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

The Journal of Chemical Physics
Srabanti Chaudhury, Dmitrii E Makarov

Abstract

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.

References

Oct 8, 1999·Biophysical Journal·D K Lubensky, D R Nelson
Apr 6, 2001·Physical Review Letters·M Muthukumar
Jan 28, 2003·Biophysical Journal·A M Berezhkovskii, I V Gopich
Jul 23, 2004·The Journal of Chemical Physics·Gerhard Hummer
Jan 11, 2005·The Journal of Chemical Physics·Alexander Berezhkovskii, Attila Szabo
Jul 13, 2005·The Journal of Chemical Physics·Serdal KirmizialtinDmitrii E Makarov
Nov 19, 2005·The Journal of Chemical Physics·Eric Vanden-Eijnden, Fabio A Tal
Apr 12, 2006·Physical Review Letters·Silvina MatysiakCecilia Clementi
Aug 16, 2006·Physical Review Letters·Alexander M BerezhkovskiiSergey M Bezrukov
Sep 13, 2006·The Journal of Chemical Physics·Philipp MetznerEric Vanden-Eijnden
Feb 20, 2007·Biophysical Journal·Tae-Hee LeeSteven Chu
Mar 3, 2007·The Journal of Chemical Physics·Bin W ZhangDaniel M Zuckerman
Nov 21, 2007·The Journal of Chemical Physics·Stanislav Kotsev, Anatoly B Kolomeisky
Feb 7, 2008·The Journal of Physical Chemistry. B·Robert B BestOlga K Dudko
Mar 26, 2008·The Journal of Chemical Physics·Lei Huang, Dmitrii E Makarov
Apr 2, 2008·The Journal of Chemical Physics·Aruna MohanMatteo Pasquali
Apr 25, 2008·The Journal of Chemical Physics·Chiu Tai Andrew Wong, M Muthukumar
Oct 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Olga K DudkoAttila Szabo
Dec 17, 2008·Accounts of Chemical Research·Dmitrii E Makarov
Apr 28, 2009·Trends in Biotechnology·Liviu Movileanu
May 28, 2009·Proceedings of the National Academy of Sciences of the United States of America·Olga K Dudko
Jul 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hoi Sung ChungWilliam A Eaton
Jan 19, 2010·The Journal of Chemical Physics·Sergey V Malinin, Vladimir Y Chernyak

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Citations

Jul 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Stefano PianaDavid E Shaw
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hao YuMichael T Woodside
Aug 21, 2013·The Journal of Chemical Physics·Alexander T HawkDmitrii E Makarov
Apr 26, 2013·The Journal of Chemical Physics·Alexander T Hawk
Jun 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Hao YuMichael T Woodside
Dec 17, 2015·The Journal of Chemical Physics·Won Kyu Kim, Roland R Netz
Mar 10, 2016·Proceedings of the National Academy of Sciences of the United States of America·Robert B Best, Gerhard Hummer
Nov 23, 2015·The Journal of Chemical Physics·Dmitrii E Makarov
Apr 29, 2016·Science·Peter Wolynes
Jun 5, 2014·Annual Review of Biophysics·Michael T Woodside, Steven M Block
Sep 19, 2016·Journal of Molecular Biology·Jörg SchönfelderRaul Perez-Jimenez
Nov 2, 2015·The Journal of Chemical Physics·Xiaoyu Bai, Peter G Wolynes
Jan 25, 2017·Proceedings of the National Academy of Sciences of the United States of America·Krishna NeupaneMichael T Woodside
Jun 21, 2017·Proceedings of the National Academy of Sciences of the United States of America·S Walter Englander, Leland Mayne
Oct 8, 2016·Faraday Discussions·Reuven Ianconescu, Eli Pollak
Oct 21, 2016·Physical Chemistry Chemical Physics : PCCP·Eli Pollak
Sep 14, 2018·Physical Chemistry Chemical Physics : PCCP·Michele CaraglioCarlo Vanderzande
Jan 30, 2020·Physical Chemistry Chemical Physics : PCCP·Michele CaraglioEnrico Carlon
Jun 20, 2015·Protein Science : a Publication of the Protein Society·Gi-Moon Nam, Dmitrii E Makarov
Jul 17, 2015·Physical Review Letters·Katherine TruexWilliam A Eaton
Oct 23, 2017·The Journal of Chemical Physics·Rohit SatijaDmitrii E Makarov
Feb 24, 2018·The Journal of Chemical Physics·Jakob Petersen, Eli Pollak
Jun 6, 2018·The Journal of Chemical Physics·Alexander M Berezhkovskii, Dmitrii E Makarov
Sep 24, 2018·The Journal of Chemical Physics·Andrew G T PyoMichael T Woodside
Nov 6, 2018·The Journal of Chemical Physics·Reuven Ianconescu, Eli Pollak
Jan 3, 2019·The Journal of Chemical Physics·R SchulzR R Netz
Sep 17, 2017·The Journal of Chemical Physics·Alexander M BerezhkovskiiSergey M Bezrukov
Dec 10, 2017·The Journal of Chemical Physics·M LalemanH Orland
Feb 24, 2017·The Journal of Chemical Physics·Dmitrii E Makarov
Dec 3, 2017·The Journal of Chemical Physics·Alexander M Berezhkovskii, Dmitrii E Makarov
Jun 15, 2020·The Journal of Chemical Physics·Alexander M Berezhkovskii, Dmitrii E Makarov
Nov 11, 2018·Nature Communications·Flurin SturzeneggerBenjamin Schuler
Dec 23, 2019·The Journal of Chemical Physics·Masoumeh Ozmaian, Dmitrii E Makarov
Oct 11, 2017·The Journal of Chemical Physics·Alexander M BerezhkovskiiSergey M Bezrukov
Apr 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Noel Q HofferMichael T Woodside
Dec 29, 2020·Frontiers in Chemistry·Alexander MehlichJohannes Stigler
Oct 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Rohit SatijaDmitrii E Makarov
Feb 23, 2021·The Journal of Physical Chemistry. B·Dmitrii E Makarov
Apr 27, 2021·The Journal of Physical Chemistry. B·Divya SinghSrabanti Chaudhury
Jul 10, 2021·The Journal of Chemical Physics·Shivangi SharmaParbati Biswas
Jul 18, 2021·Physical Review. E·Kento Yasuda, Shigeyuki Komura
Mar 21, 2018·The Journal of Physical Chemistry. a·Jakob Petersen, Eli Pollak
Sep 14, 2017·Journal of Chemical Theory and Computation·Bin W ZhangRonald M Levy

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Methods Mentioned

BETA
fluorescence

Software Mentioned

smFRET

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