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Showing papers in "Molecular Simulation in 2017"


Journal ArticleDOI
TL;DR: Artificial neural networks (NNs) are increasingly common in quantum chemistry applications and can be trained to higher-level ab-initio calculations and are capable of achieving arbitrary results as discussed by the authors.
Abstract: Artificial neural networks (NNs) are increasingly common in quantum chemistry applications. These models can be trained to higher-level ab-initio calculations and are capable of achieving arbitrary...

65 citations


Journal ArticleDOI
TL;DR: In this article, the authors investigate the degree that efficient computational methods can be used for modelling adsorbates at solid/liquid interfaces, and they have benchmarked gas phase and solvated energetics for H, O and OH.
Abstract: To investigate the degree that efficient computational methods can be used for modelling adsorbates at solid/liquid interfaces, we have benchmarked gas phase and solvated energetics for H, O and OH...

63 citations


Journal ArticleDOI
TL;DR: In this article, a comparative study was conducted to determine the effects of graphene and carbon nanotubes on the thermo-mechanical properties of asphalt binder using molecular simulations and experiments.
Abstract: A comparative study was conducted to determine the effects of graphene and carbon nanotubes on the thermo-mechanical properties of asphalt binder using molecular simulations and experiments. Micro-morphology of graphene and carbon nanotubes was measured by scanning electron microscopy. Thermal stability and glass transition temperature were investigated by differential scanning calorimeter. Simulation results indicated that the Tg had slightly changed for graphene-modified asphalt (GMA) and carbon nanotubes-modified asphalt (CNsMA) and that the thermal expansion coefficients and thermal conductivity increased along with the adding amount of graphene or carbon nanotubes. The Tg calculated by density–temperature method was closer than the experimental Tg and the Tg decreased in the order of CNsMA, GMA and asphalt. Young’s modulus of asphalt, GMA and CNsMA were 9.2658, 25.7563 and 17.8249 GPa at 298 K, respectively, which indicated that thermo-mechanical properties of asphalt showed considerable impr...

62 citations


Journal ArticleDOI
TL;DR: In this article, the role of intermolecular hydrogen bonds and ionic side chain length of monolayer systems of N-acyl amino acid-based surfactants was investigated.
Abstract: Atomic molecular dynamics simulations have been performed on the monolayer systems of N-acyl amino acid-based surfactants. The role of intermolecular hydrogen bonds and ionic side chain length of d...

45 citations


Journal ArticleDOI
TL;DR: In this article, the elastic stiffness tensor of fcc argon at 60 K and 1 bar was computed using molecular simulation tools and three different methods were investigated: explicit deformations of the simulation box, strain fluctuations at constant pressure and stress fluctuations at a constant volume.
Abstract: We compute the elastic stiffness tensor of fcc argon at 60 K and 1 bar using molecular simulation tools. Three different methods are investigated: explicit deformations of the simulation box, strain fluctuations at constant pressure and stress fluctuations at constant volume. Statistical ensemble sampling is done using molecular dynamics and Monte Carlo simulations. We observe a good agreement between the different methods and sampling algorithms excepted with molecular dynamics simulations in the (NpT) ensemble. There, we notice a strong dependence of the computed elastic constants with the barostat parameter, whereas molecular dynamics simulations in the (NVT) ensemble are not affected by the thermostat parameter.

41 citations


Journal ArticleDOI
Haoyang Sun1, Hui Zhao1, Na Qi1, Xiaoqing Qi1, Kai Zhang1, Ying Li1 
TL;DR: In this paper, the authors used the Grand Canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulation methods to investigate the adsorption and diffusion properties of CH4 and CO2 in montmorillonite slit-nanopor...
Abstract: The Grand Canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulation methods were used to investigate the adsorption and diffusion properties of CH4 and CO2 in montmorillonite slit-nanopor...

38 citations


Journal ArticleDOI
TL;DR: The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions as mentioned in this paper, and the Interface Force Field (IFF) and surface mappings.
Abstract: The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface m...

37 citations


Journal ArticleDOI
TL;DR: In this article, the authors introduce new tools for streamlining surface chemistry simulation set-up and review some of the challenges in first-principles, density functional theory (DFT) simulation of surface phenomena.
Abstract: First-principles simulation has played an ever-increasing role in the discovery and interpretation of the chemical properties of surface–adsorbate interactions. Nevertheless, key challenges remain for the computational chemist wishing to study surface chemistry: modelling the full extent of experimental conditions, managing computational cost, minimising human effort in simulation set-up and maximising accuracy. This article introduces new tools for streamlining surface chemistry simulation set-up and reviews some of the challenges in first-principles, density functional theory (DFT) simulation of surface phenomena. Furthermore, we provide a worked example of Co tetraphenylporphyrin on Au(1 1 1) in which we analyse electronic and energetic properties with semi-local DFT and compare to predictions made from hybrid functional and the so-called DFT+U correction. Through both review and the worked example, we aim to provide a pedagogical introduction to the challenges and the insight that first-princi...

35 citations


Journal ArticleDOI
TL;DR: In this article, the authors carried out a molecular dynamics simulation of the swelling patterns of Na-, Mg-, Na/Cs, Na/Mg-MMT in an isobaric isothermal ensemble (NPT) at T = 300 K and p = 1 atm.
Abstract: Over the last two decades, the swelling properties of montmorillonite (MMT) have been studied in many experimental and simulation works, but less attention has been given to MMT containing a mixture of monovalent/monovalent and monovalent/bivalent cations in the interlayer spaces. We carried out a molecular dynamics simulation of the swelling patterns of Na-, Mg-, Na/Cs-, Na/Mg-MMT in an isobaric isothermal ensemble (NPT) at T = 300 K and p = 1 atm. The simulation reproduced a swelling pattern of Na-, Mg-, Na/Cs-, Na/Mg-MMT and the swelling curves obtained showed the difference between the hydration mechanisms of the type of MMT used in this study. We also found out that the differences in size and hydration energy of Na, Cs and Na, Mg ions have strong implications on the structure of interlayer water. This has led to the difference in the swelling curves of the simulated Na-, Mg-, Na/Cs- and Na/Mg-MMT. For Na/Cs-MMT, the hydration energy of Na cations increased compared to that in Na-MMT, the hyd...

34 citations


Journal ArticleDOI
TL;DR: A brief overview of molecular simulation techniques utilised to simulate the electrode/electrolyte interfaces is given in this article, where the authors introduce a simple scheme to perform classical molecular dynami...
Abstract: This paper presents a brief overview of molecular simulation techniques utilised to simulate the electrode/electrolyte interfaces. We introduce a simple scheme to perform classical molecular dynami...

31 citations


Journal ArticleDOI
TL;DR: ReaxFF MD as discussed by the authors is a promising method for exploring complex chemical reactions, allowing large coal molecular systems simulated at high temperature, due to the amorphous and diverse nature of coal chemic...
Abstract: ReaxFF MD is a promising method for exploring complex chemical reactions, allowing large coal molecular systems simulated at high temperature. Due to the amorphous and diverse nature of coal chemic...

Journal ArticleDOI
TL;DR: In this paper, a roll-to-roll printed organic photovoltaics (OPVs) with active layer morphologies optimised for charge separation and transport is presented.
Abstract: Rationally designing roll-to-roll printed organic photovoltaics (OPVs) requires a fundamental understanding of active layer morphologies optimised for charge separation and transport, and which ing...

Journal ArticleDOI
TL;DR: In this paper, the performance of a variety of dispersion correction methods within dif-ferent non-covalent intermolecular interaction was investigated. But the performance was not evaluated.
Abstract: Accurate description of the non-covalent intermolecular interaction is significant for the study of energetic materials. Here, the performance of a variety of dispersion correction methods within d...

Journal ArticleDOI
TL;DR: In this article, a summary of experimental studies of pure hydrogen and binary large guest + hydrogen clathrate hydrate phases is presented, together with a review of the computational studies of hydrogen storage in clathrates.
Abstract: In this article, computational studies of hydrogen storage in clathrate hydrate phases are reviewed. A summary of experimental studies of pure hydrogen and binary large guest + hydrogen clathrate h...

Journal ArticleDOI
TL;DR: In this paper, the authors describe a prolific amount of computational resources used in a variety of technological applications, as well as their prevalence as naturally occurring phases in the environment, due to their widespread use in various technological applications.
Abstract: Owing to their widespread use in a variety of technological applications, as well as their prevalence as naturally occurring phases in the environment, there is a prolific amount of computational r...

Journal ArticleDOI
TL;DR: In this paper, the authors study the parameters that govern the intramolecular charge transfer and photo-injection processes in dyes for dye-sensitised solar cells (DSSC).
Abstract: We aim at providing better insight into the parameters that govern the intramolecular charge transfer (ICT) and photo-injection processes in dyes for dye-sensitised solar cells (DSSC). Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations are utilized to study the geometry, electronic structure, electrostatic potential (ESP) and absorption spectrum, for a representative donor-π bridge-acceptor (D–π–A) dye for DSSC. The coplanar geometry of the dye (D1) facilitates strong conjugation and considerable delocalization originating the π CT interaction from donor to acceptor orbitals and the hyper-conjugative interactions involving Rydberg states. A model simulating the adsorption of the dye on the TiO2 surface is utilized to estimate binding energies. The effect of fluorine substituents in the π-spacer on the quantum efficiency of DSSCs was investigated. Gibb’s free energy values, redox potentials, excited state lifetime, non-linear optical properties (NLO) and driving forces for...

Journal ArticleDOI
TL;DR: The human serotonin transporter (hSERT) played a significant role in neurological process whose structural basis had been analyzed for many years Recently, the first homology model was constructed as mentioned in this paper.
Abstract: The human serotonin transporter (hSERT) played a significant role in neurological process whose structural basis had been analysed for many years Recently, the first homology model was constructed

Journal ArticleDOI
TL;DR: In the past thirty years, molecular simulation techniques centred on density functional theory (DFT) calculations have quickly become a powerful research and technology development instrument as discussed by the authors, and have been used in many applications.
Abstract: In the past thirty years, molecular simulation techniques centred on density functional theory (DFT) calculations have quickly become a powerful research and technology development instrument. In p...

Journal ArticleDOI
TL;DR: Guaiacol is an important phenolic component present in pyrolytic bio-oils; and in this work its hydrodeoxygenation (HDO) by various reaction schemes has been considered within the framework of density functional theory.
Abstract: Guaiacol is an important phenolic component present in pyrolytic bio-oils; and in this work its hydrodeoxygenation (HDO) by various reaction schemes has been considered within the framework of density functional theory. In this computational study, primarily three reaction schemes for the HDO of guaiacol are considered. In the first reaction scheme (RS 1), guaiacol undergoes hydrogenolysis at O–CH3 bond site of methoxy group to produce catechol and methane followed by HDO of catechol forming phenol and water, followed by HDO of phenol producing benzene and water and finally benzene leading to cyclohexane formation. In the second reaction scheme (RS 2), guaiacol undergoes hydrogenolysis at Caromatic–O bond of methoxy group producing phenol and methanol followed by hydrotreatment of phenol to form cyclohexane along with same intermediates as in the first reaction scheme. In the third reaction scheme (RS 3), HDO of guaiacol compound at Caromatic–OH sigma bond produces anisole and water; and then anis...

Journal ArticleDOI
TL;DR: In this article, it was shown that ensemble averages computed in the Gibbs Ensemble with Continuous Fractional Component Monte Carlo (CFCMC GE) are different from those computed by the conventional GE.
Abstract: It is shown that ensemble averages computed in the Gibbs Ensemble with Continuous Fractional Component Monte Carlo (CFCMC GE) are different from those computed in the conventional Gibbs Ensemble (GE). However, it is possible to compute averages corresponding to the conventional GE while performing simulations in the CFCMC GE. In this way, one can benefit from the nice features of CFCMC GE (e.g. more efficient particle exchange) and at the same time compute the ensemble averages that correspond to the conventional GE. As a case study, the equilibrium pressure and densities of the systems of 256 and 512 LJ particles at different reduced temperatures () are computed in the conventional GE and CFCMC GE. The validity of the expressions derived for computation of the thermodynamic pressure and densities corresponding to the conventional GE and computed in the CFCMC GE is examined numerically. The thermodynamic pressure in the conventional GE and CFCMC GE typically differs by at most 4%. It is shown that a very ...

Journal ArticleDOI
TL;DR: In this article, the presence of high concentration of arsenic in conventional water sources can cause serious health and environmental hazards, and an urgent need is to find an efficient adsorbent for the removal of a...
Abstract: The presence of high concentration of arsenic in conventional water sources can cause serious health and environmental hazards. An urgent need is to find an efficient adsorbent for the removal of a...

Journal ArticleDOI
TL;DR: In this paper, the dependence of polarisability and hyperpolarisability on donor strength has been systematically studied by employing density functional theory method on triphenylamine (TPA) and carbazole (CZ) based compounds.
Abstract: The dependence of polarisability (α) and hyperpolarisability (β) on donor strength has been systematically studied by employing density functional theory method on triphenylamine (TPA) and carbazole (CZ) based compounds. The electronic structures, absorption spectra and non-linear optical (NLO) response were calculated by using quantum chemical methods. All the calculations were performed in gas phase in presence of solvent. The results reveal that the polarizability (α) and hyperpolarizability (β) significantly increased by the addition of second donor moiety. Similarly, the oscillator strength and light harvesting efficiency were also increased, while absorption wavelength was red-shifted by the addition of second donor moiety. These results indicate that the di-substituted donor is an effective way to improve NLO response. The TPA dyes possess a large second-order non-linear response and this is primarily because of the strong donor-π-acceptor conjugation that is ascribed to the excited state i...

Journal ArticleDOI
TL;DR: In this article, the plastic deformation behavior of Cu50Zr50/B2 CuZr amorphous/crystalline nanolaminate was studied at the atomic scale using molecular dynamics simulations.
Abstract: The plastic deformation behaviours of Cu50Zr50/B2 CuZr amorphous/crystalline nanolaminate were studied at the atomic scale using molecular dynamics simulations. For pure metallic glass, the highly ...

Journal ArticleDOI
TL;DR: In this article, molecular dynamic simulations of anionic polyelectrolyte poly(acrylic acid) (PAA) in water-ethanol solution were carried out across the solvent composition range 0.
Abstract: Molecular dynamic simulations of anionic polyelectrolyte poly(acrylic acid) (PAA) in water–ethanol solution, specifically Li+-PAA and Cs+-PAA, were carried out across the solvent composition range 0 ≤ фeth ≤ 0.9. Chain collapse (i.e. shrinkage) occurs with increase in фeth for both types of counter-ion systems and in agreement with the experiments. The qualitative difference in the collapse point is in agreement with experimental results, with counter-ion specific chain collapse of PAA following the order Li+ > Cs+. With increase in фeth the number of hydrogen-bonds between PAA and water decreases while that between PAA and ethanol increases. At higher level of ethanol content in solution, ethanol molecules displace water molecules from the vicinity of the chain. The analysis of the radial distribution functions shows that counter-ion binding distance of Li+ to chain is lesser as compared to that of Cs+, as well as a higher coordination number exhibited by Li+. Thus, as compared to Cs+-PAA, greate...

Journal ArticleDOI
Jie Ma1, Zhendian Zhang1, Yan Xiang1, Fenglei Cao1, Huai Sun1 
TL;DR: In this paper, the authors examined the Green-Kubo and Einstein-Helfand approaches for calculating diffusion coefficient, electronic conductivity and shear viscosity of ionic liquid using 1-n-butylmethylpyridinium tetrafluoroborate [C4PY][BF4] as an example.
Abstract: The Green–Kubo and Einstein–Helfand approaches are examined for calculating diffusion coefficient, electronic conductivity and shear viscosity of ionic liquid using 1-n-butylmethylpyridinium tetrafluoroborate [C4PY][BF4] as an example. Both methods suffer numerical errors accumulated at long simulation time, resulting divergences in the integrated autocorrelation time (IAT) and nonlinearity in the mean square displacement (MSD). The numerical errors can be reduced using smaller time step in the simulation. By identifying a converged plateau in IAT and a linear segment in MSD both approaches yield consistent predictions. Using a validated force field, the predicted diffusion coefficient and electrical conductivity agree reasonably well with the experimental data. However, the shear viscosity is significantly underestimated. Analysis of the simulation data indicates that a much slow relaxation in the pressure tensor must be considered, which is unfortunately infeasible due to the accumulated numeric...

Journal ArticleDOI
TL;DR: The inclusion complexation of neral, a cis-isomer of citral found in lemon grass (Cymbopogon citratus Stapf), and four different types of cyclodextrin (βCD), 2,6-dimethyl-βCD (2,6DM) were discussed in this paper.
Abstract: The inclusion complexation of neral, a cis-isomer of citral found in lemon grass (Cymbopogon citratus Stapf), and four different types of cyclodextrin (β-cyclodextrin (βCD), 2,6-dimethyl-βCD (2,6DM...

Journal ArticleDOI
TL;DR: Glycerol, which is one of the most abundant byproducts in biodiesel production, can be converted into H2 through aqueous-phase reforming (APR) as mentioned in this paper.
Abstract: Glycerol, which is one of the most abundant by-products in biodiesel production, can be converted into H2 through aqueous-phase reforming (APR). Dehydrogenation is one of the main processes in glyc...

Journal ArticleDOI
TL;DR: In this article, the effect of uniaxial and baoxial strain on the structural and electronic properties of MoS monolayers by first-principle calculations based on density functional theory was studied.
Abstract: In this paper, we study the effect of uniaxial and biaxial strain on the structural and electronic properties of MoS monolayers by first-principle calculations based on density functional theory. Our calculations show that the bond length between Mo and S atoms depends linearly on the strain. At the equilibrium state, MoS has a direct band gap of 1.72 eV opening at the K-point. However, an indirect–direct band gap transition has been found in MoS monolayer when the strain is introduced. MoS becomes a semiconductor with an indirect band gap when the uniaxial strain or the biaxial strain . Under biaxial strain, a metal–semiconductor transition occurs at of elongation. The indirect character and phase transition will largely constrain application of MoS monolayer to electronic and optical devices.

Journal ArticleDOI
TL;DR: Low-angle grain boundaries (LAGBs) may show up frequently as distinct dislocation products such as in the processes of work hardening, recovery and recrystallisation of metals and alloys as mentioned in this paper.
Abstract: Low-angle grain boundaries (LAGBs) may show up frequently as distinct dislocation products such as in the processes of work hardening, recovery and recrystallisation of metals and alloys. To reveal...

Journal ArticleDOI
Houfu Dai1, Genyu Chen1
TL;DR: In this paper, the effects of laser moving speed, laser pulse intensity and laser spot radius are thoroughly investigated in terms of atomic trajectories, phase transformation, temperature distribution, grinding temperature, grinding force and friction coefficient.
Abstract: Molecular dynamics is employed to study the mechanism of material removal and subsurface damage of monocrystalline silicon when it is under a nanoscale high-speed laser-assisted grinding of a diamond tip. Laser-assisted machining (LAM) is that the workpiece is locally heated by an intense laser beam before material removal. The effects of laser moving speed, laser pulse intensity and laser spot radius are thoroughly investigated in terms of atomic trajectories, phase transformation, temperature distribution, grinding temperature, grinding force and friction coefficient. The investigation shows that a higher laser moving speed reduces the subsurface damage and improves the material remove rate because of fewer atoms with five and six coordination atoms and more chips. Besides, both tangential grinding force (Fx) and normal grinding force (Fy) decrease as the laser moving speed increases. The distribution of high-temperature zone strongly depends upon the effect of laser pulse intensity and laser sp...