Solute-water Interactions Research Articles

Calculation of Linear and Non-linear Electric Response Properties of Systems in Aqueous Solution: A Polarizable Quantum/Classical Approach with Quantum Repulsion Effects.

We present a computational study of polarizabilities and hyperpolarizabilities of organic molecules in aqueous solutions, focusing on solute–water interactions and the way they affect a molecule’s linear and non-linear electric response properties. We employ a polarizable quantum mechanics/molecular mechanics (QM/MM) computational model that treats the solute at the QM level while the solvent is treated classically using a force field that includes polarizable charges and dipoles, which dynamically respond to the solute’s quantum-mechanical electron density. Quantum confinement effects are also treated by means of a recently implemented method that endows solvent molecules with a parametric electron density, which exerts Pauli repulsion forces upon the solute. By applying the method to a set of aromatic molecules in solution we show that, for both polarizabilities and first hyperpolarizabilities, observed solution values are the result of a delicate balance between electrostatics, hydrogen-bonding, and non-electrostatic solute solvent interactions.

Can small drugs predict the intrinsic aqueous solubility of 'beyond Rule of 5' big drugs?

The aim of the study was to explore to what extent small molecules (mostly from the Rule of 5 chemical space) can be used to predict the intrinsic aqueous solubility, S0, of big molecules from beyond the Rule of 5 (bRo5) space. It was demonstrated that the General Solubility Equation (GSE) and the Abraham Solvation Equation (ABSOLV) underpredict solubility in systematic but slightly ways. The Random Forest regression (RFR) method predicts solubility more accurately, albeit in the manner of a ‘black box.’ It was discovered that the GSE improves considerably in the case of big molecules when the coefficient of the log P term (octanol-water partition coefficient) in the equation is set to -0.4 instead of the traditional -1 value. The traditional GSE underpredicts solubility for molecules with experimental S0 < 50 μM. In contrast, the ABSOLV equation (trained with small molecules) underpredicts the solubility of big molecules in all cases tested. It was found that the errors in the ABSOLV-predicted solubilities of big molecules correlate linearly with the number of rotatable bonds, which suggests that flexibility may be an important factor in differentiating solubility of small from big molecules. Notably, most of the 31 big molecules considered have negative enthalpy of solution: these big molecules become less soluble with increasing temperature, which is compatible with ‘molecular chameleon’ behavior associated with intramolecular hydrogen bonding. The X-ray structures of many of these molecules reveal void spaces in their crystal lattices large enough to accommodate many water molecules when such solids are in contact with aqueous media. The water sorbed into crystals suspended in aqueous solution may enhance solubility by way of intra-lattice solute-water interactions involving the numerous H-bond acceptors in the big molecules studied. A ‘Solubility Enhancement–Big Molecules’ index was defined, which embodies many of the above findings.

Sampling Solvation Free Energy of Electrolytic Solvents with 3D2PT

Interactions between biomolecules and their surrounding solvation environment contribute significantly to their stability and to the driving forces for complex formation and conformational change. However, exploring the impact of solvation on these processes requires a thorough quantification of thermodynamic contributions to changes in the free energy of the system. Microscopic details available in atomistic molecular dynamics simulations allow for the extraction of solvation enthalpies from pair-wise additive protein-water and water-water interactions relative to the bulk solvent. The 3D-2PT method developed in the Heyden lab at Arizona State University complements this information with an analysis of hydration water entropies obtained from an analysis of intermolecular vibrations. Both the solvation enthalpy and entropy are analyzed on three-dimensional grids with 0.5-1.0 Å resolution allowing for direct thermodynamic insights into local hydration sites at the protein-water interface.Here, the original 3D-2PT approach is expanded to include contributions of electrolytes to the solvation enthalpy, entropy and free energy. This is achieved in a mixed resolution approach, which considers the drastic differences in concentration between water (∼55 M) and electrolytes (∼0.15 M) and resulting statistics for local environments. In addition to an analysis of water and ion vibrations in their local coordination environments, the new analysis distinguishes solute-water, solute-ion, water-water, ion-ion and water-ion interactions and their contributions to the solvation enthalpy.

Quantifying how step-wise fluorination tunes local solute hydrophobicity, hydration shell thermodynamics and the quantum mechanical contributions of solute-water interactions.

The ability to locally tune solute-water interactions and thus control the hydrophilic/hydrophobic character of a solute is key to control molecular self-assembly and to develop new drugs and biocatalysts; it has been a holy grail in synthetic chemistry and biology. To date, the connection between (i) the hydrophobicity of a functional group; (ii) the local structure and thermodynamics of its hydration shell; and (iii) the relative influence of van der Waals (dispersion) and electrostatic interactions on hydration remains unclear. We investigate this connection using spectroscopic, classical simulation and ab initio methods by following the transition from hydrophile to hydrophobe induced by the step-wise fluorination of methyl groups. Along the transition, we find that water-solute hydrogen bonds are progressively transformed into dangling hydroxy groups. Each structure has a distinct thermodynamic, spectroscopic and quantum-mechanical signature connected to the associated local solute hydrophobicity and correlating with the relative contribution of electrostatics and dispersion to the solute-water interactions.

Comparative Study of Anomalous Size Dependence of Charged and Neutral Solute Diffusion in Water.

We present a comparative study of size dependence of diffusion for charged and neutral solutes in water. Although both show nonmonotonicity of the size dependence of diffusion, their nature and origin are quite different. For neutral solutes, the peak position and the value of diffusion at the maximum are both independent of the solute-water interaction. Interestingly, for charged solutes, with an increase in solute-water interaction strength, the peak position shifts to lower solute sizes and with an increase in charge, it shifts to higher solute sizes. The diffusion value at the peak reduces with an increase in both solute-water interaction and solute charge. We show that all these features observed for charged solutes can be understood in terms of the interplay between ionic and nonionic interactions which is definitely absent for neutral solutes. Some of the earlier studies addressing the nonmonotonicity in diffusion did suggest the interplay between the two interactions to be the cause. However, this is the first time we show that such an interplay gives rise to the nonmonotonicity in the potential energy which is a prerequisite for obtaining the nonmonotonicity in the diffusion. Such nonmonotonicity in the potential energy is absent for neutral solutes.

Hydrophobic but Water-Friendly: Favorable Water-Perfluoromethyl Interactions Promote Hydration Shell Defects.

Although perfluorination is known to enhance hydrophobicity and change protein activity, its influence on hydration-shell structure and thermodynamics remains an open question. Here we address that question by combining experimental Raman multivariate curve resolution spectroscopy with theoretical classical simulations and quantum mechanical calculations. Perfluorination of the terminal methyl group of ethanol is found to enhance the disruption of its hydration-shell hydrogen bond network. Our results reveal that this disruption is not due to the associated volume change but rather to the electrostatic stabilization of the water dangling OH···F interaction. Thus, the hydration shell structure of fluorinated methyl groups results from a delicate balance of solute-water interactions that is intrinsically different from that associated with a methyl group.

A Molecular Mechanics Model for Flavins.

Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox-active isoalloxazine system, which is capable of one- and two-electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water-solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin-containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc.

Exploring the interactions of organic micropollutants with polyamide nanofiltration membranes: A molecular docking study

The solute-membrane interactions play an important role in adsorption and consequently rejection of trace organic compounds (TrOCs) by nanofiltration (NF) membranes, while the various specific interactions are yet to be identified and quantified. In this study, molecular docking was for the first time explored as a simulation and computation approach to elucidating the solute-membrane interactions. The binding modes between several pharmaceuticals (PhACs) and the polyamide (PA) material in different protonation/deprotonation states were simulated, and the specific interactions including hydrogen bonding, π-π stacking, π-cation interaction and ionic bridge binding were identified. Binding energies consisting of van der Waals and electrostatic components were calculated by the Grid scoring of docking, which quantitatively confirmed the contributions of various interactions to the adsorption of PhACs onto the membrane. Regression analysis showed that the adsorbed amounts could be well described jointly by the binding energies and two molecular descriptors of PhACs (i.e., solubility (logS) and polarity (MR)), which depict the effects of solute-membrane and solute-water interactions, respectively. This study provided valuable information to better understanding the adsorption mechanisms which greatly affect the rejection of TrOCs by NF membranes.

Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar aromatic compounds. To investigate a cause of error, we employed a novel systematic framework of quantum-mechanical/molecular-mechanical (QM/MM) coupling protocol in explicit solvation manner, termed DFT-CES, based on the grid-based mean-field treatment. With the aid of DFT-CES, we delved into multiple energy parts, thereby comparing DFT-CES and PB models component-by-component. By applying the modified PB model to estimate the hydration free energies of non-polar solutes, we find a possibility to improve the predictability of PB models. We expect that this study could shed light on providing an accurate route to study the hydration thermodynamics for various solute compounds.

The Chaotropic Effect as an Assembly Motif in Chemistry.

Following up on scattered reports on interactions of conventional chaotropic ions (for example, I−, SCN−, ClO4 −) with macrocyclic host molecules, biomolecules, and hydrophobic neutral surfaces in aqueous solution, the chaotropic effect has recently emerged as a generic driving force for supramolecular assembly, orthogonal to the hydrophobic effect. The chaotropic effect becomes most effective for very large ions that extend beyond the classical Hofmeister scale and that can be referred to as superchaotropic ions (for example, borate clusters and polyoxometalates). In this Minireview, we present a continuous scale of water–solute interactions that includes the solvation of kosmotropic, chaotropic, and hydrophobic solutes, as well as the creation of void space (cavitation). Recent examples for the association of chaotropic anions to hydrophobic synthetic and biological binding sites, lipid bilayers, and surfaces are discussed.

Soret coefficients and thermal conductivities of alkali halide aqueous solutions via non-equilibrium molecular dynamics simulations

ABSTRACTThermal gradients induce thermodiffusion, the Ludwig–Soret effect, which might be exploited in biotechnological, chemical, micro and nanofluidic applications. It has been shown that thermodiffusion depends very sensitively on the nature of the solute, suggesting that water–solute interactions play an important role in determining the preference of solutes to move towards hot or cold regions. Here we employ non-equilibrium molecular dynamics computations to gain insight into the role of water–ion interactions on the strength and sign of the Soret coefficient of alkali halide solutions. By performing simulations with different force-fields, we draw conclusions on the dependence of the thermodiffusive response with the properties of the first hydration shell of the ions. We further compute the thermal conductivity of aqueous solutions. State-of-the art force-fields reproduce the decrease of the thermal conductivity with increasing salt concentration when the thermal conductivity of pure water is corrected to match experimental data.

Hydration properties and water structure in aqueous solutions of native and modified cyclodextrins by UV Raman and Brillouin scattering

AbstractWe have studied aqueous solutions of native and chemically modified cyclodextrins (CDs) by means of UV Raman and Brillouin scattering. Analysis of the spectral profile of the OH‐stretching Raman signal, which is sensitive to the intermolecular organization of water, reveals a remarkable reduction of the population of ordered tetrahedral water structures inside the hydration shell of substituted CDs. As a remarkable result, this destructuring effect seems to be mainly related to the number of substituted hydroxyl groups in the CD ring rather than to the chemical nature of the substituent group. UV Brillouin scattering experiments confirm the structural picture emerging from the UV Raman study, also providing an estimate of the activation energy associated to the collective H‐bond restructuring mechanism in CD solutions. Overall, the results provide a coherent description of the water–solute interactions in aqueous solutions of CDs.

On negative rejection of uncharged organic solutes in forward osmosis

Negative rejection of 7 alcohols in Forward Osmosis (FO) is reported. The alcohols used in this study are uncharged, hydrophilic organic solutes. It is shown that current membrane transport models are not capable of reproducing the rejection pattern presented here, and consequently, a new model is developed. The model relies on adsorption of the solutes to the membrane followed by coupled transport. Adsorption is caused by salting out of the solutes, while coupled transport is caused by their small size and hydrophilicity, yielding comparatively strong water-solute interactions. It is calculated that the solutes are enriched 4–5 times in the membrane compared to the feed solution. Coupled transport is also demonstrated using the same membrane and solutes in RO mode. The novel model yields an excellent fit, and model parameters are discussed.

Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.

Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure-function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute-solute, solute-water, and water-water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations.

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy.

How to manipulate partition behavior of proteins in aqueous two-phase systems: Effect of trimethylamine N-oxide (TMAO)

It is shown that the partition behavior of solutes in a given aqueous two-phase systems can be manipulated using a nonionic additive, the trimethylamine N-oxide (TMAO). To this end, partitioning of a set of proteins and small organic compounds was analyzed in aqueous Dextran-75-Polyethylene glycol (PEG-600)-0.15 M sodium sulfate-0.01 M sodium/potassium phosphate buffer, pH 7.4 two-phase systems with TMAO additive at different concentrations from 0 up to 1.95 M. Partition behavior of several proteins was also examined in aqueous Ficoll-70-Polyethylene glycol (PEG-8000)-0.01 M sodium/potassium phosphate buffer, pH 7.4 two-phase systems with TMAO additive at different concentrations in a range from 0 up to 1.5 M. It has been found that protein partitioning changes with the increasing TMAO concentration in the protein specific manner. The differences between the solvent properties of water in the phases of the aqueous two-phase systems, such as hydrophobic character, electrostatic properties, solvent dipolarity/polarizability, hydrogen bonding donor acidity, and hydrogen bonding acceptor basicity were characterized with (a) analysis of partitioning of homologous series of sodium salts of dinitrophenylated amino acids with aliphatic alkyl side-chains, and (b) solvatochromic comparison method. The results obtained show that TMAO affects partitioning of solutes via its effect on the solvent properties of the phases, in agreement with the view that partition behavior of proteins and small organic compounds is governed by the solute-water interactions in the coexisting phases.

Water activity in liquid food systems: A molecular scale interpretation

Water activity has historically been and continues to be recognised as a key concept in the area of food science. Despite its ubiquitous utilisation, it still appears as though there is confusion concerning its molecular basis, even within simple, single component solutions. Here, by close examination of the well-known Norrish equation and subsequent application of a rigorous statistical theory, we are able to shed light on such an origin. Our findings highlight the importance of solute-solute interactions thus questioning traditional, empirically based “free water” and “water structure” hypotheses. Conversely, they support the theory of “solute hydration and clustering” which advocates the interplay of solute-solute and solute-water interactions but crucially, they do so in a manner which is free of any estimations and approximations.

A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

Encapsulation of small (bio-)organic molecules within water cages is governed by a subtle equilibrium between water–water and water–solute interactions. The competition between the formation of exohedral and endohedral complexes is investigated. The first step prior to a theoretical characterization of interactions involved in such complexes lies in the judicious choice of a level of theory. The β-propiolactone (BPL), a solute for which the micro-hydration was recently characterized by means of high resolution microwave spectroscopy (Angew. Chem. 2015, 127, 993), was selected for the present study, and a calibration step is carried out. It is shown that the dispersion-corrected density functional theory (DFT-D) suitably reproduce the geometric, energetic and spectroscopic features of the BPL:(H2O)1–5 complexes. The experimentally deduced structures of the BPL:(H2O)4,5 species are fully understood in terms of the maximization of interactions between complementary sites in the MESPs. DFT-D calculations followed by the topological analysis within the Quantum Theory of Atoms in Molecules framework have shown that the solute could efficiently interact with (H2O)6,10 clusters in a similar manner that the (H2O)4,5 clusters do. The interaction of the solute with two larger water clusters is further investigated. The exohedral and endohedral BPL:(H2O)20 isomers are close in energy with each other, whereas the formation of an inclusion complex is energetically more favored than the facial interaction in the case of the BPL:(H2O)24 cluster. The topological analysis suggests that the substantial energetic stability is due to interactions between the solute and almost all oxygen atoms of the water cage.

Influence of aliphatic amides on the temperature of maximum density of water

The influence of dissolved substances on the temperature of the maximum density of water has been studied in relation to their effect on water structure as they can change the equilibrium between structured and unstructured species of water. However, most work has been performed using salts and the studies with small organic solutes such as amides are scarce.In this work, the effect of acetamide, propionamide and butyramide on the temperature of maximum density of water was determined from density measurements using a magnetic float densimeter. Densities of aqueous solutions were measured within the temperature range from T=(275.65–278.65)K at intervals of 0.50K in the concentration range between (0.10000 and 0.80000)mol·kg−1.The temperature of maximum density was determined from the experimental results. The effect of the three amides is to decrease the temperature of maximum density of water and the change does not follow the Despretz equation. The results are discussed in terms of solute-water interactions and the disrupting effect of amides on water structure.

Using Grand Canonical Monte Carlo Simulations to Understand the Role of Interfacial Fluctuations on Solvation at the Water-Vapor Interface.

The present work investigates the effect of interfacial fluctuations (predominantly capillary wave-like fluctuations) on the solvation free energy (Δμ) of a monatomic solute at the water-vapor interface. We introduce a grand-canonical-ensemble-based simulation approach that quantifies the contribution of interfacial fluctuations to Δμ. This approach is used to understand how the above contribution depends on the strength of dispersive and electrostatic solute-water interactions at the temperature of 400 K. At this temperature, we observe that interfacial fluctuations do play a role in the variation of Δμ with the strength of the electrostatic solute-water interaction. We also use grand canonical simulations to further investigate how interfacial fluctuations affect the propensity of the solute toward the water-vapor interface. To this end, we track a quantity called the interface potential (surface excess free energy) with the number of water molecules. With increasing number of water molecules, the liquid-vapor interface moves across a solute, which is kept at a fixed position in the simulation. Hence, the dependence of the interface potential on the number of waters models the process of moving the solute through the water-vapor interface. We analyze the change of the interface potential with the number of water molecules to explain that solute-induced changes in the interfacial fluctuations, like the pinning of capillary-wave-like undulations, do not play any role in the propensity of solutes toward water-vapor interfaces. The above analysis also shows that the dampening of interfacial fluctuations accompanies the adsorption of any solute at the liquid-vapor interface, irrespective of the chemical nature of the solute and solvent. However, such a correlation does not imply that dampening of fluctuations causes adsorption.