Salting-Out of Methane in the Aqueous Solutions of Urea and Glycine-Betaine

Osmolyte-induced conformational stabilization of a hydrophobic polymer

Elucidating the mechanistic role of osmolytes on conformations of hydrophobic prototypical macromolecules in principle is the stepping stone towards understanding the effect of osmolytes on proteins. Motivated by this, we use equilibrium simulations and umbrella sampling techniques to dissect the underlying mechanism of osmolyte-induced conformational stability of a hydrophobic polymer. Our results unveil a remarkable osmolyte-dependent conformational stabilization of the polymer. In an aqueous solution of 4 M choline chloride (ChCl), the polymer has an even more compact structure than in water. On the other hand, an aqueous solution of 8 M urea stabilizes the extended state of the polymer. Interestingly, the polymer adopts an intermediate hairpin conformation in a mixed osmolyte solution of 4 M ChCl and 8 M urea in water due to the interplay of ChCl and urea. Our simulations identify the relative accumulation of water and the hydrophilic part of choline or preferential binding of urea near the collapsed and the extended states, respectively. Analyses split out the enthalpic and entropic contributions to the overall free energy. This decides the stabilization of the preferred conformation in the chosen osmolyte solution. Our simulations show that in an aqueous solution of ChCl, the hairpin state is stabilized by entropy gain. In contrast, the enthalpic contribution stabilizes the hairpin state in mixed environments. However, a collapsed state is energetically not favored in the presence of urea. In brief, via employing an in silico approach, the current findings indicate the importance of osmolytes in stabilizing the conformational states of hydrophobic polymers.

Exploring the Role of Hydroxy- and Phosphate-Terminated cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber: Insights from Molecular Dynamics Simulations

This study elucidates the pivotal role of terminal structures in cis-1,4-polyisoprene (PI) chains, contributing to the exceptional mechanical properties of Hevea natural rubber (NR). NR's unique networking structure, crucial for crack resistance, elasticity, and strain-induced crystallization, involves two terminal groups, ω and α. The proposed ω terminal structure is dimethyl allyl-(trans-1,4-isoprene)2, and α terminals exist in various forms, including hydroxy, ester, and phosphate groups. Among others, we investigated three types of cis-1,4-PI with different terminal combinations: HPIH (pure PI with H terminal), ωPIα6 (PI with ω and α6 terminals), and ωPIPO4 (PI with ω and PO4 terminals) and revealed significant dynamics variations. Hydrogen bonds between α6 and α6 and PO4 and PO4 residues in ωPIα6 and ωPIPO4 systems induce slower dynamics of hydroxy- and phosphate-terminated PI chains. Associations between α6 and α6 and PO4 and PO4 terminals are markedly stronger than ω and ω, and hydrogen terminals in HPIH and ω PIα6,PO4 systems. Phosphate terminals exhibit a stronger mutual association than hydroxy terminals. Potentials of mean force analysis and cluster-formation-fraction computations reveal stable clusters in ωPIα6 and ωPIPO4 , supporting the formation of polar aggregates (physical junction points). Notably, phosphate terminal groups facilitate large and highly stable phosphate polar aggregates, crucial for the natural networking structure responsible for NR's outstanding mechanical properties compared to synthetic PI rubber. This comprehensive investigation provides valuable insights into the role of terminal groups in cis-1,4-PI melt systems and their profound impact on the mechanical properties of NR.

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO-Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis

Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM+ and Cl- ions in DMSO-water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO-water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO-water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl- ions.

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene)2] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), ester-terminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., HPIH (PI0)-pure PI (Hydrogen terminal), ωPIα1 (PII), ωPIα2 (PIII), ωPIα3 (PIIII), ωPIα4 (PIIV), ωPIα5 (PIV), and ωPIα6 (PIVI). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (Ree), and radius of gyration (Rg). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2-α2, α4-α4, and α6-α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ωPIα2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]-[α2], [α4]-[α4], and [α6]-[α6] terminals in ωPIα2,α4,α6 melt systems is significantly stronger than in [ISO]-[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in HPIH and ω-ω, [α1]-[α1], [α3]-[α3], and [α5]-[α5] in ωPIα1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the HPIH, ωPIα1, ωPIα3, and ωPIα5 melt systems. Conversely, in the ωPIα2, ωPIα4, and ωPIα6 systems, we perceived stable clusters of [(α2)p] [(α4)p] and [(α6)p] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.

Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide?

The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents.

Ammonium based stabilizers effectively counteract urea-induced denaturation in a small protein: insights from molecular dynamics simulations

Room temperature ionic liquids (IL) and deep eutectic solvents (DES) are known to aid the conformational stability and activity of proteins and enzymes in aqueous solutions.