Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins.

Linear and nonlinear dielectric responses of solutions of intrinsically disordered proteins (IDPs) were analyzed by combining molecular dynamics simulations with formal theories. A large increment of the linear dielectric function over that of the solvent is found and related to large dipole moments of IDPs. The nonlinear dielectric effect (NDE) of the IDP far exceeds that of the bulk electrolyte, offering a route to interrogate protein conformational and rotational statistics and dynamics. Conformational flexibility of the IDP makes the dipole moment statistics consistent with the gamma/log-normal distributions and contributes to the NDE through the dipole moment's non-Gaussian parameter. The intrinsic non-Gaussian parameter of the dipole moment combines with the protein osmotic compressibility in the nonlinear dielectric susceptibility when dipolar correlations are screened by the electrolyte. The NDE is dominated by dipolar correlations when electrolyte screening is reduced.

Electrophoretic Mobility of Nanoparticles in Water.

Classical equations for colloidal mobility anticipate linear proportionality between the nanoparticle mobility and zeta potential caused by the combined electrostatics of free charges at the nanoparticle and screening bound charges of the polar solvent. Polarization of the interfacial liquid, either spontaneous due to molecular asymmetry of the solvent (water) or induced by nonelectrostatic (e.g., charge-transfer) interactions, is responsible for a static interface charge adding to the overall electrokinetic charge of the nanoparticle. The particle mobility gains a constant offset term that is formally unrelated to the zeta potential. The static charge is multiplied by the static dielectric constant of the solvent in the expression for the electrokinetic charge and is sufficiently large in magnitude to cause electrophoretic mobility of even neutral particles. At a larger scale, nonlinear electrophoresis linked to the interface quadrupole moment can potentially contribute a sufficiently negative charge to a micrometer-size nanoparticle.

Nonlinear dielectric response of dilute protein solutions.

A theory for the nonlinear dielectric response of dilute protein solutions is presented. The field-dependent dielectric function of the protein solution changes linearly with the electric field squared in the lowest order. The slope of this dependence is expressed in terms of the protein dipole moment M0, its volume fraction in solution η0, and the second osmotic virial coefficient. For practical conditions, the nonlinear dielectric response scales as η03M08. This strong dependence on the protein dipole moment and concentration establishes a sharp contrast between the nonlinear response of solvated proteins relative to the surrounding polar solvent. Nonlinear dielectric response can serve as a sensitive tool for monitoring protein conformations and physiological activity.

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, 25, 12479.

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.

Electron Tunneling in Biology: When Does it Matter?

Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport. In addition, universal charge-transport properties are assigned to all proteins, making protein identity, flexibility, and dynamics insignificant. This paradigm is challenged by dynamical models of electron transfer, showing that the electron hopping rate is constant within the crossover distance R* ≃ 12 Å, followed with an exponential falloff at longer distances. If this hypothesis is fully confirmed, natural and man-made energy chains for electron transport should be best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover distance. Changes in protein flexibility between forward and backward transitions contribute to vectorial charge transport. For biological energy chains, charge transport through proteins is not defined by universal parameters, and protein identity matters.

From Single-Particle to Collective Dynamics in Supercooled Liquids.

It has been recognized recently that the considerable difference between photon correlation (PCS) and dielectric (BDS) susceptibility spectra arises from their respective association with single-particle and collective dynamics. This work presents a model that captures the narrower width and shifted peak position of collective dynamics (BDS), given the single-particle susceptibility derived from PCS studies. Only one adjustable parameter is required to connect the spectra of collective and single-particle dynamics. This constant accounts for cross-correlations between molecular angular velocities and the ratio of the first- and second-rank single-particle relaxation times. The model is tested for three supercooled liquids, glycerol, propylene glycol, and tributyl phosphate, and is shown to provide a good account of the difference between BDS and PCS spectra. Because PCS spectra appear to be rather universal across a range of supercooled liquids, this model provides a first step toward rationalizing the more material-specific dielectric loss profiles.

Reorganization energy of electron transfer.

The theory of electron transfer reactions establishes the conceptual foundation for redox solution chemistry, electrochemistry, and bioenergetics. Electron and proton transfer across the cellular membrane provide all energy of life gained through natural photosynthesis and mitochondrial respiration. Rates of biological charge transfer set kinetic bottlenecks for biological energy storage. The main system-specific parameter determining the activation barrier for a single electron-transfer hop is the reorganization energy of the medium. Both harvesting of light energy in natural and artificial photosynthesis and efficient electron transport in biological energy chains require reduction of the reorganization energy to allow fast transitions. This review article discusses mechanisms by which small values of the reorganization energy are achieved in protein electron transfer and how similar mechanisms can operate in other media, such as nonpolar and ionic liquids. One of the major mechanisms of reorganization energy reduction is through non-Gibbsian (nonergodic) sampling of the medium configurations on the reaction time. A number of alternative mechanisms, such as electrowetting of active sites of proteins, give rise to non-parabolic free energy surfaces of electron transfer. These mechanisms, and nonequilibrium population of donor-acceptor vibrations, lead to a universal phenomenology of separation between the Stokes shift and variance reorganization energies of electron transfer.

Effect of Water Deuteration on Protein Electron Transfer.

Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration. H/D substitution changes the rate constant pre-exponential factor in the regime of electron transfer controlled by medium dynamics. Switching from light to heavy water increases the effective medium relaxation time. The effect is caused by both a global change in the flexibility of the protein backbone and locally stronger hydrogen bonds to charged residues.

Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin.

One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.

Multiparticle orientational correlations are responsible for the nonlinear dielectric effect: Analysis of temperature-dependent measurements for glycerol.

The nonlinear dielectric effect (NDE) is traditionally viewed as originating from saturation of the response of individual dipoles in a strong electric field. This mean-field view, mathematically described by the Langevin saturation function, predicts enhanced dielectric saturation at lower temperatures. In contrast, recent experiments for glycerol have shown a sharp increase of the NDE with increasing temperature. The formalism presented here splits the NDE into a sum of a term representing binary correlations of dipolar orientations and terms referring to three- and four-particle orientational correlations. Analysis of experimental data shows that the contribution of three- and four-particle correlations strongly increases at elevated temperatures. The mean-field picture of dielectric saturation as the origin of the NDE is inconsistent with observations. A positive NDE (increment of the field-dependent dielectric constant) is predicted for low-concentration solutions of polar molecules in nonpolar solvents. The dependence of the NDE on the concentration of the polar component is polynomial.

War and peace between electrostatic and van der Waals forces regulate translational and rotational diffusion.

In the Stokes-Einstein picture, diffusion of a Brownian particle or a molecule in a liquid solvent is caused by unbalanced fluctuations of osmotic forces on different sides of the particle. When the particle carries a charge or a higher multipolar moment, this picture is amended by fluctuations of electrostatic forces producing dielectric friction. Dielectric friction slows down both the translational and rotational diffusion. While this picture is well established and is physically sound, standard theories grossly overestimate the magnitude of dielectric friction for small dipolar solutes and larger colloidal particles, such as proteins. Motivated by recent simulation studies, this Perspective discusses the interplay between osmotic (van der Waals) and electrostatic forces in promoting molecular and colloidal diffusion. Much can be learned about microscopic friction mechanisms from statistical and dynamical correlations between osmotic and electrostatic forces.

Conformational dynamics modulating electron transfer.

Diffusional dynamics of the donor-acceptor distance are responsible for the appearance of a new time scale of diffusion over the distance of electronic tunneling in electron-transfer reactions. The distance dynamics compete with the medium polarization dynamics in the dynamics-controlled electron-transfer kinetics. The pre-exponential factor of the electron-transfer rate constant switches, at the crossover distance, between a distance-independent, dynamics-controlled plateau and exponential distance decay. The crossover between two regimes is controlled by an effective relaxation time slowed down by a factor exponentially depending on the variance of the donor-acceptor displacement. Flexible donor-acceptor complexes must show a greater tendency for dynamics-controlled electron transfer. Energy chains based on electron transport are best designed by placing the redox cofactors near the crossover distance.

Ionic mobility driven by correlated van der Waals and electrostatic forces.

Classical theories of dielectric friction make two critical assumptions: (i) friction due to van der Waals (vdW) forces is described by hydrodynamic drag and is independent of the ionic charge and (ii) vdW and electrostatic forces are statistically independent. Both assumptions turn out to be incorrect when tested against simulations of anions and cations with varying charge magnitude dissolved in water. Both the vdW and electrostatic components of the force variance scale linearly with the ionic charge squared. The two components are strongly anticorrelated producing simple relations for the total force variance in terms of self-variances. The inverse diffusion constant scales linearly with the charge squared. Solvation asymmetry between cations and anions extends to linear transport coefficients.

Strong increase of correlations in liquid glycerol observed by nonlinear dielectric techniques.

Nonlinear dielectric measurements are an important tool to access material properties and dynamics concealed in their linear counterparts, but the available data are often intermittent and, on occasion, even contradictory. Employing and refining a recently developed technique for high ac field dielectric measurements in the static limit, we ascertain nonlinear effects in glycerol over a wide temperature range from 230 to 320 K. We find that the temperature dependence of the Piekara factor a, which quantifies the saturation effect, changes drastically around 290 K, from ∂a/∂T = +1.4 to -130 in units of 10-18 V2 m-2 K-1. These high values of |a| quantify not only elevated dielectric saturation effects but also indicate a temperature driven increase in higher-order orientational correlations and considerable correction terms with respect to the central limit theorem. No signature of this feature can be found in the corresponding low field data.

Anomalously Small Reorganization Energy of the Half Redox Reaction of Azurin.

Small values of the reorganization energy, 0.2-0.3 eV, were reported by electrochemical kinetic measurements for the half redox reaction of the redox-active protein azurin. This theoretical study explores possible mechanisms for the low activation barrier for electrochemical protein electron transfer: (1) electronic polarizability of the active site, (2) altering protonation states of far-away histidine residues not directly connected to the active site, and (3) a partial desolvation of the protein when attached to the electrode. The last mechanism provides the most robust explanation of the observations. Constraints imposed by the protein fold on its ability to sample the configuration space lead to the breakdown of the fluctuation-dissipation relation (FDR) and a strong separation of the Stokes-shift and variance reorganization energies. The resulting nonergodic kinetic reorganization energy observed experimentally is significantly lowered compared to predictions of standard models based on Gibbsian statistics and the FDR. The fast rate of protein electron transfer is directly related to the ability of the protein scaffold to maintain nonequilibrium statistics of electrostatic fluctuations projected on the electron-transfer reaction coordinate.

Reorganization Energy of Electron Transfer in Ionic Liquids.

Bandshape analysis of charge-transfer optical bands in room-temperature ionic liquids (ILs) was performed to extract the reorganization energy of electron transfer. Remarkably, the reorganization energies in ILs are close to those in cyclohexane. This result runs against common wisdom in the field since conducting ILs, which are characterized by an infinite static dielectric constant, and nonpolar cyclohexane fall to the opposite ends of the polarity scale based on their dielectric constants. Theoretical calculations employing structure factors of ILs from molecular dynamics simulations support the low values of the reorganization energy. Standard dielectric arguments do not apply to solvation in ILs, and nonergodic reorganization energies are required for a quantitative analysis.

Electron-Induced Proton Transfer.

The pathway of activationless proton transfer induced by an electron-transfer reaction is studied theoretically. Long-range electron transfer produces highly nonequilibrium medium polarization that can drive proton transfer through an activationless transition during the process of thermalization, dynamically altering the screening of the electron-proton Coulomb interaction by the medium. The cross electron-proton reorganization energy is the main energy parameter of the theory, which exceeds in magnitude the proton-transfer reorganization energy roughly by the ratio of the electron-transfer to proton-transfer distance. This parameter, which can be either positive or negative, is related to the difference in pKa values in two electron-transfer states. The relaxation time of the medium is on the (sub)picosecond time scale, which establishes the characteristic time for activationless proton transfer. Microscopic calculations predict substantial retardation of the collective relaxation dynamics compared to the continuum estimates due to the phenomenology analogous to de Gennes narrowing. Nonequilibrium medium configuration promoting proton transfer can be induced by either thermal or photoinduced charge transfer.

Ewald sum corrections in simulations of ion and dipole solvation and electron transfer.

Periodic boundary conditions and Ewald sums used in standard simulation protocols require finite-size corrections when the total charge of the simulated system is nonzero. Corrections for ion solvation were introduced by Hummer, Pratt, and García, [J. Chem. Phys. 107, 9275 (1997)]. The latter approach is extended here to derive finite-size correction for the Stokes-shift and reorganization energy applied to electron-transfer reactions. The same correction term, scaling inversely with the box size, adds to the reorganization energy from the energy-gap variance but is subtracted from the reorganization energy calculated from the Stokes shift. Finite-size corrections thus widen the gap between these two quantities, which were recently found to diverge for protein electron transfer. Corrections to the free energy of dipole solvation and the variance of the electric field scale as m2/L3 with the solute dipole m and the box size L.

Enhanced Molecular Diffusivity through Destructive Interference between Electrostatic and Osmotic Forces.

Molecular charge asymmetrically distributed in a diffusing tagged particle causes a nonzero electrostatic force balanced by an opposing van der Waals (vdW) force. Fluctuations of electrostatic and vdW forces are highly correlated, and they destructively interfere in the force variance. This phenomenology is caused by the formation of a structurally frozen hydration layer for a particle diffusing in water and is responsible for a substantial speedup of translational diffusion compared to traditional theories of dielectric friction. Diffusion of proteins is insensitive to charge mutations, while smaller particles with asymmetric charge distribution can show a strong dependence of translational and rotational diffusion on molecular charge. Dielectric calculations of the electrostatic force require low values of ≃5 for the effective dielectric constant of interfacial water to be consistent with simulations.