The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge

Mixed species biofilm: Structure, challenge and its intricate involvement in hospital associated infections

Hospital associated infections or healthcare associated infections (HAIs) are a major threat to healthcare and medical management, mostly because of their recalcitrant nature. The primary cause of these HAIs is bacterial associations, especially the interspecies interactions. In interspecies interactions, more than one species co-exists in a common platform of extracellular polymeric substances (EPS), establishing a strong interspecies crosstalk and thereby lead to the formation of mixed species biofilms. In this process, the internal microenvironment and the surrounding EPS matrix of the biofilms ensure the protection of the microorganisms and allow them to survive under antagonistic conditions. The communications between the biofilm members as well as the interactions between the bacterial cells and the matrix polymers, also aid in the rigidity of the biofilm structure and allow the microorganisms to evade both the host immune response and a wide range of anti-microbials. Therefore, to design a treatment protocol for HAIs is difficult and it has become a growing point of concern. This review therefore first aims to discuss the role of microenvironment, molecular structure, cell-cell communication, and metabolism of mixed species biofilms in manifestation of HAIs. In addition, we discuss the electrochemical properties of mixed-species biofilms and their mechanism in developing drug resistance. Then we focus on the most dreaded bacterial HAI including oral and gut multi-species infections, catheter-associated urinary tract infections, surgical site infections, and ventilator-associated pneumonia. Further, we highlight the challenges to eradication of the mixed species biofilms and the current and prospective future strategies for the treatment of mixed species-associated HAI. Together, the review presents a comprehensive understanding of mixed species biofilm-mediated infections in clinical scenario, and summarizes the current challenge and prospect of therapeutic strategies against HAI.

Constant chemical potential-quantum mechanical-molecular dynamics simulations of the graphene-electrolyte double layer

We present the coupling of two frameworks-the pseudo-open boundary simulation method known as constant potential molecular dynamics simulations (CμMD), combined with quantum mechanics/molecular dynamics (QMMD) calculations-to describe the properties of graphene electrodes in contact with electrolytes. The resulting CμQMMD model was then applied to three ionic solutions (LiCl, NaCl, and KCl in water) at bulk solution concentrations ranging from 0.5 M to 6 M in contact with a charged graphene electrode. The new approach we are describing here provides a simulation protocol to control the concentration of electrolyte solutions while including the effects of a fully polarizable electrode surface. Thanks to this coupling, we are able to accurately model both the electrode and solution side of the double layer and provide a thorough analysis of the properties of electrolytes at charged interfaces, such as the screening ability of the electrolyte and the electrostatic potential profile. We also report the calculation of the integral electrochemical double layer capacitance in the whole range of concentrations analyzed for each ionic species, while the quantum mechanical simulations provide access to the differential and integral quantum capacitance. We highlight how subtle features, such as the adsorption of potassium graphene or the tendency of the ions to form clusters contribute to the ability of graphene to store charge, and suggest implications for desalination.

Electrochemistry, ion adsorption and dynamics in the double layer: a study of NaCl(aq) on graphite

Graphite and related sp² carbons are ubiquitous electrode materials with particular promise for use in e.g., energy storage and desalination devices, but very little is known about the properties of the carbon–electrolyte double layer at technologically relevant concentrations. Here, the (electrified) graphite–NaCl(aq) interface was examined using constant chemical potential molecular dynamics (CμMD) simulations; this approach avoids ion depletion (due to surface adsorption) and maintains a constant concentration, electroneutral bulk solution beyond the surface. Specific Na⁺ adsorption at the graphite basal surface causes charging of the interface in the absence of an applied potential. At moderate bulk concentrations, this leads to accumulation of counter-ions in a diffuse layer to balance the effective surface charge, consistent with established models of the electrical double layer. Beyond ∼0.6 M, however, a combination of over-screening and ion crowding in the double layer results in alternating compact layers of charge density perpendicular to the interface. The transition to this regime is marked by an increasing double layer size and anomalous negative shifts to the potential of zero charge with incremental changes to the bulk concentration. Our observations are supported by changes to the position of the differential capacitance minimum measured by electrochemical impedance spectroscopy, and are explained in terms of the screening behaviour and asymmetric ion adsorption. Furthermore, a striking level of agreement between the differential capacitance from solution evaluated in simulations and measured in experiments allows us to critically assess electrochemical capacitance measurements which have previously been considered to report simply on the density of states of the graphite material at the potential of zero charge. Our work shows that the solution side of the double layer provides the more dominant contribution to the overall measured capacitance. Finally, ion crowding at the highest concentrations (beyond ∼5 M) leads to the formation of liquid-like NaCl clusters confined to highly non-ideal regions of the double layer, where ion diffusion is up to five times slower than in the bulk. The implications of changes to the speciation of ions on reactive events in the double layer are discussed.

CμMD reveals multi-layer electrolyte screening in the double layer beyond 0.6 M, which affects ion activities, speciation and mobility; asymmetric charge screening explains concentration dependent changes to electrochemical properties.

Strong Enhancement of Nanoconfined Water Mobility by a Structure Breaking Salt

For the majority of the water present on earth, the two most important factors influencing its behavior are confinement, in either inorganic or organic matrixes, and the presence of solutes. Here, we investigate the effect of confinement in 3 nm pores on water diffusivity in aqueous solutions with archetypical solutes, a structure making (kosmotrope) NaCl and a structure breaking (chaotrope) KCl, up to 1.0 M in concentration. The water diffusivity in bulk aqueous solutions in such a concentration range is known to decrease very slightly in the presence of NaCl and increase very slightly in the presence of KCl. However, here we observe the water diffusivity in confined H₂O-KCl increases by a factor of 2 compared to the pure water diffusivity in the same confinement. This unusually strong cumulative effect of confinement and a structure breaking additive may have profound implications for the mobility and transport of aqueous species in nature.

Including diverging electrostatic potential in 3D-RISM theory: The charged wall case

Although three-dimensional site-site molecular integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of biomolecular solvation with either 3D-RISM or continuum electrostatics approaches, it still is computationally efficient. Introducing the electrostatic potential of an infinite wall, which is periodic in 2 dimensions, we avoid edge effects, permit a robust integration of Poisson's equation, and obtain the 3D electrostatic potential profile for the first time in such calculations. We show that the potential within the electrical double layer presents oscillations which are not grasped by the Debye-Hückel and Gouy-Chapman theories. This electrostatic potential deviates from its average of up to 1-2 V at small distances from the substrate along the lateral directions. Applications of this theoretical development are relevant, for example, for liquid scanning tunneling microscopy imaging.

Capacitive Energy Storage: Current and Future Challenges

Capacitive energy storage devices are receiving increasing experimental and theoretical attention due to their enormous potential for energy applications. Current research in this field is focused on the improvement of both the energy and the power density of supercapacitors by optimizing the nanostructure of porous electrodes and the chemical structure/composition of the electrolytes. However, the understanding of the underlying correlations and the mechanisms of electric double layer formation near charged surfaces and inside nanoporous electrodes is complicated by the complex interplay of several molecular scale phenomena. This Perspective presents several aspects regarding the experimental and theoretical research in the field, discusses the current atomistic and molecular scale understanding of the mechanisms of energy and charge storage, and provides a brief outlook to the future developments and applications of these devices.

Using molecular dynamics to quantify the electrical double layer and examine the potential for its direct observation in the in-situ TEM

Understanding the fundamental processes taking place at the electrode-electrolyte interface in batteries will play a key role in the development of next generation energy storage technologies. One of the most fundamental aspects of the electrode-electrolyte interface is the electrical double layer (EDL). Given the recent development of high spatial resolution in-situ electrochemical fluid cells for scanning transmission electron microscopy (STEM), there now exists the possibility that we can directly observe the formation and dynamics of the EDL. In this paper we predict electrolyte structure within the EDL using classical models and atomistic Molecular Dynamics (MD) simulations. Classical models are found to greatly differ from MD in predicted concentration profiles. It is thus suggested that MD must be used in order to accurately predict STEM images of the electrode-electrolyte interface. Using MD and image simulation together for a high contrast electrolyte (the high atomic number CsCl electrolyte), it is determined that, for a smooth interface, concentration profiles within the EDL should be visible experimentally. When normal experimental parameters such as rough interfaces and low-Z electrolytes (like those used in Li-ion batteries) are considered, observation of the EDL appears to be more difficult.

Solvation and cavity occupation in biomolecules

BACKGROUND

Solvation density locations are important for protein dynamics and structure. Knowledge of the preferred hydration sites at biomolecular interfaces and those in the interior of cavities can enhance understanding of structure and function. While advanced X-ray diffraction methods can provide accurate atomic structures for proteins, that technique is challenged when it comes to providing accurate hydration structures, especially for interfacial and cavity bound solvent molecules.

METHODS

Advances in integral equation theories which include more accurate methods for calculating the long-ranged Coulomb interaction contributions to the three-dimensional distribution functions make it possible to calculate angle dependent average solvent structure, accurately, around and inside irregular molecular conformations. The proximal radial distribution method provides another approximate method to determine average solvent structures for biomolecular systems based on a proximal or near neighbor solvent distribution that can be constructed from previously collected solvent distributions. These two approximate methods, along with all-atom molecular dynamics simulations are used to determine the solvent density inside the myoglobin heme cavity.

DISCUSSION AND RESULTS

Myoglobin is a good test system for these methods because the cavities are many and one is large, tens of Å(3), but is shown to have only four hydration sites. These sites are not near neighbors which implies that the large cavity must have more than one way in and out.

CONCLUSIONS

Our results show that main solvation sites are well reproduced by all three methods. The techniques also produce a clearly identifiable solvent pathway into the interior of the protein.

GENERAL SIGNIFICANCE

The agreement between molecular dynamics and less computationally demanding approximate methods is encouraging. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Ionic Size Effects: Generalized Boltzmann Distributions, Counterion Stratification, and Modified Debye Length

Near a charged surface, counterions of different valences and sizes cluster; and their concentration profiles stratify. At a distance from such a surface larger than the Debye length, the electric field is screened by counterions. Recent studies by a variational mean-field approach that includes ionic size effects and by Monte Carlo simulations both suggest that the counterion stratification is determined by the ionic valence-to-volume ratios. Central in the mean-field approach is a free-energy functional of ionic concentrations in which the ionic size effects are included through the entropic effect of solvent molecules. The corresponding equilibrium conditions define the generalized Boltzmann distributions relating the ionic concentrations to the electrostatic potential. This paper presents a detailed analysis and numerical calculations of such a free-energy functional to understand the dependence of the ionic charge density on the electrostatic potential through the generalized Boltzmann distributions, the role of ionic valence-to-volume ratios in the counterion stratification, and the modification of Debye length due to the effect of ionic sizes.

Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions

Using the dielectrically consistent reference interaction site model (DRISM) of molecular solvation, we have calculated structural and thermodynamic information of alkali-halide salts in aqueous solution, as a function of salt concentration. The impact of varying the closure relation used with DRISM is investigated using the partial series expansion of order-n (PSE-n) family of closures, which includes the commonly used hypernetted-chain equation (HNC) and Kovalenko-Hirata closures. Results are compared to explicit molecular dynamics (MD) simulations, using the same force fields, and to experiment. The mean activity coefficients of ions predicted by DRISM agree well with experimental values at concentrations below 0.5 m, especially when using the HNC closure. As individual ion activities (and the corresponding solvation free energies) are not known from experiment, only DRISM and MD results are directly compared and found to have reasonably good agreement. The activity of water directly estimated from DRISM is nearly consistent with values derived from the DRISM ion activities and the Gibbs-Duhem equation, but the changes in the computed pressure as a function of salt concentration dominate these comparisons. Good agreement with experiment is obtained if these pressure changes are ignored. Radial distribution functions of NaCl solution at three concentrations were compared between DRISM and MD simulations. DRISM shows comparable water distribution around the cation, but water structures around the anion deviate from the MD results; this may also be related to the high pressure of the system. Despite some problems, DRISM-PSE-n is an effective tool for investigating thermodynamic properties of simple electrolytes.

Ionic Interactions Are Everywhere

Ionic solutions are dominated by interactions because they must be electrically neutral, but classical theory assumes no interactions. Biological solutions are rather like seawater, concentrated enough so that the diameter of ions also produces important interactions. In my view, the theory of complex fluids is needed to deal with the interacting reality of biological solutions.

Integral Equation Theory of Biomolecules and Electrolytes

The so-called three-dimensional version (3D-RISM) can be used to describe the interactions of solvent components (here we treat water and ions) with a chemical or biomolecular solute of arbitrary size and shape. Here we give an overview of the current status of such models, describing some aspects of “pure” electrolytes (water plus simple ions) and of ionophores, proteins and nucleic acids in the presence of water and salts. Here we focus primarily on interactions with water and dissolved salts; as a practical matter, the discussion is mostly limited to monovalent ions, since studies of divalent ions present many difficult problems that have not yet been addressed. This is not a comprehensive review, but covers a few recent examples that illustrate current issues.

Ionizable side chains at catalytic active sites of enzymes

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

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.

Integral equations in the study of polar and ionic interaction site fluids

In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids.

Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach

Ionic size effects are significant in many biological systems. Mean-field descriptions of such effects can be efficient but also challenging. When ionic sizes are different, explicit formulas in such descriptions are not available for the dependence of the ionic concentrations on the electrostatic potential, that is, there is no explicit Boltzmann-type distributions. This work begins with a variational formulation of the continuum electrostatics of an ionic solution with such nonuniform ionic sizes as well as multiple ionic valences. An augmented Lagrange multiplier method is then developed and implemented to numerically solve the underlying constrained optimization problem. The method is shown to be accurate and efficient, and is applied to ionic systems with nonuniform ionic sizes such as the sodium chloride solution. Extensive numerical tests demonstrate that the mean-field model and numerical method capture qualitatively some significant ionic size effects, particularly those for multivalent ionic solutions, such as the stratification of multivalent counterions near a charged surface. The ionic valence-to-volume ratio is found to be the key physical parameter in the stratification of concentrations. All these are not well described by the classical Poisson-Boltzmann theory, or the generalized Poisson-Boltzmann theory that treats uniform ionic sizes. Finally, various issues such as the close packing, limitation of the continuum model, and generalization of this work to molecular solvation are discussed.

Ion and solvent density distributions around canonical B-DNA from integral equations

We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na(+) and K(+) ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.

Hydrated cation speciation at the muscovite (001)-water interface

Charged materials in aqueous systems interact according to their interfacial properties, typically described by the electrical double layer (EDL). Distributions of divalent metal cations at the muscovite (001)-solution interface observed using resonant anomalous X-ray reflectivity demonstrate an unexpected complexity with respect to the EDL structure. Three forms of adsorbed cations can coexist: the classical inner-sphere and outer-sphere complexes and a third "extended" outer-sphere complex located farther from the surface. Their relative proportions are controlled by the energy balance among cation hydration, interface hydration, and electrostatic attraction. Systematic trends in coverage and position establish the defining role of cation hydration in stabilizing the multiple coexisting species.

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an "extra layer" of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler-Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new component is added to the energy or dissipation, the Euler-Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler-Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson-Nernst-Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary "binding" in the channel, and the eventual accumulation of salts in "unstirred layers" near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions.