2023/09/14 by Benjamin A. Dalton, Dalton, Benjamin A., Henrik Kiefer +3
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Chemical Physics (physics.chem-ph) #FOS: Physical sciences #Lipid Membrane Structure and Behavior #Protein Structure and Dynamics #Soft Condensed Matter (cond-mat.soft) #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.2309.07521
openalex publication_date 2023/09/14 · openalex created_date 2023/09/16 · openalex updated_date 2026/07/28
Molecular isomerization kinetics in liquid solvents are determined by a complex interplay between the friction acting on a rotating dihedral due to interactions with the solvent, internal dissipation effects (also known as internal friction), the viscosity of the solvent, and the free energy profile over which a dihedral rotates. Currently, it is not understood how these quantities are related at the molecular scale. Here, we combine molecular dynamics simulations of isomerizing n-alkane chains and dipeptide molecules in mixed water-glycerol solvents with memory-kernel extraction techniques to directly evaluate the frequency-dependent friction acting on a rotating dihedral. We extract the friction and isomerization times over a range of glycerol concentrations and accurately evaluate the relationships between solvent viscosity, isomerization kinetics, and dihedral friction. We show that the total friction acting on a rotating dihedral does not scale linearly with solvent viscosity, thus violating the Stokes-Einstein relation. Additionally, we demonstrate that the kinetics of isomerization are significantly faster compared to the Kramers prediction in the overdamped limit. We suggest that isomerization kinetics are determined by the multi-time-scale friction coupling between a rotating dihedral and its solvent environment, which results in non-Markovian kinetic speed-up effects.