Partial Molecular Volume Research Articles

Temperature, Pressure, and Length-Scale Dependence of Solvation in Water-like Solvents. II. Large Solvophovic Solutes.

We use molecular simulation to determine solvation free energies, isochoric solvation energies and entropies, isobaric solvation enthalpies and entropies, partial molecular volumes, and isothermal density derivatives of the solvation free energy as a function of temperature and pressure for hard-sphere solutes with diameters ranging from 4 to 36 Å in TIP4P/2005 and Jagla water-like solvents exhibiting unusual thermodynamics. An important piece of our discussion focuses on the nanometer-sized solutes, for which simulation results are found to be accounted for by the most basic classical thermodynamic treatment contemplating bulk and interfacial contributions to the solvation free energy. Thus, since water's liquid-vapor surface tension is only special inasmuch as it takes unusually large values, solvent's water-like unusual thermodynamics manifests through a term proportional to the pressure in the solvation free energy. As a result, such solvent's unusual thermodynamics is found to be relevant to the temperature and pressure dependence of the isochoric solvation energy and entropy as well as to the isothermal density derivative of the solvation free energy. This sharply contrasts with the findings of the first part of this series indicating that the solvation free energy of small hard spheres responds to temperature and pressure changes as solvent's density does, with such a contrasting picture embodying a "pressure-density dichotomy." As for the length-scale dependence, we find the zero nominal pressure and the solvent's temperature of the maximum density as singular conditions for cavity surface-area size scaling of large solutes to occur for all solvation quantities. We finally argue that the overall study undertaken in this series suggests that water's unusual thermodynamics may be relevant to the thermodynamic stability of clusters of solvophobic units in the temperature-pressure plane. Some comments on the role of solute-solvent attractive interactions are also depicted.

Temperature, Pressure, and Length-Scale Dependence of Solvation in Water-like Solvents. I. Small Solvophobic Solutes.

We analyze the role of temperature, pressure, and solute's molecular size on the pattern of isochoric and isobaric solvation of small hard-sphere solutes in TIP4P/2005 water and in a water-like "Jagla" solvent exhibiting unusual thermodynamics. To this end, we employ molecular simulation to determine solvation free energies, isochoric solvation energies and entropies, isobaric solvation enthalpies and entropies, partial molecular volumes, and isothermal density derivatives of the solvation free energy along isobaric and isothermal paths covering solvent's stable liquid and supercritical states as well as supercooled and "stretched" liquid states. Results are found to be consistent with the most primitive scaled-particle theory and the Gaussian model of small-length-scale solvation. The temperature and pressure dependence of solvation quantities embraces solvent's water-like unusual thermodynamic behavior: its density is reflected in the solvation free energy; the isochoric solvation energy and entropy; and the isothermal density derivative of the solvation free energy, its isobaric thermal expansivity in the isobaric solvation enthalpy and entropy, and its isothermal compressibility in the partial molecular volume. The solute's size or length-scale dependence is found to combine with solvent's water-like behavior to produce the "convergence thermodynamics" picture characteristic of aqueous solutions of nonpolar solutes, which is unequivocally found here to be the mapping of the water-like density maximum into the isobaric solvation enthalpy and entropy versus temperature curves for a set of solutes of varying sizes.

Charge and hydration structure of dendritic polyelectrolytes: molecular simulations of polyglycerol sulphate.

Macromolecules based on dendritic or hyperbranched polyelectrolytes have been emerging as high potential candidates for biomedical applications. Here we study the charge and solvation structure of dendritic polyglycerol sulphate (dPGS) of generations 0 to 3 in aqueous sodium chloride solution by explicit-solvent molecular dynamics computer simulations. We characterize dPGS by calculating several important properties such as relevant dPGS radii, molecular distributions, the solvent accessible surface area, and the partial molecular volume. In particular, as the dPGS exhibits high charge renormalization effects, we address the challenges of how to obtain a well-defined effective charge and surface potential of dPGS for practical applications. We compare implicit- and explicit-solvent approaches in our all-atom simulations with the coarse-grained simulations from our previous work. We find consistent values for the effective electrostatic size (i.e., the location of the effective charge of a Debye-Hückel sphere) within all the approaches, deviating at most by the size of a water molecule. Finally, the excess chemical potential of water insertion into dPGS and its thermodynamic signature are presented and rationalized.

Partial molecular volumes of cholesterol and phosphatidylcholine in mixed bilayers

Abstract Dispersion of multilamellar liposomes of dimyristoylphosphatidylcholine (DMPC) and cholesterol (CHOL) were studied by vibrational densitometer for the CHOL mole fractions X = 0−0.54 in the temperature range 18−50 °C, both below and above the main phase transition. DMPC-CHOL bilayers served as a simple model for lipidic part of biological membrane. Volumetric parameters are essential not only to evaluate the data obtained by scattering and diffraction methods on model membranes but can provide valuable information about molecular packing in bilayers and the phase behaviour of lipid-CHOL mixtures. In this paper, preliminary results regarding the changes in the specific volume of lipid bilayer with increasing temperature and CHOL content are presented. Different values of apparent molecular volume of CHOL for different CHOL mole fraction pointed out the non-ideal mixing of DMPC and CHOL.

Osmotic Second Virial Coefficients of Aqueous Solutions from Two-Component Equations of State.

Osmotic second virial coefficients in dilute aqueous solutions of small nonpolar solutes are calculated from three different two-component equations of state. The solutes are five noble gases, four diatomics, and six hydrocarbons in the range C1-C4. The equations of state are modified versions of the van der Waals, Redlich-Kwong, and Peng-Robinson equations, with an added hydrogen-bonding term for the solvent water. The parameters in the resulting equations of state are assigned so as to reproduce the experimental values and temperature dependence of the density, vapor pressure, and compressibility of the solvent, the gas-phase second virial coefficient of the pure solute, the solubility and partial molecular volume of the solute, and earlier estimates of the solutes' molecular radii. For all 15 solutes, the calculations are done for 298.15 K, whereas for CH4, C2H6, and C3H8 in particular, they are also done as functions of temperature over the full range 278.15-348.15 K. The calculated osmotic virial coefficients are compared with earlier calculations of these coefficients for these solutes and also with the results derived from earlier computer simulations of model aqueous solutions of methane. They are also compared with the experimental gas-phase second virial coefficients of the pure gaseous solutes to determine the effect the mediation of the solvent has on the resulting solute-solute interactions in the solution.

Water anomalous thermodynamics, attraction, repulsion, and hydrophobic hydration.

A model composed of van der Waals-like and hydrogen bonding contributions that simulates the low-temperature anomalous thermodynamics of pure water while exhibiting a second, liquid-liquid critical point [P. H. Poole et al., Phys. Rev. Lett. 73, 1632 (1994)] is extended to dilute solutions of nonionic species. Critical lines emanating from such second critical point are calculated. While one infers that the smallness of the water molecule may be a relevant factor for those critical lines to move towards experimentally accessible regions, attention is mainly focused on the picture our model draws for the hydration thermodynamics of purely hydrophobic and amphiphilic non-electrolyte solutes. We first focus on differentiating solvation at constant volume from the corresponding isobaric process. Both processes provide the same viewpoint for the low solubility of hydrophobic solutes: it originates from the combination of weak solute-solvent attractive interactions and the specific excluded-volume effects associated with the small molecular size of water. However, a sharp distinction is found when exploring the temperature dependence of hydration phenomena since, in contrast to the situation for the constant-V process, the properties of pure water play a crucial role at isobaric conditions. Specifically, the solubility minimum as well as enthalpy and entropy convergence phenomena, exclusively ascribed to isobaric solvation, are closely related to water's density maximum. Furthermore, the behavior of the partial molecular volume and the partial molecular isobaric heat capacity highlights the interplay between water anomalies, attraction, and repulsion. The overall picture presented here is supported by experimental observations, simulations, and previous theoretical results.

In silico characterization of protein partial molecular volumes and hydration shells.

In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.

A detailed analysis of partial molecular volumes in DPPC/cholesterol binary bilayers

We examined the volumetric behavior of the dipalmitoylphosphatidylcholine (DPPC)/cholesterol binary bilayer system with high accuracy and more cholesterol concentrations to reveal the detailed molecular states in the liquid-disordered (Ld) phase, the liquid-ordered (Lo) phase and the gel phase. We measured the average specific volume of the binary bilayer at several temperatures by the neutral flotation method and calculated the average volume per molecule to estimate the partial molecular volumes of DPPC and cholesterol in each phase. As a result, we found that the region with intermediate cholesterol concentrations showed a more complicated behavior than expected from simple coexistence of Ld and Lo domains. We also measured fluorescence decay of trans-parinaric acid (tPA) added into the binary bilayer with more cholesterol concentrations to get further insight into the cholesterol-induced formation of the Lo phase. On the basis of these results we discuss the molecular interaction between DPPC and cholesterol molecule in the Lo phase and the manner of Ld/Lo phase coexistence.

Mixing Properties of Sphingomyelin Ceramide Bilayers: A Simulation Study

Ceramide is the simplest molecule in the class of glycosphingolipids composed of a sphingosine backbone and acyl moiety. It plays significant roles in cell signaling; apoptosis; binding of hormones, toxins, and viruses; and many other biologically important functions. Sphingomyelin, ceramide with a phosphotidylcholine headgroup, is another biologically vital lipid present in the myelin sheath of nerve cell axons. Regions with high concentrations of ceramide can be formed in biological membranes composed of sphingomyelin by enzymatic catalysis with sphingomyelinase. To better understand the biophysical and thermodynamic properties of these molecules and their mixtures, we have preformed NPT molecular dynamics simulations of hydrated 16:0 sphingomyelin bilayers with increasing concentrations of 16:0 ceramide at 323, 332, 340, and 358 K. From analyses of electron densities, hydrogen bonding, NMR order parameters, partial molecular volume, and partial molecular area, we have identified possible structural changes corresponding to liquid ordered and liquid disordered phases. These structural changes are the results of changes in intra- and intermolecular hydrogen bonds between SM and Cer molecules. Our results correspond to DSC experiments for sphingomyelin bilayer concentrations up to 50% Cer. Above 50% concentration, we observe conformational changes in the SM headgroup similar to that of the umbrella model for lipid cholesterol mixtures.

Simultaneous establishing of stationary growth rate and composition of supercritical droplets at isothermal binary condensation in the diffusion-controlled regime

General integral relations expressing the droplet radius and time of the droplet nonstationary growth as nonlinear functions of solution concentration in the droplet have been derived. These relations are valid for a supercritical droplet (i.e., sufficiently large droplet, for which the Laplace pressure effect on the concentration at saturation of vapors is negligible) isothermally growing via stationary diffusion in the mixture of two condensing vapors and an incondensable carrier gas. The initial composition in the droplet may be arbitrary and partial molecular volumes of components are not fixed. Explicit analytical relations have been found for droplet composition and the droplet size as functions of time at small deviations from the stationary concentration in the growing droplet. These relations show that the assumption of the steady droplet growth rate is not valid for non-small deviations from the stationary concentration. Some illustrations of the general nonlinear theory have been done in situation when solution in the droplet can be considered ideal.

Solvation of hydrophobes in water and simple liquids

The solvation of nonpolar molecules in water and that in simple liquids are compared and contrasted. First, solvation thermodynamics is reviewed in a way that focuses on how the enthalpy and entropy of solvation depend on the choice of microscopic volume change v in the solvation process--including special choices v being zero (fixed-volume condition) and v being the partial molecular volume of a solute molecule (fixed-pressure condition)--and how the solvation quantities are related with temperature derivatives of the solvation free energy. Second, the solvation free energy and the solvation enthalpy of a Lennard-Jones (LJ) atom in model water are calculated in the parameter space representing the solute size and the strength of the solute-solvent interaction, and the results are compared with those for an LJ atom in the LJ solvent. The solvation diagrams showing domains of different types of solvation in the parameter space are obtained both for the constant-volume condition and for the constant-pressure condition. Similarities between water and the simple liquid are found when the constant-volume solvation is considered while a significant difference manifests itself in the fixed-pressure solvation. The domain of solvation of hydrophobic character in the parameter space is large in the constant-volume solvation both for water and for the simple liquid. When switched to the constant-pressure condition accompanying a microscopic volume change, the hydrophobic domain remains large in water but it becomes significantly small in the simple liquid. The contrasting results are due to the smallness of the thermal pressure coefficient of water at low temperatures.

Experimental and Theoretical Determination of the Limiting Partial Molar Volume of Indole in CCl4, Tetrahydrofuran and Acetonitrile at 293.15 K: A Comparative Study with Benzimidazole and Benzothiophene

The partial molar volumes of indole(Ind) at infinite dilution (\(V_{2}^{\infty}\)) in carbon tetrachloride (CCl4), acetonitrile (ACN) and tetrahydrofuran (THF) as solvents, were estimated from densitometry measurements at 293.15 K. The results indicate that \(V_{2}^{\infty}\mbox{(ACN)}>V_{2}^{\infty}\mbox{(CCl$_{4}$)}\) \(\approx V_{2}^{\infty}\mbox{(THF)}\). The values determined in this study are close to the values calculated from reported density for Ind in the solid state. In order to make a comparison the partial molecular volume of benzimidazole (Bim) and benzothiophene (BT) in solvents with appropriate solubility were measured too, and the results have revealed that \(V_{2}^{\infty}\mbox{(BT)}>V_{2}^{\infty}\mbox{(Ind)}\) in CCl4 and \(V_{2}^{\infty}\mbox{(Ind)}>V_{2}^{\infty}\mbox{(Bim)}\) in THF. In this work the role of solvent reorganization around to solute cavity, and specific and nonspecific interactions on the volumetric behavior of these molecules in solution are discussed using the Terasawa-Itsuki-Arakawa model, the Lee-Graziano model, molar volumes of solutes calculated at the DFT-B3LYP/cc-pVTZ and aug-cc-pVTZ level in the gas phase and considering solvent presence with the Onsager’s reaction field, and the van der Waals volume. This analysis suggests that the molecular volumes of solutes are overestimated by the quantum methods employed in this work and that the volumetric contribution from the van der Waals components to the limiting partial molecular volumes of solutes is important, with the exception of Ind in CCl4 where the solvent reorganization is the dominant factor.

Computer-assisted searching for coumarins inPeucedanum alsaticumL. andPeucedanum cervaria(L.) Lap.

Summary The objective of the work was continuation of our study on identification of target coumarins in extracts from Peucedanum alsaticum L. and Peucedanum cervaria (L.) Lap., by use of ChromSword, on the basis of relationships between retention data and descriptors such as partial molecular volume of structural fragments in water and energies of electrostatic interactions of bond dipoles with water (QSRR). The coumarins were mainly identified by comparing UV spectra from gradient runs with spectra from the literature. The presence of columbianadin, ostruthin, and 8-methoxypeucedanin in the fruits of P. cervaria (L.) Lap. and oxypeucedanin and isoimperatorin in the fruits of P. alsaticum was confirmed. The optimum conditions obtained from DryLab simulation were used for both RP-HPLC and RP-UPLC.

Cholesterol Surrogates: A Comparison of Cholesterol and 16:0 Ceramide in POPC Bilayers

Experimental evidence indicates that, under some circumstances, “surrogate” molecules may play the same role as cholesterol in ordering membrane lipids. The simplest molecule in this class is Ceramide. In this article, we describe atomic-level molecular dynamics simulations designed to shed light on this phenomenon. We run simulations of hydrated phosphoryl-oleoyl phosphatidylcholine (POPC) bilayers containing cholesterol, and containing ceramide, in concentrations ranging from 5% to 33%. We also perform a simulation of a pure POPC bilayer to verify the simulation force fields against experimental structural data for POPC. Our simulation data are in good agreement with experimental data for the partial molecular volumes, areas, form factors, and order parameters. These simulations suggest that ceramide and cholesterol have a very similar effect on the POPC bilayer, although ceramide is less effective in inducing order in the bilayer compared with cholesterol at the same concentrations.

3P134 蛋白質の部分分子体積における水和効果(細胞生物学的課題(接着・運動・骨格・伝達・膜)、水・水和、電解質,口頭発表,第45回日本生物物理学会年会)

3P134 蛋白質の部分分子体積における水和効果(細胞生物学的課題(接着・運動・骨格・伝達・膜)、水・水和、電解質,口頭発表,第45回日本生物物理学会年会)

Partial molecular volumes of lipids and cholesterol

Volumetric measurements are reported for fully hydrated lipid/cholesterol bilayer mixtures using the neutral flotation method. Apparent specific volume data were obtained with the lipids DOPC, POPC and DMPC at T = 30 °C, DPPC at 50 °C, and brain sphingomyelin (BSM) at 45 and 24 °C for mole fractions of cholesterol x from 0 to 0.5. Unlike previous cholesterol mixture studies, we converted our raw data to partial molecular volume V L of the lipid and V C of the cholesterol. The partial molecular volumes were constant for POPC and DOPC as x was varied, but had sharp breaks for the other lipids at values of x C near 0.25 ± 0.05. Results for x < x C clearly exhibit the condensation effect of cholesterol on DPPC, DMPC and BSM when measured at temperatures above their main transition temperatures T M. The break points at x C are compared to phase diagrams in the literature. For x > x C the values of the partial molecular volumes of cholesterol clustered near 630 ± 10 Å 3 in all the lipids when measured for T > T M; we suggest that this is the most appropriate measure of the bare volume of cholesterol in lipid bilayers.

S3f1-2 Evaluation of Molecular Factors Involved in Determining Partial Molecular Volume of Proteins in Various Conformational States(S3-f1: "Hydration Effects on Structure and Thermodynamics of Proteins,Symposia,Abstract,Meeting Program of EABS &amp; BSJ 2006)

S3f1-2 Evaluation of Molecular Factors Involved in Determining Partial Molecular Volume of Proteins in Various Conformational States(S3-f1: "Hydration Effects on Structure and Thermodynamics of Proteins,Symposia,Abstract,Meeting Program of EABS &amp; BSJ 2006)

1P089 非天然状態にある蛋白質の部分分子容予測法の開発(蛋白質 C) 物生(安定性、折れたたみなど)))

1P089 非天然状態にある蛋白質の部分分子容予測法の開発(蛋白質 C) 物生(安定性、折れたたみなど)))

Partial molar volume as an important thermodynamic parameter. Application for uracil methyl derivatives

Quantum mechanical calculations of the solvation were performed for all 16 possible methylated uracil derivatives using the Polarizible Continuum Model (PCM) approach. The obtained results were found to reproduce the experimental data of hydration enthalpies. The decomposition of QM-derived Gibbs energy enabled to correlate the solute–solvent Gibbs energy interaction with the difference between partial molar volume and molecular volume. In aqueous medium, the change of the “effective” solute volume upon dissolution costs 1.8 kJ mol −1 per every 1 cm 3 mol −1 of the difference between solute partial molar volume and molecular volume.

Self-Assembly at High Pressures: SANS Study of the Effect of Pressure on Microstructure of C8E5 Micelles in Water

We present the results of a high-pressure small-angle neutron scattering study of the effect of pressure on surfactant microstructure. The study was carried out on a solution of 1 wt % C8E5 in D2O at 29.4 °C and pressures up to 310 MPa. The C8E5 micelles that form under these conditions are noninteracting. We find that applying pressure leads to a pronounced decrease in the micelle radius of gyration and the forward scattering intensity over the pressure range from ambient to 150 MPa. The partial molecular volume of the surfactant and the extent of hydration of the surfactant head groups in the micelle were also determined using the method of solvent contrast variation. Both quantities decrease with the application of pressure up to 150 MPa. Core−shell model fits to the scattering spectra over the entire q-range indicate that the shell radius decreases, while the hydrophobic core radius increases slightly with pressure. The pressure dependence of the shell radius is notably similar to that observed for the radius of gyration. Collectively, these observations lead to the conclusion that the effect of pressure on C8E5 micellization is to induce the dehydration of surfactant head groups and the collapse of the hydrophilic micelle shell at pressures between ambient and 150 MPa.