Tracing the Effect of Replacing [Gly]- with [Ala]- and Hydroxylation of [emim]+ on the Fine-Tuning of the Transport Properties of the Corresponding Amino Acid-Based Ionic Liquids Using MD Simulation.

Natural amino acid-based ionic liquids (AAILs) composed of deprotonated amino acids, [AA]-, as anions and hydroxylated imidazolium cations provide an eco-friendly nontoxic IL family with the growing number of chemical and biochemical revolutionary applications. In this paper, the transport properties of four AAILs composed of 1-(2-hydroxyethyl)-3-methylimidazolium ([HOemim]+) and 1-ethyl-3-methylimidazolium ([emim]+) cations with alaninate and glycinate anions were studied by molecular dynamics (MD) simulations. A nonpolarizable all-atom force field with the scaled charge (±0.8e) on each of the ions was applied and compared with the unit charge model in some cases. The tunable effects of the presence of the hydroxyl group in the side chain of the imidazolium cation, the type of amino acid anion, and the varied temperature on the dynamical behavior of AAILs were investigated in detail. The experimentally compatible trends of the simulated ionic self-diffusion coefficients, ionic conductivity, and ionicity were found to be inverse to the viscosity and ionic association of these ILs as [emim][Gly] > [emim][Ala] > [HOemim][Gly] > [HOemim][Ala]. The main reason behind these trends is the higher ability of the hydroxylated cation for the hydrogen-bond formation with [AA]-. The mean square displacement (MSD), self-diffusion, and transference number of imidazolium cations are larger than those of [AA]- anions, except in the case of [HOemim][Gly]. It was found that the activation energy for diffusion of [AA]- is lower than that of [HOemim]+ but higher than that of [emim]+ in [HOemim][AA] and [emim][AA] ILs, respectively. The computed velocity autocorrelation function (VACF) showed that [Gly]-, as the lightest ion, has the shortest mean collision time and velocity randomization time among the ions, especially in the [HOemim][Gly] IL. Replacing [emim]+ with [HOemim]+, similar to the effect of decreasing temperature, causes significant decreasing of the ionic self-diffusion and increasing of the well depth of the first minimum of the ionic VACFs. Current findings show that introducing suitable functional groups in the side chain of imidazolium cations can be a viable approach for efficient engineering design and fine-tuning of the transport properties of these AAILs.

Tracing the origin of heterogeneities in the local structure and very sluggish dynamics of [Cho][Gly] ionic liquid confined between rutile and graphite slit nanopores: A MD study.

Atomistic-level understanding of the interfacial behavior of ionic liquids (ILs) confined in slit-like nanopores is of both fundamental and practical interest. Molecular dynamics (MD) is an efficient and robust approach to characterize the properties of confined systems in contrast with some limitations in direct experimental measurements at low-dimensions. In this research, MD simulations are used to study the biocompatible IL cholinium glycinate, [Cho][Gly], confined between two parallel plates of rutile or graphite, with the separation distance of 24 Å along the z-direction. As expected, both the microscopic local structure and dynamical behavior of the confined IL are very heterogeneous and depend effectively on the position of the ions to the pore walls. The ion z-density profile is used for segmentation of the inter-wall space into a central region and two outer layers. The behavior of ions in the central region is very similar to the bulk IL, while the behavior of the arranged ionic layers adjacent to the pore walls shows the clear deviation from the bulk IL due to confinement. In general, the confined IL shows a "solid-like" dynamics at T = 353 K, especially in the outer layers near the walls as well as in the z-direction. The presence of the "IL-rutile wall" electrostatic interaction and hydrogen bonding (H-bonding) causes a significant difference in the local structure and very sluggish dynamics of the IL adjacent to the rutile walls vs the graphite walls. Simulation reveals a significant decrease in the average number of key cation-anion H-bonds at the outer layers relative to the central regions of both confined systems. The recognized [Cho]+⋯[Gly]-⋯[Cho]+ bridge structure at the central region is lost in the vicinity of the rutile walls due to inaccessibility of the hydroxyl hydrogen atom, which forms a stable H-bond with the rutile oxygen site. However, another unprecedented [Gly]- bridge is confirmed and preserved near the graphite walls, and [Cho]+ cations prefer to stay parallel to the wall surface to form the van der Waals dispersion interactions with the uncharged graphite walls.

Molecular Dynamics Insights into the Nanoscale Structural Organization and Local Interaction of Aqueous Solutions of Ionic Liquid 1-Butyl-3-methylimidazolium Nitrate.

Considering the growing number of applications of the aqueous ionic liquids (ILs), atomistic molecular dynamics (MD) simulations were used to probe the effect of water molar fraction, xw, ranging from 0.00 to 0.90, on the nanoscale local structure of 1-butyl-3-methylimidazolium nitrate, [bmim][NO3], IL. The results prove that, with water addition, the cation-anion, cation-cation, and anion-anion structural correlations are weakened, while strong anion-water and unconventional cation-water hydrogen bonds are formed in the solutions. Water molecules were detected as bridges between nitrate anions, and the water cluster size distribution at different xw's was investigated. Simulation shows a similar pattern of probability densities for water and anion around the acidic hydrogen atoms of the reference cation ring, while both species move away from the cation butyl chain. Increasing the water concentration to xw = 0.90 causes decreasing of the local arrangement of the nearest-neighboring cations, because of the weakening of cation-cation π-π stacking. In addition, this dilution reduces the probability of the in-plane cation-anion conformation, disrupts both the polar ionic network and nonpolar domains, and diminishes the nanoaggregation of the cation butyl chains compared to those of the neat IL. These results can rationalize the origins of the fluidity enhancements and transport property trends upon adding water to the imidazolium-based ILs. The current study proposes a deep atomistic-level insight into the complex coupling between water concentration, microscopic structure, and local interactions of aqueous imidazolium-based ILs with hydrophilic anions.

Tracing Local Nanostructure of the Aqueous Solutions of the Biocompatible [Cho][Gly] Ionic Liquid: Importance of Hydrogen Bond Attraction between Like-Charged Ions.

The neat and aqueous solutions of the cholinium glycinate ionic liquid (IL), [Cho][Gly], at different water mole fractions, xws, are studied by molecular dynamics simulations. The changes in the local nanostructure of systems with composition have been determined by calculation of various structural distribution functions. Hydrogen bond (H-bond) attractions determine the major relative orientations of the oppositely and like charged nearest neighbors. The cation-anion H-bonds mainly form between the hydrogen of the hydroxyl or methyl groups of the cation and the carboxylate oxygen of the anion. A preferred (antiparallel) arrangement between adjacent [Cho]+ cations is due to the effective H-bond between the hydroxyl oxygen and the methyl hydrogen sites that promotes the like-charge cluster formation. Adding water decreases the occurrence probability of the [Cho]+···[Gly]-···[Cho]+ bridge structure in the aqueous solutions due to the formation of the [Gly]-···HOH···[Gly]- structure via H-bonding. Observed density trend versus xw is interpreted based on an interstice model and investigating the water cluster size distribution. Finally, the effect of xw on the infrared (IR) vibrational spectra were studied and blue and red shifts were observed for the stretching and bending vibrational modes of the hydroxyl group of [Cho]+, respectively. Current findings will improve the efficient engineering design and task-specific applications of aqueous solutions of bio-ILs consist of [Cho]+ and amino acid anions.

Molecular dynamics simulations of nano-confined methanol and methanol-water mixtures between infinite graphite plates: Structure and dynamics.

Molecular dynamics simulations are used to investigate microscopic structures and dynamics of methanol and methanol-water binary mixture films confined between hydrophobic infinite parallel graphite plate slits with widths, H, in the range of 7-20 Å at 300 K. The initial geometric densities of the liquids were chosen to be the same as bulk methanol at the same temperature. For the two narrowest slit widths, two smaller initial densities were also considered. For the nano-confined system with H = 7 Å and high pressure, a solid-like hexagonal arrangement of methanol molecules arranged perpendicular to the plates is observed which reflects the closest packing of the molecules and partially mirrors the structure of the underlying graphite structure. At lower pressures and for larger slit widths, in the contact layer, the methanol molecules prefer having the C-O bond oriented parallel to the walls. Layered structures of methanol parallel to the wall were observed, with contact layers and additional numbers of central layers depending on the particular slit width. For methanol-water mixtures, simulations of solutions with different composition were performed between infinite graphite slits with H = 10 and 20 Å at 300 K. For the nanoslit with H = 10 Å, in the solution mixtures, three layers of molecules form, but for all mole fractions of methanol, methanol molecules are excluded from the central fluid layer. In the nanopore with H = 20 Å, more than three fluid layers are formed and methanol concentrations are enhanced near the confining plates walls compared to the average solution stoichiometry. The self-diffusion coefficients of methanol and water molecules in the solution show strong dependence on the solution concentration. The solution mole fractions with minimal diffusivity are the same in confined and non-confined bulk methanol-water mixtures.

Fine probing the effect of replacing [PF6]- with [PF3(C2F5)3]- on the local structure and nanoscale organization of [bmim]+-based ionic liquids using MD simulation.

Comparative all-atom molecular dynamics simulations are used to study the microscopic local structure and interionic interactions of two ionic liquids (ILs) composed of the 1-butyl-3-methylimidazolium cation, [bmim]+, coupled with the hexafluorophosphate, [PF6]-, or tris(pentafluoroethyl)trifluorophosphate, [FAP]-, anions. Respective distribution functions clearly reveal that the structural correlations between the cation and anion decrease when (i) replacing [PF6]- with [FAP]-, (ii) scaling the partial atomic charges, and (iii) considering the anion's structural flexibility versus rigidity. Replacement of [PF6]- with [FAP]- expands the nonpolar domains totally and causes the decreasing of the three-dimensional polar networks as well as the diminishing of the nano-aggregation of cation side chains. Current simulations show that with increasing the anion size and its charge delocalization, the probability of the in-plane cation-anion conformation, its related hydrogen bond acceptor ability, and the cation-cation π-π interaction decreases in accordance with the fluidity enhancements of the corresponding imidazolium-based IL. Hence, structural findings can explain and justify rationally the origins of the observed trends in the simulated dynamical properties of these ILs in our previous report. A complete understanding of the microscopic structure of ILs is necessary to control the outstanding properties of ILs as designer solvents that will support experimentalists for the best engineering design and a breakthrough efficiency of IL-related processes.

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.

Comprehensive molecular dynamics simulations are performed to study the average single-particle dynamics and the transport properties of 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF6], and 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate, [bmim][FAP], ionic liquids (ILs) at 400 K. We applied one of the most widely used nonpolarizable all-atom force fields for ILs, both with the original unit (±1) charges on each ion and with the partial charges uniformly scaled to 80-85%, taking into account the average polarizability and tracing the experimentally compatible transport properties. In all simulations, [bmim]+ was considered to be flexible, while the effect of a flexible vs. rigid structure of the anions and the effect of two applied charge sets on the calculated properties were separately investigated in detail. The simulation results showed that replacing [PF6]- with [FAP]-, considering anion flexibility, and applying the charge-scaled model significantly enhanced the ionic self-diffusion, ionic conductivity, inverse viscosity, and hyper anion preference (HAP). Both of the calculated self-diffusion coefficients from the long-time linear slope of the mean-square displacement (MSD) and from the integration of the velocity autocorrelation function (VACF) for the centers of mass of the ions were used for evaluation of the ionic transference number, HAP, ideal Nernst-Einstein ionic conductivity (σNE), and the Stokes-Einstein viscosity. In addition, for quantification of the degree of complicated ionic association (known as the Nernst-Einstein deviation parameter, Δ) and ionicity phenomena in the two studied ILs, the ionic conductivity was determined more rigorously by the Green-Kubo integral of the electric-current autocorrelation function (ECACF), and then the σGK/σNE ratio was evaluated. It was found that the correlated motion of the (cationanion) neighbors in [bmim][FAP] is smaller than in [bmim][PF6]. The relaxation times of the normalized reorientational autocorrelation functions were computed to gain a deep, molecular-level insight into the rotational motion of the ions. The geometric shape of the ion is a key factor in determining its reorientational dynamics. [bmim]+ shows faster translational and slower rotational dynamics in contrast to [PF6]-.

Systematic evaluation and refinement of existing all-atom force fields for the simulation of liquid acetonitrile.

The reliability of a molecular dynamics (MD) simulation study mainly depends on the accuracy of the applied force field. Unlike the ability of some potential models for reasonably predicting the thermodynamic properties of acetonitrile (ACN), simulated dynamical properties such as self-diffusion are generally underestimated compared to experimental values. The present work focuses on the evaluation and refinement of several available all-atom force fields for ACN and proposes a refined flexible six-site potential model. The main modification is related to the reduction of intermolecular LJ parameters (σ and ɛ) for hydrogen atoms, especially ɛ, significantly affecting the dynamical behavior. Besides, the adjustment of σ and ɛ for nitrile carbon and nitrogen atoms helps reach optimum results. Our refined model shows an excellent agreement with the experiment for self-diffusion coefficient and thermodynamic quantities as well as providing a qualitative description of the microscopic structure of liquid ACN. © 2018 Wiley Periodicals, Inc.

Tracing Dynamics, Self-Diffusion, and Nanoscale Structural Heterogeneity of Pure and Binary Mixtures of Ionic Liquid 1-Hexyl-2,3-dimethylimidazolium Bis(fluorosulfonyl)imide with Acetonitrile: Insights from Molecular Dynamics Simulations.

All-atom molecular dynamics (MD) simulations of the ionic liquid (IL) 1-hexyl-2,3-dimethylimidazolium bis(fluorosulfonyl)imide ([C6mmim][FSI]) and its binary mixtures with acetonitrile (ACN) have been reported for the first time. The presence of ACN as a cosolvent, similar to the effect of increasing temperature, causes enhancements in the ion translational motion and fluidity of the IL, leading to significant improvement of ionic conductivity and self-diffusion, which is well explained by a microscopic structural analysis. In neat IL and a concentrated IL mixture, self-diffusion of the cation is higher than that of the corresponding anion; however, further addition of ACN into the diluted mixtures with IL molar fractions (xIL's) below 0.50 results in more weakened interactions among the nearest ACN-anion neighbors compared to those among the ACN-cation neighbors so that the number of isolated anions is more than that of isolated cations under this condition, and the anions diffuse faster than the cations, as expected on the basis of their relative sizes. The velocity autocorrelation function analysis indicates an inverse relation between xIL and the mean collision time of each species. Additionally, at a fixed xIL, both the mean collision time and velocity randomization time of ACN are shorter than those of the ions. Gradual addition of ACN changes the morphology of nanosegregated domains and tends to disrupt ionic clusters (i.e., it scatters and decomposes both the polar and nonpolar domains) compared with pure IL, whereas both the radial and spatial distribution functions show the stabilization role of ACN in the close-contact ion-pair association. On the other hand, increasing ACN causes weakening of the structural correlations of the cation-cation and anion-anion neighbors in the solutions. ACN molecules appeared as a bridge, with balanced affinities between the polar and nonpolar domains, and no indication was observed for aggregation of ACN molecules in the studied mixtures that can rationalize good miscibility with imidazolium-based ILs.