How hydrophobic buckminsterfullerene affects surrounding water structure

Ethanol-Induced Aggregation of Nonpolar Nanoparticles in Water/Ethanol Mixed Solvents

The dispersity of nonpolar nanoparticles (NPs) in water/ethanol mixed solvents was studied using molecular dynamics simulations. Based on the rule of "like dissolves like," nonpolar NPs should be dispersed better in a solvent with a lower polarity. As the mole fraction of ethanol in a mixed solvent (R) increases from 0% (pure water) to 100% (pure ethanol), the polarity of the mixed solvent is indicated to decrease monotonically. However, the dispersity of nonpolar NP does not increase monotonically: it first decreases after the addition of a small fraction of ethanol (R < 8.0%) and then markedly increases as R further grows. When there is a small amount of ethanol, the ethanol molecules around aggregated NPs tend to simultaneously make contact with multiple NPs, which can increase the tendency of NP aggregation. Furthermore, with a considerable ethanol ratio, the interaction of the solvent with NPs becomes notably strong, which facilitates the dissolution of NPs. Our findings may help to better understand the mechanism of dispersion of NPs in mixed solvents and may provide a useful precipitation technology for NP production.

Synthesis and molecular dynamics simulation of CuS@GO–CS hydrogel for enhanced photothermal antibacterial effect

CuS@GO–CS hydrogels were prepared by a simple method and possessed an enhanced photothermal antibacterial effect against E. coli and S. aureus.

Molecular Dynamics Studies of Poly(Lactic Acid) Nanoparticles and Their Interactions with Vitamin E and TLR Agonists Pam1CSK4 and Pam3CSK4

Poly(lactic acid) (PLA) nanoparticles (NPs) are widely investigated due to their bioresorbable, biocompatible and low immunogen properties. Interestingly, many recent studies show that they can be efficiently used as drug delivery systems or as adjuvants to enhance vaccine efficacy. Our work focuses on the molecular mechanisms involved during the nanoprecipitation of PLA NPs from concentrated solutions of lactic acid polymeric chains, and their specific interactions with biologically relevant molecules. In this study, we evaluated the ability of a PLA-based nanoparticle drug carrier to vectorize either vitamin E or the Toll-like receptor (TLR) agonists Pam₁CSK₄ and Pam₃CSK₄, which are potent activators of the proinflammatory transcription factor NF-κB. We used dissipative particle dynamics (DPD) to simulate large systems mimicking the nanoprecipitation process for a complete NP. Our results evidenced that after the NP formation, Pam₁CSK₄ and Pam₃CSK₄ molecules end up located on the surface of the particle, interacting with the PLA chains via their fatty acid chains, whereas vitamin E molecules are buried deeper in the core of the particle. Our results allow for a better understanding of the molecular mechanisms responsible for the formation of the PLA NPs and their interactions with biological molecules located either on their surfaces or encapsulated within them. This work should allow for a rapid development of better biodegradable and safe vectorization systems with new drugs in the near future.

Randomized Incremental Construction of Delaunay Triangulations of Nice Point Sets

Randomized incremental construction (RIC) is one of the most important paradigms for building geometric data structures. Clarkson and Shor developed a general theory that led to numerous algorithms which are both simple and efficient in theory and in practice. Randomized incremental constructions are usually space-optimal and time-optimal in the worst case, as exemplified by the construction of convex hulls, Delaunay triangulations, and arrangements of line segments. However, the worst-case scenario occurs rarely in practice and we would like to understand how RIC behaves when the input is nice in the sense that the associated output is significantly smaller than in the worst case. For example, it is known that the Delaunay triangulation of nicely distributed points in E d or on polyhedral surfaces in E 3 has linear complexity, as opposed to a worst-case complexity of Θ ( n ⌊ d / 2 ⌋ ) in the first case and quadratic in the second. The standard analysis does not provide accurate bounds on the complexity of such cases and we aim at establishing such bounds in this paper. More precisely, we will show that, in the two cases above and variants of them, the complexity of the usual RIC is O ( n log n ) , which is optimal. In other words, without any modification, RIC nicely adapts to good cases of practical value. At the heart of our proof is a bound on the complexity of the Delaunay triangulation of random subsets of ε -nets. Along the way, we prove a probabilistic lemma for sampling without replacement, which may be of independent interest.

Effects of Water and Different Solutes on Carbon-Nanotube Low-Voltage Field-Effect Transistors

Semiconducting single-walled carbon nanotubes (swCNTs) are a promising class of materials for emerging applications. In particular, they are demonstrated to possess excellent biosensing capabilities, and are poised to address existing challenges in sensor reliability, sensitivity, and selectivity. This work focuses on swCNT field-effect transistors (FETs) employing rubbery double-layer capacitive dielectric poly(vinylidene fluoride-co-hexafluoropropylene). These devices exhibit small device-to-device variation as well as high current output at low voltages (<0.5 V), making them compatible with most physiological liquids. Using this platform, the swCNT devices are directly exposed to aqueous solutions containing different solutes to characterize their effects on FET current-voltage (FET I-V) characteristics. Clear deviation from ideal characteristics is observed when swCNTs are directly contacted by water. Such changes are attributed to strong interactions between water molecules and sp² -hybridized carbon structures. Selective response to Hg²⁺ is discussed along with reversible pH effect using two distinct device geometries. Additionally, the influence of aqueous ammonium/ammonia in direct contact with the swCNTs is investigated. Understanding the FET I-V characteristics of low-voltage swCNT FETs may provide insights for future development of stable, reliable, and selective biosensor systems.

Structural Dynamics of Neighboring Water Molecules of N-Isopropylacrylamide Pentamer

Poly(N-isopropylacrylamide) (PNIPAM) is a popular polymer widely used in smart hydrogel synthesis due to its thermo-responsive behavior in aqueous medium. Aqueous PNIPAM hydrogels can reversibly swell and collapse below and above their lower critical solution temperature (LCST), respectively. The present work used molecular dynamics simulations to explore the behavior of water molecules surrounding the side chains of a NIPAM pentamer in response to temperature changes (273-353 K range) near its experimental LCST (305 K). Results suggest a strong inverse correlation of temperature with water density and hydrophobic hydration character of the first coordination shell around the isopropyl groups. Integrity of the first and second coordination shells is further characterized by polygon ring analysis. Predominant occurrence of pentagons suggests clathrate-like behavior of both shells at lower temperatures. This predominance is eventually overtaken by 4-membered rings as temperature is increased beyond 303 and 293 K for the first and second coordination shells, respectively, losing their clathrate-like property. It is surmised that this temperature-dependent stability of the coordination shells is one of the important factors that controls the reversible swell-collapse mechanism of PNIPAM hydrogels.

Thickness and Structure of Adsorbed Water Layer and Effects on Adhesion and Friction at Nanoasperity Contact

Most inorganic material surfaces exposed to ambient air can adsorb water, and hydrogen bonding interactions among adsorbed water molecules vary depending on, not only intrinsic properties of material surfaces, but also extrinsic working conditions. When dimensions of solid objects shrink to micro- and nano-scales, the ratio of surface area to volume increases greatly and the contribution of water condensation on interfacial forces, such as adhesion (Fa) and friction (Ft), becomes significant. This paper reviews the structural evolution of the adsorbed water layer on solid surfaces and its effect on Fa and Ft at nanoasperity contact for sphere-on-flat geometry. The details of the underlying mechanisms governing water adsorption behaviors vary depending on the atomic structure of the substrate, surface hydrophilicity and atmospheric conditions. The solid surfaces reviewed in this paper include metal/metallic oxides, silicon/silicon oxides, fluorides, and two-dimensional materials. The mechanism by which water condensation influences Fa is discussed based on the competition among capillary force, van der Waals force and the rupture force of solid-like water bridge. The condensed meniscus and the molecular configuration of the water bridge are influenced by surface roughness, surface hydrophilicity, temperature, sliding velocity, which in turn affect the kinetics of water condensation and interfacial Ft. Taking the effects of the thickness and structure of adsorbed water into account is important to obtain a full understanding of the interfacial forces at nanoasperity contact under ambient conditions.

Generic Mechanism for Pattern Formation in the Solvation Shells of Buckminsterfullerene

Accurate description of solvation structure of a hydrophobic nanomaterial is of immense importance to understand protein folding, molecular recognition, drug binding, and many related phenomena. Moreover, spontaneous pattern formation through self-organization of solvent molecules around a nanoscopic solute is fascinating and useful in making template-directed nanostructures of desired morphologies. Recently, it has been shown using polarizable atomistic models that the hydration shell of a buckminsterfullerene can have atomically resolved ordered structure, in which C₆₀ atomic arrangement is imprinted. In analyzing any peculiar behavior of water, traditionally, emphasis has been placed on the long-ranged and orientation-dependent interactions in it. Here, we show through molecular dynamics simulation that the patterned solvation layer with the imprints of the hydrophobic surface atoms of the buckminsterfullerene can be obtained from a completely different mechanism arising from a spherically symmetric, short-ranged interaction having two characteristic lengthscales. The nature of the pattern can be modified by adjusting solvent density or pressure. Although solute-solvent dispersion interaction is the key to such pattern formation adjacent to the solute surface, the ordering at longer lengthscale is a consequence of mutual influence of short-range correlations among successive layers. The present study thus demonstrates that the formation of such patterned solvation shells around the buckminsterfullerene is not restricted to water, but encompasses a large class of anomalous fluids represented by two-lengthscale potential.

Water structuring above solutes with planar hydrophobic surfaces

Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a wetting type interaction to a dewetting regime as a function of the solute size, with a gradual transition in behavior taking place around characteristic lengths of ∼1 nm. Aggregations of non-polar species over this size range will undergo a transition from being dominated by entropy to being dominated by enthalpy. These transitions can be understood in part in terms of the geometries required of the solvating water molecules. We report here a series of simulations in aqueous solution of organic molecules with planar faces of increasing size, ranging from cyclopropane to circumcircumcoronene, in order to explore the transition in behavior for such solutes as their size increases. For this series, the dewetting transition occurred gradually, converging asymptotically to a limiting separation value for first layer water molecules of around 3.3 Å, while the transition in hydrogen bonding orientational structure occurred between cyclopropane and cyclopentadene. Water immediately adjacent to the largest planar hydrophobic surfaces oriented in ways that resembled on average the structural organization of the basal planes of ice.

Thermodynamics of hydration of fullerols [C60(OH)n] and hydrogen bond dynamics in their hydration shells

Molecular dynamics simulations of fullerene and fullerols [C₆₀(OH)_n, where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules. We have found that water molecules form two solvation shells around the central solute molecule. Hydrogen bonding in the bulk solvent is unaffected by increasing n. The large decrease in solvation enthalpies of these solute molecules for n > 14 enhances solubilisation. The diffusion constants of solute molecules decrease with increasing n. The solvation free energy of C₆₀ in water is positive (52.8 kJ/mol), whereas its value for C₆₀(OH)₃₀ is highly negative (-427.1 kJ/mol). The effects of surface hydroxylation become more dominant once the fullerols become soluble.

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

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

The impacts of surface polarity on the solubility of nanoparticle

In order to study the dependence of water solubility and hydration behavior of nanoparticles on their surface polarity, we designed polar nanoparticles with varying surface polarity by assigning atomic partial charge to the surface of C60. The water solubility of the nanoparticle is enhanced by several orders of magnitude after the introduction of surface polarity. Nevertheless, when the atomic partial charge grows beyond a certain value (qM), the solubility continuously decreases to the level of nonpolar nanoparticle. It should be noted that such qM is comparable with atomic partial charge of a variety of functional groups. The hydration behaviors of nanoparticles were then studied to investigate the non-monotonic dependence of solubility on the surface polarity. The interaction between the polar nanoparticle and the hydration water is stronger than the nonpolar counterpart, which should facilitate the dissolution of the nanoparticles. On the other hand, the surface polarity also reduces the interaction of hydration water with the other water molecules and enhances the interaction between the nanoparticles which may hinder their dispersion. Besides, the introduction of surface polarity disturbs and even rearranges the hydration structure of nonpolar nanoparticle. Interestingly, the polar nanoparticle with less ordered hydration structure tends to have higher water solubility.

Fullerenes in Aromatic Solvents: Correlation between Solvation-Shell Structure, Solvate Formation, and Solubility

In this work, an all-atom molecular dynamics simulation technique was employed to gain insight into the dynamic structure of the solvation shell formed around C60 and phenyl-C61-butyric acid methyl ester (PCBM) in nine aromatic solvents. A new method was developed to visualize and quantify the distribution of solvent molecule orientations in the solvation shell. A strong positive correlation was found between the regularity of solvent molecule orientations in the solvation shell and the experimentally obtained solubility limits for both C60 and PCBM. This correlation was extended to predict a solubility of 36 g/L for PCBM in 1,2,4-trimethylbenze. The relationship between solvation-shell structure and solubility provided detailed insight into solvate formation of C60 and solvation in relation to solvent molecular structure and properties. The determined dependence of the solvation-shell structure on the geometric shape of the solvent might allow for enhanced control of fullerene solution-phase behavior during processing by chemically tailoring the solvent molecular structure, potentially diminishing the need for costly and environmentally harmful halogenated solvents and/or additives.

Effect of Water Hydrogen Bonding on the Solvent-Mediated "Oscillatory" Repulsion of C60 Fullerenes in Water

The solvent-mediated interaction of C60 fullerenes in liquid water is examined by using the combination of the probabilistic hydrogen bond model with the density functional theory. This combination allows one to take into account the effect of hydrogen bonding between water molecules on their interaction with fullerenes and to construct an approximation for the distribution of water molecules in the system, which provides an efficient foundation for studying hydrophobic phenomena. Our numerical evaluations predict the solvent-induced interaction of two C60 fullerenes in water at 293 K to have an oscillatory-repulsive character (previously observed in molecular dynamics simulations) only when the vicinal water-water hydrogen bonds are slightly weaker than bulk ones. Besides indicating the direction of the energetic alteration of water-water hydrogen bonds near C60 fullerenes, our model also suggests that the hydrogen bonding ability of water plays a defining role in the solvent-mediated C60-C60 repulsion.

Functionalized fullerenes in water: a closer look

The excellent photophysical properties of C60 fullerenes have spurred much research on their application to aqueous systems for biological and environmental applications. Spontaneous aggregation of C60 in water and the consequent diminution of photoactivity present a significant challenge to aqueous applications. The mechanisms driving the reduction of photoactivity in fullerene aggregates and the effects of functionalization on these processes, however, are not well understood. Here, we take a closer look at the molecular phenomena of functionalized fullerene interactions in water utilizing simulation and experimental tools. Molecular dynamic simulations were performed to investigate time-evolved molecular interactions in systems containing fullerenes with water, oxygen, and/or neighboring fullerene molecules, complimented by physical and chemical characterizations of the fullerenes pre- and postaggregation. Aggregates with widely different photoactivities exhibit similar fullerene-water interactions as well as surface and aggregation characteristics. Photoactive fullerene aggregates had weaker fullerene-fullerene and fullerene-O2 interactions, suggesting the importance of molecular interactions in the sensitization route.

Dynamic solvation shell and solubility of C60 in organic solvents

The notion of (static) solvation shells has recently proved fruitful in revealing key molecular factors that dictate the solubility and aggregation properties of fullerene species in polar or ionic solvent media. Using molecular dynamics schemes with carefully evaluated force fields, we have scrutinized both the static and the dynamic features of the solvation shells of single C60 particle for three nonpolar organic solvents (i.e., chloroform, toluene, and chlorobenzene) and a range of system temperatures (i.e., T = 250-330 K). The central findings have been that, while the static structures of the solvation shell remain, in general, insensitive to the effects of changing solvent type or system temperature, the dynamic behavior of solvent molecules within the shell exhibits prominent dependence on both factors. Detailed analyses led us to propose the notion of dynamically stable solvation shell, effectiveness of which can be characterized by a new physical parameter defined as the ratio of two fundamental time constants representing, respectively, the solvent relaxation (or residence) time within the first solvation shell and the characteristic time required for the fullerene particle to diffuse a distance comparable to the shell thickness. We show that, for the five (two from the literature) different solvent media and the range of system temperatures examined herein, this parameter bears a value around unity and, in particular, correlates intimately with known trends of solubility for C60 solutions. We also provide evidence revealing that, in addition to fullerene-solvent interactions, solvent-solvent interactions play an important role, too, in shaping the dynamic solvation shell, as implied by recent experimental trends.

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.

Photodynamic therapy with fullerenes in vivo: reality or a dream?

Photodynamic therapy (PDT) employs the combination of nontoxic photosensitizers and visible light that is absorbed by the chromophore to produce long-lived triplet states that can carry out photochemistry in the presence of oxygen to kill cells. The closed carbon-cage structure found in fullerenes can act as a photosensitizer, especially when functionalized to impart water solubility. Although there are reports of the use of fullerenes to carry out light-mediated destruction of viruses, microorganisms and cancer cells in vitro, the use of fullerenes to mediate PDT of diseases such as cancer and infections in animal models is less well developed. It has recently been shown that fullerene PDT can be used to save the life of mice with wounds infected with pathogenic Gram-negative bacteria. Fullerene PDT has also been used to treat mouse models of various cancers including disseminated metastatic cancer in the peritoneal cavity. In vivo PDT with fullerenes represents a new application in nanomedicine.

Can nanotechnology potentiate photodynamic therapy?

Photodynamic therapy (PDT) uses the combination of non-toxic dyes and harmless visible light to produce reactive oxygen species that can kill cancer cells and infectious microorganisms. Due to the tendency of most photosensitizers (PS) to be poorly soluble and to form nonphotoactive aggregates, drug-delivery vehicles have become of high importance. The nanotechnology revolution has provided many examples of nanoscale drug-delivery platforms that have been applied to PDT. These include liposomes, lipoplexes, nanoemulsions, micelles, polymer nanoparticles (degradable and nondegradable), and silica nanoparticles. In some cases (fullerenes and quantum dots), the actual nanoparticle itself is the PS. Targeting ligands such as antibodies and peptides can be used to increase specificity. Gold and silver nanoparticles can provide plasmonic enhancement of PDT. Two-photon excitation or optical upconversion can be used instead of one-photon excitation to increase tissue penetration at longer wavelengths. Finally, after sections on in vivo studies and nanotoxicology, we attempt to answer the title question, "can nano-technology potentiate PDT?"

Carbon Nanomaterials: Efficacy and Safety for Nanomedicine

Carbon nanomaterials, including fullerenes, carbon nanohorns, and carbon nanotubes, are increasingly being used in various fields owing to these materials’ unique, size-dependent functions and physicochemical properties. Recently, because of their high variability and stability, carbon nanomaterials have been explored as a novel tool for the delivery of therapeutic molecules including peptide and nucleic acid cancer drugs. However, insufficient information is available regarding the safety of carbon nanomaterials for human health, even though such information is vital for the development of safe and effective nanomedicine technologies. In this review, we discuss currently available information regarding the safety of carbon nanomaterials in nanomedicine applications, including information obtained from our own studies; and we discuss types of carbon nanomaterials that demonstrate particular promise for safe nanomedicine technologies.

Remarkable patterns of surface water ordering around polarized buckminsterfullerene

Accurate description of water structure affects simulation of protein folding, substrate binding, macromolecular recognition, and complex formation. We study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere, by molecular dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3), derived from quantum mechanical data at the MP2/aug-cc-pVTZ(-hp) level augmented by CCSD(T). QMPFF3 calculation of the hydrophobic effect is compared to that obtained with empirical force fields. Using a novel and highly sensitive method, we see polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range. We see less water order for empirical force fields. The greater order seen with QMPFF3 will affect biological processes through a stronger hydrophobic effect.

Non-bulk-like solvent behavior in the ribosome exit tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.

Hydration structure on crystalline silica substrates

The structure of interfacial water at the silica solid surfaces was investigated using molecular dynamics simulations. Different degrees of surface hydroxylation were employed to assess the effect of the surface chemistry on the structure of interfacial water. Density profiles, in-plane radial distribution functions, in-plane density distribution, and hydrogen-bond profiles were calculated. Our results show that the surface hydroxylation affects the structure, orientation, and hydrogen-bond network of interfacial water molecules. Data analysis suggests that the degree of hydroxylation controls the amount of water molecules in the first interfacial layer as well as the distance between the first adsorbed layer and the substrate. Well-organized and uniform structures of interfacial water appear on the homogeneously hydroxylated surface, while a heterogeneous interfacial structure, characterized by extensive water-water hydrogen bonds, forms on the partially hydroxylated surface. We demonstrate that both the local surface chemistry and water-water hydrogen bonds are the dominant factors that determine the structural properties of interfacial water.

Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability

Confinement effects on protein stability are relevant in a number of biological applications ranging from encapsulation in the cylindrical cavity of a chaperonin, translocation through pores, and structure formation in the exit tunnel of the ribosome. Consequently, free energies of interaction between amino acid side chains in restricted spaces can provide insights into factors that control protein stability in nanopores. Using all-atom molecular dynamics simulations, we show that 3 pair interactions between side chains--hydrophobic (Ala-Phe), polar (Ser-Asn) and charged (Lys-Glu)--are substantially altered in hydrophobic, water-filled nanopores, relative to bulk water. When the pore holds water at bulk density, the hydrophobic pair is strongly destabilized and is driven to large separations corresponding to the width and the length of the cylindrical pore. As the water density is reduced, the preference of Ala and Phe to be at the boundary decreases, and the contact pair is preferred. A model that accounts for the volume accessible to Phe and Ala in the solvent-depleted region near the pore boundary explains the simulation results. In the pore, the hydrogen-bonded interactions between Ser and Asn have an enhanced dependence on their relative orientations, as compared with bulk water. When the side chains of Lys and Glu are restrained to be side by side, parallel to each other, then salt bridge formation is promoted in the nanopore. Based on these results, we argue and demonstrate that for a generic amphiphilic sequence, cylindrical confinement is likely to enhance thermodynamic stability relative to the bulk.

Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study

Carbon nanotubes (CNTs) are possible nanoinjectors for the introduction of therapeutic agents into cells. To explore their interactions with a lipid bilayer membrane and to model the nanoinjection process, we used coarse-grained molecular dynamics to simulate the penetration of dipalmitoylphosphatidylcholine (DPPC) bilayers by single-walled CNTs. Lipids are extracted from a bilayer during CNT penetration and reside on both the inner and the outer tube surfaces. Lipids that interact with the CNT interior wall spread out and hence can "block" the tube. However, the degree of lipid lining of the inner surface is strongly dependent upon the tube penetration velocity, with fewer lipids extracted from the bilayer at higher rates. There is no apparent effect on bilayer integrity after CNT penetration, with the bilayer able to self-seal. Our findings reveal some of the complexities of the interactions of lipids with CNT nanoinjectors and suggest a need to further characterize the influence of, for example, CNT functionalization and cargo on lipid blocking of CNTs.