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A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements

Source: J. Chem. Phys. 133, 034118 (2010); doi:10.1063/1.3459058

Published 20 July 2010

KEYWORDS and PACS
Keywords
PACS
  • 82.20.Db
    Transition state theory and statistical theories of rate constants (chemical kinetics)
  • 82.20.Wt
    Computational modeling and simulation of chemical kinetics
  • 87.15.hp
    Conformational changes of biomolecules
  • 87.15.R-
    Biochemical reactions and kinetics
  • YEAR: 2010
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PUBLICATION DATA
ISSN:
1553-9628 (online)
Publisher:
AIP is a member of CrossRef AIP
Srabanti Chaudhury and Dmitrii E. Makarov
Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
Motivated by recent experimental efforts to measure the time a molecular system spends in transit between the reactants and the products of a chemical reaction, here we study the properties of the distribution of such transit times for the case of conservative dynamics on a multidimensional energy landscape. Unlike reaction rates, transit times are not invariant with respect to the order parameter (a.k.a. the experimental signal) used to monitor the progress of a chemical reaction. Nevertheless, such order parameter dependence turns out to be relatively weak. Moreover, for several model systems we find that the probability distribution of transit times can be estimated analytically, with reasonable accuracy, by assuming that the order parameter coincides with the direction of the unstable normal mode at the transition state. Although this approximation tends to overestimate the actual mean transit time measured using other order parameters, it yields asymptotically correct long-time behavior of the transit time distribution, which is independent of the order parameter. ©2010 American Institute of Physics
History: Received 13 April 2010; accepted 11 June 2010; published 20 July 2010
Permalink: http://link.aip.org/link/?JCPSA6/133/034118/1

REFERENCES (31)

For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. A. H. Zewail, Angew. Chem., Int. Ed. Engl. 39, 2586 (2000).
  2. H. S. Chung, J. M. Louis, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 106, 11837 (2009).
  3. T. H. Lee, L. J. Lapidus, W. Zhao, K. J. Travers, D. Herschlag, and S. Chu, Biophys. J. 92, 3275 (2007).
  4. D. M. Zuckerman and T. B. Woolf, J. Chem. Phys. 116, 2586 (2002).
  5. G. Hummer, J. Chem. Phys. 120, 516 (2004).
  6. B. W. Zhang, D. Jasnow, and D. M. Zuckerman, J. Chem. Phys. 126, 074504 (2007).
  7. S. V. Malinin and V. Y. Chernyak, J. Chem. Phys. 132, 014504 (2010).
  8. E. Weinan and E. Vanden-Eijnden, J. Stat. Phys. 123, 503 (2006).
  9. P. Metzner, C. Schutte, and E. Vanden-Eijnden, J. Chem. Phys. 125, 084110 (2006).
  10. E. Vanden-Eijnden, in Computer Simulations in Condensed Matter: From Materials to Chemical Biology, edited by M. M. Ferrario, G. Ciccotti, and K. Binder (Springer, Berlin Heidelberg, 2006).
  11. S. Kirmizialtin, L. Huang, and D. E. Makarov, Phys. Status Solidi B 243, 2038 (2006)
    12. S. Matysiak, A. Montesi, M. Pasquali, A. B. Kolomeisky, and C. Clementi, Phys. Rev. Lett. 96, 118103 (2006).
  12. D. E. Makarov, Acc. Chem. Res. 42, 281 (2009).
  13. A. Berezhkovskii and A. Szabo, J. Chem. Phys. 122, 014503 (2005).
  14. M. Muthukumar, J. Chem. Phys. 111, 10371 (1999)
    15. Phys. Rev. Lett. 86, 3188 (2001)
    J. Chem. Phys. 118, 5174 (2003)
    C. T. Wong and M. Muthukumar, ibid. 128, 154903 (2008)
    A. M. Berezhkovskii and I. V. Gopich, Biophys. J. 84, 787 (2003)
    A. M. Berezhkovskii, M. A. Pustovoit, and S. M. Bezrukov, J. Chem. Phys. 126, 134706 (2007)
    B. Hornblower, A. Coombs, R. D. Whitaker, A. Kolomeisky, S. J. Picone, A. Meller, and M. Akeson, Nat. Methods 4, 315 (2007)
    S. Kotsev and A. B. Kolomeisky, J. Chem. Phys. 127, 185103 (2007)
    A. Mohan, A. B. Kolomeisky, and M. Pasquali, ibid. 128, 125104 (2008)
    E. Slonkina and A. B. Kolomeisky, ibid. 118, 7112 (2003).
  15. D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999).
  16. A. M. Berezhkovskii, G. Hummer, and S. M. Bezrukov, Phys. Rev. Lett. 97, 020601 (2006).
  17. L. Movileanu, Trends Biotechnol. 27, 333 (2009).
  18. A. O. Caldeira and A. J. Leggett, Ann. Phys. (N.Y.) 149, 374 (1983).
  19. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, New York, 2001).
  20. A. Voter and J. Doll, J. Chem. Phys.82, 80 (1985).
  21. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990).
  22. D. E. Makarov and H. Metiu, J. Chem. Phys. 108, 8155 (1998).
  23. D. Chandler, J. Chem. Phys. 68, 2959 (1978)
    24. A. F. Voter, Phys. Rev. Lett. 63, 167 (1989).
  24. T. Van Erp and P. Bolhuis, J. Comput. Phys. 205, 157 (2005)
    25. E. Vanden-Eijnden and F. Tal, J. Chem. Phys. 123, 184103 (2005).
  25. R. B. Best, E. Paci, G. Hummer, and O. K. Dudko, J. Phys. Chem. B 112, 5968 (2008)
    26. O. K. Dudko, Proc. Natl. Acad. Sci. U.S.A. 106, 8795 (2009)
    O. K. Dudko, G. Hummer, and A. Szabo, ibid. 105, 15755 (2008)
    S. Kirmizialtin, L. Huang, and D. E. Makarov, J. Chem. Phys. 122, 234915 (2005)
    P. -C. Li and D. E. Makarov, ibid. 119, 9260 (2003)
    J. Phys. Chem. B 108, 745 (2004).
  26. O. K. Dudko, J. Mathe, A. Szabo, A. Meller, and G. Hummer, Biophys. J. 92, 4188 (2007)
    27. L. Huang and D. E. Makarov, J. Chem. Phys. 128, 114903 (2008).
  27. E. Pollak, Chem. Phys. Lett. 127, 178 (1986).
  28. R. Elber and M. Karplus, Chem. Phys. Lett. 139, 375 (1987)
    29. G. Henkelman and H. Jonsson, J. Chem. Phys. 111, 7010 (1999)
    G. Henkelman, B. P. Uberuaga, and H. Jonsson, ibid. 113, 9901 (2000).
  29. C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences (Springer-Verlag, Berlin, 1983).
  30. A. Szabo (private communication).
  31. H. Risken, The Fokker Planck Equation: Methods of Solution and Applications (Springer-Verlag, Berlin, 1984).

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