Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

Canonical Sampling Method for Initial Conditions for Reactive Flux Calculations Using Nose-Hoover Chains

  • Published : 2004.04.20
Download PDF
⟨ Previous Next ⟩

Abstract

Canonical sampling method has been presented to generate the initial conditions for reactive flux studies of organic reactions in water. Velocity Verlet version of Nose-Hoover chain dynamics algorithm has been employed to sample the initial conditions according to canonical distribution. The unstable normal mode of a transition state has been introduced to define a dividing plane separating reactant and product regions in reaction processes. This method has been implemented and tested for the case iels-Alder reaction of methyl vinyl ketone (MVK) and cyclopentadiene (CPD) in water, providing a reliable tool for further reactive flux molecular dynamics studies in condensed media.

Keywords

References

  1. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.;DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. https://doi.org/10.1063/1.448118
  2. den Otter, W. K.; Briels, W. J. J. Chem. Phys. 1996, 106, 5494.
  3. Jang, S.; Voth, G. A. J. Chem. Phys. 1998, 107, 9514. https://doi.org/10.1063/1.475247
  4. Berne, B. J. In Multiple Time Scales; Brackbill, J. U.; Cohen, B. I.,Eds.; Academic: New York, 1985.
  5. Wilson, Jr., E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations;Dover Publications: New York, 1955.
  6. Papousek, D.; Aliev, M. R. Molecular Vibrational-RotationalSpectra; Elsevier: New York, 1982.
  7. Eckart, C. Phys. Rev. 1935, 47, 552. https://doi.org/10.1103/PhysRev.47.552
  8. Louck, J. D.; Galbraith, H. W. Rev. Mod. Phys. 1976, 48, 69. https://doi.org/10.1103/RevModPhys.48.69
  9. Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys.Lett. 1989, 156, 472. https://doi.org/10.1016/S0009-2614(89)87314-2
  10. Cornell, W. D. et al. J. Am. Chem. Soc. 1995, 117, 5179. https://doi.org/10.1021/ja00124a002
  11. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys.Chem. 1993, 97, 10269. https://doi.org/10.1021/j100142a004
  12. Lobaugh, J.; Voth, G. A. J. Chem. Phys. 1997, 106, 2400. https://doi.org/10.1063/1.473151
  13. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.;Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.;Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.;Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe,M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J.L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.;Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. GAUSSIAN 94, RevisionE.2; Gaussian, Inc.: Pittsburgh, PA, 1995.

Cited by

  1. Physical Chemistry Research Articles Published in the Bulletin of the Korean Chemical Society: 2003-2007 vol.29, pp.2, 2008, https://doi.org/10.5012/bkcs.2008.29.2.450