Computational insight into the effect of alkyl chain length in tetraalkylammonium-based deep eutectic solvents

The effect of the increase in the alkyl chain length of cation on the properties of deep eutectic solvents based on ethylene glycol has been investigated employing classical molecular dynamics simulations. The change in the structural and dynamic properties in both the bulk and liquid-vapor interface is explored through various analyses. The interaction between the anion and the ethylene glycol increases with an increase in the alkyl chain length of the cation, as observed in the increase of the lifetime of the hydrogen bond formed between the two. The terminal carbon atoms are found to be closer to each other when the cation changes from tetraethylammonium to tetrabutylammonium. The cations are located closer to the interface, and the association of the alkyl chains becomes more significant with increased alkyl chain length, decreasing the surface tension values.

Effect of electronegative atoms on π - π stacking and hydrogen bonding behavior in simple aromatic molecules - An Ab initio MD study

Ab initio molecular dynamics studies have been performed on fluorobenzene, phenol, and aniline, which have the three most electronegative atoms, fluorine, oxygen, and nitrogen, respectively. Radial distribution functions show strong hydrogen bonding in the phenolic -OH group, whereas it is less prominent in the -NH2 group of aniline. Fluorobenzene does not show strong hydrogen bonds as no solvation shell is found between the fluorine atom and different aromatic hydrogens of the molecule. Spatial distribution functions show that the nitrogen atom of aniline interacts with the aromatic plane, the oxygen atom of phenol is concentrated near the -OH group and fluorobenzene's fluorine atom interacts with the para hydrogen. Liquid phase dimer structures of these systems reveal that perpendicular orientation (Y-shaped) is preferred over parallel ones. Almost half of the total dimer population tends to prefer 90∘±30° angle. H-bond analyses show that fluorobenzene has the longest mean H-bond lifetime for the H-bond between the aromatic hydrogens and the fluorine atoms, whereas the aniline has the least. The mean lifetime between aromatic hydrogens and electronegative atoms increases steadily from aniline to fluorobenzene. Phenolic -OH and amino -NH2 groups show considerably longer mean H-bond lifetime than the aromatic hydrogens. Gas-phase binding energies obtained from quantum chemical calculations show that aniline and phenol dimers have higher binding energy values than the fluorobenzene dimer. Only the phenol dimer shows a perpendicular structure as a stable one, while aniline and fluorobenzene prefer the parallel orientation.

Deciphering the Role of Anions of Ionic Liquids in Modulating the Structure and Stability of ct-DNA in Aqueous Solutions

Stabilizing biomolecules under ambient conditions can be extremely beneficial for various biological applications. In this context, the utilization of ionic liquids (ILs) in enhancing the stability and preservation of nucleic acids in aqueous solutions is found to be promising. While the role of the cationic moiety of ILs in the said event has been thoroughly explored, the importance of the anionic moiety in ILs, if any, is rather poorly understood. Herein, we examine the function of anions of ILs in nucleic acid stabilization by examining the stability and structure of calf thymus-DNA (ct-DNA) in the presence of various ILs composed of a common 1-ethyl-3-methylimidazolium cations (Emim+) and different anions, which includes Cl-, Br-, NO 3 - , Ac - , HS O 4 - and B F 4 - by employing various spectroscopic techniques as well as Molecular Dynamics (MD) simulation studies. Analysis of our data suggests that the chemical nature of anions including polarity, basicity, and hydrophilicity become an important factor in the overall DNA-IL interaction event. At lower concentrations, the interplay of intermolecular interaction between the IL anions with their respective cations and the solvent molecules becomes a very crucial factor in inducing their stabilizing effect on ct-DNA. However, at higher concentrations of ILs, the ct-DNA stabilization is additionally governed by specific-ion effect. MD simulation studies have also provided valuable insights into molecular-level understanding of the DNA-IL interaction event. Overall, the present study clearly demonstrated that along with the cationic moiety of ILs, the anions of ILs can play a significant role in deciding the stability of duplex DNA in aqueous solution. The findings of this study are expected to enhance our knowledge on understanding of IL-DNA interactions in a better manner and will be helpful in designing optimized IL systems for nucleic acid based applications.

Interaction of the tau fibrils with the neuronal membrane

Tau proteins are recently gaining a lot of interest due to their active role in causing a range of tauopathies. Molecular mechanisms underlying the tau interaction with the neuronal membrane are hitherto unknown and difficult to characterize using experimental methods. Using the cryo-EM structure of the tau-fibrils we have used atomistic molecular dynamics simulation to model the tau fibril and neuronal membrane interaction using explicit solvation. The dynamics and structural characteristics of the tau fibril with the neuronal membrane are compared to the tau fibril in the aqueous phase to corroborate the effect of the neuronal membrane in the tau structure. Tau fibrils have been modelled using CHARMM-36m force field and the six component neuronal membrane composition is taken from the earlier simulation results. The timescale conceivable in our molecular dynamics simulations is of the order of microseconds which captures the onset of the interaction of the tau fibrils with the neuronal membrane. This interaction is found to impact the tau pathogenesis that finally causes neuronal toxicity. Our study initiates the understanding of tau conformational ensemble in the presence of neuronal membrane and sheds the light on the significant tau-membrane interactions.

Understanding the screening effect of aqueous DES on the IDPs: A molecular dynamics simulation study using amyloid β42 monomer

Deep eutectic solvents (DESs) have emerged as the promising replacement to the ionic liquids in solvent engineering for bio-compatibility. We aim to understand the effect of aqueous deep eutectic solvents on the conformation of intrinsically disordered proteins (IDPs). In this context, we have studied the effect on amyloid beta (Aβ₄₂) monomer in the hydrated DES composed of tetrabutylammonium chloride and ethylene glycol in a 3:1 ratio using all-atom molecular dynamics simulations. DES is found to effectively screen the interaction of four zones of the amyloid beta monomer with water. Water molecules and the DES constituents modulate the local protein-solvent interactions, in the solvation shell of the protein. In addition, the aqueous DES medium conserves the secondary structure of the Aβ₄₂ monomer by increasing the intramolecular hydrogen bonding and D23-K28 salt-bridge interactions when compared to the pure water medium. The current study provides insights into the impact of DES in stabilizing an IDP, at molecular level. We envisage the hindered aggregation of the amyloid beta structures in DES medium over the pure water medium due to the screening of hydrophobic intramolecular interactions.

Understanding the conformational changes in the influenza B M2 ion channel at various protonation states

The characterization of influenza (A/B M2) ion channels is very important as they are potential binding sites for the drugs. We report the all-atom molecular dynamics study of the influenza B M2 ion channel in the presence of explicit solvent and lipid bilayers using the high resolution solid-state NMR structures. The importance of the various protonation states of histidine in the activation of the ion channel is discussed. The conformational changes at the closed and the open structures clearly show that the increase in tilt angle is necessary for the activation of the ion channel. Additionally, the free energy surfaces of the eight systems show the importance of the protonation state of the histidine residues in the activation of the influenza B M2 ion channel. The protonation of the histidine residues increases the tilt angle and the intra-helix distance which is evident from the superimposition of the structures corresponding to the maxima and the minima in the free energy landscape. The findings imply differences in the singly protonated and double protonated conformational states of BM2 ion channel and provide insights to help further studies of these ion channels as the drug targets for the influenza virus.

The effect of external salts on the aggregation of the multiheaded surfactants: All-atom molecular dynamics studies

Tailoring the molecular design of the surfactants leads to changes in the aggregation properties. The role of external salts on the aggregation properties of the multiheaded surfactants is investigated using molecular dynamics simulations. The multiheaded surfactants show differential aggregation properties on addition of external salts, as reported earlier from experimental studies. We have modelled the multiheaded surfactants to study the effect of external salts (potassium bromide and sodium salicylate) at three different concentrations using the all-atom modelling and explicit solvation. The influence of external salts on the hydration and aggregation propensity, hydrogen bonding, and the structural characteristics of the surfactant aggregates are probed using various analyses across the four groups of multiheaded surfactants. The larger salicylate ion masks the repulsion between the cationic head groups and acts as an effective promoter of aggregation.

Helix-coil transition and conformational deformity in Aβ42-monomer: a case study using the Zn2+ cation

The metal ions (like Fe2+, Zn²⁺, Cu2+) are known to influence the amyloid beta (Aβ) aggregation. In this study, we have examined the conformational and dynamical changes during the coordination of Aβ-monomer with the Zn2+ ion using all-atom molecular dynamics (MD) simulations using explicit solvent models. We have probed the unfolding of the full-length Aβ₄₂ monomer both inclusive and exclusive of the Zn2+ cation, with 1:1 ratio of the peptide and the Zn2+ cation. The inclusion of the Zn2+ cation shows differential intra-peptide interactions which has been probed using various analyses. The Helix - Coil transition of the wild type Aβ42 monomer is studied using the steered molecular dynamics simulations by taking the end-to-end C-α distance across the peptide. This gives an idea of the unequal intra - peptide and peptide - water interactions being found across the length of the Aβ monomer. The transition of an α-helix dominated wild-type (WT) Aβ structure to the unfolded coil structure gives significant evidence of the intra-peptide hydrogen bonding shifts in the presence of the Zn2+ cation. This accounts for the structural and the dynamical variations that take place in the Aβ monomer in the presence of the Zn2+ cation to mimic the conditions/environment at the onset of fibrillation.Communicated by Ramaswamy H. Sarma.

Exploring the candidates for a new protein folding - cross-α amyloid - in available protein databases

Amyloid fibrils are formed from the assembly of soluble proteins and are responsible for many diseases. They are known to have a cross-β structure, where the fibril runs perpendicular to the β-sheets. A new type of tertiary structure formed by the aggregation of peptides in their α-helical form, in naturally occurring as well as synthetic peptides, termed cross-α amyloid has been reported recently. We have studied the interactions responsible for the formation of these cross-α amyloids and proposed a model to determine the peptides that could form these structures. Eight such peptides obtained using the model have been shown to form a cross-α structure using molecular dynamics simulations. The formation of a cross-α structure from eight copies of a randomly chosen peptide and its stability over a microsecond simulation have been demonstrated. A software named Cross-Alpha-Det has been developed that can determine whether a protein can form a cross-α structure from its secondary structure.

Self-Assembly of Cations in Aqueous Solutions of Multiheaded Cationic Surfactants: All Atom Molecular Dynamics Simulation Studies

Self-assembly of multiheaded surfactants in aqueous solutions has been investigated using atomistic molecular dynamics simulations. The model multiheaded surfactants contain multiple head groups ranging from one to four for a single tail group. Increase in the number of charged head groups has substantial consequences in the aggregation properties of surfactants in their aqueous solutions. Polydisperse aggregates of surfactants are formed in the aqueous solution. The shape and size of the aggregates are dictated by the number of charged head groups present in the surfactant. Our simulations demonstrate that with the increase in the number of charged head groups on the surfactants, the aggregation number decreases, which corroborates previous experimental and theoretical studies. Though experimental studies on the surfactant with four head groups is yet to be performed, we have included the surfactant having four head groups in our studies and compared the results with previous coarse-grained computational study involving four head groups.

Effect of spacer chain length on the liquid structure of aqueous dicationic ionic liquid solutions: molecular dynamics studies

Cations in an aqueous [C₁₆(MIm)₂][2Br] solution aggregate spontaneously to form micelles, with a hydrophobic core composed of spacer alkyl chains and a hydrophilic surface composed of imidazolium head groups.

Segregation of ions at the interface: molecular dynamics studies of the bulk and liquid–vapor interface structure of equimolar binary mixtures of ionic liquids

Ions in an equimolar binary mixture of [emim][TfO] and [omim][TfO] segregate at the liquid–vapor interface to form a hydrophobic surface composed of octyl chains.

Ionic liquids at nonane-water interfaces: molecular dynamics studies

The structures of ternary systems with water, nonane, and an ionic liquid, with the ionic liquid placed between water and nonane, have been studied using atomistic molecular dynamics simulations. Three different ionic liquids with 1-n-butyl-3-methylimidazolium cation and bromide, tetrafluoroborate, and trifluoromethanesulfonate anions have been studied. The ionic liquids disperse into the aqueous phase quickly and are solubilized in water within 15 ns to form two equivalent nonane-aqueous ionic liquid interfaces. The interfacial region is enriched with ionic liquids due to the amphiphilicity of the cations. The presence of ionic liquids at the interface reduces the interfacial tension between the nonane and water, thus facilitating the mixing of aqueous and nonane phases. The reduction in the interfacial tension is found to be inversely related to the solubility of the corresponding ionic liquid in water. The butyl chains of the cations and the trifluoromethanesulfonate anions present in the interfacial region are found to be preferentially oriented parallel to the interface normal.

Refined potential model for atomistic simulations of ionic liquid [bmim][PF6]

Refined parameters of an atomistic interaction potential model for the room temperature ionic liquid 1-n-butyl,3-methylimidazolium hexafluorophosphate are presented. Classical molecular dynamics simulations have been carried out to validate this fully flexible all-atom model. It predicts the density of the liquid at different temperatures between 300 and 500 K within 1.4% of the experimental value. Intermolecular radial distribution functions and the spatial distribution functions obtained from the new model are in close agreement with ab initio simulations. The calculated diffusion coefficients of ions and the surface tension of the liquid agree well with experiment.

Dynamics in a room-temperature ionic liquid: a computer simulation study of 1,3-dimethylimidazolium chloride

The transport properties and solvation dynamics of model 1,3-dialkylimidazolium chloride melt at 425 K is studied using molecular-dynamics simulations. Long trajectories of a large system have been generated and quantities such as the self-diffusion coefficient of ions, shear viscosity, and ionic conductivity have been calculated. Interestingly, the diffusion of the heavier cation is found to be faster than the anion, in agreement with experiment. The interaction model is found to predict a higher viscosity and lower electrical conductivity compared to experimental estimates. Analysis of the latter calculations points to correlated ion motions in this melt. The solvation time correlation function for dipolar and ionic probes studied using equilibrium simulations exhibits three time components, which include an ultrafast (subpicosecond) part as well as one with a time constant of around 150 ps. The ultrafast solvent relaxation is ascribed to the rattling of anions in their cage, while the slow component could be related to the reorientation of the cations as well as to ion diffusion.

Insights into the Structure and Dynamics of a Room-Temperature Ionic Liquid: Ab Initio Molecular Dynamics Simulation Studies of 1-n-Butyl-3-methylimidazolium Hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]−CO2 Mixture

Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.

Layering at an Ionic Liquid−Vapor Interface: A Molecular Dynamics Simulation Study of [bmim][PF6]

The structure of the planar liquid-vapor interface of a room-temperature ionic liquid, 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]), is studied using atomistic molecular dynamics simulations. Layering of the ions at the interface is observed as oscillations in the corresponding number density profiles. These oscillations, however, are diminished in amplitude in the electron density profile, due to a near cancellation in the contributions from the anions and the cations. An enhancement by 12% in the electron density at the interface over its value in the bulk liquid is observed, in excellent agreement with X-ray reflectivity experiments. The anions are found to predominantly contribute to this increase in the interfacial electron density. The cations present at the interface are oriented anisotropically. Their butyl chains are observed to be preferentially oriented along the interface normal and to project outside the liquid surface, thus imparting a hydrophobic character. In the densest region of the interface, the imidazolium ring plane is found to lie parallel to the surface normal, in agreement with direct recoil spectroscopy experiments.