The impact of charges in force field parameterization for molecular dynamics simulations of deep eutectic solvents

Investigating Biomolecules in Deep Eutectic Solvents with Molecular Dynamics Simulations: Current State, Challenges and Future Perspectives

Deep eutectic solvents (DESs) have recently gained increased attention for their potential in biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond acceptor and a hydrogen bond donor, which allows for tailoring their properties for particular applications. If produced from sustainable resources, they can provide a greener alternative to many traditional organic solvents for usage in various applications (e.g., as reaction environment, crystallization agent, or storage medium). To navigate this large design space, it is crucial to comprehend the behavior of biomolecules (e.g., enzymes, proteins, cofactors, and DNA) in DESs and the impact of their individual components. Molecular dynamics (MD) simulations offer a powerful tool for understanding thermodynamic and transport processes at the atomic level and offer insights into their fundamental phenomena, which may not be accessible through experiments. While the experimental investigation of DESs for various biotechnological applications is well progressed, a thorough investigation of biomolecules in DESs via MD simulations has only gained popularity in recent years. Within this work, we aim to provide an overview of the current state of modeling biomolecules with MD simulations in DESs and discuss future directions with a focus for optimizing the molecular simulations and increasing our fundamental knowledge.

Analysis of temperature effect in the CO2 absorption using a deep eutectic solvent: An in silico approach

The excess level of carbon dioxide in the atmosphere has contributed a lot to global warming, occasioning several damages to the planet. Therefore, it is urgent to find ways to capture this gas. Then, the present work analyzed the temperature effect in CO2 absorption through deep eutectic solvents (DESs) based on urea and choline chloride using an in silico approach. The Molecular Dynamics (MD) simulations indicated that the increased temperature reduced the interaction potential of carbon dioxide molecules with the DESs components, indicating that the absorption process is more favorable at 303 K. On the other hand, the Noncovalent Interactions (NCI) simulations suggest that the increased temperature reduced the strong attractions and increased repulsive interactions between the carbon dioxide molecules with the solvent analyzed. Therefore, both in silico approaches suggest that the carbon dioxide absorption is more indicated at 303 K.

Nature of a Tetrabutylammonium Chloride-Levulinic Acid Deep Eutectic Solvent

A deep eutectic solvent was formed by considering the mixtures of tetrabutylammonium chloride and levulinic acid, and it is studied via a combined theoretical and experimental approach. Physicochemical properties were measured as a function of temperature, providing a macroscopic characterization of the fluid. Quantum chemistry and classical molecular dynamics simulations were carried out for the nanoscopic characterization, providing attention to the nature, extension, and dynamics of the hydrogen bonding network, which is at the root of the properties of the fluid. The reported study allows multiscale characterization of this fluid as an archetypical example of a natural, low-cost, and sustainable fluid.

Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole

The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.

Water Influence on the Physico-Chemical Properties and 3D Printability of Choline Acrylate-Bacterial Cellulose Inks

The aim of this work was to study the influence of water as a co-solvent on the interaction between a polymerizable ionic liquid-choline acrylate (ChA)-and bacterial cellulose. Bacterial cellulose dispersed in ChA is a new type of UV-curable biopolymer-based ink that is a prospective material for the 3D printing of green composite ion-gels. Higher cellulose content in inks is beneficial for the ecological and mechanical properties of materials, and leads to increased viscosity and the yield stress of such systems and hampers printability. It was found that the addition of water results in (1) a decrease in the solvent viscosity and yield stress; and (2) a decrease in the stability of dispersion toward phase separation under stress. In this work, an optimal composition in the range of 30-40 wt% water content demonstrating 97-160 Pa of yield stress was found that ensures the printability and stability of inks. The rheological properties of inks and mechanical characteristics (0.7-0.8 MPa strength and 1.1-1.2 MPa Young's modulus) were obtained. The mechanism of influence of the ratio ChA/water on the properties of ink was revealed with atomic force microscopy, wide-angle X-ray diffraction studies of bacterial cellulose after regeneration from solvent, and computer simulation of ChA/water mixtures and their interaction with the cellulose surface.

Structural and dynamic properties of eutectic mixtures based on menthol and fatty acids derived from coconut oil: a MD simulation study

The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. To this end, the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs are studied. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions (CDFs), radial distribution functions (RDFs), angular distribution functions (ADFs), hydrogen bonding networks, and spatial distribution functions (SDF). Additionally, our Results indicated robust interactions between menthol and Caprylic acid molecules Finally, the transport properties of the mixtures were investigated using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. Overall, our simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solvents

Deep eutectic solvents (DESs) are an emerging class of non-aqueous solvents that are potentially scalable, easy to prepare and functionalize for many applications ranging from biomass processing to energy storage technologies. Predictive understanding of the fundamental correlations between local structure and macroscopic properties is needed to exploit the large design space and tunability of DESs for specific applications. Here, we employ a range of computational and experimental techniques that span length-scales from molecular to macroscopic and timescales from picoseconds to seconds to study the evolution of structure and dynamics in model DESs, namely Glyceline and Ethaline, starting from the parent compounds. We show that systematic addition of choline chloride leads to microscopic heterogeneities that alter the primary structural relaxation in glycerol and ethylene glycol and result in new dynamic modes that are strongly correlated to the macroscopic properties of the DES formed.

Tailoring the macroscopic properties of deep eutectic solvents requires knowing how these depend on the local structure and microscopic dynamics. The authors, with computational and experimental tools spanning a wide range of space- and timescales, shed light into the relationship between micro and macroscopic properties in glyceline and ethaline.

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can predict and reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline

Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular, for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable, and polarizable force field for MD simulations of different types of DESs. The original formulation contains, however, some problems that appear in simulations of ethaline and may also have a broader impact. First, the originally proposed atomic diameter parameters are unbalanced, resulting in too weak interactions between the chlorides and the hydroxyl groups of the ethylene glycol molecules. This, in turn, causes an artificial phase separation in long simulations. Second, there is an overpolarization of chlorides due to strong induced dipoles that give rise to the presence of peaks and antipeaks at very low q-vector values (2.4 nm^-1) in the partial components of the structure factors. In physical terms, this is equivalent to overestimated spatial nanoscale heterogeneity. To correct these problems, we adjusted the chloride-hydroxyl radial distribution functions against ab initio data and then extended the use of the Tang-Toennis damping function for the chlorides' induced dipoles. These adjustments correct the problems without losing the robustness of the CL&Pol force field. The results were also compared with the nonpolarizable version, the CL&P force field. We expect that the corrections will facilitate reliable use of the CL&Pol force field for other types of DESs.

Bulk and interfacial nanostructure and properties in deep eutectic solvents: Current perspectives and future directions

Deep eutectic solvents (DESs) are a tailorable class of solvents that are rapidly gaining scientific and industrial interest. This is because they are distinct from conventional molecular solvents, inherently tuneable via careful selection of constituents, and possess many attractive properties for applications, including catalysis, chemical extraction, reaction media, novel lubricants, materials chemistry, and electrochemistry. DESs are a class of solvents composed solely of hydrogen bond donors and acceptors with a melting point lower than the individual components and are often fluidic at room temperature. A unique feature of DESs is that they possess distinct bulk liquid and interfacial nanostructure, which results from intra- and inter-molecular interactions, including coulomb forces, hydrogen bonding, van der Waals interactions, electrostatics, dispersion forces, and apolar-polar segregation. This nanostructure manifests as preferential spatial arrangements of the different species, and exists over several length scales, from molecular- to nano- and meso-scales. The physicochemical properties of DESs are dictated by structure-property relationships; however, there is a significant gap in our understanding of the underlying factors which govern their solvent properties. This is a major limitation of DES-based technologies, as nanostructure can significantly influence physical properties and thus potential applications. This perspective provides an overview of the current state of knowledge of DES nanostructure, both in the bulk liquid and at solid interfaces. We provide definitions which clearly distinguish DESs as a unique solvent class, rather than a subset of ILs. An appraisal of recent work provides hints towards trends in structure-property relationships, while also highlighting inconsistencies within the literature suggesting new research directions for the field. It is hoped that this review will provide insight into DES nanostructure, their potential applications, and development of a robust framework for systematic investigation moving forward.

Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase

Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.

A computational study on the interactions between a layered imine-based COF structure and selected anticancer drugs

The covalent organic frameworks (COFs) are important materials in drug delivery. Herein, the interactions between an imine-based COF with selected commercially available anticancer drugs are studied. Molecular dynamics (MD) simulation studies were used. The studies were carried out in four different temperatures to find out the impact of the temperature on the binding free energies between the drugs and COF structure. It was found that the effect of temperature on binding free energy is ignorable. Between the hydrogen bonding, electrostatic, and van der Waals interactions, the last one is the most important one to keep the drug and COF next to each other. Also, the van der Waals interaction is keeping the layers of COF next to each other to create cavities. The cavities can be loaded with different drugs and the system can be used in drug delivery systems. Based on the obtained results, the drugs that are more lipophilic prefer to adhere more strongly to the COF in comparison with hydrophilic drugs.

Deep Eutectic Solvents: A Review of Fundamentals and Applications

Deep eutectic solvents (DESs) are an emerging class of mixtures characterized by significant depressions in melting points compared to those of the neat constituent components. These materials are promising for applications as inexpensive "designer" solvents exhibiting a host of tunable physicochemical properties. A detailed review of the current literature reveals the lack of predictive understanding of the microscopic mechanisms that govern the structure-property relationships in this class of solvents. Complex hydrogen bonding is postulated as the root cause of their melting point depressions and physicochemical properties; to understand these hydrogen bonded networks, it is imperative to study these systems as dynamic entities using both simulations and experiments. This review emphasizes recent research efforts in order to elucidate the next steps needed to develop a fundamental framework needed for a deeper understanding of DESs. It covers recent developments in DES research, frames outstanding scientific questions, and identifies promising research thrusts aligned with the advancement of the field toward predictive models and fundamental understanding of these solvents.

Molecular approach about the effect of water on the electrochemical behaviour of Ag+ ions in urea-choline chloride-water mixture

The water influence on electrochemical behaviour of Ag⁺ ions in urea and choline chloride mixture was investigated by cyclic voltammetry technique, while the molecular insights about the investigated systems were obtained from molecular dynamic (MD) simulation. The water content was variated from 0 up to 10% (v/v). Cyclic voltammetry technique showed that the peak potential for Ag⁺/Ag redox couples shifted in direction to more positive potentials with the gradual increase of water content in solution, indicating that the addition of water electrocatalyses the kinetics of the reduction of Ag⁺ ions. The MD simulations demonstrated that water molecules do not interact strongly with Ag⁺ ions but induce a small reduction in the number of urea molecules around of the ion and that the water molecules adjust to free spaces in the mixture.

Modeling the Physicochemical Properties of Natural Deep Eutectic Solvents

Natural deep eutectic solvents (NADES) are mixtures of naturally derived compounds with a significantly decreased melting point owing to specific interactions among the constituents. NADES have benign properties (low volatility, flammability, toxicity, cost) and tailorable physicochemical properties (by altering the type and molar ratio of constituents); hence, they are often considered to be a green alternative to common organic solvents. Modeling the relation between their composition and properties is crucial though, both for understanding and predicting their behavior. Several efforts have been made to this end. This Review aims at structuring the present knowledge as an outline for future research. First, the key properties of NADES are reviewed and related to their structure on the basis of the available experimental data. Second, available modeling methods applicable to NADES are reviewed. At the molecular level, DFT and molecular dynamics allow density differences and vibrational spectra to be interpreted, and interaction energies to be computed. Additionally, properties at the level of the bulk medium can be explained and predicted by semi-empirical methods based on ab initio methods (COSMO-RS) and equation of state models (PC-SAFT). Finally, methods based on large datasets are discussed: models based on group-contribution methods and machine learning. A combination of bulk-medium and dataset modeling allows qualitative prediction and interpretation of phase equilibria properties on the one hand, and quantitative prediction of melting point, density, viscosity, surface tension, and refractive index on the other. Multiscale modeling, combining molecular and macroscale methods, is expected to strongly enhance the predictability of NADES properties and their interaction with solutes, and thus yield truly tailorable solvents to accommodate (bio)chemical reactions.

Deep Eutectic Solvents Mixed with Fluorinated Refrigerants for Absorption Refrigeration: A Molecular Simulation Study

Molecular simulations were performed to evaluate mixtures of fluorinated refrigerants with deep eutectic solvents (DESs), for potential use in single-effect absorption refrigeration cycles that use low quality waste heat sources at temperatures of ∼80 °C. The refrigerants considered were the hydrofluorocarbon R245fa and the hydrofluoroolefins R1234zeE and HFO1336mzzE, whereas the DESs evaluated were 1:2 molar mixtures of choline chloride with either ethylene glycol (ethaline) or levulinic acid (levuline) as hydrogen bond donors (HBDs). Assuming the same cycle operating conditions, the waste heat cycle efficiency η was computed for all working fluid mixtures from molecular simulation results of the mixture densities and Henry's law constants of the refrigerants in the DESs, coupled with phase equilibrium calculations and the enthalpies of the pure refrigerants. The largest efficiency was obtained for the mixture R245fa-ethaline (η = 6.82), followed by R245fa-levuline (η = 4.64) and HFO1336mzzE-levuline (η = 2.10). These modest efficiency values could be further increased by tailoring the cycle operating conditions to each particular refrigerant-DES system, as well as optimizing our choice of working fluid mixtures, neither of which we attempted in this study. Strong interactions were observed between the chlorine anions and some of the hydrogen atoms of the refrigerants, but in general the cation-refrigerant and HBD-refrigerant interactions are weaker compared to the refrigerant-refrigerant interactions. Refrigerant molecules have the largest diffusivities and make the cations, anions and HBD to move faster compared to systems of DESs without refrigerant; in general, species in refrigerant-ethaline mixtures have larger diffusivities compared to those for refrigerant-levuline mixtures. We also computed waste heat cycle efficiencies for the same R134a-DES mixtures studied in our previous work, finding significant differences between the efficiencies determined from molecular simulation data and those determined before using the COSMO-RS approach using two standard parametrizations. This observation suggests that further work is needed to improve the accuracy of the COSMO-RS predictions for these systems.

Modeling of Solid-Liquid Equilibria in Deep Eutectic Solvents: A Parameter Study

Deep eutectic solvents (DESs) are potential alternatives to many conventional solvents in process applications. Knowledge and understanding of solid-liquid equilibria (SLE) are essential to characterize, design, and select a DES for a specific application. The present study highlights the main aspects that should be taken into account to yield better modeling, prediction, and understanding of SLE in DESs. The work is a comprehensive study of the parameters required for thermodynamic modeling of SLE-i.e., the melting properties of pure DES constituents and their activity coefficients in the liquid phase. The study is carried out for a hypothetical binary mixture as well as for selected real DESs. It was found that the deepest eutectic temperature is possible for components with low melting enthalpies and strong negative deviations from ideality in the liquid phase. In fact, changing the melting enthalpy value of a component means a change in the difference between solid and liquid reference state chemical potentials which results in different values of activity coefficients, leading to different interpretations and even misinterpretations of interactions in the liquid phase. Therefore, along with reliable modeling of liquid phase non-ideality in DESs, accurate estimation of the melting properties of their pure constituents is of clear significance in understanding their SLE behavior and for designing new DES systems.

Ionic deep eutectic solvents for the extraction and separation of natural products

Room ionic liquids (ILs) used as green solvents have received considerable attention and wide application in different research and industrial fields, such as chemistry, biology, catalysis, energy, and even environmental sciences. Recently, a new class of sustainable solvents named deep eutectic solvents (DESs) have been developed, which share the promising solvent characteristics of ILs, such as thermal and chemical stability, low vapor pressure and design ability. In addition, the major advantages of DESs over ILs are their lower prices and easier preparation. Therefore, DESs have been considered to be a potential alternative to replace conventional organic solvents and ILs. Currently, the developed DESs may be classified into ionic and nonionic liquids. Typically, choline chloride (ChCl)/urea (1:2) is an ionic DES, while glucose/sucrose (1:1) is a nonionic DES. Although several reviews have covered advancements in DESs, in this review, we aim to provide a general insight into DESs, particularly ionic DESs, like choline-based DES, in terms of their preparation and application in the extraction of natural products (NPs) mainly from traditional Chinese medicines and the recovery of extracted compounds from their extracts. Additionally, various factors affecting the extraction efficiency of DESs are discussed.

On the Performance of Confined Deep Eutectic Solvents and Ionic Liquids for Separations of Carbon Dioxide from Methane: Molecular Dynamics Simulations

Classical molecular dynamics simulations were used to investigate the performance of slit graphite and titania (rutile) pores of 5.2 nm in width, partially and completely filled with deep eutectic solvents (DESs) or ionic liquids (ILs), for gas separations of a carbon dioxide-methane mixture of 5:95 molar ratio and temperatures and pressures on the order of 318 K and 100 bar, respectively. The DESs studied were ethaline and levuline (1:2 molar mixtures of choline chloride with ethylene glycol or levulinic acid), and the IL considered was 1- n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [bmim⁺][NTf₂^-]. The performance of these systems in terms of solubility selectivity, diffusion selectivity, and permselectivity was compared against the performance of the bulk solvents (which could also be viewed as a model system for the micrometer-sized pores of a supported IL or DES membrane) and against carbon and rutile pores without preadsorbed solvent. The best performance in terms of permselectivity is obtained for bulk levuline and by rutile pores fully filled by ethaline, followed by graphite pores filled by ethaline and the IL. Empty rutile pores have the largest value of solubility selectivity, followed by bulk ethaline and rutile pores completely filled by the IL. The largest values of diffusivity selectivity were observed for bulk levuline, followed by ethaline completely filling a rutile nanopore and a graphite nanopore completely filled with the IL. These observations are rationalized by examining local density profiles and interaction energies among the different entities in our systems. In general, systems of nanopores fully filled by solvents, as well as the bulk solvents, have larger permselectivities than pores partially filled by the IL or the DESs. Drops of 2-3 orders of magnitude are observed in the gas diffusivity in pores filled with solvents with respect to systems of empty pores, which may be problematic if gas permeation is mainly controlled by diffusion. However, if adsorption dominates the gas permeation within the membrane, our results suggest that systems of levuline in the micrometer-sized pores of a supported DES membrane or ethaline confined in the rutile nanopores of a supported DES phase material might represent promising systems for gas separation.

The effect of water on the physicochemical properties of an ethylene glycol and choline chloride mixture containing Cu2+ ions: electrochemical results and dynamic molecular simulation approach

The molecular dynamic indicated that the water molecules replace the ethylene glycol molecules that are coordinated with Cu²⁺ ions.

Atomic charges of sulfur in ionic liquids: experiments and calculations

A wide variety of experimental and computational methods are used to probe sulfur atomic charges in ionic liquids.

Potential applications of deep eutectic solvents in natural gas sweetening for CO2 capture

Novel solvents named deep eutectic solvents (DESs) have been intensively investigated in recent years. Their non-toxicity, biodegradability, low volatility, easy preparation and low cost make them promising green solvents for several industrial processes. This article provides a status review of the possible applications of DESs in natural gas (NG) sweetening by carbon dioxide (CO

Doubly ionic hydrogen bond interactions within the choline chloride–urea deep eutectic solvent

Computational analysis indicates flexibility and diversity in the hydrogen bonding, but limited charge delocalisation, within the choline chloride–urea eutectic.

Insights into choline chloride–phenylacetic acid deep eutectic solvent for CO2 absorption

Choline chloride plus phenylacetic acid deep eutectic solvent in neat liquid state and upon CO₂ absorption is analyzed using a theoretical approach combining quantum chemistry using Density Functional Theory and classic molecular dynamics methods.