Density-Functional Theory and Molecular Dynamics: A New Perspective for Simulations of Biological Systems

Perspectives in Drug Discovery and Design

Volumn 9, Issue , 1998, Pages 161-167

  Andreoni, Wanda ^a  

^a IBM RESEARCH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0010035925     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1027212022542     Document Type: Review

References (40)

1. Dreizier, R.M. and Gross, E.K.U., Density-functional theory, Springer-Verlag, Berlin, 1990.
2. Parr, R.G. and Yang, W., Density-functional theory of atoms and molecules, Oxford Science Publications, New York, 1989.
3. Hohenberg, P. and Kohn, W., Inhomogeneous electron gas, Phys. Rev., 136 (1964) B864-B887.
4. See also Lieb, E.H., Density functionals for Coulomb systems, In Dreizler, R.M. and Providencia, J. (Eds.) Density functional methods in physics, Plenum, New York, 1985, pp. 31-80; Levy, M. and Perdew, J.P., The constrained search formulation of density functional theory, ibid., pp. 11-30.
5. See also Lieb, E.H., Density functionals for Coulomb systems, In Dreizler, R.M. and Providencia, J. (Eds.) Density functional methods in physics, Plenum, New York, 1985, pp. 31-80; Levy, M. and Perdew, J.P., The constrained search formulation of density functional theory, ibid., pp. 11-30.
6. Kohn, W. and Sham, L.J., Self-consistent equations including exchange and correlation effects, Phys. Rev., 140(1965) A1133-A1138.
7. Gunnarsson, O., Jonson, M. and Lundqvist, B.I., Description of exchange and correlation effects in inhomogeneous electron systems, Phys. Rev. B, 20 (1979) 3136-3164.
8. Car, R. and Parrinello, M., Unified density-functional theory and molecular dynamics, Phys. Rev. Lett., 55 (1985) 2471-2474.
9. Car, R., Molecular dynamics from first principles, In Binder, K. and Ciccotti G. (Eds.) Monte Carlo and molecular dynamics of condensed matter systems, Italian Physical Society Publications, Bologna, Italy, 1995, pp. 601-634.
10. See e.g. Sponer, J., Leszczynski, J. and Hobza, P., Structures and energies of hydrogen-bonded DNA base pairs: A nonempirical study with inclusion of electron correlation, J. Phys. Chem., 100 (1996) 1965-1974.
11. Hutter, J., Carloni, P. and Parrinello, M., Non-empirical calculations of a hydrated RNA duplex, J. Am. Chem. Soc., 118 (1996) 8710-8712.
12. Carloni, P. and Andreoni, W., Platinum-modified nucleobase pairs in the solid state: theoretical study, J. Phys. Chem., 100 (1996) 17797-17800.
13. Carloni, P. and Alber, F., Density-functional theory investigations of enzyme-substrate interactions, this volume and references therein.
14. Karplus, M. and Petsko, G. A., Molecular dynamics simulations in biology. Nature, 347 (1990) 631-639.
15. Sprik, M., Hutter, J. and Parrinello, M., Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient-corrected density functionals, J. Chem. Phys., 105 (1996) 1142-1152.
16. Beveridge, D.L., Swaminathan, S., Ravishanker, G., Withka, J.M., Srinivasan, J., Prevost, C., Louise-May, S., Langley, D.R., DiCapua, F.M. and Bolton, P.H., Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers, In Westhof, E. (Ed.) Water and biological macro-molecules, Macmillan, London, U.K., 1993, pp. 165-225.
17. 3 in the gas phase and in aqueous solution, J. Phys. Chem. (in press).
18. Carloni, P., Sprik, M. and Andreoni, W., Cisplatin-DNA binding mechanism: Key steps from ab initio molecular dynamics (in preparation).
19. Marx, D. and Parrinello, M., Ab-initio path integral molecular dynamics: Basic ideas, J. Chem. Phys., 104 (1996) 4077-4082.
20. Tuckerman, M.E., Marx, D., Klein, M.L. and Parrinello, M., On the quantum nature of the shared proton in hydrogen bonds, Science, 275 (1997) 817-819, and references therein.
21. Kristyán, S. and Pulay, P., Can (semi) local density functional theory account for the London dispersion forces? Chem. Phys. Lett., 229 (1994) 175-180.
22. 8 van der Waals dispersion coefficients for molecules, J. Chem. Phys. 106 (1997) 5091.
23. Kohn, W. and Meir, Y., Van der Waals energies in density functional theory, Phys. Rev. Lett. (submitted)
24. Gross, E.K.U., Dobson, J.F. and Petersilka, M., Density functional theory time-dependent phenomena, In Nalewajski, R.F. (Ed.) Density functional theory: Topics in Current Chemistry, Vol. 181, Springer, Heidelberg, 1996, pp. 81-172.
25. Mauri, F. and Galli, G., Electronic structure calculations and molecular dynamics simulations with linear system-size scaling, Phys. Rev. B, 50 (1994) 4316-4326.
26. Carlsson A.E., Order-N density-matrix electronic-structure method for general potentials, Phys. Rev. B, 51 (1995) 13935-13941.
27. Kohn, W., Density functional and density matrix methods scaling linearly with the number of atoms, Phys. Rev. Lett., 76 (1996) 3168-3171.
28. van Gunsteren, W.F., Molecular dynamics and stochastic dynamics simulations: A primer, In van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J. (Eds.) Computer simulation of biomolecular systems, Vol. 2, ESCOM, Leiden, The Netherlands, 1993,pp. 3-36.
29. Tuckerman, M.E. and Parrinello, M., Integrating the Car-Parrinello equations II: Multiple time scale techniques, J. Chem. Phys., 101 (1994) 1316-1329.
30. Carter, E.A., Ciccotti, G. and Hynes, J.T., Constrained reaction coordinate dynamics for the simulation of rare events, Chem. Phys. Lett., 156 (1989) 472-477; Ciccotti, G., Ferrario, M. and Hynes, J.T., Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent, Chem. Phys. 129 (1989) 241-251.
31. Carter, E.A., Ciccotti, G. and Hynes, J.T., Constrained reaction coordinate dynamics for the simulation of rare events, Chem. Phys. Lett., 156 (1989) 472-477; Ciccotti, G., Ferrario, M. and Hynes, J.T., Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent, Chem. Phys. 129 (1989) 241-251.
32. Curioni, A., Sprik, M., Andreoni, W., Schiffer, H., Hutter, J. and Parrinello, M., Density-functional-theory based molecular dynamics simulation of acid catalyzed reactions in liquid trioxane, J. Am. Chem. Soc. 119 (1997) 7218.
33. Perákylá, M. and Kollman, P.A., A simulation of the catalytic mechanism of aspartyl-glucosaminidase using ab-initio quantum mechanics and molecular dynamics, J. Am. Chem. Soc., 119 (1997) 1189-1196.
34. Stanton, R.V., Hartsough, D.S. and Merz, K.M., Jr., An examination of a density functional/molecular mechanical coupled potential, J. Comput. Chem., 16 (1995) 113-128.
35. See e.g. Cramer, C.J. and Truhlar, D.G., Molecular obital theory calculations of aqueous solvation effects in chemical equilibria, J. Am. Chem. Soc., 113 (1991) 8552-8554; Giesen, D.J., Gu, M.Z., and Truhlar, D.G., A universal organic solvation model, J. Org. Chem., 61(1996) 8720-8721.
36. See e.g. Cramer, C.J. and Truhlar, D.G., Molecular obital theory calculations of aqueous solvation effects in chemical equilibria, J. Am. Chem. Soc., 113 (1991) 8552-8554; Giesen, D.J., Gu, M.Z., and Truhlar, D.G., A universal organic solvation model, J. Org. Chem., 61(1996) 8720-8721.
37. Wei, D. and Salahub, D.R., A combined density functional and molecular dynamics simulation of a quantum water molecular in aqueous solution, Chem. Phys. Lett., 224 (1994) 291-296.
38. Buda, F., deGroot, H. and Bifone, A., Charge localization and dynamics in rhodopsin, Phys. Rev. Lett., 77 (1996) 4474-4477.
39. Rovira, C., Ballone, P. and Parrinello, M., A density functional study of iron-porphyrin complexes, Chem. Phys. Lett., 271 (1997) 247-250.
40. Sagnella, D.E., Laasonen, K. and Klein, M.L., Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A, Biophys. J., 71 (1996) 1172-1178.