Formation of spanning water networks on protein surfaces via 2D percolation transition

The formation of spanning hydrogen-bonded water networks on protein surfaces by a percolation transition is closely connected with the onset of their biological activity. To analyze the structure of the hydration water at this important threshold, we performed the first computer simulation study of the percolation transition of water in a model protein powder and on the surface of a single protein molecule. The formation of an infinite water network in the protein powder occurs as a 2D percolation transition at a critical hydration level, which is close to the values observed experimentally. The formation of a spanning 2D water network on a single rigid protein molecule can be described by adapting the cluster analysis of conventional percolation studies to the characterization of the connectivity of the hydration water on the surface of finite objects. Strong fluctuations of the surface water network are observed close to the percolation threshold. Our simulations also furnish a microscopic picture for understanding the specific values of the experimentally observed hydration levels, where different steps of increasing mobility in the hydrated powder are observed.     

Thermal breaking of spanning water networks in the hydration shell of proteins

The presence of a spanning hydrogen-bonded network of water at the surface of biomolecules is important for their conformational stability, dynamics, and function. We have studied by computer simulations the clustering and percolation of water in the hydration shell of a small elastinlike peptide (ELP) and the medium-size protein staphylococcal nuclease (SNase), in aqueous solution. We have found that in both systems a spanning network of hydration water exists at low temperatures and breaks up with increasing temperature via a quasi-two-dimensional percolation transition. The thermal breaking of the spanning water network occurs at biologically relevant temperatures, in the temperature range, which is close to the temperature of the "inverse temperature transition" of ELP and the unfolding temperature of SNase, respectively.     

Properties of spanning water networks at protein surfaces

The formation of a spanning two-dimensional hydrogen-bonded water network at the surface of proteins via a percolation transition enables their biological function. We show in detail how the spanning (percolating) water network appears at the surfaces of model hydrophilic spheres and at the surface of a single protein (lysozyme) molecule. We have found essential correlations of the linear extension, radius of gyration, and position of the center of mass of the largest water cluster with its size. The specific two-peak structure of the probability distribution of the largest cluster size allowed us to study various properties separately for spanning and nonspanning largest clusters. The radius of gyration of the spanning cluster always exceeds the radii of the spheres or the effective radius of the protein. Any spanning cluster envelops essentially more than half of the surface area. The temporal decay of the spanning networks shows a stretched exponential character. Their average lifetime at the percolation threshold is about the lifetime of a water-water hydrogen bond.     

The Electrostatic Origin of Low‐Hydration Polymorphism in DNA

In recent years, significant progress has been made towards uncovering the physical mechanisms of low‐hydration polymorphism in double‐helical DNA. The effect appears to be mechanistically similar in different biological systems, and it is due to the ability of water to form spanning H‐bonded networks around biomacromolecules via a quasi‐two‐dimensional percolation transition. In the case of DNA, disintegration of the spanning H‐bonded network leads to electrostatic condensation of DNA strands because, below the percolation threshold, water loses its high dielectric permittivity, whereas the concentration of neutralizing counterions becomes high. In this Concept article arguments propose that this simple electrostatic mechanism represents the universal origin of low‐hydration polymorphism in DNA.     

Origin of the dynamic transition upon pressurization of crystalline proteins

We study the role of hydration water in the dynamic transition of low-hydrated proteins upon pressurization found recently (Meinhold, L.; Smith, J. C. Phys. Rev. E 2005, 72, 061908). Clustering and percolation of water in the hydration shells of protein molecules in crystalline Staphylococcal nuclease are analyzed at various pressures. The number of water molecules in the hydration shell increases and the hydrogen-bonded network of hydration water spans with increasing pressure. The dynamic transition of protein occurs when the spanning water network exists with the probability of about 50% and hydration water shows large density fluctuations. Formation of a spanning water network upon pressurization promotes protein dynamics as in the case of the dynamic transition with increasing hydration. Properties of hydration water in various thermodynamic states and their influence on biological function are discussed.     

Water clustering and percolation in low hydration DNA shells

The hydrogen-bonded networks of water at the surface of a model DNA molecule are analyzed. At low hydrations, only small water clusters are attached to the DNA surface, whereas, at high hydrations, it is homogeneously covered by a spanning water network. The spanning water network is formed via a percolation transition at an intermediate hydration number of about 15 water molecules per nucleotide, which is very close to the midpoint of polymorphic transitions between A- and B-forms of the double helix. The percolation transition can occur in both A- and B-DNA hydration shells with nearly identical percolation thresholds. However, the mechanism of the percolation transition in A- and B-DNA is qualitatively different in regard to the roles played by the two opposite grooves of the double helix. Free ions can shift the percolation threshold by preventing some water molecules from hydrogen bond networking. The results corroborate the suggested relationship between water percolation and the low hydration polymorphism in DNA.     

Which Properties of a Spanning Network of Hydration Water Enable Biological Functions?

The central role of water in biological functions is well‐recognized, but numerous questions concerning the physical mechanisms behind the importance of water for life remain unanswered. Water in biosystems exists mainly as hydration water. Analysis of the phase diagram of hydration water shows that biological functions are possible only when the surfaces of biomolecules are covered by spanning hydrogen‐bonded networks of hydration water. The comparative studies of the various properties of hydrated biosystems in the presence and in the absence of a spanning water network should clarify its specific physical properties, which are crucial for biological functions. Herein, we summarize the recent progress in these studies. The biological activity of the living organisms is maximal in a narrow temperature interval, where the spanning network of hydration water breaks up with heating via a percolation transition. The entropy of the hydration water related to the diversity of cluster size diverges at this percolation threshold. The possible role of this phenomenon in life processes is discussed.     

Unraveling the Oxidation Behaviors of MXenes in Aqueous Systems by Active-Learning-Potential Molecular-Dynamics Simulation

MXenes are 2D materials with great potential in various applications. However, the degradation of MXenes in humid environments has become a main obstacle in their practical use. Here we combine deep neural networks and an active learning scheme to develop a neural network potential (NNP) for aqueous MXene systems with ab initio precision but low cost. The oxidation behaviors of super large aqueous MXene systems are investigated systematically at nanosecond timescales for the first time. The oxidation process of MXenes is clearly displayed at the atomic level. Free protons and oxides greatly inhibit subsequent oxidation reactions, leading to the degree of oxidation of MXenes to exponentially decay with time, which is consistent with the oxidation rate of MXenes measured experimentally. Importantly, this computational study represents the first exploration of the kinetic process of oxidation of super-sized aqueous MXene systems. It opens a promising avenue for the future development of effective protection strategies aimed at controlling the stability of MXenes.     

Conductive Flow Parameters of Mixed Nonionic Surfactants Microemulsions

This article focuses on the electrical conductivity study of the brine solution/sucrose laurate/ethoxylated mono-di-glyceride/oil + ethanol system. The oils were R (+)-limonene, isopropylmyristate and caprylic-capric triglyceride. The mixing ratio (w/w) of ethanol/oil and that of sucrose laurate/ethoxylated mono-di-glyceride equal unity. The brine solution was 0.01 M aqueous sodium chloride solution. No observable effect was observed on the phase boundaries by replacing pure water with brine solution in the case of R (+)-limonene based microemulsions. In the systems based on isopropylmyristate and caprylic-capric triglyceride, the replacement of pure water by brine significantly affected the phase boundaries, the microemulsion region shrink and the total monophasic area of microemulsions decreased. Electrical conductivity increases with the increase in the water volume fraction and percolation thresholds were observed. The critical volume fractions where the percolation thresholds appear depend on the type of oil used in the microemulsion formulation. Electrical conductivity was measured at different temperatures and the activation energy of conduction flow was evaluated. At the percolation threshold the activation energy of conduction flow reaches a minimum value. Beyond the percolation threshold, a small increase is observed in the activation energy of conduction flow then it decreases with the increase in the water volume fraction indicating structural transitions.     

Percolation transition in supercritical water: a Monte Carlo simulation study

Computer simulations of water have been performed on the canonical ensemble at 15 different molecular number densities, ranging from 0.006 to 0.018 A-3, along the supercritical isotherm of 700 K, in order to characterize the percolation transition in the system. It is found that the percolation transition occurs at a somewhat higher density than what is corresponding to the supercritical extension of the boiling line. We have shown that the fractal dimension of the largest cluster and the probability of finding a spanning cluster are the most appropriate properties for the location of the true percolation threshold. Thus, percolation transition occurs when the fractal dimension of the largest cluster reaches 2.53, and the probability of finding a cluster that spans the system in at least one dimension and in all the three dimensions reaches 0.97 and 0.65, respectively. On the other hand, the percolation threshold cannot be accurately located through the cluster size distribution, as it is distorted by appearance of clusters crossing the finite simulated system even far below the percolation threshold. The structure of the largest water cluster is dominated by a linear, chainlike arrangement, which does not change noticeably until the largest cluster becomes infinite.     

Ultrathin transparent conductive films of polymer-modified multiwalled carbon nanotubes

Deposition of multiwalled carbon nanotubes modified by poly(2-vinylpyridine) (CNT-g-P2VP) from aqueous dispersions at low pH is an effective method to prepare homogeneous ultrathin films with a tunable CNTs density. A percolation threshold of 0.25 mug/cm2 and a critical exponent alpha = 1.24 have been found from dc conductivity measurements. The sheet resistance value agrees with the percolation theory for 2D films. According to AFM and electrical measurements, even when only 5% of the surface is covered by CNT-g-P2VPs, the sheet resistance is of the order of 1 MOmega/sq, which indicates that conductivity is imparted by a network of an ultralow density. When the film transmittance decreases down to approximately 70% at 550 nm, the occupied surface area is approximately 15% and sheet resistance falls down to approximately 90 kOmega/sq. These data show that undesired in-plane clustering does not occur upon the dispersion casting of the films and that high-quality networks of CNT-g-P2VPs are built up. The electrosteric stabilization of the CNT-g-P2VP dispersions in water at low pH is at the origin of this desired behavior. Although the multiwalled CNT films prepared in this work are less conductive and less transparent than the SWNTs films, they could find applications, e.g., in touch screens, reflective displays, EMI shielding, and static charge dissipation.     

Particle connectedness and cluster formation in sequential depositions of particles: integral-equation theory

We applied the integral-equation theory to the connectedness problem. The method originally applied to the study of continuum percolation in various equilibrium systems was modified for our sequential quenching model, a particular limit of an irreversible adsorption. The development of the theory based on the (quenched-annealed) binary-mixture approximation includes the Ornstein-Zernike equation, the Percus-Yevick closure, and an additional term involving the three-body connectedness function. This function is simplified by introducing a Kirkwood-like superposition approximation. We studied the three-dimensional (3D) system of randomly placed spheres and 2D systems of square-well particles, both with a narrow and with a wide well. The results from our integral-equation theory are in good accordance with simulation results within a certain range of densities.     

Circular hydrogen bond networks on the surface of beta-ribofuranose in aqueous solution

This paper examines the hydration structure on the surface of beta-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of beta-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of beta-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.     

Percolation phenomenon in mixed reverse micelles: the effect of additives

The conductivity of AOT/IPM/water reverse micellar systems as a function of temperature, has been found to be non-percolating at three different concentrations (100, 175 and 250 mM), while the addition of nonionic surfactants [polyoxyethylene(10) cetyl ether (Brij-56) and polyoxyethylene(20) cetyl ether (Brij-58)] to these systems exhibits temperature-induced percolation in conductance in non-percolating AOT/isopropyl myristate (IPM)/water system at constant compositions (i.e., at fixed total surfactant concentration, omega and X(nonionic)). The influence of total surfactant concentration (micellar concentration) on the temperature-induced percolation behaviors of these systems has been investigated. The effect of Brij-58 is more pronounced than that of Brij-56 in inducing percolation. The threshold percolation temperature, Tp has been determined for these systems in presence of additives of different molecular structures, physical parameters and/or interfacial properties. The additives have shown both assisting and resisting effects on the percolation threshold. The additives, bile salt (sodium cholate), urea, formamide, cholesteryl acetate, cholesteryl benzoate, toluene, a triblock copolymer [(EO)13(PO)30(EO)13, Pluronic, PL64], polybutadiene, sucrose esters (sucrose dodecanoates, L-1695 and sucrose monostearate S-1670), formamide distinctively fall in the former category, whereas sodium chloride, cholesteryl palmitate, crown ether, ethylene glycol constitute the latter for both systems. Sucrose dodecanoates (L-595) had almost marginal effect on the process. The observed behavior of these additives on the percolation phenomenon has been explained in terms of critical packing parameter and/or other factors, which influence the texture of the interface and solution properties of the mixed reverse micellar systems. The activation energy, Ep for the percolation process has been evaluated. Ep values for the AOT/Brij-56 systems have been found to be lower than those of AOT/Brij-58 systems. The concentration of additives influence the parameters Tp and Ep for both systems. A preliminary report for the first time on the percolation phenomenon in mixed reverse micelles in presence of additives has been suggested on the basis of these parameters (Tp and Ep).     

Theoretical consideration of osmotic pressure in aqueous protein/salt systems based on extended hard core Lennard-Jones potential

A simple and analytical pair potential function was developed to represent the osmotic pressures in aqueous protein/salt systems under various conditions. Based on a hard core Lennard-Jones (HCLJ) potential model, the new potential function considers various interactions by extending the attractive Lennard-Jones potential. A temperature-dependent coefficient term was introduced to take into account the specific properties of given materials. Comparison of the new potential function with the HCLJ model in hydrocarbon and water systems showed that consideration of the temperature dependence in the potential function was effective, especially for strong polar systems such as water. To predict the osmotic pressures of aqueous lysozyme/(NH(4))(2)SO(4) solutions of various ionic strength and pH, the energy parameters of lysozyme were correlated with the experimental cloud point temperature. The proposed model agreed fairly well with the experimental osmotic pressure data with only previously obtained parameters.     

Dispersing behavior of recycled rubber particles

The hydrophobic nature of recycled rubber particles presently limits their use only in non-aqueous media. Recycled rubber particles were chemically modified by preparation of amphiphilic semi-interpenetrating polymer networks using poly(acrylic acid) as the hydrophilic polymer. The resulting composite particles are water dispersible and suitable for various aqueous media applications.     

The Conductance Percolation and Droplets Dimension of AOT in Alkanol Systems

The conductance behaviors of AOT in alkanol (hexanol, heptanol, octanol, and decanol) reverse microemulsions have been investigated. The percolation phenomenon induced by water is observed in the water/AOT/decanol system at 15°C and 30°C, and the water/AOT/octanol system at 15°C. The percolation phenomenon of water/AOT/alkanol systems is discussed from the interaction between the hydroxy group of alkanol and the polar group of AOT, droplets diffusion coefficient, and the rate constant for droplets collision. The droplets size and diffusion coefficient of the water/AOT/alkanol systems have also been studied by modifying the water concentration. The results show that hydrodynamic diameter of droplets decreases and diffusion coefficient increases with the increasing of water content, which may be explained by the polarity of alkanol phase.     

Fracture behavior of triglyceride‐based adhesives

The use of natural plant oils in the production of adhesives has been the focus of much research because natural oils are a renewable resource which have environmental and economic advantages over the petroleum‐derived chemicals used in traditional adhesives. The network formation and the stress–strain behavior of these plant oil–based adhesives is studied using a combination of simulation techniques. An off‐lattice Monte Carlo simulation has been developed to model the formation of these networks via the free‐radical copolymerization of the triglycerides present in natural oils. Networks of systems representing the triglycerides found in soybean oil, linseed oil, and olive oil are generated, as are networks made from other “theoretical” natural oils. The structure of the networks is characterized by percolation analysis. The stress–strain behavior of these networks is studied using large‐scale molecular dynamics simulations. Tensile strains are applied to the networks and it is observed that with increasing n the failure stress increases but the failure strain decreases. Also, for systems with low values of n, large voids form while the system is strained and then the system fails cohesively. However, for large n, no significant voiding is observed and the system fails close to the interface. The simulation results are shown to be consistent with the vector percolation theoretical prediction for how the failure stress relates to n. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3333–3343, 2004     

Molecular dynamics simulation of quasi-two-dimensional water clusters on ice nucleation protein

We performed molecular dynamics simulations of systems that consisted of the ice nucleation protein and the quasi-two-dimensional water cluster on it. The angle distributions, percolation probabilities, mean cluster sizes, cluster size distributions, and hydrogen bond relaxation times were analyzed. We concluded that the behavior of the water clusters on the ice nucleation protein was elaborately intertwined by the interaction between the ice nucleation protein and water, the interaction between the water molecules and the effect of temperature. The percolation probability and mean cluster size depended on the interactions and temperatures.