The Dependence of Hydrophobic Interactions on the Shape of Solute Surface

According to our recent studies on hydrophobicity, this work is aimed at understanding the dependence of hydrophobic interactions on the shape of a solute's surface. It has been observed that dissolved solutes primarily affect the structure of interfacial water, which refers to the top layer of water at the interface between the solute and water. As solutes aggregate in a solution, hydrophobic interactions become closely related to the transition of water molecules from the interfacial region to the bulk water. It is inferred that hydrophobic interactions may depend on the shape of the solute surface. To enhance the strength of hydrophobic interactions, the solutes tend to aggregate, thereby minimizing their surface area-to-volume ratio. This also suggests that hydrophobic interactions may exhibit directional characteristics. Moreover, this phenomenon can be supported by calculated potential mean forces (PMFs) using molecular dynamics (MD) simulations, where different surfaces, such as convex, flat, or concave, are associated with a sphere. Furthermore, this concept can be extended to comprehend the molecular packing parameter, commonly utilized in studying the self-assembly behavior of amphiphilic molecules in aqueous solutions.

Assessing Weak Anion Binding to Small Peptides

Since Hofmeister's seminal studies in the late 19th century, it has been known that salts and buffers can drastically affect the properties of peptides and proteins. These Hofmeister effects can be conceived of in terms of three distinct phenomena/mechanisms: water-salt interactions that indirectly induce the salting-out of a protein by water sequestration by the salt, and direct salt-protein interactions that can either salt-in or salt-out the protein. Unfortunately, direct salt-protein interactions responsible for Hofmeister effects are weak and difficult to quantify. As such, they are frequently construed of as being nonspecific. Nevertheless, there has been considerable effort to better specify these interactions. Here, we use pentapeptides to demonstrate the utility of the H-dimension of nuclear magnetic resonance (NMR) spectroscopy to assess anion binding using N-H signal shifts. We qualify binding using these, demonstrating the upfield shifts induced by anion association and revealing how they are much larger than the corresponding downfield shifts induced by magnetic susceptibility and other ionic strength change effects. We also qualify binding in terms of how the pattern of signal shifts changes with point mutations. In general, we find that the observed upfield shifts are small compared with those induced by anion binding to amide-based hosts, and MD simulations suggest that this is so. Thus, charge-diffuse anions associate mostly with the nonpolar regions of the peptide rather than directly interacting with the amide N-H groups. These findings reveal the utility of 1H NMR spectroscopy for qualifying affinity to peptides─even when affinity constants are very low─and serve as a benchmark for using NMR spectroscopy to study anion binding to more complex systems.

Free Energy Density of a Fluid and Its Role in Solvation and Binding

The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. First, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f(R), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, fbulk, near a solute but should asymptotically approach fbulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential. Second, we use statistical thermodynamics to formulate a definition of the free energy density that satisfies these desiderata. Third, we show how any free energy density satisfying the desiderata may be used to analyze molecular processes in solution. In particular, because the spatial integral of f(R) equals the free energy of the system, it can be used to compute free energy changes that result from the rearrangement of solutes as well as the forces exerted on the solutes by the solvent. This enables the use of a thermodynamic analysis of water in protein binding sites to inform ligand design. Finally, we discuss related literature and address published concerns regarding the thermodynamic plausibility of a position-dependent free energy density. The theory presented here has applications in theoretical and computational chemistry and may be further generalizable beyond fluids, such as to solids and macromolecules.

Distinction and Quantification of Noncovalent Dispersive and Hydrophobic Effects

The possibilities of comparing computational results of noncovalent interactions with experimental data are discussed, first with respect to intramolecular interactions. For these a variety of experimental data such as heats of formation, crystal sublimation heats, comparison with energy minimized structures, and spectroscopic data are available, but until now largely have not found widespread application. Early force field and QM/MP2 calculations have already shown that the sublimation heats of hydrocarbons can be predicted with an accuracy of ±1%. Intermolecular interactions in solution or the gas phase are always accompanied by difficult to compute entropic contributions, like all associations between molecules. Experimentally observed T∆S values contribute 10% to 80% of the total ∆G, depending on interaction mechanisms within the complexes, such as, e.g., hydrogen bonding and ion pairing. Free energies ∆G derived from equilibrium measurements in solution allow us to define binding increments ∆∆G, which are additive and transferable to a variety of supramolecular complexes. Data from more than 90 equilibrium measurements of porphyrin receptors in water indicate that small alkanes do not bind to the hydrophobic flat surfaces within a measuring limit of ∆G = ±0.5 kJ/mol, and that 20 functions bearing heteroatoms show associations by dispersive interactions with up to ∆G = 8 kJ/mol, roughly as a function of their polarizability. Aromatic systems display size-dependent affinities ∆G as a linear function of the number of π-electrons.

How do water-mediated interactions and osmotic second virial coefficients vary with particle size?

We examine quantitatively the solute-size dependences of the effective interactions between nonpolar solutes in water and in a simple liquid. The potential w(r) of mean force and the osmotic second virial coefficients B are calculated with high accuracy from molecular dynamics simulations. As the solute diameter increases from methane's to C60's with the solute-solute and solute-solvent attractive interaction parameters fixed to those for the methane-methane and methane-water interactions, the first minimum of w(r) lowers from -1.1 to -4.7 in units of the thermal energy kT. Correspondingly, the magnitude of B (<0) increases proportional to σα with some power close to 6 or 7, which reinforces the solute-size dependence of B found earlier for a smaller range of σ [H. Naito, R. Okamoto, T. Sumi and K. Koga, J. Chem. Phys., 2022, 156, 221104]. We also demonstrate that the strength of the attractive interactions between solute and solvent molecules can qualitatively change the characteristics of the effective pair interaction between solute particles, both in water and in a simple liquid. If the solute-solvent attractive force is set to be weaker (stronger) than a threshold, the effective interaction becomes increasingly attractive (repulsive) with increasing solute size.

Dual Effect of Secondary Solutes on Binding Equilibria: Contributions from Solute-Reactant Interactions and Solute-Water Interactions

This study examines the role of water in binding equilibria with a special focus on secondary solutes (cosolutes) that influence the equilibrium but are not constituents of the final product. Using a thermodynamic framework that includes an explicit term for the release of water molecules upon binding, this investigation reveals how solutes may alter equilibria by changing the activity of the reactants, reflected in ΔG°(obs), and by changing the chemical potential of the solvent, reflected in ΔGS. The framework is applied to four experimental binding systems that differ in the degree of electrostatic contributions. The model systems include the chelation of Ca2+ by EDTA and three host-guest reactions; the pairings of p-sulfonatocalix[4]arene with tetramethylammonium ion, cucurbit[7]uril with N-acetyl-phenylalanine-amide, and β-cyclodextrin with adamantane carboxylate are tested. Each reaction pair is examined by isothermal titration calorimetry at 25 °C in the presence of a common osmolyte, sucrose, and a common chaotrope, urea. Molar solutions of trehalose and phosphate were also tested with selected models. In general, cosolutes that enhance binding tend to reduce the solvation free energy penalty and cosolutes that weaken binding tend to increase the solvation free energy penalty. Notably, the nonpolar-nonpolar interaction between adamantane carboxylate and β-cyclodextrin is characterized by a ΔGS value near zero. The results with β-cyclodextrin, in particular, prompt further discussions of the hydrophobic effect and the biocompatible properties of trehalose. Other investigators are encouraged to test and refine the approach taken here to further our understanding of solvent effects on molecular recognition.

Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl Alcohol Solutions Using Vibrational Spectroscopy

The microheterogeneous structure of aqueous tert-butyl alcohol (TBA) solutions is quantified by combining experimental, simulations, and theoretical results. Experimental Raman multivariate curve resolution (Raman-MCR) C-H frequency shift measurements are compared with predictions obtained using combined quantum mechanical and effective fragment potential (QM/EFP) calculations, as well as with molecular dynamics (MD), random mixture (RM), and finite lattice (FL) predictions. The results indicate that the microheterogeneous aggregation in aqueous TBA solutions is slightly less than that predicted by MD simulations performed using either CHARMM generalized force field (CGenFF) or optimized parameters for liquid simulations all atom (OPLS-AA) force fields but slightly more than that in a self-avoiding RM of TBA-like molecules. The results imply that the onset of microheterogeneity in aqueous solutions occurs when solute contact free energies are about an order of magnitude smaller than thermal fluctuations, thus suggesting a fundamental bound of relevance to biological self-assembly.

Medium viscosity influence on the open states genesis in a DNA molecule

The studies were carried out by the mathematical modeling of DNA mechanical deformations. Numerical calculations done for the interferon alpha 17 gene, which consists of 980 base pairs. It has been established that the genesis and dynamics of open states in the DNA molecule depends on the magnitude of the external influence (torque) and on the viscosity of the environment. In addition, it is shown that the dynamics of open states zones can have a jump-like character with a small change in the magnitude of the torque. When torque is applied to all 980 base pairs of the gene, the following effect is observed: an increase in the viscosity of the medium leads to an increase in the value of the torque necessary for the occurrence of OS and DNA unwinding, i.e. viscosity plays an important stabilizing role in DNA dynamics. Under the influence of a localized torque on different (by the content of A-T and G-C pairs and location) regions of the interferon alpha 17 gene, it was found that the magnitude of the external torque necessary for the occurrence of open states at all calculated values of viscosity depends on the nucleotide composition. The dependence of the torque magnitude required for the open states occurrence on viscosity is observed when the torque is applied to areas close to the gene boundaries. At the same time, the significance of the end effect, which weakens DNA, decreased with increasing viscosity of the medium.Communicated by Ramaswamy H. Sarma.

Zirconium Coordination Chemistry and Its Role in Optimizing Hydroxymate Chelation: Insights from Molecular Dynamics

In the past decade, there has been a growth in using Zirconium-89 (89Zr) as a radionuclide in nuclear medicine for cancer diagnostic imaging and drug discovery processes. Although one of the most popular chelators for 89Zr, desferrioxamine (DFO) is typically presented as a hexadentate ligand, our work suggests a different scenario. The coordination structure of the Zr4+-DFO complex has primarily been informed by DFT-based calculations, which typically ignore temperature and therefore entropic and dynamic solvent effects. In this work, free energy calculations using molecular dynamics simulations, where the conformational fluctuations of both the ligand and the solvent are explicitly included, are used to compare the binding of Zr4+ cations with two different chelators, DFO and 4HMS, the latter of which is an octadentate ligand that has been recently proposed as a better chelator due to the presence of four hydroxymate groups. We find that thermally induced disorder leads to an open hexadentate chelate structure of the Zr4+-DFO complex, leaving the Zr4+ metal exposed to the solvent. A stable coordination of Zr4+ with 4HMS, however, is formed by involving both hydroxamate groups and water molecules in a more closely packed structure.

Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain

Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These results provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.

Molecular Dynamics Study of the Antifouling Mechanism of Hydrophilic Polymer Brushes

We perform all-atom molecular dynamics simulations of the adsorption of amino acid side-chain analogues on polymer brushes. The analogues examined are nonpolar isobutane, polar propionamide, negatively charged propionate ion, and positively charged butylammonium ion. The polymer brushes consist of a sheet of graphene and strongly hydrophilic poly(carboxybetaine methacrylate) (PCBMA) or weakly hydrophilic poly(2-hydroxyethyl methacrylate) (PHEMA). The effective interactions between isobutane and polymer chains are repulsive for PCBMA and attractive for PHEMA. Gibbs energy decomposition analysis shows that this is due to the abundance of water in the PCBMA brush, which increases the steric repulsion and decreases the Lennard-Jones attraction. The affinity of the hydrophilic analogues is low for both PCBMA and PHEMA chains, but the balance between the components of the Gibbs energy is different for the two polymers. The simulations are performed at several θ, where θ is the degree of overlap of polymer chains. The antifouling performance against the neutral analogues is better for PCBMA than for PHEMA in the low and high θ regimes. However, in the middle θ regime, the antifouling performance of PHEMA is close to or better than that of PCBMA. This is attributed to the formation of a dense layer of PHEMA on the graphene surface that inhibits direct adsorption of analogue molecules on graphene. The charged analogues do not bind to either the PHEMA or PCBMA brush irrespective of θ.

Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau

A known imbalance between intra-protein and protein-water interactions in many empirical force fields results in collapsed conformational ensembles of intrinsically disordered proteins in explicit solvent simulations that disagree with experiments. Multiple strategies have been introduced in the literature to modify protein-water interactions, which improve agreement between experiments and simulations. In this work, we combine simulations with standard and modified force fields with a spatially resolved analysis of solvation free energy contributions and compare the consequences of each strategy. We find that enhanced Lennard-Jones (LJ) interactions between protein atoms and water oxygens primarily improve the solvation of nonpolar functional groups of the protein. In contrast, modified electrostatics in the water model or strengthened LJ interactions between the protein and water hydrogens mainly affect the hydration of polar functional groups. Modified electrostatics further impact the average orientation of water molecules in the hydration shell. As a result, protein-water interactions with the first hydration layers are strengthened, while interactions with water molecules in higher hydration shells are weakened. Hence, distinct strategies to balance intra-protein and protein-water interactions in simulations have qualitatively different effects on protein solvation. These differences are not necessarily captured by comparisons to experiments that report on global parameters describing protein conformational ensembles, e.g., the radius of gyration, but will influence the tendency of a protein to form aggregates or phase-separated droplets.

Using Implicit-Solvent Potentials to Extract Water Contributions to Enthalpy-Entropy Compensation in Biomolecular Associations

Biomolecular assembly typically exhibits enthalpy-entropy compensation (EEC) behavior whose molecular origin remains a long-standing puzzle. While water restructuring is believed to play an important role in EEC, its contribution to the entropy and enthalpy changes, and how these changes relate to EEC, remains poorly understood. Here, we show that water reorganization entropy/enthalpy can be obtained by exploiting the temperature dependence in effective, implicit-solvent potentials. We find that the different temperature dependencies in the hydrophobic interaction, rooted in water reorganization, result in substantial variations in the entropy/enthalpy change, which are responsible for EEC. For lower-critical-solution-temperature association, water reorganization entropy dominates the free-energy change at the expense of enthalpy; for upper-critical-solution-temperature association, water reorganization enthalpy drives the process at the cost of entropy. Other effects, such as electrostatic interaction and conformation change of the macromolecules, contribute much less to the variations in entropy/enthalpy.

Solvation thermodynamics from cavity shapes of amino acids

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.

Formation of a traditional Chinese medicine self-assembly nanostrategy and its application in cancer: a promising treatment

Traditional Chinese medicine (TCM) has been used for centuries to prevent and treat a variety of illnesses, and its popularity is increasing worldwide. However, the clinical applications of natural active components in TCM are hindered by the poor solubility and low bioavailability of these compounds. To address these issues, Chinese medicine self-assembly nanostrategy (CSAN) is being developed. Many active components of TCM possess self-assembly properties, allowing them to form nanoparticles (NPs) through various noncovalent forces. Self-assembled NPs (SANs) are also present in TCM decoctions, and they are closely linked to the therapeutic effects of these remedies. SAN is gaining popularity in the nano research field due to its simplicity, eco-friendliness, and enhanced biodegradability and biocompatibility compared to traditional nano preparation methods. The self-assembly of active ingredients from TCM that exhibit antitumour effects or are combined with other antitumour drugs has generated considerable interest in the field of cancer therapeutics. This paper provides a review of the principles and forms of CSAN, as well as an overview of recent reports on TCM that can be used for self-assembly. Additionally, the application of CSAN in various cancer diseases is summarized, and finally, a concluding summary and thoughts are proposed. We strongly believe that CSAN has the potential to offer fresh strategies and perspectives for the modernization of TCM.

Recent Advances in Nanocellulose Aerogels for Efficient Heavy Metal and Dye Removal

Water pollution is a significant environmental issue that has emerged because of industrial and economic growth. Human activities such as industrial, agricultural, and technological practices have increased the levels of pollutants in the environment, causing harm to both the environment and public health. Dyes and heavy metals are major contributors to water pollution. Organic dyes are a major concern because of their stability in water and their potential to absorb sunlight, increasing the temperature and disrupting the ecological balance. The presence of heavy metals in the production of textile dyes adds to the toxicity of the wastewater. Heavy metals are a global issue that can harm both human health and the environment and are mainly caused by urbanization and industrialization. To address this issue, researchers have focused on developing effective water treatment procedures, including adsorption, precipitation, and filtration. Among these methods, adsorption is a simple, efficient, and cheap method for removing organic dyes from water. Aerogels have shown potential as a promising adsorbent material because of their low density, high porosity, high surface area, low thermal and electrical conductivity, and ability to respond to external stimuli. Biomaterials such as cellulose, starch, chitosan, chitin, carrageenan, and graphene have been extensively studied for the production of sustainable aerogels for water treatment. Cellulose, which is abundant in nature, has received significant attention in recent years. This review highlights the potential of cellulose-based aerogels as a sustainable and efficient material for removing dyes and heavy metals from water during the treatment process.

Acidic Conditions Impact Hydrophobe Transfer across the Oil-Water Interface in Unusual Ways

Molecular dynamics simulation and enhanced free energy sampling are used to study hydrophobic solute transfer across the water-oil interface with explicit consideration of the effect of different electrolytes: hydronium cation (hydrated excess proton) and sodium cation, both with chloride counterions (i.e., dissociated acid and salt, HCl and NaCl). With the Multistate Empirical Valence Bond (MS-EVB) methodology, we find that, surprisingly, hydronium can to a certain degree stabilize the hydrophobic solute, neopentane, in the aqueous phase and including at the oil-water interface. At the same time, the sodium cation tends to "salt out" the hydrophobic solute in the expected fashion. When it comes to the solvation structure of the hydrophobic solute in the acidic conditions, hydronium shows an affinity to the hydrophobic solute, as suggested by the radial distribution functions (RDFs). Upon consideration of this interfacial effect, we find that the solvation structure of the hydrophobic solute varies at different distances from the oil-liquid interface due to a competition between the bulk oil phase and the hydrophobic solute phase. Together with an observed orientational preference of the hydroniums and the lifetime of water molecules in the first solvation shell of neopentane, we conclude that hydronium stabilizes to a certain degree the dispersal of neopentane in the aqueous phase and eliminates any salting out effect in the acid solution; i.e., the hydronium acts like a surfactant. The present molecular dynamics study provides new insight into the hydrophobic solute transfer across the water-oil interface process, including for acid and salt solutions.

Recent advances in natural small molecules as drug delivery systems

Drug delivery systems (DDSs) are a multidisciplinary approach toward the effective delivery of drugs to their target sites. Natural small molecule (NSM) compounds with anticancer activity, self-assembly and co-assembly functions show great potential for application as novel DDSs in the biomedical field. NSMs are widely sourced, have many modification sites, and readily form hydrogen bonds, π-π interactions, van der Waals interactions, and other non-covalent bonds in solvents, resulting in ordered structures. Moreover, their good biocompatibility and bioactivity allow compositions based on these compounds to be used in life science applications such as tissue engineering, drug delivery and cell imaging, showing the potential medical value of NSMs as DDSs. In this review, we summarise the role, assembly principles and applications of natural products such as triterpenoids, diterpenoids, sterols, alkaloids and polysaccharides in the construction of small molecule systems, which are expected to provide an important reference for the development of more active natural nanomaterials and the study of single or multi-component interactions.

Solvation free energy arithmetic for small organic molecules

Solvent-mediated interactions contribute to ligand binding affinities in computational drug design and provide a challenge for theoretical predictions. In this study, we analyze the solvation free energy of benzene derivatives in water to guide the development of predictive models for solvation free energies and solvent-mediated interactions. We use a spatially resolved analysis of local solvation free energy contributions and define solvation free energy arithmetic, which enable us to construct additive models to describe the solvation of complex compounds. The substituents analyzed in this study are carboxyl and nitro-groups due to their similar sterical requirements but distinct interactions with water. We find that nonadditive solvation free energy contributions are primarily attributed to electrostatics, which are qualitatively reproduced with computationally efficient continuum models. This suggests a promising route for the development of efficient and accurate models for the solvation of complex molecules with varying substitution patterns using solvation arithmetic.

Lipophilic NO-Driven Nanomotors as Drug Balloon Coating for the Treatment of Atherosclerosis

Drug-coated balloons (DCB) intervention is an important approach for the treatment of atherosclerosis (AS). However, this therapeutic approach has the drawbacks of poor drug retention and penetration at the lesion site. Here, a lipophilic drug-loaded nanomotor as a modified balloon coating for the treatment of AS is reported. First, a lipophilic nanomotor PMA-TPP/PTX loaded with drug PTX and lipophilic triphenylphosphine (TPP) compounds is synthesized. The PMA-TPP/PTX nanomotors use nitric oxide (NO) as the driving force, which is produced from the reaction between arginine on the motor substrate and excess reactive oxygen species (ROS) and inducible nitric oxide synthase (iNOS) in the AS microenvironment. The final in vitro and in vivo experimental results confirm that the introduction of the lipophilic drug-loaded nanomotor technology can greatly enhance the drug retention and permeability in atherosclerotic lesions. In particular, NO can also play an anti-AS role in improving endothelial cell function and reducing oxidative stress. The chemotherapeutic drug PTX loaded onto the nanomotors can inhibit cell division and proliferation, thereby exerting the effect of inhibiting vascular intimal hyperplasia, which is helpful for the multiple therapies of AS. Using nanomotor technology to solve cardiovascular diseases may be a promising research direction.

Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions

Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions but present conceptual and computational challenges to both theory and simulations. We review recent developments in an approach addressing these challenges─local molecular field (LMF) theory. LMF theory exploits an exact and physically suggestive separation of intermolecular Coulomb interactions into strong short-range and uniformly slowly varying long-range components. This allows us to accurately determine the averaged effects of the long-range components on the short-range structure using effective single particle fields and analytical corrections, greatly reducing the need for complex lattice summation techniques used in most standard approaches. The simplest use of these ideas in aqueous solutions leads to the short solvent (SS) model, where both solvent-solvent and solute-solvent Coulomb interactions have only short-range components. Here we use the SS model to give a simple description of pairing of nucleobases and biologically relevant ions in water.

Observation of Strong Synergy in the Interfacial Water Response of Binary Ionic and Nonionic Surfactant Mixtures

Interfacial vibrational footprints of the binary mixture of sodium dodecyl sulfate (SDS) and hexaethylene glycol monododecyl ether (C₁₂E₆) were probed using heterodyne detected vibrational sum frequency generation (HDVSFG). Our results show that in the presence of C₁₂E₆ at CMC (70 μM) the effect of SDS on the orientation of interfacial water molecules is enhanced 10 times compared to just pure surfactants. The experimental results contest the traditional Langmuir adsorption model predictions. This is also evidenced by our molecular dynamics simulations that show a remarkable restructuring and enhanced orientation of the interfacial water molecules upon DS^- adsorption to the C₁₂E₆ surface. The simulations show that the adsorption free energy of DS^- ions to a water surface covered with C₁₂E₆ is an enthalpy-driven process and more attractive by ∼10 k_BT compared to the adsorption energy of DS^- to the surface of pure water.

Molecular dynamics study of the interactions between a hydrophilic polymer brush on graphene and amino acid side chain analogues in water

We perform all-atom molecular dynamics simulations of poly(2-hydroxyethyl methacrylate) (PHEMA) brushes in aqueous solutions of isobutane, propionamide, and sodium propionate. These solutes are side chain analogues to leucine, glutamine, and glutamic acid, respectively. We compute the Gibbs energy profile of the solute's adsorption to the polymer brush and decompose it into the contributions from the steric repulsion, van der Waals interaction, and Coulomb interaction to reveal the energetic origin of repulsion or attraction of the solute by the polymer brush. The Henry adsorption constant is the amount of adsorption normalized by the concentration in aqueous solution. We examine the dependence of this quantity on the grafting density and chain length. Our results suggest that the concurrent primary and ternary adsorption mechanism may be more important than previously expected when the solute is hydrophobic.

Connecting Non-Gaussian Water Density Fluctuations to the Lengthscale Dependent Crossover in Hydrophobic Hydration

We connect density fluctuations in liquid water to lengthscale dependent crossover in hydrophobic hydration. Specifically, we employ indirect umbrella sampling (INDUS) simulations to characterize density fluctuations in observation volumes of various sizes and shapes in water and as a function of temperature and salt concentration. Consistent with previous observations, density fluctuations are Gaussian in small molecular scale volumes, but they display non-Gaussian "low-density fat tails" in larger volumes. These non-Gaussian tails are indicative of the proximity of water to its liquid to vapor phase transition and have implications on biomolecular interactions and function. We show that the onset of non-Gaussian fluctuations in large volumes is accompanied by the formation of a cavity in the observation volume. We develop a model that uses the physics of cavity-water interface formation as a key ingredient and show that it captures the nature of non-Gaussian density fluctuations over a broad region in water and in salt solutions. We discuss the limitations of this model in the very low density region of the distribution. Our calculations provide new insights into the origins of non-Gaussian density fluctuations in water and their connections to lengthscale dependent crossover in hydrophobic hydration.

Different Temperature- and Pressure-Effects on the Water-Mediated Interactions between Hydrophobic, Hydrophilic, and Hydrophobic-Hydrophilic Nanoscale Surfaces

Water-mediated interactions (WMI) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic-hydrophilic) interactions have been mostly overlooked. Here we study the role of T and P of the WMI between nanoscale (i) hydrophobic-hydrophobic, (ii) hydrophilic-hydrophilic, and (iii) hydrophilic-hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic and hybrid interactions are all sensitive to P. However, while hydrophobic interactions [case (i)] are sensitive to T-variations, hydrophilic [case (ii)] and hybrid interactions [case (iii)] are practically T-independent. An analysis of the entropic and enthalpic contributions to the PMF for cases (i)-(iii) is also presented. Our results are important in understanding T- and P-induced protein denaturation, and the interactions of biomolecules in solution, including protein aggregation andphase separation processes. From the computational point of view, the results presented here are relevant in the design of implicit water models for the study of molecular and colloidal/nanoparticle systems at different thermodynamic conditions.

Learning Efficient, Collective Monte Carlo Moves with Variational Autoencoders

Discovering meaningful collective variables for enhancing sampling, via applied biasing potentials or tailored MC move sets, remains a major challenge within molecular simulation. While recent studies identifying collective variables with variational autoencoders (VAEs) have focused on the encoding and latent space discovered by a VAE, the impact of the decoding and its ability to act as a generative model remains unexplored. We demonstrate how VAEs may be used to learn (on-the-fly and with minimal human intervention) highly efficient, collective Monte Carlo moves that accelerate sampling along the learned collective variable. In contrast to many machine learning-based efforts to bias sampling and generate novel configurations, our methods result in exact sampling in the ensemble of interest and do not require reweighting. In fact, we show that the acceptance rates of our moves approach unity for a perfect VAE model. While this is never observed in practice, VAE-based Monte Carlo moves still enhance sampling of new configurations. We demonstrate, however, that the form of the encoding and decoding distributions, in particular the extent to which the decoder reflects the underlying physics, greatly impacts the performance of the trained VAE.

Osmotic second virial coefficients for hydrophobic interactions as a function of solute size

To gain quantitative insight into how the overall strength of the hydrophobic interaction varies with the molecular size, we calculate osmotic second virial coefficients B for hydrophobic spherical molecules of different diameters σ in water based on molecular simulation with corrections to the finite-size and finite-concentration effects. It is shown that B (<0) changes by two orders of magnitude greater as σ increases twofold and its solute-size dependence is best fit by a power law B ∝ σ^α with the exponent α ≃ 6, which contrasts with the cubic power law that the second virial coefficients of gases obey. It is also found that values of B for the solutes in a nonpolar solvent are positive but they obey the same power law as in water. A thermodynamic identity for B derived earlier [K. Koga, V. Holten, and B. Widom, J. Phys. Chem. B 119, 13391 (2015)] indicates that if B is asymptotically proportional to a power of σ, the exponent α must be equal to or greater than 6.

Spatially Resolved Hydration Thermodynamics in Biomolecular Systems

Water is essential for the structure, dynamics, energetics, and thus the function of biomolecules. It is a formidable challenge to elicit, in microscopic detail, the role of the solvation-related driving forces of biomolecular processes, such as the enthalpy and entropy contributions to the underlying free-energy landscape. In this Perspective, we discuss recent developments and applications of computational methods that provide a spatially resolved map of hydration thermodynamics in biomolecular systems and thus yield atomic-level insights to guide the interpretation of experimental observations. An emphasis is on the challenge of quantifying the hydration entropy, which requires characterization of both the motions of the biomolecules and of the water molecules in their surrounding.

On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding

The complexity of macromolecular surfaces means that there are still many open questions regarding how specific areas are solvated and how this might affect the complexation of guests. Contributing to the identification and classification of the different possible mechanisms of complexation events in aqueous solution, and as part of the recent SAMPL8 exercise, we report here on the synthesis and conformational properties of TEEtOA 2, a cavitand with conformationally flexible ethyl groups at its portal. Using a combination of ITC and NMR spectroscopy, we report the binding affinities of a series of carboxylates to 2 and compare it to a related cavitand TEMOA 1. Additionally, we report MD simulations revealing how the wetting of the pocket of 2 is controlled by the conformation of its rim ethyl groups and, correspondingly, a novel triggered wetting, guest complexation mechanism, whereby the approaching guest opens up the pocket of the host, inducing its wetting and ultimately allows the formation of a hydrated host-guest complex (H·G·H2O). A general classification of complexation mechanisms is also suggested.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water‐mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor‐substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

Solubility of Hydrophobes into Macrocyclic Hosts

The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.

Contribution of the Induced-Dipole Interaction to Methane Aggregation in Water

Apolar molecules in the gas phase have no dipole moments. However, when placed in an aqueous environment, they acquire a dipole moment induced by the electric fields of the surrounding water molecules. Could these induced dipole moments, not present in the gas phase but present in solution, play an important role in the hydrophobic interaction between two apolar molecules? In particular, for two methane molecules, our results show that the interaction between the induced-dipole moments only very weakly plays a role in the aggregation of a pair of methane molecules in water. The induced-dipole-induced-dipole interaction has a magnitude as large as 1 kcal/mol for certain mutual orientations of the induced dipole moments, which is larger than the magnitude of the free energy of aggregation of the methane solutes in water. However, when averaged over all physically occurring conformations for a fixed intersolute separation, this interaction averages to an insignificant value (magnitude less than 0.01 kcal/mol) except, possibly, for some very short intermolecular separation.

Evidence of Many-Body Interactions in the Virial Coefficients of Polyelectrolyte Gels

Simulation studies of aqueous polymer solutions, and heuristic arguments by De Gennes for aqueous polyethylene oxide polymer solutions, have suggested that many-body interactions can give rise to the ‘anomalous’ situation in which the second osmotic virial coefficient is positive, while the third virial coefficient is negative. This phenomenon was later confirmed in analytic calculations of the phase behavior and the osmotic pressure of complex fluids exhibiting cooperative self-assembly into extended dynamic polymeric structures by Dudowicz et al. In the present study, we experimentally confirm the occurrence of this osmotic virial sign inversion phenomenon for several highly charged model polyelectrolyte gels (poly(acrylic acid), poly(styrene sulfonate), DNA, hyaluronic acid), where the virial coefficients are deduced from osmotic pressure measurements. Our observations qualitatively accord with experimental and simulation studies indicating that polyelectrolyte materials exhibit supramolecular assembly in solution, another symptomatic property of fluids exhibiting many-body interactions. We also find that the inversion in the variation of the second (A₂) and third (A₂) virial coefficients upon approach to phase separation does not occur in uncharged poly(vinyl acetate) gels. Finally, we briefly discuss the estimation of the osmotic compressibility of swollen polyelectrolyte gels from neutron scattering measurements as an alternative to direct, time-consuming and meticulous osmotic pressure measurements. We conclude by summarizing some general trends and suggesting future research directions of natural and synthetic polyelectrolyte hydrogels.

Model Folded Hydrophobic Polymers Reside in Highly Branched Voids

By using advanced data analysis techniques, we characterize the shape of the voids surrounding model polymers of different sizes in water, observed in molecular dynamics simulations. We find that even when the model polymer is folded, the voids are extremely rough, with branches that can extend to over 1 nm away from the polymer. Water molecules in contact with the void retain close-to-bulk properties in terms of local structure. The branches disappear, and the voids start resembling the quasispherical shape predicted by dewetting theory only when they surround particles with a radius ∼1 nm, well above the size occupied by a folded hydrophobic polymer. Our results provide fresh insights into the microscopic origins of the vapor-like interfaces underlying dewetting and drying transitions.

Solutions, in Particular Dilute Solutions of Nonelectrolytes: A Review

The liquid state is one of the three principal states of matter and arguably the most important one; and liquid mixtures represent a large research field of profound theoretical and practical interest. This topic is of importance in many areas of the applied sciences, such as in chemical engineering, geochemistry, the environmental sciences, biophysics and biomedical technology. First, I will concisely present a review of important concepts from classical thermodynamics of nonelectrolyte solutions; this will be followed by a survey of (semi-)empirical approaches to representing the composition and temperature dependence of selected thermodynamic mixture properties, and finally the focus will be on dilute binary nonelectrolyte solutions where one component, a supercritical solute, is present in much smaller quantity than the other component, called the solvent. Partial molar properties in the limit of infinite dilution (indicated by a superscript ∞) are of particular interest. For instance, activity coefficients (Lewis–Randall (LR) convention) are customarily used to characterize mixing behavior, and infinite-dilution values $$\gamma_{i}^{{{\text{LR,}}\infty }}$$ γ i LR, ∞ provide a convenient route for obtaining binary parameters for several popular solution models. When discussing solute (j)—solvent (i) interactions in solutions where the solute is supercritical, the Henry fugacity $$h_{j,i} \left( {T,P} \right)$$ h j , i T , P , also known as Henry’s law (HL) constant, is a measurable thermodynamic key quantity. Its temperature dependence yields information on the partial molar enthalpy change on solution $$\Delta H_{j}^{\infty } \left( {T,P} \right)$$ Δ H j ∞ T , P , while its pressure dependence yields information on the partial molar volume $$V_{j}^{{{\text{L,}}\infty }} \left( {T,P} \right)$$ V j L, ∞ T , P of solute j in the liquid phase (superscript L). I will clarify issues frequently overlooked, touch upon solubility data reduction and correlation, report a few recent high-precision experimental results on dilute aqueous solutions of supercritical nonelectrolytes, and show the equivalency of results for caloric quantities (e.g. $$\Delta H_{j}^{\infty }$$ Δ H j ∞ ) obtained via van ’t Hoff analysis of high-precision solubility data with directly measured calorimetric data.

Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both?

There are many open questions regarding the supramolecular properties of ions in water, a fact that has ramifications within any field of study involving buffered solutions. Indeed, as Pielak has noted (Buffers, Especially the Good Kind, Biochemistry, 2021, in press. DOI:10.1021/acs.biochem.1c00200) buffers were conceived of with little regard to their supramolecular properties. But there is a difficulty here; the mathematical models supramolecular chemists use for affinity determinations do not account for screening. As a result, there is uncertainty as to the magnitude of any screening effect and how this compares to competitive salt/buffer binding. Here we use a tetra-cation cavitand to compare halide affinities obtained using a traditional unscreened model and a screened (Debye-Hückel) model. The rule of thumb that emerges is that if ionic strength is changed by >1 order of magnitude─either during a titration or if a comparison is sought between two different buffered solutions─screening should be considered. We also build a competitive mathematical model showing that binding attenuation in buffer is largely due to competitive binding to the host by said buffer. For the system at hand, we find that the effect of competition is approximately twice that of the effect of screening (∼RT at 25 °C). Thus, for strong binders it is less important to account for screening than it is to account for competitive complexation, but for weaker binders both effects should be considered. We anticipate these results will help supramolecular chemists unravel the properties of buffers and so help guide studies of biomacromolecules.

Less-Ordered Hydration Shell around Poly(N,N-diethylacrylamide) Is Insensitive to the Clouding Transition

Raman multivariate curve resolution (Raman-MCR) is applied to examine how the hydration shell around poly(N,N-diethylacrylamide) (PDEAM) changes upon heating, in comparison with poly(N-isopropylacrylamide) (PNIPAM), both of which undergo a clouding transition near room temperature. We report that PDEAM possesses a less-ordered and smaller hydration shell than PNIPAM. Furthermore, the PDEAM hydration-shell structure is insensitive to the occurrence of clouding, indicating the coil-globule transition and aggregation of multiple chains can be achieved without the hydration-shell structural transformation.

Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

The insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol^-1 and yields a net stabilization of also ≈5 kJ mol^-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system.

Water-mediated interactions destabilize proteins

Proteins are folded to avoid exposure of the nonpolar groups to water because water‐mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins—which is a well‐accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free‐energy calculation for a thermodynamic cycle of a protein folding using a liquid‐state density functional theory. Here, the solvation‐free energy for a leucine zipper formation was examined in the coiled‐coil protein GCN4‐p1, a typical model for hydrophobic interactions, which demonstrated that water‐mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.

Crowding effects on water-mediated hydrophobic interactions

Understanding the fundamental forces such as hydrophobic interactions in a crowded intracellular environment is necessary to comprehensively decipher the mechanisms of protein folding and biomolecular self-assemblies. The widely accepted entropic depletion view of crowding effects primarily attributes biomolecular compaction to the solvent excluded volume effects exerted by the "inert" crowders, neglecting their soft interactions with the biomolecule. In this study, we examine the effects of chemical nature and soft attractive energy of crowders on the water-mediated hydrophobic interaction between two non-polar neopentane solutes using molecular dynamics simulations. The crowded environment is modeled using dipeptides composed of polar and non-polar amino acids of varying sizes. The results show that amongst the non-polar crowders, Leu₂ strengthens the hydrophobic interactions significantly, whereas the polar and small-sized non-polar crowders do not show significant strengthening. Distinct underlying thermodynamic driving forces are illustrated where the small-sized crowders drive hydrophobic interaction via a classic entropic depletion effect and the bulky crowders strengthen it by preferential interaction with the solute. A crossover from energy-stabilized solvent-separated pair to entropy-stabilized contact pair state is observed in the case of bulky non-polar (Leu₂) and polar (Lys₂) crowders. The influence of solute-crowder energy in affecting the dehydration energy penalty is found to be crucial for determining the neopentane association. The findings demonstrate that along with the entropic (size) effects, the energetic effects also play a crucial role in determining hydrophobic association. The results can be extended and have implications in understanding the impact of protein crowding with varying chemistry in modulating the protein free energy landscapes.

Atomic Force Microscopy Study of Non-DLVO Interactions between Drops and Bubbles

The heterointeraction between liquid drops and air bubbles dispersed in another immiscible liquid is studied with the application of the atomic force microscopy (AFM) probe techniques. The tetradecane drops and air bubbles readily coalescence to form a lens-like structure in 100 mM sodium chloride aqueous solution, demonstrating strong hydrophobic (HB) attraction. The interaction range and strength of this hydrophobic attraction between oil drops and air bubbles is investigated by fine control of electrical double layer thicknesses related to specific electrolyte concentrations, and a midrange term in combination with a short-range term is found to present a proper characterization of this hydrophobic attraction. A further step is taken by introducing a triblock copolymer (Pluronic F68) into the aqueous solution, with results indicating that a relatively long-range steric hindrance (SH) furnished by a polymer "brush" surmounts the hydrophobic attraction. Finally, the interaction between a water drop and an air bubble in tetradecane is also measured as a comparison. The repelling action between a hydrophobic body (air bubble) and water drop indicates a strong repulsion. The present results show an interesting understanding of hydrophobic interactions between drops and bubbles, which is of potential application in controlling dispersion stability.

Length-Scale Effects in Hydrophobic Polymer Collapse Transitions

The study of molecular mechanisms for cosolvent-driven hydrophobic polymer collapse transitions in water is of pivotal importance in the field of smart responsive materials. Computational studies together with complementary experimental data have led to the discovery and understanding of new phenomena in recent years. However, elementary mechanisms, generally contributing to polymer coil-globule transitions in different classes of cosolvent-water systems, remain elusive due to compensating energy-entropy effects. Herein, I discuss the role of length scales in polymer solubility problems. New ideas on surfactant mechanisms are discussed based on examples in which these mechanisms drive polymer swelling or collapse.