Density-functional theory and molecular dynamics: a new perspective for simulations of biological systems

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References

  1. 1.

    Dreizler, R.M. and Gross, E.K.U., Density-functional theory, Springer-Verlag, Berlin, 1990.

    Google Scholar 

  2. 2.

    Parr, R.G. and Yang, W., Density-functional theory of atoms and molecules, Oxford Science Publications, New York, 1989.

    Google Scholar 

  3. 3.

    Hohenberg, P. and Kohn, W., Inhomogeneous electron gas, Phys. Rev., 136 (1964) B864-B887.

    Google Scholar 

  4. 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.

    Google Scholar 

  5. 5.

    Kohn, W. and Sham, L.J., Self-consistent equations including exchange and correlation effects, Phys. Rev., 140 (1965) A1133-A1138.

    Google Scholar 

  6. 6.

    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.

    Google Scholar 

  7. 7.

    Car, R. and Parrinello, M., Unified density-functional theory and molecular dynamics, Phys. Rev. Lett., 55 (1985) 2471–2474.

    Google Scholar 

  8. 8.

    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.

    Google Scholar 

  9. 9.

    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.

    Google Scholar 

  10. 10.

    Hutter, J., Carloni, P. and Parrinello, M., Non-empirical calculations of a hydrated RNA duplex, J. Am. Chem. Soc., 118 (1996) 8710–8712.

    Google Scholar 

  11. 11.

    Carloni, P. and Andreoni, W., Platinum-modified nucleobase pairs in the solid state: theoretical study, J. Phys. Chem., 100 (1996) 17797–17800.

    Google Scholar 

  12. 12.

    Carloni, P. and Alber, F., Density-functional theory investigations of enzyme-substrate interactions, this volume and references therein.

  13. 13.

    Karplus, M. and Petsko, G.A., Molecular dynamics simulations in biology, Nature, 347 (1990) 631–639.

    Google Scholar 

  14. 14.

    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.

    Google Scholar 

  15. 15.

    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.

    Google Scholar 

  16. 16.

    See e.g. Mejer, E.J. and Sprik, M., A density-functional study of the addition of water to SO3 in the gas phase and in aqueous solution, J. Phys. Chem. (in press).

  17. 17.

    Carloni, P., Sprik, M. and Andreoni, W., Cisplatin-DNA binding mechanism: Key steps from ab initio molecular dynamics (in preparation).

  18. 18.

    Marx, D. and Parrinello, M., Ab-initio path integral molecular dynamics: Basic ideas, J. Chem. Phys., 104 (1996) 4077–4082.

    Google Scholar 

  19. 19.

    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.

    Google Scholar 

  20. 20.

    Kristyán, S. and Pulay, P., Can (semi) local density functional theory account for the London dispersion forces? Chem. Phys. Lett., 229 (1994) 175–180.

    Google Scholar 

  21. 21.

    Osinga, V.P., van Gisbergen, S.J.A. and Baerends, E.J., Density functional results for isotropic and anisotropic multipole polarizabilities and C6, C7 and C8 van der Waals dispersion coefficients for molecules, J. Chem. Phys. 106 (1997) 5091. s

    Google Scholar 

  22. 22.

    Kohn, W. and Meir, Y., Van der Waals energies in density functional theory, Phys. Rev. Lett. (submitted)

  23. 23.

    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.

    Google Scholar 

  24. 24.

    Mauri, F. and Galli, G., Electronic structure calculations and molecular dynamics simulations with linear system-size scaling, Phys. Rev. B, 50 (1994) 4316–4326.

    Google Scholar 

  25. 25.

    Carlsson A.E., Order-N density-matrix electronic-structure method for general potentials, Phys. Rev. B, 51 (1995) 13935–13941.

    Google Scholar 

  26. 26.

    Kohn, W., Density functional and density matrix methods scaling linearly with the number of atoms, Phys. Rev. Lett., 76 (1996) 3168–3171.

    Google Scholar 

  27. 27.

    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.

    Google Scholar 

  28. 28.

    Tuckerman, M.E. and Parrinello, M., Integrating the Car-Parrinello equations II: Multiple time scale techniques, J. Chem. Phys., 101 (1994) 1316–1329.

    Google Scholar 

  29. 29.

    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.

    Google Scholar 

  30. 30.

    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.

    Google Scholar 

  31. 31.

    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.

    Google Scholar 

  32. 32.

    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.

    Google Scholar 

  33. 33.

    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.

    Google Scholar 

  34. 34.

    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.

    Google Scholar 

  35. 35.

    Buda, F., deGroot, H. and Bifone, A., Charge localization and dynamics in rhodopsin, Phys. Rev. Lett., 77 (1996) 4474–4477.

    Google Scholar 

  36. 36.

    Rovira, C., Ballone, P. and Parrinello, M., A density functional study of iron-porphyrin complexes, Chem. Phys. Lett., 271 (1997) 247–250.

    Google Scholar 

  37. 37.

    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.

    Google Scholar 

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Andreoni, W. Density-functional theory and molecular dynamics: a new perspective for simulations of biological systems. Perspectives in Drug Discovery and Design 9, 161–167 (1998). https://doi.org/10.1023/A:1027212022542

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Keywords

  • Polymer
  • Molecular Dynamic
  • Biological System