Molecular dynamics simulation study for ion mobility of alkali earth metal cations in water at 25°C

We present the results of molecular dynamics simulations for alkali earth metal cations (Mg²⁺, Ca²⁺, Sr²⁺ and Ba²⁺) in an aqueous solution at 25°C using the extended simple point charge water potential with Ewald summation. The ion mobilities (defined by u_i = D_iz_iF/RT) obtained from the simulations are in good accord with the experimental measures. The strong divalent cation–water interactions explain well the static and dynamic properties of the alkali earth metal cations. The classical solvent-berg picture describes the ion mobilities of these cations in water adequately.     

Quantum mechanical study of the inclusion process of adamantanol isomers by l-tryptophan-modified-β-cyclodextrin

The complexation processes of 1 and 2-adamantanol with l-tryptophan-β-cyclodextrin have been studied using ab initio Hartree–Fock and density functional theory levels. For the host: guest inclusion processes, the up mode with the OH group of the alcohol oriented towards the secondary rim, is found to be in qualitative agreement with the experimental finding. A molecular recognition mechanism is proposed based on the host: guest relative dipole orientation. For the complex with the 2-Ada isomer the host and guest the dipoles are parallels favoring the interaction energy and. This mechanism can explain the small energy difference for the processes involving the adamantanol isomers and modified cyclodextrins.     

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 simulation of film size and vacancy defect effects on the thermal conductivities of argon thin films

It is well known that there is a size effect for the thermal conductivity of thin films and that vacancy defects in film reduce the film's thermal conduction. In this paper, the film size and vacancy defect effects on the thermal conductivities of argon thin films were studied by molecular dynamics simulations. The results show the existence of phonon boundary scattering. The results also confirm that the theoretical model based on the Boltzmann equation can accurately model the thermal conduction of thin argon films. Both the theoretical and MD results illustrate that, although, both the defect and the thickness of the thin film deduce the thermal conductivity, their physical mechanisms differ.     

Accelerating all-atom protein folding simulations through reduced dihedral barriers

Protein folding requires extensive changes of backbone and sidechain dihedral angles, whose energy barriers constitute obstacles for the folding kinetics. Folding of small proteins is furthermore thought to be path-independent. Here, we propose that time-consuming all-atom protein folding simulations may be accelerated through a reduction of the dihedral barriers of the force field. In order to investigate this hypothesis, we performed various folding simulations of two small proteins. We report an acceleration towards smaller root-mean-square deviations from the native protein structure using our proposed method.     

Cell size dependence of orientational order of uniaxial liquid crystals in flat slit

In order to investigate the ordered structure of nematic liquid crystal molecules confined in a nanoslit, we carried out a classical molecular dynamics simulation of uniaxial prolate Gay–Berne particles in a flat, structureless slit at several temperatures. When the slit gap is so small that the system is not assumed as the bulk, particles in the slit possess orientationally ordered structures different from ones in the bulk. The weak spacial orientational correlation existed when the temperature corresponded to the isotropic phase in the bulk system. The first order isotropic–nematic phase transition was not clearly observed and the transitional phenomenon of the creation and annihilation of the uniaxial domains were observed. These results revealed that the ordered structure depends on the number of particles, in other words, cell size, and that the system with 100,000 or more particles gives reasonable results of an infinitely wide slit. The number of particles is converted into up to 220 particles of the length of the base.     

A novel model for the molecular dynamics simulation study on mechanical properties of HMX/F2311 polymer-bonded explosive

The ‘insert’ model for β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)-based polymer-bonded explosive (PBX) was proposed for finding the relation of temperatures with mechanical properties. This model was simulated by using molecular dynamics models. The elastic constants and the effective moduli were calculated with static analysis method. Cauchy pressure was also calculated. It is found that the rigidity is weakened and the ductibility is improved by adding a small amount of F₂₃₁₁ in the crystalline HMX. The rigidity is also weakened with increasing temperature. However, the ductibility of HMX/F₂₃₁₁ PBX changes as a parabola with increasing temperature duo to the enhancement of F₂₃₁₁ molecular chain movement and simultaneously the increment of high energy conformation ratio in this molecular chain, i.e. the increment of the molecular chain rigidity.     

Molecular simulation of swelling and structure for Na-Wyoming montmorillonite in supercritical CO2

Gibbs ensemble Monte Carlo (GEMC) simulations were used to study the swelling stability and interlayer structures of Na-montmorillonite clay in supercritical CO₂ (scCO₂). From the GEMC simulation, it was found that there exist several stable mechanical spacings for Na-Wyoming montmorillonite immersed in scCO₂, which are larger than the stable spacing in vacuum condition. The swelling behaviour of Na-montmorillonite clay in scCO₂ fluid is thermodynamically favourable. However, it was also observed that the clay swelling is inhibited when in contact with CO₂ gas at atmospheric pressure. The interlayer structures were applied to investigate the mechanism of swelling. In the case of stable spacings, the interlayer sodium cations are not only well solvated with the surrounding CO₂ molecules but also show stronger tendency to adhere to the clay surface.     

Monte Carlo Study of the Buckingham Exponential-six Fluid

Abstract

In this paper we report the results of extensive Monte Carlo simulations of a pure fluid of Buckingham modified exponential-six molecules. Data are presented for the configurational energy and pressure covering a wide range of temperatures and densities. These data are interpreted using the generalized van der Waals partition function with a novel separation into free volume and mean potential terms. We find, surprisingly, that the Buckingham fluid is described by a simple van der Waals-like equation of state provided that the b parameter is temperature dependent and chosen in a theoretically correct manner.