Counterion Dynamics Research Articles

The Role of Oxidation Pattern and Water Content in the Spatial Arrangement and Dynamics of Oxidized Graphene-Based Aqueous Dispersions.

In this work, we employ fully atomistic molecular dynamics simulations to elucidate the effects of the oxidation pattern and of the water content on the organization of graphene sheets in aqueous dispersions and on the dynamic properties of the different moieties at neutral pH conditions. Analysis of the results reveals the role of the oxidation motif (peripherally or fully oxidized flakes) in the tendency of the flakes to self-assemble and in the control of key structural characteristics, such as the interlayer distance between the sheets and the average size and the distribution of the formed aggregates. In certain cases, the results are compared to a pertinent experimental system, validating further the relevant computational models. Examination of the diffusional motion of the oxidized flakes shows that different degrees of spatial restriction are imposed upon the decrease in the water content and elucidates the conditions under which a motional arrest of the flakes takes place. At constant water content, the structural differences between the formed aggregates appear to additionally impart distinct diffusional characteristics of a water molecule. A detailed examination of the counterion dynamics describes their interaction with the oxidized flakes and their dependence on the water content and on the oxidation pattern, offering new insight into the expected electrical properties of the dispersions. The detailed information provided by this work will be particularly useful in applications such as molecular sieving, nanofiltration, and in cases where conductive membranes based on oxidized forms of graphene are used.

Explicit characterization of counterion dynamics around a flexible polyelectrolyte.

The article presents a comprehensive study of counterion dynamics around a generic linear polyelectrolyte chain with the help of coarse-grained computer simulations. The ion-chain coupling is discussed in the form of binding time, mean-square displacement (MSD) relative to the chain, local ion transport coefficient, and spatiotemporal correlations in the effective charge. We have shown that a counterion exhibits subdiffusive behavior 〈δR^{2}〉∼t^{δ}, δ≈0.9 w.r.t. chain's center of mass. The MSD of ions perpendicularly outward from the chain segment exhibits a smaller subdiffusive exponent compared to the one along the chain backbone. The effective diffusivity of ion is the lowest in chain's close proximity, extending up to the length-scale of radius of gyration R_{g}. Beyond R_{g} at larger distances, they attain diffusivity of free ion with a smooth cross-over from the adsorbed regime to the free ion regime. We have shown that the effective diffusivity drastically decreases for the multivalent ions, while the crossover length scale remains the same. Conversely, with increasing salt concentration the coupling-length scale reduces, while the diffusivity remains unaltered. The effective diffusivity of adsorbed-ion reveals an exponential reduction with electrostatic interaction strength. We further corroborate this from the binding time of ions on the chain, which also grows exponentially with the coupling strength of the ion-polymer duo. Moreover, the binding time of ions exhibits a weak dependence with salt concentration for the monovalent salt, while for multivalent salts the binding time decreases dramatically with concentration. Our work also elucidates fluctuations in the effective charge per site, where it exhibits strong negative correlations at short length-scales.

Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study.

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K+ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K+ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.

Detecting Counterion Dynamics in DNA-Protein Association.

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called "ion atmosphere". Although the release of counterions upon DNA-protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA-protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA-protein association.

Detecting Counterion Dynamics in DNA–Protein Association

AbstractDue to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so‐called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR‐based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.

Recent advances in the physics of polymer systems

Recent advances in the physics of polymer systems

Electron transfer controlled by solvent and counter-anion dynamics in electrochemistry of viologen-type ionic liquid

Temperature-dependent diffusion coefficients (DO) and heterogeneous electron transfer rate constants (k0) were measured for the viologen dication (V2+) in 1-butyl-1′-heptyl-4,4′-bipyridinium bis[(trifluoromethane)sulfonyl]imide [C4VC7][Tf2N]2 redox-active ionic liquid (RAIL) and its solution. The measurements were made in three systems: (1) 10 mM of [C4VC7][Tf2N]2 dissolved in 0.1 M K[Tf2N]/acetonitrile (an organic electrolyte), (2) 10 mM [C4VC7][Tf2N]2 dissolved in a 1-n-hexyl-3-methylimidazolium tris(pentafluoroethyl)-trifluorophosphate, [HMIm][FEP] ionic liquid (IL) (an ionic liquid (IL) electrolyte), and (3) the undiluted RAIL of 1.68 M [C4VC7][Tf2N]2 with no additional solvents or supporting electrolytes. At 25 °C, the DO values in systems (1), (2), and (3) were 8.2 × 10−6, 6.7 × 10−8, and 1.3 × 10−9 cm2 s−1, and the k0 values were 1.1 × 10−2, 3.6 × 10−3, and 2.0 × 10−5 cm s−1, respectively. Temperature-dependent DO and k0 values were further interrelated to investigate heterogeneous interfacial electron transfer processes in systems (2) and (3). Solvent dynamics and counter-ion relaxation processes were used to describe the results. In system (3), k0 values were proportional to both DO and counter-ion diffusion coefficients (DCIon) but inversely proportional to the viscosity (η). Moreover, almost the same magnitude of thermal activation barrier (∼64 kJ mol−1) was found for k0, DO, DCIon, and η−1 in the system (3). In system (2), k0 values showed a non-linear relationship with DO, DCIon and η−1, and a thermal activation barrier was found to be 22.2 kJ mol−1. These results enabled us to conclude that the V+/V2+ heterogeneous electron transfer in system (3) is controlled concurrently by solvent dynamics (segmental motion of alkyl chains attached to viologen centers) and electro-inactive counter anion motion. This work reveals an inherent dependency of heterogeneous electron transfer kinetics on the solvent and counter-ion dynamics in viologen IL systems.

Structure of Superabsorbent Polyacrylate Hydrogels and Dynamics of Counterions by Nuclear Magnetic Resonance

AbstractPolyacrylate hydrogels PAAM (M = 7Li+, 23Na+, 39K+, 87Rb+, and 133Cs+) are synthesized by free‐radical copolymerization and are studied by Nuclear Magnetic Resonance (NMR) over wide time and length scales to get an insight into the polymer network structure and the dynamics of alkali ions and water. 1H double‐quantum NMR (1H DQ‐NMR) indicates that neutralization by different alkali ions influences the polymer structure in swollen PAAM hydrogels. Relaxation rates of alkali ions are found to be dominated by quadrupolar relaxation. 1H relaxation varies with the chain fraction obtained from 1H DQ‐NMR. Pulsed field gradient NMR reveals diffusion coefficients of alkali ions and water for different swelling degrees. Network structure and dynamics as well as the interactions between water, alkali ions, and polymer chains are discussed.

Accurate Multi-Physics Numerical Analysis of Particle Preconcentration Based on Ion Concentration Polarization

This paper studies the mechanism of preconcentration of charged particles in a straight microchannel embedded with permselective membranes by numerically solving the coupled transport equations of ions, charged particles and solvent fluid without any simplifying assumptions. It is demonstrated that trapping and preconcentration of charged particles are determined by the interplay between drag force from the electroosmotic fluid flow and the electrophoretic force applied through the electric field. Several insightful characteristics are revealed, including the diverse dynamics of co-ions and counter ions, replacement of co-ions by focused particles, lowered ion concentrations in particle-enriched zone, and enhanced electroosmotic pumping effect, etc. Conditions for particles that can be concentrated are identified in terms of charges, sizes and electrophoretic mobilities of particles and co-ions. Dependences of enrichment factor on cross-membrane voltage, initial particle concentration and buffer ion concentrations are analyzed and the underlying reasons are elaborated. Finally, post priori condition for the validity of decoupled simulation model is given based on the charges carried by focused particles and buffer co-ions. These results provide an important guidance in the design and optimization of nanofluidic preconcentration and other related devices.

Influence of Divalent Counterions on the Dynamics in DNA as Probed by Using a Minor-Groove Binder.

DNA dynamics, to which water, counterions, and DNA motions contribute, is a topic of considerable interest because it is closely related to the efficiency of biological functions performed by it. Simulation studies and experiments suggest that the counterion dynamics in DNA probed by a minor-groove binder are similar for various monovalent counterions. To date, the influence on DNA dynamics of higher-valence counterions, which are also present around DNA and are known to bind more strongly to it than monovalent ions, has not been studied. Herein we investigated DNA dynamics in the presence of Mg2+ and Ca2+ , chosen for their relative abundance in cells, by using minor-groove binder 4',6-diamidino-2-phenylindole (DAPI) as a fluorescence probe. The dynamics, as measured from the time-resolved fluorescence Stokes shifts of DAPI bound to calf thymus DNA on a subpicosecond-to-nanosecond timescale, were found to be very similar in the presence of both the divalent ions and Na+ ions. The observation is explained by considering the screening of the electric field of the divalent ion by its hydration shell, preferential binding of the ions to the phosphate groups, and displacement of ions from the minor groove by DAPI due to the stronger binding interaction of the latter. Furthermore, the similarity of our results in the presence of Na+ to those reported for smaller oligonucleotides suggests that the chain length of DNA does not influence the DNA dynamics.

Effects of counterion size and backbone rigidity on the dynamics of ionic polymer melts and glasses.

It is well-known that the nature and size of the counterions affect the ionic conductivity and glass transition temperature of ionic polymers in a significant manner. However, the microscopic origin of the underlying changes in the dynamics of chains and counterions is far from completely understood. Using coarse-grained molecular dynamics simulations of flexible and semi-flexible ionic polymers, we demonstrate that the glass transition temperature of ionic polymeric melts depends on the size of monovalent counterions in a non-monotonic manner. The glass transition temperature is found to be the highest for the smallest counterions and decreases with an increase in the counterion radii up to a point, after which the glass transition temperature increases with a further increase in the radii. This behavior is because the counterions have significant effects on the coupled dynamics of the charges on the chains and counterions. In particular, increase in the radii of the counterions leads to strongly coupled dynamics between the charges on the chains and the counterions. The static dielectric constant of the polymer melts also has a significant effect on the coupling and the glass transition temperature. The glass transition temperature is predicted to decrease with an increase in the dielectric constant. This, in turn, leads to an increase in the diffusion constant of the counterions at a given temperature. Backbone rigidity is shown to increase the glass transition temperature and decrease the coupling. Furthermore, faster counterion dynamics is predicted for the melts of semi-flexible chains in comparison with flexible chains at the same segmental relaxation time. As the semi-flexible chains tend to have a longer segmental relaxation time, semi-flexible polymers with high dielectric constants are predicted to have diffusion constants of counterions comparable with flexible polymers.

Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics.

Molecular models of 5 nm sized ZnO/Zn(OH)2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization) and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution.

Possible Magnetic Resonance Signal Due to the Movement of Counterions around a Polyelectrolyte with Rotational Symmetry

Experimental, theoretical and computational studies revealed that the characteristic time scales involved in counterion dynamics in polyelectrolytes systems might span several orders of magnitude ranging from subnanosecond times to time scales corresponding to acoustic-like phonon mode frequencies, with an structural organization of counterions in charge density waves (CDWs). These facts raise the possibility of observing Magnetic Resonance (MR) signals due to the movement of counterions in polyelectrolytes. In case that this signal is detected in macroions or other biological systems, like micelles, vesicles, organeles, etc. with rotational symmetry, this method opens a new tool to measure with precission the counterions velocity.

Diffusion behavior of polyelectrolytes in dilute solution: coupling effects of hydrodynamic and Coulomb interactions

The diffusion behavior of polyelectrolytes in dilute salt-free solution is studied through a hybrid mesoscale simulation technique that combines the molecular dynamics method and the multiparticle collision dynamics approach. To elucidate the effects of hydrodynamic interactions (HI), we compare results for hydrodynamic and random solvents. When HI are taken into account, we find that the chain diffusivity decreases initially and then increases gradually with the increasing strength of the Coulomb interaction. By contrast, when HI are switched off, the electrostatic-dependent diffusivity shows three distinct regions, and a plateau of approximately constant diffusivity manifests between two decreasing regions. The findings reveal that the dynamics of polyelectrolytes in dilute solution depend on the coupling effects of hydrodynamic and Coulomb interactions, and that these dynamics can be understood by considering the conformational changes of chains, the counterion condensation, and the dynamics of counterions.

Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore.

The application of recent advances in nanopore technology to high-throughput DNA sequencing requires a more detailed understanding of solvent, ion and DNA interactions occurring within these pores. Here we present a combination of atomistic and coarse-grained modeling studies of the dynamics of short single-stranded DNA (ssDNA) homopolymers within the alpha-hemolysin pore, for the two single-stranded homopolymers poly(dA)40 and poly(dC)40. Analysis of atomistic simulations along with the per-residue decomposition of protein-DNA interactions in these simulations gives new insight into the very complex issues that have yet to be fully addressed with detailed MD simulations. We discuss a modification of the solvent properties and ion distribution around DNA within nanopore confinement and put it into the general framework of counterion condensation theory. There is a reasonable agreement in computed properties from our all-atom simulations and the resulting predictions from analytical theories with experimental data, and our equilibrium results here support the conclusions from our previous non-equilibrium Brownian dynamics studies with a recently developed BROMOC protocol that cations are the primary charge carriers through alpha-hemolysin nanopores under an applied voltage in the presence of ssDNA. Clustering analysis led to an identification of distinct conformational states of captured polymer and depth of the current blockade. Therefore, our data suggest that confined polymer may act as a flickering gate, thus contributing to excess noise phenomena. We also discuss the extent of water structuring due to nanopore confinement and the relationship between the conformational dynamics of a captured polymer and the distribution of blocked current.

Electro-optics of polyelectrolyte multilayers on colloidal particles

Electric light scattering method is used to study electrical properties and structure of polyelectrolyte multilayer films adsorbed on non-spherical particles in the absence of salt. Attention is focused on the advantage of electro-optics to give information simultaneously on the dynamics of counterions and the thickness of the multilayer films adsorbed on the particles in stabilized suspensions. Based on the electro-optical experiment, it is demonstrated that polarization of counterions along the chains of the last-deposited polymer governs the behavior of the whole multilayer film. Evidence is given that the film thickness can increase exponentially with the number of deposited layers even in the absence of salt when a fully charged polyelectrolyte is combined with a weakly charged one. Examples are presented for electro-optical characterization of multilayer films on colloidal particles with potential applications in anticorrosion coatings and medicine.

Dynamics of Dilute Solutions of Poly(aspartic acid) and Its Sodium Salt Elucidated from Atomistic Molecular Dynamics Simulations with Explicit Water

The use of forward osmosis (FO) process for seawater desalination has attracted tremendous interest in recent years. Besides the manufacture of suitable membranes, the major technical challenge in the efficient deployment of the FO technology lies in the development of a suitable "draw solute". Owing to its inherent advantages, poly(aspartic acid) has arisen to be an attractive candidate for this purpose. However, an investigation of its molecular level properties has not been studied in detail. In this paper, the dynamics of poly(aspartic acid) and its sodium salt in the dilute concentration regime have been reported. The quantification of the polymer conformational properties, its solvation behavior, and the counterion dynamics are studied. The neutral polymer shows a preferentially coiled structure whereas the fully ionized polymer has an extended structure. Upon comparing with poly(acrylic acid) polymer, another polymer which has been used as a draw solute, poly(aspartic acid) forms more number of hydrogen bonds as well as fewer ion pairs.

Dielectric Relaxation Spectroscopy Shows a Sparingly Hydrated Interface and Low Counterion Mobility in Triflate Micelles

The properties of ionic micelles are affected by the nature of the counterion. Specific ion effects can be dramatic, inducing even shape and phase changes in micellar solutions, transitions apparently related to micellar hydration and counterion binding at the micellar interface. Thus, determining the hydration and dynamics of ions in micellar systems capable of undergoing such transitions is a crucial step in understanding shape and phase changes. For cationic micelles, such transitions are common with large organic anions as counterions. Interestingly, however, phase separation also occurs for dodecyltrimethylammonium triflate (DTATf) micelles in the presence of sodium triflate (NaTf). Specific ion effects for micellar solutions of dodecyltrimethylammonium chloride (DTAC), bromide (DTAB), methanesulfonate (DTAMs), and triflate (DTATf) were studied with dielectric relaxation spectroscopy (DRS), a technique capable of monitoring hydration and counterion dynamics of micellar aggregates. In comparison to DTAB, DTAC, and DTAMs, DTATf micelles were found to be considerably less hydrated and showed reduced counterion mobility at the micellar interface. The obtained DTATf and DTAMs data support the reported central role of the anion's -CF3 moiety with respect to the properties of DTATf micelles. The reduced hydration observed for DTATf micelles was rationalized in terms of the higher packing of this surfactant compared to that of other DTA-based systems. The decreased mobility of Tf(-) anions condensed at the DTATf interface strongly suggests the insertion of Tf(-) in the micellar interface, which is apparently driven by the strong hydrophobicity of -CF3.

Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis

This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.

Counterion Dynamics in an Interpenetrated Coordination Cage Capable of Dissolving AgCl

In solution, the eight BF(4)(-) counterions of a positively charged D(4)-symmetric interpenetrated [Pd(4)ligand(8)](8+) double cage (1) are localized in distinct positions. At low temperatures, one BF(4)(-) ion is encapsulated inside the central pocket of the supramolecular structure, two BF(4)(-) ions are bound inside the equivalent outer pockets, and the remaining five BF(4)(-) ions are located outside the cage structure (expressed by the formula [3 BF(4)@1][BF(4)](5)). On warming, the two BF(4)(-) ions in the outer pockets are found to exchange with the exterior ions in solution whereas the central BF(4)(-) ion stays locked inside the central cavity (here written as [BF(4)@1][BF(4)](7)). The exchange kinetics were determined by exchange spectroscopy (EXSY) NMR experiments and line-shape fitting in different solvents. The tremendously high affinity of this double cage for the binding of two chloride ions inside the outer pockets allows for complete exchange of two BF(4)(-) ions by the addition of solid AgCl to give [2 Cl+BF(4)@1][BF(4)](5). The uptake of the two chloride ions is allosteric and is thus accompanied by a structural rearrangement (compression along the Pd(4) axis) of the double cage structure. An analysis by using 900 MHz NOESY NMR spectroscopy shows that this compression of about 3.3% is associated with a helical twist of 8°, which together resemble a screw motion. As a consequence of squeezing each of the outer two pockets by 53%, the volume of the central pocket is increased by 43%, which results in an increase of 36% in the (19)F spin-lattice relaxation time (T(1)) of the central BF(4)(-) ion. The packing coefficients (PC) for the ions in the outer pockets (103% for BF(4)(-) and 96% for Cl(-)) were calculated.