Non-electrostatic Forces Research Articles

Calculation of the binding free energy for magnesium–RNA interactions

The nature of the interaction between nucleic acids and divalent ions in solution is complex. It includes long-range electrostatic and short-range nonelectrostatic forces. Water molecules can be in an inner coordination shell that intervenes between the ion and its binding site. This work describes a method for calculating the binding free energy and applies it to a specific Mg-RNA system in the presence of monovalent salt. The approach combines high-level ab initio theory with Poisson-Boltzmann calculations and provides an accurate description of all terms of the binding free energy for magnesium ions located at the RNA surface (including nonelectrostatic interactions). Some alternative macroscopic approaches are also discussed.

Formation of vortex dust structures in inhomogeneous gas-discharge plasmas

A generalized analytical model of instabilities in a dusty plasma with a nonzero grain charge gradient in a field of nonelectrostatic forces is considered. A review is given of different experimental observations of the dust self-oscillations that occur in the plasmas of an rf capacitive discharge and a dc glow discharge and whose appearance can be explained in terms of the proposed model. It is shown that the change in the grain charge gives rise to dynamic dust structures in laboratory gas-discharge plasmas. Attention is focused on the analysis of the onset of vortex motion of the dust grains.

Interaction Between Tomato spotted wilt virus N Protein Monomers Involves Nonelectrostatic Forces Governed by Multiple Distinct Regions in the Primary Structure

ABSTRACT The ambisense RNA genome of Tomato spotted wilt virus (TSWV) isby interaction with numerous copies of the virus encoded nucleocapsid (N) protein to form a subvirion structure called a ribonucleo-protein (RNP). RNPs are central to the viral replication cycle because they, and not free viral RNA, serve as templates for viral gene expression and genome replication. N protein monomers bind to viral RNA molecules in a cooperative manner. We have examined regions of the N protein that are involved in the N-N interactions that likely contribute to the cooperative binding of N to viral RNA. We created random and alanine scanning mutants of N and then screened the mutants for defects in N-N interaction using reverse and forward yeast two-hybrid assays. Our experiments identified residues in three distinct regions of the primary structure of the protein, residues 42 to 56, 132 to 152, and in the C-terminal 26 amino acids, that contribute to N-N dimerization or multimerization.interactions between N monomers mediated by the residues we identified are of a nonelectrostatic nature.

Protein adsorption modalities on polyelectrolyte multilayers.

Protein adsorption on polyelectrolyte multilayers (PEMUs) was evaluated using a combination of synthetic polyelectrolytes and proteins, including serum albumin, fibrinogen, and lysozyme. Variables such as surface and protein charge, polymer hydrophobicity, and hydrophilic repulsion were introduced to probe interaction mechanisms. Quantitative analysis with reflectance Fourier transform infrared spectroscopy, optical waveguiding, and UV-vis absorption, together with qualitative information from atomic force microscopy, provided a coordinated picture for what drives protein adsorption and how the molecules are disposed on the multilayer surface. It was found that multilayers bearing a particular surface charge sorbed biomolecules if they were of opposite charge, yielding significant loadings within the bulk PEMU. Adsorption of like-charged proteins, as surface aggregates, occurred to a much lower extent, driven by nonelectrostatic forces. A diblock copolymer comprising a hydrophilic poly(ethylene oxide) block was capable of further minimizing protein adsorption as a result of hydrophilic repulsion, although none of the surfaces tested defeated protein adsorption completely. However, poly(acrylic acid) homopolymer was quite effective in this respect. A composition gradient, formed during multilayer buildup, induced a gradient in hydrophilicity through the PEMU, which is an efficient and economical method of creating a protein-resistant surface.

Micellar effect on protonation equilibria of L-arginine and L-histidine

The protonation equilibria of L-arginine and L-histidine have been studied pH-metrically in varying concentrations (0.0-2.5%, w/v) of CTAB, SLS and TX-100 solutions maintaining an ionic strength of 0.16 mol dm - 3 at 303 K. The protonation constants have been evaluated with MINIQUAD75. They exhibited a non-linear trend with increase in micellar content due to changed dielectric constant of the medium as well as electrostatic and non-electrostatic forces operating on the equilibria due to zwitterionic form of the ligands.

Relative importance of electrostatic forces on powder particles

The phenomenon of electrostatic attraction between charged materials has been recognized since early Greek times. Despite its long history, the relative importance of electrostatic forces (compared with non-electrostatic forces) on powder particles is still a subject of debate among today's scientists. In this article, we attempt to present a systematic evaluation of the possible magnitudes of electrostatic forces and van der Waals forces, based on theoretical analysis and existing experimental data. For small particles (about 10 μm as used in electrophotographic toner), both van der Waals and electrostatic forces may play a significant role. Without setting up appropriate constraints (or conditions) for comparison, measurements of powder samples can show either dominant van der Waals forces or dominant electrostatic forces and therefore lead to controversial conclusions. Our mathematical evaluation indicates that the electrostatic adhesion on a charged particle under the condition that it can be detached by an applied electric field is likely to be greater than van der Waals forces. However, for particles of the same surface structures, the relative significance of van der Waals forces is expected to increase as the particle size is reduced. But many electrophotographic processes require that the net electrostatic force is sufficiently greater than the magnitude of van der Waals forces. Hence, it becomes a practical trend to use more surface additives on smaller toner particles desired in high quality electrophotographic printing, to effectively reduce van der Waals forces so as to ensure that the electrostatic forces become relatively dominant.

Influence of Na-humate on electric surface properties and stability of γ-Al2O3 dispersions

Electro-optical properties and electrophoretic mobility of γ-Al2O3 particles in the presence of different Na-humate (NaHS) concentrations at pH 4–6 have been studied. The adsorption layer thickness was determined by measuring the rotation diffusion coefficient. The NaHS concentration corresponding to the charge reversal (isoelectric point, IEP of the γ-Al2O3/NaHS complex) decreases with pH increase. In the IEP, the dispersion system is fully precipitated and above the IEP it is restabilized. The increase of the electrophoretic mobility above the IEP supposes that some specific (non-electrostatic) forces operate after the charge reversal, leading to further adsorption of NaHS on alumina. The adsorption layer thickness under the IEP is ≈10 nm and above the IEP it is ≈30 nm. This considerable thickness value is an indication for some electrosteric stabilization. The frequency dependence of the electro-optic effect above the IEP is shifted to lower frequency, showing a considerably reduced mobility of counterions, probably as result of their condensation on the humate backbone. The comparison between the concentration dependencies of the electrophoretic mobility, the surface electric polarizability (determined electrooptically) and the particles’ stability shows that under the IEP the stability correlates better with the electric polarizability than with the electrokinetic potential.

Effect of surfactants on protonation equilibria of oxalic and malonic acids

Protonation equilibria of oxalic and malonic acids are investigated in aqua-miccllar media of varying composition (0-2.5%, w/w) electrometrically at an ionic strength of 0.17 mol dm - 3 and at temperature 303 K. The best-fit chemical models are, arrived at based on statistical grounds employing crystallographic R factor, Χ 2 , skewness and kurtosis. The variation in the protonation constants with the dielectric constant of the medium is attributed to the electrostatic and non-electrostatic forces.

Effect of solvent on protonation equilibria of L-glutamine and succinic acid

Protonation equilibria of L-glutamine and succinic acid are investigated in 0-60% (v/v) aquo-acetonitrile media at an ionic strength of 0.1 mol dm - 3 and temperature 303 K. The best fit chemical models are arrived at using MINIQUAD75 based on statistical parameters. The change in protonation constants with the dielectric constant of the medium is attributed to the electrostatic and non-electrostatic forces.

Speciation of ternary complexes of calcium(II) and magnesium(II) with L-glutamine and succinic acid in ethylene glycol-water mixtures

A computer-assisted pH-metric investigation has been made on the speciation of Ca I I and Mg I I complexes of L-glutamine (Gln) and succinic acid (Sue). The titrations are carried out with sodium hydroxide in varying concentrations (0-60%, v/v) of ethylene glycol (EG)-water mixtures at ionic strength of 0.16 mol dm - 3 and temperature 303 K. Ca I I and Mg I I form the ternary complexes MLX 2 H 2 . ML 2 XH 2 , MLX 2 H and ML 2 XH in EG-water mixtures. The variation of stability constants with dielectric constant is explained on the basis of electrostatic and non-electrostatic forces.

Speciation of calcium(II) and magnesium(II) complexes of L-glutamine and succinic acid in ethylene glycol-water mixture

A pH-metric investigation has been made on the speciation of Ca I I and Mg I I complexes of glutamine (Gln) and succinic acid (Suc) in varying concentrations (0-60%, v/v) of ethylene glycol-water mixtures at an ionic strength of 0.16 mol dm - 3 and temperature 303 K. The active form of ligands is LH. The predominant species detected for Gin complexes are MLH, ML 2 H and ML 2 and of Suc are ML 2 H and ML 2 . The trend in variation in values of protonation and complex stability constants with dielectric constant is explained on the basis of electrostatic and non-electrostatic forces.

The role of dispersive and electrostatic interactions in the aqueous phase adsorption of naphthalenesulphonic acids on ozone-treated activated carbons

The adsorption of 1-naphthalenesulphonic (NS), 1,5-naphthalenedisulphonic (NDS) and 1,3,6-naphthalenetrisulphonic (NTS) acids on ozonated activated carbons was assessed. Commercial activated carbon (Filtrasorb 400) was treated with different ozone doses in order to study the effect of ozone treatment on their surface properties, and investigate the behaviour of these carbon samples in the adsorption of the above naphthalenesulphonic acids. Experimental results showed that the adsorption capacity sharply decreased as the number of sulphonic groups in the aromatic ring increased. As the concentration of oxygenated electron-withdrawing groups on the carbon surface increased, a significant reduction in adsorption capacity of aromatic sulphonic compounds was observed. These results indicate that the adsorption process takes place mainly by π–π dispersion interactions between the aromatic ring electrons of the naphthalenesulphonic acids and the basal plane of the activated carbon. Moreover, in all cases, the adsorption capacity of aromatic sulphonic acids decreased as the pH increased. This indicates that electrostatic interactions between the adsorbate and the carbon surface also took place, as a result of the ionisation of oxygenated surface groups on the carbon surface. Nevertheless, the dispersive (non-electrostatic) forces govern these adsorption processes.

The Physical Basis of Nucleic Acid Base Stacking in Water

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.

Phase diagram of MgO from density-functional theory and molecular-dynamics simulations

We use first-principles methods~no empirical parameters! to establish the phase diagram for the B1~NaCl!, B2~CsCl!, and liquid phases of MgO. We used density-functional theory with the generalized gradient approximation to predict the equation-of-state @volume versus pressure NV( P)O# at 0 K for MgO in the low-density B1 ~NaCl! phase and the high-density B2 ~CsCl! phase. We find a pressure-induced phase transition at P5400 GPa. We then fitted an MS-Q type force field~FF! to the quantum results. This FF, denoted as qMS-Q FF, was then used in molecular dynamics ~MD! simulations to investigate the phase coexistence curves of the B1-B2 and B1-liquid phases. This leads to a first-principles phase diagram for MgO for pressures up to 500 GPa and temperatures up to 8000 K. The accuracy of the fit of the qMS-Q FF to the quantum mechanics validates the functional form of the qMS-Q FF in which the charges are obtained from charge equilibration ~QEq! and the nonelectrostatic forces are described with simple two-body Morse potentials. Such qMS-Q FF using no empirical data should be useful for MD or Monte Carlo simulations of many other materials. @S0163-1829~99!02346-2#

Drug release from a porous ion-exchange membrane in vitro.

The effect of environmental ionic strength on the rate of drug release from a cation exchange membrane was evaluated. Cationic propranolol-HCl, timolol, sotalol-HCl, atenolol and dexmedetomidine-HCl and neutral diazepam were adsorbed onto a porous poly(vinylidene fluoride) (PVDF) membrane that was grafted with bioadhesive poly(acrylic acid) chains (PAA-PVDF). Despite its porosity, the PAA-PVDF membrane acted as a cation exchange membrane. The release of adsorbed drug from the PAA-PVDF membrane was investigated by using a USP rotating basket apparatus. Adsorption of cationic drugs onto the PAA-PVDF membrane tended to increase with increasing lipophilicity of the drug. A decrease in the ionic strength of the adsorption medium increased the amount of the cationic drugs adsorbed onto the membrane, but had no effect on diazepam adsorption. The release of cationic drugs from the PAA-PVDF membrane was greatly affected by the ionic strength of both the adsorption medium and the dissolution medium, while ionic strengths did not affect diazepam release. Our results suggest that the ionic strength of both the adsorption and dissolution media substantially affects the release rate of a drug that has been adsorbed onto the ion exchange membrane, primarily via electrostatic interactions, while ionic strength has no effect on the release of a drug which has been adsorbed onto the membrane via non-electrostatic forces.

Complex formation between the anionic polymer (PAA) and a cationic drug (procaine HCI): characterization by microcalorimetric studies.

Due to the importance of drug-polymer interactions in, inter alia, drug loading/release, supramolecular assemblies and DNA delivery for gene therapy, the aim of this study was therefore to establish the mechanism of interaction between a model polymer (Polyacrylic acid, PAA) and a model drug (procaine HCl). This was performed by studying the effect of salt (KCl) concentration on their heat released values using Isothermal Titration Microcalorimetry (ITM). The integrated released heat data were computer fitted to a one class binding model and the thermodynamic parameters (Kobs, deltaH, and N) were determined. As the KCl concentration was increased, Kobs decreased thus establishing the salt dependence of the interaction. The linear variation of deltaGobs with deltaSobs indicated that their interaction was entropically driven. The stoichiometry of the interaction was calculated to be one procaine molecule per monomer of PAA. Dissection of the total observed free energy at each KCI concentration indicated that the contribution of the non-electrostatic attractions to the interaction of PAA with procaine HCl was greater than those of the electrostatic attractions. We have shown that the interaction between PAA and procaine HCl is dependent upon the presence of counterions (monovalent ions) and is mainly entropically driven. The calculated stoichiometry indicated that one procaine HCl molecule neutralised one carboxylic acid group on PAA. Although electrostatic interactions were necessary for initiating complex formation, the non-electrostatic forces were dominant in stabilising the PAA-procaine HCl complex.

Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides

Fluorescence-based solution methods have been used to study the binding of the trp repressor of Escherichia coli to a series of oligonucleotides bearing all or partial determinants for high affinity specific binding. The tryptophan, salt concentration and competitor DNA dependence of the binding affinities was examined for these targets. Binding to a fluorescein-labeled 20 base-pair hairpin structure oligonucleotide, which contains a palindromic repressor binding site (GAACTAGTTAACTAGTAC) and is known to bind repressor in a 1 : 1 dimer-DNA complex, resulted in a protein concentration-dependent, competable static quenching of fluorescence in presence of co-repressor, l-tryptophan. The affinity recovered from the fits of these intensity profiles at 100 mM KCl was on the order of 4 × 108M−1. In absence of co-repressor an increase in intensity at high repressor concentration (>10−7M) was observed. The salt concentration dependence of the specific binding of the holo-repressor to this oligonucleotide was approximately half as large as what would be predicted by the number of phosphate contacts in the crystal structures of the complex. Repressor binding to the fluorescein-labeled hairpin 20mer was compared with binding to a rhodamine-labeled 36 base-pair oligonucleotide bearing two inverted structural half-sites GNACT separated by an eight base-pair spacer containing none of the natural intervening sequence. The rather low affinity observed for the 36mer revealed that the intervening sequence in the natural operators contains energetic specificity determinants. Binding to a rhodamine-labeled oligonucleotide bearing a completely non-specific sequence was shown to occur over the same concentration range (>100 nM), regardless of tryptophan concentration, whereas binding to sequences bearing partial specificity ratio between 100 and 1000, depending upon the salt concentration. Even in abscence of added KCl, the specificity ratio of trp repressor was greater than 100, implicating a significant free energy contribution from non-electrostatic interaction forces.

A comparative study of the sorption of serum albumin, lysozyme, and cytochrome C at phospholipid membranes using surface tensiometry, electrophoresis, and leakage of probe molecules

Protein sorption at phospholipid membranes is studied when proteins are injected into the solution, by measuring the change in the surface tension of lipid monolayers spread on the water surface. A method for analyzing the surface tension data is proposed. The results of this analysis are in agreement with the results of experiments on liposomes: an investigation of the change in electrophoretic mobilities and leakage tests of probe molecules from inside the liposomes, when proteins are added to the dispersion medium. The conclusion is that serum albumin, a rather flexible protein, absorbs into lipid membranes through non-electrostatic forces, whereas cytochrome C and lysozyme adsorb onto the membranes mainly by electrostatic attraction.

Deposition Kinetics of Two Viruses in Packed Beds of Quartz Granular Media

The removal of waterborne viruses by packed bed filtration was examined using a model system consisting of two different bacteriophages (MS2 and λ) and saturated beds of ultrapure quartz grains. The majority of these experiments were conducted at a solution pH of 5, where the viruses and quartz possess a net negative surface charge. On the basis of a simple model that correctly predicts the isoelectric point (pI) of MS2, the surface charge on this virus appears to originate from the ionization of amino acid residues located on the exterior of the virus particle. The deposition rates of both MS2 and λ at pH 5 are sensitive to the ionic composition of the suspending fluid, with more rapid filtration occurring at the higher salt concentrations. The filtration rate of λ approaches the theoretical value estimated using the Smoluchowski−Levich (S−L) approximation at pH 5 and high salt concentrations (300 mM NaCl) or at the pI of the virus, suggesting that electrostatic repulsive forces effectively dominate the filtration dynamics of λ. The filtration rate of MS2, on the other hand, is at least 800% less than the theoretical S−L value at high salt or at the pI of this virus, suggesting that both electrostatic and nonelectrostatic repulsive forces influence the filtration of MS2. We investigate the possibility that this nonelectrostatic force is steric in nature, arising from hydrophilic polypeptide loops which extend a maximum of 1 nm off the MS2 surface.

The electrostatic contribution to the B to Z transition of DNA.

In this paper, the finite difference nonlinear Poisson-Boltzmann (NLPB) equation is used to calculate the electrostatic contribution to the B to Z transition of DNA using detailed molecular structures of each DNA form. The electrostatic transition free energy is described as a balance between the change in intramolecular Coulombic interactions and charge-dependent interactions between the DNA and the solvent. As in many prior studies, we find that the larger electrostatic repulsions among the more closely spaced Z-DNA phosphates destabilize this form compared to B-DNA in the absence of solvent. However, as a result of the more compact three-dimensional geometry of Z-DNA, both water and salt are found to strongly stabilize this conformation to the extent that the total electrostatic free energy favors the B to Z transition in aqueous solution. Water acts not only by screening the inter-phosphate repulsions but also by solvating both charged and polar groups on Z-DNA more favorably than B-DNA. In addition, Z-DNA is stabilized by a substantially higher concentration of nearby counterions than B-DNA. The relative stabilization of Z-DNA by salt increases with increasing bulk salt concentration, leading to the high-salt B to Z transition. We find that the salt dependence of the B to Z transition free energy calculated with the NLPB equation agrees reasonably well with experimental results. Since electrostatic interactions are found to favor the Z-form, nonelectrostatic forces must be responsible for the relative stability of B-DNA in solution. An analysis of these forces suggests that the conformational entropy may play an important role.