Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes

Investigating the Vapor-Phase Adsorption of Aroma Molecules on the Water-Vapor Interface using Molecular Dynamics Simulations

Surfactants are amphiphilic additives primarily used to reduce the surface tension of water and manipulate its wettability on various surfaces. Recent reports suggest that volatile surfactants, such as aroma molecules, diffuse more quickly to the interface from the vapor-phase than conventional surfactants typically used in the aqueous phase. The ability to adsorb from the vapor phase, in addition to their use as cosurfactants, expands the potential applications of volatile surfactants, particularly in situations where adding surfactants from the liquid phase is difficult. Here, we present a molecular level understanding of the adsorption kinetics of linalool, a common aroma molecule, on the water interface using molecular dynamics simulations. We note that the value of surface tension while adsorption from vapor and liquid phases is dependent only on the surface coverage. A minimum surface tension of 32 ± 1.8 mN/m is obtained in both cases at a maximum surface coverage of 4.88 μmol/m2 at 300 K. We observe the extent of decrease of the H-bonds between linalool-water and linalool-linalool molecules at various surface coverages to explain the mechanism of surface tension reduction. We solve Gibb's adsorption equation to establish a correlation between the surface coverage of linalool and the corresponding bulk concentration in experiments. We investigate the free energy profile of linalool's adsorption behavior at different surface coverages and temperatures. Our report suggests that linalool adsorption onto the water interface is an enthalpy-driven process primarily dependent on the strength of the interaction between the hydroxyl group of linalool and water molecules. These insights are crucial for selecting a suitable aroma molecule for various applications that target the vapor-phase adsorption mechanism.

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.

Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study

It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)₂] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.

Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies

Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM⁺ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.

Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties

The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions.

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.

Physical insight into the entropy-driven ion association

The ion association is widely believed to be dominated by the favorable entropy change arising from the release of water molecules from ion hydration shells. However, no direct thermodynamic evidence exists to validate the reliability and suitability of this view. Herein, we employ complicated free energy calculations to rigorously split the free energy including its entropic and enthalpic components into the water-induced contributions and ion-ion interaction terms for several ion pairs from monatomic to polyatomic ions, spanning the size range from small kosmotropes to large chaotropes (Na⁺ , Cs⁺ , Ca²⁺ , F^- , I^- , CO₃ ^2- , and HPO₄ ^2- ). Our results successfully reveal that though ion associations are indeed determined by a delicate balance between the favorable entropy variation and the repulsive enthalpy change, the entropy gain dominated by the solvent occurs only for the monatomic ion pairing. The water-induced entropic contribution significantly goes against the ion pairing between polyatomic anion and cation, which is, alternatively, dominated by the favorable entropy from the ion-ion interaction term, due to the configurational arrangement of polyatomic anions involved in ion association. The structural and dynamic analysis demonstrates that the entropy penalty from the water phase is primarily ascribed to the enhanced stability of water molecules around the cation imposed by the incoming anion. Our study successfully provides a fundamental understanding of water-mediated ion associations and highlights disparate lengthscale dependencies of the dehydration thermodynamics on the specific types of ions.

Quantifying Energetic and Entropic Pathways in Molecular Systems

When examining dynamics occurring at nonzero temperatures, both energy and entropy must be taken into account to describe activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe different metastable states and the transition mechanisms between them. Here we use a physics-based machine learning method called state predictive information bottleneck (SPIB) to find nonlinear reaction coordinates for three systems of varying complexity. SPIB is able to correctly predict an entropic bottleneck for an analytical flat-energy double-well system and identify the entropy- and energy-dominated pathways for an analytical four-well system. Finally, for a simulation of benzoic acid permeation through a lipid bilayer, SPIB is able to discover the entropic and energetic barriers to the permeation process. Given these results, we thus establish that SPIB is a reasonable and robust method for finding the important entropy, energy, and enthalpy barriers in physical systems, which can then be used to enhance the understanding and sampling of different activated mechanisms.

Absorption of Volatile Organic Compounds Toluene and Acetaldehyde in Choline Chloride-Based Deep Eutectic Solvents

Unrestricted emission of volatile organic compounds (VOCs)─a threat to human health and the environment─can be controlled to a large extent by the capturing mechanism. Few recent experimental studies explored the efficacy of the deep eutectic solvent (DES), a designer solvent with some fascinating properties, as a VOC-capturing medium. Through the partition coefficient measurement, it was found that the choline chloride-based DESs exhibit excellent VOC-capturing potencies. However, a molecular picture of the above absorption process is still lacking. Here, we study the molecular mechanism of the absorption of two commonly occurring VOCs, toluene and acetaldehyde, in two different choline chloride-based DESs with varying donor molecules, urea, and levulinic acid via the molecular dynamics simulation technique. Strong absorption of the VOCs is observed in both the DESs. The free energy profile for the absorption process has been explored using the umbrella sampling method. The VOCs are preferentially solvated near the liquid/vapor interface. The simulated partition coefficients for the VOCs from the vapor to the liquid phase show good agreement with the experimental results. Detailed analyses of the spatial and orientational structure of the VOCs and different components of DESs are performed to elucidate the interaction among them. The above analyses have indicated that DES is a better VOC-capturing medium compared to a room-temperature ionic liquid, which is more extensively studied in the literature.

Adsorption of Epoxy Oligomers on Iron Oxide Surfaces: The Importance of Surface Treatment and the Role of Entropy

Epoxy-based coatings are widely used in a range of industries as protective coatings. The performance of the final solid-polymer system is dependent on the physicochemical properties of the interface and the interaction between the polymer and the solid substrate. In this study, we perform atomistic molecular dynamics simulations to investigate the binding of a common component in epoxy resins, diglycidyl ether of bisphenol A (DGEBA), on two iron oxide surfaces, hematite (0001) and magnetite (100), and investigate the effect of surface hydroxylation on the binding energy. We show that adsorption of DGEBA on hematite is more favorable than on magnetite and that the adsorbed molecules are highly localized on the pristine hematite surface but mobile on highly hydroxylated hematite surfaces and magnetite surfaces irregardless of surface hydroxylation fraction. A high degree of hydroxylation significantly reduces the binding energy of DGEBA on hematite but not on magnetite. The free-energy calculations confirm the trends observed upon hydroxylation, but the magnitude of the potential of mean force is lower than the binding energy due to the entropic contributions. Therefore, it can be suggested that DGEBA will adsorb more strongly on a surface containing a higher content of hematite than magnetite and that the presence of hydroxyl groups will weaken this adsorption. The presence of hydroxyl groups increases mobility of the chains, which can affect the coating rigidity.

Molecular-level understanding of gibbsite particle aggregation in water

Using molecular dynamics simulations, we investigate the molecular scale origin of crystal face selectivity when one gibbsite particle attaches to another in water. A comparison of the free energy per unit surface area of particle-particle attachment indicates that particle attachment through edge surfaces, where the edge surfaces are either (1 0 0) or (1 1 0) crystal faces, is more energetically favorable compared to attachment between two basal surfaces (i.e., (0 0 1) crystal faces) or between the basal surface of one particle and the edge surface of another. This result suggests that gibbsite crystals with low basal/edge surface area ratio will preferentially attach through edge surfaces, potentially helping the crystals grow laterally. However, for larger gibbsite particles (high basal/edge surface area ratio) the total free energy, not normalized by surface area, of particle attachment through the basal surfaces is lower (more negative) than attachment through the edge surfaces, indicating that larger gibbsite particles will preferentially aggregate through basal surface attachments. The short-range electrostatic interactions including the interparticle hydrogen bonds from surface -OH groups drive particle attachment, and the dominant contribution to the free energy minimum is enthalpic rather than entropic. However, the enthalpy of basal-edge attachment is significantly offset by the entropy leading to a higher free energy (less negative) compared to that of basal-basal attachment. Study of the free energy for a few imperfect attachments of two particles indicates a higher free energy (i.e., less negative, less stable), compared to a perfect attachment.

Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution

Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue surface hydrophilization, frequently motivated by macroscopic measures of hydrophilicity, because hydrophobicity is thought to increase solute-surface affinity. While this heuristic has driven diverse membrane functionalization strategies, here we build on advances in the theory of hydrophobicity to critically examine the relevance of macroscopic characterizations of solute-surface affinity. Specifically, we use molecular simulations to quantify the affinities to model hydroxyl- and methyl-functionalized surfaces of small, chemically diverse, charge-neutral solutes represented in produced water. We show that surface affinities correlate poorly with two conventional measures of solute hydrophobicity, gas-phase water solubility and oil-water partitioning. Moreover, we find that all solutes show attraction to the hydrophobic surface and most to the hydrophilic one, in contrast to macroscopically based hydrophobicity heuristics. We explain these results by decomposing affinities into direct solute interaction energies (which dominate on hydroxyl surfaces) and water restructuring penalties (which dominate on methyl surfaces). Finally, we use an inverse design algorithm to show how heterogeneous surfaces, with multiple functional groups, can be patterned to manipulate solute affinity and selectivity. These findings, importantly based on a range of solute and surface chemistries, illustrate that conventional macroscopic hydrophobicity metrics can fail to predict solute-surface affinity, and that molecular-scale surface chemical patterning significantly influences affinity-suggesting design opportunities for water purification membranes and other engineered interfaces involving aqueous solute-surface interactions.

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

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

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association

We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free-energy profile also captured the crucial role of allosteric IN inhibitors in promoting multimerization and explained why several C-terminal domain mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation, the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, interprotein water molecules are expelled to the bulk, resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side-chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. Although the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.

Properties of Entropy-Based Topological Measures of Fullerenes

A fullerene is a cubic three-connected graph whose faces are entirely composed of pentagons and hexagons. Entropy applied to graphs is one of the significant approaches to measuring the complexity of relational structures. Recently, the research on complex networks has received great attention, because many complex systems can be modelled as networks consisting of components as well as relations among these components. Information—theoretic measures have been used to analyze chemical structures possessing bond types and hetero-atoms. In the present article, we reviewed various entropy-based measures on fullerene graphs. In particular, we surveyed results on the topological information content of a graph, namely the orbit-entropy Ia(G), the symmetry index, a degree-based entropy measure Iλ(G), the eccentric-entropy Ifσ(G) and the Hosoya entropy H(G).

Detection of C60 in environmental water using dispersive liquid-liquid micro-extraction followed by high-performance liquid chromatography

The wide application of fullerene C₆₀ nanoparticles would inevitably lead to their release into the environment. In order to evaluate the environment risks of C₆₀ and the subsequent effects on ecosystem health, a reliable quantitative methodology of C₆₀ should be established. In this study, a rapid pretreatment method called low-density solvent-based dispersive liquid-liquid micro-extraction (DLLME) combined high-performance liquid chromatography-UV detector (HPLC-UV) was developed to detect C₆₀ in environmental water. In this proposed method, toluene and methanol were chosen as the extraction solvent and the dispersive solvent, respectively. The optimized volume of extraction solvent and dispersive solvent were 100 μL and 10 μL, respectively. And the best shaking time was chosen as 10 min at room temperature for the optimal homogenization procedure for the extraction of C₆₀ in water samples. The enrichment factor of 50 was obtained with 100 μL toluene, and the recoveries of C₆₀ from various environmental samples were in the range of 81.4 ± 5.0-101.4 ± 6.2% at 1.25-5.00 µg/L spiked levels. The detection limits of C₆₀ in tap water, surface water, living sewage and mining waste water were 0.19, 0.29, 0.34 and 0.22 μg/L, respectively. The low detection limit, good linear range and high recoveries of C₆₀ in environmental water indicated that the proposed method could provide an efficient approach for the analysis and tracking of C₆₀ in the environment.

Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study

Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.

Hydrophobic residues of melittin mediate its binding to αA-crystallin

The molecular chaperone αA-crystallin, mainly localized in the human ocular lens, is believed to protect the lens from opacification and cataract, by suppressing the aggregation of the other lens proteins. The present study provides structural and thermodynamic insights into the ability of human αA-crystallin (HAA) to bind to its partially unfolded clients in the lens, using a small peptide, melittin from bee venom, as a model client. We characterized the thermodynamic parameters of the binding process between melittin and HAA through isothermal titration calorimetry (ITC), and found the binding to be endothermic and entropy-driven. We identified the amino acids in melittin important for binding to HAA by saturation-transfer difference (STD) nuclear magnetic resonance (NMR) experiments, and analysis of NMR line broadening upon titration of melittin with HAA. Our results suggest that hydrophobic residues Ile17 and Ile20 on the C-terminal region of melittin are in close contact with HAA in the melittin-HAA complex. Information obtained from NMR experiments was used to generate structural models of the melittin-HAA complex by molecular docking with high-ambiguity driven docking (HADDOCK). Structural models of the melittin-HAA complex reveal important principles underlying the interaction of HAA with its clients.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.

Understanding of Structure and Thermodynamics of Melamine Association in Aqueous Solution from a Unified Theoretical and Experimental Approach

The aggregation propensity of melamine molecules in aqueous solutions in a range of melamine concentrations is investigated by means of a combination of theoretical and experimental approaches. It is observed that the hydrogen bonding interactions of sp³ nitrogen atoms of one melamine with sp² nitrogen atoms of another melamine play a major role in the melamine association. This finding is complemented by the observed favorable electrostatic energies between melamine molecules. The estimation of the orientational probability of melamine aromatic ring rules out any role of π-π interaction in melamine association. Further, the quantum chemical calculations suggest that a melamine molecule prefers to bind with another like molecule with a dihedral angle ranging from 36° to 46°. We have also determined the dimer existence autocorrelation functions to investigate the melamine-dimer stability with time in aqueous solution. Our results are well validated by the experimental findings (Chapman, R. P.; Averell, P. R.; Harris, R. R. Solubility of Melamine in Water. Ind. Eng. Chem. 1943, 35, 137-138. Ahromi, A. J.; Moosheimer, U. Oxygen Barrier Coatings Based on Supramolecular Assembly of Melamine. Macromolecules 2000, 33, 7582-7587. Yang, C.; Liu. Y. Studying on the Steady-State and Time-Resolved Fluorescence Characteristics of Melamine. Spectrochim. Acta A 2010, 75, 1329-1332. Mircescu, N. E.; Oltean, M.; Chis, V.; Leopold, N. FTIR, FT-Raman, SERS and DFT study on Melamine. Vib. Spectrosc. 2012, 62, 165-171. Makowski. S. J.; Lacher. M.; Schnick. W. Supramolecular Hydrogenbonded Structures between Melamine and N-Heterocycles. J. Mol. Struct. 2012, 1013, 19-25. Li, Z.; Chen, G.; Xu, Y.; Wang, X.; Wang, Z. Study of the Structural and Spectral Characteristics of C₃N₃(NH₂)₃(n = 1-4) Clusters. J. Phys. Chem. A 2013, 117, 12511-12518. Li, P.; Arman, D. H.; Wang, H.; Weng, L.; Alfooty, K.; Angawi, R. F.; Chen. B. Solvent Dependent Structures of Melamine: Porous or Non-porous. Cryst. Growth Des. 2015, 15, 1871-1875. Chen, J.; Lei, X.; Peng, B. Study on the Fluorescence Spectra of Melamine in Pure Milk. J. Opt. 2017, 46, 183-186.). Moreover, the thermodynamics of melamine association reveals that the association process is essentially driven by enthalpy, and this enthalpy-driven phenomenon is also confirmed by the experimental isothermal titration calorimetry measurements.

Molecular Insights into the Membrane Affinities of Model Hydrophobes

Membrane-active antibiotics are of great interest in fighting bacterial resistance. α-Mangostin is a membrane-active molecule, but there are no details of its mechanism of action at the atomistic level. We have employed free-energy simulations and microsecond-long conventional molecular dynamics simulations to study the mode of interaction of α-mangostin with a model bacterial membrane and compare it with the mechanisms of three hydrophobic molecules (ciprofloxacin, xanthone, and tetracycline). We find that α-mangostin is thermodynamically more favored to insert into the membrane compared to the other three molecules. Apart from tetracycline, which is largely hydrophilic, the other three molecules aggregate in water; however, only α-mangostin can penetrate into the lipid tail region of the membrane. When it reaches a high concentration in the lipid tail region, α-mangostin can form tubular clusters that span the two head group regions of the membrane, resulting in a large number of water translocations along the transmembrane aggregates. Structure-activity relationship analysis revealed two structural properties that characterize α-mangostin, namely, the two isoprenyl groups and the polar groups present in the aromatic rings, which result in "disruptive amphiphilicity" and hence its excellent membrane activity.

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains.

Dispersion of non-covalently modified graphene in aqueous medium: a molecular dynamics simulation approach

Electric potential variation between two graphene sheets upon adsorption of Na-AHA molecules.

Unified elucidation of the entropy-driven and -opposed hydrophobic effects

The association of nonpolar solutes is generally believed to be entropy driven, which has been shown to be true for the contact of small molecules, ellipsoids, and plates.

Water-Mediated Interactions between Hydrophilic and Hydrophobic Surfaces

All surfaces in water experience at short separations hydration repulsion or hydrophobic attraction, depending on the surface polarity. These interactions dominate the more long-ranged electrostatic and van der Waals interactions and are ubiquitous in biological and colloidal systems. Despite their importance in all scenarios where the surface separation is in the nanometer range, the origin of these hydration interactions is still unclear. Using atomistic solvent-explicit molecular dynamics simulations, we analyze the interaction free energies of charge-neutral model surfaces with different elastic and water-binding properties. The surface polarity is shown to be the most important parameter that not only determines the hydration properties and thereby the water contact angle of a single surface but also the surface-surface interaction and whether two surfaces attract or repel. Elastic properties of the surfaces are less important. On the basis of surface contact angles and surface-surface binding affinities, we construct a universal interaction diagram featuring three different interaction regimes-hydration repulsion, cavitation-induced attraction-and for intermediate surface polarities-dry adhesion. On the basis of scaling arguments and perturbation theory, we establish simple combination rules that predict the interaction behavior for combinations of dissimilar surfaces.

Recent developments in the theoretical, simulational, and experimental studies of the role of water hydrogen bonding in hydrophobic phenomena

Hydrophobic effects (hydrophobic hydration and hydrophobic interaction) constitute an important element of a wide variety of phenomena relevant to biological, physical, chemical, environmental, engineering, and pharmaceutical sciences, such as the immiscibility of oil and water, self-assembly of amphiphiles leading to micelle and membrane formation, folding and stability and unfolding of the native structure of a biologically active protein, gating of ion channels, wetting, froth floatation, and adhesion. On the other hand, the hydrogen bonding ability of water plays a major (if not crucial) role in hydrophobic phenomena. We present a review of most important and relatively recent experimental, simulational, and theoretical research on hydrophobic phenomena in various systems. With a particular interest we survey investigations clarifying the role of water hydrogen bonding therein, because it has been the main object of our own recent research. We have developed a probabilistic hydrogen bond (PHB) model that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of its distance to a hydrophobe, hydrophobe radius, and temperature. Knowing that function, one can explicitly identify a water hydrogen bond contribution to the external potential whereto a water molecule is subjected near a hydrophobe. Combining the PHB model with the classical density functional theory (DFT), one can examine the contribution of water hydrogen bonding to the temperature and lengthscale effects on the hydration of particles and on their solvent-mediated interactions over the entire low-to-high temperature and small-to-large lengthscale ranges. We applied the combined DFT/PHB model to study a variety of hydrophobic phenomena such as (liquid) water in contact with a hydrophobic plate, solvation of spherical solutes of various radii in associated and non-associated liquids at various temperatures, the solvent-mediated interaction of spherical solutes and its temperature dependence, interaction of C60 fullerenes in water, temperature effect on the evaporation lengthscale of water confined between two hydrophobes, temperature dependence of the effective width of the solute-solvent transition layer and average density therein. These applications demonstrated that the DFT/PHB model can serve as a valuable tool in studying hydrophobic phenomena because it constitutes a balanced combination of simplicity, accuracy, and detail. The predictions of the combined DFT/PHB approach for the solvent density profiles and thermodynamic aspects of hydrophobic phenomena are generally in good agreement with experiments and simulations. For example, it predicts the small-to-large crossover lengthscale of its mechanism to be approximately in the range from 1nm to 4nm, and decreasing with increasing temperature. It also suggests that, in terms of the average fluid density in the solute-solvent transition layer, the transition layer for small hydrophobes (of radii ≲2 nm) becomes enriched with rather than depleted of fluid when both the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of these parameters, needed for the depletion-to-enrichment crossover, are predicted to decrease with increasing temperature.

Water ordering controls the dynamic equilibrium of micelle-fibre formation in self-assembly of peptide amphiphiles

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides remains elusive. Here, we use a multistage atomistic-coarse-grained approach, complemented by circular dichroism/infrared spectroscopy and dynamic light scattering experiments to highlight the dual nature of water in driving the self-assembly of peptide amphiphiles (PAs). We show computationally that water cage formation and breakage near the hydrophobic groups control the fusion dynamics and aggregation of PAs in the micellar stage. Simulations also suggest that enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards the fibre phase and stimulates structure and order during the PA assembly into nanofibres. Experiments validate our simulation findings; the measured infrared O–H bond stretching frequency is reminiscent of an ice-like bond which suggests that the solvated water becomes increasingly ordered with time in the assembled peptide network, thus shedding light on the role of water in a self-assembly process.

The role of water in the kinetics of the self-assembly process of amphiphilic peptides still remains unknown. Sankaranarayanan et al. have shown through computational study that water has a dual nature when dictating the mechanism and dynamics of self-assembly of peptide amphiphiles.

Ultrasmall polymersomes of poly-α,β-(N-2-hydroxyethyl l-aspartamide)-graft-poly(l-lactic acid) copolymers as a potential drug carrier

Ultrasmall polymersomes are suggested as a drug delivery platform based on their suitable size, narrow size distribution, uniform morphology, and high thermodynamic stability.

Molecular dynamics simulation elucidates the preferential binding affinity of sodium and tetramethylammonium ions for tetrameric Nafion unit under aqueous conditions

Preferential binding interaction of sodium and tetramethylammonium cations with Nafion pendant and backbone sites respectively.

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces.