Presence Of Counterions Research Articles

Charge transport and magnetoresistance of G4-DNA molecular device modulated by counter ions and dephasing effect

The charge transport properties of the G4-DNA molecular device in the presence of counter ions and dephasing effect are investigated based on the Green function method and Landauer–Büttiker theory. The currents through the G4-DNA molecular device depend on the interference patterns at different coupling configurations. There is an effective electrostatic interaction between the counter ions and the G4-DNA molecule which introduces disorder into the on-site energies of G bases. The current through the device can be enhanced by the small disorder which avoids the strong interference of electrons at the same energy in some coupling configurations, however the diagonal disorder can suppress the overall current due to the Anderson localization of charge carriers when the disorder is large. In the presence of dephasing effect the current through the device at all coupling configurations can be enhanced as a result of the phase coherence losing of electron. As for the magnetic field response, the magnetoresistance of the device is always suppressed by the counter ions and dephasing effect.

Ammonia mobility in chabazite: insight into the diffusion component of the NH3-SCR process.

The diffusion of ammonia in commercial NH3-SCR catalyst Cu-CHA was measured and compared with H-CHA using quasielastic neutron scattering (QENS) and molecular dynamics (MD) simulations to assess the effect of counterion presence on NH3 mobility in automotive emission control relevant zeolite catalysts. QENS experiments observed jump diffusion with a jump distance of 3 Å, giving similar self-diffusion coefficient measurements for both Cu- and H-CHA samples, in the range of ca. 5-10 × 10(-10) m(2) s(-1) over the measured temperature range. Self-diffusivities calculated by MD were within a factor of 6 of those measured experimentally at each temperature. The activation energies of diffusion were also similar for both studied systems: 3.7 and 4.4 kJ mol(-1) for the H- and Cu-chabazite respectively, suggesting that counterion presence has little impact on ammonia diffusivity on the timescale of the QENS experiment. An explanation is given by the MD simulations, which showed the strong coordination of NH3 with Cu(2+) counterions in the centre of the chabazite cage, shielding other molecules from interaction with the ion, and allowing for intercage diffusion through the 8-ring windows (consistent with the experimentally observed jump length) to carry on unhindered.

Dispersion and Blocking Properties of Sulfonated Phenol Formaldehyde Resin

Dispersion properties of sulfonated phenol formaldehyde (SPF) resin were studied by measuring the hydrodynamic diameter and zeta potential of SPF resin aggregates. And the solution turbidity as a function of time at different NaCl concentrations and pH values was measured to evaluate the dispersion stability. The results show that when dissolved in water, the SPF resin was negatively charged. Dispersion stability of SPF resin solution was destroyed when NaCl concentration was higher than 0.7 wt%. The hydrodynamic diameter and zeta potential of SPF resin aggregates increased with NaCl concentration, which corresponds well with DLVO theory. In the presence of counterions (Na−), surface charge of SPF resin molecules can be screened leading to the decreased repulsive force, which results in the unstability of SPF resin dispersion. When pH was smaller than 6.0, the SPF resin solution was unstable due to the protonation of phenolic –O− and groups. The hydrodynamic diameter and zeta potential increased with the decrease of pH values. Moreover, membrane filtration results show that the formation of SPF resin aggregates can effectively block the cellulose membrane. This result indicates that SPF resin aggregates have certain mechanical strength to block pore throat in porous media showing potential applications in enhanced oil recovery.

Fluxional behaviour of tricyclo[2.2.1.02,6]heptaphosphide trisanion: a DFT investigation

AbstractThe structures of the tricyclo[2.2.1.02,6]heptaphosphide trisanion, tricyclo[2.2.1.02,6]heptaphosphane triradical and their carbocyclic analogues have been investigated theoretically at the density functional theory (DFT) (B3LYP/6-31 + G*) level. The existence of negative hyperconjugation in these molecules could be established by natural bond orbital analysis. The weakening of theσbonds combined with the possibility of the valence-shell expansion at the anionic charge carrying phosphorus atoms in the tricyclo[2.2.1.02,6]heptaphosphide trisanion induces a degenerate [2,2]sigmatropic rearrangement with a low energy barrier making all the phosphorus atoms equivalent, as detected by31P NMR experimentally. This energy barrier is enhanced in the presence of counterions. Its carbocyclic analogue trisanion fails to undergo a [2,2]sigmatropic rearrangement due to the inability of the anionic carbon centres to expand their valence shell. The tricyclo[2.2.1.02,6]heptaphosphane triradical and its carbocyclic analogue undergo a [2,2]sigmatropic rearrangement, as valence-shell expansion at the carbon atom is not required in this case. A lower activation energy barrier for the [2,2]sigmatropic rearrangement of the tricyclo[2.2.1.02,6]heptane triradical as compared to that for its phospha-analogue can be rationalised on the basis of the higher ring strain of cyclopropane than triphosphirane.

Contribution of counterions and degree of ionization for birefringence creation and relaxation kinetics parameters of PAH/PAZO films

Photo induced birefringent materials can be used to develop optical and conversion energy devices, and consequently, the study of the variables that influences the creation and relaxation of birefringence should be carefully analyzed. In this work, the parameters of birefringence creation and relaxation kinetics curves obtained on layer-by-layer (LBL) films, prepared from azo-polyectrolyte poly[1-[4-(3-carboxy-4 hydroxyphenylazo) benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) and poly(allylamine hydrochloride)(PAH), are related with the presence of counterions and the degree of ionization of the polyelectrolytes. Those kinetics curves obtained on PAH/PAZO LBL films, prepared from PAH solutions with different pHs and maintaining the pH of PAZO solution constant at pH = 9, were analyzed taking into account the films composition which was characterized by X-ray photoelectron spectroscopy. The creation and relaxation birefringence curves are justified by two processes: one associated to local mobility of the azobenzene with a characteristic time 30 s and intensity constant and other associated with polymeric chains mobility with the characteristic time and intensity decreasing with pH. These results allow us to conclude that the birefringence creation process, associated to local mobility of azobenzenes is independent of the degree of ionization and of number of counterions or co-ions present while the birefringence creation process associated to mobility of chains have its characteristic time and intensity dependent of both degree of ionization and number of counterions. The birefringence relaxation processes are dependent of the degree of ionization. The analysis of the films composition revealed, in addition, the presence of a protonated secondary or tertiary amine revealing that PAZO may have positive charges and consequently a zwitterionic behavior.

Exploring LacI-DNA dynamics by multiscale simulations using the SIRAH force field.

The lac repressor protein (LacI) together with its target regulatory sequence are a common model for studying DNA looping and its implications on transcriptional control in bacteria. Owing to the molecular size of this system, standard all-atom (AA) simulations are prohibitive for achieving relevant biological time scales. As an alternative, multiscale models, which combine AA descriptions at particular regions with coarse-grained (CG) representations of the remaining components, were used to address this computational challenge while preserving the relevant details of the system. In this work, we implement a new multiscale approach based on the SIRAH force field to gain deeper insights into the dynamics of the LacI-DNA system. Our methodology allows for a dual resolution treatment of the solute and solvent, explicitly representing the protein, DNA, and solvent environment without compromising the AA region. Starting from the P1 loop configuration in an undertwisted conformation, we were able to observe the transition to the more stable overtwisted state. Additionally, a detailed characterization of the conformational space sampled by the DNA loop was done. In agreement with experimental and theoretical evidence, we observed the transient formation of kinks at the loop, which were stabilized by the presence of counterions at the minor groove. We also show that the loop's intrinsic flexibility can account for reported FRET measurements and bent conformations required to bind the CAP transcription factor.

Applicability of Positive Cooperativity Model of Enzyme Catalysis on Surfactant-Mediated Reaction of Pararosaniline Hydrochloride Carbocation with Hydroxide Ion

The reaction of hydroxide ion with stabilized pararosaniline hydrochloride carbocation was investigated in the presence of cationic micelles of cetyltrimethylammonium bromide (CTAB) and anionic micelles of sodium dodecyl sulfate (SDS). Pseudo-first-order kinetics were followed by the reaction system and rate constant depends on surfactant concentration. The reaction was strongly inhibited in the presence of SDS micelles whereas catalyzed in the presence of CTAB micelles. Micellar data were analyzed by applying positive cooperativity model of enzyme catalysis. The value of index of cooperativity (n) was greater than 1 for all reaction systems. Inhibitory and catalytic effect in the presence of micelles had been explained on the basis of hydrophobic and electrostatic interactions of various species present in the reaction systems. Presence of counterions in the reaction system inhibited the reaction rate.

Reversible hydrophobic ion-paring complex strategy to minimize acylation of octreotide during long-term delivery from PLGA microparticles

Acylation of peptide has been reported for a number of peptides and proteins during release from polymers comprising of lactide and glycolide. We hypothesize that reversible hydrophobic ion-pairing (HIP) complex may minimize octreotide acylation during release. Sodium dodecyl sulfate (SDS), dextran sulfate A (DSA, Mw 9–20kDa) and dextran sulfate B (DSB, Mw 36–50kDa) were selected as ion-pairing agents to prepare reversible HIP complex with octreotide. Complexation efficiency was optimized with respect to the mole ratio of ion-pairing agent to octreotide to achieve 100% complexation of octreotide. Dissociation studies suggested that DSA-octreotide and DSB-octreotide complexes dissociate completely at physiological pH in presence of counter ions unlike SDS-octreotide complex. DSA-octreotide and DSB-octreotide complex encapsulated PLGA microparticles (DSAMPs and DSBMPs) were prepared using the S/O/W emulsion method. Entrapment efficiencies for DSAMPs and DSBMPs were 74.7±8.4% and 81.7±6.3%, respectively. In vitro release of octreotide was performed by suspending MPs in gel. A large fraction of peptide was released in chemically intact form and <7% was acylated from DSAMPs and DSBMPs in gel over 55 days. Therefore, HIP complexation could be a viable strategy to minimize acylation of peptides and proteins during extended release from lactide and glycolide based polymers.

High density monolayers of plasmid protein on latex particles: experiments and theoretical modeling

Monolayers obtained by adsorption of the plasmid protein KfrA on negatively charged polystyrene latex particles under diffusion-controlled conditions at pH 3.5 were interpreted in terms of the random sequential adsorption (RSA) model. A quantitative agreement of the theoretical results derived from these calculations with experimental data was attained for the ionic strength from 0.15 up to 10−2 M. This confirmed the adsorption mechanism of KfrA molecules on latex in the form of tetramers up to 10−2 M. On the other hand, for the ionic strength of 10−3 M the experimental coverage agreed with theoretical predictions under the assumption that screening of electrostatic interaction is enhanced by the presence of counterions and negatively charged polymer chains stemming from latex particles.

Free Energies for Trans-Membrane Pore Formation in the Presence of Arginine-Rich Peptides from Molecular Dynamics Simulations

Antimicrobial peptides are unique and diverse group of molecules, where the amino acid composition, cationic charge and size enables them to attach and insert into plasma membrane to form pores. These trans-membrane pores eventually lead to the cell death of the microbe. Several mechanisms were proposed for the activity of antimicrobial peptides, but a quantitative understanding of those mechanisms has remained elusive. Therefore, we modeled the formation of a trans-membrane pore in the presence of a cationic Arginine-rich model peptide using coarse-grained and atomistic molecular dynamics (MD) simulations. Free energies for trans-membrane pore formation were calculated as a function of peptide concentration and lipid composition. We find that electrostatics and presence of counter-ions; esp. for the case of charged lipids and peptides, play a critical role in free energy calculations. We address the following questions: a) does insertion of a peptide or several of them, influence the free energy of pore-formation; and b) is pore-formation a required step, or is the increased disorder of the lipids sufficient to insert a peptide? Finally, we present a quantitative comparison between the free energy of trans-membrane pore in the absence and presence of N-Arginine peptides, with the aim to provide a quantitative description of the activity of antimicrobial peptides on lipid membranes.

Modelling the effects of competing anions on fluoride removal by functionalized polyacrylonitrile coated with iron oxide nanoparticles

Fe 2 O 3 nano particles supported on functionalized poly-acrylonitrile was prepared. PAN-oxime-nano Fe 2 O 3 was characterized by XRD, FTIR andTEMand used for fluoride adsorption. The adsorption capacity increased with increasing initial fluoride concentration and reaction time. Fluoride-removal performance of PAN-oxime-nano Fe 2 O 3 was also tested in the presence of various competing anions usually found in drinking water. Competitive sorption between fluoride and competing anions showed a minimum preference for chloride counterions. Carbonate was the greatest competitor for fluoride removal followed by phosphate and sulphate. Counterion presence decreased fluoride adsorption capacity in order of CO 3 2− > PO 4 3− > SO 4 2− > Cl − . The presence of anions at various concentrations decreased fluoride adsorption capacity on PAN-oxime-nano Fe 2 O 3 by 1.22 to 6.51 mg g –1 . Effects of each two anions exist simultaneously in aqueous solution on fluoride adsorption was investigated using Tukey’s test (called also a pairwise comparison). Tukey’s HSD results indicate that the differences between various pairs of anions are significant (P < 0.05), except for chloride–sulphate (P = 0.08). In the design of PAN-oxime-nano Fe 2 O 3 for environmental applications, the strong influence of the counter ions must be considered. KEYWORDS Fluoride, PAN-oxime- nano Fe 2 O 3 , counterion, adsorption.

Multi-scale simulation studies on interaction between anionic surfactants and cations

In this paper, a dissipative particle dynamics (DPD) simulation method was used to investigate the impact of cations on the rheological properties of dodecyl sulfonate surfactant solutions. In order to obtain reasonable interaction between head groups of the surfactant, the geometric structure and interaction between dodecyl sulfonate and cations are optimized using density function theory (DFT) at the B3LYP/6-31G level. The DFT calculated results indicate that α-methylene nearest the head group can be classified as a part of the polar head. After binding, the charge on polar head decreases, thus greatly reduces the repulsion between the head groups. It is found that the presence of counterions is one of induction factors on the formation of wormlike micelles, thus greatly enhances the viscosity of surfactant solution. With the increasing in shear strengthen, the wormlike micelles are gradually oriented in the x direction and then broken up into small spherical micelles. This process is also shown by the decrease of viscosity, which decreases quickly at the low shear rates, then keeps almost a constant at the moderate shear rates and at last decreases again at the shear rates larger than a critical value. Compared with monovalent cations, divalent cations have a stronger effect on the rheological properties of dodecyl sulfonate solutions.

Ionically cross-linkable hyaluronate-based hydrogels for injectable cell delivery

Although hyaluronate is an attractive biomaterial for many biomedical applications, hyaluronate hydrogels are generally formed using chemical cross-linking reagents that may cause unwanted side effects, including toxicity. We thus propose to design and prepare ionically cross-linkable hyaluronate compounds that can form gels in the presence of counter-ions. This study is based on the hypothesis that introduction of alginate to hyaluronate backbones (hyaluronate-g-alginate) could allow for gel formation in the presence of calcium ions. Here, we demonstrated ease of formation of cross-linked structures with calcium ions without additional chemical cross-linking reagents in hyaluronate-g-alginate (HGA) gels. The mechanical properties of HGA gels were regulated through changes in polymer composition and calcium concentration. We also confirmed that HGA gels could be useful in regenerating cartilage in a mouse model following subcutaneous injection into the dorsal region with primary chondrocytes. This finding was supported by histological and immunohistochemical analyses, glycosaminoglycan quantification and chondrogenic marker gene expression. This approach to the design and tailoring of ionically cross-linkable biomedical polymers may be broadly applicable to the development of biomaterials, especially in the drug delivery and tissue engineering fields.

Electrosynthesis and characterization of poly methylene blue and its nanocomposite with ZnO nanoparticles

The poly methylene blue (PMB) films were deposited on ITO electrode by cyclic voltammetry. The fractal dimension of PMB films in the presence of counter ions was investigated. Theoretical calculations for methylene blue polymerization were carried out at density functional theory (DFT) level using the 6-31G(d,p) basis set for all atoms with Gaussian 03 program package. ZnO nanoparticles were dispersed into the polymer matrix via in situ electropolymerisation. Surface morphology of the composite film was studied by surface microscopy techniques (SEM). The presence of ZnO in the films was confirmed by EDS analysis. Furthermore experimental absorbance spectra of PMB/ZnO compared with results obtained from the Maxwell–Garnett theory (MGT) and the values of energy Eg of composite were determined as Eg1=3.3eV, Eg2=2.7eV and Eg3=1.7eV, respectively. The results show that composite films are photosensitive and they can be used as photoluminescent materials in optoelectronic devices.

A COMBINED APPROACH OF ION CHROMATOGRAPHY AND QUANTITATIVE NMR TO ACCURATELY DETERMINE COUNTERION STOICHIOMETRY

Early phase pharmaceutical research compounds must be fully characterized in order to have confidence in any testing results. Traditional methods such as HPLC/MS do not give any indication of counterion presence or identity for many common counterions such as trifluoroacetate, acetate, or succinate. Herein, we describe a combined approach of ion chromatography and quantitative nuclear magnetic resonance spectroscopy in order to identify and quantify counterions in research samples of limited quantity. Forty-two research samples were analyzed and compared for trifluoroacetate, acetate, and succinate salts.

Electrochemical control of specific adhesion between amine-functionalized polymers and noble metal electrode interfaces

Polymers are widely utilized as protective coatings to prevent metal surfaces from wear, corrosion, or bio-fouling. Yet, stability and adhesive properties of polymer to metal bondings are not fully understood at the molecular level. Here, we measured the interaction forces between a gold electrode surface and amine-functionalized polymers (PEG) using a novel electrochemical surface forces apparatus. We examined the potential dependence of specific amine–gold interactions and measured that the binding strength of amine–gold bonds can range from 0.5 to 40 kBT per binding site, depending on the applied electrochemical potential. Notably, this interaction exhibits a pronounced minimum around the potential of zero charge, where the polymer–gold adhesion is dominated by non-specific interactions between the polymer backbone and electrode surface, consistent with the adhesion of PEG polymers with gold surfaces in the absence of amine functionalization. Further, repulsive hydration interactions were observed to be stronger for amine-terminated PEG compared to non-functionalized PEG, due to increased hydration and presence of counterions in the case of amine-terminated PEG. Our results provide molecular-scale insight into design and optimization of polymer coatings for numerous applications requiring strong, specific binding interactions between polymers and metals (or their native oxides), for example passivating layers in biomedical implants and electronic devices.

Enhancement and in vitro evaluation of amifostine permeation through artificial membrane (PAMPA) via ion pairing approach and mechanistic selection of its optimal counter ion

This study presents the results of in vitro evaluation of a series of organic counter ions that form ion pairs with amifostine. The selected counter ions have different lipophilicity, shape and flexibility. Intrinsic octanol buffer partition coefficient and binding constant of the ion pairs were calculated using quasi-equilibrium analysis. Permeation through hydrophobic PAMPA membranes of amifostine and its ion pairs with different counter ions was studied. Three counter ions, succinic acid, benzoic acid and phthalic acid demonstrated an increase in the apparent partition coefficient of amifostine in n-octanol. These counter ions were selected for permeability experiments in PAMPA membranes and an increase of the apparent permeability value Papp (cm/s) was also observed as a function of the counter ion concentration. Phthalic acid produced 1.6-fold increase of log PAB while for benzoic acid and succinic acid the values were 1.2 and 0.75-fold respectively. PAMPA permeability of amifostine significantly increased in the presence of phthalic acid (42-fold), benzoic acid (37-fold) and succinic acid (10.5-fold). This study showed that the permeability of amifostine across a lipophilic membrane was enhanced in the presence of counter-ions resulting ion pair formation.

The roles of counterion and water in a stereoselective cysteine-catalyzed Rauhut-Currier reaction: a challenge for computational chemistry.

The stereoselective Rauhut-Currier (RC) reaction catalyzed by a cysteine derivative has been explored computationally with density functional theory (M06-2X). Both methanethiol and a chiral cysteine derivative were studied as nucleophiles. The complete reaction pathway involves rate-determining elimination of the thiol catalyst from the Michael addition product. The stereoselective Rauhut-Currier reaction, catalyzed by a cysteine derivative as a nucleophile, has also been studied in detail. This reaction was experimentally found to be extremely sensitive to the reaction conditions, such as the number of water equivalents and the effect of potassium counterion. The E1cB process for catalyst elimination has been explored computationally for the eight possible stereoisomers. The effect of explicit water solvation and the presence of counterion (either K(+) or Na(+) ) has been studied for the lowest energy enantiomer pair (1S, 2R, 3S)/(1R, 2S, 3R).

Erratum to: Reflections on the conformation, topology and thermodynamics of a polyelectrolyte chain in the presence of counterions with plausible applications

The simulation results from a basic polyelectrolyte chain consisting of an anionic string of 150 univalent negatively charged particles connected under various harmonic-like potential interactions with each other in the presence of a similar number of positive and free counter ions found in Jesudason et al. (EPJE $$30$$ :341–350, 2009) forms the focal point for further discussion on chain models based on a survey of more recent developments in general polyelectrolyte theory. The topics discussed include persistence length definition, forcefields and methods of controlling simulation parameters, and thermodynamics. The data for the basic system was derived for the temperature range $$0.1$$ – $$10.0$$ in reduced units (corresponding to $$\xi =10\text{-- }0.1$$ ); the augmented data involves a $$360$$ monomer chain. The data include the total and Coulombic energies, radial distribution functions, radii of gyration, end-to-end distances and snapshots of the system which are all discussed anew. Polyelectrolyte systems have been overwhelmingly associated with biophysical interpretations, but here it is suggested that these detailed studies and the consequent theoretical formulations could be extended further afield; non-biological ionic liquid systems with catalytic and energy storage applications are some of many other possibilities. However, the approach used by MD simulations to validate ionic liquid systems as carriers of molecules with catalytic moieties often refer to CPMD and DFT quantum methods, which is not the current norm as judged by the literature in especially coarse grained polyelectrolyte MD. The quantum approach could also be used for more detailed analysis of biophysical systems where one trend seems to be that the incorporation of details in simulations accounts for phenomena not explicable in coarser grained MD, for instance if conventional atomic ionic charges are assigned to all atom modeling. This is illustrated by a linear chain modeling a DNA polymer using different charge and size assignments for the same linear charge density. The trends are such that it might be expected that some form of routine standardization of force fields in the spirit of the Jorgensen OPLS-AA method that incorporates quantum calculations specific to a system will be implemented as a routine as refinements are seen to lead to more comprehensive rationalization.

Molecular force fields for aqueous electrolytes: SPC/E-compatible charged LJ sphere models and their limitations

Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.