Hydrophobic Solutes Research Articles

Water Tetrahedrons, Hydrogen-Bond Dynamics, and the Orientational Mobility of Water around Hydrophobic Solutes

Despite being intensively studied, the magnitude of specific structural and dynamic perturbations of water next to hydrophobic surfaces remains a matter of debate. Here we show, from molecular dynamics, that the structure of a subset of water molecules in the first hydration layer, those preserving four nearest water neighbors, resembles that of water at ∼10 °C, and that the origin of the orientational slowdown is mainly a decrease of the hydrogen-bond (HB) acceptor switch frequency, while water structuring plays a minor role, slightly accelerating HB acceptor switches. By portraying the mean HB dynamics of water as a doubly periodic event, we demonstrate that the orientational retardation factor is effectively defined by the ratio of the HB acceptor switch period in the hydration layer and bulk. Excluded volume delays HB acceptor switches, accelerating the orientational relaxation of ∼1/3 of the water molecules on the hydration layer in this time scale, but this is largely exceeded by the decrease of the HB switch frequency, consistent with 2D IR spectroscopy experiments, and at the origin of longer HB lifetimes. The orientational mobility of water populations with long HB lifetimes is also probed, and although a relaxation plateau is observed at ∼10 ps consistent with fs IR spectroscopy experiments, no water molecule is rotationally frozen at any time scale. The proposed molecular picture is consistent with fs IR, 2D IR, and NMR experimental results on the orientational retardation of water and reveals the magnitude of "hidden" enhanced ordered water pentamers formed near hydrophobic solutes.

Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction

Weak intermolecular interactions, such as hydrophobic associations, underlie numerous biomolecular recognition processes. Ubiquitin is a small protein that represents a biochemical model for exploring thermodynamic signatures of hydrophobic association as it is widely held that a major component of ubiquitin's binding to numerous partners is mediated by hydrophobic regions on both partners. Here, we use atomistic molecular dynamics simulations in conjunction with the Adaptive Biasing Force sampling method to compute potentials of mean force (the reversible work, or free energy, associated with the binding process) to investigate the thermodynamic signature of complexation in this well-studied biochemical model of hydrophobic association. We observe that much like in the case of a purely hydrophobic solute (i.e., graphene, carbon nanotubes), association is favored by entropic contributions from release of water from the interprotein regions. Moreover, association is disfavored by loss of enthalpic interactions, but unlike in the case of purely hydrophobic solutes, in this case protein-water interactions are lost and not compensated for by additional water-water interactions generated upon release of interprotein and moreso, hydration, water. We further find that relative orientations of the proteins that mutually present hydrophobic regions of each protein to its partner are favored over those that do not. In fact, the free energy minimum as predicted by a force field based method recapitulates the experimental NMR solution structure of the complex.

Comment on “Water’s Structure around Hydrophobic Solutes and the Iceberg Model”

Comment on “Water’s Structure around Hydrophobic Solutes and the Iceberg Model”

Reply to “Comment on ‘Water’s Structure around Hydrophobic Solutes and the Iceberg Model’”

Reply to “Comment on ‘Water’s Structure around Hydrophobic Solutes and the Iceberg Model’”

Electrophoretic mobility without charge driven by polarisation of the nanoparticle–water interface

Polarisation of the interface, spontaneously occurring when water is in contact with hydrophobic solutes or air, couples with the uniform external field to produce a non-zero force acting on a suspended particle. This force exists even in the absence of a net particle charge, and its direction is affected by the first-order, dipolar and the second-order, qudrupolar orientational order parameters of the interfacial water. The quadrupolar polarisation gives rise to an effectively negative charge. The corresponding surface charge density is inversely proportional to the area of the shear surface. As a result, the overall contribution from the quadrupolar polarisation to the particle mobility becomes negligible compared to experimentally reported values for particles exceeding a few nanometres in size. In contrast, the contribution of the dipolar order of the interface to the effective surface charge scales inversely with the particle size and dominates the zero-charge mobility of submicron particles. The corresponding electrokinetic charge is determined by the preferential orientation of interfacial dipoles relative to the surface normal.

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.

Solvation of Hydrogen Sulfide in Liquid Water and at the Water–Vapor Interface Using a Polarizable Force Field

Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (H2S) in water. Pairwise H2O-H2S Lennard-Jones interactions were optimized to the experimental H2S gas solubility at 298 K. These parameters yield hydration free energies and diffusion coefficients for H2S that are in good agreement with the experiment over 273-323 K and 298-368 K, respectively. H2S is sparingly soluble in water, with a ΔG(hydr)° of -0.5 kcal mol(-1). The free energy perturbation (FEP) calculations and analysis of the radial distribution functions show that H2S has limited hydrogen bonding and electrostatic interactions with the water solvent and generally behaves like a hydrophobic solute. These features were confirmed by ab initio MD simulations. Umbrella sampling simulations were used to calculate the free energy profile of the transition of H2S across the water-vapor interface, which showed that H2S has a sizable surface excess, with a ΔG(surf) of 1.3 kcal mol(-1). This high surface excess is consistent with our calculations of the surface tension, which decreases to 20 dyn cm(-1) under high densities of H2S (g). The dipole moment of H2S increases from its gas phase value of 0.98 to 1.25 D in bulk water as it moves across the interface. Adsorbed H2S tends to be oriented perpendicular to the interface, with the sulfur atom pointing toward the vapor phase.

Magnetic effects on the hydration of nanoscopic hydrophobic paraffin-like plates

The effect of an external static magnetic field on the hydration behavior of nanoscopic paraffin-like plates has been investigated using molecular dynamics simulation in an isothermal–isobaric ensemble. The “normal” and “hard-wall-like” hydrophobic potentials were both utilized to represent the water–solute interaction. Results demonstrate that water at ambient temperature was expelled from the confined region between two “normal” plates upon applying relatively low magnetic field, and attracted back under magnetic field beyond 0.7T. The transition of magnetodesorption to magnetoadsorption is firstly achieved theoretically, which is in good agreement with experimental results reported by Ozeki et al. In contrast, water confined in the “hard-wall-like” plates is more sensitive to magnetic treatment. A liquid-to-vapor-like phase transition has been observed at the center of confined region at 0.7T, similar to the behavior of confined water under the influence of an electric field. This indicates that aggregation of hydrophobic solutes can be induced by applying a magnetic field and could shed light on the mechanism of magnetic dewetting of hydrophobic surfaces.

NEW SORBENT WITH LOWER HYDROPHOBICITY FOR SOLID PHASE EXTRACTION: PREPARATION AND CHARACTERIZATION

C18 chemically bonded sorbents have been the main materials used in solid phase extraction (SPE). However, due their high hydrophobicity some hydrophobic solutes are strongly retained leading to the consumption of larger quantities of organic solvent for efficient recoveries. This work presents a sorbent with lower hydrophobicity but similar selectivity to the C18 sorbent, prepared by thermal immobilization of poly(dimethylsiloxane-co-alkylmethylsiloxane) (PDAS) on silica. PDAS has organic chains with methyl groups alternating with octadecyl or hexadecyl groups in its monomeric unities. For the Si(PDAS) sorbent presented, the polymeric layer was physically adsorbed on the silica surface with 12% carbon load. Although the coating of silica with the polymeric layer was incomplete, the PDAS provided better protection for the silica surface groups, promoting mostly hydrophobic interactions between analytes and the sorbent. Sorption isotherm studies revealed that the retention of hydrophobic solutes on Si(PDAS) was less intense than on conventional sorbents, confirming the lower hydrophobicity of the lab-made sorbent. Additional advantages of Si(PDAS) include simplicity and low cost of preparation, making this material a potential sorbent for the analysis of highly hydrophobic solutes.

Small-scale Triton X-114 Extraction of Hydrophobic Proteins.

Here we introduce a protocol for Triton X-114 extraction which we used in our recently-published paper (Taguchi et al., 2013). It is a versatile method to concentrate or partially purify hydrophobic proteins. The presented protocol is based on the protocol published by Bordier (Bordier, 1981) but more simplified and down-scaled for more small-scale and simpler use (Taguchi et al., 2013). Triton X-114 (TX114) is a non-ionic detergent which has a relatively low clouding point at 22 °C and separates into detergent (Det) and aqueous (Aq) phase at temperatures above the clouding point. During phase separation, hydrophobic solutes in the TX114 solution are sequestered to the Det phase, while hydrophilic solutes are sequestered to the Aq phase. Utilizing this phenomenon, TX114 extraction is a very versatile technique to efficiently concentrate hydrophobic proteins, especially glycosylphosphatidylinositol (GPI)-anchored proteins like the prion protein (PrP), because they have substantial amounts of highly hydrophobic moieties. Besides, phase separation using TX114 tolerates a variety of conditions, e.g. different pH or relatively low concentrations of guanidine hydrochloride. Since the hydrophobic proteins are sequestered to the Det phase as long as the phase separation occurs, and if the hydrophobicity of the protein of interest is not affected by pH or denaturant, this technique can be also utilized to change buffers or to remove denaturants. When using enzymes or proteases which maintain activities in detergent solutions, TX114 can also be used to separate hydrophobic from the water-soluble hydrophilic moieties upon enzymatic digestion of proteins, as done by us using in vitro digestion of PrP with phosphatidylinositol-specific phospholipase C (Taguchi et al., 2013).

Understanding the Membrane Permeability of Hydrogen Sulfide through Molecular Dynamics Simulations using a Polarizable Force Field

Hydrogen sulfide (H2S) is an acutely toxic gas, with a threshold toxicity of 200 ppm. It is also a gasotransmitter, acting through the S-sulfhydration of cysteine side chains [1]. Despite being chemically analogous to water, H2S can permeate biological membranes without a facilitator [1]. To examine this process, we used molecular dynamics simulations to calculate the potential of mean force (PMF) of H2S crossing a model lipid bilayer. As H2S is a highly polarizable molecule, we used the Drude polarizable force field for H2S developed in our group [2], in conjunction with a polarizable model for DPPC lipid bilayers [3]. Our computed PMFs show that H2S is sparingly soluble in bulk water and partitions readily into the interior of the membrane. Free energies are lowest when H2S is in the tail region of the lipids and the barriers corresponding to H2S crossing the water/lipid interface are small. This is in contrast the high free energies that occur when water molecules enter the membrane interior. Induced polarization plays a secondary role in H2S permeation, with H2S being most strongly polarized in the bulk solvent and near the lipid head groups, but having a dipole moment near the gas phase value of 0.98 D in the membrane interior. Despite a significant dipole moment and large polarizability, H2S is solvated and permeates membranes like a hydrophobic solute.[1] Gadalla, Snyder, J. Neurochem. 2010, 113, 14.[2] Mathai et al. PNAS 2009, 106, 16633.[3] Riahi, Rowley, J. Phys. Chem. B 2013, 117, 5222.[4] Chowdhary et al. J. Phys. Chem. B, 2013, 117, 9142.

Effects of salt on the ‘drying’ transition and hydrophobic interaction between nano-sized spherical solutes

The effects of sodium halide salts on the hydration and effective interaction between two nanometer-sized, spherical hydrophobic solutes are studied using explicit-water molecular dynamics computer simulations. The system exhibits bimodal wet–dry hydration oscillations that are found to be significantly shifted to dryer states by the presence of salt at and above physiological concentrations. We find that the wet–dry equilibrium of the confined solvent and the resulting interaction between the two solutes can be sensitively tuned by varying the salt type and concentration. A free energy analysis indicates that the strong salt effects can be traced back to large changes in the water chemical potential for the transfer process of a water molecule from the bulk reservoir into the ion-depleted confined region. Our results provide a better understanding of salt effects at the onset of aggregation and self-assembly of large hydrophobic solutes such as globular proteins.

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

The permeability of lipid membranes for metabolic molecules or drugs is routinely estimated from the solute’s oil/water partition coefficient. However, the molecular determinants that modulate the permeability in different lipid compositions have remained unclear. Here, we combine scanning electrochemical microscopy and molecular-dynamics simulations to study the effect of cholesterol on membrane permeability, because cholesterol is abundant in all animal membranes. The permeability of membranes from natural lipid mixtures to both hydrophilic and hydrophobic solutes monotonously decreases with cholesterol concentration [Chol]. The same is true for hydrophilic solutes and planar bilayers composed of dioleoyl-phosphatidylcholine or dioleoyl-phosphatidyl-ethanolamine. However, these synthetic lipids give rise to a bell-shaped dependence of membrane permeability on [Chol] for very hydrophobic solutes. The simulations indicate that cholesterol does not affect the diffusion constant inside the membrane. Instead, local partition coefficients at the lipid headgroups and at the lipid tails are modulated oppositely by cholesterol, explaining the experimental findings. Structurally, these modulations are induced by looser packing at the lipid headgroups and tighter packing at the tails upon the addition of cholesterol.

The analysis of water network for kinase selectivity based on the MD simulations

We studied the effect of water molecules correlated with a hydrophobic environment by analyzing a hydrogen-bonded water network using molecular dynamics simulations to explain kinase selectivity within two example systems, a variant of Gleevec and a series of substituted JNK ligands. We carried out the analysis of the five-membered ring (R5) structure for water molecules, which is a dominant structure in aqueous solutions containing hydrophobic solutes due to hydrophobic effects. The patterns of water network using the R5 structure are well mapped to the selective activity profile for the kinase inhibitors.

Effects of large volume injection of aliphatic alcohols as sample diluents on the retention of low hydrophobic solutes in reversed-phase liquid chromatography

Recent studies showed that injection of large volume of hydrophobic solvents used as sample diluents could be applied in reversed-phase liquid chromatography (RP-LC). This study reports a systematic research focused on the influence of a series of aliphatic alcohols (from methanol to 1-octanol) on the retention process in RP-LC, when large volumes of sample are injected on the column. Several model analytes with low hydrophobic character were studied by RP-LC process, for mobile phases containing methanol or acetonitrile as organic modifiers in different proportions with aqueous component. It was found that starting with 1-butanol, the aliphatic alcohols can be used as sample solvents and they can be injected in high volumes, but they may influence the retention factor and peak shape of the dissolved solutes. The dependence of the retention factor of the studied analytes on the injection volume of these alcohols is linear, with a decrease of its value as the sample volume is increased. The retention process in case of injecting up to 200μL of upper alcohols is dependent also on the content of the organic modifier (methanol or acetonitrile) in mobile phase.

Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining.

We present a multiresolution simulation scheme for the solvent environment where four atomistic water molecules are mapped onto one coarse-grained bead. Soft restraining potentials are used to allow a resolution exchange of four water molecules into a single coarse-grained site. We first study the effect of adding restraining potentials in liquid water using full all-atom simulations. The usage of very soft restraining potentials to bundle four nearest neighbor water molecules does not disrupt the hydrogen bonding patterns in the liquid water. The structural properties of the first solvation shell around hydrophobic, hydrophilic, and ionic solutes are well preserved when soft restraining potentials are added. By modeling a bundle of four water molecules as a single molecule, a smooth transition and free exchange between coarse-grained and all-atom resolution is possible by using the adaptive resolution scheme (AdResS).

Molecular density functional theory of water describing hydrophobicity at short and long length scales

We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619 (2013)] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields: the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast, the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density, and making the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.

Characterization of the Methane-Graphene Hydrophobic Interaction in Aqueous Solution from Ab Initio Simulations.

In this article, the interaction between a methane molecule and a graphene plane in liquid water has been characterized employing DFT-based free energy Molecular Dynamics calculations. This system represents a good model to understand the generic interaction between a small hydrophobic solute (methane molecule) and an extense hydrophobic surface (graphene plane). The structural and dynamical properties of graphene and methane hydration water are analyzed and found to be closely related to the main features of the potential of mean force. The results could be used in coarse-grained models to take into account the effect of the hydrophobic interaction in realistic systems relevant to experiment.

On the Thermodynamics and Kinetics of Hydrophobic Interactions at Interfaces

We have studied how primitive hydrophobic interactions between two or more small nonpolar solutes are affected by the presence of surfaces. We show that the desolvation barriers present in the potential of mean force between the solutes in bulk water are significantly reduced near an extended hydrophobic surface. Correspondingly, the kinetics of hydrophobic contact formation and breakage are faster near a hydrophobic surface than near a hydrophilic surface or in the bulk. We propose that the reduction in the desolvation barrier is a consequence of the fact that water near extended hydrophobic surfaces is akin to that at a liquid-vapor interface and is easily displaced. We support this proposal with three independent observations. First, when small hydrophobic solutes are brought near a hydrophobic surface, they induce local dewetting, thereby facilitating the reduction of desolvation barriers. Second, our results and those of Patel et al. (Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 17678-17683) show that, whereas the association of small solutes in bulk water is driven by entropy, that near hydrophobic surfaces is driven by enthalpy, suggesting that the physics of interface deformation is important. Third, moving water away from its vapor-liquid coexistence, by applying hydrostatic pressure, leads to recovery of bulklike signatures (e.g., the presence of a desolvation barrier and an entropic driving force) in the association of solutes. These observations for simple solutes also translate to end-to-end contact formation in a model peptide with hydrophobic end groups, for which lowering of the desolvation barrier and acceleration of contact formation are observed near a hydrophobic surface. Our results suggest that extended hydrophobic surfaces, such as air-water or hydrocarbon-water surfaces, could serve as excellent platforms for catalyzing hydrophobically driven assembly.

Platform for High-Throughput Testing of the Effect of Soluble Compounds on 3D Cell Cultures

In vitro 3D culture could provide an important model of tissues in vivo, but assessing the effects of chemical compounds on cells in specific regions of 3D culture requires physical isolation of cells and thus currently relies mostly on delicate and low-throughput methods. This paper describes a technique ("cells-in-gels-in-paper", CiGiP) that permits rapid assembly of arrays of 3D cell cultures and convenient isolation of cells from specific regions of these cultures. The 3D cultures were generated by stacking sheets of 200-μm-thick paper, each sheet supporting 96 individual "spots" (thin circular slabs) of hydrogels containing cells, separated by hydrophobic material (wax, PDMS) impermeable to aqueous solutions, and hydrophilic and most hydrophobic solutes. A custom-made 96-well holder isolated the cell-containing zones from each other. Each well contained media to which a different compound could be added. After culture and disassembly of the holder, peeling the layers apart "sectioned" the individual 3D cultures into 200-μm-thick sections which were easy to analyze using 2D imaging (e.g., with a commercial gel scanner). This 96-well holder brings new utilities to high-throughput, cell-based screening, by combining the simplicity of CiGiP with the convenience of a microtiter plate. This work demonstrated the potential of this type of assays by examining the cytotoxic effects of phenylarsine oxide (PAO) and cyclophosphamide (CPA) on human breast cancer cells positioned at different separations from culture media in 3D cultures.