Hydration and Dewetting near Fluorinated Superhydrophobic Plates

Unraveling the hydrophobic interaction mechanisms of hydrocarbon and fluorinated surfaces

HYPOTHESIS

Numerous hydrocarbon and fluorine-based hydrophobic surfaces have been widely applied in various engineering and bioengineering fields. It is hypothesized that the hydrophobic interactions of hydrocarbon and fluorinated surfaces in aqueous media would show some differences.

EXPERIMENTS

The hydrophobic interactions of hydrocarbon and fluorinated surfaces with air bubbles in aqueous solutions have been systematically and quantitatively measured using a bubble probe atomic force microscopy (AFM) technique. Ethanol was introduced to water for modulating the solution polarity. The experimental force profiles were analyzed using a theoretical model combining the Reynolds lubrication theory and augmented Young-Laplace equation by including disjoining pressure arisen from the Derjarguin-Landau-Verwey-Overbeek (DLVO) and non-DLVO interactions (i.e., hydrophobic interactions).

FINDINGS

The experiment results show that the hydrophobic interactions were firstly weakened and then strengthened by increasing ethanol content in the aqueous media, mainly due to the variation in interfacial hydrogen bonding network. The fluorinated surface exhibited less sensitivity to ethanol than hydrocarbon surface, which is attributed to the presence of ordered interfacial water layer. Our work reveals the different hydrophobic effects of hydrocarbon and fluorinated surfaces, with useful implications on modulating the interfacial interactions of relevant materials in various engineering and bioengineering applications.

Novel Inhibitory Role of Fenofibric Acid by Targeting Cryptic Site on the RBD of SARS-CoV-2

The emergence of the recent pandemic causing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an alarming situation worldwide. It also prompted extensive research on drug repurposing to find a potential treatment for SARS-CoV-2 infection. An active metabolite of the hyperlipidemic drug fenofibrate (also called fenofibric acid or FA) was found to destabilize the receptor-binding domain (RBD) of the viral spike protein and therefore inhibit its binding to human angiotensin-converting enzyme 2 (hACE2) receptor. Despite being considered as a potential drug candidate for SARS-CoV-2, FA's inhibitory mechanism remains to be elucidated. We used molecular dynamics (MD) simulations to investigate the binding of FA to the RBD of the SARS-CoV-2 spike protein and revealed a potential cryptic FA binding site. Free energy calculations were performed for different FA-bound RBD complexes. The results suggest that the interaction of FA with the cryptic binding site of RBD alters the conformation of the binding loop of RBD and effectively reduces its binding affinity towards ACE2. Our study provides new insights for the design of SARS-CoV-2 inhibitors targeting cryptic sites on the RBD of SARS-CoV-2.

Selective Fabrication of Robust and Multifunctional Super Nonwetting Surfaces by Diverse Modifications of Zirconia-Ceria Nanocomposites

The creation of surfaces with various super nonwetting properties is an ongoing challenge. We report diverse modifications of novel synthesized zirconia-ceria nanocomposites by different low surface energy agents to fabricate nanofluids capable of regulating surface wettability of mineral substrates to achieve selective superhydrophobic, superoleophobic-superhydrophilic, and superamphiphobic conditions. Surfaces treated with these nanofluids offer self-cleaning properties and effortless rolling-off behavior with sliding angles ≤7° for several liquids with surface tensions between 26 and 72.1 mN/m. The superamphiphobic nanofluid coating imparts nonstick properties to a solid surface whereby liquid drops can be effortlessly displaced on the coating with a near-zero tilt and conveniently lifted off using a needle tip, leaving no trace. Further, the superamphiphobic surface demonstrates good oil repellency toward ultralow surface tension liquids such as n-hexane and n-heptane. The superoleophobic-superhydrophilic surface repels oil droplets well regardless of whether it is in the air or underwater conditions. In addition, reaping the benefits of the ZrO₂-CeO₂ nanocomposites' photocatalysis feature, the superoleophobic-superhydrophilic coating exhibits self-cleaning ability by the degradation of color dyes. Modification of the wettability of substrates is carried out by a cost-effective and facile solution-immersion approach, which creates surfaces with hierarchical nano-submicron-scaled structures. The multipurpose coated surfaces have outstanding durability and mechanical stability. They also resist well high-temperature-high-pressure conditions, which will provide various practical applications in different fields, including the condensate banking removal in gas reservoirs or the separation of oil/water mixtures.

Unexpected hydrophobicity on self-assembled monolayers terminated with two hydrophilic hydroxyl groups

Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)₂-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)₂-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)₂-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.

Ordered Water Layer on the Macroscopically Hydrophobic Fluorinated Polymer Surface and Its Ultrafast Vibrational Dynamics

Hydrophobic-like water monolayers have been predicted at the metal and some polar surfaces by theoretical simulations. However, direct experimental evidence for the presence of this water layer at surfaces, particularly at biomolecule and polymer surfaces, is yet to be validated at room temperature. Here we observe experimentally that an ordered molecular water layer is present at the hydrophobic fluorinated polymer such as polytetrafluoroethylene (PTFE) surface by using sum frequency generation vibrational spectroscopy. The macroscopic hydrophobicity of PTFE surface is actually hydrophilic at the molecular level. The macroscopically hydrophobic character of PTFE is indeed resulting from the hydrophobicity of the ordered two-dimension (2D) water layer, in which cyclic water tetramer structure is found. The water layer at humidity of ≤40% has a vibrational relaxation time of 550 ± 60 fs. The vibrational relaxation time in the frequency range of 3200-3400 cm^-1 shows remarkable difference from the interfacial water at the air/H₂O interface and the lipid/H₂O interface. No discernible frequency dependence of the vibrational relaxation time is observed, indicating the homogeneous dynamics of OH groups in the water layer. These insights into the water layer at the macroscopically hydrophobic surface may contribute to a better understanding of the hydrophobic interaction and interfacial water dynamics.

Evolution of Temperature-Driven Interfacial Wettability and Surface Energy Properties on Hierarchically Structured Porous Superhydrophobic Pseudoboehmite Thin Films

Interaction of water on heterogeneous nonwetting interfaces has fascinated researchers' attention for wider applications. Herein, we report the evolution of hierarchical micro-/nanostructures on superhydrophobic pseudoboehmite surfaces created from amorphous Al₂O₃ films and unraveled their temperature-driven wettability and surface energy properties. The influence of hot water immersion temperature on the dissolution-reprecipitation mechanism and the surface geometry of the Al₂O₃ film have been extensively analyzed, which helped in attaining the optimal Cassie-Baxter state. The evolution of pseudoboehmite films has been structurally characterized using grazing incidence X-ray diffraction, field-emission scanning electron microscopy, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy and atomic force microscopy. Interfacial surface energy components on the structured superhydrophobic surface exhibited a very low surface energy of ∼4.6 mN/m at room temperature and ultrahigh water contact angle >175°. The interaction between water droplets on the nonwetting surface was comprehended and correlated to the temperature-dependent surface energy properties. The surface energy and wettability of the structured pseudoboehmite superhydrophobic surface exhibited an inverse behavior as a function of temperature. Interestingly, the superhydrophobic surface exhibited "Leidenfrost effect" below the boiling point of water (67 °C), which is further correlated with the intermolecular forces, interfacial water molecules and surface-terminated groups. These high-temperature wetting transition studies could be potentially valuable for solid-liquid systems working at nonambient temperatures, and also this approach can pave new pathways for better understanding of the solid/liquid interfacial interactions on nanoengineered superhydrophobic surfaces.

Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains

Tungsten oxide nanodot (WO_3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO_3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO_3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO_3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO_3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO_3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.

Electric Field Induced Dewetting of Hydrophobic Nanocavities at Ambient Temperature

The understanding of water dewetting in nanoporous materials is of great importance in various fields of science and technology. Herein, we report molecular dynamics simulation results of dewetting of water droplet in hydrophobic nanocavities between graphene walls under the influence of electric field. At ambient temperature, the rate of dewetting induced by electric field is significantly large. Whereas, it is a very low rate of dewetting induced by high temperature (423 K) due to the strong interaction of the hydrogen-bonding networks of water droplets in nanocavities. In addition, the electric filed induced formation of a water column has been found in a vacuum chamber. When the electric field is turned off, the water column will transform into a water droplet. Importantly, the results demonstrate that the rate of electric field-induced dewetting increases with growth of the electric field. Overall, our results suggest that electric field may have a great potential application for nanomaterial dewetting.

The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide

Molybdenum disulfide (MoS2), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS2 and PEGylated MoS2 (MoS2-PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS2 and MoS2-PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS2-PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS2-PEG exhibits a lower binding free energy than pristine MoS2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS2-PEG or MoS2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS2-PEG eliciting stronger cytokine secretion than the pristine MoS2. The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS2-PEG compared to pristine MoS2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS2-PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.

Modeling and Structural Characterization of the Sweet Taste Receptor Heterodimer

Sweet taste receptor, a heterodimer belonging to the class C G-protein coupled receptor (GPCR) family and composed of the T1R2 and T1R3 subunits, is responsible for the perception of natural sugars, sweet proteins, various d-amino acids, as well as artificial sweeteners. Despite the critical importance of the sweet receptor not only in mediating gustation but also in its role in the food industry, the architecture of the T1R2-T1R3 complex and the mechanism by which extracellular stimuli induce conformational changes that are propagated to the intracellular milieu, i.e., the signal transduction pathway, remain largely unknown. Here, we constructed and characterized a full-length structural model of the T1R2-T1R3 receptor, including both the transmembrane (TM) and extracellular (EC) domains of the heterodimer, using comparative modeling and extensive all-atom molecular dynamics simulations. Several heterodimer interfaces were first examined for the TM domain, and conformational changes occurring at the intracellular side and associated with the receptor's activation were characterized. From the analysis on the simulated data, putative allosteric binding sites for ligands, ions, and cholesterol were proposed. Also, insights into the protein interface of the TM domain upon activation are provided. The EC domain of the heterodimer, including both the Venus flytrap and cysteine-rich domains, was also investigated. Several important intersubunit interactions located at regions responsible for the receptor's proper function were observed, which resemble those recently identified in other class C GPCR members. Integration of the results from the TM and EC domains facilitates the generation of a full-length T1R2-T1R3 receptor. These findings along with the full-length structural model of the T1R2-T1R3 receptor provide a structural framework that may assist in understanding the mechanistic details associated with the receptor activation process for the sweet T1R2-T1R3 receptor as well as other members of the same family.

Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ16-21 Peptide Assembly

Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ_16-21 peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations. Interestingly, nonuniform GO nanosheets (in terms of oxidation sites) have a much stronger perturbation effect on the structure of Aβ_16-21 assembly. The Aβ peptides exhibit a remarkable tendency in binding to the scattered interfaces between unoxidized and oxidized regions, which induces the dissociation of Aβ amyloid fibril. These findings should deepen our understanding of surface-induced peptide dissociation and stimulate discovery of alternative AD treatments.

Robust Antibacterial Activity of Tungsten Oxide (WO3-x) Nanodots

Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO_3-x), synthesized by a simple one-pot synthetic approach, were found to exhibit strong antibacterial capabilities. The analyses with colony-forming units (CFU) showed an excellent antibacterial activity of WO_3-x against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damages to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase the germicidal activity of WO_3-x nanodots, a 30 min exposure to sunlight combined with 50 μg/mL WO_3-x nanodots showed a 70% decrease in E. coli viability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. The cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO_3-x nanodots on eukaryotic cells, which demonstrated their general biocompatibility. In summary, our results suggest WO_3-x nanodots have considerable potential in antibacterial applications, while also being biocompatible at large.

Study of distance dependence of hydrophobic force between two graphene-like walls and a signature of pressure induced structure formation in the confined water

We examine the separation distance dependence of the hydrophobic force by systematically varying the distance (d) between two walls. The hydrophobic force exhibits a distance mediated crossover from a liquid-like to a gas-like behavior at around d ∼ 12 Å for 1 atm pressure. The distance dependence can be fitted to a bi-exponential form, with the longer distance part displaying a correlation length of 20 Å. In addition, the crossover is found to be accompanied by a divergent-like growth of the local relative number fluctuation of the water molecules confined between the two surfaces. Furthermore, at a fixed separation (d = 20 Å), we observe a pressure induced structural modification of confined water at high pressure. The confined water is found to form an ordered structure at high pressure (10 000 atm) and room temperature, in agreement with the experimental study [G. Algara-Siller et al. Nature 519(7544), 443 (2015)].

Surface microstructure engenders unusual hydrophobicity in phyllosilicates

We present a mechanism of intriguing polar hydrophobicity of a series of naturally formed minerals: their surface cavities can effectively trap water molecules, and the water trapping remarkably disrupts the hydrogen bond interaction among interfacial water and leads to considerable hydrophobicity. Diminishing water trapping by decreasing surface roughness can considerably enhance wettability, which illustrates that a Wenzel model is no longer valid for polar materials with atomic-scale roughness.

A nonmonotonic dependence of the contact angles on the surface polarity for a model solid surface

We found an unusual nonmonotonic contact angle dependence of the surface polarity (denoted as q) on a solid surface with specific charge patterns, where the contact angle firstly decreases and then increases as q increases from 0 e to 1.0 e.

Semifluorinated Alkylphosphonic Acids Form High-Quality Self-Assembled Monolayers on Ag-Coated Yttrium Barium Copper Oxide Tapes and Enable Filamentization of the Tapes by Microcontact Printing

A custom-designed semifluorinated phosphonic acid, (9,9,10,10,11,11,12,12,13,13,14,14,15,15,16,16,16-heptadecafluorohexadecyl)phosphonic acid (F8H8PA), and a normal hexadecylphosphonic acid (H16PA) were synthesized and used to generate self-assembled monolayers (SAMs) on commercially available yttrium barium copper oxide (YBCO) tapes. In this study, we wished to evaluate the effectiveness of these monolayer films as coatings for selectively etching YBCO. Initial films formed by solution deposition and manual stamping using a non-patterned polydimethylsiloxane stamp allowed for a comparison of the film-formation characteristics. The resulting monolayers were characterized by X-ray photoelectron spectroscopy (XPS), contact angle goniometry, and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). To prepare line-patterned (filamentized) YBCO tapes, standard microcontact printing (μ-CP) procedures were used. The stamped patterns on the YBCO tapes were characterized by scanning electron microscopy (SEM) before and after etching to confirm the effectiveness of the patterning process on the YBCO surface and energy-dispersive X-ray spectroscopy (EDX) to obtain the atomic composition of the exposed interface.

Potential disruption of protein-protein interactions by graphene oxide

Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers

By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups.

Mechanisms for Enhanced Hydrophobicity by Atomic-Scale Roughness

It is well known that the close-packed CF₃-terminated solid surface is among the most hydrophobic surfaces in nature. Molecular dynamic simulations show that this hydrophobicity can be further enhanced by the atomic-scale roughness. Consequently, the hydrophobic gap width is enlarged to about 0.6 nm for roughened CF₃-terminated solid surfaces. In contrast, the hydrophobic gap width does not increase too much for a rough CH₃-terminated solid surface. We show that the CF₃-terminated surface exists in a microscopic Cassie–Baxter state, whereas the CH₃-terminated surface exists as a microscopic Wenzel state. This finding elucidates the underlying mechanism for the different widths of the observed hydrophobic gap. The cage structure of the water molecules (with integrated hydrogen bonds) around CH₃ terminal assemblies on the solid surface provides an explanation for the mechanism by which the CH₃-terminated surface is less hydrophobic than the CF₃-terminated surface.

Dissecting the contributions of β-hairpin tyrosine pairs to the folding and stability of long-lived human γD-crystallins

Ultraviolet-radiation-induced damage to and aggregation of human lens crystallin proteins are thought to be a significant pathway to age-related cataract. The aromatic residues within the duplicated Greek key domains of γ- and β-crystallins are the main ultraviolet absorbers and are susceptible to direct and indirect ultraviolet damage. The previous site-directed mutagenesis studies have revealed a striking difference for two highly conserved homologous β-hairpin Tyr pairs, at the N-terminal domain (N-td) and C-terminal domain (C-td), respectively, in their contribution to the overall stability of HγD-Crys, but why they behave so differently still remains a mystery. In this paper, we systematically investigated the underlying molecular mechanism and detailed contributions of these two Tyr pairs with large scale molecular dynamics simulations. A series of different tyrosine-to-alanine pair(s) substitutions were performed in either the N-td, the C-td, or both. Our results suggest that the Y45A/Y50A pair substitution in the N-td mainly affects the stability of the N-td itself, while the Y133A/Y138A pair substitution in the C-td leads to a more cooperative unfolding of both N-td and C-td. The stability of motif 2 in the N-td is mainly determined by the interdomain interface, while motif 1 in the N-td or motifs 3 and 4 in the C-td are mainly stabilized by the intradomain hydrophobic core. The damage to any tyrosine pair(s) can directly introduce some apparent water leakage to the hydrophobic core at the interface, which in turn causes a serious loss in the stability of the N-td. However, for the C-td substitutions, it may further impair the stable "sandwich-like" Y133-R167-Y138 cluster (through cation-π interactions) in the wild-type, thus causing the loop regions near the residue A138 to undergo large fluctuations, which in turn results in the intrusion of water into the hydrophobic core of the C-td and induces the C-td to lose its stability. These findings help resolve the "mystery" on why these two Tyr pairs display such a striking difference in their contributions to the overall protein stability despite their highly homologous nature.

Effect of urea concentration on aggregation of amyloidogenic hexapeptides (NFGAIL)

We have performed large-scale all-atom molecular dynamics (MD) simulations to study the aggregation behavior of four NFGAIL hexapeptides in the aqueous urea solution, with a urea concentration ranging from 0 to 5 M. We find that urea in general suppresses the peptide aggregation, but suppression slows down in the intermediation concentration regime around 3 M. Two competing mechanisms of urea are determined: urea molecules accumulated near the first solvation shell (FSS) tend to unfold the hexapeptide, which favors aggregation; on the other hand, the tight hydrogen bonds formed between urea and peptide mainchains hinder the association of peptides which disfavors the formation of the β-sheet. Furthermore, the different nonlinear urea concentration dependences of the urea-peptide and peptide-peptide hydrogen bonds lead to a nonmonotonic behavior, with a weak enhancement in the peptide aggregation around 3 M.

Hydrophobic interaction drives surface-assisted epitaxial assembly of amyloid-like peptides

The molecular mechanism of epitaxial fibril formation has been investigated for GAV-9 (NH(3)(+)-VGGAVVAGV-CONH(2)), an amyloid-like peptide extracted from a consensus sequence of amyloidogenic proteins, which assembles with very different morphologies, "upright" on mica and "flat" on the highly oriented pyrolytic graphite (HOPG). Our all-atom molecular dynamics simulations reveal that the strong electrostatic interaction induces the "upright" conformation on mica, whereas the hydrophobic interaction favors the "flat" conformation on HOPG. We also show that the epitaxial pattern on mica is ensured by the lattice matching between the anisotropic binding sites of the basal substrate and the molecular dimension of GAV-9, accompanied with a long-range order of well-defined β-strands. Furthermore, the binding free energy surfaces indicate that the longitudinal assembly growth is predominantly driven by the hydrophobic interaction along the longer crystallographic unit cell direction of mica. These findings provide a molecular basis for the surface-assisted molecular assembly, which might also be useful for the design of de novo nanodevices.

Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study

Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting in the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validated this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation in experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids [isoleucine, leucine, and valine (ILV) clusters] were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with less hydrophobic alanines showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with isosteric, polar asparagines enhanced the wetting of the N- and C-terminal clusters. The experimental results on the stability, secondary structure, and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster experiences only partial drying in the intermediate, and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying within hydrophobic ILV clusters in the folding and stability of the αTS TIM barrel.

Biomolecular electrostatics and solvation: a computational perspective

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Coherent microscopic picture for urea-induced denaturation of proteins

In a previous study, we explored the mechanism of urea-induced denaturation of proteins by performing molecular dynamics (MD) simulations of hen lysozyme in 8 M urea and supported the "direct interaction mechanism" whereby urea denatures protein via dispersion interaction (Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16928). Here we perform large scale MD simulations of five representative protein/peptide systems in aqueous urea to investigate if the above mechanism is common to other proteins. In all cases, accumulations of urea around proteins/peptide are observed, suggesting that urea denatures proteins by directly attacking protein backbones and side chains rather than indirectly disrupting water structure as a "water breaker". Consistent with our previous case study of lysozyme, the current energetic analyses with five protein/peptide systems reveal that urea's preferential binding to proteins mainly comes from urea's stronger dispersion interactions with proteins than with bulk solution, whereas the electrostatic (hydrogen-bonded) interactions only play a relatively minor (even negative) role during this denaturation process. Furthermore, the simulations of the peptide system at different urea concentrations (8 and 4.5 M), and with different force fields (CHARMM and OPLSAA) suggest that the above mechanism is robust, independent of the urea concentration and force field used. Last, we emphasize the importance of periodic boundary conditions in pairwise energetic analyses. This article provides a comprehensive study on the physical mechanism of urea-induced protein denaturation and suggests that the "dispersion-interaction-driven" mechanism should be general.

Water-induced ethanol dewetting transition

The dewetting transitions of two hydrophobic plates immersed in pure water, aqueous ethanol solutions with concentrations from 25% to 90%, and pure ethanol were investigated by molecular dynamics simulations, where the dewetting transition was analogous to a first-order phase transition from liquid to vapor. It was found that the dewetting transitions occurred except that in the pure ethanol system. Although the ethanol molecules prefer to locate in the vicinity of the two plates, the inter-plate region is unfavorable for water molecules, due to losing more than one hydrogen bond. Moreover, each inter-plate water molecule forms hydrogen bonds on average with about two ethanol molecules. These intermolecular hydrogen bonds cause water and ethanol to cooperatively fill or exit the inter-plate region. Thus, water molecules play a more important role in the inter-plate filling/empty process, and induce the ethanol dewetting transition. Our results provide insight into the effect of water on the ethanol dewetting phenomena.

Critical Dipole Length for the Wetting Transition Due to Collective Water-dipoles Interactions

The wetting behavior of water on the solid surfaces is fundamental to various physical, chemical and biological processes. Conventionally, the surface with charges or charge dipoles is hydrophilic, whereas the non-polar surface is hydrophobic though some exceptions were recently reported. Using molecular dynamics simulations, we show that there is a critical length of the charge dipoles on the solid surface. The solid surface still exhibited hydrophobic behavior when the dipole length was less than the critical value, indicating that the water molecules on the solid surface seemed not "feel" attractive interactions from the charge dipoles on the solid surface. Those unexpected observations result from the collective interactions between the water molecules and charge dipoles on the solid surface, where the steric exclusion effect between water molecules greatly reduces the water-dipole interactions. Remarkably, the steric exclusion effect is also important for surfaces with charge dipole lengths greater than this critical length.

Free-energy simulations reveal that both hydrophobic and polar interactions are important for influenza hemagglutinin antibody binding

Antibodies binding to conserved epitopes can provide a broad range of neutralization to existing influenza subtypes and may also prevent the propagation of potential pandemic viruses by fighting against emerging strands. Here we propose a computational framework to study structural binding patterns and detailed molecular mechanisms of viral surface glycoprotein hemagglutinin (HA) binding with a broad spectrum of neutralizing monoclonal antibody fragments (Fab). We used rigorous free-energy perturbation (FEP) methods to calculate the antigen-antibody binding affinities, with an aggregate underlying molecular-dynamics simulation time of several microseconds (∼2 μs) using all-atom, explicit-solvent models. We achieved a high accuracy in the validation of our FEP protocol against a series of known binding affinities for this complex system, with <0.5 kcal/mol errors on average. We then introduced what to our knowledge are novel mutations into the interfacial region to further study the binding mechanism. We found that the stacking interaction between Trp-21 in HA2 and Phe-55 in the CDR-H2 of Fab is crucial to the antibody-antigen association. A single mutation of either W21A or F55A can cause a binding affinity decrease of ΔΔG > 4.0 kcal/mol (equivalent to an ∼1000-fold increase in the dissociation constant K(d)). Moreover, for group 1 HA subtypes (which include both the H1N1 swine flu and the H5N1 bird flu), the relative binding affinities change only slightly (< ±1 kcal/mol) when nonpolar residues at the αA helix of HA mutate to conservative amino acids of similar size, which explains the broad neutralization capability of antibodies such as F10 and CR6261. Finally, we found that the hydrogen-bonding network between His-38 (in HA1) and Ser-30/Gln-64 (in Fab) is important for preserving the strong binding of Fab against group 1 HAs, whereas the lack of such hydrogen bonds with Asn-38 in most group 2 HAs may be responsible for the escape of antibody neutralization. These large-scale simulations may provide new insight into the antigen-antibody binding mechanism at the atomic level, which could be essential for designing more-effective vaccines for influenza.

Role of spatial ionic distribution on the energetics of hydrophobic assembly and properties of the water/hydrophobe interface

We present results from all-atom molecular dynamics simulations of large-scale hydrophobic plates solvated in NaCl and NaI salt solutions. As observed in studies of ions at the air-water interface, the density of iodide near the water-plate interface is significantly enhanced relative to chloride and in the bulk. This allows for the partial hydration of iodide while chloride remains more fully hydrated. In 1 M solutions, iodide directly pushes the hydrophobes together (contributing -2.51 kcal mol(-1)) to the PMF. Chloride, however, strengthens the water-induced contribution to the PMF by ~-2.84 kcal mol(-1). These observations are enhanced in 3 M solutions, consistent with the increased ion density in the vicinity of the hydrophobes. The different salt solutions influence changes in the critical hydrophobe separation distance and characteristic wetting/dewetting transitions. These differences are largely influenced by the ion-specific expulsion of iodide from bulk water. Results of this study are of general interest to the study of ions at interfaces and may lend insight to the mechanisms underlying the Hofmeister series.

How water meets a very hydrophobic surface

Is there a low-density region ("gap") between water and a hydrophobic surface? Previous x-ray and neutron reflectivity results have been inconsistent because the effect (if any) is subresolution for the surfaces studied. We have used x-ray reflectivity to probe the interface between water and more hydrophobic smooth surfaces. The depleted region width increases with contact angle and becomes larger than the resolution, allowing definitive measurements. Large fluctuations are predicted at this interface; however, we find that their contribution to the interface roughness is too small to measure.

Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly

Hydrophobic effects continue to be an active area of research due to implications for a wide range of physicochemical phenomena. Molecular dynamics simulations have been used extensively in the study of such effects using various water potential models, with few studies addressing the differences between models. In particular, studies considering the explicit treatment of water polarizability are underrepresented in the literature. We present results from molecular dynamics simulations that systematically compare the dependence of large-scale hydrophobic effects on the water model. We consider three common nonpolarizable models (SPC/E, TIP3P, and TIP4P) and two common polarizable models (TIP4P-FQ and SWM4-NDP). Results highlight the similarities and differences of the different water models in the vicinity of two large hydrophobic plates. In particular, profiles of average density, density fluctuations, orientation, and hydrogen bonding show only minor differences among the water models studied. However, the potential of mean force for the hydrophobe dimerization is significantly reduced in the polarizable water systems. TIP4P-FQ shows the deepest minimum of approximately -54(+/-3) kcal/mol compared to -40(+/-3), -40(+/-2), -42(+/-3), and -45(+/-5) kcal/mol for TIP4P, TIP3P, SPC/E, and SWM4-NDP (all relative to the dissociated state). We discuss the relationship between hydrophobic association and the strength of water-water interactions in the liquid phase. Results suggest that models treating polarizability (both implicitly and explicitly) influence a stronger driving force toward hydrophobic assembly. Implications of these results, as well as prospectives on future work, are discussed.

Hydrophobic-induced Surface Reorganization: Molecular Dynamics Simulations of Water Nanodroplet on Perfluorocarbon Self-Assembled Monolayers

We carried out molecular dynamics simulations of water droplets on self-assembled monolayers of perfluorocarbon molecules. The interactions between the water droplet and the hydrophobic fluorocarbon surface were studied by systematically changing the molecular surface coverage and the mobility of the tethered head groups of the surface chain molecules. The microscopic contact angles were determined for different fluorocarbon surface densities. The contact angle at a nanometer length scale does not show a large change with the surface density. The structure of the droplets was studied by looking at the water density profiles and water penetration near the hydrophobic surface. At surface densities near close packed coverage of fluorocarbons, the water density shows an oscillating pattern near the boundary with a robust layered structure. As the surface density decreased and more water molecules penetrated into the fluorocarbon surface, the ordering of the water molecules at the boundary became less pronounced and the layered density structure became diffuse. The water droplet is found to induce the interfacial surface molecules to rearrange and form unique topological structures that minimize the unfavorable water-surface contacts. The local density of the fluorocarbon molecules right below the water droplet is measured to be higher than the density outside the droplet. The density difference increases as the overall surface density decreases. Two different surface morphologies emerge from the water-induced surface reorganization over the range of surface coverage explored in the study. For surface densities near closed packed monolayer coverage, the height of the fluorocarbons is maximum at the center of the droplet and minimum at the water-vapor-surface triple junction, generating a convex surface morphology under the droplet. For lower surface densities, on the other hand, the height of the fluorocarbon surface becomes maximal at and right outside the water-vapor-surface contact line and decreases quickly towards the center of the droplet, forming a concave shape of the surface. The interplay between the fluorocarbon packing and the water molecules is found to have profound consequences in many aspects of surface-water interactions, including water depletion and penetration, hydrogen bonding, and surface morphologies.

Recognition mechanism of siRNA by viral p19 suppressor of RNA silencing: a molecular dynamics study

The p19 protein (p19) encoded from Tombusvirus is involved in various activities such as pathogenicity and virus transport. Recent studies have found that p19 is a plant suppressor of RNA silencing, which binds to short interfering RNAs (siRNAs) with high affinity. We use molecular dynamics (MD) simulations of the wild-type and mutant p19 protein (W39 and W42G) binding with a 21-nt siRNA duplex to study the p19-siRNA recognition mechanism and mutation effects. Our simulations with standard MD and steered molecular dynamics have shown that the double mutant structure is indeed much less stable than the wild-type, consistent with the recent experimental findings. Comprehensive structural analysis also shows that the W39/42G mutations first induce the loss of stacking interactions between p19 and siRNA, Trp(42)-Cyt1 (Cyt1 from the 5' to 3' strand) and Trp(39)-Gua'19 (Gua19 from the 3' to 5' strand), and then breaks the hydrophobic core formed by W39-W42 with nucleotide basepairs in the wild-type. The steered molecular dynamics simulations also show that the mutant p19 complex is "decompounded" very fast under a constant separation force, whereas the wild-type remains largely intact under the same steering force. Moreover, we have used the free energy perturbation to predict a binding affinity loss of 6.98 +/- 0.95 kcal/mol for the single mutation W39G, and 12.8 +/- 1.0 kcal/mol loss for the double mutation W39/42G, with the van der Waals interactions dominating the contribution ( approximately 90%). These results indicate that the W39/42G mutations essentially destroy the important p19-siRNA recognition by breaking the strong stacking interaction between Cyt1 and Gua'19 with end-capping tryptophans. These large scale simulations might provide new insights to the interactions and co-evolution relationship between RNA virus proteins and their hosts.

Dewetting and hydrophobic interaction in physical and biological systems

Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments

The role of water in promoting the formation of protofilaments (the basic building blocks of amyloid fibrils) is investigated using fully atomic molecular dynamics simulations. Our model protofilament consists of two parallel beta-sheets of Alzheimer Amyloid-beta 16-22 peptides (Ac-K(16)-L(17)-V(18)-F(19)-F(20)-A(21)-E(22)-NH2). Each sheet presents a distinct hydrophobic and hydrophilic face and together self-assemble to a stable protofilament with a core consisting of purely hydrophobic residues (L(17), F(19), A(21)), with the two charged residues (K(16), E(22)) pointing to the solvent. Our simulations reveal a subtle interplay between a water mediated assembly and one driven by favorable energetic interactions between specific residues forming the interior of the protofilament. A dewetting transition, in which water expulsion precedes hydrophobic collapse, is observed for some, but not all molecular dynamics trajectories. In the trajectories in which no dewetting is observed, water expulsion and hydrophobic collapse occur simultaneously, with protofilament assembly driven by direct interactions between the hydrophobic side chains of the peptides (particularly between F-F residues). For those same trajectories, a small increase in the temperature of the simulation (on the order of 20 K) or a modest reduction in the peptide-water van der Waals attraction (on the order of 10%) is sufficient to induce a dewetting transition, suggesting that the existence of a dewetting transition in simulation might be sensitive to the details of the force field parametrization.

Effect of Surface Polarity on Water Contact Angle and Interfacial Hydration Structure

We perform molecular dynamics simulations of water in the presence of hydrophobic/hydrophilic walls at T = 300 K and P = 0 GPa. For the hydrophilic walls, we use a hydroxylated silica model introduced in previous simulations [Lee, S. H.; Rossky, P. J. J. Chem. Phys. 1994, 100, 3334. Giovambattista, N.; Rossky, P. J.; Debenedetti, P. G.; Phys. Rev. E 2006, 73, 041604.]. By rescaling the physical partial atomic charges by a parameter 0 <or= k <or= 1, we can continuously transform the hydrophilic walls (hydroxylated silica, k = 1) into hydrophobic apolar surfaces (k = 0). From a physical point of view, k is the normalized magnitude of a surface dipole moment, and thus it quantifies the polarity of the surface. We calculate the contact angle of water for 0 <or= k <or= 1. We find that, at least for the present homogeneous, atomically flat, and defect-free surface model, the magnitude of the surface dipole correlates with the contact angle in a one-to-one correspondence. In particular, we find that polar surfaces with 0 < k <or= kc = 0.4 are macroscopically hydrophobic; that is, the contact angle is larger than 90 degrees . For the cutoff value k = kc, the magnitude of the dipole moment of the polar silica surface unit is 41% that of the water molecule dipole moment. We also study the water orientation distributions next to the walls (a microscopic property). We find that these distributions also correlate with the contact angle in a one-to-one correspondence. Thus, the structure of confined water, the surface polarity, and the contact angle are in a direct correspondence to each other, and therefore, each quantifies the hydrophobicity/hydrophilicity of the surface.