A molecular dynamics simulation study of the effect of water–graphene interaction on the properties of confined water

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsive r^?12 potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r^?12 potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential.     

Structures,intermolecular interactions,and chemical hardness of binary water–organic solvents: a molecular dynamics study

The evolution of structural properties, thermodynamics and averaged (dynamic) total hardness values as a function of the composition of binary water–organic solvents, was rationalized in view of the intermolecular interactions. The organic solvents considered were ethanol, acetonitrile, and isopropanol at 0.25, 0.5, 0.75, and 1 mass fractions, and the results were obtained using molecular dynamics simulations. The site-to-site radial distribution functions reveal a well-defined peak for the first coordination shell in all solvents. A characteristic peak of the second coordination shell exists in aqueous mixtures of acetonitrile, whereas in the water–alcohol solvents, a second peak develops with the increase in alcohol content. From the computed coordination numbers, averaged hydrogen bonds and their lifetimes, we found that water mixed with acetonitrile largely preserves its structural features and promotes the acetonitrile structuring. Both the water and alcohol structures in their mixtures are disturbed and form hydrogen bonds between molecules of different kinds. The dynamic hardness values are obtained as the average over the total hardness values of 1200 snapshots per solvent type, extracted from the equilibrium dynamics. The dynamic hardness profile has a non-linear evolution with the liquid compositions, similarly to the thermodynamic properties of these non-ideal solvents.

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Graphical abstract Computed dynamic total hardness, as a function of the cosolvent mass fraction for water–ethanol (EtOH), water–isopropanol (2PrOH) and water–acetonitrile (AN)

     

Molecular dynamics simulation of the melting processes of core–shell and pure nanoparticles

Core–shell nanoparticles are nanosized particles that consist of a core and a shell, constructed from different metallic elements. Core–shell nanoparticles have received extensive attention, owing to their various potential applications such as paints, optical films and catalysts. Herein, we investigate the melting behaviours of different core–shell nanoparticles under continuous heating using molecular dynamics simulation. Different metallic elements were examined as core–shell and pure nanoparticles. Five different processes were observed during the melting of core–shell nanoparticles. In contrast, only one process was identified during the melting of pure nanoparticles. These processes were influenced by the nanoparticle size, shell thickness and differences between the lattice constants and melting point temperatures of the metallic elements. Our simulation provides microscopic insights into the melting behaviours of existing and proposed core–shell nanoparticles that would be highly beneficial towards the fabrication of materials with different chemical coatings.     

The dynamics of irreversible evaporation of a water–protein droplet and the problem of structural and dynamic experiments with single molecules

The effect of isothermal and adiabatic evaporation on the state of a water–protein droplet is discussed. The considered problem relates to the design of various approaches for structural and dynamic experiments with single molecules involving X-ray lasers. The delivery of the sample into the X-ray beam is performed by a microdroplet injector in these experiments; and the approach time is in the microsecond range. A version of molecular-dynamics simulation for all-atom modeling of an irreversible isothermal evaporation process is developed. The parameters of the isothermal evaporation of a water–protein droplet that contains sodium and chloride ions at concentrations of approximately 0.3 M have been determined in computational experiments for different temperatures. The in silico experiments showed that the energy of irreversible evaporation at the initial stages of the process was virtually the same as the specific heat of evaporation for water. An exact analytical solution of the problem for the kinetics of irreversible adiabatic evaporation has been obtained in the limit of the high heat conductivity of the droplet (or a droplet size not exceeding ~100 Å). This solution contains parameters that were derived from simulation of the isothermal evaporation of the droplets. The kinetics of the evaporation and adiabatic cooling of the droplet were shown to be scalable according to the size of the droplet. Estimation of the rate of freezing of the water–protein droplet upon adiabatic evaporation in a vacuum chamber revealed the necessity of using additional procedures for stabilizing the temperature in the droplet nucleus that contains the protein molecule. Isothermal or quasi-isothermal conditions are more favorable for the investigation of macro-molecular structural rearrangements that are related to the functioning of the object. However, the effects of dehydration and a sharp increase in the ionic strength of the aqueous microenvironment of the protein must be taken into account in this case.     

The effect of phosphorylation on the conformation of oligo-peptides with Ser–Pro motif: a molecular dynamics simulation

Model tetrapeptide system was designed to investigate the cis/trans isomerization of peptidyl-prolyl imide bond of Ser–Pro motif. To establish the side-chain O-phosphorylation effect in regulating the peptides conformations, molecular dynamics (MD) simulations where carried out on the designed tetrapeptides and their corresponding phosphorylated forms by MD Insight II Discovery3 approach. The most stable configurations and the statistic cis/trans concentration distribution demonstrated that the phosphorylation evidently influences the peptidyl-prolyl imide bond isomerization and works as a key effect in regulating the peptide conformations. The charge state and the site provided for the charge of the phosphate moiety might be an important key. The results also demonstrated that phosphorylation changes the cis conformation ratio of the peptide and the maximum cis value is obtained when the phosphate group has no negative charge.     

Effects of ground water and harvest intensity on alkaline grassland ecosystem dynamics – a simulation study

A model for the alkaline grassland ecosystems, MAGE, was applied to plant communities dominated by three species. Field observations on two communities dominated respectively by Puccinellia tenuiflora and Suaeda corniculata were used to parameterize the model for multiple species interaction. The model behaves reasonably in following the seasonal variations of water content, soluble sodium cation and calcium cation in surface soil, as well as biomass of the plant communities.Simulations were run to investigate the effects of ground water quality, ground water table depth, maximum non-capillary porosity in surface soil and harvest intensity, on ecosystem dynamics. The results indicated that ground water sodium concentration and ground water table depth had primary control on soil alkalization and vegetation status. The improvement of soil conditions by vegetation is limited to an extent with moderate ground water depth and sodium concentration. Non-capillary pores are critical for vegetation to affect the soil alkalization/de-alkalization process, but the effect of non-capillary pores tends to saturate when maximum non-capillary porosity is greater than 0.1.     

Molecular dynamics simulation of Axillaridine–A: A potent natural cholinesterase inhibitor

Molecular Dynamics (MD) simulations were carried out for human acetylcholinesterase (hAChE) and its complex with Axillaridine–A, in order to dynamically explore the active site of the protein and the behaviour of the ligand at the peripheral binding site. Simulation of the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues while Tyr72 is almost perpendicular to the Trp286, which is responsible for stable π -π interactions. The complexation of AChE with Axillaridine-A, results in the reduction of gorge size due to interaction between the ligand and the active site residues. The gorge size was determined by the distance between the center of mass of Glu81 and Trp286. As far as the geometry of the active site is concerned, the presence of ligand in the active site alters its specific conformation, as revealed by stable hydrogen bondings established between amino acids. With the increasing interaction between ligand and the active amino acids, size of the active site of the complex decreases with respect to time. Axillaridine-A, forms stable π -π interactions with the aromatic ring of Tyr124 that results in inhibition of catalytic activity of the enzyme. This π -π interaction keeps the substrate stable at the edge of the catalytic gorge by inhibiting its catalytic activity. The MD results clearly provide an explanation for the binding pattern of bulky steroidal alkaloids at the active site of AChE.     

Lees–Edwards boundary condition for simulation of polymer suspension with dissipative particle dynamics method

The Lees–Edwards boundary condition (LEbc) is widely used in particle-based simulation for producing shear flow. Application of traditional LEbc in dissipative particle dynamics (DPD) method may encounter certain problems, e.g. it will destroy the momentum conservation law at the near boundary region, and the coordinate system gives an incorrect end-to-end vector for polymer beads. Special treatments of the implementation of LEbc in DPD method are introduced in this paper. A single side ghost layer is used to keep the momentum conservation, and the global coordinate system is employed to obtain a correct calculation of the spring force between polymer beads. The simulation results give a good prediction of velocity profile and system temperature, and the elastic dumbbell model for current method can well represent the Oldroyd-B fluid.     

Molecular dynamics simulation of the reciprocal fused LiF–KBr mixture: local structure and self-diffusion coefficients

This paper describes the molecular dynamics simulation of the reciprocal fused LiF–KBr mixture, which is located above the critical mixing point, in the temperature range 1280–1450 K. The first coordination sphere is found to form as follows: a smaller ion is formed around a smaller counter-ion, and a larger ion is formed around a larger counter-ion. The calculated concentration dependence of the self-diffusion coefficients and the radial distribution functions of all ion pairs indicate that the degree of association of the Li–F pair increases as the lithium fluoride fraction in the mixture decreases.     

Effect of glycerol–water binary mixtures on the structure and dynamics of protein solutions

We have performed 20?ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30, and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The solvent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the incoherent intermediate scattering function, shows a nonmonotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water-containing solvents, but different from the pure glycerol case. The increase in the number of protein–glycerol hydrogen bonds in glycerol–water binary mixtures explains the slowing down of protein dynamics as the glycerol content increases. We also explored the dynamic behavior of the hydration layer. We show that the short length scale dynamics of this layer are insensitive to glycerol concentration. However, the long length scale behavior shows a significant dependence on glycerol content. We also provide insights into the behavior of bound and mobile water molecules.     

Binding of 1-substituted carbazolyl-3,4-dihydro-β-carbolines with DNA: Molecular dynamics simulation and MM-GBSA analysis

Molecular Mechanics-Generalized Born-Solvent Accessibility free energy calculations were used to analyse DNA binding affinity of 1-substituted carbazolyl-3,4-dihydro-β-carboline molecules. In this study, DNA structure with sequence of d(CGATCG)2 was used for simulations. 15 ns molecular dynamics simulations of the studied complexes were performed. The calculated free energy was compared with experimental antitumor activity (IC₅₀). The predicted free energies decreased with the increase of IC₅₀ values. It was shown that molecules 1–6 bind to DNA via intercalation mode, while molecules 7–9 bind through groove binding mode. Also, it was found that the vdW energy term (ΔE_vdW) and the non-polar desolvation energy (ΔG_SA) are the favorable terms for binding energy, whereas net electrostatic energies (ΔE_ele + ΔG_GB) and conformational entropy energy (TΔS) are unfavorable ones.     

Conformational and dynamics simulation study of antimicrobial peptide hedistin—heterogeneity of its helix–turn–helix motif

Hedistin is an antimicrobial peptide isolated from the coelomocytes of Nereis diversicolor, possessing activity against a large spectrum of bacteria including the methicillin resistant Staphylococcus aureus and Vibrio alginolyticus. The three-dimensional structure of hedistin in both aqueous solution and deuterated dodecylphosphocholine (DPC) micelles was examined using circular dichroism (CD) and nuclear magnetic resonance (NMR) techniques. And, the early events of the antibacterial process of hedistin were simulated using palmitoyl-oleoyl-phophatidylcholine (POPC) lipid bilayers and molecular dynamics (MD) simulation methods. Hedistin lacks secondary structure in aqueous solution, however, in DPC micelles, it features with a heterogeneous helix–turn–helix moiety and exhibits obvious amphipathic nature. The turn region (residues Val9–Thr12) in the moiety is a four-residue hinge, lying in between the first N-terminal α-helix (residues Leu5–Lys8) and the second α-helix (residues Val13–Ala17) regions and causing an ～ 120° angle between the axes of the two helices. The segmental and nonlinear nature of hedistin structure is referred to as the heterogeneity of its helix–turn–helix motif which was found to be corresponding to a kind of discrete dynamics behavior, herein coined as its dynamical heterogeneity, at the early stage (0–50 ns) of the MD simulations. That is, the first helix segment, prior to (at 310 K) or following (at 363 K) the second helix, binds to the lipid head-group region and subsequently permeates into the hydrophobic lipid tail region, and the hinge is the last portion entering the lipid environment. This result implies that hedistin may adopt a “carpet” model action when disrupting bacterial membrane.     

Molecular dynamics simulations and contact angle of surfactant at the coal–water interface

Wettability of nonylphenol ethoxylate with four ethylene oxide groups (NP-4) on a subbituminous coal was carried out. As the concentration of NP-4 gradually increases, the contact angle firstly increases and then decreases with maximum contact angle at about critical micelle concentration (CMC) of NP-4. The monolayer adsorption behaviour of NP-4 on the model surface of Hatcher subbituminous coal was investigated by means of molecular dynamics simulations. The surfactant molecules could be detected at the water–coal interface. The water molecules are repelled and stronger hydrophobicity of the coal is obtained in the presence of NP-4, which are consistent with contact angle results at low concentration. The aggregated structure of the surfactant molecules on the coal surface in terms of head group and tail group density profiles along the perpendicular direction shows that the ethoxylate groups of the surfactant are attached at the solid surfaces. The negative interaction energy between NP-4 and the subbituminous coal surface calculated suggests that adsorption process is spontaneous. The self-diffusion coefficients results indicate that the presence of NP-4 causes higher water mobility meaning improving the hydrophobicity of low-rank coal, which is consistent with the experimental results of contact angle.     

Quantum chemical molecular dynamics simulation of carbon nanotube–graphene fusion

Abstract

Here we report a quantum mechanical molecular dynamics (QM/MD) study of a fusion process of an open-ended carbon nanotube on a graphene hole, which results in the formation of a so-called pillared graphene structure – a three-dimensional nanomaterial consisting entirely of sp²-carbons. The self-consistent-charge density-functional tight-binding potential was adopted in this study. Two different sizes of graphene holes with 12 or 24 central carbon atoms removed from a graphene flake, and a (6,6) carbon nanotube with a compatible diameter were adopted. Formations of 6–7–6/5–8–5 defect structures were found on the fusion border between tube and graphene hole. The 6–7–6 structure was found to bear less curvature-induced strain energy and therefore to be more stable and much easier to form than the 5–8–5 structure.     

Free energy landscapes of two model peptides: α-helical and β-hairpin peptides explored with Brownian dynamics simulation

We applied an atomistic Brownian dynamics (BD) simulation with multiple time step method for the folding simulation of a 13-mer α-helical peptide and a 12-mer β-hairpin peptide, giving successful folding simulations. In this model, the driving energy contribution towards folding came from both electrostatic and van der Waals interactions for the α-helical peptide and from van der Waals interactions for the β-hairpin peptide. Although, many non-native structures having the same or lower energy than that of native structure were observed, the folded states formed the most populated cluster when the structures obtained by the BD simulations were subjected to the cluster analysis based on distance-based root mean square deviation of side-chains between different structures. This result indicates that we can predict the native structures from conformations sampled by BD simulation.     

Modeling soil–root water transport and competition for single and mixed crops

A knowledge of above and below ground plant interactions for water is essential to understand the performance of intercropped systems. In this work, root water potential dynamics and water uptake partitioning were compared between single crops and intercrops, using a simulation model. Four root maps having 498, 364, 431 and 431 soil-root contacts were used. In the first and second cases, single crops with deep and surface roots were considered, whereas in the third and fourth cases, roots of two mixed crops were simultaneously considered with different row spacing (40 cm and 60 cm). Two soils corresponding to a clay and a silty clay loam were used in the calculations. A total maximum evapotranspiration of 6 mm d^-1 for both single or mixed crops was considered, for the mixed crops however, two transpiration distributions between the crops were analyzed (3:3 mm d^-1, or 4:2 mm d^-1 for each crop, respectively). The model was based on a previous theoretical framework applied to single or intercropped plants having spatially distributed roots in a two-dimensional domain. Although water stress occurred more rapidly in the loam than in the clay, due to the rapid decrease of the soil water reserve in the loam, the role of the root arrangement appeared to be crucial for water availability. Interactions between the distribution of transpiration among mixed crops and the architecture of the root systems which were in competition led to water movements from zones with one plant to another, or vice versa, which corresponded to specific competition or facilitation effects. Decreasing the distances between roots may increase competition for water, although it may determine greater water potential gradients in the soil that increase lateral or vertical water fluxes in the soil profile. The effects of the root competition on water uptake were quite complicated, depending on both environmental conditions, soil hydrodynamic properties, and time scales. Although some biological adaptive mechanisms were disregarded in the analysis, the physically 2-D based model may be considered as a tool to study the exploitation of environmental heterogeneity at microsite scales.     

Solvent-responsiveness of PS–PEO binary mixed polymer brushes: a coarse-grained molecular dynamics study

Abstract

Systems of mixed polymer brushes (polystyrene–polyethylene oxide, PS–PEO) uniformly grafted on solid substrate were investigated by coarse-grained molecular dynamics simulations. The effects of grafting density and relatively degree of polymerisation of PS and PEO on the switching property of PS–PEO mixed polymer brushes in water and solvent are explored and discussed. Simulation results indicate that PS dominated the thickness of PS–PEO mixed polymer brushes in different solvents, which can be controlled by adjusting the grafting density. Brush heights of mixed PS–PEO polymer brushes fluctuate in different solvents when grafting density varies. The chemical composition of the very top surface of these mixed polymer brushes are largely determined by the relative polymerisation degree of PS and PEO.     

Phase Behavior, Stability, and Mesomorphism of Monostearin–oil–water Gels

This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase $ {\left( {L_{\alpha } } \right)} This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase with a (001) reflection occurring at 50 ?. In addition to the 50 ? reflection at small angles, a wide angle reflection at 4.2 ? was observed upon cooling below 60°C, indicating a transition from the to the phase, which upon storage at 22°C for one day converted to the coagel, or β-gel phase.