Study on the β Peak of χ″ for a Two-Dimensional Supercooled Fluid State Via Molecular Dynamics Simulation

Abstract

We have computed the generalized susceptibility (imaginary part of χ) of two-dimensional supercooled fluid states through molecular dynamics simulations with different system sizes. It is found that when the temperature of the system is higher than T_c (critical temperature) there is no significant difference between the large (10,000-particle) and small (100-particle) systems in the χ obtained, but for much lower temperatures the spectra of the χ″ obtained reveal a remarkable system-size dependent behavior such as the β peak becomes much broader for the large system. This phenomenon is physically understood in terms of the strongly correlated motion of atoms extending over a wide range of space of the system. We will discuss in this work about the relaxations on two-dimensional supercooled fluids and their microscopic origins as well as their system-size dependence.     

Self-aggregation of trehalose in the mixed solvents of 1,3-dimethylimidazolium ionic liquid and water

Abstract

Conformational variations of solvated trehaloses in binary mixtures of 1,3-dialkylimidazolium ([dmim]Cl) ionic liquids and trehalose as well as ternary mixtures of trehalose, [dmim]Cl and water have been studied by molecular dynamics (MD) simulations with and without polarisable force fields. The interaction energy between anion Cl^? and water is stronger than that between water itself in the [dmim]Cl-water mixtures. Isolated water clusters were found in the binary [dmim]Cl-water mixtures with 60.0 and 75.0% mole fraction of water, but a continuous water network appears when the concentration of the mixture increases to 99.9%. In the case of binary mixtures of trehalose and [dmim]Cl, both non-polarisable and polarisable models demonstrated that the pyranose rings of trehalose displayed chair conformations. MD simulations with polarisation model could sample larger conformation space than that with non-polarisable model. A self-aggregation behaviour of trehalose was found in the ternary trehalose-[dmim]Cl-water mixtures, which can be rationalised by the stronger non-bonded interaction energy between trehalose molecules and anion Cl^? than that between trehalose molecules and water.     

Study of the molecular array behaviours and interfacial activities of green surfactant alkyl polyglycoside and the mixed systems with other surfactants on oil–water interface

Abstract

The widely performance of surfactants is closely related to their interfacial activity, which is essentially determined by the molecular array behaviours at the interface, of which the studies are significance for clearly understanding their structure-performance relationships. In this paper, the detailed molecular array behaviours of green surfactant alkyl polyglycoside (APG) and the mixed systems with other types of surfactants on oil/water interface have been studied using molecular dynamics simulations, and the key theoretical principle was confirmed by quantum chemistry calculations. It was found that the hydrophilic maltose ring head groups of decyl polyglycoside (C₁₀-APG) are prone to lie flatly at the oil–water interface, the steric hindrance results in the low interfacial density, which critically determines the limit of the interfacial activity. The interfacial adsorption behaviours of the binary mixtures of C₁₀-APG and SDS or DATB and the ternary mixtures of C₁₀-APG, SDS and DATB were studied in detail, how the efficient synergism effect could be achieved for the mixture to get super high interfacial activity was discussed. This study provides a strategy to reveal how the molecular interfacial behaviours determine the key interfacial characteristics of the novel surfactants, which might provide help to promote their applications.     

Formation of binary complexes of Pb(II), Cd(II) and Hg(II) with maleic acid in CTAB-water mixtures

Abstract

Complexation of toxic metal ions with maleic acid in (0.0–2.5% w/v) cetyltrimethylammonium bromide (CTAB)–water mixtures has been studied pH-metrically at ambient conditions and an ionic strength of 0.16 mol L^-1. The existence of different binary species was established from modelling studies using the computer program MINIQUAD75. The best-fit chemical models were selected based on statistical parameters such as the crystallographic R factor and sum of the squares of residuals in mass-balance equations. The models for binary complex systems contain the chemical species ML₂, ML₂H and ML₃ for Pb(II), Cd(II) and Hg(II) in CTAB–water mixtures. The trend in the variation of stability constants with change in the mole fraction of the medium was explained based on electrostatic and non-electrostatic forces. Distribution of the species with pH at different compositions of CTAB–water mixtures was also presented.     

Nonsputtering impulse magnetron discharge

Experiments with quasi-steady high-current discharges in crossed E × B fields in various gases (Ar, N₂, H₂, and SF₆) and gas mixtures (Ar/SF₆ and Ar/O₂) at pressures from 10⁻³ to 5 Torr in discharge systems with different configurations of electric and magnetic fields revealed a specific type of stable low-voltage discharge that does not transform into an arc. This type of discharge came to be known as a high-current diffuse discharge and, later, a nonsputtering impulse magnetron discharge. This paper presents results from experimental studies of the plasma parameters (the electron temperature, the plasma density, and the temperature of ions and atoms of the plasma-forming gas) of a high-current low-pressure diffuse discharge in crossed E × B fields.     

Molecular Simulation of Adsorption of Guest Molecules in Zeolitic Materials: A Comparative Study of Intermolecular Potentials

Abstract

Grand Canonical Monte Carlo simulation, together with an appropriate guest-host forcefield is shown to provide reasonably accurate predictions of adsorption properties of guest molecules in a variety of zeolitic materials. The use of a simple guest-host Kiselev-type potential permits the calculations to capture the essence of the behavior of simple guest-host systems such as rare gases or methane molecules in neutral AlPO₄-5. However, a full scale potential is needed in the more complex cases of large anisotropic molecules adsorbed in cationic zeolites (such as xylene isomers in faujasite). The guest-host potential model developed by Nicholson and coworkers is shown to allow an excellent transferability of the potential parameters from one guest/host system to another.     

Gelation of sickle cell hemoglobin in mixtures with normal adult and fetal hemoglobins.

We report the results of thermodynamic and kinetic studies on the gelation of mixtures of sickle cell (S) deoxyhemoglobin with normal human adult (A) and fetal (F) deoxyhemoglobins. The delay time of thermally induced gelation was monitored by the increase in turbidity. At the completion of gelation the solubility was determined by sedimenting the polymers and measuring the supernatant concentration spectrophotometrically. Addition of hemoglobins A or F, at mole fractions from 0 to 0.6, resulted in large increases in both the solubility and the delay time. For a 50:50 mixture of deoxyhemoglobin F with deoxyhemoglobin S, the solubility increased by a factor of 1.8 and the delay time by a factor of 10⁷ relative to pure deoxyhemoglobin S at the same total concentration, while for a 50:50 mixture of deoxyhemoglobins A and S the solubility increased by a factor of 1.4 and the delay time by a factor of 10⁴. The relative delay times were independent of both temperature and total hemoglobin concentration. The data have been analyzed according to theoretical models which treat the effects of temperature, concentration, non-ideality and solution composition on the thermodynamics and kinetics of gelation. The increased solubility in mixtures with deoxyhemoglobin F is fully explained by a model in which only deoxyhemoglobin S molecules polymerize. The effect of fetal hemoglobin (α₂γ₂) and hybrid α₂γβ^S molecules is to increase the solution non-ideality through the contribution of their excluded volume. The smaller increase in the solubility observed in comparable mixtures with deoxyhemoglobin A requires that the hybrid α₂β^Aβ^S molecules copolymerize with the deoxyhemoglobin S. The kinetic results for the mixtures can be quantitatively accounted for using a nucleation model in which the equilibrium properties of the polymer are used to describe the critical nucleus. The very large increases in delay time observed for the $\text{S}\text{F}$ mixtures can be explained by assuming that only α₂β₂^S molecules participate in the formation of a nucleus containing about 25 monomers. As in the thermodynamic analysis, the smaller effect of adding deoxyhemoglobin A can be attributed to the contribution of the hybrid molecules in forming the critical nucleus. Thus the difference between the polymerization properties of mixtures of deoxyhemoglobin S with deoxyhemoglobins A and F can be attributed solely to the copolymerization of the α₂β^Aβ^S hybrid molecule and the absence of any significant copolymerization of the α₂γβ^S hybrid.     

Catalysis by Laccase (From Coriolus uersicolor) in Microheterogeneous Media of the Water/Organic Solvent/Surfactant Type

Catalysis by laccase from Coriolus uersicolor solubilized in the ternary systems of surfactant/water/organic solvent type, namely, Aerosol OT/water/octane, Brij 56/water/cyclohexane and egg lecithin/water/octane + pentanol + methanol mixture, has been studied. The laccase activity is found to depend, in principle, not only on the water/surfactant molar ratio, but on the surfactant concentration (with its hydration degree being constant) as well. The following inferences should be emphasized. Firstly, in all the systems under study, the catalytic activity (k_cat) of laccase entrapped into surfactant reversed micelles increases more than 50 times (when the surfactant concentration is extrapolated to zero) compared with the k_cat value in aqueous solution. Secondly, the catalytic activity (k_cat) of laccase entrapped in hydrated Aerosol OT aggregates, having lamellar, reversed cylindrical (hexagonal) and reversed micellar structure, depends greatly on the aggregate type. In other words, the phase transitions, i.e. an alteration in the packing of hydrated Aerosol OT molecules, evokes a sharp reversible change in the enzymatic activity. Thirdly, in the same phase, the catalytic activity of the solubilized enzyme depends on the linear dimensions of water cavities inside the surfactant aggregates (i.e. on the water content in the system under study). All these effects, regulating enzymatic activity, are probably caused by an alteration of the conformational mobility of laccase molecules incorporated into the inner polar cavities inside the surfactant aggregates.     

An Extended Gibbs Ensemble

Abstract

A general extended Gibbs ensemble, obtained by augmenting the standard Gibbs ensemble by intermediate states in the spirit of the scaled particle method of Nezbeda and Kolafa [Molec. Simul., 5, 391 (1991)], is introduced. The intermediate states span the states with different number of particles in the simulation boxes and facilitate the transfer of particles even in such complex systems as e.g., mixtures of very different components, systems of flexible polymeric molecules, or systems at very high densities. A general formulation of the ensemble is given and two implementations are considered in detail. The method is very general and is exemplified by studying the fluid-fluid coexistence in a dense binary mixture of the hard-sphere and square-well fluids. It is found that its efficiency is about by factor three greater in comparison with the standard Gibbs ensemble simulations.     

Investigating lithium ion conductivity in amorphous solids containing [V10O28]6− clusters by computer simulation

Computer simulation method was applied to investigate the migration of lithium ion in three amorphous solid systems containing polyoxovanadate (POV) clusters [V₁₀O₂₈]^6 ? . The cluster was adopted from a recently synthesized crystalline poly[octa-μ-aqua-octaaqua-μ-decavanadato-hexalithium] (POAODH). The simulated POV systems correspond to amorphous solid half-dehydrated solid and completely dehydrated solid doped with LiCl salt. The simulation results show large diffusion constants of lithium ions in all systems in spite of highly negatively charged [V₁₀O₂₈]^6 ?  clusters presented in the system. The estimated ionic conductivity due to the migration of lithium ions reaches a magnitude of 10^? 4 S/m. The conductivity increases as the water content in the system decreases. The analysis of moving trajectories shows the lithium ion moves around the oxygen sites of POV clusters and hops between them. The estimated displacement of lithium ion is about 4～5 Å, which is much larger than the corresponding displacement of lithium ion in a polymer matrix. Rapidly rotating clusters shown by orientation correlation function analysis, in conjunction with the large separation between clusters in the system, provides favorable conditions for the large amplitude migration of lithium ions.     

Screening of Ligand Binding on Melatonin Receptor Using Non-Peptide Combinatorial Libraries

Abstract

The screening of combinatorial libraries requires a deconvolution procedure to obtain, in fine, the most active compound of the starting library. the standard screening assays used in regular molecular pharmacology, have been poorly assessed when transposed to combinatorial chemistry-related experiments, particularly those involving large numbers of chemicals in a single assay. One key issue is the effect of the inactive analogs on the identification of the active ligand in mixtures. We chose melatonin receptors to measure the apparent affinity of a single ligand when tested alone or in mixtures of non-peptide low molecular weight compounds. Using ligands with IC₅₀ from the micro- to the picomolar range, mixed with increasingly complex mixtures of 5 to 20 or 25 inactive compounds, we analyzed the displacements from the mt₁ and MT₂ melatonin receptor subtypes of the radioligand 2-iodomelatonin (K_d= 25pmol/l and 200pmol/l, respectively). the behavior of equimolar mixtures in displacement curves led to the conclusion that the observed binding affinity reflects the dilution effect of mixing the active component with inactive compounds but does not reveal noticeable interactions which would interfere with the binding process. From the practical point of view, the concentrations of the active species in the binding assay should be large enough to displace significantly the radioligand, a requirement which may be limited by the solubility of the ligand mixtures. in contrast, previous observations with peptide libraries report that the dilution effect is often compensated by additive or synergic action of structurally related analogs, thus making possible the deconvolution of very large (typically up to 10⁷ compounds) peptide libraries.     

Emulsifying and surface active agents from Corynebacterium hydrocarboclastus

A Corynebacterium hydrocarboclastus culture isolated in our laboratory (see, Zajic and Knettig, Developments in Industrial Microbiology, 1971, p. 87) has been shown to produce an extracellular biopolymer with emulsifying properties when grown on a mixture of linear hydrocarbons. This microorganism was found to grow well on a variety of carbohydrates and hydrocarbons. However, the best substrates were pure linear hydrocarbons and particularly, n-C₁₂, n-C₁₃, and n-C₁₄. The substrates supporting good growth gave good polymer production. Maximum cell mass of 10–11 g/liter and a maximum amount of polymer of 5–6 g/liter were recorded. The polymers recovered from the different substrates were found to be complex molecules or mixtures with a protein, a lipid, and a carbohydrate moiety. All the polymers are surface active and have two critical micelle concentrations.     

Refinement of histamine H3 ligands pharmacophore model leads to a new class of potent and selective naphthalene inverse agonists

The refinement of our original five point pharmacophore model for the H₃ receptor with the addition of a new acceptor feature is presented. The importance of this new acceptor feature for the binding and the selectivity against H₁, H₂ and H₄ has been validated using a newly synthesized naphthalene series. With the SAR deduced from several hundred naphthalene derivatives in various sub-classes the specific role of each pharmacophoric feature, by varying the geometry, size and charge of the molecules, was elucidated. This led to the discovery of a highly potent and selective new compounds series.     

Effect of neurosteroids on a model lipid bilayer including cholesterol: An Atomic Force Microscopy study

Amphiphilic molecules which have a biological effect on specific membrane proteins, could also affect lipid bilayer properties possibly resulting in a modulation of the overall membrane behavior. In light of this consideration, it is important to study the possible effects of amphiphilic molecule of pharmacological interest on model systems which recapitulate some of the main properties of the biological plasma membranes. In this work we studied the effect of a neurosteroid, Allopregnanolone (3α,5α-tetrahydroprogesterone or Allo), on a model bilayer composed by the ternary lipid mixture DOPC/bSM/chol. We chose ternary mixtures which present, at room temperature, a phase coexistence of liquid ordered (L_o) and liquid disordered (L_d) domains and which reside near to a critical point. We found that Allo, which is able to strongly partition in the lipid bilayer, induces a marked increase in the bilayer area and modifies the relative proportion of the two phases favoring the L_d phase. We also found that the neurosteroid shifts the miscibility temperature to higher values in a way similarly to what happens when the cholesterol concentration is decreased. Interestingly, an isoform of Allo, isoAllopregnanolone (3β,5α-tetrahydroprogesterone or isoAllo), known to inhibit the effects of Allo on GABA_A receptors, has an opposite effect on the bilayer properties.     

Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems

The Nafion, Dow and Aciplex systems – where the prime differences lies in the side-chain length – have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO₃ end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H₃O⁺/H₂O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility. Figure The simulation box for Aciplex with 5 water molecules per sulphonate end-group (yellow spheres). The polymer backbone is black; while side-chains are brown. The water-channel iso-surfaces are represented as blue clouds     

Reducing acidic discharges from coastal wetlands in eastern Australia

Much of eastern Australia's coastal lowlands are underlain by Holocene sulfidic sediments. Large areas have been drained for agriculture. Drained, sulfidic sediments oxidize and produce highly acidic discharge (pH<4) with significant impacts on estuarine ecosystems. The rate of production of acid from drained floodplains is between 100 to 300 kg H₂SO₄ /ha/y and hundreds of tonnes of H₂SO₄ can be discharged in a single flood from the floodplain. Generation and export of acidity is controlled by the water balance of the floodplain, the characteristics of the drainage system and the distribution of sulfides. Evapotranspiration by native plants and crops plays a dominant role in the oxidation of sediments in dry periods. In wet periods, upland discharges to floodplains dominate the water balance. Drain spacing and drain depth are critical factors in the export of acidity into coastal streams. Amelioration of acidic outflows requires an understanding of the interaction between chemical and hydrological processes in sulfidic landscapes. Redesign of drainage systems to manage surface waters and reduce drain density with the treatment of drains with lime offer promise for treating acidic discharge and reducing impacts. Reflooding of drained, partially oxidized floodplains with freshwater may not be a panacea because of the large volumes of acid stored in the soil, a lack of labile organic matter in the sediments needed to reduce sulfate and irreversible changes to the soil due to oxidation. Tidal brackish water reflooding of unproductive acidified lowlands offers promise for rehabilitating wetlands. Sulfidic wetlands which are still undrained should remain so unless all acidic discharge can be treated.     

Molecular Dynamics Simulation Studies of the Limiting Conductances of CaCl2 using Extended Simple Point Charge and Revised Polarizable Models

We have carried out molecular dynamics (MD) simulations of the limiting conductances of CaCl₂ in ambient and supercritical states as a function of water density using extended simple point charge (SPC/E) and revised polarizable (RPOL) models for ions and water molecules. Both models predict the limiting conductances of CaCl₂ in supercritical water that are a linear dependence on water density. The effect of the electronic polarization on the limiting conductances is too small to cause a deduction in the lower water density of 0.6?～?0.7?g/cc in this study. The most significant effect of the electronic polarization is appeared in a decrease in the ion–water potential energy and, as a result, an increase in the limiting conductances for both ions. Different charge distributions of water molecules in the first hydration shell around the ions lead the opposite behavior of the induced dipole moment with water density for a positive and a negative ion in supercritical water; the induced dipole moment of Ca²⁺ decreases with increasing water density but for Cl^-, the opposite is observed. The same kind of opposite behavior due to the structure of water molecules around the ions is also found in hydrogen-bond correlations of water around the ions and of bulk water; hydrogen bonding around Ca²⁺ persists longer than in bulk water whereas the opposite is observed for Cl^-.     

Impact of lyoprotectors on protein-protein separation in the solid state: Neutron- and X-ray-scattering investigation

BackgroundPolyhydroxycompounds (PHC) are used as lyoprotectors to minimize aggregation of pharmaceutical proteins during freeze-drying and storage.MethodsLysozyme/PHC mixtures with 1:1 and 1:3 (w/w) ratios are freeze-dried from either H₂O or D₂O solutions. Disaccharides (sucrose and trehalose), monosaccharide (glucose), and sugar alcohol (sorbitol) are used in the study. Small-angle neutron and X-ray scattering (SANS and SAXS) are applied to study protein-protein interaction in the freeze-dried samples.ResultsProtein interaction peak in the freeze-dried mixtures has been detected by both SANS (D₂O-based samples only) and SAXS (both D₂O- and H₂O-based). In the 1:1 mixtures, protein separation distances are similar (center-of-mass distance of approx. 31 Å) between all lyoprotectors studied. Mixtures with a higher content of the disaccharides (1:3 ratio) have a higher separation distance of approx 40 Å. The higher separation could reduce protein-protein contacts and therefore be associated with less favourable aggregation conditions. In the 1:3 mixtures with glucose and sorbitol, complex SANS and SAXS/WAXS patterns are observed. The pattern for the glucose sample indicate two populations of lysozyme molecules, while the origin of multiple SAXS peaks in the lysozyme/sorbitol 1:3 mixture is uncertain.ConclusionsProtein-protein separation distance is determined predominantly by the lyoprotector/protein weight ratio.General significanceUse of SANS and SAXS improves understanding of mechanisms of protein stabilization by sugars in freeze-dried formulations, and provide a tool to verify hypothesis on relationship between protein/protein separation and aggregation propensity in the dried state.     

Comparative microcalorimetric and dilatometric analysis of the interactions of quinacrine,chloroquine, and ethidium bromide with DNA

The enthalpies of binding of chloroquine and quinacrine to DNA at different molar ratios of drug to DNA and at different ionic strengths have been measured. The limiting values obtained with quinacrine fall in the range found for typical intercalating agents (e.g., ethidium, proflavin, adriamycin), whereas the value obtained with chloroquine is always zero, independent of the ratio of drug to DNA and ionic strength. The dilatometric measurements performed on the same systems and on the ethidium–DNA system show that when ethidium and quinacrine bind to DNA at low drug/DNA ratios, a volume decrease of about 16 mL/mol of bound drug occurs. No change in volume is observed when the two drugs bind to DNA through external, electrostatic forces. The volume change can be attributed to the loss of structured water around hydrophobic moieties of the drug molecules, following intercalation. In contrast, chloroquine binding to DNA at low drug/DNA ratios is characterized by a volume change distinctly smaller than that shown by quinacrine. The low ΔV_B and ΔH_B values shown by chloroquine are discussed in terms of the mechanism of interaction with DNA.