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Kinetics and energetics of chemical reactions through intermediate states

Author

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  • Arango-Restrepo, A.
  • Rubi, J.M.
  • Barragán, D.

Abstract

We analyze the kinetics and the energetics of chemical reactions passing through an intermediate state. Two approaches are adopted. The first one is a mesoscopic description in which the state of the reaction undergoes a diffusion process in a tristable potential along a reaction coordinate which parametrizes different molecular configurations in the reaction pathway. The second consists of a two-level system model. We show that the reaction flux and the energy dissipated (lost work) depend significantly on the mean life of the intermediate state. It is found that the values of these quantities obtained through both approaches differ especially at early stages, in the presence of high chemical potential differences for low energies of the intermediate state. The analysis presented unifies kinetics and energetics of chemical reactions steps and can be applied to explain the mechanism of enzymatic and organic reactions, RNA and protein folding and sorption processes.

Suggested Citation

  • Arango-Restrepo, A. & Rubi, J.M. & Barragán, D., 2018. "Kinetics and energetics of chemical reactions through intermediate states," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 509(C), pages 86-96.
    • Handle: RePEc:eee:phsmap:v:509:y:2018:i:c:p:86-96
    DOI: 10.1016/j.physa.2018.05.132
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    References listed on IDEAS

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    1. Pagonabarraga, I. & Pérez-Madrid, A. & Rubí, J.M., 1997. "Fluctuating hydrodynamics approach to chemical reactions," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 237(1), pages 205-219.
    2. Diwakar Shukla & Yilin Meng & Benoît Roux & Vijay S. Pande, 2014. "Activation pathway of Src kinase reveals intermediate states as targets for drug design," Nature Communications, Nature, vol. 5(1), pages 1-11, May.
    3. Reguera, David & Rubı́, J.M & Pérez-Madrid, A, 1998. "Fokker–Planck equations for nucleation processes revisited," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 259(1), pages 10-23.
    4. Gomila, G. & Pérez-Madrid, A. & Rubí, J.M., 1996. "Non-equilibrium thermodynamics of thermionic emission processes in abrupt semiconductor junctions, including the effects of surface states," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 233(1), pages 208-220.
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    Cited by:

    1. Drigo Filho, Elso & Chahine, Jorge & Araujo, Marcelo Tozo & Ricotta, Regina Maria, 2022. "Probability distribution to obtain the characteristic passage time for different tri-stable potentials," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 606(C).

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