing: Jülich, Germany, 2000; Vol. 1, pp 257-277.
40. Laio, A.; VandeVondele, J.; Roethlisberger, U. J. Chem. Phys. 2002, 116, 6941.
41. Sebastiani, D.; Rothlisberger, U. J. Phys. Chem. B 2004, 108, 2807.
42. Cui, Q.; Karplus, M. J. Phys. Chem. B 2000, 104, 3721.
43. Kongsted, J.; Nielsen, C. B.; Mikkelsen, K. V.; Christiansen, O.; Ruud, K. J. Chem. Phys. 2007, 126, 034510.
44. Wang, B.; Merz, K. M. J. Chem. Theory Comp. 2000, 2, 209.
45. Ramalho, T. C.; da Cunha, E. F. F.; de Alencastro, R. B. J. Phys. Condens. Matter 2004, 16, 6159.
46. Sebastiani, D.; Parrinello, M. J. Phys. Chem. A 2001, 105, 1951.
47. Sebastiani, D.; Goward, G.; Schnell, I.; Spiess, H. W. J. Mol. Struct. (THEOCHEM) 2003, 625, 283.
48. Gauss, J. J. Chem. Phys. 1993, 99, 3629.
49. Gauss, J.; Stanton, J. J. Chem. Phys. 1995, 102, 251.
50. Gauss, J.; Stanton, J. J. Chem. Phys. 1995, 103, 3561.
51. Case, D. A.; et al. Computer code AMBER, Copyright University of California.
52. Hutter, J. et al. Computer code CPMD, version 3.12,1990-2005; Copyright IBM Corp, and MPI-FKF Stuttgart; http://www.cpmd.org.
53. Hutter, J.; Curioni, A. ChemPhysChem 2005, 6, 1788.
54. Marx, D.; Hutter, J. Ab-initio molecular dynamics: Theory and implementation. In Modern Methods and Algorithms in Quantum Chemistry; Forschungzentrum: Juelich, Germany, 2000; pp 301-449.
55. Becke, A. D. Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098.
56. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785.
57. Troullier, N.; Martins, J. L. Phys. Rev. B: Condens. Matter Mater. Phys.. 1991, 43, 1993.
58. Martyna, G.; Tuckerman, M. J. Chem. Phys. 1999, 110, 2810.
59. van Gunsteren, W.; Berendsen, H. Computer code GROMOS96; Copyright BIOMOS b.v., Biomolecular Software, ETH-ZUrich.
60. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
61. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comp. Phys. 1977, 23, 327.
62. Putrino, A.; Sebastiani, D.; Parrinello, M. J. Chem. Phys. 2000, 113, 7102.
63. Baroni, S.; de Gironcoli, S.; del Corso, A.; Giannozzi, P. Rev. Mod. Phys. 2001, 73, 515.
64. Mauri, F.; Pfrommer, B.; Louie, S. Phys. Rev. Lett. 1996, 77, 5300.
65. Day, P. N.; et al. J. Chem. Phys. 1996, 105, 1968.
66. Cossi, M.; Barone, V.; Cammi, R.; Tomasi, J. Chem. Phys. Lett. 1996, 255, 327.
67. Amovilli, C.; et al. Adv. Quant. Chem. 1999, 32, 227.
68. Tomasi, J.; Mennucci B.; Cancès, E. J. Mol. Struct. (THEOCHEM) 1999, 464, 211.
69. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.03; Gaussian, Inc.: Wallingford, CT, 2003.
70. Schreckenbach, G.; Wolff, S. K.; Ziegler, T. J. Phys. Chem. A 2000, 104, 8244.
71. Straka, M.; Kaupp, M. Chem. Phys. Lett. 2005, 311, 45.
72. Mauri, F.; Louie, S. Phys. Rev. Lett. 1996, 76, 4246.
73. Gervais, C.; et al. J. Phys. Chem. A 2005, 109, 6960.
74. Mauri, F.; Vast, N.; Pickard, C. J. Phys. Rev. Lett. 2001, 88, 085506.
75. Pickard, C. J.; Mauri, F. Phys. Rev. B: Condens. Matter Mater. Phys. 2001, 63, 245101.
76. Sebastiani, D. Int. J. Quantum Chem. 2005, 101, 849.
77. von Lilienfeld-Toal, A.; Tavernelli, I.; Rothlisberger, U.; Sebastiani, D. Phys. Rev. B: Condens. Matter Mater. Phys. 2005, 71, 195119.
78. von Lilienfeld-Toal, A.; Tavernelli, I.; Rothlisberger, U.; Sebastiani, D. J. Chem. Phys. 2005, 122, 014113.
79. Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. J. Phys. Chem. A 2000, 104, 1720.
80. OO.