Electrode screening by ionic liquids

In this work we are concerned with the short-range screening provided by the ionic liquid dimethylimidazolium chloride near a charged wall. We study the free energy profiles (or potentials of mean force) for charged and neutral solutes as a function of distance from a charged wall. Four different wall charge densities are used in addition to a wall with zero charge. The highest magnitude of the charge densities is ±1 e nm(-2) which is close to the maximum limit of charge densities accessible in experiments, while the intermediate charges ±0.5 e nm(-2) are in the range of densities typically used in most of the experimental studies. Positively and negatively charged solutes of approximately the size of a BF ion and a Cl(-) ion are used as probes. We find that the ionic liquid provides excellent electrostatic screening at a distance of 1-2 nm. The free energy profiles show minima which are due to layering in the ionic liquid near the electrodes. This indicates that the solute ions tend to displace ionic liquid ions in the layers when approaching the electrode. The important role of non-electrostatic forces is demonstrated by the oscillations in the free energy profiles of uncharged solutes as a function of distance from the wall.     

Comparing the Predictions of the Nonlinear Poisson-Boltzmann Equation and the Ion Size-Modified Poisson-Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution

The ion size-modified Poisson Boltzmann equation (SMPBE) is applied to the simple model problem of a low-dielectric spherical cavity containing a central charge, in an aqueous salt solution to investigate the finite ion size effect upon the electrostatic free energy and its sensitivity to changes in salt concentration. The SMPBE is shown to predict a very different electrostatic free energy than the nonlinear Poisson-Boltzmann equation (NLPBE) due to the additional entropic cost of placing ions in solution. Although the energy predictions of the SMPBE can be reproduced by fitting an appropriatelysized Stern layer, or ion-exclusion layer to the NLPBE calculations, the size of the Stern layer is difficult to estimate a priori. The SMPBE also produces a saturation layer when the central charge becomes sufficiently large. Ion-competition effects on various integrated quantities such the total number of ions predicted by the SMPBE are qualitatively similar to those given by the NLPBE and those found in available experimental results.     

Acyclic distonic acylium ions: Dual free radical and acylium ion reactivity in a single molecule

Three gaseous acyclic distonic acylium ions: *CH2-CH2-C+=O, *CH2-CH2-CH2-C+=O, and *CH2=C(CH2)-C+=O, are found to display dual free radical and acylium ion reactivity; with appropriate neutrals, they react selectively either as free radicals with inert charge sites, or (and more pronouncedly) as acylium ions with inert radical sites. The free radical reactivity of the ions is demonstrated via the Kenttamaa reaction: CH3S* abstraction with the spin trap dimethyl disulfide; their ion reactivity by two reactions most characteristic of acylium ions: transacetalization with 2-methyl-1,3-dioxolane and the gas-phase Meerwein reaction, that is, expansion of the three-membered epoxide ring of epichlorohydrin to the five-membered 1,3-dioxolanylium ion ring. In "one-pot" reactions with gaseous mixtures of epichlorohydrin and dimethyl disulfide, the ions react selectively at either site, but more readily at the acylium charge site, to form the two mono-derivatized ions. Further reaction at either the remaining free radical or acylium charge site forms a single bi-derivatized ion as the final product. Becke3LYP/6-31G(d) calculations predict the reactions at the acylium charge sites of the three distonic ions to be highly exothermic, and both the "hot" transacetalization and epoxide ring expansion products of *CH2-CH2-CH2-C+=O to dissociate rapidly by H2C=CH2 loss in overall exothermic processes. The calculations also predict highly spatially separate odd spin and charge sites for the novel cyclic distonic ketal ions formed by the reactions at the acylium charge sites.     

Charge separation in water molecule clusters under thermal fluctuations: 1. Intermolecular interactions

A detailed model of intermolecular interactions in water molecule clusters is developed that makes it possible to describe their disintegration to ions under conditions of finite temperatures by the stochastic simulation methods. In this model, the Hamiltonian in explicit form includes Coulomb, dispersion, exchange, and polarization interactions; many-particle covalent interactions and hydrogen bonds; the interaction of induced dipoles; charge transfers from ions to molecules; and the recombination of counterion charges, as well as the effect of an ion field on the unpaired interactions of molecules. The model is consistent with experimental data on the free energy and entropy of ion hydration in water vapors and the free energy of the hydration of a recombined ion pair.     

Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions

The ability to predict and characterize free energy differences associated with conformational equilibria or the binding of biomolecules is vital to understanding the molecular basis of many important biological functions. As biological studies focus on larger molecular complexes and properties of the genome, proteome, and interactome, the development and characterization of efficient methods for calculating free energy becomes increasingly essential. The aim of this study is to examine the robustness of the end-point free energy method termed the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM/PBSA) method. Specifically, applications of MM/PBSA to the conformational equilibria of nucleic acid (NA) systems are explored. This is achieved by comparing A to B form DNA conformational free energy differences calculated using MM/PBSA with corresponding free energy differences determined with a more rigorous and time-consuming umbrella sampling algorithm. In addition, the robustness of NA MM/PBSA calculations is also evaluated in terms of the sensitivity towards the choice of force field and the choice of solvent model used during conformational sampling. MM/PBSA calculations of the free energy difference between A-form and B-form DNA are shown to be in very close agreement with the PMF result determined using an umbrella sampling approach. Further, it is found that the MM/PBSA conformational free energy differences were also in agreement using either the CHARMM or AMBER force field. The influence of ionic strength on conformational stability was particularly insensitive to the choice of force field. Finally, it is also shown that the use of a generalized Born implicit solvent during conformational sampling results in free energy estimates that deviate slightly from those obtained using explicitly solvated MD simulations in these NA systems.     

Effect of ions on the hydrophobic interaction between two plates

We use molecular dynamics simulations to investigate the solvent mediated attraction and drying between two nanoscale hydrophobic surfaces in aqueous salt solutions. We study these effects as a function of the ionic charge density, that is, the ionic charge per unit ionic volume, while keeping the ionic diameter fixed. The attraction is expressed by a negative change in the free energy as the plates are brought together, with enthalpy and entropy changes that both promote aggregation. We find a strong correlation between the strength of the hydrophobic interaction and the degree of preferential binding/exclusion of the ions relative to the surfaces. The results show that amplification of the hydrophobic interaction, a phenomenon analogous to salting-out, is a purely entropic effect and is induced by high-charge-density ions that exhibit preferential exclusion. In contrast, a reduction of the hydrophobic interaction, analogous to salting-in, is induced by low-charge-density ions that exhibit preferential binding, the effect being either entropic or enthalpic. Our findings are relevant to phenomena long studied in solution chemistry, as we demonstrate the significant, yet subtle, effects of electrolytes on hydrophobic aggregation and collapse.     

Direct Observation of a Li‐Ionic Space‐Charge Layer Formed at an Electrode/Solid‐Electrolyte Interface

When two different materials come into contact, mobile carriers redistribute at the interface according to their potential difference. Such a charge redistribution is also expected at the interface between electrodes and solid electrolytes. The redistributed ions significantly affect the ion conduction through the interface. Thus, it is essential to determine the actual distribution of the ionic carriers and their potential to improve ion conduction. We succeeded in visualizing the ionic and potential profiles in the charge redistribution layer, or space‐charge layer (SCL), formed at the interface between a Cu electrode and Li‐conductive solid electrolyte using phase‐shifting electron holography and spatially resolved electron energy‐loss spectroscopy. These electron microscopy techniques clearly showed the Li‐ionic SCL, which dropped by 1.3 V within a distance of 10 nm from the interface. These techniques could contribute to the development of next‐generation electrochemical devices.     

Modification of Surface Forces by Metal Ion Adsorption

Abstract

Sorption of ions may lead to variations in interparticle forces and, thus, changes in the stability of colloidal particles. Chemical interactions between metal ions and colloidal particles modify the molecular structure of the surface, the surface charge, and the electrical potential between colloidal particles. These modifications to the surface and to the electrical double layer due to metal ion sorption are reflected in the interaction force between a particle and another surface, which is measured in this study by atomic force microscopy (AFM). Specifically, AFM is used to investigate the sorption of copper ions from aqueous solutions by silica particles. The influence of metal ion concentration and solution ionic strength on surface forces is studied under transient conditions. Results show that as the metal ion concentration is decreased, charge reversal occurs and a longer period of time is required for the system to reach equilibrium. The ionic strength has no significant effect on sorption kinetics. Furthermore, neither metal concentration nor ionic strength exhibits any effect on sorption equilibria, indicating that for the experimental conditions used in this study, the surface sites of the silica particle are fully occupied by copper ions.     

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin

The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.     

On the mechanism of uptake of globular proteins by polyelectrolyte brushes: a two-gradient self-consistent field analysis

We present model calculations for the interaction of a protein-like inhomogeneously charged nanoscale object with a layer of densely grafted polyelectrolytes ("polyelectrolyte brush"). The motivation of this work is the recent experimental observation that proteins that carry an overall negative charge are absorbed into negatively charged polyelectrolyte brushes. Two-gradient self-consistent field (2G-SCF) calculations have been performed to unravel the physical mechanism of the uptake of protein thus effected. Our results prove that an overall neutral, protein-like object can electrostatically be attracted and therefore spontaneously driven into a polyelectrolyte brush when the object has two faces (patches, domains), one with a permanent positive charge and the other with a permanent negative charge. Using a 2G-SCF analysis, we evaluate the free energy of insertion, such that the electric dipole of the inclusion is oriented parallel to the brush surface. An electroneutral protein-like object is attracted into the brush because the polyelectrolyte brush interacts asymmetrically with the charged patches of opposite sign. At high ionic strength and low charge density on the patches, the attraction cannot compete with the repulsive excluded-volume interaction. However, for low ionic strengths and sufficiently high charge density on the patches, a gain on the order of k(B)T per charge becomes possible. Hence, the asymmetry of interaction for patches of different charges may result in a total attractive force between the protein and the brush. All results obtained herein are in excellent agreement with recent experimental data.     

Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs

Different microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long-range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.     

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA.     

Highly charged ion induced nanostructures at surfaces by strong electronic excitations

Nanostructure formation by single slow highly charged ion impacts can be associated with high density of electronic excitations at the impact points of the ions. Experimental results show that depending on the target material these electronic excitations may lead to very large desorption yields in the order of a few 1000 atoms per ion or the formation of nanohillocks at the impact site. Even in ultra-thin insulating membranes the formation of nanometer sized pores is observed after ion impact. In this paper, we show recent results on nanostructure formation by highly charged ions and compare them to structures and defects observed after intense electron and light ion irradiation of ionic crystals and graphene. Additional data on energy loss, charge exchange and secondary electron emission of highly charged ions clearly show that the ion charge dominates the defect formation at the surface.     

Is there a ‘matrix suppression effect’ under fast‐atom bombardment liquid secondary ion mass spectrometry of ionic surfactants in glycerol?

Some features of a ‘matrix suppression effect’ caused by ionic surface‐active compounds under fast‐atom bombardment (FAB) liquid secondary ion mass spectrometry (LSIMS) are being revised. It is shown that abundant transfer of the glycerol matrix molecules to the gas phase does occur under FAB‐LSIMS of ionic surfactants, contrary to popular belief. This process can be obscure because of the dependence of the charge state of the glycerol‐containing cluster ions on the type of ionic surfactant. It is revealed that, while glycerol matrix signals are really completely suppressed in the positive ion mass spectra of cationic surfactants (decamethoxinum, aethonium), abundant deprotonated glycerol and glycerol‐anion clusters are recorded in the negative ion mode. In the case of an anionic surfactant (sodium dodecyl sulfate), on the contrary, glycerol is completely suppressed in the negative ion mode, but is present in the protonated and cationized forms in the positive ion mass spectra. It is suggested that such patterns of positive and negative ion FAB‐LSIMS spectra of ionic surfactants solutions reflect the structure and composition of the electric double layer formed at the vacuum‐liquid interface by organic cations or anions and their counterions. Processes leading to the formation of the glycerol‐containing ions preferentially of positive or negative charge are discussed. The most obvious of them is efficient binding of glycerol to inorganic counterions of the salts Cl^? or Na⁺, which is confirmed by data from quantum chemical calculations. The high content of the counterions and relatively small content of glycerol in the sputtered zone may be responsible for the charge‐selective suppression of neat glycerol clusters of opposite charge to the counterions. In the case of a mixture of cationic and anionic surfactants the substitution of inorganic counterions by organic ones was observed. The dependence of the exchange rate in the surface layer is not a linear function of the bulk solution concentration, and an effect of abrupt recharging of the surface can be registered. No both positively or negatively charged pure glycerol and glycerol‐inorganic counterion clusters are recorded for the mixture. Correlations between the mass spectrometric observations and some phenomena of surface and colloid chemistry and physics are discussed. Copyright © 2007 John Wiley & Sons, Ltd.     

Interfacial biocatalysis on charged and immobilized substrates: the roles of enzyme and substrate surface charge

An enzyme charge ladder was used to examine the role of electrostatic interactions involved in biocatalysis at the solid-liquid interface. The reactive substrate consisted of an immobilized bovine serum albumin (BSA) multilayer prepared using a layer-by-layer technique. The zeta potential of the BSA substrate and each enzyme variant was measured to determine the absolute charge in solution. Enzyme adsorption and the rate of substrate surface hydrolysis were monitored for the enzyme charge ladder series to provide information regarding the strength of the enzyme-substrate interaction and the rate of interfacial biocatalysis. First, each variant of the charge ladder was examined at pH 8 for various solution ionic strengths. We found that for positively charged variants the adsorption increased with the magnitude of the charge until the surface became saturated. For higher ionic strength solutions, a greater positive enzyme charge was required to induce adsorption. Interestingly, the maximum catalytic rate was not achieved at enzyme saturation but at an invariable intermediate level of adsorption for each ionic strength value. Furthermore, the maximum achievable reaction rate for the charge ladder was larger for higher ionic strength values. We propose that diffusion plays an important role in interfacial biocatalysis, and for strong enzyme-substrate interaction, the rate of diffusion is reduced, leading to a decrease in the overall reaction rate. We investigated the effect of substrate charge by varying the solution pH from 6.1 to 8.7 and by examining multiple ionic strength values for each pH. The same intermediate level of adsorption was found to maximize the overall reaction rate. However, the ionic strength response of the maximum achievable rate was clearly dependent on the pH of the experiment. We propose that this observation is not a direct effect of pH but is caused by the change in substrate surface charge induced by changing the pH. To prove this hypothesis, BSA substrates were chemically modified to reduce the magnitude of the negative charge at pH 8. Chemical modification was accomplished by the amidation of aspartic and glutamic acids to asparagine and glutamine. The ionic strength response of the chemically modified substrate was considerably different than that for the native BSA substrate at an identical pH, consistent with the trend based on substrate surface charge. Consequently, for substrates with a low net surface charge, the maximum achievable catalytic rate of the charge ladder was relatively independent of the solution ionic strength over the range examined; however, at high net substrate surface charge, the maximum rate showed a considerable ionic strength dependence.     

Controlling the transport of cations through permselective mesoporous alumina layers by manipulation of electric field and ionic strength

The electric field-driven transport of ions through supported mesoporous gamma-alumina membranes was investigated. The influence of ion concentration, ion valency, pH, ionic strength, and electrolyte composition on transport behavior was determined. The permselectivity of the membrane was found to be highly dependent on the ionic strength. When the ionic strength was sufficiently low for electrical double-layer overlap to occur inside the pores, the membrane was found to be cation-permselective and the transport rate of cations could be tuned by variation of the potential difference over the membrane. The cation permselectivity is thought to be due to the adsorption of anions onto the pore walls, causing a net negative immobile surface charge density, and consequently, a positively charged mobile double layer. The transport mechanism of cations was interpreted in terms of a combination of Fick diffusion and ion migration. By variation of the potential difference over the membrane the transport of double-charged cations, Cu2+, could be controlled accurately, effectively resulting in on/off tunable transport. In the absence of double-layer overlap at high ionic strength, the membrane was found to be nonselective.