Density-functional theory and Monte Carlo simulation study on the electric double layer around DNA in mixed-size counterion systems

Surface charging parameters of charged particles in symmetrical electrolyte solutions

Surface electric charge of dispersed particles is an essential determinant of physicochemical properties, coagulation and flocculation processes, and stability of colloidal solutions. Size-dependence of surface potential, charge density, and total surface charge of suspended charged particles has recently received attention in the literature. Despite the clear significance of understanding such dependence, very few studies have been devoted to this problem, with contradictory results of the relationship type. Currently, there is no analytical formula to represent explicit relationships between surface charging parameters and particle size. This research work is directed at development of accurate physics-based formulas for quantification of curvature-dependence of surface potential, surface charge density, and total surface charge for cylindrical and spherical charged particles immersed in a symmetrical electrolyte solution. First, a non-dimensional approach is adopted to simplify the problems, overcoming the difficulty of dealing with multiple influential variables. Then, to reduce the degrees of freedom of the problems under consideration, Gauss's law is combined with the condition of electro-neutrality in an electrical double layer (EDL). Next, the resulting complex integral equations are solved to construct characteristic curves and to express the dimensionless surface charging parameters explicitly as a function of the dimensionless particle radius. The new theoretical expressions are founded on approximate analytical and numerical solutions of the nonlinear Poisson-Boltzmann (PB) equation in cylindrical and spherical geometries. Afterwards, the solutions of the non-dimensionalized problems are dimensionalized to derive accurate explicit closed-form expressions, describing how surface charging parameters are related to the radius of a charged particle, properties of the solution, and thermodynamic conditions. These analytical formulas enable researchers to properly determine surface potential, surface charge density, total surface charge, and radius of dispersed particles by characterizing only one of them. Finally, the validity of the commonly-held hypothesis that surface charge density is independent of particle size is examined at the end of this study.

Competitive interaction of monovalent cations with DNA from 3D-RISM

The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.

Structure of fully asymmetric mixed electrolytes around a charged nanoparticle: a density functional and simulation investigation

A systematic study on the structure of mixed electrolytes with arbitrary size and charge asymmetry around a charged nanoparticle is carried out using density functional theory and Monte Carlo simulation.

Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments

The ionic atmosphere around a nucleic acid regulates its stability in aqueous salt solutions. One major source of complexity in biological activities involving nucleic acids arises from the strong influence of the surrounding ions and water molecules on their structural and thermodynamic properties. Here, we implement a classical density functional theory for cylindrical polyelectrolytes embedded in aqueous electrolytes containing explicit (neutral hard sphere) water molecules at experimental solvent concentrations. Our approach allows us to include ion correlations as well as solvent and ion excluded volume effects for studying the structural and thermodynamic properties of highly charged cylindrical polyelectrolytes. Several models of size and charge asymmetric mixtures of aqueous electrolytes at physiological concentrations are studied. Our results are in good agreement with Monte Carlo simulations. Our numerical calculations display significant differences in the ion density profiles for the different aqueous electrolyte models studied. However, similar results regarding the excess number of ions adsorbed to the B-DNA molecule are predicted by our theoretical approach for different aqueous electrolyte models. These findings suggest that ion counting experimental data should not be used alone to validate the performance of aqueous DNA-electrolyte models.

Structure of spherical electric double layers with fully asymmetric electrolytes: a systematic study by Monte Carlo simulations and density functional theory

A systematic investigation of the spherical electric double layers with the electrolytes having size as well as charge asymmetry is carried out using density functional theory and Monte Carlo simulations. The system is considered within the primitive model, where the macroion is a structureless hard spherical colloid, the small ions as charged hard spheres of different size, and the solvent is represented as a dielectric continuum. The present theory approximates the hard sphere part of the one particle correlation function using a weighted density approach whereas a perturbation expansion around the uniform fluid is applied to evaluate the ionic contribution. The theory is in quantitative agreement with Monte Carlo simulation for the density and the mean electrostatic potential profiles over a wide range of electrolyte concentrations, surface charge densities, valence of small ions, and macroion sizes. The theory provides distinctive evidence of charge and size correlations within the electrode-electrolyte interface in spherical geometry.

Competitive adsorption and ordered packing of counterions near highly charged surfaces: From mean-field theory to Monte Carlo simulations

Competitive adsorption of counterions of multiple species to charged surfaces is studied by a size-effect-included mean-field theory and Monte Carlo (MC) simulations. The mean-field electrostatic free-energy functional of ionic concentrations, constrained by Poisson's equation, is numerically minimized by an augmented Lagrangian multiplier method. Unrestricted primitive models and canonical ensemble MC simulations with the Metropolis criterion are used to predict the ionic distributions around a charged surface. It is found that, for a low surface charge density, the adsorption of ions with a higher valence is preferable, agreeing with existing studies. For a highly charged surface, both the mean-field theory and the MC simulations demonstrate that the counterions bind tightly around the charged surface, resulting in a stratification of counterions of different species. The competition between mixed entropy and electrostatic energetics leads to a compromise that the ionic species with a higher valence-to-volume ratio has a larger probability to form the first layer of stratification. In particular, the MC simulations confirm the crucial role of ionic valence-to-volume ratios in the competitive adsorption to charged surfaces that had been previously predicted by the mean-field theory. The charge inversion for ionic systems with salt is predicted by the MC simulations but not by the mean-field theory. This work provides a better understanding of competitive adsorption of counterions to charged surfaces and calls for further studies on the ionic size effect with application to large-scale biomolecular modeling.

An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces

In this work, a Monte-Carlo algorithm in the constant-voltage ensemble for the calculation of 3d charge concentrations at charged surfaces functionalized with biomolecules is presented. The motivation for this work is the theoretical understanding of biofunctionalized surfaces in nanowire field-effect biosensors (BioFETs). This work provides the simulation capability for the boundary layer that is crucial in the detection mechanism of these sensors; slight changes in the charge concentration in the boundary layer upon binding of analyte molecules modulate the conductance of nanowire transducers. The simulation of biofunctionalized surfaces poses special requirements on the Monte-Carlo simulations and these are addressed by the algorithm. The constant-voltage ensemble enables us to include the right boundary conditions; the dna strands can be rotated with respect to the surface; and several molecules can be placed in a single simulation box to achieve good statistics in the case of low ionic concentrations relevant in experiments. Simulation results are presented for the leading example of surfaces functionalized with pna and with single- and double-stranded dna in a sodium-chloride electrolyte. These quantitative results make it possible to quantify the screening of the biomolecule charge due to the counter-ions around the biomolecules and the electrical double layer. The resulting concentration profiles show a three-layer structure and non-trivial interactions between the electric double layer and the counter-ions. The numerical results are also important as a reference for the development of simpler screening models.

Molecular solvent model of spherical electric double layers: a systematic study by Monte Carlo simulations and density functional theory

The structure of spherical electric double layers is studied using Monte Carlo simulation and density functional theory by considering solvent as the third component. In this molecular solvent model (MSM), ions and solvent molecules are considered as charged and neutral hard spheres, respectively, having equal diameter. The macroion is considered as an isolated hard sphere having uniform surface charge density surrounded by the electrolyte and the solvent. The theory is partially perturbative as the hard-sphere contribution to the one particle correlation function is evaluated using suitably averaged weighted density, and the ionic part is obtained through a second-order functional Taylor expansion around the bulk electrolyte. The Monte Carlo simulations have been performed in a canonical ensemble. The system is studied at varying concentrations of electrolytes, and the solvent molecules, at different valences of the electrolyte, at different macroion radii, and at varying surface charge densities. The theory is found to be in good agreement with the simulation results over a wide range of parametric conditions. The excluded volume effects due to the molecular nature of the solvent are shown to have much richer features in diffuse layer phenomena like layering and charge inversion.

Simulational and theoretical study of the spherical electrical double layer for a size-asymmetric electrolyte: the case of big coions

Monte Carlo simulations of a spherical macroion, surrounded by a size-asymmetric electrolyte in the primitive model, were performed. We considered 1:1 and 2:2 salts with a size ratio of 2 (i.e., with coions twice the size of counterions), for several surface charge densities of the macrosphere. The radial distribution functions, electrostatic potential in all the space and at the Helmholtz surfaces, and integrated charge are reported. We compare these simulational data with original results obtained from the Ornstein-Zernike integral equation, supplemented by the hypernetted chain-hypernetted chain (HNC-HNC) and hypernetted chain-mean spherical approximation (HNC-MSA) closures, and with the corresponding calculations using the modified Gouy-Chapman and unequal-radius modified Gouy-Chapman theories. The HNC-HNC and HNC-MSA integral equations formalisms show good concordance with Monte Carlo "experiments," whereas the notable limitations of point-ion approaches are evidenced. Most importantly, the simulations confirm our previous theoretical predictions of the nondominance of the counterions in the size-asymmetric spherical electrical double layer [J. Chem. Phys. 123, 034703 (2005)], the appearance of anomalous curvatures at the outer Helmholtz plane, and the enhancement of the charge reversal and screening at high colloidal surface charge densities due to the ionic size asymmetry.

Insights from theory and simulation on the electrical double layer

Despite the fact that our conceptual understanding of the electrical double layer has advanced during the past few decades, the interpretation of experimental and applied work is still largely based on the venerable Poisson-Boltzmann theory of Gouy, Chapman and Stern. This is understandable since this theory is simple and analytic. However, it is not very accurate because the atomic/molecular nature of the ions/solvent and their correlations are ignored. Simulation and some theoretical studies by ourselves and others that have advanced our understanding are discussed. These studies show that the GCS theory predicts a narrow double layer with monotonic profiles. This is not correct. The double layer is wider, and there can be substantial layering that would be even more pronounced if explicit solvent molecules are considered. For many years, experimental studies of the double layer have been directed to the use of electrochemistry as an analytical tool. This is acceptable for analytic chemistry studies. However, the understanding of electrochemical reactions that typically occur at the electrode surface, where simulation and theory indicate that the GCS theory can have substantial errors, requires modern approaches. New, fundamental experimental studies that would lead to deeper insights using more novel systems would be desirable. Further, biophysics is an interesting field. Recent studies of the selectivity of ion channels and of the adsorption of ions in a binding sites of a protein have shown that the linearized GCS theory has substantial errors.

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model

A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.

Ionic correlations in the inhomogeneous atmosphere surrounding cylindrical polyions: catalytic effects of polyions

The structural properties of linear polyelectrolyte solutions in the presence of a salt as evidenced through ionic correlations in the inhomogeneous atmosphere around a polyion and their consequence such as the catalytic potential are studied by using Monte Carlo simulation techniques. The simulations are performed on the cylindrical cell model where a uniformly charged hard cylinder mimics the linear polyion, which is caged in its own cylindrical cell containing counterions and salt. The cell (volume) average of the interionic correlations is presented as a function of the polyion and salt concentrations and ion radius. These results are utilized to study the catalytic effects of polyions as manifested through the changes in the collision frequency between ions in the double layer surrounding the polyion relative to that in the pure electrolyte solution. The reported results suggest a strong influence of the added salt/polyelectrolyte concentration ratio on the structural properties of the solution and hence on ion-ion collision frequency. The machine simulations are supplemented by nonlinear Poisson-Boltzmann results. Fair agreement between two different theoretical methods of calculating the collision frequency is obtained.

Counterion-counterion correlation in the double layer around cylindrical polyions: counterion size and valency effects

Monte Carlo simulation and Poisson-Boltzmann results on some aspects of structure and thermodynamics of aqueous polyelectrolyte solutions are presented. The polyelectrolyte solution is described by an infinitely long cylindrical polyion surrounded by counterions modeled as rigid ions moving in a continuum dielectric. Ion-ion correlations in the form of volume average of the counterion-counterion distribution function in the double layer surrounding the polyion are reported for mono- and divalent counterions and for a range of polyion concentrations and charge density parameters in each case. These results confirm again strong influence of the charge density parameter of polyions on properties of polyelectrolyte solutions. The structural information is supplemented by the calculated thermodynamic properties such as osmotic coefficients and heats of dilutions; the latter quantity has not been examined yet in detail by computer simulations. The results are discussed in view of the existing experimental data from the literature for these properties.

Structure of spherical electric double layers: A density functional approach

A density functional theory is presented for the structure of spherical electric double layers within the restricted primitive model, where the macroion is considered as a hard sphere having uniform surface charge density, the small ions as charged hard spheres, and the solvent is taken as a dielectric continuum. The theory is partially perturbative as the hard-sphere contribution to the one-particle correlation function is evaluated using suitably averaged weighted density and the ionic part is obtained through a second-order functional Taylor expansion around the uniform fluid. The theory is in quantitative agreement with Monte Carlo simulation for the density profiles and the zeta potentials over a wide range of macroion sizes and electrolyte concentrations. The theory is able to provide interesting insights about the layering and the charge inversion phenomena occurring at the interface.

Preferential interaction between DNA and small ions in mixed-size counterion systems: Monte Carlo simulation and density functional study

Competitive binding between counterions around DNA molecule is characterized using the preferential interaction coefficient of individual ion in single and mixed electrolyte solutions. The canonical Monte Carlo (MC) simulation, nonlinear Poisson-Boltzmann (PB) equation, and density functional theory (DFT) proposed in our previous work [Wang, Yu, Gao, and Luo, J. Chem. Phys. 123, 234904 (2005)] are utilized to calculate the preferential interaction coefficients. The MC simulations and theoretical results show that for single electrolyte around DNA, the preferential interaction coefficient of electrolyte decreases as the cation size is increased, indicating that the larger cation has less accumulation ability in the vicinity of DNA. For the mixed electrolyte solution, it is found that cation diameter has a significant effect on the competitive ability while anion diameter has a negligible effect. It proves that the preferential interaction coefficients of all ions decrease as the total ionic concentration is increased. The DFT generally has better performance than the PB equation does when compared to the MC simulation data. The DFT behaves quite well for the real ionic solutions such as the KCl-NaCl-H2O, NaCl-CaCl2-H2O, and CaCl2-MgCl2-H2O systems.

Simple density functional approach to adsorption of biomolecules on solid surfaces

A simple density functional approach for modeling the adsorption of biomolecules is considered. The model comprises a three-component mixture consisting of spherical and differently charged ions and chain molecules. Spherical ions can form associative bonds with selected segments of a chain. To enable the formation of bonds between chain segments and spherical ions, the statistical associating fluid theory is applied. The present theory is used to study the structure of adsorbed layers, the excess adsorption isotherms, and the capacitance of the double layer.

Van der Waals-Like Isotherms in a Confined Electrolyte by Spherical and Cylindrical Nanopores

Electrolytes confined by spherical, cylindrical, and slit-like charged nanopores are studied. Results for ionic distribution profiles, pressures of the confined fluid, and absorption isotherms are obtained through the hypernetted chain/mean spherical approximation (HNC/MSA) integral equations theory. In spherical and cylindrical geometries, an inward, non-monotonic behavior of the pressure is found as confinement increases, implying a negative compressibility. The pressure vs volume isotherms resemble liquid-vapor van der Waals-like phase transition diagrams. This effect is correlated with a charge separation inside a spherical pore previously reported (Phys. Rev. Lett., 79, 3656, 1997). Here, the mechanism of charge separation and negative compressibility are explored in detail. When compared with the slit-like pore pressure, important qualitative differences are found.

Computer Simulation of the Ionic Atmosphere around Z-DNA

We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively small number of repulsive interaction sites. In addition, negative charges are placed at the phosphate positions. The ionic atmosphere around this grooved Z-DNA model is then investigated with Monte Carlo simulation. Cylindrically averaged concentration profiles as well as the spatial distribution of ions have been calculated. The results are compared to those for other DNA models differing in the repulsive core. This allows the examination of the effect of the DNA shape in the ionic distribution. It is seen that the penetrability of the ions to the DNA groove plays an important role in the ionic distribution. The results are also compared with those reported for B-DNA. In both conformers the ions are structured in alternating layers of positive and negative charge. In Z-DNA the layers are more or less concentric to the molecular axis. Besides, no coions enter into the single groove of this conformer. On the contrary, the alternating layers of B-DNA are also structured along the axial coordinate with some coions penetrating into the major groove. In both cases we have found five preferred locations of the counterions and two for the coions. The concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove and at the minor groove of B-DNA, the value of the maximum being higher in the Z conformer.