Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

Adsorption Energetics of Amino Acid Analogs on Polymer/Water Interfaces Studied by All-Atom Molecular Dynamics Simulation and a Theory of Solutions

Energetics of adsorption was addressed with all-atom molecular dynamics simulation on the interfaces of poly(2-methoxyethyl acrylate) (PMEA), poly(methyl methacrylate) (PMMA), and poly(butyl acrylate) (PBA) with water. A wide variety of adsorbate solutes were examined, and the free energy of adsorption was computed with the method of energy representation. It was found that the adsorption free energy was favorable (negative) for all the combinations of solute and polymer, and among PMEA, PMMA, and PBA, the strongest adsorption was observed on PMMA for the hydrophobic solutes and on PMEA for the hydrophilic ones. According to the decomposition of the adsorption free energy into the contributions from polymer and water, it was seen that the polymer contribution is larger in magnitude with the solute size. The total free energy of adsorption was correlated well with the solvation free energy in bulk water only for hydrophobic solutes. The roles of the intermolecular interaction components such as electrostatic, van der Waals, and excluded-volume were further studied, and the electrostatic component was influential only in determining the polymer dependences of the adsorption propensities of hydrophilic solutes. The extent of adsorption was shown to be ranked by the van der Waals component in the solute-polymer interaction separately over the hydrophilic and hydrophobic solutes, with the excluded-volume effect from water pointed out to also drive the adsorption.

Controlling desolvation through polymer-assisted grinding

We demonstrate the ability to controllably desolvate a crystal-solvate system in step-wise fashion through polymer-assisted grinding by varying the type and proportion of polymer agent used. A plausible mechanistic explanation...

Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation

Solvation is a controlling factor for the structure and function of proteins. This article addresses the effects of solvation from an energetic perspective for the fluctuations and cosolvent-induced changes in protein structures and the equilibrium of aggregate formation for a peptide. A theoretical framework to analyze the solvation effects with an explicit solvent is introduced by adopting the energy-representation theory of solvation, and the connection of the solvation free energy to the protein structure and the aggregation tendency is quantitatively described in combination with all-atom molecular dynamics simulations. The interaction components that govern the solvation effects on the structural variations of proteins are further identified through correlation analysis, and a computational scheme to assess the shift of an aggregation equilibrium due to the addition of a cosolvent is provided.

Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions

The performance of a polymer medium as a separation membrane is determined by the dissolution free energy ΔG and diffusion coefficient D of the permeant. In this work, ΔG and D of water are investigated with all-atom molecular dynamics simulation in a wide variety of polymer species in the amorphous state. The computed ΔG is shown to agree well with the experimental value for linear homopolymers, and the degrees of polymerization of the homopolymers do not affect ΔG when they are beyond ∼10. The copolymers of ethylene-vinylidene difluoride, ethylene-vinyl acetate, and ethylene-acrylamide are then examined by changing the repeating patterns of the constituent monomers in both the periodic and graft forms. It is found that ΔG is determined primarily by the overall compositions of the monomers and is not affected by the copolymerization topology (periodic or graft). The hydrophobicity of the copolymer is enhanced, furthermore, when the hydrophobicity and hydrophilicity of the ethylene and non-ethylene parts are well contrasted and those parts are fragmented along the polymer chain. According to the computed D, the diffusivity of water tends to be larger when the (co)polymer is more hydrophobic and ΔG is more positive. D is actually seen to vary by orders of magnitude with the polymer structures, while the effect of the polymer species on the water permeation is stronger for ΔG than for D.

Solvation Thermodynamics from the Perspective of Endpoints DFT

Solvation thermodynamics is concerned with the evaluation and physical interpretation of solvation free energies. Endpoints DFT provides a framework for computing solvation free energies by combining molecular simulations with a version of the classical density-functional theory of solutions which focuses on ω, the indirect (solvent-mediated) part of the solute-solvent potential of mean force (indirect PMF). The simulations are performed at the endpoints of a hypothetical charging process which transforms the solvent density from the pure liquid state to that of the solution state. The endpoints DFT expression for solvation free energy can be shown to be equivalent to the standard expression for which the key quantity is the direct correlation function, but it has the advantage that the indirect term ω is more focused on the change in solvent-solvent correlations with respect to the pure liquid as the solute is inserted into the solution. In this Perspective, we review recent developments of endpoints DFT, highlighting a series of papers we have written together beginning in 2017. We emphasize the importance of dimensionality reduction as the key to the evaluation of endpoints DFT expressions and present a recently developed, spatially resolved version of the theory. The role of interfacial water at certain positions which stabilize or destabilize a solute in solution can be analyzed with the spatially resolved version, and it is of considerable interest to investigate how changes in solvation affect protein-ligand binding and conformational landscapes from an endpoints DFT perspective. Endpoints DFT can also be employed in materials science; an example involving the rational design strategy for polymer membrane separation is described. The endpoints DFT method is a scheme to evaluate the solvation free energy by introducing approximations to integrate the classical density functional over a charging parameter. We have further proposed a new functional which captures the correct dependence of the indirect PMF ω at both endpoints of the charging process, and we review how it might be employed in future work.

Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation

Physisorption of urea on its crystal in contact with water was subject to energetics analysis with all-atom molecular dynamics simulation. The transfer free energy of urea to an adsorption site was treated in the framework of the energy-representation theory of solutions, which allows a fast computation of the free energy in an inhomogeneous environment with solid-liquid interface. The preference of adsorption was then compared between the (001) and (110) faces, and it was found that the physisorption is more favorable on (001) than on (110) in correspondence to the hydrogen bonding between the adsorbed urea and the crystal urea. Among the terrace configurations of adsorption, the attractive interaction governs the preferable site with a minor role of the repulsive interaction. The effect of an edge was also treated by examining the terrace and step and was shown to be strongly operative on the (110) face when the CO group of the adsorbed urea points toward the edge. The present work demonstrates that the solution theory can be a framework for analyzing the energetics of physisorption and addressing the roles of the crystal and liquid at the interface through the systematic decomposition of free energy.

Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

Ionomers play a key role in forming the catalyst layer of polymer electrolyte fuel cells. In the present work, we performed atomistic molecular dynamics simulations and free-energy calculations with the energy-representation method for sulfonated polyethersulfone (SPES) and its derivatives toward the rational design of ionomers for carbon alloy catalysts. It was observed that H₂O aggregates strongly in the branched SPES systems with fluorocarbons and is located homogeneously in the systems without fluorocarbons. The O₂ permeability was then examined within the framework of the solubility-diffusion mechanism. The permeability was seen to be large for the branched SPES with fluorocarbons, indicating that the performance of ionomers as a permeation medium for O₂ may be tuned by the flexibility and branching of the polymer chain.

Probabilistic analysis for identifying the driving force of protein folding

Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions

The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.

Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent

Energetics was analyzed for Trp-cage miniprotein in water to elucidate the solvation effect in heat denaturation. The solvation free energy was computed for a set of protein structures at room and high temperatures with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were investigated against the intramolecular (structural) energy of the protein and the average interaction energy of the protein with the solvent water. It was observed both at room and high temperatures that the solvation free energy is anticorrelated to the structural energy and varies in parallel to the electrostatic component of the protein-water interaction energy without correlations to the van der Waals and excluded-volume components. When the set of folded structures sampled at room temperature was compared with the set of unfolded ones at high temperature, it was found that the preference order of the two sets is in correspondence to the van der Waals and excluded-volume components in the sum of the protein intramolecular and protein-water intermolecular interactions and is not distinguished by the electrostatic component.