The Effect of Urea on the Structure of Water: A Molecular Dynamics Simulation

Widom Line in Supercritical Water in Terms of Changes in Local Structure: Theoretical Perspective

Performing molecular dynamics simulations with the TIP4P/2005 water model along 9 isobars (from 175 to 375 bar) in the temperature range between 300 and 1100 K, we have found that the loci of the extrema in the rate of change of specific structural properties can be used to define purely structure-based Widom lines. We have examined several parameters that describe the local structure of water, such as the tetrahedral arrangement, nearest neighbor distance, local density around the molecules, and the size of the largest dense domain. The last two parameters were determined using the Voronoi polyhedral and density-based spatial clustering of applications with noise methods, respectively. By analyzing the moments of the associated distributions, we show that along a given isobar, the temperature at which we observe a maximum in the fluctuation, the rate of change of the average values, or in the skewness values unambiguously determines the Widom line that is in agreement with the experimentally detected, thermodynamic response function-based ones.

Counteracting Effects of Trimethylamine N-Oxide against Urea in Aqueous Solutions: Insights from Theoretical Two-Dimensional Infrared Spectroscopy

The study of small osmolytes in their aqueous solutions has gained significant attention because of their relevance to structure and thermodynamics of proteins in aqueous media. Special attention has been given to the binary and ternary aqueous solutions of urea and trimethylamine N-oxide (TMAO). Urea is a well-known protein denaturant, while TMAO protects proteins in their native states. Interestingly, TMAO counteracts urea's ability to denature proteins when present in solutions with approximately half of the concentration of urea. Vibrational spectroscopy can improve our understanding of the molecular origin of this counteracting effect because of its sensitivity to local structure and dynamics. We present results of theoretical linear vibrational and two-dimensional infrared (2DIR) spectroscopy of water in the binary and ternary aqueous solutions of TMAO and urea. The 2DIR spectra are calculated using the electronic structure/molecular dynamics approach. The non-Condon effects in spectral transitions are incorporated in the theoretical calculations of 2DIR spectra. It is found that TMAO disrupts the local structure of water, while urea leaves it essentially unaffected. The 2DIR results show that both TMAO and urea slow down the dynamics of spectral diffusion of water. The extent of slowing down is found to be particularly significant for both hydration and bulk water in the presence of TMAO which can be attributed to strong hydrogen bonds between the water and TMAO molecules. The water molecules present in the hydration layer of the solutes in the ternary solutions are found to relax at even slower rates compared to that in their binary solutions in water. The hydrogen bonds between TMAO and urea are found to be not stable. Thus, the counteracting effect of TMAO against urea is seen to take place mainly through water-mediated interactions. Such TMAO-induced effects giving rise to more structured and slower hydrogen-bonded network are successfully captured through 2DIR spectroscopic calculations.

Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study

Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.

Urea Disrupts the AOT Reverse Micelle Structure at Low Temperatures

Aside from its prominent role in the excretory system, urea is also a known protein denaturant. Here, we characterize urea as it behaves in confined spaces of AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reverse micelles as a model of tight, confined spaces found at the subcellular level. Dynamic light scattering revealed that low temperatures (275 K) caused the smallest of the reverse micelle sizes, w₀ = 10, to destabilize and dramatically increase in apparent hydrodynamic diameter. We attribute this to urea embedded into the surfactant interface as confirmed by 2D ¹H-NOESY NMR spectroscopy. This increase in size in turn caused the hydrogen exchange between urea and water within the nanosized reverse micelles to increase as measured by 1D EXSY-NMR. A minimal enlarging effect and no increase in hydrogen exchange were observed when aqueous urea was introduced into w₀ = 15 or 20 reverse micelles, suggesting that this effect is unique to particularly small-diameter spaces (∼7 nm).

Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence

In this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme—hewl) and unfolded protein models (glycine—GLY and N-methylglycine—NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with caution. We isolated the spectral share of water changed simultaneously by the biomacromolecule/model molecule and the osmolyte, which allowed us to provide unambiguous experimental arguments for the mechanism of stabilization/destabilization of proteins by osmolytes. In the case of both types of osmolytes, the decisive factor determining the equilibrium folded/unfolded state of protein was the enthalpy effect exerted on the hydration spheres of proteins in both forms. In the case of stabilizing osmolytes, enthalpy was also favored by entropy, as the unfolded state of a protein was more entropically destabilized than the folded state.

Direct Observation of the Orientation of Urea Molecules at Charged Interfaces

Dissolving urea into water induces special solvation properties that play a crucial role in many biological processes. Here we probe the properties of urea molecules at charged aqueous interfaces using heterodyne-detected vibrational sum-frequency generation (HD-VSFG) spectroscopy. We find that at the neat water/air interface urea molecules do not yield a significant sum-frequency generation signal. However, upon the addition of ionic surfactants, we observe two vibrational bands at 1660 and 1590 cm^-1 in the HD-VSFG spectrum, assigned to mixed bands of the C═O stretch and NH₂ bend vibrations of urea. The orientation of the urea molecules depends on the sign of the charge localized at surface and closely follows the orientation of the neighboring water molecules. We demonstrate that urea is an excellent probe of the local electric field at aqueous interfaces.

Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis

Water structure in aqueous osmolyte solutions, deduced from the slight alteration in the water-water radial distribution function, the decrease in water-water hydrogen bonding, and tetrahedral ordering based only on the orientation of nearest water molecules derived from the molecular dynamics simulations, appears to have been perturbed. A careful analysis, however, reveals that the hydrogen bonding and the tetrahedral ordering around a water molecule in binary solutions remain intact as in neat water when the contribution of osmolyte-water interactions is appropriately incorporated. Furthermore, the distribution of the water binding energies and the water excess chemical potential of solvation in solutions are also pretty much the same as in neat water. Osmolytes are, therefore, well integrated into the hydrogen-bond network of water. Indeed, osmolytes tend to preferentially hydrogen bond with water molecules and their interaction energies are strongly correlated to their hydrogen-bonding capability. The graph network analysis, further, illustrates that osmolytes act as hubs in the percolated hydrogen-bond network of solutions. The degree of hydrogen bonding of osmolytes predominantly determines all of the network properties. Osmolytes like ethanol that form fewer hydrogen bonds than a water molecule disrupt the water hydrogen-bond network, while other osmolytes that form more hydrogen bonds effectively increase the connectivity among water molecules. Our observation of minimal variation in the local structure and the vitality of osmolyte-water hydrogen bonds on the solution network properties clearly imply that the direct interaction between protein and osmolytes is solely responsible for the protein stability. Further, the relevance of hydrogen bonds on solution properties suggests that the hydrogen-bonding interaction among protein, water, and osmolyte could be the key determinant of the protein conformation in solutions.

Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation

Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.

Structure and Interactions in Perfluorooctanoate Micellar Solutions Revealed by Small-Angle Neutron Scattering and Molecular Dynamics Simulations Studies: Effect of Urea

The self-assembly of surfactants in aqueous solution can be modulated by the presence of additives including urea, which is a well-known protein denaturant and also present in physiological fluids and agricultural runoff. This study addresses the effects of urea on the structure of micelles formed in water by the fluorinated surfactant perfluoro-n-octanoic acid ammonium salt (PFOA). Analysis of small-angle neutron scattering (SANS) experiments and atomistic molecular dynamics (MD) simulations provide consensus strong evidence for the direct mechanism of urea action on micellization: urea helps solvate the hydrophobic micelle core by localizing at the surface of the core in the place of some water molecules. Consequently, urea decreases electrostatic interactions at the micelle shell, changes the micelle shape from prolate ellipsoid to sphere, and decreases the number of surfactant molecules associating in a micelle. These findings inform the interactions and behavior of surface active per- and polyfluoroalkyl substances (PFAS) released in the aqueous environment and biota.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.

Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this paper, we propose to use the weighted persistent homology to systematically study the osmolytes molecular aggregation and their hydrogen-bonding network from a local topological perspective. We consider two weighted models, i.e., localized persistent homology (LPH) and interactive persistent homology (IPH). Boltzmann persistent entropy (BPE) is proposed to quantitatively characterize the topological features from LPH and IPH, together with persistent Betti number (PBN). More specifically, from the localized persistent homology models, we have found that TMAO and urea have very different local topology. TMAO is found to exhibit a local network structure. With the concentration increase, the circle elements in these networks show a clear increase in their total numbers and a decrease in their relative sizes. In contrast, urea shows two types of local topological patterns, i.e., local clusters around 6 Å and a few global circle elements at around 12 Å. From the interactive persistent homology models, it has been found that our persistent radial distribution function (PRDF) from the global-scale IPH has same physical properties as the traditional radial distribution function. Moreover, PRDFs from the local-scale IPH can also be generated and used to characterize the local interaction information. Other than the clear difference of the first peak value of PRDFs at filtration size 4 Å, TMAO and urea also shows very different behaviors at the second peak region from filtration size 5 Å to 10 Å. These differences are also reflected in the PBNs and BPEs of the local-scale IPH. These localized topological information has never been revealed before. Since graphs can be transferred into simplicial complexes by the clique complex, our weighted persistent homology models can be used in the analysis of various networks and graphs from any molecular structures and aggregation systems.

Urea's match in the hydrogen-bond network? A high pressure THz study

We present results of the measurement of the low frequency spectrum of solvated urea. The study revealed a blue shift of the intramolecular mode of urea centered at 150 cm^-1 of Δν= 17 cm^-1 upon increasing the pressure up to 10 kbar. The blue shift scaled linearly with the increase in density and was attributed to a stiffening of the water-urea intermolecular potential. We deduced an increase in the number of affected water molecules from 1 to 2 up to 5-7, which corresponds to the sterical coordination number of urea. The increase in hydration number can be explained by an suppression of the NH₂ inversion and the hydrogen bond switching around the NH₂ group. Pressure induced sterical constraints are proposed to hinder the rapid switching of hydrogen bond partners and make the water around urea less bulk-like than under ambient conditions.

Distance Angle Descriptors of the Interionic and Ion-Solvent Interactions in Imidazolium-Based Ionic Liquid Mixtures with Aprotic Solvents: A Molecular Dynamics Simulation Study

The aim of this paper is to quantify the changes of the interionic and ion-solvent interactions in mixtures of imidazolium-based ionic liquids, having tetrafluoroborate (BmimBF₄), hexafluorophosphate (BmimPF₆), trifluoromethylsulfonate (BmimTFO), or bis(trifluoromethanesulfonyl)imide (BmimTFSI), anions, and polar aprotic molecular solvents, such as acetonitrile (AN), γ-butyrolactone (GBL), and propylene carbonate (PC). For this purpose, we calculate, using the nearest-neighbor approach, the average distance between the imidazolium ring H atom in positions 2, 4, and 5 (H^2,4,5) and the nearest high-electronegativity atom of the solvent or anion (X) as distance descriptors, and the mean angle formed by the C^2,4,5-H^2,4,5 bond and the H^2,4,5···X axis around the H^2,4,5 atom as angular descriptors of the cation-anion and cation-solvent interactions around the ring C-H groups. The behavior of these descriptors as a function of the ionic liquid mole fraction is analyzed in detail. The obtained results show that the extent of the change of these descriptors with respect to their values in the neat ionic liquid depends both on the nature of the anion and on the mixture composition. Thus, in the case of the mixtures of the molecular solvents with BmimBF₄ and BmimTFO, a small change of the distance and a drastic increase of the angular descriptor corresponding to the cation-anion interactions are observed with decreasing mole fraction of the ionic liquid, indicating that the anion moves from the above/below position (with respect to the imidazolium ring plane) to a position that is nearly linearly aligned with the C²-H² bond and hinders the possible interaction between the C²-H² group and the solvent molecules. On the other hand, in the case of mixtures of BmimTFSI and BmimPF₆ with the molecular solvents, both the observed increase of the distance descriptor and the slight change of the angular descriptor with decreasing ionic liquid mole fraction are compatible with the direct interactions of the solvent with the C²-H² group. The behavior of these descriptors is correlated with the experimentally observed ¹H chemical shift of the C²-H² group and the red shift of the C²-H² vibrational mode, particularly at low ionic liquid mole fractions. The present results are thus of great help in interpreting these experimental observations.

On the Solute-Induced Structure-Making/Breaking Effect: Rigorous Links among Microscopic Behavior, Solvation Properties, and Solution Non-Ideality

We studied the solute-induced perturbation of the solvent environment around a solute species from a microscopic viewpoint and propose a novel approach to the understanding of the structure-making/breaking process, regardless of the type and nature of the solute-solvent interactions. Based on the Kirkwood-Buff fluctuation formalism, we present a rigorous statistical mechanics description of the evolution of the solvent structure around the solute, analyze its response to small perturbations of the ( TP) state conditions and composition of the system, and make direct connections between a few equivalent micro- and macroscopic manifestations as probes for, and targets of, experimental measurements. We illustrate the analysis with theoretical results from integral equation calculations of model fluids and experimental evidence from available data for a variety of aqueous electrolyte and nonelectrolyte real fluid solutions. Finally, we provide a critical discussion about the inadequacy underlying a widely used de facto criterion for the classification of structure-making/breaking solutes.

Permeability of P and K-nutrient through polystyrene membrane from aqueous solutions of urea + KH2PO4

With the polymer-coated fertilizer as background, the permeability of P- and K-nutrient through a representative polymer membrane-polystyrene membrane were investigated by measuring their permeability in the solutions of KH2PO4-water and urea-KH2PO4-water at nominal temperature of 298 K using the Ussing chamber method. To analyze and interpret the variation of permeability with solute concentration, the solubility of permeate in polymer membrane were determined experimentally and the permeate diffusion coefficient were assessed by the measurements of density and apparent molar volume of the aqueous fertilizer solutions. An interesting “increase-decrease” trend for the permeability of both phosphorous (P)-nutrient, and potassium (K)-nutrient fertilizer with permeate concentration was observed, in which the increases in permeability at low concentrations of permeate could be attributed to the increase in solubility of KH2PO4 in polymer while the decreases in permeability at high concentrations was due to the decrease in diffusion coefficient of permeate in polymer membrane. Finally, the release kinetics of these nutrients from a PS-coated urea-KH2PO4 compound fertilizer granule was predicted using the Shaviv’s model along with the permeability data of P- and K-nutrient generated.

Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks

Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.

Effect of Urea, Arginine, and Ethanol Concentration on Aggregation of 179CVNITV184 Fragment of Sheep Prion Protein

Understanding protein aggregation is of utmost importance as it is responsible for causing several neurodegenerative diseases and one of the serious impediments in large-scale biopharmaceutical production. The prion protein is responsible for pathological states in fatal transmissible spongiform conditions, such as Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. The peptide fragment 178-191 of Syrian hamster prion protein is known to be amyloidogenic. Here, we identified the fragment ₁₇₉CVNITV₁₈₄ as an aggregation-prone fragment in sheep prion protein. This fragment is conserved sequence among sheep and Syrian hamster prion protein and also falls in the previously identified amyloidogenic sequence. The mechanistic details of the aggregation behavior are analyzed in three different concentrations of urea, arginine, and ethanol. Urea and arginine are found to be aggregation suppressors, but ethanol enhances the protein aggregation through β-sheet formation. We have also analyzed the influence of these osmolyte on water dynamics in the presence of the octamer of this aggregation-prone fragment and correlated this water dynamics with the aggregation behavior of the octamer.

Noncovalent Interactions between Trimethylamine N-Oxide (TMAO), Urea, and Water

Trimethylamine N-oxide (TMAO) and urea are two important osmolytes with their main significance to the biophysical field being in how they uniquely interact with proteins. Urea is a strong protein destabilizing agent, whereas TMAO is known to counteract urea's deleterious effects. The exact mechanisms by which TMAO stabilizes and urea destabilizes folded proteins continue to be debated in the literature. Although recent evidence has suggested that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored, it has also been suggested that urea acts indirectly to denature proteins by destabilizing the surrounding hydrogen bonding water networks. Here, we elucidate the molecular level mechanism of TMAO's unique ability to counteract urea's destabilizing nature by comparing Raman spectroscopic frequency shifts to the results of electronic structure calculations of microsolvated molecular clusters. Experimental and computational data suggest that the addition of TMAO into an aqueous solution of urea induces blue shifts in urea's H-N-H symmetric bending modes, which is evidence for direct interactions between the two cosolvents.

Study of distance dependence of hydrophobic force between two graphene-like walls and a signature of pressure induced structure formation in the confined water

We examine the separation distance dependence of the hydrophobic force by systematically varying the distance (d) between two walls. The hydrophobic force exhibits a distance mediated crossover from a liquid-like to a gas-like behavior at around d ∼ 12 Å for 1 atm pressure. The distance dependence can be fitted to a bi-exponential form, with the longer distance part displaying a correlation length of 20 Å. In addition, the crossover is found to be accompanied by a divergent-like growth of the local relative number fluctuation of the water molecules confined between the two surfaces. Furthermore, at a fixed separation (d = 20 Å), we observe a pressure induced structural modification of confined water at high pressure. The confined water is found to form an ordered structure at high pressure (10 000 atm) and room temperature, in agreement with the experimental study [G. Algara-Siller et al. Nature 519(7544), 443 (2015)].

Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation

Sensitivity of thermodiffusion to urea–water interactions was studied experimentally and by NEMD simulations, identifying the hydrophobic behaviour of urea.

The local structure in the BmimPF6/acetonitrile mixture: the charge distribution effect

The effect of the charge distribution on the local structure in the binary mixture of 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF₆) ionic liquid and acetonitrile is investigated over the entire composition range.

Urea hydration from dielectric relaxation spectroscopy: old findings confirmed, new insights gained

We report results on urea hydration obtained by dielectric relaxation spectroscopy (DRS) in a broad range of concentrations and temperatures. In particular, the effective hydration number and dipole moment of urea have been determined. The observed changes with composition and temperature were found to be insignificant and mainly caused by the changing number density of urea. Similarly, solute reorientation scaled simply with viscosity. In contrast, we find that water reorientation undergoes substantial changes in the presence of urea, resulting in two water fractions. The first corresponds to water molecules strongly bound to urea. These solvent molecules follow the reorientational dynamics of the solute. The second fraction exhibits only a minor increase of its relaxation time (in comparison with pure water) which is not linked to solution viscosity. Its activation energy decreases significantly with urea concentration, indicating a marked decrease of the number of H-bonds among the H2O molecules belonging to this fraction. Noncovalent interactions (NCI) analysis, capable to estimate the strength of the interactions within a cluster, shows that bound water molecules are most probably double-hydrogen bonded to urea via the oxygen atom of the carbonyl group and a cis-hydrogen atom. Due to the increased H-bond strength compared to the water dimer and the rigid position in the formed complex the reorientation of these bound H2O molecules is strongly impeded.

Local Structure in Terms of Nearest-Neighbor Approach in 1-Butyl-3-methylimidazolium-Based Ionic Liquids: MD Simulations

Description of the local microscopic structure in ionic liquids (ILs) is a prerequisite to obtain a comprehensive understanding of the influence of the nature of ions on the properties of ILs. The local structure is mainly determined by the spatial arrangement of the nearest neighboring ions. Therefore, the main interaction patterns in ILs, such as cation-anion H-bond-like motifs, cation-cation alkyl tail aggregation, and ring stacking, were considered within the framework of the nearest-neighbor approach with respect to each particular interaction site. We employed classical molecular dynamics (MD) simulations to study in detail the spatial, radial, and orientational relative distribution of ions in a set of imidazolium-based ILs, in which the 1-butyl-3-methylimidazolium (C4mim(+)) cation is coupled with the acetate (OAc(-)), chloride (Cl(-)), tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), or bis(trifluoromethanesulfonyl)amide (TFSA(-)) anion. It was established that several structural properties are strongly anion-specific, while some can be treated as universally applicable to ILs, regardless of the nature of the anion. Namely, strongly basic anions, such as OAc(-) and Cl(-), prefer to be located in the imidazolium ring plane next to the C-H(2/4-5) sites. By contrast, the other four bulky and weakly coordinating anions tend to occupy positions above/below the plane. Similarly, the H-bond-like interactions involving the H(2) site are found to be particularly enhanced in comparison with the ones at H(4-5) in the case of asymmetric and/or more basic anions (C4mimOAc, C4mimCl, C4mimTfO, and C4mimTFSA), in accordance with recent spectroscopic and theoretical findings. Other IL-specific details related to the multiple H-bond-like binding and cation stacking issues are also discussed in this paper. The secondary H-bonding of anions with the alkyl hydrogen atoms of cations as well as the cation-cation alkyl chain aggregation turned out to be poorly sensitive to the nature of the anion.

Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water

Using extensive molecular dynamics simulations of a single eight-residue alanine polypeptide in explicit water, we investigate the influence of α-helix formation on the dielectric spectrum. For this, we project long equilibrium trajectories into folded and unfolded states and thereby obtain dielectric spectra representative for disordered as well α-helical conformations without the need to change any other system parameter such as pH or temperature. The absorption spectrum in the α-helical state exhibits a feature in the sub-GHz range that is significantly stronger than in the unfolded state. As we show by an additional decomposition into peptide and water contributions, this slow dielectric mode, the relaxation time of which matches the independently determined peptide rotational relaxation time, is mostly caused by peptide polarization correlations, but also contains considerable contributions from peptide-water correlations. In contrast, the peptide spectral contribution shows no features in the GHz range where bulk water absorbs, not even in the peptide-water correlation part, we conclude that hydration water around Ala8 is more influenced by peptide polarization relaxation effects than the other way around. A further decomposition into water-self and water-collective polarization correlations shows that the dielectric response of hydration water is, in contrast to electrolyte solutions, retarded and that this retardation is mostly due to collective effects, the self relaxation of hydration water molecules is only slightly slowed down compared to bulk water. We find the dynamic peptide-water polarization cross correlations to be rather long-ranged and to extend more than one nanometer away from the peptide-water interface into the water hydration shell, in qualitative agreement with previous simulation studies and recent THz absorption experiments.