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The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media

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Listed:
  • Benjamin A. Dalton

    (Fachbereich Physik)

  • Henrik Kiefer

    (Fachbereich Physik)

  • Roland R. Netz

    (Fachbereich Physik)

Abstract

Molecular isomerization kinetics in liquid solvent depends on a complex interplay between the solvent friction acting on the molecule, internal dissipation effects (also known as internal friction), the viscosity of the solvent, and the dihedral free energy profile. Due to the absence of accurate techniques to directly evaluate isomerization friction, it has not been possible to explore these relationships in full. By combining extensive molecular dynamics simulations with friction memory-kernel extraction techniques we consider a variety of small, isomerising molecules under a range of different viscogenic conditions and directly evaluate the viscosity dependence of the friction acting on a rotating dihedral. We reveal that the influence of different viscogenic media on isomerization kinetics can be dramatically different, even when measured at the same viscosity. This is due to the dynamic solute-solvent coupling, mediated by time-dependent friction memory kernels. We also show that deviations from the linear dependence of isomerization rates on solvent viscosity, which are often simply attributed to internal friction effects, are due to the simultaneous violation of two fundamental relationships: the Stokes-Einstein relation and the overdamped Kramers prediction for the barrier-crossing rate, both of which require explicit knowledge of friction.

Suggested Citation

  • Benjamin A. Dalton & Henrik Kiefer & Roland R. Netz, 2024. "The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48016-7
    DOI: 10.1038/s41467-024-48016-7
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    References listed on IDEAS

    as
    1. David de Sancho & Anshul Sirur & Robert B. Best, 2014. "Molecular origins of internal friction effects on protein-folding rates," Nature Communications, Nature, vol. 5(1), pages 1-10, September.
    2. Alessandro Borgia & Beth G. Wensley & Andrea Soranno & Daniel Nettels & Madeleine B. Borgia & Armin Hoffmann & Shawn H. Pfeil & Everett A. Lipman & Jane Clarke & Benjamin Schuler, 2012. "Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
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