Volumetric properties for the monosaccharide (D-xylose, D-arabinose, D-glucose, D-galactose)-NaCl-water systems at 298.15 K

Densities have been measured for monosaccharide (D-xylose, D-arabinose, D-glucose and D-galactose)-NaCl-water solutions at 298.15 K. These data have been used to determine the apparent molar volumes of these saccharides and NaCl in the studied solutions. Infinite-dilution apparent molar volumes for the saccharides (V0(phi,S)) in aqueous NaCl and those for NaCl (V0(phi,E)) in aqueous saccharide solutions have been evaluated, together with the standard transfer volumes of the saccharides (delta(t) V0S) from water to aqueous NaCl and of NaCl (delta(t) V0E) from water to aqueous saccharide solutions. It is shown that the delta(t) V0S and delta (t) V0E values are positive and increase with increasing co-solute molalities. Volumetric parameters indicating the interactions of NaCl with saccharides in water have been obtained, respectively, by using transfer volumes of the saccharides and NaCl, and the resulting values are in good agreement with each other within experimental error. The interactions between saccharides and NaCl are discussed in terms of the structural interaction model and the stereochemistry of the saccharide molecules in water.     

Mid-infrared spectroscopic analysis of saccharides in aqueous solutions with sodium chloride

The infrared spectral characteristics of three different types of disaccharides (trehalose, maltose, and sucrose) and four different types of monosaccharides (glucose, mannose, galactose, and fructose) in aqueous solutions with sodium chloride (NaCl) were determined. The infrared spectra were obtained using the FT-IR/ATR method and the absorption intensities respected the interaction between the saccharide and water with NaCl were determined. This study also focused on not only the glycosidic linkage position and the constituent monosaccharides, but also the concentration of the saccharides and NaCl and found that they have a significant influence on the infrared spectroscopic characterization of the disaccharides in an aqueous solution with NaCl. The absorption intensities representing the interaction between a saccharide and water with NaCl were spectroscopically determined. Additionally, the applications of MIR spectroscopy to obtain information about saccharide–NaCl interactions in foods and biosystems were suggested.     

Calorimetric study of the interaction between amino acids and sugars in water at 298.15 K

The enthalpies of dissolving glycine and DL-alanine in water solutions of D-glucose, D-maltose, and sucrose at 298.15 K were determined by calorimetry. From the results obtained, the coefficients of enthalpy for pairwise interactions hxy of the amino acids and saccharides in water were calculated. It was found that the hxy values for glycine in solutions of all saccharides studied are negative; in the case of DL-alanine, the hxy values are positive for all saccharides except for sucrose solution. It was shown that the hxy values reflect the sum effect of interactions between the amino acids and saccharides in aqueous solutions and the contribution of hydration of the solutes.     

Modeling of preparative reversed-phase HPLC of insulin

The adsorption isotherms of three recombinant proteins, human insulin, porcine insulin, and Lispro, were measured by frontal analysis on a YMC-ODS C18 column with an aqueous solution at 31% acetonitrile (0.1% TFA) as the mobile phase. The retention behavior of insulin, its related molecular structure, its conformation, and its aggregation in this phase system are discussed. The experimental isotherm data were fitted to the Langmuir, the Langmuir-Freundlich, and the Toth models. The results allow for a quantitative comparison of the saturation capacities, the equilibrium constants, and the exponents that represent the heterogeneity of the stationary phase obtained for the different insulin variants studied. The Toth model provided the best fit of the experimental data. The overloaded band profiles were calculated using the lumped pore diffusion and the equilibrium-dispersive model of chromatography. An excellent agreement between calculated and experimental profiles was demonstrated.     

Spatial structure of angiotensin in an aqueous solution

The spatial structure of spin-labeled angiotensin in aqueous solution wa investigated with the combined use of NMR, fluorescence spectroscopy and energy calculation including Monte-Carlo techniques. The calculated mean values of molecular parameters were compared with the experimental ones. The calculated and experimental mean values were regarded as statistically indistinguishable when the corresponding mean values occurred within the 95% confidence limit. The experimental parameters were shown to be adequately described by calculated conformers only with the assumption of the existence of dynamic equilibrium of conformers in solution. The mean values of statistical weights and their limits providing the agreement between the calculated and experimental data were determined. Two geometrically different forms of backbone structure for C-terminal hexapeptide in aqueous solution were revealed using the discussed approach; the N-terminal part of the molecule appeared to be much more conformationally labile. The model of molecule spatial structure is consistent with available literature data upon angiotensin titration experiments, its complexing with heavy metal ions etc.     

Simulating the vapour–liquid equilibria of 1,4-dioxane

1,4-dioxane, a cyclic ether, is an emerging contaminant which is difficult to remove from water with conventional water treatment methods and resistant to biodegradation. Once a reliable force field is developed for 1,4-dioxane, molecular simulation techniques can be useful to study alternative adsorbents for its removal. For this purpose, we carried out Monte Carlo simulations in a constant volume Gibbs Ensemble to generate a force field which is capable of predicting the vapour–liquid coexistence curve and critical data of 1,4-dioxane. Results are given in comparison with experimental data and results from simulations with other force fields. Liquid densities and critical temperature are predicted in excellent agreement with experimental data using the new force field. At high temperatures, predicted vapour densities are in good agreement with experimental data, however, at lower temperatures the predicted vapour densities deviate about an order of magnitude from the experimental values. The critical density is slightly underestimated with our new force field. However, overall, the results of simulations with the new parameters give much better agreement with experimental data compared to the results obtained using other force fields.     

Computational electrode potential of a coumestan derivative: theoretical and experimental studies

Electrode potential of a coumestan derivative, an important biological molecule, in aqueous solution is computed theoretically using Self-Consistent Field (SCF) theory at the level of Hartree--Fock and employing 6-31G(d) basis set and also obtained experimentally by employing electrochemical technique of cyclic voltammetry (CV). Frequency calculations have been carried out and thermal corrections and entropies have been taken into account. Polarizable continuum model is used to describe the solvent. The theoretical and experimental values for the standard electrode potential of the studied coumestan are in excellent agreement with each other and there is only 0.001 V discrepancy between experiment and theory. The agreement mutually verifies the accuracy of experimental method and the validity of mathematical model.     

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.     

Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket

We present free energy calculations using molecular dynamics on different substrates of alpha-lytic protease in the gas phase, in solution, while forming a noncovalent Michaelis complex with the enzyme, and in a tetrahedral structure representing a transition state/intermediate for acylation by the enzyme. Various P1 substrates were studied, with P1 = Gly, Ala, Val, and Leu. In qualitative agreement with experiment, the enzyme was calculated to bind and catalyze most effectively substrates with P1 = Ala over those with P1 = Gly, Val or Leu. Also, the calculated relative solvation free energies of Gly----Ala and Ala----Val were in qualitative agreement with experimental values in corresponding model systems. However, the level of quantitative agreement with experiment achieved in our earlier study of relative binding and catalysis of native subtilisin and an Asn-155----Ala mutant was not achieved. We surmise that this is due to the greater difficulty in quantitatively simulating effects that are predominantly van der Waals and hydrophobic compared to those that are hydrogen bonding/electrostatic.     

Predicting Liquid–Vapour Equilibria for Water Using an ab-initio Potential from Histogram Reweighting Monte Carlo Simulations

Abstract

The coexisting densities for an ab-initio model for water have been calculated using grand canonical Monte Carlo simulations with the histogram reweighting technique. Although good agreement with experimental data is found for the radial distribution function at room temperature, the predicted critical density and temperature are well below both the experimental value as well as predictions from semi-empirical potentials. Improvement in the repulsive part of the ab-initio potential is suggested as a way to obtain better agreement with experiment.     

Determination of the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system and a comparison between two theoretical methods for synthetic phase diagrams

Characterization of the thermodynamic properties of multi-solute aqueous solutions is of critical importance for biological and biochemical research. For example, the phase diagrams of aqueous systems, containing salts, saccharides, and plasma membrane permeating solutes, are indispensible in the field of cryobiology and pharmacology. However, only a few ternary phase diagrams are currently available for these systems. In this study, an auto-sampler differential scanning calorimeter (DSC) was used to determine the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system. To improve the accuracy of melting point measurement, a “mass-redemption” method was also applied for the DSC technique. Base on the analyses of these experimental data, a comparison was made between the two practical approaches to generate phase diagrams of multi-solute solutions from those of single-solute solutions: the summation of cubic polynomial melting point equations versus the use of osmotic virial equations with cross coefficients. The calculated values of the model standard deviations suggested that both methods are satisfactory for characterizing this quaternary system.     

Thermodynamic modeling of the partitioning of biomolecules in aqueous two-phase systems using a modified Flory–Huggins equation

A modified Flory–Huggins equation accounting for the solvation of polymer molecules by water molecules was used to model the phase behavior of aqueous two-phase systems (ATPS) formed by poly(ethylene glycol) (PEG) and dextran. The parameters of the equation were obtained by fitting experimental equilibrium data either accounting for or disregarding dextran polidispersity. The modified equation was subsequently applied to calculate partition coefficients of biomolecules in these systems. It was found that accounting for polidispersity did not affect significantly the calculated phase equilibrium, but increased the agreement of calculated partition coefficients with experimental data. Further improvement was obtained by using a size dependent interaction parameter for dextran pseudo-components.     

Highly sensitive, quick and simple quantification method for mono and disaccharides in aqueous media using liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS)

A highly sensitive, rapid LC-APCI-MS method for identification and quantification of mono and disaccharides in simple or complex aqueous phase has been developed. This original method is easy to use, no derivation and no post-column injection are needed. The separation is performed with a hydrophilic amino interaction (HILIC) column allowing high-throughput analysis with analysis times of 15 min for monosaccharides to 22 min for disaccharides. The development of the method carried out with 9 standard saccharides allowed to point out a dynamic range from 0.1-25.6 to 1-256 μg mL(-1) depending on the considered sugar. Next, the method was validated on saccharides at known concentrations in water and on 2 real samples: orange juice and aqueous phase obtained after enzymatic hydrolysis of sunflower seeds.     

Effect of potassium citrate salts on the vapor-liquid equilibrium properties of aqueous solutions of alanine at different temperatures

Water activity measurements by isopiestic method have been carried out on the aqueous solutions of alanine + potassium di-hydrogen citrate (KH₂Cit) and alanine + tri-potassium citrate (K₃Cit) over a range of temperatures at atmospheric pressure. From these measurements, values of the vapor pressure of solutions were determined. The effect of temperature and charge on the anion of salts on the vapor–liquid equilibrium of the investigated systems has been studied. The experimental water activities have been correlated successfully with the segment-based local composition Wilson and NRTL models. The agreement between the correlations and the experimental data is good.     

Aqueous viscosity is the primary source of friction in lipidic pore dynamics

A new theory, to our knowledge, is developed that describes the dynamics of a lipidic pore in a liposome. The equations of the theory capture the experimentally observed three-stage functional form of pore radius over time—stage 1, rapid pore enlargement; stage 2, slow pore shrinkage; and stage 3, rapid pore closure. They also show that lipid flow is kinetically limited by the values of both membrane and aqueous viscosity; therefore, pore evolution is affected by both viscosities. The theory predicts that for a giant liposome, tens of microns in radius, water viscosity dominates over the effects of membrane viscosity. The edge tension of a lipidic pore is calculated by using the theory to quantitatively account for pore kinetics in stage 3, rapid pore closing. This value of edge tension agrees with the value as standardly calculated from the stage of slow pore closure, stage 2. For small, submicron liposomes, membrane viscosity affects pore kinetics, but only if the viscosity of the aqueous solution is comparable to that of distilled water. A first-principle fluid-mechanics calculation of the friction due to aqueous viscosity is in excellent agreement with the friction obtained by applying the new theory to data of previously published experimental results.     

Molecular Parameterisation and the Theoretical Calculation of Electrode Potentials

The difference in reduction potentials between ortho and para-benzoquinones has been calculated. The employs gas phase ab initio and semi-empirical computations in combination with free energy perturbation theory applied to gas and solution phase Monte Carlo simulations. The effects on calculated results of altering solute electrostatic parameterisation in solution phase simulations is examined. Atom centred charges derived from the molecular electrostatic potentials, MEPs, from optimised ab initio wavefunctions and charges generated by consideration of hydrogen bonded complexes are considered. Parameterisation of hydroxyl torsions in hydroquinone molecules is treated in a physically realistic manner. The coupled torsional system of the ortho-hydrobenzoquinone molecule is described by a potential energy surface calculated using gas phase AM1 semi-empirical computations rather than the simple torsional energy functions frequently employed in such calculations. Calculated differences in electrode potentials show that the electrostatic interactions of quinone and hydroquinone molecules in aqueous solution are not well described by atom centred charges derived from ab initio calculated MEPs. Moreover, results in good agreement with the experimental reduction potential difference can be obtained by employing high level ab initio calculations and solution phase electrostatic parameters developed by consideration of hydrogen bonded complexes.     

Solvent selection for solid-to-solid synthesis

Thermolysin catalyzed solid-to-solid synthesis of the model peptide Z-L-Phe-L-Leu-NH(2) is practically feasible in water and a range of organic solvents with different physicochemical properties. Excellent overall conversions were obtained in acetonitrile, ethyl acetate, n-hexane, methanol, 2-propanol, tert-amyl alcohol, tetrahydrofuran, toluene and water, while no product precipitation was observed in dichloromethane resulting in a much lower yield. In precipitation driven synthesis the product accumulates both in solution and in the solid phase. It was shown that the highest overall yields (yield in the liquid plus yield in the solid) can be expected in solvents where the substrate solubilities are minimized. The best yields of solid product can be expected in solvents where both product and substrate solubilities are lowest. This was in agreement with experimental observations and should be generally valid.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.     

CD spectrum and conformational distribution of cyclotuftsin in solution

CD spectra for low-energy conformations of the tuftsin cycloanalogue, , were calculated. A theoretical spectrum obtained as the weighted average of calculated spectra for individual peptide backbone conformers is qualitatively consistent with an experimental CD spectrum in aqueous solution. The conformational distribution allows one to achieve agreement between calculated and experimental values of structural parameters of the cyclotuftsin molecule investigated by NMR spectroscopy.

CD spectrum calculation Theoretical conformational analysis Tuftsin cycloanalog Peptide conformation