Conformational analysis of dimethyl phosphate in aqueous solution: A density functional theory-based molecular dynamics study

Journal of Molecular Structure: THEOCHEM

Volumn 489, Issue 2-3, 1999, Pages 237-245

  Alber, F ^a,b   Folkers, G ^b   Carloni, P ^a,c  

^a SISSA   (Italy)

^b ETH ZURICH   (Switzerland)

^c INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

Car Parrinello method; Density functional; Dimethyl phosphate; Molecular dynamics; Solvent effects

Indexed keywords

PHOSPHATE;

AQUEOUS SOLUTION; ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; THEORY;

EID: 0033595834     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-1280(99)00057-3     Document Type: Article

References (33)

1. Blackburn M.G., Gait M.G. Nucleic Acids in Chemistry and Biology. 1996;Oxford University Press, Oxford.
2. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer, New York. p. 88.
3. Govil G. Biopolymers. 15:1976;2303.
4. Newton M.D. J. Am. Chem. Soc. 95:1973;256.
5. Schneider B., Kabeláč M., Hobza P. J. Am. Chem. Soc. 118:1996;12207. and references therein.
6. Florián J., Štrajbl M., Warshel A. J. Am. Chem. Soc. 120:1998;7959.
7. Cornell W.D., Cieplak P., Bayly I., Gould I.R., Merz K.M. Jr., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. J. Am. Chem. Soc. 117:1995;5179.
8. Car R., Parrinello M. Phys. Rev. Lett. 55:1985;2471.
9. Galli G., Parrinello M. Meyer M., Pontikis V. Computer Simulations in Material Science. NATO ASI Series. 205:1991;283 Kluwer, Dordrecht.
10. Molteni C., Parrinello M. J. Am. Soc. Chem. 120:1998;2168. and references therein.
11. Sagnella D.E., Laasonen K., Klein M.L. Biophys. J. 71:1996;1172.
12. Hütter J., Carloni P., Parrinello M. J. Am. Chem. Soc. 18:1996;8710.
13. Carloni P., Andreoni W., Parrinello M. Phys. Rev. Lett. 79:1997;761.
14. Parrinello M. Solid State Commun. 102:1997;107.
15. Carloni P., Andreoni W. J. Phys. Chem. 100:1996;17797.
16. Brooks C.L. III, Karplus M., Montgomery-Pettitt B. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. 1988;Wiley, New York.
17. Becke A. Phys. Rev. A. 38:1988;3098.
18. Lee C., Yang W., Parr R.G. Phys. Rev. B. 37:1988;785.
19. Sprik M., Hütter J., Parrinello M. J. Chem. Phys. 105:1996;1142.
20. Alber F., Folkers G., Carloni P. J. Phys. Chem. B. 103:1999;6121.
21. Giarda L., Garbassi F., Calcaterra M. Acta Cryst. B29:1973;1826.
22. Jorgensen W.L., Chandrasekhar J., Madura J., Impey R.W., Klein M.L. J. Chem. Phys. 79:1983;926.
23. The classical molecular dynamics simulation was performed using the Cerius2 program (Molecular Simulations Inc., 1997, San Diego Inc., San Diego CA) running on an SGI Octane machine. We have used the force field developed by Mayo et al. (S.L. Mayo, B.D. Olafson, W.A. Goddard III, J. Phys. Chem., 94 (1990) 8897.) in combination with the Charge Equilibration method (A.K. Rappe, W.A. Goddard III, J. Phys. Chem., 95 (1991) 3358.) The simulation was carried out using periodic boundary conditions. Ewald summations were used to treat the long-range electrostatics. The timestep was set to 1 fs and the dielectric constant to 1. The system was coupled to a Nosé thermostat at 300 K with a relaxation time of 0.1 ps. The non hydrogen atoms of the HDMP molecule were kept fixed during this simulation.
24. The classical molecular dynamics simulation was performed using the Cerius2 program (Molecular Simulations Inc., 1997, San Diego Inc., San Diego CA) running on an SGI Octane machine. We have used the force field developed by Mayo et al. (S.L. Mayo, B.D. Olafson, W.A. Goddard III, J. Phys. Chem., 94 (1990) 8897.) in combination with the Charge Equilibration method (A.K. Rappe, W.A. Goddard III, J. Phys. Chem., 95 (1991) 3358.) The simulation was carried out using periodic boundary conditions. Ewald summations were used to treat the long-range electrostatics. The timestep was set to 1 fs and the dielectric constant to 1. The system was coupled to a Nosé thermostat at 300 K with a relaxation time of 0.1 ps. The non hydrogen atoms of the HDMP molecule were kept fixed during this simulation.
25. Nosé S. J. Chem. Phys. 81:1984;511.
26. Ewald P. Ann. Phys. 64:1921;253.
27. Allen M.P., Toldesley D.J. Computer Simulation of Liquids. 1986;Oxford Science Publications.
28. Clementi E. MOTECC, Modern Techniques in Computational Chemistry. 1991;ESCOM, Leiden.
29. Jeffrey G.A., Saenger W. Hydrogen bonding in biological structures. 1991;Springer, Berlin.
30. Jayaram B., Mezei M., Beveridge D.L. J. Am. Chem. Soc. 110:1988;1691. and references therein.
31. Jayaram B., Mezei M., Beveridge D.L. J. Comput. Chem. 8:1987;917.
32. Florián J., Baumruk V., Štrajbl M., Bednárová L., Štěpánek J. J. Phys. Chem. 100:1996;1559.
33. Taga K., Miyagai K., Hirabayashi N., Yoshida T., Okabayashi H. J. Mol. Struc. 245:1991;1.