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.     

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.     

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.     

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.     

Molecular dynamics simulation of the gGAPDH–NAD+ complex from Trypanosoma cruzi

A 50-ns molecular dynamics simulation has been used to study the homotetramer of the enzyme glycosomal glyceraldehyde 3-phosphate dehydrogenase (gGAPDH) complexes, from Trypanosoma cruzi, with nicotinamide adenine dinucleotide (NAD⁺) cofactors in aqueous solution. The root mean square deviation indicates that the overall structure of the homotetramer does not undergo significant change. The largest structural change observed was in the NAD⁺ binding domain of subunit (chain) D; as a consequence, the NAD⁺ cofactor was dislocated from its initial position. However, the other subunits were not affected, suggesting that the gGAPDH enzyme exhibits non-cooperative behaviour. Our simulation estimates that the NAD⁺ binding domain rotates about 4.8° relative to the catalytic domain in the apo–holo form transition. The hydrogen bond analysis reveals that the residues R12, I13, D38 and M39 are essential for gGAPDH–NAD⁺ interaction. Furthermore, two promising cavities to be explored in drug design were found: one formed by residues I13, R12, T197, T199, E336 and Y339, and the other by residues C166, H194, R249, I13, R12, T197, T199, E336 and Y339. The results presented in this paper offer new insight into the search for inhibitors of the gGAPDH enzyme of T. cruzi protozoan.     

Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface

The conformation of the tridecapeptide α-melanocyte stimulating hormone in the presence of a double water-membrane interface was studied by molecular dynamics simulation, using the computational package THOR. In this program the solvent is represented by a continuous medium with dielectric constant ɛ, and the interface between different media is simulated by a surface of discontinuity of the dielectric constant. The electrostatic image method was used to write down the terms, added to the force field, that describe the polarisation effects induced in the interface by the atomic charges. The program was further improved by the introduction of a second surface, parallel to the first one, to mimic the membrane. A conformational search using the software Prelude was employed to find an initial geometry for the peptide in water. The molecular dynamics simulation performed during 10 ns showed that the peptide structure is flexible in water, without stabilisation of any preferential conformation. In the presence of the model membrane, the peptide moved to the medium representing the interior of the membrane. Inside the low dielectric constant medium, the structure of the peptide showed a turn in the central sequence of amino acids and a packed conformation remained stabilised during more than 7.0 ns of simulation. Received: 27 November 1998 / Revised version: 11 March 1999 / Accepted: 8 April 1999     

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.     

Molecular dynamics simulation approach for the prediction of transmembrane helix–helix heterodimers assembly

Computational methods are useful to identify favorable structures of transmembrane (TM) helix oligomers when experimental data are not available or when they cannot help to interpret helix-helix association. We report here a global search method using molecular dynamics (MD) simulations to predict the structures of transmembrane homo and heterodimers. The present approach is based only on sequence information without any experimental data and is first applied to glycophorin A to validate the protocol and to the HER2-HER3 heterodimer receptor. The method successfully reproduces the experimental structures of the TM domain of glycophorin A (GpA(TM)) with a root mean square deviation of 1.5 A. The search protocol identifies three energetically stable models of the TM domain of HER2-HER3 receptor with favorable helix-helix arrangement, including right-handed and left-handed coiled-coils. The predicted TM structures exhibit the GxxxG-like motif at the dimer interface which is presumed to drive receptor oligomerization. We demonstrate that native structures of TM domain can be predicted without quantitative experimental data. This search protocol could help to predict structures of the TM domain of HER heterodimer family.     

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.     

Molecular dynamics simulation of diffusion of hydrogen in binary hydrogen–tetrahydrofuran hydrate

The binary structure II hydrogen–tetrahydrofuran (THF) hydrate was studied with molecular dynamics simulation. The simulations were carried out at 300, 310 K and 10.1 MPa, and with various contents of hydrogen and THF. The migrations of hydrogen molecules from cage to cage were observed. The migration process of hydrogen was also analysed, and the diffusion coefficients of hydrogen in the hydrate were calculated. The calculated diffusion coefficients qualitatively agreed with the experimental data. Double and quintet occupancies of hydrogen molecules were observed in the small and large cages, respectively, without changing the hydrate structure.     

Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

The Na⁺-translocating NADH:quinone oxidoreductase (Na⁺-NQR) is the major Na⁺ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na⁺-NQR. While the mechanisms underlying Na⁺-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na⁺-NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na⁺-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.

     

Molecular dynamics simulation of helium–argon gas mixture under various wall conditions

As computational capabilities increase, molecular dynamics (MD) simulations become important tools of simulating reality. These simulations are especially useful for compressible gas mixture problems. In this study, binary diffusion of helium and argon was examined using a hard-sphere MD simulation method. For the sake of computational speed, low spacing ratios were chosen. Binary mass diffusion of gases in two equally sized halves of a box was simulated for identical initial kinetic energies and number densities. It has been noted that a purely mass diffusion mechanism of different gases is not physically possible. The resultant gas mixtures of several diffusion simulations were used as initial conditions for combined heat transfer – Couette flow, and heating and cooling experiments. The results showed the interesting behaviour of the mixture, which was subjected to various wall conditions. Energy of heavier molecules is found to be more sensitive to the wall velocities and less sensitive to the wall temperatures than lighter molecules. Diffusion, heat transfer, viscosity and heat capacity coefficients are deduced as well.     

Excited-state proton-transfer reactions of 7-azaindole with water,ammonia and mixed water–ammonia: microsolvated dynamics simulation

Dynamics simulations of excited-state multiple proton transfer (ESMPT) reactions in 7-azaindole (7AI) with ammonia, mixed water–ammonia, and water molecules were investigated by quantum dynamics simulations in the first-excited state using RI-ADC(2)/SVP-SV(P) in the gas phase. 7AI(WW), 7AI(WA), 7AI(AW) and 7AI(AA) clusters (W, water and A, ammonia) show very high probability of the excited-state triple proton transfer (ESTPT) occurrence in ranges from 20% for 7AI(WA) to 60% for 7AI(AW), respectively. Furthermore, 7AI(AW) clusters with ammonia placed near N–H of 7AI has the highest probability among other isomers. In 7AI with three molecules of bridged-planar of water, ammonia and mixed water–ammonia clusters, the excited-state quadruple proton transfer reactions occur ineffectively and rearrangement of hydrogen-bonded network on solvents also takes place prior to either ESTPT or excited-state double proton transfer. The role played by mixed-solvent is revealed with replacing H₂O with NH₃ in which the ESMPT is found to be more efficient corresponding to lower barrier in the excited state. The preferential number of solvent surrounding 7AI that facilitates the proton transfer process is two for methanol and water but this preferential number for ammonia is one.

Highlights: (i) replacing H₂O with NH₃ assists ESPT corresponding to lower barrier in the excited state; (ii) the ESMPT time of 7AI with mixed water–ammonia is in the sub-picosecond timescale; (iii) the PT tends to be concerted process with at least one ammonia, but synchronous without ammonia.     

Molecular dynamics simulation of diffusion behaviour of gas molecules within oil–paper insulation system

The diffusion behaviour of hydrogen, carbon monoxide, carbon dioxide, methane, acetylene, ethylene and ethane in oil and paper medium was examined using molecular dynamics to reveal the diffusion mechanism of gas molecules in transformer oil–paper insulation system at the microscopic level. These compounds are commonly used in the dissolved gas analysis of power transformers and produced during the ageing process of oil–paper composite insulating material. Two groups of models were constructed using molecular dynamics simulation software to simulate the diffusion behaviour of the aforementioned seven types of small gas molecules in oil and paper. The diffusion coefficients, displacement features, free volume characteristics and interaction energies of the gas molecules were investigated. In particular, the diffusion micro-mechanism of the gas molecules was observed. The differences in diffusion features among the gas molecules were discussed, and the factors influencing the diffusion of the gas molecules were compared. Simulation results indicate that the diffusion coefficients of gas molecules in cellulose is an order of magnitude lower than that in oil, and the diffusion coefficients of these gas molecules in the two types of insulation media have different orders. Free volume of gas molecules is the main factor that influences the diffusion behaviour in oil, whereas intermolecular interaction is the main influencing factor of diffusion behaviour in cellulose.     

Host–parasitoid spatial models: the interplay of demographic stochasticity and dynamics

Host–parasitoid metapopulation models have typically been deterministic models formulated with population numbers as a continuous variable. Spatial heterogeneity in local population abundance is a typical (and often essential) feature of these models and means that, even when average population density is high, some patches have small population sizes. In addition, large temporal population fluctuations are characteristic of many of these models, and this also results in periodically small local population sizes. Whenever population abundances are small, demographic stochasticity can become important in several ways. To investigate this problem, we have reformulated a deterministic, host–parasitoid metapopulation as an integer-based model in which encounters between hosts and parasitoids, and the fecundity of individuals are modelled as stochastic processes. This has a number of important consequences: (1) stochastic fluctuations at small population sizes tend to be amplified by the dynamics to cause massive population variability, i.e. the demographic stochasticity has a destabilizing effect; (2) the spatial patterns of local abundance observed in the deterministic counterpart are largely maintained (although the area of ''spatial chaos'' is extended); (3) at small population sizes, dispersal by discrete individuals leads to a smaller fraction of new patches being colonized, so that parasitoids with small dispersal rates have a greater tendency for extinction and higher dispersal rates have a larger competitive advantage; and (4) competing parasitoids that could coexist in the deterministic model due to spatial segregation cannot now coexist for any combination of parameters.     

Investigating the effects of wettability and gaseous nanobubbles on roughened wall–fluid interface using molecular dynamics simulation

This paper reports on the use of molecular dynamics (MD) simulation to investigate the coupling effects of wettability, surface roughness and interfacial nanobubbles (INBs) on wall–fluid interfaces. The fluid properties close to the wall–fluid interface, such as potential energy, density, diffusion coefficients of fluid molecules and effective slip length are simulated. In the cases without surface nanobubbles, regions with lower potential energy have a higher probability of hosting water molecules. The local translational and rotational diffusion coefficients of water within the cavities are strongly influenced by wettability but largely unaffected by hydrodynamic effects. In cases where INBs exist, variations in wettability result in distinctly different argon morphologies. Argon nanobubbles form a convex shape on Wenzel-like interfaces but a shallow concave shape on Cassie-like interfaces. The phenomenon of water molecules invading grooves tends to occur on Wenzel-like interfaces; however, this depends largely on the morphology of the grooves. The high mobility and high density of argon molecules indicate that the state of the argon molecules within the grooves may require further investigation. Our results also show that the effective slip length is significantly influenced by wall–fluid wettability as well as the morphology of INBs.     

Molecular dynamics simulation on the effect of transition metal binding to the N-terminal fragment of amyloid-β

Abstract

We report molecular dynamics simulations of three possible adducts of Fe(II) to the N-terminal 1–16 fragments of the amyloid-β peptide, along with analogous simulations of Cu(II) and Zn(II) adducts. We find that multiple simulations from different starting points reach pseudo-equilibration within 100–300?ns, leading to over 900?ns of equilibrated trajectory data for each system. The specifics of the coordination modes for Fe(II) have only a weak effect on peptide secondary and tertiary structures, and we therefore compare one of these with analogous models of Cu(II) and Zn(II) complexes. All share broadly similar structural features, with mixture of coil, turn and bend in the N-terminal region and helical structure for residues 11–16. Within this overall pattern, subtle effects due to changes in metal are evident: Fe(II) complexes are more compact and are more likely to occupy bridge and ribbon regions of Ramachandran maps, while Cu(II) coordination leads to greater occupancy of the poly-proline region. Analysis of representative clusters in terms of molecular mechanics energy and atoms-in-molecules properties indicates similarity of four-coordinate Cu and Zn complexes, compared to five-coordinate Fe complex that exhibits lower stability and weaker metal–ligand bonding.

Communicated by Ramaswamy H. Sarma     

Molecular dynamics simulation integrating the inhibition kinetics of hydroxysafflor yellow A on α-glucosidase

Inhibition of α-glucosidase has attracted the attention of researchers due to its connection to type-2 diabetes. Hydroxysafflor yellow A (HSYA) extracted from Carthamus tinctorius L. is a natural antioxidant used in traditional Chinese medicine. In this study, the effect of HSYA on α-glucosidase was evaluated using inhibitory kinetics based on the antioxidant properties of HSYA and by performing computational simulation integration methods. HSYA reversibly inhibited α-glucosidase in a competitive inhibition manner and the evaluated kinetic parameters were IC₅₀ = 1.1 ± 0.22 mM and K_i = 1.04 ± 0.23 mM, respectively. The results of spectrofluorimetry showed that the inner hydrophobic regions of α-glucosidase, which are mostly in the active site, were exposed to the surface with increasing HSYA concentrations, indicating that the inactivation of α-glucosidase by HSYA was accompanied by regional unfolding. The molecular dynamics simulations indicated that the four rings of HSYA interact with four residues such as G217, A278, H279, and G280 at the entrance of the active site. Our study provides insight into the inhibition of α-glucosidase and the accompanying structural changes by HSYA. Based on its α-glucosidase-inhibiting effect and its potential as a natural antioxidant, HSYA is a potential agent for treating α-glucosidase-associated type-2 diabetes.