Toward Greater DNA Stability by Leveraging the Proton-Donating Ability of Protic Ionic Liquids

Deoxyribonucleic acid (DNA) stability is a prerequisite in many applications, ranging from DNA-based vaccines and data storage to gene therapy. However, the strategies to enhance DNA stability are limited, and the underlying mechanisms are poorly understood. Ionic liquids (ILs), molten salts of organic cations and organic/inorganic anions, are showing tremendous prospects in myriads of applications. With a judicious choice of constituent ions, the protic nature of ILs can be tuned. In this work, we investigate the relative stability of full-length genomic DNA in aqueous IL solutions of increasing protic nature. Our experimental measurements show that the protic ionic liquids (PILs) enhance the DNA melting temperature significantly while unaltering its native B-conformation. Molecular dynamics simulations and quantum mechanical calculation results suggest that the intramolecular Watson-Crick H-bonding in DNA remains unaffected and, in addition, the PILs induce stronger H-bonding networks in solution through their ability to make multiple intermolecular H-bonds with the nucleobases and among its constituent ions, thus aiding greater DNA stability. The detailed understanding obtained from this study could bring about the much-awaited breakthrough in improved DNA stability for its sustained use in the aforesaid applications!

Classical Molecular Dynamics Simulation of Glyonic Liquids: Structural Insights and Relation to Conductive Properties

Rhamnolipids are biosurfactants that have obtained wide industrial and environmental interests with their biodegradability and great surface activity. Besides their important roles as surfactants, they are found to function as a new type of glycolipid-based protic ionic liquids (ILs)─glyonic liquids (GLs). GLs are reported to have impressive physicochemical properties, especially superionic conductivity, and it was reported in experiments that specific ion selections and the fraction of water content have a strong effect on the conductivity. Also, the shape of the conductivity curve as a function of water fraction in GLs is interesting with a sharp increase first and a long plateau. We related the conductivities to the three-dimensional (3D) networks composed of -OH inside the GLs utilizing classical molecular dynamics (MD) simulations. The amount and size of these networks vary with both ion species and water fractions. Before reaching the first hydration layer, the -OH networks with higher projection/box length ratios indicate better conductivity; after reaching the first hydration layer and forming continuous structures, the conductivity retains with more water molecules participating in the continuous networks. Therefore, networks are found to be a qualitative predictor of actual conductivity. This is explained by the analysis of the atomic structures, including radial distribution function, fraction free volume, anion conformations, and hydrogen bond occupancies, of GLs and their water mixtures under different chemical conditions.

Structural Transitions at the Water/Oil Interface by Ionic-Liquid-like Surfactant, 1-Butyl-3-methylimidazolium Dioctyl Sulfosuccinate: Measurements and Mechanism

Reverse micelle (RM) aggregates have a wide range of applications in various areas of science and technology. A continuous demand exists to replace interfacial surfactant molecules with various nonconventional amphiphiles. Ionic liquid (IL)-like surfactants (IL-surf's) constitute a class of such molecules that are being researched extensively. Here, we have formulated several water/IL-surf/oil microemulsions by optimizing the core droplet size with varying oil phases. The best composition of water/[BMIM][AOT]/IPM ([BMIM][AOT]: 1-butyl-3-methylimidazolium dioctyl sulfosuccinate; IPM: isopropyl myristate) was then analyzed in detail through experimental and computer simulations. Our results from DLS measurements suggest a structural transition from spherical aggregates in the parent water/[Na][AOT]/IPM solution to cylindrical droplets in the IL-surf-based system. The Raman and ATR-FTIR spectral analysis suggest a variation in the microstructure of the water/oil interface due to the differential interaction of the counterions with AOT headgroups and water. Molecular dynamics simulation results provided the direct image of the interface showing a structured versus uneven water/oil interface in [Na][AOT] versus [BMIM][AOT] RMs, where the larger [BMIM] cations weakly bind with the AOT headgroups due to their low charge density. Finally, an application of this IL-surf-based formulation was tested by carrying out a Heck cross-coupling reaction that showed significantly higher yield under milder reaction conditions.

Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation

Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.

Extended H-Bonding through Protic Ionic Liquids Facilitates the Growth and Stability of Water Domains in Hydrophobic Environment

Discrete water domains in hydrophobic environment find relevance in aerosols, oil refinery, the human body, etc. The interfacial microstructure plays a crucial role in the stability of such water domains. Over the decades, the amphiphile-induced electrostatic interaction is considered to be the major stabilizing factor operating at these interfaces. Here we take the representative water/AOT/oil microemulsion to show that creating a strong H-bonding network through suitable additive, such as protic ionic liquid (IL) at the interface, helps both the growth and stability of water domains in the hydrophobic phase. On the other hand, common electrolytes and aprotic ILs fail to replicate such behavior as seen by Raman, Fourier transform infrared spectroscopy, dynamic light scattering (DLS), and electron microscopy measurements. Experimental results are further supported by the all-atomic molecular dynamics (MD) simulations that showed extended H-bonding mediated by the protic IL cations that were localized at the interface. High temperature DLS and rheology studies have shown greater thermal stability and mechanical strengths of our biocompatible microemulsions, which have potential to become suitable templates for in situ synthesis of nanoparticle and various organic compounds.

Anomalous and Not-So-Common Behavior in Common Ionic Liquids and Ionic Liquid-Containing Systems

This work highlights unexpected, not so well known responses of ionic liquids and ionic liquid-containing systems, which are reported in a collective manner, as a short review. Examples include: (i) Minima in the temperature dependence of the isobaric thermal expansion coefficient of some ILs; (ii) Viscosity Minima in binary mixtures of IL + Molecular solvents; (iii) Anomalies in the surface tension within a family of ILs; (iv) The constancy among IL substitution of C_p/V_m at and around room temperature; (v) ILs as glass forming liquids; (vi) Alternate odd-even side alkyl chain length effects; (vii) Absolute negative pressures in ILs and IL-containing systems; (viii) Reversed-charged ionic liquid pairs; (ix) LCST immiscibility behavior in IL + solvent systems.

New dimensions in salt-solvent mixtures: a 4th evolution of ionic liquids

In the field of ionic liquids (ILs) it has long been of fundamental interest to examine the transition from salt-in-solvent behaviour to pure liquid-salt behaviour, in terms of structures and properties. At the same time, a variety of applications have beneficially employed IL-solvent mixtures as media that offer an optimal set of properties. Their properties in many cases can be other than as expected on the basis of simple mixing concepts. Instead, they can reflect the distinct structural and interaction changes that occur as the mixture passes through the various stages from pure coulombic medium, to "plasticised" coulombic medium, into a meso-region where distinct molecular and ionic domains can co-exist. Such domains can persist to quite a high dilution into the salt-in-solvent regime and their presence manifests itself in a number of important synergistic interaction effects in diverse areas such as membrane transport and corrosion protection. Similarly, the use of ionic liquids in synthetic processes where there is a significant volume fraction of molecular species present can produce a variety of distinct and unexpected effects. The range of these salt-solvent mixtures is considerably broader than just those based on ionic liquids, since there is only minor value in the pure salt being a liquid at the outset. In other words, the extensive families of organic and metal salts become candidates for study and use. Our perspective then is of an evolution of ionic liquids into a broader field of fundamental phenomena and applications. This can draw on an even larger family of tuneable salts that exhibit an exciting combination of properties when mixed with molecular liquids.

Water Clathrates in Nanostructural Organization of Hydrated Ionic Liquids Manifest a Peculiar Density Trend

Ionic liquid-water binary solutions have significantly expanded the applications of ionic liquids (ILs) in chemical and biological research. Therefore, considerable research has focused on measuring the thermophysical properties of these binary mixtures. From low-to-moderate concentrations of water, several IL/water mixtures exhibit deviations from expected trends in thermophysical behavior. One such example is a unique density trend observed for certain IL classes, which exhibit a characteristic increase in density with the addition of small amounts of water. Since water primarily interacts with the IL anion, such deviations have always been explained in the context of anion-water associations. Surprisingly, however, IL/water mixtures containing different cations but a common lactate anion exhibit similar peculiarities in density trends. Using atomistic level molecular dynamics simulations, we show that diverse density trends are caused by cation-mediated modulations in the IL nanostructure. Depending on its nature, the IL cation can play a dual role in modulating the IL nanostructure: (i) resist water-mediated breakdown of the nanostructure by interacting with the anion very strongly, (ii) further strengthen the nanostructure by incorporating water in the IL framework. The [emim] cation fails to play both roles resulting in the density decrease, while the [tmg] cation fulfills both roles leading to a density rise. The choline cation resists the density fall by inducing the formation of "water-clathrates" in the solution. Such occurrence of clathrates in IL/water binary mixtures, reported for the first time in this study, further emphasizes that the properties of ILs and its mixtures are not merely determined by the chemical nature of the component ions, but also by their unique nanostructural organizations. These unique nanostructural organizations also manifest in their unusual dynamics.

The peculiar effect of water on ionic liquids and deep eutectic solvents

Ionic liquids (ILs) and deep eutectic solvents (DESs) have been suggested as eco-friendly alternatives to organic solvents. A trace amount of water is often unavoidable as impurity, and water is also added on purpose to reduce their problematically high viscosity and lower their high price. Understanding the distinct effects of water on the properties of ILs/DESs is highly important. In this review, we collect published experimental and theoretical results for IL/DES-H2O systems at varied water concentrations and analyze them. Results from mechanistic studies, thermodynamic modelling and advanced experiments are collected and critically discussed. Six commonly studied IL/DES-H2O systems were selected to map experimental observations onto microscopic results obtained in mechanistic studies. A great variety of distinct contours of the excess properties can be observed over the entire compositional range, indicating that the properties of IL/DES-H2O systems are highly unpredictable. Mechanistic studies clearly demonstrate that the added H2O rapidly changes the heterogeneous 3D structures of pure ILs/DESs, leading to very different properties and behaviour. There are similarities between aqueous electrolytes and IL/DES solutions but the bulky and asymmetric organic cations in ILs/DESs do not conform to the standard salt dissolution and hydration concepts. Thermodynamic modelling previously assumes ILs/DESs to be either a neutral ion-pair or completely dissociated ions, neglecting specific ion hydration effects. A new conceptual framework is suggested for thermodynamic modelling of IL/DES-H2O binary systems to enable new technologies for their practical applications.

Experimental and computational study of guanidinoacetic acid self-aggregation in aqueous solution

In this work for the first time the physicochemical and thermal properties of guanidinoacetic acid (GAA) and its aqueous solutions have been performed to test for its viability as a potential dietary supplement. Thermal stability, viscosity, solubility and experimental density are determined. From measured densities the volumetric properties were estimated and discussed in the scope of GAA self-aggregation in aqueous solutions using experimental and computational results. Based on thermal stability and solubility measurements, it is found that GAA is more thermally stable but less soluble comparing to creatine due to a self-aggregation process that occurs at GAA concentrations higher than 0.013mol·dm^-3. Existence of self-aggregation influences the macroscopic properties of aqueous GAA solutions, but also its bioavailability.

How water manifests the structural regimes in ionic liquids

Ionic liquids (ILs) are being considered as greener alternatives to the conventional organic solvents. However, highly viscous nature of ILs often limits their applications. Hence studies on IL/water binary mixtures have received tremendous attention. These mixtures exhibit much lower viscosity, but almost similar density, compressibility and other properties as that of the neat ILs, up to certain water content. Hence, determining the IL-water ratio till which the solution behaves like IL and subsequently changes to a state of solute IL dissolved in continuous water phase is of paramount importance. Noting the very different and characteristic behaviours of neat ILs and pure water over a temperature range, herein, we measured the various thermophysical properties of the binary mixtures of tetramethylguanidinium benzoate/water and tetramethylguanidinium salicylate/water with water content varying from 20 wt% to 95 wt% for a temperature range of 298 K to 343 K. The results show that similar to neat ILs, the measured densities and compressibility of these mixtures display a linear change, and viscosity decreases rapidly as temperature is increased for water content up to 50 wt%. At higher water concentrations, the measured density and compressibility exhibit nonlinear behaviour and the decrease in viscosity with increased temperature is minute, mimicking the behaviour of bulk water. MD simulations were carried out to explain the experimental observations. Simulation results show a greater temperature-induced disintegration of IL ion-water interactions in dense systems, explaining the rapid decay of the properties with temperature. The results also exhibit the presence of a neat, IL-like, H-bond mediated expanded structure in concentrated solution versus a collapsed IL structure in dilute solution.

Enhanced stability and water solubilizing capacity of water-in-oil microemulsions based on protic ionic liquids

In view of this limited research on pILs in microemulsions, here we study the formation and characterization of a series of pIL–water/oil microemulsions with specific questions on the effect of pILs on water uptake capacity and thermal stability of W/O microemulsions.

Environmentally benign tetramethylguanidinium cation based ionic liquids

Ionic liquids (ILs) are being considered as greener alternatives to conventional organic solvents.

Effective asymmetric bioreduction of ethyl 4-chloro-3-oxobutanoate to ethyl (R)-4-chloro-3-hydroxybutanoate by recombinant E. coli CCZU-A13 in [Bmim]PF6-hydrolyzate media

It was the first report that the concentrated hydrolyzates from the enzymatic hydrolysis of dilute NaOH (3wt%)-soaking rice straw at 30°C was used to form [Bmim]PF6-hydrolyzate (50:50, v/v) media for bioconverting ethyl 4-chloro-3-oxobutanoate (COBE) into ethyl (R)-4-chloro-3-hydroxybutanoate [(R)-CHBE] (>99% e.e.) with recombinant E. coli CCZU-A13. Compared with pure glucose, the hydrolyzates could promote both initial reaction rate and the intracellular NADH content. Furthermore, emulsifier OP-10 (20mM) was employed to improve the reductase activity. Moreover, Hp-β-cyclodextrin (0.01mol Hp-β-cyclodextrin/mol COBE) was also added into this bioreaction system for enhancing the biosynthesis of (R)-CHBE from COBE by E. coli CCZU-A13 whole-cells. The yield of (R)-CHBE (>99% e.e.) from 800mM COBE was obtained at 100% in the [Bmim]PF6-hydrolyzate (50:50, v/v) media by supplementation of OP-10 (20mM) and Hp-β-CD (8mM). In conclusion, an effective strategy for the biosynthesis of (R)-CHBE was successfully demonstrated.

Ion-water wires in imidazolium-based ionic liquid/water solutions induce unique trends in density

Ionic liquid/water binary mixtures are rapidly gaining popularity as solvents for dissolution of cellulose, nucleobases, and other poorly water-soluble biomolecules. Hence, several studies have focused on measuring the thermophysical properties of these versatile mixtures. Among these, 1-ethyl-3-methylimidazolium ([emim]) cation-based ILs containing different anions exhibit unique density behaviours upon addition of water. While [emim][acetate]/water binary mixtures display an unusual rise in density with the addition of low-to-moderate amounts of water, those containing the [trifluoroacetate] ([Tfa]) anion display a sluggish decrease in density. The density of [emim][tetrafluoroborate] ([emim][BF4])/water mixtures, on the other hand, declines rapidly in close accordance with the experimental reports. Here, we unravel the structural basis underlying this unique density behavior of [emim]-based IL/water mixtures using all-atom molecular dynamics (MD) simulations. The results revealed that the distinct nature of anion-water hydrogen bonded networks in the three systems was a key in modulating the observed unique density behaviour. Vast expanses of uninterrupted anion-water-anion H-bonded stretches, denoted here as anion-water wires, induced significant structuring in [emim][Ac]/water mixtures that resulted in the density rise. Conversely, the presence of intermittent large water clusters disintegrated the anion-water wires in [emim][Tfa]/water and [emim][BF4]/water mixtures to cause a monotonic density decrease. The differential nanostructuring affected the dynamics of the solutions proportionately, with the H-bond making and breaking dynamics found to be greatly retarded in [emim][Ac]/water mixtures, while it exhibited a faster relaxation in the other two binary solutions.