Solvent Shear Viscosity Research Articles

Transport properties of zwitterion glycine, diglycine, and triglycine in water

Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work, we have studied about the diffusion of zwitterion glycine, zwitterion diglycine and zwitterion triglycine in SPC/E model of water using classical molecular dynamics. Self and binary diffusion coefficients of aqueous solution of these molecules have been estimated using Einstein’s method. Our results agree with experimental data reported in literatures. Temperature dependency of diffusion of glycine in water has been explored using estimated values of self and binary diffusion coefficients at four different temperature. Effects of peptide bond formation in diffusion has been studied using peptide chain composed of up to three monomers of glycine. The system-size dependence of diffusion coefficient has been studied and the shear viscosity of solvent and system has been calculated. Also, the diffusion coefficient of zwitterion glycine in other water model TIP4P/2005 has been estimated. The structure of the system has been analyzed using radial distribution function of different atoms.

Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.

We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction kB T/6 ηV with kB Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.

Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution

Recently, the method of enveloping distribution sampling (EDS) to efficiently obtain free enthalpy differences between different molecular systems from a single simulation has been generalized to compute free enthalpy differences between different conformations of a system [Z. X. Lin, H. Y. Liu, S. Riniker, and W. F. van Gunsteren, J. Chem. Theory Comput. 7, 3884 (2011)]. However, the efficiency of EDS in this case is hampered if the parts of the conformational space relevant to the two end states or conformations are far apart and the conformational diffusion from one state to the other is slow. This leads to slow convergence of the EDS parameter values and free enthalpy differences. In the present work, we apply the EDS methodology to a challenging case, i.e., to calculate the free enthalpy difference between a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix of a hexa-β-peptide in solution from a single simulation. No transition between the two helices was detected in a standard EDS parameter update simulation, thus enhanced sampling techniques had to be applied, which included adiabatic decoupling (AD) of solute and solvent motions in combination with increasing the solute temperature, and lowering the shear viscosity of the solvent. AD was found to be unsuitable to enhance the sampling of the solute conformations in the EDS parameter update simulations. Lowering the solvent shear viscosity turned out to be useful during EDS parameter update simulations, i.e., it did speed up the conformational diffusion of the solute, more transitions between the two helices were observed. This came at the cost of more CPU time spent due to the shorter time step needed for simulations with the lower solvent shear viscosity. Using an improved EDS parameter update scheme, parameter convergence was five-fold enhanced. The resulting free enthalpy difference between the two helices calculated from EDS agrees well with the result obtained through direct counting from a long MD simulation, while the EDS technique significantly enhances the sampling of both helices over non-helical conformations.

Resolving the Turnover of Temperature Dependence of the Reaction Rate in Barrierless Isomerization

In this work, the temperature dependence of the barrierless cis−trans isomerization reaction in the excited state of 1,1‘-diethyl-4,4‘-cyanine (1144-C) has been investigated. Transient absorption kinetics as well as transient absorption spectra were measured at different temperatures and viscosities, making it possible to obtain dynamic information regarding the isomerization process at constant viscosity. Our experimental results suggest a crossover of the reaction rate from a negative temperature dependence (decreasing relaxation rate with increasing temperature) at low viscosities to a positive temperature dependence at higher viscosities. This crossover of the relaxation rate was observed to occur at ∼17 cP; the range of viscosities studied was from ∼2 to ∼30 cP. We discuss the origin of this turnover behavior in terms of the BFO (Bagchi, Fleming, and Oxtoby) theory and show that the turnover can be explained by this model, as the competition between two processes following the excitation, namely transport of the population on the excited-state surface and internal conversion. We also discuss the validity of using the solvent shear viscosity as a measure of the friction experienced by the isomerizing group. Our results suggest that, at least for 1144-C in short-chain alcohols (methanol to hexanol), the shear viscosity can indeed be used as a reasonable measure of the solvent friction in the barrierless isomerization process.

Pressure tuning of solvent viscosity for the formation of twisted intramolecular charge-transfer state in 4,4′-diaminodiphenyl sulfone in alcohol solution

The effect of solvent shear viscosity on the formation of twisted intramolecular charge-transfer (TICT) state in the excited state for 4,4′-diaminodiphenyl sulfone (DAPS) in three linear alcohol solvents has been investigated by measuring the picosecond fluorescence lifetime as a function of pressure. At lower pressures the kinetics of the TICT-state formation is controlled by solvent relaxation. While with increasing pressure, the reaction path shifts toward the ‘‘high viscosity regime’’ in which the reaction proceeds through the nonrelaxed path independent of solvent coordinate on the free energy surface of the S1 excited state. This behavior could be called as ‘‘pressure tuning effect’’ of solvent viscosity. The power law parameter (α) is used as a measure of the viscosity dependence. For the high viscosity regime, α=0.2 can be attributed to the intrinsic viscosity dependence for barrier crossing.

Size Dependence of Tracer Diffusion in Supercooled Liquids

We have determined by forced Rayleigh scattering the diffusion coefficients D of several photochromic tracers with van der Waals radii between 0.38 and 8 nm (the largest ones being photolabeled polystyrene micronetworks) in 10 glass-forming liquids at temperatures between the glass temperature Tg and ∼1.2Tg. The results were analyzed in terms of power law plots, D(T) ∝ T/η(T)ξ, where η is the solvent shear viscosity, and temperature shifts, D(T) ∝ T/η(T + ΔT). The shift ΔT was related with the width of the rotational correlation time distribution via the time−temperature superposition principle.

Universality in Isomerization Reactions in Polar Solvents

Recently it has been shown by Singh and Robinson (SR) that universality and scaling occur in the van der Zwan−Hynes (ZH) model of dipole isomerization reactions near a critical point. This advance in the understanding of chemical reactions was accomplished through the discovery of an analogy of this critical point with the one in the van der Waals equation of state for an imperfect gas. In the present paper, the experimental data of Onganer et al. on the cis−trans photoisomerization of merocyanine 540 in n-alkyl alcohol and n-alkanenitrile solvents, as a function of the solvent shear viscosity and temperature, is analyzed in terms of the ZH model. This model, based on the Grote−Hynes theory, uses a non-Markovian solvent friction characterized by a reactant−solvent coupling strength parameter β, the solvent inertial response time r, and the solvent frictional or viscous response time x. It is found that the photoisomerization data with alcohol solvents fit the ZH model reasonably well, and the fitted param...

High-Pressure Studies on the Excited-State Intramolecular Charge Transfer of 4-(N,N-Dimethylamino)triphenylphosphine in Alcohols

The influence of solvent viscosity on the intramolecular charge-transfer (CT)-state formation in the excited S1 state for 4-(N,N-dimethylamino) triphenylphosphine (DMATP) in alcohol solvents has been investigated by measuring the steady-state and time-resolved fluorescence spectra at high pressures. The kinetic mechanism of the intramolecular CT reaction has been examined as a function of solvent shear viscosity. In the lower viscosity region the reaction is controlled by the solvent relaxation. With increasing pressure, the reaction path shifts toward the “high-viscosity regime” in which the molecule moves along the nonrelaxed path on the free energy surface. The viscosity dependence of α ≅ 0.33, where α is the power law parameter, can be interpreted as the extreme value in which the reaction is controlled by the dynamic solvent effect due to intrinsic collisional interaction of barrier crossing. The coupling between the intramolecular CT-state formation dynamics of DMATP and the solvent relaxation dynam...

Dynamical solvation effects on the cis-trans isomerization reaction: photoisomerization of merocyanine 540 in polar solvents

The fluorescence quantum yield, Φ f , of merocyanine 540 in n-alkyl alcohol and n-alkanenitrile solvents was measured as a function of temperature and solvent shear viscosity at ambient pressure. The Strickler-Berg equation was used to calculate the radiative rate, k r , from the absorption and fluorescence spectra. Te values of Φ f and k r were used to obtain the rate of photoisomerization, k iso . This rate is consistent with the Smoluchowski limit of the Kramers theory for activated barrier crossing. The intrinsic barrier height, which is taken to be equal to the difference between the single-solvent activation energy and the viscosity activation energy, is lower in alcohols than in nitriles

High Pressure NMR Studies of the Kramers Turnover for Reactions in Liquid Solutions

AbstractAdvantages of NMR techniques to obtain the rate data for simple isomerizations in liquid solutions and advantages of using high pressure to change the viscosity of the solution are discussed. After a brief overview of our experiments on cyclohexane, 1,1‐difluorocyclohexane, and N,N‐dimethyltrichloroacetamide, the discussion focuses on the ethylene rotation in μ‐cyclopentadienylethylenetetrafluoroethylene‐rhodium in several solvents. – The experimental data, as interpreted in terms of stochastic models of isomerization reactions, indicate a Kramers turnover for the pressure dependence of the rotation of coordinated ethylene in the Rh complex in solution. In fact, the observation of the energy‐controlled regime in this system may be the consequence of the so‐called heavy metal atom bottleneck effect which reduces the intramolecular energy transfer within the molecule. The experimental dependences of the rates upon solvent viscosity and/or Enskog collision frequency show that solvent shear viscosity represents only an approximative measure of the coupling of the reaction coordinate to the medium.

Picosecond photodissociation and geminate radical recombination in alkane solutions of tetraphenylhydrazine

Tetraphenylhydrazine is observed to dissociate in less than 1 ps in alkane solution after 288 nm excitation. The diphenylaminyl radicals produced undergo rapid geminate recombination at a rate proportional to solvent shear viscosity. A strong magnetic field decreases the recombination yield. A model for the recombination is proposed which involves initial separation of nitrogen atoms and recombination of the radicals by rotational rather than translational motion alone. In a different approach the rates of radical recombination are also well described by Kramers' model of barrier crossing.

High pressure nuclear magnetic resonance study of the dynamical solvent effects on the rotation of coordinated ethylene in an organometallic compound

The effect of temperature and pressure on the internal rotation rate of coordinated ethylene in π–cyclopentadienylethylenetetrafluoroethylene–rhodium in liquid solution has been investigated by using 1H Fourier transform (FT) nuclear magnetic resonance spectroscopy. The solvents used in this study are n–pentane–d12, carbon disulfide, and methylcyclohexane–d14. The activation energy (13.4±0.2 kcal/mol) for the internal rotation of ethylene is independent of solvent and pressure as determined from conventional Arrhenius type plots and isoviscosity plots. It is found that the rotation of the coordinated ethylene is initially accelerated by pressure, reaches a maximum and then decreases at high pressure. The strong pressure dependence of the observed activation volume for the rotation suggests a strong collisional contribution to the activation volume and the presence of dynamical solvent effects. The experimental data, as interpreted in terms of stochastic models of isomerization reactions, indicate a Kramers’ turnover for the pressure dependence of the rotation of coordinated ethylene in the Rh complex in solution. The observation of the energy-controlled regime in this system may be the consequence of the so-called heavy metal atom bottleneck effect which reduces the intramolecular energy transfer within the molecule. The experimental dependences of the rates upon solvent viscosity and/or Enskog collision frequency show that solvent shear viscosity represents only an approximative measure of the coupling of the reaction coordinate to the medium.

Picosecond ground-state rotational diffusion of merocyanine 540 in polar solvents

The ground-state rotational diffusion of merocyanine 540 in polar solvents was studied by using picosecond polarized transient bleaching. The rotational diffusion time τ rot was obtained from fits of a single exponential to the absorption anisotropy. The value of τ rot was 78±5 ps in acetone, 100±24 ps in methanol, 190±19 ps in dimethylformamide, 270±00 ps in ethanol, 490±50 ps in 1-propanol, 500±10 ps in dimethyl sulfoxide, and 700±100 ps in 1-butanol. The dependence of the observed rotational diffusion time on the solvent's shear viscosity was the same in protic and aprotic solvents. The reorientational dynamics of this dye in these solvents can be explained by hydrodynamics for a prolate ellipsoid using stick boundary conditions

High-pressure NMR study of the dynamical solvent effects on the rotation of coordinated ethylene in (π-C5H5)Rh(C2H4)2

Preliminary results of the high-pressure NMR study show that the rate of rotation of coordinated ethylene groups in (π-C5H5)Rh(C2H4)2 dissolved in benzene and chloroform solvents increases with increasing pressure. The rate constants obtained in different solutions correlate with the solvent shear viscosity, and the viscosity dependence of the rate constant indicates inertial behavior in agreement with the prediction of the Skinner and Wolynes model.

Dielectric friction and dielectric dispersion in electrolyte solutions with spin

A self-consistent continuum model of dielectric friction on a moving ion is developed in which the only adjustable parameters are the hydrodynamic boundary conditions and a ’’rotational viscosity’’ hR. Ion mobility and the solution dielectric properties are calculated as a function of ion size, ion charge, low and high frequency dielectric constants of the solvent, dielectric relaxation time of the solvent, rotational viscosity, and solvent shear viscosity. The consequences of varying hR are investigated: For hR→∞ the continuum theory analyzed by Hubbard and Onsager (HO) is recovered; for small hR, however, the polarization and ’’spin’’ fields in the solvent near the ion differ significantly from the HO model. While this has remarkably little effect on calculated ionic mobilities, the solution dielectric properties are noticeably altered. In particular, the kinetic dielectric decrement diverges as ln hR as hR vanishes.