Counterion binding in the aqueous solutions of bile acid salts, as studied by computer simulation methods

We investigate the structural and dynamical properties of counterion binding in sodium cholate and sodium deoxycholate micelles at three different concentration, namely, 30, 90, and 300 mM, by means of molecular dynamics simulations at the atomistic level. The obtained results can resolve a long-standing, apparent contradiction between different experiments that reported discordant values for the degree of counterion binding. Namely, our results suggest that certain experimental techniques, such as freezing point depression, are only sensitive to the contact counterions, and hence, the degree of contact binding of the counterions is measured. On the other hand, in experiments employing, e.g., electrode potential or nuclear magnetic resonance measurements, the solvent-separated counterions also contribute to the signal detected, and hence, the counterions that are measured as bound ones do include the solvent-separated counterions as well.     

Molecular dynamics simulation of aqueous solutions of glycine betaine

Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine-N-oxide, a bioprotectant closely related to glycine betaine.     

Molecular dynamics study on hydrophobic effects in aqueous urea solutions.

Hydrophobic effects in aqueous urea were analyzed by molecular dynamics simulations. The contribution of solvents to the potential of mean force between two methane molecules was calculated by using molecular dynamics simulations and was compared with the solubility data of hydrocarbons in aqueous urea. Both the simulation results and the solubility data indicated that urea stabilizes methane-methane association. The stabilization was due to increasing the solvation free energies of small hydrocarbons such as methane by addition of urea. The solvation free energies of larger hydrocarbons, on the other hand, are decreased by addition of urea. This effect of the solute size on hydrophobic free energies in aqueous urea was also analyzed by using molecular dynamics simulations by means of division of the solvation process into two parts: the cavity formation and the introduction of the solute-solvent attractive interactions. In the cavity formation, urea increased hydrophobic free energies, and in the introduction of the solute-solvent attractive interactions, urea decreased hydrophobic free energies. The influence of urea on hydrophobic free energies was determined by the balance of effects of the two parts of the solvation process.     

First-principles molecular dynamics study on aqueous sulfuric acid solutions

The properties of aqueous sulfuric acid have been studied employing density functional theory-based molecular dynamics simulations in conjunction with norm-conserving pseudopotentials. The simulations were carried out for two different concentrations whose molar concentrations were fixed at 0.84 and 10.2 mol/l. The structural features of aqueous sulfuric acid solutions show a strong dependency on the concentration. The Gr?tthuss-type proton transfer mechanism is not effectively operative at the higher concentration because of the broken hydrogen bond network of water induced by ions generated by the dissociation of sulfuric acid. In addition, to evaluate electrical properties, we carried out a simulation that takes an electric field into account. Results are compared with those of the simulation undertaken with no external electric field.     

Raman spectroscopic study of the conformation of dicarboxylic acid salts in aqueous solutions

It is already known that the molecules of long chain monocarboxylic acid salts have a tendency to form micelles in aqueous solutions, the molecular chain taking the all-trans zigzag structure. However it is considered difficult for dicarboxylic acid salts to adopt the same structure as the monocarboxylic acid salts as they have two carboxyl groups, one on each end of the molecular chain. Therefore, a special structure is expected to exist for dicarboxylic acid salts in aqueous solution. In order to examine this, Raman spectra of suberic acid salt and azelaic acid salt in aqueous solution were measured and the normal vibrational calculation carried out, showing that dicarboxylic acid salts have a helical structure in aqueous solution.     

不同浓度下NaCl水溶液的分子动力学模拟

采用分子动力学模拟的方法在298K时对1.33mol/L,2.71mol/L,4.14mol/L和5.12mol/L的NaCl水溶液的微观结构进行了研究。模拟发现浓度对离了近程水化结构的影响不大,浓溶液中Na^+,Cl^-之间有两种缔合方式,接触缔合离子对和溶剂分隔的缔合离子对。这表明在建立可适用于高浓度条件下的电解质溶液热力学模型时应考虑离子缔合的贡献。     

Molecular dynamics simulation of aqueous NaF and NaI solutions near a hydrophobic surface

We present results from molecular dynamics simulation of aqueous solutions of alkali halide salts (NaI and NaF) at the interface with hydrophobic objects. The primary objective of this study is to investigate the structural properties of the salt solutions at the hydrophobic surface. An alkane crystal has been taken as the parent model for a hydrophobic surface. A hexagonal hole was created on it, which was half a nm deep and 2.5 nm wide. The density distributions of different species (water, anions, and cations) are studied as a function of distance from the surface. While iodide prefers the interface, the fluoride ions stay inside the bulk water region. The higher concentration of iodide ions at the interface drags sodium counterions to the interface. It also decreases the water density at the interface because of steric effects of the iodide ions. The number of contacts between the surface carbons and water decreases in the case of NaI solutions but is unchanged for NaF solutions. The orientation of the water-ion and the water-water hydrogen bond vector orientations near the interface is discussed in detail.     

Concentration-dependent aggregation patterns of conjugated bile salts in aqueous sodium chloride solutions

Based on light scattering intensity measurements, a critical concentration for micelle formation can be assigned to sodium taurodeoxycholate in aqueous electrolyte solutions. For sodium taurocholate a progressive aggregation even at very low concentrations of bile salt is indicated. Surface tension and diffusion coefficients are also reported.     

A molecular dynamics simulation of micellar aggregates in aqueous solutions of hexadecyltrimethylammonium chloride with admixtures of low-molecular-weight substances

A molecular dynamics simulation was performed for spherical and cylindrical hexadecyltrimethylammonium chloride micelles in aqueous solutions containing admixtures of isopropanol, acetone, and sodium benzoate. Local particle (atom, atomic group, and ion) density profiles were obtained depending on the distance to the center of a micelle. The stationary size of aggregates was determined, and the micelle surface area per surfactant polar head was estimated.     

Molecular dynamics simulations of aqueous solutions of ethanolamines

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.     

Aggregation of perfluoropolyether carboxylic salts in aqueous solutions. Fluorescence probe study

Aqueous solutions of anionic surfactants Cl(C3F6O)nCF2COOX, consisting of n = 2 and 3 perfluoroisopropoxy units and the counterion X = Na+ or NH4+, were studied by the method of fluorescence quenching with the use of (1-pyrenylbutyl)trimethylammonium bromide as a luminophore, and 1,1'-dimethyl-4,4'bipyridinium dichloride (methyl viologen) as a quencher. From the kinetics of fluorescence decay (time-resolved experiments) micellar aggregation numbers, N, and rate constants of the intramicellar quenching were determined for a wide range of surfactant concentrations, on the basis of the model developed by Infelta and Tachiya. The results are discussed in terms of the shape of the aggregates and the degree of counterion binding. The most important conclusions include: (i) a significant increase of N with increasing surfactant concentration suggests that spherical micelles formed at critical micellar concentration (CMC) transform into ellipsoidal aggregates, (ii) the degree of counterion binding to micelles is higher for NH4+ than for Na+, leading to higher N values in the case of the ammonium salt (n = 2), and (iii) at concentrations close to CMC the longer chain surfactant (n = 3) forms loose aggregates suggesting significant permeation with water molecules. An additional finding of this study is that the micelle-bound luminophore and quencher can form a ground-state complex, and for this reason the N values cannot be evaluated properly from the steady-state fluorescence intensity data using the equation proposed by Turro and Yekta.     

Molecular dynamics simulation of glycine zwitterion in aqueous solution

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.     

Activities and viscosities of aqueous bile acid salt-lecithin solutions

Isopiestic and viscosity measurements on aqueous sodium cholate-lecithin solutions are reported at high concentrations which include the physiological region as a lower limit. At low cholate concentration, the addition of lecithin increases the activity of water, consistent with earlier studies showing increases of micellar weights. At higher cholate concentrations, the activity of water is independent of lecithin concentrations. Studies of binary solutions of bile acid salts and detergents agree very closely with earlier work.     

Micellization of bile salts in aqueous medium: a fluorescence study

Owing to the physiological importance of the micellization process of bile salts, the critical micelle concentration (CMC) becomes a fundamental parameter in the evaluation of their biological activities. The present study suggests fluorescence probing, using 1,6-diphenylhexatriene (DPH), as a simple, convenient, sensitive and economic method for monitoring the micellization process of bile salts in aqueous medium. Three independent parameters: fluorescence intensity, anisotropy and lifetime of DPH have been employed successfully for determining the CMC of two bile salts, sodium deoxycholate (NaDC) and sodium cholate (NaC), in aqueous medium. The CMC values reported by all the above three parameters of DPH are found to be same and it is 16 mM for NaC and 6 mM for NaDC at 25 degrees C in unbuffered solution. The effect of temperature and ionic strength on the micellization process has also been investigated employing DPH as a fluorescent probe. Increasing temperature leads to the formation of fluffier micelles with less rigid interior for both NaC and NaDC. The micelle core of NaC is less perturbed by the presence of NaCl whereas in case of NaDC, the aggregates provide DPH a more nonpolar and rigid environment in presence of NaCl than that in absence of salt.     

Molecular dynamics simulation of solution structure and dynamics of aqueous sodium chloride solutions from dilute to supersaturated concentration

Constant-temperature and constant-pressure (NpT) molecular dynamics simulations were performed to study the effects of salt concentration ranging from dilute to supersaturated concentrations on solution structure and dynamical properties of aqueous sodium chloride solutions at 298 K. The rigid SPC/E model was used for water molecules, and sodium and chloride ions were modeled as charged Lennard–Jones particles. Na⁺–Cl⁻ radial distribution functions showed the presence of contact ion pairs and solvent separated ion pairs. The coordination numbers of Na⁺–Cl⁻ ion pairs increased with salt concentration up to saturated concentration, although the number of contact ion pairs was almost constant in supersaturated regions. The tracer diffusion coefficients of both ions decreased with salt concentration up to saturated concentration, while that of sodium ion was almost constant in supersaturated regions. The tracer diffusion coefficients of both ions were therefore quite close to each other. The constant number of the contact ion pairs and the almost equality of the tracer diffusion coefficients of both ions would lead to the formation of clusters in supersaturated solutions.     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

Structure of small associates of glycyrrhizic acid with cholesterol in aqueous solution: Molecular dynamics simulation

In a recent work by Zelikman et al.(J. Struct. Chem., 2015, 56(1)), the molecular dynamics simulation of dimers of glycyrrhizic acid (GA) arising from the spontaneous collision of two GA molecules in water is performed. Several relatively stable dimer structures are found, and when a cholesterol molecule is inserted, associates are observed constituting a GA dimer with a cholesterol molecule “stuck” to it. Here, we simulate the associates consisting of three and four GA molecules and a cholesterol molecule. It appears that the cholesterol molecule, as a rule, also locates at the surface of the GA associate. Therewith, the trimers do not form any clear characteristic structures, as dimers do, and the tetramers can be two stuck dimers.     

Ultrafast dynamics in aqueous polyacrylamide solutions.

We have investigated the ultrafast dynamics of aqueous polyacrylamide ([-CH(2)CH(CONH(2))-](n), or PAAm) solutions using femtosecond optical heterodyne-detected Raman-induced Kerr effect spectroscopy (OHD-RIKES). The observed aqueous PAAm dynamics are nearly identical for both M(w) = 1500 and 10 000. Aqueous propionamide (CH(3)CH(2)CONH(2), or PrAm) solutions were also studied, because PrAm is an exact model for the PAAm constitutional repeat unit (CRU). The longest time scale dynamics observed for both aqueous PAAm and PrAm solutions occur in the 4-10 ps range. Over the range of concentrations from 0 to 40 wt %, the picosecond reorientation time constants for the aqueous PAAm and PrAm solutions scale linearly with the solution concentration, despite the fact that the solution shear viscosities vary exponentially from 1 to 264 cP. For a given value of solution concentration in weight percent, constant ratios of measured reorientation time constants for PAAm to PrAm are obtained. This ratio of PAAm to PrAm reorientation time constants is equal to the ratio of the volume for the PAAm constitutional repeat unit (-CH(2)CHCONH(2)-) to the molecular volume of PrAm. For these reasons, we assign the polymer reorientation dynamics to motions of the entire constitutional repeat unit, not only side group motions. Simple molecular dynamics simulations of H[-CH(2)CH(CONH(2))-](7)H in a periodic box with 180 water molecules support this assignment. Amide-amide and amide-water hydrogen-bonding interactions lead to strongly oscillatory femtosecond dynamics in the Kerr transients, peaking at 80, 410, and 750 fs.     

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.