Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory

Assessing the mechanism of fast-cycling cancer-associated mutations of Rac1 small Rho GTPase

Rho-GTPases proteins function as molecular switches alternating from an active to an inactive state upon Guanosine triphosphate (GTP) binding and hydrolysis to Guanosine diphosphate (GDP). Among them, Rac subfamily regulates cell dynamics, being overexpressed in distinct cancer types. Notably, these proteins are object of frequent cancer-associated mutations at Pro29 (P29S, P29L, and P29Q). To assess the impact of these mutations on Rac1 structure and function, we performed extensive all-atom molecular dynamics simulations on wild-type (wt) and oncogenic isoforms of this protein in GDP- and GTP-bound states. Our results unprecedentedly elucidate that P29Q/S-induced structural and dynamical perturbations of Rac1 core domain weaken the binding of the catalytic site Mg2+ ion, and reduce the GDP residence time within protein, enhancing the GDP/GTP exchange rate and Rac1 activity. This broadens our knowledge of the role of cancer-associated mutations on small GTPases mechanism supplying valuable information for future drug discovery efforts targeting specific Rac1 isoforms.

Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters

Polarization plays important roles in charged and hydrogen bonding containing systems. Much effort ranging from the construction of physics-based models to quantum mechanism (QM)-based and machine learning (ML)-assisted models have been devoted to incorporating the polarization effect into the conventional force fields at different levels, such as atomic and coarse grained (CG). The application of polarizable force fields or polarization models was limited by two aspects, namely, computational cost and transferability. Different from physics-based models, no predetermining parameters were required in the QM-based approaches. Taking advantage of both the accuracy of QM calculations and efficiency of molecular mechanism (MM) and ML, polarization effects could be treated more efficiently while maintaining the QM accuracy. The computational cost could be reduced with variable electrostatic parameters, such as the charge, dipole, and electronic dielectric constant with the help of linear scaling fragmentation-based QM calculations and ML models. Polarization and entropy effects on the prediction of partition coefficient of druglike molecules are demonstrated by using both explicit or implicit all-atom molecular dynamics simulations and machine learning-assisted models. Directions and challenges for future development are also envisioned.

Nonpolarizable Force Fields through the Self-Consistent Modeling Scheme with MD and DFT Methods: From Ionic Liquids to Self-Assembled Ionic Liquid Crystals

A key to achieve the accuracy of molecular dynamics (MD) simulation is the set of force fields used to express the atomistic interactions. In particular, the electrostatic interaction remains the main issue for the precise simulation of various ionic soft materials from ionic liquids to their supramolecular compounds. In this study, we test the nonpolarizable force fields of ionic liquids (ILs) and self-assembled ionic liquid crystals (ILCs) for which the intermolecular charge transfer and intramolecular polarization are significant. The self-consistent modeling scheme is adopted to refine the atomic charges of ionic species in a condensed state through the use of density functional theory (DFT) under the periodic boundary condition. The atomic charges of the generalized amber force field (GAFF) are effectively updated to express the electrostatic properties of ionic molecules obtained by the DFT calculation in condensed phase, which improves the prediction accuracy of ionic conductivity with the obtained force field (GAFF-DFT). The derived DFT charges then suggest that the substitution of a hydrophobic liquid-crystalline moiety into IL-based cations enhances the charge localization of ionic groups in the amphiphilic molecules, leading to the amplification of the electrostatic interactions among the hydrophilic/ionic groups in the presence of hydrophobic moieties. In addition, we focus on an ion-conductive pathway hidden in the self-assembled nanostructure. The MD results indicate that the ionic groups of cation and anion interact strongly for keeping the bicontinuous nanosegregation of ionic nanochannel. The partial fractions of hydrophilic/ionic and hydrophobic nanodomains are then quantified with the volume difference from referenced IL systems, while the calculated ionic conductivity decreases in the self-assembled ILCs more than the occupied volume of ionic nanodomains. These analyses suggest that the mobility of ions in the self-assembled ILCs remains quite restricted even with small tetrafluoroborate anions because of strong attractive interaction among ionic moieties.

Dynamical Ion Association and Transport Properties in PEO-LiTFSI Electrolytes: Effect of Salt Concentration

The association of ions describes the formation of ion species in electrolyte solutions and is strongly related to the salt concentration. However, the discussion of ion species and their transport is ambiguous in some studies on electrolyte materials due to the assumption of ideal solutions. Accordingly, in this work, molecular dynamics simulations are used to study ion association and transport properties of poly(ethylene)oxide (PEO)-lithium bis(trifluoromethanesulfonyl)imide electrolytes over a range of salt concentrations (r = [Li]/[EO]) from 0.01 to 0.20. Based on the analysis of the solvation environment and ion species, it is revealed that the distinct ion-ion correlations exist in two different characteristic areas, with a salt concentration of 0.10 as the limit. Below the critical concentration, the dynamic equilibrium between free ions and ion pairs is the most important process affecting the transport properties of electrolytes, but the process may have a minor influence on the applicability of the Nernst-Einstein relation. In concentrated solutions, a large number of ion pairs, triplets, and so forth appear in the electrolytes. The high-order ion clusters, with an average size of 3.95 at r = 0.20, are the main stable structures for transporting Li⁺, but the trapped free ions are the most abundant ion species. Meanwhile, the effect of salt concentrations on the average transport of ion clusters is to increase their average lifetime, but their transport rates remain unchanged. In addition, the coupling dynamics between ions and polymers is also discussed in order to gain a complete insight into the importance of salt concentrations.

Controlling Li+ transport in ionic liquid electrolytes through salt content and anion asymmetry: a mechanistic understanding gained from molecular dynamics simulations

In this work, we report the results from molecular dynamics simulations of lithium salt-ionic liquid electrolytes (ILEs) based either on the symmetric bis[(trifluoromethyl)sulfonyl]imide (TFSI^-) anion or its asymmetric analogue 2,2,2-(trifluoromethyl)sulfonyl-N-cyanoamide (TFSAM^-). Relating lithium's coordination environment to anion mean residence times and diffusion constants confirms the remarkable transport behaviour of the TFSAM^--based ILEs that has been observed in recent experiments: for increased salt doping, the lithium ions must compete for the more attractive cyano over oxygen coordination and a fragmented landscape of solvation geometries emerges, in which lithium appears to be less strongly bound. We present a novel, yet statistically straightforward methodology to quantify the extent to which lithium and its solvation shell are dynamically coupled. By means of a Lithium Coupling Factor (LCF) we demonstrate that the shell anions do not constitute a stable lithium vehicle, which suggests for this electrolyte material the commonly termed "vehicular" lithium transport mechanism could be more aptly pictured as a correlated, flow-like motion of lithium and its neighbourhood. Our analysis elucidates two separate causes why lithium and shell dynamics progressively decouple with higher salt content: on the one hand, an increased sharing of anions between lithium limits the achievable LCF of individual lithium-anion pairs. On the other hand, weaker binding configurations naturally entail a lower dynamic stability of the lithium-anion complex, which is particularly relevant for the TFSAM^--containing ILEs.

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

Self-assembled ionic liquid crystals can transport water and ions via the periodic nanochannels, and these materials are promising candidates as water treatment membranes. Molecular insights on the water transport process are, however, less investigated because of computational difficulties of ionic soft matters and the self-assembly. Here we report specific behavior of water molecules in the nanochannels by using the self-consistent modeling combining density functional theory and molecular dynamics and the large-scale molecular dynamics calculation. The simulations clearly provide the one-dimensional (1D) and 3D-interconnected nanochannels of self-assembled columnar and bicontinuous structures, respectively, with the precise mesoscale order observed by x-ray diffraction measurement. Water molecules are then confined inside the nanochannels with the formation of hydrogen bonding network. The quantitative analyses of free energetics and anisotropic diffusivity reveal that, the mesoscale geometry of 1D nanodomain profits the nature of water transport via advantages of dissolution and diffusion mechanisms inside the ionic nanochannels.

Efficient Parametrization of Force Field for the Quantitative Prediction of the Physical Properties of Ionic Liquid Electrolytes

The prediction of transport properties of room-temperature ionic liquids from nonpolarizable force field-based simulations has long been a challenge. The uniform charge scaling method has been widely used to improve the agreement with the experiment by incorporating the polarizability and charge transfer effects in an effective manner. While this method improves the performance of the force fields, this prescription is ad hoc in character; further, a quantitative prediction is still not guaranteed. In such cases, the nonbonded interaction parameters too need to be refined, which requires significant effort. In this work, we propose a three-step semiautomated refinement procedure based on (1) atomic site charges obtained from quantum calculations of the bulk condensed phase; (2) quenched Monte Carlo optimizer to shortlist suitable force field candidates, which are then tested using pilot simulations; and (3) manual refinement to further improve the accuracy of the force field. The strategy is designed in a sequential manner with each step improving the accuracy over the previous step, allowing the users to invest the effort commensurate with the desired accuracy of the refined force field. The refinement procedure is applied on N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide (DEME-TFSI), a front-runner as an electrolyte for electric double-layer capacitors and single-molecule-based devices. The transferability of the refined force field is tested on N,N-dimethyl-N-ethyl-N-methoxyethoxyethylammonium bis(trifluoromethanesulfonyl)imide (N_112,2O2O1-TFSI). The refined force field is found to be better at predicting both structural and transport properties compared to the uniform charge scaling procedure, which showed a discrepancy in the X-ray structure factor. The refined force field showed quantitative agreement with structural (density and X-ray structure factor) and transport properties-diffusion coefficients, ionic conductivity, and shear viscosity over a wide temperature range, building a case for the wide adoption of the procedure.

Spatial-Decomposition Analysis of Electrical Conductivity in Mixtures of Ionic Liquid and Sodium Salt for Sodium-Ion Battery Electrolytes

Ionic liquid (IL)-based electrolytes are a promising material for the development of sodium-ion batteries, and their performance can be quantified by electrical conductivity. In this highly concentrated ionic system, the correlated motions of ion pairs are influential on the ionic transport properties. Herein, all-atom analyses are conducted through molecular dynamics simulations to bridge the macroscopically observable electrical conductivity with the molecular pictures of correlated motion of ion pairs. The analysis is applied to three mixtures of IL with sodium salt that are relevant to the electrolyte for a sodium-ion battery: [1-ethyl-3-methylimidazolium, Na][bis(fluorosulfonyl)amide] ([C₂C₁im, Na][FSA]), [N-methyl-N-propylpyrrolidinium, Na][FSA] ([C₃C₁pyrr, Na][FSA]), and [K, Na][FSA]. The computational results on electrical conductivities are in agreement with the experimental reports, and their dependency on temperature and sodium-ion composition is reproduced well. The overall contributions from cross-correlated motions are found to be negative in all the IL mixtures; thus, the total conductivities are less than their Nernst-Einstein estimates. The spatial view of cross-correlated motions is further obtained by decomposing the time correlation functions of velocities according to the distances between ion pairs. It is observed that ion pairs are moving in the same direction for ∼0.3 ps when they were initially within the first coordination shell, followed by motions toward opposite directions. The cross-correlation terms are also dissected into local and nonlocal components, and it is commonly seen for all the ion pairs that the local component is negative for cation-anion pairs and is positive for cation-cation and anion-anion pairs. The motions of ion pairs are accompanied by a "backflow" that manifests in the form of the nonlocal component whose sign is opposite to the corresponding local component. In fact, the contributions of the correlated motions of ions to the electrical conductivity are not localized to contact pairs and extend spatially beyond the first coordination shell of the cation-anion pairs.

The Effect of Phenyl Substitutions on Microstructures and Dynamics of Tetraalkylphosphonium Bis(trifluoro- methylsulfonyl)imide Ionic Liquids

Extensive atomistic simulations demonstrated that a gradual substitution of hexyl chains with phenyl groups in tetraalkylphosphonium cations results in remarkable changes in hydrogen bonding interactions, liquid structures and scattering structural functions, and rotational dynamics of hexyl chains and phenyl groups in tetraalkylphosphonium bis(trifluoromethylsulfonyl)imide ionic liquids. Hydrogen donor sites in hexyl chains present competitive characteristics with those in phenyl groups in coordinating anions, as well as their continuous and intermittent hydrogen bonding dynamics. Cation-cation and anion-anion spatial correlations show concomitant shift to short distances with decreased peak intensities with variations of cation structures, whereas cation-anion correlations have a distinct shift to large radial distances due to decreased associations of anions with neighboring cations. These microstructural changes are qualitatively manifested in shifts of prominent peaks for prevalent charge alternations and adjacency correlations between ion species in scattering structural functions. Meanwhile, rotational dynamics of hexyl chains speed up, which, in turn, slow down rotations of phenyl groups, whereas anions exhibit imperceptible changes in their rotational dynamics. These computational results are intrinsically correlated with conformational flexibilities, molecular sizes, and steric hindrance effects of phenyl groups in comparison with hexyl chains, and constrained distributions of anions around cations in heterogeneous ionic environments.

How Molecular Chiralities of Bis(mandelato)borate Anions Affect Their Binding Structures With Alkali Metal Ions and Microstructural Properties in Tetraalkylphosphonium Ionic Liquids

Spiroborate anion-based inorganic electrolytes and ionic liquids (ILs) have fascinating electrochemical and tribological properties and have received widespread attention in industrial applications. The molecular chiralities of spiroborate anions have a significant effect on the microstructures and macroscopic functionalities of these ionic materials in application and thus deserve fundamental consideration. In the current work, we performed quantum chemistry calculations to address the binding strength and coordination structures of chiral bis(mandelato)borate ([BMB]) anions with representative alkali metal ions, as well as the electronic properties of alkali metal ion-[BMB] ion pair complexes. The optimized [BMB] conformers are categorized into V-shaped, bent, and twisted structures with varied electrostatic potential contours and conformational energies and distinct alkali metal ion-[BMB] binding structures. Alkali metal ions have additional associations with phenyl groups in V-shaped [BMB] conformers owing to preferential cation-π interactions. Furthermore, the effects of the molecular chiralities of [BMB] anions on the thermodynamics and microstructural properties of tetraalkylphosphonium [BMB] ILs were studied by performing extensive atomistic interactions. Oxygen atoms in [BMB] anions have competitive hydrogen bonding interactions with hydrogen atoms in cations depending on the molecular chiralities and steric hindrance effects of [BMB] anions. However, the molecular chiralities of [BMB] anions have a negligible effect on the liquid densities of tetraalkylphosphonium [BMB] ILs and the spatial distributions of boron atoms in anions around phosphorous atoms in cations. Enlarging tetraalkylphosphonium cation sizes leads to enhanced cation-anion intermolecular hydrogen bonding and Coulombic interactions due to enhanced segregation of polar groups in apolar networks in heterogeneous IL matrices, as verified by scattering structural functions.

Self-Consistent Scheme Combining MD and Order-N DFT Methods: An Improved Set of Nonpolarizable Force Fields for Ionic Liquids

The nonpolarizable force field of ionic liquids is tuned by using the self-consistent scheme of molecular dynamics (MD) simulation and first-principles calculation based on the order-N density functional theory (DFT). The atomic charges are determined by using the whole MD cell for DFT calculation and accounts effectively for the many-body effects of charge transfer and intramolecular polarization. The charges represent effective interactions in the condensed phase within the framework of the nonpolarizable force field and can be an alternative for an explicitly many-body model incorporating, for example, polarizability. Here we demonstrate the performance of nonpolarizable force field determined with the MD-DFT self-consistent scheme in imidazolium-, pyrrolidinium-, and ammonium-based ionic liquids. The variation ranges of molecular charges are much larger with the compositions of the ionic liquid than with the thermodynamic conditions, and the charge-ordering structures become systematically weaker with the effective charges. For energetic properties, while the calculated heat of vaporization depends on the atomic and molecular charges, the corresponding heat capacity is not strongly affected by the DFT-based variation. For transport properties, the self-diffusion coefficient, electrical conductivity, and viscosity vary much more in the self-consistent scheme. The effective DFT charge is observed to enhance the fluidity of ionic liquids and improve the accuracy of electrical conductivity and viscosity. This is due to the weakened interactions among the ions, and the too slow motions observed with a full-charge model are well corrected through the iteration of MD and DFT. We therefore conclude that the set of nonpolarizable force fields obtained with the MD-DFT self-consistent scheme leads to better description of transport properties of ionic liquids.

Dynamics and Vibrational Spectroscopy of Alcohols in Ionic Liquids: Methanol and Ethanol

The structure, dynamics, and vibrational spectroscopy of dilute HOD, methanol, and ethanol in the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [emim][NTf₂], ionic liquid (IL) are investigated with molecular dynamics (MD) simulations. The structure of the ILs around the solutes is qualitatively similar, where the OD bond of the deuterated alcohols donates an interaction to an [NTf₂] anion and the [emim] cations interact with the oxygen atom of the OD group. The slowest time scale for the reorientational dynamics of the OD bond varied considerably for HOD, methanol, and ethanol (27, 71, and 87 ps, respectively). In contrast, the slowest time scales for spectral diffusion of the OD vibrational frequency were 11 ps for each of the three solutes, which indicates that the dynamics of the IL is relatively unchanged by the presence of the alcohols at dilute concentration. The theoretical results for the reorientational and spectral diffusion dynamics compare favorably with prior two-dimensional infrared (2D IR) spectroscopic measurements.

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.

Cation effect on small phosphonium based ionic liquid electrolytes with high concentrations of lithium salt

Ionic liquid electrolytes with high alkali salt concentrations have displayed some excellent electrochemical properties, thus opening up the field for further improvements to liquid electrolytes for lithium or sodium batteries. Fundamental computational investigations into these high concentration systems are required in order to gain a better understanding of these systems, yet they remain lacking. Small phosphonium-based ionic liquids with high concentrations of alkali metal ions have recently shown many promising results in experimental studies, thereby prompting us to conduct further theoretical exploration of these materials. Here, we conducted a molecular dynamics simulation on four small phosphonium-based ionic liquids with 50 mol. % LiFSI salt, focusing on the effect of cation structure on local structuring and ion diffusional and rotational dynamics-which are closely related to the electrochemical properties of these materials.

Rheology of phosphonium ionic liquids: a molecular dynamics and experimental study

Comparison between the theoretical and experimental viscosity of an ionic liquid.

Capturing the effect of [PF3(C2F5)3]−vs. [PF6]−, flexible anion vs. rigid, and scaled charge vs. unit on the transport properties of [bmim]+-based ionic liquids: a comparative MD study

Effect of [PF₃(C₂F₅)₃]⁻vs. [PF₆]⁻, flexible anion vs. rigid, and scaled charge vs. unit on the transport properties of ILs.

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.

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc.

A relationship between the force curve measured by atomic force microscopy in an ionic liquid and its density distribution on a substrate

A relationship between the force curve measured in an ionic liquid and the solvation structure is studied. Applying the obtained relationship, candidates of the solvation structure are estimated from a measured force curve.