Fluid of fused spheres as a model for protein solution

In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the fused-sphere particles. The model can be used to study the non-spherical (or dimerized) proteins in solution. Thermodynamic quantities of the system are calculated using a modification of Wertheim's thermodynamic perturbation theory and the results compared with new Monte Carlo simulations under isobaric-isothermal conditions. In particular, we are interested in the liquid-liquid phase separation in such systems. The model fluid serves to evaluate the effect of the shape of the molecules, changing from spherical to more elongated (two fused spheres) ones. The results indicate that the effect of the non-spherical shape is to reduce the critical density and temperature. This finding is consistent with experimental observations for the antibodies of non-spherical shape.Comment: 12 pages, 5 figure

Correlation between flexibility of chain-like polyelectrolyte and thermodynamic properties of its solution

Structural and thermodynamic properties of the model solution containing charged oligomers and the equivalent number of counterions were studied by means of the canonical Monte Carlo simulation technique. The oligomers are represented as (flexible) freely jointed chains or as a linear (rigid) array of charged hard spheres. In accordance with the primitive model of electrolyte solutions, the counterions are modeled as charged hard spheres and the solvent as dielectric continuum. Significant differences in the pair distribution functions, obtained for the rigid (rod-like) and flexible model are found but the differences in thermodynamic properties, such as, enthalpy of dilution and excess chemical potential, are less significant. The results are discussed in light of the experimental data an aqueous polyelectrolyte solutions. The simulations suggest that deviations from the fully extended (rod-like) conformation yield slightly stronger binding of counterions. On the other hand, the flexibility of polyions, even when coupled with the ion-size effects, cannot be blamed for qualitative differences between the theoretical results and experimental data for enthalpy of dilution.Comment: 14 pages, 10 figure

Effects of translational and rotational degrees of freedom on the properties of model water

Molecular dynamics simulations with separate thermostats for rotational and translational motions were used to study the effects of these degrees of freedom on the structure of water at a fixed density. To describe water molecules, we used the SPC/E model. The results indicate that an increase of the rotational temperature, $T_\textrm{R}$, causes a significant breaking of the hydrogen bonds. This is not the case, at least not to such an extent, when the translational temperature, $T_\textrm{T}$, is raised. The probability of finding an empty spherical cavity (no water molecule present) of a given size, strongly decreases with an increase of $T_\textrm{R}$, but this only marginally affects the free energy of the hydrophobe insertion. The excess internal energy increases proportionally with an increase of $T_\textrm{R}$, while an increase of $T_\textrm{T}$ yields a much smaller effect at high temperatures. The diffusion coefficient of water exhibits a non-monotonous behaviour with an increase of the rotational temperature.Comment: 9 pages, 9 figure

Primitive model electrolytes. A comparison of the HNC approximation for the activity coefficient with Monte Carlo data

Accuracy of the mean activity coefficient expression (Hansen-Vieillefosse-Belloni equation), valid within the hypernetted chain (HNC) approximation, was tested in a wide concentration range against new Monte Carlo (MC) data for +1:-1 and +2:-2 primitive model electrolytes. The expression has an advantage that the excess chemical potential can be obtained directly, without invoking the time consuming Gibbs-Duhem calculation. We found the HNC results for the mean activity coefficient to be in good agreement with the machine calculations performed for the same model. In addition, the thermodynamic consistency of the HNC approximation was tested. The mean activity coefficients, calculated via the Gibbs-Duhem equation, seem to follow the MC data slightly better than the Hansen-Vieillefosse-Belloni expression. For completeness of the calculation, the HNC excess internal energies and osmotic coefficients are also presented. These results are compared with the calculations based on other theories commonly used to describe electrolyte solutions, such as the mean spherical approximation, Pitzer's extension of the Debye-H\"uckel theory, and the Debye-H\"uckel limiting law.Comment: 15 pages, 6 figure

Modelling the ion-exchange equilibrium in nanoporous materials

Distribution of a two component electrolyte mixture between the model adsorbent and a bulk aqueous electrolyte solution was studied using the replica Ornstein-Zernike theory and the grand canonical Monte Carlo method. The electrolyte components were modelled to mimic the HCl/NaCl and HCl/CaCl_2 mixtures, respectively. The matrix, invaded by the primitive model electrolyte mixture, was formed from monovalent negatively charged spherical obstacles. The solution was treated as a continuous dielectric with the properties of pure water. Comparison of the pair distribution functions (obtained by the two methods) between the various ionic species indicated a good agreement between the replica Ornstein-Zernike results and machine calculations. Among thermodynamic properties, the mean activity coefficient of the invaded electrolyte components was calculated. Simple model for the ion-exchange resin was proposed. The selectivity calculations yielded qualitative agreement with the following experimental observations: (i) selectivity increases with the increasing capacity of the adsorbent (matrix concentration), (ii) the adsorbent is more selective for the ion having higher charge density if its fraction in mixture is smaller.Comment: 12 pages, 9 figure

Modelling Bi-specific Antibodies in Aqueous Solution

This study presents theoretical results for physico-chemical properties of system of molecules modeling bi-specific antibodies, such as, dual-variable-domain monoclonal antibodies (DVD-Ig) and Fabs-In-Tandem Immunoglobulin (FIT-Ig). These molecules are representatives of the engineered proteins that combine the function and specificity of two monoclonal antibodies. Individual molecules are here depicted as an assembly of nine (or in case of the Fit-Ig eleven) hard spheres, organized to resemble the Y-shaped object. The effects of the increased size, asymmetry, and flexibility of individual molecules on measurable properties of such systems of molecules are investigated. We examined the liquid-liquid phase separation, the second virial coefficient $B_2$, and viscosity under various experimental conditions. The calculations are compared with the data for regular monoclonal antibodies and discussed in view of the experimental results for DVD-Ig solutions available in literature

The Activity Coefficients of Amino Acids and Peptides in Aqueous Solutions Containing Guanidinium Chloride

Six systems of the type amino acid- or peptide-guanidinium chloride-water have been investigated over wide solute molality ranges using vapor pressure osmometry. The amino acids used were glycine and L-leucine, while the peptides were diglycine, triglycine, glycyl-L-leucine and L-leucyl-L-leucine. Equations for the ratios of the activity coefficients of these compounds in the salt solutions and water, respectively, were obtained in terms of the molalities of the solutes. The activity coefficient ratios for glycine are not much below one, whereas those for i.-leucine are considerably smaller reflecting the presence of the leucyl side chain. The activity coefficient ratios for the peptides are generally smaller than those for the amino acids which can be attributed to . the presence of the peptide group

The Activity Coefficients of Amino Acids and Peptides in Aqueous Solutions Containing Guanidinium Chloride

Six systems of the type amino acid- or peptide-guanidinium chloride-water have been investigated over wide solute molality ranges using vapor pressure osmometry. The amino acids used were glycine and L-leucine, while the peptides were diglycine, triglycine, glycyl-L-leucine and L-leucyl-L-leucine. Equations for the ratios of the activity coefficients of these compounds in the salt solutions and water, respectively, were obtained in terms of the molalities of the solutes. The activity coefficient ratios for glycine are not much below one, whereas those for i.-leucine are considerably smaller reflecting the presence of the leucyl side chain. The activity coefficient ratios for the peptides are generally smaller than those for the amino acids which can be attributed to . the presence of the peptide group

On the nature of long-range contributions to pair interactions between charged colloids in two dimensions

We perform a detailed analysis of solutions of the inverse problem applied to experimentally measured two-dimensional radial distribution functions for highly charged latex dispersions. The experiments are carried out at high colloidal densities and under low-salt conditions. At the highest studied densities, the extracted effective pair potentials contain long-range attractive part. At the same time, we find that for the best distribution functions available the range of stability of the solutions is limited by the nearest neighbour distance between the colloidal particles. Moreover, the measured pair distribution functions can be explained by purely repulsive pair potentials contained in the stable part of the solution.Comment: 6 pages, 5 figure