On the validity of Stokes' law at the molecular level

Walser, Regula; Mark, Alan E.; Gunsteren, Wilfred F. van

doi:10.1016/s0009-2614(99)00266-3

Cited by 58 publications

(42 citation statements)

References 24 publications

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“…Computationally, changing the mass of water is a very elegant and clean way to explore the viscosity dependence of the switching process, without changing anything else but the solvent friction. 10,[49][50][51] That is, it can been shown on very general grounds that within the framework of classical mechanics, any thermodynamic property of a system is not dependent on atom masses, 52 only dynamical properties are. In particular, the starting and ending ensembles before and after switching, respectively, ought to be the same.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

Waldauer

Stucki-Buchli

Frey

et al. 2014

The Journal of Chemical Physics

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By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein.The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations. By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations. © 2014 AIP Publishing LLC.

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

Waldauer

Stucki-Buchli

Frey

et al. 2014

The Journal of Chemical Physics

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“…The density F is within 0.1% of the experimental value at 1 bar for a range of temperature from 293 to 313 K. As with other solvent models, the pressure at constant volume is very sensitive to the method used for the calculation of long-range interactions. 27 Reducing the long-range cutoff radius from 1.4 to 1.2 nm, results in an increase in the average pressure of ≈100 bar. Other properties remain almost unaffected.…”

Section: Physicochemical Properties Of Pure Tfementioning

confidence: 99%

A New 2,2,2-Trifluoroethanol Model for Molecular Dynamics Simulations

Fioroni¹,

Burger²,

Mark³

et al. 2000

J. Phys. Chem. B

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108

120

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A new model for 2,2,2-trifluoroethanol is proposed. It is a 7-atom model with the methylene group treated as an united atom. The model was optimized to reproduce the physicochemical properties of the pure liquid. The properties of the new model were compared with the available experimental data over a range of temperatures. Furthermore, mixtures with the SPC water model were simulated to assess the ability to reproduce available thermodynamic and kinetic data as well as dielectric properties. The model provides a good agreement with experimental data for the neat liquid and for mixtures with water.

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“…Electronic mail: tcc.chan@polyu.edu.hk found in computer simulations and theoretical studies. [4][5][6][7] Although many modified SE relations have been developed, it appears insofar that none could satisfactorily account for a broad range of diffusivities. The SE relation and its modifications have been reviewed by Cussler 8 and Reid et al 9 The other major approach in diffusion study is Enskog's kinetic theory, which takes binary collisions of molecules into account.…”

Section: Introductionmentioning

confidence: 99%

Diffusion of aromatic compounds in nonaqueous solvents: A study of solute, solvent, and temperature dependences

Chan

Tang

2013

The Journal of Chemical Physics

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Tracer diffusivities (limiting mutual diffusion coefficients) of nonassociated aromatic compounds in n-hexane and cyclohexane have been measured at 298.2 K by Taylor's dispersion method. These new data, together with other diffusivities of nonassociated pseudoplanar solutes reported in the literature, are used to determine the separate effects of solute and solvent on tracer diffusion. The data show that for a given pseudoplanar solute diffusing in different solvents at 298.2 K, the tracer diffusivity is dependent not only on the fractional viscosity of the solvent but also on a function of the solvent's molar density, molecular mass, and free volume fraction. For different pseudoplanar aromatic solutes diffusing in a particular solvent at a constant temperature, there is a linear relationship between the reciprocal of the tracer diffusivity and the molecular volume of the solutes. The results are discussed in respect to relevant theories and experimental studies in the literature. An idealized relation, developed on the basis of the Einstein equation by incorporating the newly found solute and solvent dependences, is capable of describing a total of 176 diffusivities of nonassociated pseudoplanar solutes in various solvents at different temperatures to within an average error of ±2.8%. © 2013 AIP Publishing LLC. [http://dx

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On the validity of Stokes' law at the molecular level

Cited by 58 publications

References 24 publications

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

A New 2,2,2-Trifluoroethanol Model for Molecular Dynamics Simulations

Diffusion of aromatic compounds in nonaqueous solvents: A study of solute, solvent, and temperature dependences

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