Molecular dynamics study of the volumetric and hydrophobic properties of the amphiphilic molecule C8E6

Insight to the Local Structure of Mixtures of Imidazolium-Based Ionic Liquids and Molecular Solvents from Molecular Dynamics Simulations and Voronoi Analysis

While the physicochemical properties as well as the NMR and vibration spectroscopic data of the mixtures of ionic liquids (ILs) with molecular solvents undergo a drastic change around the IL mole fraction of 0.2, the local structure of the mixtures pertaining to this behavior remains unclear. In this work, the local structure of 12 mixtures of 1-butyl-3-methylimidazolium cation (C₄mim⁺) combined with perfluorinated anions, such as tetrafluoroborate (BF₄^-), hexafluorophosphate (PF₆^-), trifluoromethylsulfonate (TFO^-), and bis(trifluoromethanesulfonyl)imide, (TFSI^-), and aprotic dipolar solvents, such as acetonitrile (AN), propylene carbonate (PC), and gamma butyrolactone (γ-BL) is studied by molecular dynamics simulations in the entire composition range, with an emphasis on the IL mole fractions around 0.2. Distributions of metric properties corresponding to the Voronoi polyhedra of the particles (volume assigned to the particles, local density, radius of spherical voids) are determined, using representative sites of the cations, anions, and the solvent molecules, to characterize the changes in the local structure of these mixtures. By analyzing the mole fraction dependence of the average value, fluctuation, and skewness parameter of these distributions, the present study reveals that, around the IL mole fraction of 0.2, the local structure of the mixture undergoes a transition between that determined by the interionic interactions and that determined by the interactions between the ions and solvent molecules. It should be noted that the strength of the interactions between the ions and the solvent molecules, modulated by the change in the composition of the mixture, plays an important role in the occurrence of this transition. The signature of the change in the local structure is traced back to the nonlinear change of the mean values, fluctuations, and skewness values of the metric Voronoi polyhedra distributions.

Voronoi Polyhedra as a Tool for the Characterization of Inhomogeneous Distribution in 1-Butyl-3-methylimidazolium Cation-Based Ionic Liquids

The inhomogeneity distribution in four imidazolium-based ionic liquids (ILs) containing the 1-butyl-3-methylimidazolium (C₄mim) cation, coupled with tetrafluoroborate (BF₄), hexafluorophosphate (PF₆), bis(trifluoromethanesulfonyl)amide (TFSA), and trifluoromethanesulfonate (TfO) anions, was characterized using Voronoi polyhedra. For this purpose, molecular dynamic simulations have been performed on the isothermal-isobaric (NpT) ensemble. We checked the ability of the potential models to reproduce the experimental density, heat of vaporization, and transport properties (diffusion and viscosity) of these ionic liquids. The inhomogeneity distribution of ions around the ring, methyl, and butyl chain terminal hydrogen atoms of the C₄mim cation was investigated by means of Voronoi polyhedra analysis. For this purpose, the position of the C₄mim cation was described successively by the ring, methyl, and butyl chain terminal hydrogen atoms, while that of the anions was described by their F or O atom. We calculated the Voronoi polyhedra distributions of the volume, the density, and the asphericity parameters as well as that of the radius of the spherical intermolecular voids. We carried out the analysis in two steps. In the first step, both ions were taken into account. The calculated distributions gave information on the neighboring ions around a reference one. In the second step, to distinguish between like and oppositely charged ions and then to get information on the inhomogeneity distribution of the like ions, we repeated the same calculations on the same sample configurations and removed one of the ions and considered only the other one. Detailed analysis of these distributions has revealed that the ring hydrogen atoms are mainly solvated by the anions, while the methyl and butyl terminal H atoms are surrounded by like atoms. The extent of this inhomogeneity was assessed by calculating the cluster size distribution that shows that the dimers are the most abundant ones.

Nanospikes-mediated Anomalous Dispersities of Hydropobic Micro-objects and their Application for Oil Emulsion Cleaning

Many fields of applications require dispersion of hydrophobic particles in water, which is traditionally achieved by using surfactants or amphiphilic molecules to modify particle surfaces. However, surfactants or amphiphilic molecules may disturb the native solution or particles' surface hydrophobicity, limiting extended applications such as oil emulsion cleaning. Recently one example of 2 μm-size polystyrene microparticles covered with ZnO nanospikes has been shown to exhibit excellent dispersity in water in spite of surface hydrophobicity. Whether this anomalous dispersion phenomenon was applicable to other hydrophobic microparticle systems was still unclear and its application scope was limited. Here the anomalous dispersities of different hydrophobic spiky micro-objects were systematically explored. The results show that the anomalous dispersion phenomenon was universally observed on different hydrophobic spiky micro-objects including different hydrophobic coating, particle sizes, material compositions and core particle morphologies. In addition, the spiky micro-objects displayed anomalous dispersity in water without compromising surface hydrophobicity, and their applications for oil spills absorption and oil emulsion cleaning were demonstrated. This work offers unique insight on the nanospikes-mediated anomalous dispersion phenomenon of hydrophobic micro-object and potentially extends its applicability and application scopes.

Connections between the Anomalous Volumetric Properties of Alcohols in Aqueous Solution and the Volume of Hydrophobic Association

The partial molar volumes of alcohols in water exhibit a non-monotonic dependence on concentration at room temperature, initially decreasing with increasing concentration before passing through a minimum and rising to the pure liquid plateau. This anomalous behavior is associated with hydrophobic interactions. We report molecular simulations of short chain alcohols and alkanes in water to examine the volumetric properties of these mixtures at infinite dilution over a range of temperatures. Our simulations find this anomaly disappears at a crossover temperature, above which the solute volume only varies monotonically with concentration. A Voronoi volume analysis of solution configurations finds that solutes in clusters take up less space than individual solutes at low temperature and more space at elevated temperatures. These changes in cluster volumes are subsequently shown to correlate with the derivative of the solute partial molar volume with respect to solute concentration. The changes in solute volume upon nonpolar solute association impact the response of molecular-scale hydrophobic interactions for assembly with increasing pressure.

TMAO and urea in the hydration shell of the protein SNase

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures.

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.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes.

Determination of partial molar volumes from free energy perturbation theory

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

Exploring volume, compressibility and hydration changes of folded proteins upon compression

Understanding the physical basis of the structure, stability and function of proteins in solution, including extreme environmental conditions, requires knowledge of their temperature and pressure dependent volumetric properties. One physical-chemical property of proteins that is still little understood is their partial molar volume and its dependence on temperature and pressure. We used molecular dynamics simulations of aqueous solutions of a typical monomeric folded protein, staphylococcal nuclease (SNase), to study and analyze the pressure dependence of the apparent volume, Vapp, and its components by the Voronoi-Delaunay method. We show that the strong decrease of Vapp with pressure (βT = 0.95 × 10(-5) bar(-1), in very good agreement with the experimental value) is essentially due to the compression of the molecular volume, VM, ultimately, of its internal voids, V. Changes of the intrinsic volume (defined as the Voronoi volume of the molecule), the contribution of the solvent to the apparent volume, and of the contribution of the boundary voids between the protein and the solvent have also been studied and quantified in detail. The pressure dependences of the volumetric characteristics obtained are compared with the temperature dependent behavior of these quantities and with corresponding results for a natively unfolded polypeptide.

Infinitely dilute partial molar properties of proteins from computer simulation

A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.