Rodlike Micelle Structure and Formation of Ionic liquid in Aqueous Solution by Molecular Simulation

Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations

Inspired by the recent work from Noé and coworkers on the development of machine learning based implicit solvent model for the simulation of solvated peptides [Chen et al., J. Chem. Phys., 2021, 155, 084101], here we report another investigation of the possibility of using machine learning (ML) techniques to "derive" an implicit solvent model directly from explicit solvent molecular dynamics (MD) simulations. For alanine dipeptide, a machine learning potential (MLP) based on the DeepPot-SE representation of the molecule was trained to capture its interactions with its average solvent environment configuration (ASEC). The predicted forces on the solute deviated only by an RMSD of 0.4 kcal mol-1 Å-1 from the reference values, and the MLP-based free energy surface differed from that obtained from explicit solvent MD simulations by an RMSD of less than 0.9 kcal mol-1. Our MLP training protocol could also accurately reproduce combined quantum mechanical molecular mechanical (QM/MM) forces on the quantum mechanical (QM) solute in ASEC environment, thus enabling the development of accurate ML-based implicit solvent models for ab initio-QM MD simulations. Such ML-based implicit solvent models for QM calculations are cost-effective in both the training stage, where the use of ASEC reduces the number of data points to be labelled, and the inference stage, where the MLP can be evaluated at a relatively small additional cost on top of the QM calculation of the solute.

Degradation of o-, m-, p-cresol isomers using ozone in the presence of V2O5-supported Mn, Fe, and Ni catalysts

Oxidative degradation of o-, m- and p-cresols using ozone in the presence of V2O5-supported metal (Mn, Fe, Ni) catalysts was studied under ambient reaction conditions. Metal (Mn, Fe, Ni) loaded V2O5 catalysts were prepared using a wet-impregnation method, thereafter, characterized, and analyzed by use of the XRD, FT-IR, SEM-EDX, TEM, and ICP-OES. Results show the effect of the amount of a metal that was loaded on the support, particularly, how it affects the resultant catalysts’ (i) crystallite size, (ii) dispersion of an active metal over the surface of a support, and (iii) catalytic activity. Mn-loaded catalysts were found to be relatively more active for the conversion of individual cresol isomers and the activity of this catalyst was significantly enhanced at a lower Mn to V2O5 ratio (2.5 wt%). Mn(2.5 %)/V2O5 catalyst led to conversions of 66.78, 71.01 and 73.68 % with o-, m-, and p-cresols respectively within 24 h of oxidation. Oxidation products were derivatized by ethanol and a few were positively detected using GC-MS. o-Tolyl acetate and 2,5-dihydroxy toluene were detected from o-cresol, m-tolyl acetate, and 2,3-dihydroxy toluene from m-cresol and p-tolyl acetate and 3,4-dihydroxy toluene from p-cresol oxidation. Dimethyl maleate and dimethyl oxalate were detected as common products in all three isomers’ oxidation.

Insights into Ionic Liquids: From Z-Bonds to Quasi-Liquids

Ionic liquids (ILs) hold great promise in the fields of green chemistry, environmental science, and sustainable technology due to their unique properties, such as a tailorable structure, the various types available, and their environmentally friendly features. On the basis of multiscale simulations and experimental characterizations, two unique features of ILs are as follows: (1) strong coupling interactions between the electrostatic forces and hydrogen bonds, namely in the Z-bond, and (2) the unique semiordered structure and properties of ultrathin films, specifically regarding the quasi-liquid. In accordance with the aforementioned theoretical findings, many cutting-edge applications have been proposed: for example, CO₂ capture and conversion, biomass conversion and utilization, and energy storage materials. Although substantial progress has been made recently in the field of ILs, considerable challenges remain in understanding the nature of and devising applications for ILs, especially in terms of e.g. in situ/real-time observation and highly precise multiscale simulations of the Z-bond and quasi-liquid. In this Perspective, we review recent developments and challenges for the IL research community and provide insights into the nature and function of ILs, which will facilitate future applications.

Multi-Interactions in Ionic Liquids for Natural Product Extraction

Natural products with a variety of pharmacological effects are important sources for commercial drugs, and it is very crucial to develop effective techniques to selectively extract and isolate bioactive natural components from the plants against the background of sustainable development. Ionic liquids (ILs) are a kind of designable material with unique physicochemical properties, including good thermal stability, negligible vapor pressure, good solvation ability, etc. ILs have already been used in pharmaceuticals for extraction, purification, drug delivery, etc. It has been reported that multi-interactions, like hydrogen bonding, hydrophobic interactions, play important roles in the extraction of bioactive components from the plants. In this review, recent progress in the understanding of scientific essence of hydrogen bonding, the special interaction, in ILs was summarized. The extraction of various natural products, one important area in pharmaceutical, by conventional and functional ILs as well as the specific roles of multi-interactions in this process were also reviewed. Moreover, problems existing in bioactive compound extraction by ILs and the future developing trends of this area are given, which might be helpful for scientists, especially beginners, in this field.

Use of Ionic Liquids in Protein and DNA Chemistry

Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.

The effect of anion on aggregation of amino acid ionic liquid: Atomistic simulation

Aggregation behavior of dodecyl betaine chloride [DB][Cl], as an amino acid ionic liquid, and dodecyl betaine N-acetyl glycinate [DB][AG], as a bio ionic liquid, in aqueous media was studied through molecular dynamics simulation. The aggregating was investigated by radial distribution function, coordination numbers, and hydrogen bond numbers. The results demonstrated the hydrogen bond between [DB]⁺ and [AG]^- that leads to aggregation. The number of hydrogen bonds of [DB][AG] is greater than [DB][Cl] and causes a decrease in the gradient of the mean square displacement, thereby the diffusion coefficient of cation, anion, and water in [DB][AG]. The results point to a stable aggregation of [DB][AG] which is in agreement with the results of root mean square deviations. The aggregation number for [DB][AG] is 50 and 44 for [DB][Cl]. Computing the radius of gyration and geometrical radius shows that the aggregation size is 23.0 Å and 26.4 Å for [DB][AG] and [DB][Cl], respectively. It was also observed that the shape of the aggregates is quasi-spherical that points to a sub-diffusive regime.

Insight into the formation and permeability of ionic liquid unilamellar vesicles by molecular dynamics simulation

Unilamellar vesicles in solution could open up new horizons for reaction and material delivery, but the formation mechanism especially for the permeability of the small molecule through the vesicle membrane is still unknown. In this study, the formation and permeability of the unilamellar vesicles formed by the ionic liquid 1-dodecyl-3-methylimidazolium salicylate ([C12mim][Sal]) have been investigated by molecular dynamics simulation. Starting from a random distribution of ionic liquids, the entire process of vesicle formation could be observed on a nanosecond time scale, during which planar and cup-like structures are formed at the intermediate stage. Energy analysis reveals that the electrostatic interactions between cations and anions play a dominant role in forming and stabilizing the vesicle. Radial density distribution functions indicate that the final stable vesicle is a spherical bilayer structure. Besides, it was found that the structure of vesicles is maintained with the increase of temperature, while the water molecules in the vesicles could be completely exchanged quickly. These results suggest that vesicles may be beneficial for the enrichment or release of molecules.

Photo-Triggered Reversible Phase Transfer of Azobenzene-Based Ionic Liquid Surfactants between Oil and Water

The reversible phase transfer of compounds between two immiscible liquid phases has many applications in a wide range of fields, and ionic liquids have been widely used as potential functional solvents and catalysts. However, photo-triggered reversible phase transfer of ionic liquids between the organic phase and water phase has not been reported so far. In the present work, the reversible phase transfer of six kinds of azobenzene-based ionic liquid surfactants between the organic phase and water phase is investigated by alternative irradiation of UV and visible light. Factors affecting the transfer efficiency, such as chemical structure and concentration of the ionic liquid surfactants, equilibrium photo-isomerization degree, and the aggregation state of ionic liquid surfactants are investigated in detail. It is shown that transfer efficiency greater than 89% was achieved under optimal conditions, equilibrium photo-isomerization degree of the ionic liquid surfactants is the main factor to determine their transfer efficiencies, and the aggregation of cis-isomers is not beneficial for the transfer.

Effect of water and ionic liquids on biomolecules

The remarkable progress in the field of ionic liquids (ILs) in the last two decades has involved investigations on different aspects of ILs in various conditions. The nontoxic and biocompatible nature of ILs makes them a suitable substance for the storage and application of biomolecules. In this regard, the aqueous IL solutions have attracted a large number of studies to comprehend the role of water in modulating various properties of biomolecules. Here, we review some of the recent studies on aqueous ILs that concern the role of water in altering the behavior of ILs in general and in case of biomolecules solvated in ILs. The different structural and dynamic effects caused by water have been highlighted. We discuss the different modes of IL interaction that are responsible for stabilization and destabilization of proteins and enzymes followed by examples of water effect on this. The role of water in the case of nucleic acid storage in ILs, an area which has mostly been underrated, also has been emphasized. Our discussions highlight the fact that the effects of water on IL behavior are not general and are highly dependent on the nature of the IL under consideration. Overall, we aim to draw attention to the significance of water dynamics in the aqueous IL solutions, a better understanding of which can help in developing superior storage materials for application purposes.

Colloidal paradigm in supercapattery electrode systems

Among decades of development, electrochemical energy storage systems are now sorely in need of a new design paradigm at the nano size and ion level to satisfy the higher energy and power demands. In this review paper, we introduce a new colloidal electrode paradigm for supercapattery that integrates multiple-scale forms of matter, i.e. ion clusters, colloidal ions, and nanosized materials, into one colloid system, coupled with multiple interactions, i.e. electrostatic, van der Waals forces, and chemical bonding, thus leading to the formation of many redox reactive centers. This colloidal electrode not only keeps the original ionic nature in colloidal materials, but also creates a new attribute of high electroactivity. Colloidal supercapattery is a perfect application example of the novel colloidal electrode, leading to higher specific capacitance than traditional electrode materials. The high electroactivity of the colloidal electrode mainly comes from the contribution of exposed reactive centers, owing to the confinement effect of carbon and a binder matrix. Systematic and thorough research on the colloidal system will significantly promote the development of fundamental science and the progress of advanced energy storage technology.

Understanding the hydrogen bonds in ionic liquids and their roles in properties and reactions

Ionic liquids (ILs) have many potential applications in the chemical industry. In order to understand ILs, their molecular details have been extensively investigated. Intuitively, electrostatic forces are solely important in ILs. However, experiments and calculations have provided strong evidence for the existence of H-bonds in ILs and their roles in the properties and applications of ILs. As a structure-directing force, H-bonds are responsible for ionic pairing, stacking and self-assembling. Their geometric structure, interaction energy and electronic configuration in the ion-pairs of imidazolium-based ILs and protic ionic liquids (PILs) show a great number of differences compared to conventional H-bonds. In particular, their cooperation with electrostatic, dispersion and π interactions embodies the physical nature of H-bonds in ILs, which anomalously influences their properties, leading to a decrease in their melting points and viscosities and thus fluidizing them. Using ILs as catalysts and solvents, many reactions can be activated by the presence of H-bonds, which reduce the reaction barriers and stabilize the transition states. In the dissolution of lignocellulosic biomass by ILs, H-bonds exhibit a most important role in disrupting the H-bonding network of cellulose and controlling microscopic ordering into domains. In this article, a critical review is presented regarding the structural features of H-bonds in ILs and PILs, the correlation between H-bonds and the properties of ILs, and the roles of H-bonds in typical reactions.

Dissolving process of a cellulose bunch in ionic liquids: a molecular dynamics study

In recent years, a variety of ionic liquids (ILs) were found to be capable of dissolving cellulose and mechanistic studies were also reported. However, there is still a lack of detailed information at the molecular level. Here, long time molecular dynamics simulations of cellulose bunch in 1-ethyl-3-methylimidazolium acetate (EmimAc), 1-ethyl-3-methylimidazolium chloride (EmimCl), 1-butyl-3-methylimidazolium chloride (BmimCl) and water were performed to analyze the inherent interaction and dissolving mechanism. Complete dissolution of the cellulose bunch was observed in EmimAc, while little change took place in EmimCl and BmimCl, and nothing significant happened in water. The deconstruction of the hydrogen bond (H-bond) network in cellulose was found and analyzed quantitatively. The synergistic effect of cations and anions was revealed by analyzing the whole dissolving process. Initially, cations bind to the side face of the cellulose bunch and anions insert into the cellulose strands to form H-bonds with hydroxyl groups. Then cations start to intercalate into cellulose chains due to their strong electrostatic interaction with the entered anions. The H-bonds formed by Cl(-) cannot effectively separate the cellulose chain and that is the reason why EmimCl and BmimCl dissolve cellulose more slowly. These findings deepen people's understanding on how ILs dissolve cellulose and would be helpful for designing new efficient ILs to dissolve cellulose.