Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.     

Studies on the Effect of Organic Solvents and Temperature on the Micellar Solution of Pentamethylene-1,5-bis(tetradecyldimethylammonium bromide) Gemini Surfactant

Effects of three organic solvents, viz. methyl cellosolve, acetonitrile, and formamide, on the micellization process of Gemini surfactant pentamethylene-1,5-bis(tetradecyldimethylammonium bromide) aqueous solutions, with the volume percentages of the organic solvents up to 50%, have been investigated conductometrically. The studies were made at different temperatures and the data were used to find out different micellization parameters. From the study, it was observed that, although an increment in the amount of the organic solvents delays the micellization, the increase in the critical micelle concentration (cmc) is comparatively less below 20%(v/v) showing the predominance of water character in the bulk phase at lower compositions of the organic solvents. Applying equilibrium model for micelle formation, various thermodynamic parameters were also calculated from the temperature dependence of the cmc values and the results show that the micellization process becomes less spontaneous as the volume % of the organic solvent increases in the system due to the action of water-organic solvent mixed media as better solvent than pure water (solvophobic effect) for the studied Gemini molecules.     

Potentiometric determination of the dissociation constants of L-histidine, proline and tryptophane in various hydroorganic media

The dissociation constant values of L-histidine, proline and tryptophane were determined at 25 +/- 0.1 degrees C by potentiometric pH titration in pure water and different hydroorganic solvent media. The organic solvents used were methanol, ethanol, N,N-dimethylformamide, dimethyl sulfoxide, acetone and dioxane. Initial estimates of the dissociation constant values of the different amino acids studied have been refined with ESAP2M computer program. It was observed that changing the medium permittivity as the solvent is enriched in methanol or ethanol has little influence on the pK*(a) values of the amino acids studied. The results obtained are discussed in terms of average macroscopic properties of the mixed solvents and the possible variation in microheterogeneity of the salvation shells around the solute.     

Solvent extraction of europium from aqueous-organic solutions by solvating extractants

The partition of Eu(III) between benzene containing solvating extractants (TBP, TOPO, dioctylsulfoxide) and aqueous nitrate, perchlorate and thiocyanate solutions containing various organic solvents miscible with water (alcohols, acetone, acetonitrile, ethylene glycol, dimethyl sulfoxide and dimethylformamide) was investigated. Depending on the specific extraction system, the presence of organic solvents in the mixed phase showed various effects on the distribution ratio of Eu(III). These were discussed in terms of solute-solvent interactions. The results in the systems containing dimethylformamide and dimethyl sulfoxide indicated complexation of Eu(III) with these solvents in the polar phase.     

Solvent effects in the absorption spectra of the Ninhydrin chromophore

Visible spectra of the Ninhydrin chromophore, Ruhemann's purple, were studied in dimethyl sulfoxide (DMSO), formamide, N, N-dimethylformamide (DMF), and pyridine, as well as in mixed aqueous-nonaqueous solvent media. Large differences in both the position of absorption maxima and extinction coefficients for the two bands in the visible spectra in the various solvent media were observed. Both the absorption maxima and the extinction coefficients of the Ninhydrin chromophore were a linear function of the composition of dimethyl sulfoxide-H₂O solvent media. The experimental evidence allows predictions of values for the two absorption maxima of Ruhemann's purple as a function of the nature of the solvent medium. In nonaqueous aprotic solvents (i.e., DMSO and DMF), the maxima should be near 605 and 420 mμ; in nonaqueous aprotic solvents capable of undergoing charge-transfer interactions (i.e., pyridine), near 550 and 420 mμ; and in nonaqueous protic solvents (i.e., formamide), near 575 and 410 mμ. The maxima in aprotic media will be displaced to about 575 mμ (higher wavelength band) and 410 mμ (lower wavelength band) on dilution with protic solvents.     

Spectrophotometric study of acidity constants of Alizarine Red S in various water-organic solvent

The acidity constants of Alizarine Red S were determined spectrophotometrically at 25 degrees C and at constant ionic strength 0.1 M (KNO3) in pure water as well as in aqueous media containing variable mole percentages (5-70%) of organic solvents. The organic solvents used were methanol, ethanol, N,N-dimethyl formamide (DMF), dimethyl sulfoxide (DMSO), acetonitrile and dioxan. The acidity constants of all related equilibria are estimated using the whole spectral fitting of the collected data to an established factor analysis model. DATAN program was applied for determining of acidity constants and pure spectra of different form of Alizarine Red S. The obtained results indicated that acidity constants decrease as the content of an organic solvent in the medium increases. There are linear relationship between acidity constants and the mole fraction of various organic solvents in the solvent mixtures. Effect of various solvents on acidity constants and pure spectrum of each component are also discussed.     

Measurement of reduced sulphur compounds contained in aqueous matrices by direct injection into a gas chromatograph with a flame photometric detector

An analytical method was developed to measure the concentration of hydrogen sulphide, methyl mercaptan, dimethyl sulphide and dimethyl disulphide contained in aqueous matrices (distilled water, tap water, kraft mill condensates and membrane bioreactor mixed liquor) by direct injection of aqueous samples into a gas chromatograph with a flame photometric detector. The analytical method requires a small sample volume (2 ml), sample preparation and analysis can be completed within 20 min and no complex sampling apparatus is needed. Consistent results and good recoveries were observed in all matrices investigated over the range of concentrations examined. The relationship between the normalized peak area obtained from GC–flame photometric detection and the concentration of the reduced sulphur compounds (RSCs) examined did not follow the theoretical power law exponent of two. The power law exponent appeared to decrease with the organic fraction associated with each RSC. The observed power law exponents for hydrogen sulphide, methyl mercaptan, dimethyl sulphide and dimethyl disulphide were 1.92, 1.90, 1.66 and 1.72, respectively.     

Effect of the composition of aqueous-organic mixtures on the sensitivity of thermal lens measurements

Thermooptical properties of aqueous solutions of methanol, acetonitrile, dimethyl sulfoxide, ethylene glycol, glycerol, 1,4-dioxane, and sucrose were studied, and it was found that the analytical thermal lens signal depends on the nature of the organic component, most of all, on the polarity and molecular size. The sensitivity coefficient of thermal lens measurements is increased to a maximum extent in methanol solutions (by 7.3 times at the concentration 50 vol %) and acetonitrile (by 8.8 times at 26 vol %). It was found that a small concentration of water slightly affects the thermooptical properties of polar organic solvents.     

Solvent Effects on a Diels-Alder Reaction Involving a Cationic Diene: Consequences of the Absence of Hydrogen-Bond Interactions for Accelerations in Aqueous Media

In order to study the influence of hydrogen-bond interactions on the accelerations of Diels-Alder reactions in water and highly aqueous mixed solvent systems, second-order rate constants for the Diels-Alder reaction of acridizinium bromide (1a) with cyclopentadiene (CP) have been measured in aqueous media and organic solvents. Only modest rate accelerations were found in water-rich media. This is attributed to the absence of hydrogen-bonding groups in the reactants. Comparison with cycloadditions of CP with 9-carbomethoxyacridizinium bromide (1b), acrylonitrile (3), and methyl vinyl ketone (4), which do contain hydrogen-bond acceptors, reveals substantially larger aqueous accelerations. These results demonstrate that hydrogen bonding is a major factor in aqueous accelerations. Also rate constants for the cycloaddition of CP to 1a in surfactant solutions were determined. Micellar catalysis is observed in SDS solutions, due to binding of both the diene and the dienophile to the anionic micellar surface.     

Temperature Dependence of Solubility for Ibuprofen in Some Organic and Aqueous Solvents

The thermodynamic functions—Gibbs energy, enthalpy, and entropy of solution—were evaluated from the solubilities of ibuprofen determined at several temperatures in the pure solvents: octanol, isopropyl myristate, chloroform, cyclohexane, and water. The organic solvent-saturated aqueous media and water-saturated organic solvents were also studied, except for cyclohexane. In aqueous media, the solubility was determined at pH = 7.4 and an ionic strength 0.15 mol-L^–1 (physiological values). The excess Gibbs energy and the activity coefficients of the solutes were also determined. The solubilities are higher in organic media such as chloroform and octanol than in aqueous media and cyclohexane.     

Headspace needle-trap analysis of priority volatile organic compounds from aqueous samples: application to the analysis of natural and waste waters

Combining headspace (HS) sampling with a needle-trap device (NTD) to determine priority volatile organic compounds (VOCs) in water samples results in improved sensitivity and efficiency when compared to conventional static HS sampling. A 22 gauge stainless steel, 51-mm needle packed with Tenax TA and Carboxen 1000 particles is used as the NTD. Three different HS-NTD sampling methodologies are evaluated and all give limits of detection for the target VOCs in the ng L⁻¹ range. Active (purge-and-trap) HS-NTD sampling is found to give the best sensitivity but requires exhaustive control of the sampling conditions. The use of the NTD to collect the headspace gas sample results in a combined adsorption/desorption mechanism. The testing of different temperatures for the HS thermostating reveals a greater desorption effect when the sample is allowed to diffuse, whether passively or actively, through the sorbent particles. The limits of detection obtained in the simplest sampling methodology, static HS-NTD (5 mL aqueous sample in 20 mL HS vials, thermostating at 50 °C for 30 min with agitation), are sufficiently low as to permit its application to the analysis of 18 priority VOCs in natural and waste waters. In all cases compounds were detected below regulated levels.     

Utilization of Makgeolli Sludge Filtrate (MSF) as Low-Cost Substrate for Bacterial Cellulose Production by Gluconacetobacter xylinus

Search for efficient low-cost substrate/additives are gaining significant impetus in bacterial cellulose (BC) production. Makgeolli sludge (a traditional Korean wine distillery waste) is enriched with organic acid, alcohol, and sugar. Using makgeolli sludge filtrate (MSF) and Hestrin–Schramm (HS) medium (g/l of distilled water: glucose, 10.0; peptone, 5.0; yeast extract, 5.0; disodium phosphate, 2.7; citric acid, 1.15; pH 5.0), two different media—namely the modified HS media (ingredients of HS media except glucose dissolved in MSF) and mixed modified HS media (equal volume mixture of original and modified HS media)—were formulated. BC production with Gluconacetobacter xylinus was studied using the two above referred medium. Keeping HS medium as reference, effect of initial pH, glucose, ethanol, and organic acid concentration on BC production was also studied. It suggests that increasing initial glucose (up to 25 g/l) though improves BC production but results in poor BC yield above 15 g/l of glucose. However, addition of alcohol (up to 1%v/v) or citric acid (up to 20 mM) escalate productivity up to four and two times, respectively. In both modified HS media and mixed modified HS medium, BC production was four to five times higher than that of original HS medium. Even MSF alone surpassed HS medium in BC production. Scanning electron microscopy showed that BC microfibrils from MSF based media were several micrometers long and about 25–60 nm widths. X-ray diffraction patterns suggested the produced BC were of cellulose I polymorph.     

Poly(ionic liquid)s as phase-transporter for graphene oxide liquid crystals from aqueous to non-polar organic phase via noncovalent functionalization

We synthesise a novel poly(ionic liquid) (PIL) and develop a procedure that allows the phase transfer of graphene oxides (GO) from water to organic solvent, retaining graphene oxide liquid crystal (GOLC) phase in various organic solvents, especially non-polar organic solvents. PIL ([PEP-MIM]DBS) is exploited in this procedure as a noncovalent functional material that is capable of transporting GO from aqueous to non-polar organic phase. PILs can decorate GO noncovalently and keep GO nano-sheets exfoliated in solid-state PILs/GO hybrids, which can well redisperse in organic solvents without any agglomeration. This expands the number of known solvents which can support GOLC phase to dimethyl formamide, dimethyl sulfoxide, acetonitrile, tetrahydrofuran, and a number of other non-polar organic solvents, many of which were not known to afford GOLC phase prior to this report, such as dichloromethane, tetrachloromethane, dichloroethane and tetrachloroethane.     

Enthalpy characteristics of L-proline dissolution in certain water–organic mixtures at 298.15 K

A thermochemical study of the processes of L-proline dissolution in aqueous solutions of acetonitrile, 1,4-dioxane, acetone, dimethyl sulfoxide, nitromethane and tetrahydrofuran at Т = 298.15 K in the range of organic solvent concentrations x₂ = 0–0.25 mole fractions is performed. Standard values of the enthalpies of solution and transfer of L-proline from water to mixed solvent, and the enthalpy coefficients of pairwise interactions between L-proline and molecules of organic solvents, are calculated. The effect the composition of a water–organic mixture and the structure of organic solvents have on the enthalpy characteristics of L-proline dissolution and transfer is examined. The effect the energy properties of intermolecular interactions between components of a mixed solvent has on the intermolecular interactions between L-proline and molecules of cosolvent is estimated. The correlation between the enthalpy characteristics of L-proline dissolution and electron-donor properties of organic cosolvent in aqueous solutions is determined.     

Surface charge properties of Fe2O3 in aqueous and alcoholic mixed solvents

Iron oxide (Fe2O3) was identified and characterized by surface area, X-ray diffractometry, and FTIR analyses. Surface charge densities, point of zero charge (PZC), and surface ionization constants were determined from the potentiometric titration data in various aqueous and aqueous organic mixed solvents in the temperature range 293-313 K. The surface charge densities were observed to decrease with the increase in temperature and concentration of metal ions in both the aqueous and aqueous organic mixed solvents. The absolute values of the surface charge density were found to change in the order aqueous > aqueous/methanol > aqueous/ethanol. Further, the PZC of the iron oxide was observed to shift to the higher pH values in the order ethanol > methanol > aqueous solution, which indicated a decrease in the acidity of the surface -OH groups. The pKa1 and pKa2 values of iron oxide were also determined and then used for determination of the surface potential (psi0) of the solid in aqueous and aqueous organic mixed solvents. The surface potential-surface charge curves generally supplemented the results derived from psi0-pH curves.     

Hydrophobic Silica Sol Coatings on Textiles—the Influence of Solvent and Sol Concentration

Hydrophobic silica sol coatings on textiles were investigated with respect to the influence of the solvents and the concentration of the sol. For this purpose, two silica sols, prepared with the hydrophobic additives octyltriethoxysilane and perfluoroctyltriethoxysilane were diluted by different solvents: water, ethanol and aceton.In case of using pure water for dilution, the hydrophobicity of coated textiles decreases drastically with increasing dilution of the applied sol. For coatings on polyester fabrics or mixed fabrics made from polyester and cotton, the use of the organic solvents ethanol or aceton leads to significant hydrophobicity even in case of strong dilution down to a sol concentration < 1%. The hydrophobic effect of coated polyamide textile is less. The reason for different hydrophobicity of coated textiles resulting from the use of water instead of organic solvents is explained by different surface morphologies of the coatings deposited on the textile fibres, as observed by REM. In case of using organic solvents the coatings contain a more flat morphology which covers the fibres completely. In contrast, sols with higher water content lead to less adhesive coatings with crack formation.The use of a combination of water with less inflammable organic solvents such as di(propylene glycol) n-propyl ether (Dowanol^TM DPnP) in hydrophobic silica sols yields textile coatings with good hydrophobicity, even in case of low sol concentration. For practical application of textile coatings, especially silica sols with high water content are of interest, due to less risk of inflammation and lower ecological impact. Therefore, the use of water diluted hydrophobic silica sols with small amounts of DPnP offers a chance for textile refinement by the sol–gel technique.     

Limiting partial molar excess enthalpies by flow calorimetry: Some organic solvents in water

A Picker flow microcalorimeter was employed in conjunction with asymmetric syringe-type pumps to measure heats of mixing of highly dilute aqueous solutions of organic solvents. These data were used in turn to determine limiting partial molar excess enthalpies of the examined solvents in water. The measurements were carried out at 298.15 K for 29 common, oxygen and/or nitrogen containing solvents exhibiting complete miscibility with water. Except for only one compound, formamide, the limiting partial molar excess enthalpies are exothermic indicating that the process of dissolution is energetically favored. Comparison to literature data (in most cases to solution enthalpies at infinite dilution measured by batch calorimetry) proved the technique applied to be sufficiently accurate.     

Determination of dissociation constants of weak acids by deconvolution of proton binding isotherms derived from potentiometric data

Potentiometric titration of six carboxylic acid analytes were measured in aqueous and semiaqueous solvents to determine the effect of the solvent composition on the dissociation constants of the acids. The analytes studied were monoprotic (formic acid, acetic acid), diprotic (maleic and succinic acid) and triprotic (1, 2, ranging in composition from 0 to 80% by volume dioxane. The methodology used to assess the acidity constants was deconvolution of the proton binding isotherm of each analyte in each of the solvents. The dissociation constants agreed with those reported in the literature for titration in water. In the presence of the organic component, correlations relating the acidity constants with properties of the media were also found. In particular, affinity distributions derived from potentiometric titration data were used to assess the solvent media for resolving dissociation constants of weak acids and bases.     

Enhancement of intramolecular excimer formation and photodimerization of anthrylmethyl α,ω-alkanedioates via hydrophobic interactions

The fluorescence spectra and photodimerization of anthrylmethyl a,w-alkanedioates (A-Mn-A) both in organic and in aqueous organic mixed solvents have been studied.In aqueous organic mixed solvents strong intramolecular excimer emission is detected and the quantum yield for the intramolecular photodimerization is significantly greater than those in organic solvents.These observations suggest that hydrophobic interactions force A-Mn-A molecule to self-coil.The ratio of the head-to-head to head-to-tail products in the intramolecular photodimers of A-Mn-A depends on the length of the linking chain.This work presents a successful example of application of hydrophobic interactions to enhancement of large-ring formation.     

Thermodynamic Study of Poly(vinyl pyrrolidone) in Water/Dimethyl Sulfoxide Solutions by Viscometry

In this work, the intrinsic viscosities of poly(vinyl pyrrolidone) with a molar mass of 58?kg?mol^?1 were measured in water?Cdimethyl sulfoxide solutions at temperatures from (298.15 to 318.15)?K. The expansion factors of the polymer chains were calculated from the intrinsic viscosity data. The thermodynamic parameters (entropy of dilution parameter, the heat of dilution parameter, theta temperature, polymer?Csolvent interaction parameter and second osmotic virial coefficient) were derived by the temperature dependence of the polymer chain expansion factor. The thermodynamic parameters indicate that mixtures of water/dimethyl sulfoxide become poorer solvents for poly(vinyl pyrrolidone) as the temperature is increased. Also, the thermodynamic parameters indicate that water/dimethyl sulfoxide mixtures become better solvents for poly(vinyl pyrrolidone) by increasing the volume fractions of dimethyl sulfoxide.