Nonadditivities of the Particle Sizes Hidden in Model Pair Potentials and Their Effects on Physical Adsorptions.

It is important to understand the mechanism of colloidal particle assembly near a substrate for development of drug delivery systems, micro-/nanorobots, batteries, heterogeneous catalysts, paints, and cosmetics. Understanding the mechanism is also important for crystallization of the colloidal particles and proteins. In this study, we calculated the physical adsorption of colloidal particles on a flat wall mainly using the integral equation theory, wherein small and large colloidal particles were employed. In the calculation system, like-charged electric double-layer potentials were used as pair potentials. In some cases, it was found that the small particles are more easily adsorbed. This result is unusual from the viewpoint of the Asakura-Oosawa theory, and we call it a "reversal phenomenon". Theoretical analysis revealed that the reversal phenomenon originates from the nonadditivities of the particle sizes. Using the knowledge obtained from this study, we invented a method to analyze the size nonadditivity hidden in model pair potentials. The method will be useful for confirmation of various simulation results regarding the adsorption and development of force fields for colloidal particles, proteins, and solutes.

Comparison of atomic force microscopy force curve and solvation structure studied by integral equation theory.

Atomic force microscopy can observe structures of liquids (solvents) on solid surfaces as oscillating force curves. The oscillation originates from the solvation force, which is affected by the interaction between the probe, substrate, and solvents. To investigate the effects of the interactions on the force curve, we calculated the force curves by integral equation theory with various probe and substrate conditions. The probe solvophilicity affected the force curves more than the substrate solvophilicity in our calculation, and its reason is qualitatively explained by the amount of the desolvated solvents. We evaluated the probes and parameters in terms of the qualitative estimation of the number density distribution of the solvent on the wall. The negative of the force curve's derivative with respect to the surface separation reflected the number density distribution better than the force curve. This parameter is based on the method that is proposed previously by Amano et al. [Phys. Chem. Chem. Phys. 18, 15534 (2016)]. The normalized frequency shift can also be used for the qualitative estimation of the number density distribution if the cantilever amplitude is small. Solvophobic probes reflected the number density distribution better than the solvophilic probes. Solvophilic probes resulted in larger oscillation amplitudes than solvophobic probes and are suitable for measurements with a high S/N ratio.

An electric double layer structure and differential capacitance at the electrode interface of tributylmethylammonium bis(trifluoromethanesulfonyl)amide studied using a molecular dynamics simulation.

A molecular dynamics simulation at the electrode interface of a quaternary ammonium ionic liquid, tributylmethylammonium bis(trifluoromethanesulfonyl)amide ([N1444+][TFSA-]), has been performed. Unlike the commonly used cations, such as 1-alkyl-3-methylimidazolium and 1,1-alkylmethylpyrrolidinium cations, N1444+ has multiple long-alkyl groups (three butyl groups). The behavior of ions at the electrode interface, especially these butyl groups, has been investigated. N1444+ at the first layer mainly has two types of orientations, lying and standing. The lying orientation is dominant at moderately negative potentials. However, the standing one becomes dominant at the more negative potentials. Due to this orientational change, the number of N1444+ increases at the first layer as the potential becomes negative even at the potentials where the anions are completely depleted there. The change in orientation results in the upward deviation of the differential capacitance from the theoretical prediction at the negative potentials. The results suggest that the orientational preference caused by the steric constraint between alkyl groups plays an important role in the behavior of the electric double layer of the ionic liquids.

Janus-Type Gold/Polythiophene Composites Formed via Redox Reaction at the Ionic Liquid|Water Interface.

Janus-type Au/polythiophene (PT) composites have been prepared by utilizing the liquid/liquid interface between water (W) and a hydrophobic ionic liquid (IL) as the redox reaction site. AuCl4- is reductively deposited, and terthiophene is oxidatively polymerized spacio-selectively at the IL|W interface, leading to the formation of the Au/PT composites. The composites are Janus-type Au-attached PT plates with two surface morphologies, flat surface and flowerlike surface at the W and IL sides of the plates at the IL|W interface, respectively. Not only surface morphologies but also attached Au structures are different at the two surfaces; Au microurchins on the flat surface and dendritic Au nanofibers on the flowerlike surface. Optical and scanning electron microscopic observations have revealed that nanofibers and microurchins are formed at the early and later stage of the reaction, respectively. Electrochemistry at the IL|W interface has illustrated that electron transfer across the IL|W interface during the formation of the Janus-type Au/PT composites is coupled with ion transfer of AuCl4- to compensate for the charge unbalance in the two liquid phases. AuCl4- transferred into IL is found to be the source of the dendritic Au nanofibers formed at the IL side of the PT plates.

A relationship between the force curve measured by atomic force microscopy in an ionic liquid and its density distribution on a substrate.

An ionic liquid forms a characteristic solvation structure on a substrate. For example, when the surface of the substrate is negatively or positively charged, cation and anion layers are alternately aligned on the surface. Such a solvation structure is closely related to slow diffusion, high electric capacity, and chemical reactions at the interface. To analyze the periodicity of the solvation structure, atomic force microscopy is often used. The measured force curve is generally oscillatory and its characteristic oscillation length corresponds not to the ionic diameter, but to the ion-pair diameter. However, the force curve is not the solvation structure. Hence, it is necessary to know the relationship between the force curve and the solvation structure. To find physical essence in the relationship, we have used statistical mechanics of a simple ionic liquid. We found that the basic relationship can be expressed by a simple equation and the reason why the oscillation length corresponds to the ion-pair diameter. Moreover, it is also found that Derjaguin approximation is applicable to the ionic liquid system.

Number Density Distribution of Small Particles around a Large Particle: Structural Analysis of a Colloidal Suspension.

Some colloidal suspensions contain two types of particles-small and large particles-to improve the lubricating ability, light absorptivity, and so forth. Structural and chemical analyses of such colloidal suspensions are often performed to understand their properties. In a structural analysis study, the observation of the number density distribution of small particles around a large particle (gLS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain gLS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (ΦLL). We propose a theory that transforms ΦLL into gLS. The transform theory is explained in detail and tested. We demonstrate for the first time that LOT can be used for the structural analysis of a colloidal suspension. LOT combined with the transform theory will facilitate structural analyses of the colloidal suspensions, which is important for both understanding colloidal properties and developing colloidal products.

Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy.

Atomic force microscopy (AFM) in liquids can measure a force curve between a probe and a buried substrate. The shape of the measured force curve is related to hydration structure on the substrate. However, until now, there has been no practical theory that can transform the force curve into the hydration structure, because treatment of the liquid confined between the probe and the substrate is a difficult problem. Here, we propose a robust and practical transform theory, which can generate the number density distribution of solvent molecules on a substrate from the force curve. As an example, we analyzed a force curve measured by using our high-resolution AFM with a newly fabricated ultrashort cantilever. It is demonstrated that the hydration structure on muscovite mica (001) surface can be reproduced from the force curve by using the transform theory. The transform theory will enhance AFM's ability and support structural analyses of solid/liquid interfaces. By using the transform theory, the effective diameter of a real probe apex is also obtained. This result will be important for designing a model probe of molecular scale simulations.

Correction: Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy.

Correction for 'Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy' by Ken-ichi Amano et al., Phys. Chem. Chem. Phys., 2016, 18, 15534-15544.

Dynamics of the entropic insertion of a large sphere into a cylindrical vessel.

Insertion of a solute into a vessel comprising biopolymers is a fundamental function in a biological system. The entropy originating from the translational displacement of solvent particles plays an essential role in the insertion. Here we study the dynamics of entropic insertion of a large spherical solute into a cylindrical vessel. The solute and the vessel are immersed in small spheres forming the solvent. We develop a theoretical method formulated using the Fokker-Planck equation. The spatial distribution of solute-vessel entropic potential, which is calculated by the three-dimensional integral equation theory combined with rigid-body models, serves as input data. The key quantity analyzed is the density of the probability of finding the solute at any position at any time. It is found that the solute is inserted along the central axis of the vessel cavity and trapped at a position where the entropic potential takes a local minimum value. The solute keeps being trapped without touching the vessel inner surface. In a significantly long time τ, the solute transfers to the position in contact with the vessel bottom possessing the global potential minimum along the central axis. As the solute size increases, τ becomes remarkably longer. We also discuss the relevance of our result to the functional expression of a chaperonin/cochaperonin in the assistance of protein folding.

On the physics of multidrug efflux through a biomolecular complex.

Insertion and release of a solute into and from a vessel comprising biopolymers is a fundamental function in a biological system. A typical example is found in a multidrug efflux transporter. "Multidrug efflux" signifies that solutes such as drug molecules with diverse properties can be handled. In our view, the mechanism of the multidrug efflux is not chemically specific but rather has to be based on a physical factor. In earlier works, we showed that the spatial distribution of the solute-vessel potential of mean force (PMF) induced by the solvent plays imperative roles in the insertion∕release process. The PMF can be decomposed into the energetic and entropic components. The entropic component, which originates from the translational displacement of solvent molecules, is rather insensitive to the solute-solvent and vessel inner surface-solvent affinities. This feature is not shared with the energetic component. When the vessel inner surface is neither solvophobic nor solvophilic, the solvents within the vessel cavity and in the bulk offer almost the same environment to any solute with solvophobicity or solvophilicity, and the energetic component becomes much smaller than the entropic component (i.e., the latter predominates over the former). Our idea is that the multidrug efflux can be realized if the insertion/release process is accomplished by the entropic component exhibiting the insensitivity to the solute properties. However, we have recently argued that the entropic release of the solute is not feasible as long as the vessel geometry is fixed. Here we consider a model of TolC, a cylindrical vessel possessing an entrance at one end and an exit at the other end for the solute. The spatial distribution of the PMF is calculated by employing the three-dimensional integral equation theory with rigid-body models in which the constituents interact only through hard-body potentials. Since the behavior of these models is purely entropic in origin, our analysis is focused on the entropic component. We show that the entropically inserted solute can be released by a continuous variation of the vessel geometry which forms a time-dependent entropic force continuing to accelerate the solute motion to the exit. Solutes with a wide range of sizes are entropically released using the same vessel-geometry variation. The results obtained are fairly general and also applicable to the efflux pump protein AcrB and ATP-binding cassette transporter.

The relationship between local liquid density and force applied on a tip of atomic force microscope: a theoretical analysis for simple liquids.

The density of a liquid is not uniform when placed on a solid. The structured liquid pushes or pulls a probe employed in atomic force microscopy, as demonstrated in a number of experimental studies. In the present study, the relation between the force on a probe and the local density of a liquid is derived based on the statistical mechanics of simple liquids. When the probe is identical to a solvent molecule, the strength of the force is shown to be proportional to the vertical gradient of ln(ρDS) with the local liquid's density on a solid surface being ρDS. The intrinsic liquid's density on a solid is numerically calculated and compared with the density reconstructed from the force on a probe that is identical or not identical to the solvent molecule.

Interaction between the substrate and probe in liquid metal Ga: experimental and theoretical analysis.

Interaction between two bodies in a liquid metal is an important topic for development of metallic products with high performance. We conducted atomic force microscopy measurements and achieved the interaction between the substrate and the probe in liquid Ga of an opaque and highly viscous liquid. The interaction cannot be accessed with the normal atomic force microscopy, electron microscopy, and beam reflectometry. We performed a theoretical calculation using statistical mechanics of simple liquids by mixing an experimentally derived quantum effect. From both experiment and theory, we found an unusual behaviour in the interaction between the solvophobic substances, which has never been reported in water and ionic liquids. Shapes of the interaction curves between several solvophobic and solvophilic pairs in liquid Ga are also studied.

Implication of antigenic conversion of Helicobacter pylori lipopolysaccharides that involve interaction with surfactant protein D.

We propose two antigenic types of Helicobacter pylori lipopolysaccharides (LPS): highly antigenic epitope-carrying LPS (HA-LPS) and weakly antigenic epitope-carrying LPS (WA-LPS) based on human serum reactivity. Strains carrying WA-LPS are highly prevalent in isolates from gastric cancer patients. WA-LPS exhibits more potent biological activities compared to HA-LPS, namely, upregulation of Toll-like receptor 4 (TLR4) expression and induction of enhanced epithelial cell proliferation. The results of competitive binding assays using monosaccharides and methylglycosides, as well as binding assays using glycosidase-treated LPS, suggested that ß-linked N-acetyl-D-glucosamine and ß-linked D-galactose residues largely contributed to the highly antigenic epitope and the weakly antigenic epitope, respectively. WA-LPS exhibited greater binding activity to surfactant protein D (SP-D) in a Ca(2+)-dependent manner, and this interaction was inhibited by methyl-ß-D-galactoside. The biological activities of WA-LPS were markedly enhanced by the addition of SP-D. Lines of evidence suggested that removal of ß-N-acetyl-D-glucosamine residue, which comprises the highly antigenic epitope, results in exposure of the weakly antigenic epitope. The weakly antigenic epitope interacted preferentially with SP-D, and SP-D enhanced the biological activity of WA-LPS.

Helicobacter pylori lipopolysaccharides upregulate toll-like receptor 4 expression and proliferation of gastric epithelial cells via the MEK1/2-ERK1/2 mitogen-activated protein kinase pathway.

Helicobacter pylori is recognized as an etiological agent of gastroduodenal diseases. H. pylori produces various toxic substances, including lipopolysaccharide (LPS). However, H. pylori LPS exhibits extremely weakly endotoxic activity compared to the typical LPS, such as that produced by Escherichia coli, which acts through Toll-like receptor 4 (TLR4) to induce inflammatory molecules. The gastric epithelial cell lines MKN28 and MKN45 express TLR4 at very low levels, so they show very weak interleukin-8 (IL-8) production in response to E. coli LPS, but pretreatment with H. pylori LPS markedly enhanced IL-8 production induced by E. coli LPS by upregulating TLR4 via TLR2 and the MEK1/2-ERK1/2 pathway. The transcription factor NF-Y was activated by this signal and promoted transcription of the tlr4 gene. These MEK1/2-ERK1/2 signal-mediated activities were more potently activated by LPS carrying a weakly antigenic epitope, which is frequently found in gastric cancers, than by LPS carrying a highly antigenic epitope, which is associated with chronic gastritis. H. pylori LPS also augmented the proliferation rate of gastric epithelial cells via the MEK1/2-ERK1/2 pathway. H. pylori LPS may be a pathogenic factor causing gastric tumors by enhancing cell proliferation and inflammation via the MEK1/2-ERK1/2 mitogen-activated protein kinase cascade in gastric epithelial cells.

Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models.

We report a new progress in elucidating the mechanism of the unidirectional movement of a linear-motor protein (e.g., myosin) along a filament (e.g., F-actin). The basic concept emphasized here is that a potential field is entropically formed for the protein on the filament immersed in solvent due to the effect of the translational displacement of solvent molecules. The entropic potential field is strongly dependent on geometric features of the protein and the filament, their overall shapes as well as details of the polyatomic structures. The features and the corresponding field are judiciously adjusted by the binding of adenosine triphosphate (ATP) to the protein, hydrolysis of ATP into adenosine diphosphate (ADP)+Pi, and release of Pi and ADP. As the first step, we propose the following physical picture: The potential field formed along the filament for the protein without the binding of ATP or ADP+Pi to it is largely different from that for the protein with the binding, and the directed movement is realized by repeated switches from one of the fields to the other. To illustrate the picture, we analyze the spatial distribution of the entropic potential between a large solute and a large body using the three-dimensional integral equation theory. The solute is modeled as a large hard sphere. Two model filaments are considered as the body: model 1 is a set of one-dimensionally connected large hard spheres and model 2 is a double helical structure formed by two sets of connected large hard spheres. The solute and the filament are immersed in small hard spheres forming the solvent. The major findings are as follows. The solute is strongly confined within a narrow space in contact with the filament. Within the space there are locations with sharply deep local potential minima along the filament, and the distance between two adjacent locations is equal to the diameter of the large spheres constituting the filament. The potential minima form a ringlike domain in model 1 while they form a pointlike one in model 2. We then examine the effects of geometric features of the solute on the amplitudes and asymmetry of the entropic potential field acting on the solute along the filament. A large aspherical solute with a cleft near the solute-filament interface, which mimics the myosin motor domain, is considered in the examination. Thus, the two fields in our physical picture described above are qualitatively reproduced. The factors to be taken into account in further studies are also discussed.

Reactivity of Zinc Cations under Spontaneous Accumulation of Hydrophobic Coexisting Cations in Hydrophobic Nanoporous Silicon.

The ion enrichment behavior due to surface-induced phase separation and the concomitant phase transition of electrolyte solutions between a liquid and a solid confined within nanopores of porous silicon is examined using concentrated aqueous solutions. We performed open-circuit potential measurements and differential scanning calorimetry (DSC) while varying the concentration of aqueous tetraethylammonium chloride (TEACl) solution. Open-circuit potential measurements revealed that the local OH- concentration within the nanopores increases as the bulk TEACl concentration increases. DSC measurements indicated that TEA+ cations are enriched within the nanopores and an extremely high concentration of TEA+ remarkably increases the local OH- concentration. This increase in the local pH should realize the selective precipitation of metal hydroxides within the nanopores. However, such precipitation was not observed in our investigations using aqueous solutions containing zinc cations. The experimental results suggest that ionic species within the nanopores of porous silicon are more stable than those in a bulk solution due to the formation of ion pairs with enhanced stability as well as kinetic factors that increase the activation energy for precipitation.

Evolution and Reversible Polarity of Multilayering at the Ionic Liquid/Water Interface.

Highly correlated positioning of ions underlies Coulomb interactions between ions and electrified interfaces within dense ionic fluids such as biological cells and ionic liquids. Recent work has shown that highly correlated ionic systems behave differently than dilute electrolyte solutions, and interest is focused upon characterizing the electrical and structural properties of the dense electrical double layers (EDLs) formed at internal interfaces. It has been a challenge for experiments to characterize the progressive development of the EDL on the nanoscale as the interfacial electric potential is varied over a range of positive and negative values. Here we address this challenge by measuring X-ray reflectivity from the interface between an ionic liquid (IL) and a dilute aqueous electrolyte solution over a range of interfacial potentials from -450 to 350 mV. The growth of alternately charged cation-rich and anion-rich layers was observed along with a polarity reversal of the layers as the potential changed sign. These data show that the structural development of an ionic multilayer-like EDL with increasing potential is similar to that suggested by phenomenological theories and MD simulations, although our data also reveal that the excess charge beyond the first ionic layer decays more rapidly than predicted.

A theoretical analysis on characteristics of protein structures induced by cold denaturation.

Yeast frataxin is a protein exhibiting cold denaturation at an exceptionally high temperature (280 K). We show that the microscopic mechanism of cold denaturation, which has recently been suggested by us [Yoshidome and Kinoshita, Phys. Rev. E 79, 030905(R) (2009)], is also applicable to yeast frataxin. The hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach is employed for calculating hydration thermodynamic quantities of the protein with a prescribed structure. In order to investigate the characteristics of the cold-denatured structures of yeast frataxin, we consider the entropy change upon denaturation comprising the loss of the water entropy and the gain in the protein conformational entropy. The minimum and maximum values of the conformational-entropy gain (i.e., the range within which the exact value lies) are estimated via two routes. The range of the water-entropy loss is then determined from the entropy change experimentally obtained [Pastore et al., J. Am. Chem. Soc. 129, 5374 (2007)]. We calculate the water-entropy loss upon the transition from the native structure to a variety of unfolded structures. We then select the unfolded structures for which the water-entropy loss falls within the determined range. The selection is performed at cold and heat denaturation temperatures of yeast frataxin. The structures characterizing cold and heat denaturations are thus obtained. It is found that the average values of the radius of gyration, excluded volume, and water-accessible surface area for the cold-denatured structures are almost the same as those for the heat-denatured ones. We theoretically estimate the cold denaturation temperature of yeast frataxin from the experimental data for the enthalpy, entropy, and heat-capacity changes upon denaturation. The finding is that the temperature is considerably higher than 273 K. These results are in qualitatively good accord with the experimental observations.

[Clinical trials of Escherichia coli O-serogroup serodiagnosis in patients with diarrhea by Ec-LPS array].

After developing the Ec-LPS array for Escherichia coli O-serogroup serodiagnosis (J. Jpn. Infect. Dis., 2007; 81: 26-32), we tested the array's usefulness in sera bled over 8 years ago from 24 patients with pediatric diarrhea. IgM and IgA antibodies in 20 sera among sera from the 24 reacted with a single LPS spot, making it possible to diagnose the O-serogroup. IgG antibodies in almost all patient sera reacted with many LPS among the 58 O-serogroup LPS of E. coli. O-serogroup strains of E. coli isolated from the 24 patients numbered 15. Among 11 patients in who O-serogroups were serodiagnosed by both methods, 7 were diagnosed with the same O-serogroups. Based on these results, this array appears useful in the O-serogroup serodiagnosis of E. coli.