Hydrophobic effects and modeling of biophysical aqueous solution interfaces

Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures

Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting a considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoylphosphatidylcholine (DPPC) and palmitoyl sphingomyelin; they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with a particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303 K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5-2.5. In the liquid-crystalline phase at 323 K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems.

Variations in the Protein Hydration and Hydrogen-Bond Network of Water Molecules Induced by the Changes in the Secondary Structures of Proteins Studied through Near-Infrared Spectroscopy

This study investigated how the secondary structural changes of proteins in aqueous solutions affect their hydration and the hydrogen-bond network of water molecules using near-infrared (NIR) spectroscopy. The aqueous solutions of three types of proteins, i.e., ovalbumin, β-lactoglobulin, and bovine serum albumin, were denatured by heating, and changes in the NIR bands of water reflecting the states of hydrogen bonds induced via protein secondary structural changes were investigated. On heating, the intermolecular hydrogen bonds between water molecules as well as between water and protein molecules were broken, and protein molecules were no longer strongly bound by the surrounding water molecules. Consequently, the denaturation was observed to proceed depending on the thermodynamic properties of the proteins. When the aqueous solutions of proteins were cooled after denaturation, the hydrogen-bond network was reformed. However, the state of protein hydration was changed owing to the secondary structural changes of proteins, and the variation patterns were different depending on the protein species. These changes in protein hydration may be derived from the differences in the surface charges of proteins. The elucidation of the mechanism of protein hydration and the formation of the hydrogen-bond network of water molecules will afford a comprehensive understanding of the protein functioning and dysfunctioning derived from the structural changes in proteins.

Peptides and protein hydrolysates exhibiting anti-inflammatory activity: sources, structural features and modulation mechanisms

Inflammation is the response of the immune system to harmful stimuli such as tissue injury, infection or toxic chemicals, which has the aim of eliminating irritants or pathogenic microorganisms and enhancing tissue repair. Uncontrolled long-lasting acute inflammation can gradually progress to chronic, causing a variety of chronic inflammatory diseases that are usually treated with anti-inflammatory drugs, but most of them are inadequate to control chronic responses and are also associated with adverse side effects. Thus, many efforts are being directed to develop alternative and more selective anti-inflammatory therapies from natural products. One main field of interest is the obtaining of bioactive peptides exhibiting anti-inflammatory activity from sustainable protein sources like edible insects or agroindustry and fishing by-products. This work highlighted the structure-activity relationship of anti-inflammatory peptides. Small peptides with molecular weight under 1 kDa and amino acid chain length between 2 to 20 residues are generally the most active because of the higher probability to be absorbed in the intestine and penetrate into cells when compared with the larger size peptides. The presence of hydrophobic (Val, Ile, Pro) and positively charged (His, Arg, Lys) amino acids is another common occurrence for anti-inflammatory peptides. Interestingly, a high percentage (77%) of these bioactive peptides can be found in alternative sustainable protein sources such as Tenebrio molitor or sunflower, apart from its original protein source. However, not all of these peptides with anti-inflammatory potential in vitro achieve good scores by the in silico bioactivity predictors studied. Therefore, it is essential to implement current bioinformatics tools, in order to complement in vitro experiments with prior prediction of potential bioactive peptides.

Variable Interfacial Water Nanosized Arrangements Measured by Atomic Force Microscopy

While there seems to be broad agreement that cluster formation does exist near solid surfaces, its presence at the liquid/vapor interface is controversial. We report experimental studies we have carried out on interfacial water attached on hydrophobic and hydrophilic surfaces. Nanosized steps in the measured force vs distance to the surface curves characterize water cluster profiles. An expansion of the interfacial structure with time is observed; the initial profile extent is typically ∼1 nm, and for longer times expanded structures of ∼70 nm are observed. Our previous results showed that the interfacial water structure has a relative permittivity of ε ≈ 3 at the air/water interface homogeneously increasing to ε ≈ 80 at 300 nm inside the bulk, but here we have shown that the interfacial dielectric permittivity may have an oscillating profile describing the spatial steps in the force vs distance curves. This low dielectric permittivity arrangements of clusters extend the region with ε ≈ 3 inside bulk water and exhibit a behavior similar to that of water networks that expand in time.

Prolonged Association between Water Molecules under Hydrophobic Nanoconfinement

We present an investigation of the dynamics of water confined among rigid carbon rods and between parallel graphene sheets with molecular dynamics simulations. Diffusion coefficients, activation energy of diffusion, and residence-time correlation functions as a function of confinement geometry reveal a retardation of water dynamics under hydrophobic confinement compared to bulk water. In fact, water under various confinements possesses longer associations with its neighbors and exhibits diffusion dynamics characteristic of a lower temperature. Analysis of the residence-time correlation functions reveals long and short residence times, which we relate to the diffusion coefficient and activation energy of diffusion, respectively. Additional investigations reveal how the level of confining surface hydrophobicity affects water dynamics, further broadening our understanding of water diffusion inside diverse media. Overall, this study sheds light on the physical origin of retarded water dynamics under hydrophobic confinement and the close relationship between residence times and diffusion behavior.

Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy

Understanding the physical and chemical properties of viral infections at molecular scales is a major challenge for the scientific community more so with the outbreak of global pandemics. There is currently a lot of effort being placed in identifying molecules that could act as putative drugs or blockers of viral molecules. In this work, we computationally explore the importance in antiviral activity of a less studied class of molecules, namely surfactants. We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water. Our microsecond simulations show a preferential binding of lecithin to the receptor-binding motif of SARS-CoV-2 with binding free energies significantly larger than [Formula: see text]. Furthermore, hydrophobic interactions involving lecithin non-polar tails dominate these binding events, which are also accompanied by dewetting of the receptor binding motif. Through an analysis of fluctuations in the radius of gyration of the receptor-binding domain, its contact maps with lecithin molecules, and distributions of water molecules near the binding region, we elucidate molecular interactions that may play an important role in interactions involving surfactant-type molecules and viruses. We discuss our minimal computational model in the context of lecithin-based liposomal nasal sprays as putative mitigating therapies for COVID-19.

Water-Air Interfaces as Environments to Address the Water Paradox in Prebiotic Chemistry: A Physical Chemistry Perspective

The asymmetric water-air interface provides a dynamic aqueous environment with properties that are often very different than bulk aqueous or gaseous phases and promotes reactions that are thermodynamically, kinetically, or otherwise unfavorable in bulk water. Prebiotic chemistry faces a key challenge: water is necessary for life yet reduces the efficiency of many biomolecular synthesis reactions. This perspective considers water-air interfaces as auspicious reaction environments for abiotic synthesis. We discuss recent evidence that (1) water-air interfaces promote condensation reactions including peptide synthesis, phosphorylation, and oligomerization; (2) photochemistry at water-air interfaces may have been a significant source of prebiotic molecular complexity, given the lack of oxygen and increased availability of near-ultraviolet radiation on early Earth; and (3) water-air interfaces can promote spontaneous reduction and oxidation reactions, potentially providing protometabolic pathways. Life likely began within a relatively short time frame, and water-air interfaces offer promising environments for simultaneous and efficient biomolecule production.

Fast bilayer-micelle fusion mediated by hydrophobic dipeptides

To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.

Design and Applications of Water-Soluble Coordination Cages

Compartmentalization of the aqueous space within a cell is necessary for life. In similar fashion to the nanometer-scale compartments in living systems, synthetic water-soluble coordination cages (WSCCs) can isolate guest molecules and host chemical transformations. Such cages thus show promise in biological, medical, environmental, and industrial domains. This review highlights examples of three-dimensional synthetic WSCCs, offering perspectives so as to enhance their design and applications. Strategies are presented that address key challenges for the preparation of coordination cages that are soluble and stable in water. The peculiarities of guest binding in aqueous media are examined, highlighting amplified binding in water, changing guest properties, and the recognition of specific molecular targets. The properties of WSCC hosts associated with biomedical applications, and their use as vessels to carry out chemical reactions in water, are also presented. These examples sketch a blueprint for the preparation of new metal-organic containers for use in aqueous solution, as well as guidelines for the engineering of new applications in water.

Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity

We address the association of the hydrophobic driving forces in protein folding with the inverse temperature dependence of protein hydration, wherein stabilizing hydration effects strengthen with increasing temperature in a physiological range. All-atom calculations of the free energy of hydration of aqueous deca-alanine conformers, holistically including backbone and side-chain interactions together, show that attractive peptide-solvent interactions and the thermal expansion of the solvent dominate the inverse temperature signatures that have been interpreted traditionally as the hydrophobic stabilization of proteins in aqueous solution. Equivalent calculations on a methane solute are also presented as a benchmark for comparison. The present study calls for a reassessment of the forces that stabilize folded protein conformations in aqueous solutions and of the additivity of hydrophobic/hydrophilic contributions.

Highly Selective Anion Template Effect in the Synthesis of Constrained Pseudopeptidic Macrocyclic Cyclophanes

Herein, we report the synthesis of a novel family of constrained pseudopeptidic macrocyclic compounds containing the hexahydropyrrolo[3,4-f]isoindolocyclophane scaffold and involving four coupled substitution reactions in the macrocyclization process. Although the increase in the number of steps involved in the macrocyclization could lead to a larger number of possible side products, the optimization of the methodology and the study of the driving forces have made it possible to obtain the desired macrocycles in excellent yields. A thorough computational study has been carried out to understand the macrocyclization process, and the results obtained nicely agree with experimental data. Moreover, the bromide anion had a clear catalytic template effect in the macrocyclization reaction, and surprisingly, the chloride anion had a negative template effect in opposition to the results obtained for analogous macrocycles. The parameters responsible for the specific kinetic template effect observed have been studied in detail.

Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies

Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new heterogeneous dielectric implicit membrane model, with respect to free energy simulations in explicit membrane and explicit water, and implemented it into the Amber software suite. This new model supersedes our previous uniform, single dielectric implicit membrane model by allowing the dielectric constant to vary with depth within the membrane. We calculated MMPBSA binding free energies for the human purinergic platelet receptor (P2Y₁₂R) and two of the muscarinic acetylcholine receptors (M2R and M3R) bound to various antagonist ligands using both membrane models, and we found that the heterogeneous dielectric membrane model has a stronger correlation with experimental binding affinities compared to the older model under otherwise identical conditions. This improved membrane model increases the utility of MMPBSA calculations for the rational design and improvement of future drug candidates.

The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives

Side chain as the main conformational and self-assembly structural factor for C₂-pseudopeptides.

Surface Water as a Mediator and Reporter of Adhesion at Aqueous Interfaces

Understanding the adsorption of molecules onto surfaces is integral to a wide variety of fields with scientific, engineering, and industrial applications. The surface-adsorbed structure is governed by the nature of the molecule, surface characteristics, and solution environment. There are therefore three critical interactions that govern adhesion: solvent-analyte, substrate-analyte, and substrate-solvent. The last two interactions require a surface-specific probe restricted to a few nanometers or less. This is particularly true of efforts to probe polymer surface structure without being overwhelmed by bulk polymer signal or interfacial water structure in the presence of bulk water. Second-order nonlinear optical techniques are ideal probes of such interactions, as their reporting depth is determined by the polar arrangement of molecules (a break in the macroscopic inversion symmetry) rather than the penetration of the optical fields. This Account begins with an introduction of surface water structure from the perspective of a nonlinear probe. Details about the unique view of the water orientation distribution are discussed and contrasted with information obtained from conventional vibrational techniques. The salient features of water next to model hydrophobic and hydrophilic surfaces are discussed, in preparation for a discussion of solute interactions that follows. We then present three examples using a combination of linear and nonlinear vibrational spectroscopy and molecular dynamics simulations to illustrate how water is both a mediator and a marker of adhesion. The first is a study of amphipathic peptide adhesion onto hydrophobic and hydrophilic surfaces, characterizing the adsorbed structure in relation to the water surrounding the molecule and trapped near the surface. Water is found to be especially important in mediating adhesion to hydrophilic surfaces, where it aids in solvating the peptide as well as facilitating interactions with the surface. In the second example, we look at adhesion of a multicomponent polymer adhesive using surface-bulk heterospectral correlation analysis, in which surface vibrational spectroscopy is combined with bulk infrared absorption to determine interfacial structure development during the evaporation of water. When acrylic acid is added to the polymer, there is a change in orientation of the polymer before an increase in population. This is opposite to what is observed when no additive is present. In our third example, we show how interfacial water provides a unique window into the surface microenvironment during bacterial adhesion, highlighting the role of solution conditions at the surface in cell attachment and biofilm growth. Changes in the nonlinear vibrational response of interfacial water reflect changes occurring in the pH and ionic strength only at the surface, due to the presence of polymeric adhesives secreted by the bacteria. These studies underline the importance of surface water in governing the structure of adhered molecules and in mediating changes in the interfacial environment as a result of adhesion and provide insight into a nanoscale region that is otherwise difficult to query. They also illustrate the importance of combining surface-sensitive and bulk spectroscopic probes with computer modeling to gain a better understanding of the interplay between water and adsorbate structure.

The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations

We use end point simulations to estimate the excess chemical potential of water in the homogeneous liquid and at the interface with a protein in solution. When the pure liquid is taken as the reference, the excess chemical potential of interfacial water is the difference between the solvation free energy of a water molecule at the interface and in the bulk. Using the homogeneous liquid as an example, we show that the solvation free energy for growing a water molecule can be estimated by applying UWHAM to the simulation data generated from the initial and final states (i.e., "the end points") instead of multistate free energy perturbation simulations because of the possible overlaps of the configurations sampled at the end points. Then end point simulations are used to estimate the solvation free energy of water at the interface with a protein in solution. The estimate of the solvation free energy at the interface from two simulations at the end points agrees with the benchmark using 32 states within a 95% confidence interval for most interfacial locations. The ability to accurately estimate the excess chemical potential of water from end point simulations facilitates the statistical thermodynamic analysis of diverse interfacial phenomena. Our focus is on analyzing the excess chemical potential of water at protein receptor binding sites with the goal of using this information to assist in the design of tight binding ligands.

Binding of Hydrophobic Guests in a Coordination Cage Cavity is Driven by Liberation of "High-Energy" Water

The cavity of an M8 L12 cubic coordination cage can accommodate a cluster of ten water molecules in which the average number of hydrogen bonds per water molecule is 0.5 H-bonds less than it would be in the bulk solution. The presence of these "hydrogen-bond frustrated" or "high-energy" water molecules in the cavity results in the hydrophobic effect associated with guest binding being predominantly enthalpy-based, as these water molecules can improve their hydrogen-bonding environment on release. This contrasts with the classical form of the hydrophobic effect in which the favourable entropy change associated with release of ordered molecules from hydrophobic surfaces dominates. For several guests Van't Hoff plots showed that the free energy of binding in water is primarily enthalpy driven. For five homologous pairs of guests related by the presence or absence of a CH2 group, the incremental changes to ΔH and TΔS for guest binding-that is, ΔΔH and TΔΔS, the difference in contributions arising from the CH2 group-are consistently 5(±1) kJ mol-1 for ΔΔH and 0(±1) kJ mol-1 for TΔΔS. This systematic dominance of ΔH in the binding of hydrophobic guests is consistent with the view that guest binding is dominated by release of "high energy" water molecules into a more favourable solvation environment, as has been demonstrated recently for some members of the cucurbituril family.

Molecular Shape and the Hydrophobic Effect

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.

Sequence-Dependent Interfacial Adsorption and Permeation of Dipeptides across Phospholipid Membranes

We investigate permeation of three blocked dipeptides with different side chain polarity across a phospholipid membrane and their behavior at the water-membrane interface by way of molecular dynamics simulations. Hydrophilic serine-serine dipeptide is found to desorb from the interface to aqueous phase, whereas hydrophobic phenylalanine-leucine and amphiphilic serine-leucine tend to accumulate at the interface with a free energy minimum of -3 kcal/mol. All three dipeptides exhibit free energy barriers to permeation across the membrane located at the center of the bilayer. The height of the barrier is strongly sequence dependent and increases with the dipeptide polarity. It is equal to 3.5, 6.4, and 10.0 kcal/mol for phenylalanine-leucine, serine-leucine, and serine-serine, respectively. The corresponding permeability coefficients are equal to 4.6 × 10^-3, 4.5 × 10^-5, and 8.7 × 10^-8 cm/s. The apparent insensitivity of membrane permeability to hydrophobicity of dipeptides, found in some experiments, is attributed to neglecting corrections for unstirred water layers near membrane surface, which are significant for hydrophobic species. Different hydrophobicity of the dipeptides also influences their conformations and orientations, both at the interface and inside the membrane. In particular, penetration of hydrophilic serine-serine dipeptide causes the formation of water-filled defects in the bilayer. These results are relevant to the delivery of peptide-based therapeutic agents.

How Water's Properties Are Encoded in Its Molecular Structure and Energies

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.

Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H₂ O, Ala₂ H⁺ ⋅18 H₂ O, and Ala₂ ⋅18 H₂ O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.

Pharmacophore Mapping Approach for Drug Target Identification: A Chemical Synthesis and in Silico Study on Novel Thiadiazole Compounds

INTRODUCTION

Compounds containing thiadiazole moiety are cognized to possess with variety of clinical and therapeutic activity. Finding a suitable drug target for newly synthesized compounds remain a major bottle neck in current high throughout medicinal chemistry era.

AIM

To effectively synthesize di substituted thiadiazole compounds and demonstrate drug target identification using an in silico pharmacophore probing approach. Moreover, we also aim to validate the suitability of identified drug target.

MATERIALS AND METHODS

A cost-effective and environmental friendly chemical synthesis scheme for production of di substituted thiadiazole compounds was employed. Target identification was conducted by Pharmmapper software. Validation was accomplished by performing molecular docking and further Molecular Hydrophobic Potential (MHP) analysis.

RESULTS

Pharmacophore probing base approach identified hepatocyte growth factor receptor (c-Met) as a suitable biological target for newly synthesized compounds. Binding free energy values indicate that compound 4b, 4e, 4g and 4h has tremendous potential to be further used as lead compound to design selective inhibitors of c-Met receptor. MHP data from current study supports the possibility that hydrophobic contacts might act as major factor stabilizing thiadiazole- c-Met complex. Moreover, in silico observations of current study are in absolute accordance with previously described in vitro and crystallographic analysis.

CONCLUSION

We demonstrate that thiadiazole compounds synthesized in current investigation has high potential to act in modulation of hepatocyte growth factor receptor (c-Met) activity and thereby act as putative therapeutic agent in cancer therapy.

Interfacial Solvation and Surface pH of Phenol and Dihydroxybenzene Aqueous Nanoaerosols Unveiled by Aerosol VUV Photoelectron Spectroscopy

Although the significance of aqueous interfaces has been recognized in numerous important fields, it can be even more prominent for nanoscaled aqueous aerosols because of their large surface-to-volume ratios and prevalent existence in nature. Also, considering that organic species are often mixed with aqueous aerosols in nature, a fundamental understanding of the electronic and structural properties of organic species in aqueous nanoaerosols is essential to learn the interplay between water and organic solutes under the nanoscaled size regime. Here, we report for the first time the vacuum ultraviolet photoelectron spectroscopy of phenol and three dihydroxybenzene (DHB) isomers including catechol, resorcinol, and hydroquinone in the aqueous nanoaerosol form. By evaluating two photoelectron features of the lowest vertical ionization energies originated from the b₁(π) and a₂(π) orbitals for phenolic aqueous nanoaerosols, their interfacial solvation characteristics are unraveled. Phenolic species appear to reside primarily on/near the aqueous nanoaerosol interface, where they appear only partially hydrated on the aqueous interface with the hydrophilic hydroxyl group more solvated in water. An appreciable proportion of phenol is found to coexist with phenolate at/near the nanoaerosol interface even under a high bulk pH of 12.0, indicating that the nanoaerosol interface exhibits a composition distribution and pH drastically different from those of the bulk. The surface pH of phenol-containing aqueous nanoaerosols is found to be ∼2.2 ± 0.1 units more acidic than that of the bulk interior, as measured at the bulk pH of 12.0. From the photoelectron spectra of DHB aqueous nanoaerosols, the effects of numbers/arrangements of -OH groups are assessed. This study shows that the hydration extents, pH values, deprotonation status, and numbers/relative arrangements of -OH groups are crucial factors affecting the ionization energies of phenolic aqueous nanoaerosols and thus their redox-based activities. The multifaceted implications of the present study in the aerosol science, atmospheric/marine chemistry, and biological science are also addressed.

A Quantitative Study of the Effects of Guest Flexibility on Binding Inside a Coordination Cage Host

We have performed a systematic investigation of the effects of guest flexibility on their ability to bind in the cavity of a coordination cage host in water, using two sets of isomeric aliphatic ketones that differ only in the branching patterns of their alkyl chains. Apart from the expected increase in binding strength for C9 over C7 ketones associated with their greater hydrophobic surface area, within each isomeric set there is a clear inverse correlation between binding free energy and guest flexibility, associated with loss of conformational entropy. This can be parameterized by the number of rotatable C-C bonds in the guest, with each additional rotatable bond resulting in a penalty of around 2 kJ mol-1 in the binding free energy, in good agreement with values obtained from protein/ligand binding studies. We used the binding data for the new flexible guests to improve the scoring function that we had previously developed that allowed us to predict binding constants of relatively rigid guests in the cage cavity using the molecular docking programme GOLD (Genetic Optimisation of Ligand Docking). This improved scoring function resulted in a significant improvement in the ability of GOLD to predict binding constants for flexible guests, without any detriment to its ability to predict binding for more rigid guests.

On the role of water density fluctuations in the inhibition of a proton channel

Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.

On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water

Density fluctuations in liquid water are at the heart of numerous phenomena associated with hydrophobic effects such as protein folding and the interaction between biomolecules. One of the most fundamental processes in this regard is the solvation of hydrophobic solutes in water. The vast majority of theoretical and numerical studies examine density fluctuations at the short length scale focusing exclusively on spherical cavities. In this work, we use both first-principles and classical molecular dynamics simulations to demonstrate that density fluctuations in liquid water can deviate significantly from the canonical spherical shapes. We show that regions of empty space are frequently characterized by exotic, highly asymmetric shapes that can be quite delocalized over the hydrogen bond network. Interestingly, density fluctuations of these shapes are characterized by Gaussian statistics with larger fluctuations. An important consequence of this is that the work required to create non spherical cavities can be substantially smaller than that of spheres. This feature is also qualitatively captured by the Lum-Chandler-Weeks theory. The scaling behavior of the free energy as a function of the volume at short length scales is qualitatively different for the nonspherical entities. We also demonstrate that nonspherical density fluctuations are important for accommodating the hydrophobic amino acid alanine and are thus likely to have significant implications when it comes to solvating highly asymmetrical species such as alkanes, polymers, or biomolecules.

Statistical Analyses of Hydrophobic Interactions: A Mini-Review

This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. First, the inverse temperature phenomenology of hydrophobic interactions, i.e., strengthening of hydrophobic bonds with increasing temperature, is decisively exhibited by hydrophobic interactions between atomic-scale hard sphere solutes in water. Second, inclusion of attractive interactions associated with atomic-size hydrophobic reference cases leads to substantial, nontrivial corrections to reference results for purely repulsive solutes. Hydrophobic bonds are weakened by adding solute dispersion forces to treatment of reference cases. The classic statistical mechanical theory for those corrections is not accurate in this application, but molecular quasi-chemical theory shows promise. Finally, because of the masking roles of excluded volume and attractive interactions, comparisons that do not discriminate the different possibilities face an interpretive danger.

Dissecting the Molecular Structure of the Air/Water Interface from Quantum Simulations of the Sum-Frequency Generation Spectrum

The molecular characterization of the air/water interface is a key step in understanding fundamental multiphase phenomena ranging from heterogeneous chemical processes in the atmosphere to the hydration of biomolecules. The apparent simplicity of the air/water interface, however, masks an underlying complexity associated with the dynamic nature of the water hydrogen-bond network that has so far hindered an unambiguous characterization of its microscopic properties. Here, we demonstrate that the application of quantum many-body molecular dynamics, which enables spectroscopically accurate simulations of water from the gas to the condensed phase, leads to a definitive molecular-level picture of the interface region. For the first time, excellent agreement is obtained between the simulated vibrational sum-frequency generation spectrum and the most recent state-of-the-art measurements, without requiring any empirical frequency shift or ad hoc scaling of the spectral intensity. A systematic dissection of the spectral features demonstrates that a rigorous representation of nuclear quantum effects as well as of many-body energy and electrostatic contributions is necessary for a quantitative reproduction of the experimental data. The unprecedented accuracy of the simulations presented here indicates that quantum many-body molecular dynamics can enable predictive studies of aqueous interfaces, which by complementing analogous experimental measurements will provide unique molecular insights into multiphase and heterogeneous processes of relevance in chemistry, biology, materials science, and environmental research.

Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach

Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.