Dissolution of cellulose in ionic liquid and water mixtures as revealed by molecular dynamics simulations

Sorption of PFOS onto polystyrene microplastics potentiates synergistic toxic effects during zebrafish embryogenesis and neurodevelopment

Microplastics (MPs) have become an emerging anthropogenic pollutant, and their ability to sorb contaminants potentially enhances the threats to the ecosystem. Only a few studies are available to understand the combined effects of microplastics and other pollutants. The present study investigated the sorption of perfluorooctane sulfonic acid (PFOS) onto polystyrene microplastics (PS-MPs) at varying concentrations, using molecular dynamics simulation (MDS) to preliminarily explore the adsorption behavior. The MDS results revealed negative interaction energies between PFOS and PS-MPs, underscoring PS-MPs' role as a potential adsorbent for PFOS in an aqueous solution. Thereafter, zebrafish embryos were employed to explore the toxic effects of combined exposure to PS-MPs and PFOS. Fluorescence and Scanning Electron Microscopy (SEM) suggested PS-MP accumulation individually and in combination with PFOS on the embryonic chorion membrane. As a result, the exposed group showed increased inner pore size of the chorionic membrane and accelerated heartbeat, indicating hypoxic conditions and hindered gaseous exchange. PS-MPs aggravated the toxicity of PFOS during larval development manifested by delayed hatching rate, increased mortality, and malformation rate. Additionally, increased ROS accumulation and altered antioxidant enzymatic status were observed in all the exposed groups suggesting perturbation of the redox state. Additionally, co-exposure of zebrafish larvae to PS-MPs and PFOS resulted in an abrupt behavioral response, which decreased AChE activity and altered neurotransmitter levels. Taken together, our results emphasize that PS-MPs can act as a potential vector for PFOS, exerting synergistic toxic effects in the aquatic environment, and hence their health risks cannot be ignored.

Study of Cellulose Dissolution in ZnO/NaOH/Water Solvent Solution and Its Temperature-Dependent Effect Using Molecular Dynamics Simulation

Cellulose is a biopolymer with numerous advantages that make it an ecological, economical, and high-performing choice for various applications. To fully exploit the potential of cellulose, it is often necessary to dissolve it, which poses a current challenge. The aqueous zinc oxide/sodium hydroxide (ZnO/NaOH/Water) system is a preferred solvent for its rapid dissolution, non-toxicity, low cost, and environmentally friendly nature. In this context, the behavior of cellulose chains in the aqueous solution of ZnO/NaOH and the impact of temperature on the solubility of this polymer were examined through a molecular dynamics simulation. The analysis of the root means square deviation (RMSD), interaction energy, hydrogen bond curves, and radial distribution function revealed that cellulose is insoluble in the ZnO/NaOH solvent at room temperature (T = 298 K). Decreasing the temperature in the range of 273 K to 268 K led to a geometric deformation of cellulose chains, accompanied by a decrease in the number of interchain hydrogen bonds over the simulation time, thus confirming the solubility of cellulose in this system between T = 273 K and T = 268 K.

Molecular insights into mutation-induced conformational changes in Acetyl CoA Carboxylase for improved activity

Acetyl-CoA carboxylase (ACCase) is crucial for fatty acid biosynthesis and has potential applications in lipid accumulation and advanced biofuel production. Mutations like S659A and S1157A in Saccharomyces cerevisiae ACCase remove the Snf1-regulation sites, resulting in increased enzyme activity with positive effects on the fatty acid pathway. However, the molecular-level understanding of these mutations on ACCase activity remains unexplored. Here, molecular dynamics simulation was conducted to investigate the mutations-induced conformational changes in S. cerevisiae ACCase. The wild-type ACCase was observed to have significant deviation in structure compared to mutant. Additionally, fluctuation of residues associated with biotin binding and Snf1-recognition were reduced in mutant compared to wild-type. Furthermore, the wild-type demonstrated opening motions of the domains, whereas the mutant showed closing movement. The mutation-induced conformational changes were analysed using network parameters, i.e., cliques/communities. The mutant showed an increase in sizes of several communities in AC3-AC4-AC5 domains leading to rigidification. Also, a new community was added in AC1-BT in the mutant, which suggested a substantial shift in the protein conformation. Thus, this study provides a theoretical understanding of the increased activity of ACCase due to two mutations, which can pave the path for enzyme engineering towards improved fatty acid-based fuel and chemical production.

Elucidating the Ionic Liquid-Induced Mixed Inhibition of GH1 β-Glucosidase H0HC94

Deciphering the ionic liquid (IL) tolerance of glycoside hydrolases (GHs) to improve their hydrolysis efficiency for fermentable sugar synthesis in the "one-pot" process has long been a hurdle for researchers. In this work, we employed experimental and theoretical approaches to investigate the 1-ethyl-3-methylimidazolium acetate ([C2C1im][MeCO2])-induced inhibition of GH1 β-glucosidase (H0HC94) from Agrobacterium tumefaciens 5A. At 10-15% [C2C1im][MeCO2] concentration, H0HC94 experiences competitive inhibition (R2 = 0.97, alpha = 2.8). As the IL content increased to 20-25%, the inhibition pattern shifted to mixed-type inhibition (R2 = 0.98, alpha = 3.4). These findings were further confirmed through characteristic inhibition plots using Lineweaver-Burk plots. Atomistic molecular dynamics simulations conducted with 0% [C2C1im][MeCO2], 10% [C2C1im][MeCO2], and 25% [C2C1im][MeCO2] revealed the accumulation of [C2C1im]+ at the negatively charged active site of H0HC94 in 10% [C2C1im][MeCO2], supporting the occurrence of competitive inhibition at lower IL concentrations. At higher IL concentrations, the cations and anions bound to the secondary binding sites (SBSs) of H0HC94, leading to a tertiary conformational change, as captured by the principal component analysis based on the free-energy landscape and protein structure networks. The altered conformation of H0HC94 affected the interaction with [C2C1im][MeCO2], which could possibly shift the inhibition from competitive to more mixed-type (competitive + noncompetitive) inhibition, as observed in the experiments. For the first time, we report a combined experimental and theoretical insight behind the mixed inhibition of a GH1 β-glucosidase. Our findings indicated the role of SBS in IL-induced inhibition, which could aid in developing more IL-tolerant β-glucosidases for biorefinery applications.

Molecular Insights into Antioxidant Efficiency of Melanin: A Sustainable Antioxidant for Natural Rubber Formulations

N-(1,3-Dimethyl butyl)-N'-phenyl-p-phenylenediamine (6-PPD) is a worldwide antioxidant commonly added to delay the thermo-oxidative degradation of tire rubbers. Unfortunately, 6PPD and its transformation product 6PPD-quinone are toxic to aquatic organisms (e.g., coho salmon). Herein, we explore the free radical scavenging activity and protective mechanism of melanin (MLN) on natural rubber's (NR's) oxidative resistance using molecular dynamics (MD) and quantum mechanical (QM) calculations. The relationship between the molecular structure and the chemical nature of the antioxidant molecules via transition state calculations is explored to unravel the reaction mechanisms of antioxidants interacting with peroxy radicals (ROO·) of NR with the estimation of reaction barriers. Following this, the radical scavenging activity of antioxidants was quantified via a hydrogen atom transfer mechanism and bond dissociation energy calculations. Parallel MD simulations were considered to study the interfacial interactions of antioxidant molecules with polymer chains and fillers with a quantifiable structure-property correlation. Given these results, the nanocomposite (NR-MLN-SiO2) with natural antioxidant melanin manifested outstanding antioxidant properties by preferentially bagging the ROO· radicals, thus improving NR's thermal-oxidative aging relative to 6-PPD. The MD results revealed that the intermolecular interactions at the NR/antioxidant interface benefited the antioxidant MLN to bind tightly to the NR in NR-MLN-SiO2 composite, thus exhibiting improved dispersion, O2 barrier properties, and thermo-oxidative stability, which could extend the service life of NR products (e.g., tires). In addition, as a sustainable antioxidant, MLN could replace toxic antioxidants like 6-PPD. More importantly, the QM/MD simulations provided a fundamental understanding of the mechanistic pathways of antioxidant molecules in NR composites, which are conducive to designing high-performance and sustainable green elastomers.

Dissolution mechanism of cellulose in a benzyltriethylammonium/urea deep eutectic solvent (DES): DFT-quantum modeling, molecular dynamics and experimental investigation

In this paper, a benzyltriethylammonium/urea DES was investigated as a new green and eco-friendly medium for the progress of organic chemical reactions, particularly the dissolution and the functionalization of cellulose. In this regard, the viscosity-average molecular weight of cellulose (M̄w) during the dissolution/regeneration process was investigated, showing no significant degradation of the polymer chains. Moreover, X-ray diffraction patterns indicated that the cellulose dissolution process in the BTEAB/urea DES decreased the crystallinity index from 87% to 75%, and there was no effect on type I cellulose polymorphism. However, a drastic impact of the cosolvents (water and DMSO) on the melting point of the DES was observed. Besides, to understand the evolution of cellulose-DES interactions, the formation mechanism of the system was studied in terms of H-bond density and radial distribution function (RDF) using molecular dynamics modeling. Furthermore, density functional theory (DFT) was used to evaluate the topological characteristics of the polymeric system such as potential energy density (PED), laplacian electron density (LED), energy density, and kinetic energy density (KED) at bond critical points (BCPs) between the cellulose and the DES. The quantum theory of atoms in molecules (AIM), Bader's quantum theory (BQT), and reduced density gradient (RDG) scatter plots have been exploited to estimate and locate non-covalent interactions (NCIs). The results revealed that the dissolution process is attributed to the physical interactions, mainly the strong H-bond interactions.

A force field for bio-polymers in ionic liquids (BILFF) - part 2: cellulose in [EMIm][OAc]/water mixtures

We present the extension of our force field BILFF (Bio-Polymers in Ionic Liquids Force Field) to the bio-polymer cellulose. We already published BILFF parameters for mixtures of ionic liquid 1-ethyl-3-methylimidazolium acetate ([EMIm][OAc]) with water. Our all-atom force field focuses on a quantitative reproduction of the hydrogen bonds in the complex mixture of cellulose, [EMIm]⁺, [OAc]^- and water when compared to reference ab initio molecular dynamics (AIMD) simulations. To enhance the sampling, 50 individual AIMD simulations starting from different initial configurations were performed for cellulose in solvent instead of one long simulation, and the resulting averages were used for force field optimization. All cellulose force field parameters were iteratively adjusted starting from the literature force field of W. Damm et al. We were able to obtain a very good agreement with respect to both the microstructure of the reference AIMD simulations and experimental results such as the system density (even at higher temperatures) and the crystal structure. Our new force field allows performing very long simulations of large systems containing cellulose solvated in (aqueous) [EMIm][OAc] with almost ab initio accuracy.

Ionic liquids as a useful tool for tailoring active pharmaceutical ingredients

Ionic liquids (ILs) have been widely used in biomedical and pharmaceutical fields as solvents or permeation enhancers. Recently, more and more researchers focused on optimizing the physicochemical properties of active pharmaceutical ingredient (API) by ILs technology. Converting APIs into ILs (API-ILs) has shown great potential for drug delivery by eliminating polymorphism, tailoring solubility, improving thermal stability, increasing dissolution, controlling drug release, modulating the surfactant properties, enhancing permeability of APIs and modulating cytotoxicity on tumor cells. In addition, API-ILs are also used in various formulations as active ingredients, such as solutions, emulsions, even tablets or nanoparticles. This paper aims to review current status of API-ILs, including the rational and design, preparation and characterization, the improvement on the physicochemical characteristics of APIs, the compatibility of API-ILs with various formulations, and the future prospects of API-ILs in biomedical and pharmaceutical fields.

Understanding the dissolution of softwood lignin in ionic liquid and water mixed solvents

Lignin is the most abundant heterogeneous aromatic polymer on earth to produce a large number of value-added chemicals. Besides, the separation of lignin from the lignocellulosic biomass is essential for cellulosic biofuel production. For the first time, we report a cosolvent-based approach to understand the dissolution of lignin with 61 guaiacyl subunits at the molecular level. Atomistic molecular dynamics simulations of the lignin were performed in 0%, 20%, 50%, 80%, and 100% 1-Ethyl-3-Methylimidazolium Acetate (EmimOAc) systems. The lignin structure was significantly destabilized in both 50%, and 80% EmimOAc cosolvents, and pure EmimOAc systems leading to the breakdown of intrachain hydrogen bonds. Lignin-OAc and lignin-water hydrogen bonds were formed with increasing EmimOAc concentration, signifying the dissolution process. The OAc anions mostly solvated the alkyl chains and hydroxy groups of lignin. Besides, the imidazolium head of Emim cations contributed to solvation of methoxy groups and hydroxy groups, whereas ethyl tail interacted with the benzene ring of guaiacyl subunits. Effective dissolution was obtained in both the 50% and 80% EmimOAc cosolvent systems. Overall, our study presents a molecular view of the lignin dissolution focusing on the role of both cation and anion, which will help to design efficient cosolvent-based methods for lignin dissolution.

Dissolution and Interaction of Cellulose Carbamate in NaOH/ZnO Aqueous Solutions

The dissolution and molecular interactions of cellulose carbamate (CC) in NaOH/ZnO aqueous solutions were studied using optical microscopy, differential scanning calorimetry (DSC), ¹H NMR, dynamic light scattering (DLS), atomic force microscopy (AFM), transmission electron microscopy (TEM), and molecular dynamic simulation. The dissolution of CC in NaOH/ZnO aqueous solutions using the freezing–thawing method was an exothermic process, and the lower temperature was favorable for the dissolution of CC. ZnO dissolved in NaOH aqueous solutions with the formation of Zn(OH)₄²⁻, and no free Zn²⁺ ions existed in the solvents. NaOH/Na₂Zn(OH)₄ system formed strong interactions with the hydroxyl groups of CC to improve its solubility and the stability of CC solution. The results indicate that 7 wt% NaOH/1.6 wt% ZnO aqueous solution was the most appropriate solvent for the dissolution of CC. This work revealed the dissolution interaction of CC-NaOH/ZnO solutions, which is beneficial for the industrialization of the CarbaCell process.

A force field for bio-polymers in ionic liquids (BILFF) - part 1: [EMIm][OAc]/water mixtures

We present BILFF, a novel force field for bio-polymers in ionic liquids. In the first part of our study, we introduce optimized force field parameters for mixtures of the ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate ([EMIm][OAc]) with water. This imidazolium-based IL is of particular practical importance as it can dissolve significant amounts of cellulose even at room temperature. An understanding of this dissolution process via molecular dynamics simulations requires a quantitative description of the microscopic structure and the strong hydrogen bonds with a method able of simulating at least several dozen nanoseconds, which is the main aim of our novel force field. To reach this goal, we optimize the force field parameters to reproduce radial, spatial, and combined distribution functions, hydrogen bond lifetimes, diffusion coefficients, and several other quantities from reference ab initio molecular dynamics (AIMD) simulations. Non-trivial effects such as dispersion interactions between the side chains and π-π stacking of the cations are reproduced very well. We further validate the force field by comparison to experimental data such as thermal expansion coefficients, bulk modulus, and density at different temperatures, which yields good agreement and correct trends. No other force field with optimized parameters for mixtures of [EMIm][OAc] and water has been presented in the literature yet. Optimized force field parameters for cellulose and other ILs will be published in upcoming articles.

Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus

Economic deconstruction of lignocellulose remains a challenge due to the complex architecture of cellulose, hemicellulose, and lignin. Advancements in pretreatment processes have introduced ionic liquids (ILs) as promising non-derivatizing solvents for reducing biomass recalcitrance and for promoting enzymatic hydrolysis. However, available commercial cellulases are destabilized or inactivated even in low concentration of residual ILs. Thus, a molecular understanding of IL-enzyme interactions is crucial for developing IL-tolerant enzymes with high catalytic activity. In this study, molecular insight behind the IL tolerance of hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus (RmCel12A) has been investigated in 20%, 40%, and 60% 1-ethyl-3-methylimidazolium acetate (EmimAc) through molecular dynamic simulations at 368 K. Though the enzyme retained its stability in all EmimAc concentrations, the activity was affected due to the loss of essential dynamic motions. A protein structure network was constructed using the snapshots of protein structures from the simulation trajectories and the hub properties of residues R20, Y59, W68, W197, E203, and F220 were found to be lost in 60% EmimAc. Emim cations were observed to intrude the active site tunnel and interact with more number of catalytic residues with higher cumulative fractional occupancy in 60% EmimAc than in 20% or 40% EmimAc. Some non-catalytic residues have also been identified at the active site, which can be probable mutation targets for improving the IL tolerance. Our findings reveal the molecular understanding behind the origin of activity loss of RmCel12A and proposed insights for the further improvement of IL sensitivity.

Understanding the behavior of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus in different concentrations of EmimAc.

Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines

This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.