Solution of the linearized Poisson-Boltzmann equation

Improved methods are formulated for solution of the linearized Poisson-Boltzmann equation, to be used in conjunction with electronic structure calculation on a solute together with dielectric continuum representation of the salt-containing solvent. Volume polarization effects due to quantum mechanical penetration of solute charge density outside the cavity that excludes solvent are treated by exact and by approximate methods analogous to those previously developed for the salt-free case. With boundary element approaches, exact solutions lead to coupled equations for a pair of cavity surface distributions that mimic the polarization of the solvent dielectric and the ionic atmosphere. A novel means is found to effectively decouple these equations, yielding more efficient practical methods for their numerical solution. Detailed comparisons are given to related boundary element formulations previously reported in the literature, which neglect volume polarization, and analogous decoupling is also found for the pair of surface distributions invoked there. Illustrative results are provided for a simple spherical example.     

Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute∕liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response.     

Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time‐dependent charges

A boundary element formulation of continuum electrostatics is used to examine time‐independent dielectric relaxation and screening in two proteins, and time‐dependent relaxation in two simpler solutes. Cytochrome c oxidation is modeled by inserting partial charges on the heme, using one to three dielectric regions in the protein. It was suggested recently that for charge insertion on a protein‐bound ligand, all or part of the ligand should be treated as a cavity within the protein medium. Here, the effect of an internal cavity surrounding the central heme atoms is examined, considering separately the static and relaxation (or reorganization) free energies. The former is the free energy to remove the redox electron while maintaining the rest of the structure and charge distribution fixed; the latter is the free energy associated with the relaxation into the product state after the corresponding constraints are released. The effect of the cavity is found to be small for the static free energy, while for the relaxation free energy it is large, as polarization of groups immediately around the heme dominates the relaxation. If the protein surface groups are treated as a distinct medium with a dielectric of 25 (as suggested by recent molecular dynamics simulations), the relaxation free energy decreases significantly (from −37.0 to −43.9 kcal/mol), compared to a model where the whole protein has a dielectric constant of two. Therefore, with this model, although polarization of groups immediately around the heme still dominates the relaxation, polar groups near the protein surface also contribute significantly, and solvent negligibly. The screening of an applied field within myoglobin is calculated, with the protein surrounded by either a low‐dielectric or a high‐dielectric glass. In the vicinity of the CO ligand, the screening is approximately isotropic with a low‐dielectric glass. It is anisotropic with a high‐dielectric glass, but the applied and local fields are still approximately parallel. This has implications for experiments that probe dielectric screening in proteins with the newly developed technique of vibrational Stark spectroscopy: with a high‐dielectric glass, a single, rotationally averaged screening factor can be used, the local field being about 1.65 times the applied field. Finally, we calculate the time‐dependent relaxation in response to instantaneous charge insertion within a spherical cavity in a Debye solvent, and to photoexcitation of a tryptophan solute, illustrating the extension of the boundary element formulation to time‐dependent problems. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 290–305, 2001     

Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects

A method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system. No limitations are imposed on the composition and dimension of the solute, on the goodness of the corresponding wavefunction, or on the shape of the cavity in the dielectric. Several levels of approximation, which evidence the effect of self-polarization of the system of surface charges, the influence of the tails of the solute charge distribution going beyond the limits of the cavity, and the effect of the polarization of the solute, are examined and discussed.     

Electrokinetic actuation of an uncharged polarizable dielectric droplet in charged hydrogel medium

Electrokinetic transport of an uncharged nonconducting microsized liquid droplet in a charged hydrogel medium is studied. Dielectric polarization of the liquid drop under the action of an externally imposed electric field induces a non-homogeneous charge density at the droplet surface. The interactions of the induced surface charge of the droplet with the immobile charges of the hydrogel medium generates an electric force to the droplet, which actuates the drop through the charged hydrogel medium. A numerical study based on the first principle of electrokinetics is adopted. Dependence of the droplet velocity on its dielectric permittivity, bulk ionic concentration, and immobile charge density of the gel is analyzed. The surface conduction is significant in presence of charged gel, which creates a concentration polarization. The impact of the counterion saturation in the Debye layer due to the dielectric decrement of the medium is addressed. The modified Nernst–Planck equation for ion transport and the Poisson equation for the electric field is considered to take into account the dielectric polarization. A quadrupolar vortex around the uncharged droplet is observed when the gel medium is considered to be uncharged, which is similar to the induced charge electroosmosis around an uncharged dielectric colloid in free-solution. We find that the induced charge electrokinetic mechanism creates a strong recirculation of liquid within the droplet and the translational velocity of the droplet strongly depends on its size for the dielectric droplet embedded in a charged gel medium.     

Electric polarization effects on the electronic spectral shift of centrosymmetric compounds

The classic dielectric dipolar Onsager model was extended to include quadrupolar interactions between solute molecules and solvents with different polarities. A multiparametric solvatochromic expression, based on the point quadrupole moment inside a spherical cavity embedded in a dielectric continuum, is applied to centrosymmetric sulfonamide porphyrins, zinc tetraphenyl porphyrin, squaraine and 9,10-dicyanoanthracene, in order to account for the quadrupolar polarization effect of solute molecules. The reaction field polarity functions created respectively by dipole and quadrupole moments are compared and found to be linearly correlated.     

Electrostatic contribution to the ion solvation energy: cavity effects

Ion solvation process has been analysed for the spherically symmetrical system where an ion is located inside a cavity surrounded by an isotropic nonlocal dielectric medium. It has been proven that for any dielectric properties of the medium, the electric field outside the cavity as well as the ion solvation energy depend only on the total ion charge but not of the particular distribution of the ion charge density inside the cavity. These characteristics remain unchanged if the charge is displaced from the external boundary of the cavity into it. Analytical formulas for them have been derived for a particular model of the nonlocal dielectric function. Comparison of results for the solvation energy on the basis of this new theory and of the conventional approach (disregarding the existence of the cavity) shows a significant difference between their predictions if the ion charge is displaced inside the ion cavity.     

New formulation and implementation for volume polarization in dielectric continuum theory

In the use of dielectric continuum theory to model bulk solvation effects on the electronic structure and properties of a solute, volume polarization contributions due to quantum mechanical penetration of the solute charge density outside the cavity nominally enclosing it are known to be significant. This work provides a new formulation and implementation of methods for solution of the requisite Poisson equation. In previous formulations the determination of the surface polarization contribution required evaluation of the difficult to calculate electric field generated by the volume polarization. It is shown that this problematic quantity can be eliminated in favor of other more easily evaluated quantities. That formal advance also opens the way for a more efficient apparatus to be implemented for calculation of the direct contribution of volume polarization to the solvation energy. The new formulation and its practical implementation are described, and illustrative numerical results are given for several neutral and ionic solutes to study the convergence and precision in practice.     

Dipolar response of hydrated proteins

The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins in solution. We calculate the effective dielectric constant representing the average dipole moment induced at the protein by a uniform external field. The dielectric constant shows a remarkable variation among the proteins, changing from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility, that is a dia-electric dipolar response and negative dielectrophoresis. It means that ubiquitin, carrying an average dipole of ?240 D, is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The study suggests that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending ~2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is seen for the electrostatic potential produced by the hydration water inside the protein. The analysis of numerical simulations suggests that the polarization of the protein-water interface is highly heterogeneous and does not follow the standard dielectric results for cavities carved in dielectrics. The polarization of the water shell gains in importance, relative to the intrinsic protein dipole, at high frequencies, above the protein Debye peak. The induced interfacial dipole can be either parallel or antiparallel to the protein dipole, depending on the distribution of the protein surface charge. As a result, the high-frequency absorption of the protein solution can be either higher or lower than the absorption of water. Both scenarios have been experimentally observed in the THz window of radiation.     

An automatic three-dimensional finite element mesh generation system for the Poisson–Boltzmann equation

We present an automatic three-dimensional mesh generation system for the solution of the Poisson–Boltzmann equation using a finite element discretization. The different algorithms presented allow the construction of a tetrahedral mesh using a predetermined spatial distribution of vertices adapted to the geometry of the dielectric continuum solvent model. A constrained mesh generation strategy, based on Bowyer's algorithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of triangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interface. This will allow an accurate calculation of the induced polarization charge to be carried out while maintaining a sparse grid structure in the rest of the computational space. The inclusion of an ionic boundary at some finite distance from the dielectric interface can be automatically achieved as the grid point distribution outside the solute molecule is constructed using a set of surfaces topologically equivalent to this boundary. The meshes obtained by applying the algorithm to real molecular geometries are described. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1570–1590, 1997     

Electro-osmosis of the second kind near the heterogeneous ion-exchange membrane

The features of concentrated polarization by an electric current passing through an ion-exchange membrane, with heterogeneous ionic conductivity, are considered in this paper. A space charge appears inside the concentrated polarization zone caused by a strong electric field. In the case of a surface with nonuniform conductivity, the tangential to the surface component of electric field occurs. The action of the tangential component on the induced space charge produces electro-osmotic whirlwinds, which change the main characteristics of the concentrated polarization and increase the current through the membrane.

The peculiarities of the polarization processes are analyzed for laminar and turbulent flows of liquid along the interface. It has been shown that a combination of electro-osmotic convection with turbulent pulsation leads to a significant rise in current above the limiting value.     

Simulation of volume polarization for the influence of solvation on chemical shielding

The effect of bulk dielectric solvation on chemical shielding at nitrogen in CH₃CN is studied with reaction field theory. A previous work has demonstrated the strong influence on this property from volume polarization, which describes that part of the reaction field arising from solute charge density penetrating outside its cavity. The essentially exact treatment of volume polarization used in that work is computationally demanding, and a more facile method for simulation of the volume polarization has recently been proposed. It is found in the present work that this simulation of the volume polarization yields results in excellent agreement with the essentially exact treatment of the strong volume polarization effects on nitrogen shielding in CH₃CN.Contribution to the Jacopo Tomasi Honorary Issue     

Towards a modellisation of the solvation energy in multi-component solvents. The interesting case of a charged solute imbedded in a polymer-containing electrolyte solution

In this paper we propose a mean-field theory to calculate the solvation free energy of a charged solute imbedded in a complex multi-component solvent. We considered a solvent made up of a mixture of small (electrolyte solution) and large (polymer) components. The presence of macromolecules ensures reduced mixing entropy among the different solvent components, an effect due to polymer connectivity. The reduced entropy favours strong preferential distribution of a particular solvent even in the presence of weak preferential solute–solvent interactions. In addition, two energy terms must be considered: (a) the interaction between the solute electrostatic potential and the electrolyte solution and (b) the formation of a polymer–solute interface. Because of the different dielectric permittivity of the solvent components, the electrolyte and polymer distribution functions are strongly coupled: ions, indeed, are more solvated in regions of higher local dielectric permittivity arising from the inhomogeneous mixing of solvent and polymer. We combined together the different energy terms in the framework of the de Gennes free energy functional for polymer solutions along with a generalised Poisson–Boltzmann equation developed for inhomogeneous dielectric media. Moreover, the preferential electrolyte solvation in regions of greater polarity was considered by an extension of the Born equation. Setting the polymer dielectric permittivity smaller than the solvent one and making null the specific polymer–solute interactions, we calculated enhanced electrolyte concentration and reduced polymer concentration near the solute surface on raising the solute surface charge density. The theory shows also the breakdown of the widely used separation between electrostatic and surface tension-dependent contributions to solvation energy when non-ideal mixed solvents are considered. In fact, according to the model, the surface tension of such mixed solvents strongly depends on the solute surface charge density: at high potentials the interfacial tension may increase rather than decrease on raising the polymer volume fraction. The theoretical results have been compared with experimental data on polymer+electrolyte solution surface tension and with solubility data of colloidal particles. The comparison evidences the complex behaviour of multi-component solvents going well beyond the trivial weighted average of the dielectric permittivity and surface tension of the isolated chemical components. Deviations from the simple behaviour predicted by an average picture of multi-component solvents could be understood by developing more sophisticated, but still simple, approaches like that proposed in this paper.Contribution to the Jacopo Tomasi Honorary Issue. This paper is dedicated to Jacopo Tomasi. I learned much of the difficult art of transforming complex problems into simple models after reading his early works on solvation energy.     

Polarization effects on peptide conformations at water–membrane interface by molecular dynamics simulation

The electrostatic image method was applied to investigate the conformation of peptides characterized by different hydrophobicities in a water–membrane interface model. The interface was represented by a surface of discontinuity between two media with different dielectric constants, taking into account the difference between the polarizabilities of the aqueous medium and the hydrocarbon one. The method consists of a substitution of the real problem, which involves the charges and the induced polarization at the surface of discontinuity, by a simpler problem formed with charges and their images. The electric field due to the polarization induced at the surface by charge q was calculated using a hypothetical charge q′ (image of q), symmetrically located on the opposite side of the surface. The value of q′ was determined using the appropriate electrostatic boundary conditions at the surface. By means of this procedure, the effect of the interface can be introduced easily in the usual force field. We included this extension in the computational package that we are developing for molecular dynamics simulations (Thor ). The peptides studied included hydrophilic tetraaspartic acid (Asp–Asp–Asp–Asp), tetralysine (Lys–Lys–Lys–Lys), hydrophobic tetrapeptide (His–Phe–Arg–Trp), an amphiphilic fragment of β-endorphin, and the signal sequence of the E. coli λ-receptor. The simulation results are in agreement with known experimental data regarding the behavior of peptides at the water–membrane interface. An analysis of the conformational dynamics of the signal sequence peptide at the interface was performed over the course of a few nanoseconds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 971–982, 1999     

The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations

A new technique is presented for incorporating hydration forces into molecular mechanics simulations. The method assumes the classical continuum approximation, where a solvated molecule is represented as a low-dielectric cavity of arbitrary shape embedded in a continuous region of high dielectric constant. Electrostatic effects are computed by first calculating the distribution of polarization charge (induced by the configuration of solute fixed charges) at the molecular surface. The hydration force at a particular atom is then found as the sum of the coulombic interaction with the induced surface charge, plus a purely mechanical contribution that arises from the pressure of the polarized solvent as it is pulled toward the solute. A procedure is developed to use the computed hydration forces in conjunction with the CHARMM molecular mechanics package to carry out energy minimizations in which the effects of solvation are explicitly included. This new technique also allows a detailed analysis of the relative balance of coulombic, hydration, and steric energies as a function of molecular conformation. The method is applied to the test case of a zwitterionic tripeptide (LYS-GLY-GLU), and the computational results suggest that hydration effects can play a significant role in determining a stable conformation for a solvated polar molecule. The future application to larger molecules is discussed.     

Electrorheological toners for electrophotography

The electrorheological (ER) behavior of pigment suspensions dispersed in a nonaqueous solvent was examined for their application as liquid toners for electrophotography. In electric fields, particles can align into chains along the field vector by dielectric polarization forces and the suspensions undergo a rapid transition from Newtonian fluids to Bingham bodies. However, the migration and deposition of particles can take place by the electrophoretic effect, because charge control agents are added to liquid toners for fast development. The combined effects of dielectric polarization forces, electrophoretic forces, and hydrodynamic forces make rheological behavior very complicated. To simulate the ER behavior of liquid toners in reprographic processes, viscosity measurements were carried out in electrodes with a honeycomb pattern. Nonuniform electric fields enhance the dipole-dipole interactions between particles and give rise to a striking ER effect. Based on measurements in honeycomb pattern electrodes, new ER toners were developed which can reproduce images with high quality.     

Electrostatic interactions of a neutral dipolar solute with a fused salt: a new model for solvation in ionic liquids

Ionic liquids represent a novel and poorly understood class of solvents, and one challenge in understanding these systems is how one should view the electrostatic character of solute-solvent interactions. The highly structured nature of a fused salt makes a dielectric continuum approximation difficult to implement, and there is no obvious connection between the structure of an individual ion and the polarization character of the medium. We address this problem by making the ansatz that rather than polarizing the medium, the solute may be viewed as intercalating in the charge distribution of the neat liquid such that the solvent screens the electric field of the solute. This approach allows derivation of an analytical expression for the distribution of solvent charge about the solute, and this distribution is found to be a close match to simulation data. The theory also predicts that the electrostatic character of solute-solvent interactions should be determined primarily by the number density of solvent ions, a prediction proven correct by analysis of existing experimental data. The approach represents a new model for the interpretation of solvation phenomena in ionic liquids.     

Polarized states of hybrid aligned nematic layers

Electric polarization arising in hybrid aligned nematic liquid crystal layers with rigid boundary conditions is studied numerically by solving the torques equation and Poisson equation. Three phenomena that give rise to the polarization are taken into account: flexoelectricity, surface polarization and adsorption of ions. The director orientation within the layer, as well as the distribution of electric potential and space charge density are calculated for layers deformed by an external magnetic field. The role of the ionic space charge is investigated. For a particular set of parameters of a model substance, the voltage arising between the layer surfaces varies from 10^-1 V (in an extremely pure nematic) to 10^-3 V (in material with a typical ion concentration). The surface polarization yields an additional voltage (of the order 10^-2 V) nearly independent of the ion concentration. The effect of simultaneous flexoelectric polarization and ion adsorption is evidently different from a linear superposition of their separate contributions. The flexoelectric polarization leads to partial separation of ions of opposite signs. In the case of positive flexoelectric coefficients, a thin sublayer of positive charge arises at the planar-orienting boundary plate. The negative charge is displaced towards the homeotropically aligning plate. The magnitude of this effect increases with the magnetic field. The surface phenomena introduce additional subsurface charges.