Long-Time Correlations and Hydrophobe-Modified Hydrogen-Bonding Dynamics in Hydrophobic Hydration

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

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

How stereochemistry of lipid components can affect lipid organization and the route of liposome internalization into cells

Though liposome-based drugs are in clinical use, the mechanism of cell internalization of liposomes is yet an object of controversy. The present experimental investigation, carried out on human glioblastoma cells, indicated different internalization routes for two diastereomeric liposomes. Molecular dynamics simulations of the lipid bilayers of the two formulations indicated that the different stereochemistry of a lipid component controls some parameters such as area per lipid molecule and fluidity of lipid membranes, surface potential and water organization at the lipid/water interface, all of which affect the interaction with biomolecules and cell components.

Insignificant Effect of Temperature on the Structure and Angular Jumps of Water near a Hydrophobic Cation

The ambiguity in the behavior of water molecules around hydrophobic solutes is a matter of interest for many studies. Motivated by the earlier results on the dynamics of water molecules around tetramethylammonium (TMA) cation, we present the effect of temperature on the structure and angular jumps of water due to hydrophobicity using first principles molecular dynamics simulations. The average intermolecular distance between the central oxygen and four nearest neighbors is found to be the highest for water molecules in the solvation shell of TMA at 400 K, followed by the same at 330 K. The hydrogen bond (HB) donor-acceptor count, HB per water molecule, and tetrahedral order parameter suggests the loss of tetrahedrality in the solvation shell. Elevated temperature affects the tetrahedral parameter in local regions. The HB jump mechanism is studied for methyl hydrogen and water molecules in the solvation shell. Observations hint at the presence of dangling water molecules in the vicinity of the hydrophobic cation, and no evidence is found for the enhanced structural ordering of nearby water molecules.

Hydrophobic pattern of alkylated ureas markedly affects water rotation and hydrogen bond dynamics in aqueous solution

Alkylated ureas are frequently used amphiphiles to mediate biomolecule water interactions, yet their hydrophobic substitution pattern critically affects their function. These differences can be traced back to their hydration, which is poorly understood. Here, we investigate subtle effects of the hydrophobic pattern of ureas on hydration dynamics using a combination of linear and non-linear infrared spectroscopies on the OD stretching vibration of HDO. Isomeric 1,3-dimethylurea (1,3-DMU), 1,1-dimethylurea (1,1-DMU) and 1-ethylurea (1-EU) exhibit very similar and rather weak modulation of the water hydrogen-bond strength distribution. Yet, only 1,3-DMU and 1,1-DMU enhance the hydrogen-bond heterogeneity and slow-down its fluctuation dynamics. In turn, rotational dynamics of water molecules, which is dominated by hydrogen bond switches, is significantly impeded in the presence of 1,3-DMU and only weakly by 1,1-DMU and 1-EU. These marked differences can be explained by both excluded volume effects in hydration and self-aggregation, which may be the key to their biotechnological function.

Hydrogen Bond Networks in Binary Mixtures of Water and Organic Solvents

We here present an approach for the optical in situ characterization of hydrogen bond networks (HBNs) in binary mixtures of water and organic solvents (OSs), such as methanol, ethanol, and acetonitrile. HBNs are characterized based on (i) the analysis of experimental molar Raman spectra of the mixture, (ii) partial molar Raman spectra of the mixture constituents, and (iii) computed ideal molar Raman spectra of the mixture. Especially, the consideration of the partial molar Raman spectra provides insights into the development of hydrogen bonds of molecules of one species with their neighbors. The obtained Raman spectra are evaluated with respect to the centroid of the symmetric stretching vibration Raman signal of water and to the hydroxyl stretching vibration of alcohols. We show the influence of composition and temperature on the development of the HBN of the mixtures, the HBN of water, and the HBN of the OS molecules.

Temperature-Dependent Segregation in Alcohol-Water Binary Mixtures Is Driven by Water Clustering

Previous neutron scattering work, combined with computer simulated structure analysis, has established that binary mixtures of methanol and water partially segregate into water-rich and alcohol-rich components. It has furthermore been noted that, between methanol mole fractions of 0.27 and 0.54, both components, water and methanol, simultaneously form percolating clusters. This partial segregation is enhanced with decreasing temperature. The mole fraction of 0.27 also corresponds to the point of maximum excess entropy for ethanol-water mixtures. Here, we study the degree of molecular segregation in aqueous ethanol solutions at a mole fraction of 0.27 and compare it with that in methanol-water solutions at the same concentration. Structural information is extracted for these solutions using neutron diffraction coupled with empirical potential structure refinement. We show that ethanol, like methanol, bi-percolates at this concentration and that, in a similar manner to methanol, alcohol segregation, as measured by the proximity of neighboring methyl sidechains, is increased upon cooling the solution. Water clustering is found to be significantly enhanced in both alcohol solutions compared to the water clustering that occurs for random, hard sphere-like, mixing with no hydrogen bonds between molecules. Alcohol clustering via the hydrophobic groups is, on the other hand, only slightly sensitive to the water hydrogen bond network. These results support the idea that it is the water clustering that drives the partial segregation of the two components, and hence the observed excess entropy of mixing.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers

We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.

Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects

We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (<2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly increases with solute concentration. In addition, the slowdown factor is found to vary very little with temperature, thus suggesting an entropic origin. All of these results are in quantitative agreement with prior classical molecular dynamics simulations and with the previously suggested excluded-volume model. The hydrophilic TMAO headgroup is found to affect water dynamics more strongly than the hydrophobic moiety, and the magnitude of this slowdown is very sensitive to the strength of the water-solute hydrogen-bond.

Water is an active matrix of life for cell and molecular biology

Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.

Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical transition at a lower temperature (∼200 K) vis-à-vis the zero-field case (∼220 K).

Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes

Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level. We present unequivocal and model-free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10-15 per methane molecule. Ab initio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous, and more tetrahedrally oriented hydrogen bonds than those in bulk water and that their mobility is restricted. We show the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration.

Enthalpic and Entropic Contributions to Hydrophobicity

Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called "unhappy water" molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.

Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide

Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules.

Fast and slow dynamics and the local structure of liquid and supercooled water next to a hydrophobic amino acid

We study, through molecular dynamics simulations, the structure and orientational dynamics of water next to a blocked hydrophobic amino acid, valine (Val), above and below the freezing point of water.

Hydrophobicity: effect of density and order on water's rotational slowing down

Ab initio molecular dynamics (AIMD) simulations of over 4.5 ns were performed in the temperature range of T = 260-350 K with van der Waals corrections to investigate the relationship between local water density and tetrahedral order in bulk water and in the presence of a hydrophobe, tetramethylurea (TMU). We demonstrate that in bulk water, defects consisting of 5- and higher coordinated water are a major contributor to dynamics. Close to a hydrophobe, 3-coordinated defects take over. The co-existence of these defects gives rise to very different local densities. We propose that the slowing down of rotational motion close to a hydrophobe is induced by an interplay between density and order with the slowing down decreasing in the following order: (i) low-density ordered-water, (ii) normal-density ordered-water, (iii) high-density ordered-water and (iv) disordered-water. The proportions of these water environments vary with temperature. These local environments also support the idea of water's polymorphism, i.e., the existence of the high- and low-density states in supercooled water.

Slow-to-fast transition of hydrogen bond dynamics in acetamide hydration shell formation

The acetamide hydration shell dynamics speeds up in a remarkable way upon increasing the water amount.

On the slowdown mechanism of water dynamics around small amphiphiles

Partitioning the water molecules depending on their location with respect to the solute makes it possible to probe the cause of the orientational slowdown in aqueous tetramethylurea.

Cholesterol level affects surface charge of lipid membranes in saline solution

Cholesterol is an important component of all biological membranes as well as drug delivery liposomes. We show here that increasing the level of cholesterol in a phospholipid membrane decreases surface charge in the physiological environment. Through molecular dynamics simulation we have shown that increasing the level of cholesterol decreases Na+ ion binding. Complementary experimental ζ--potential measurements have shown a decreased ζ--potential with increasing cholesterol content, indicative of reduced surface charge. Both experiments and simulations have been carried out on both saturated 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and monounsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. This result is particularly important because membrane surface charge plays an important role in the interactions of biomembranes with peripheral membrane proteins and drug delivery liposomes with the immune system.

Temperature dependence of hydrophobic hydration dynamics: from retardation to acceleration

The perturbation induced by a hydrophobic solute on water dynamics is essential in many biochemical processes, but its mechanism and magnitude are still debated. A stringent test of the different proposed pictures is provided by recent NMR measurements by Qvist and Halle (J. Am. Chem. Soc. 2008, 130, 10345-10353) which showed that, unexpectedly, the perturbation changes in a non-monotonic fashion when the solution is cooled below room temperature. Here we perform and analyze molecular dynamics simulations of a small paradigm amphiphilic solute, trimethylamine N-oxide (TMAO), in dilute aqueous solutions over the 218-350 K temperature range. We first show that our simulations properly reproduce the non-monotonic temperature dependence. We then develop a model which combines our previously suggested entropic excluded-volume effect with a perturbation factor arising from the difference between local structural fluctuations in the shell and the bulk. Our model provides a detailed molecular understanding of the hydrophobic perturbation over the full temperature range investigated. It shows that the excluded-volume factor brings a dominant temperature-independent contribution to the perturbation at all temperatures, and provides a very good approximation at room temperature. The non-monotonic temperature dependence of the perturbation is shown to arise from the structural factor and mostly from relative shifts between the shell and bulk distributions of local structures, whose amplitude remains very small compared to the widths of those distributions.

Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity

Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine

The environment of sulfur in dissolved aqueous L-cysteine has been examined using K-edge x-ray absorption spectroscopy (XAS), extended continuum multiple scattering (ECMS) theory, and density functional theory (DFT). For the first time, bound-state and continuum transitions representing the entire XAS spectrum of L-cysteine sulfur are accurately reproduced by theory. Sulfur K-edge absorption features at 2473.3 eV and 2474.2 eV represent transitions to LUMOs that are mixtures of S-C and S-H σ∗ orbitals significantly delocalized over the entire L-cysteine molecule. Continuum features at 2479, 2489, and 2530 eV were successfully reproduced using extended continuum theory. The full L-cysteine sulfur K-edge XAS spectrum could not be reproduced without addition of a water-sulfur hydrogen bond. Density functional theory analysis shows that although the Cys(H)S⋯H-OH hydrogen bond is weak (∼2 kcal) the atomic charge on sulfur is significantly affected by this water. MXAN analysis of hydrogen-bonding structures for L-cysteine and water yielded a best fit model featuring a tandem of two water molecules, 2.9 Å and 5.8 Å from sulfur. The model included a S(cys)⋯H-O(w1)H hydrogen-bond of 2.19 Å and of 2.16 Å for H(2)O(w1)⋯H-O(w2)H. One hydrogen-bonding water-sulfur interaction alone was insufficient to fully describe the continuum XAS spectrum. However, density functional theoretical results are convincing that the water-sulfur interaction is weak and should be only transient in water solution. The durable water-sulfur hydrogen bond in aqueous L-cysteine reported here therefore represents a break with theoretical studies indicating its absence. Reconciling the apparent disparity between theory and result remains the continuing challenge.

More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water

Biological interfaces characterized by a complex mixture of hydrophobic, hydrophilic, or charged moieties interfere with the cooperative rearrangement of the hydrogen-bond network of water. In the present study, this solute-induced dynamical perturbation is investigated by extended frequency range depolarized light scattering experiments on an aqueous solution of a variety of systems of different nature and complexity such as small hydrophobic and hydrophilic molecules, amino acids, dipeptides, and proteins. Our results suggest that a reductionist approach is not adequate to describe the rearrangement of hydration water because a significant increase of the dynamical retardation and extension of the perturbation occurs when increasing the chemical complexity of the solute.

Hydration properties of small hydrophobic molecules by Brillouin light scattering

We study the relaxation of water molecules next to hydrophobic solutes with different functional groups by Brillouin light scattering. Evidence is given for (i) water activation energy in trimethylamine-N-oxide, proline and t-butyl alcohol diluted solutions which is comparable to that of neat water, almost independent from solute mole fraction and (ii) moderate slowdown of relaxation time of proximal water compared to the bulk, which is consistent with excluded volume models. Assuming that the main contribution to viscosity comes from bulk and hydration water, a rationale is given of the phenomenological Arrhenius' laws for the viscosity of diluted aqueous solutions.

Physical origin underlying the entropy loss upon hydrophobic hydration

The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the molecular scale HE has an entropic origin. It is believed that hydrophobic particles induce order in the surrounding water by reducing the volume of configuration space available for hydrogen bonding. Here we show with computer simulation results that this traditional picture, based on average structural features of hydration water, configurational properties of single water molecules, and up to pairwise correlations, is not correct. Analyzing collective fluctuations in water clusters we are able to provide a fundamentally new picture of HE based on pronounced many-body correlations affecting the switching of hydrogen bonds (HBs) between molecules. These correlations emerge as a nonlocal compensation of reduced fluctuations of local electrostatic fields in the presence of an apolar solute. We propose an alternative view which may also be formulated as a maximization principle: The electrostatic noise acting on water molecules is maximized under the constraint that each water molecule on average maintains as many HBs as possible. In the presence of the solute the maximized electrostatic noise is a result of nonlocal fluctuations in the labile HB network giving rise to strong correlations among at least up to four water molecules.