Hiromitsu Takaba

A Computational Chemistry Study on Friction of h-MoS2. Part I. Mechanism of Single Sheet Lubrication

In this work, we theoretically investigated the friction mechanism of hexagonal MoS(2) (a well-known lamellar compound) using a computational chemistry method. First, we determined several parameters for molecular dynamics simulations via accurate quantum chemistry calculations and MoS(2) and MoS(2-x)O(x) structures were successfully reproduced. We also show that the simulated Raman spectrum and peak shift on X-ray diffraction patterns were in good agreement with those of experiment. The atomic interactions between MoS(2) sheets were studied by using a hybrid quantum chemical/classical molecular dynamics method. We found that the predominant interaction between two sulfur layers in different MoS(2) sheets was Coulombic repulsion, which directly affects the MoS(2) lubrication. MoS(2) sheets adsorbed on a nascent iron substrate reduced friction further due to much larger Coulombic repulsive interactions. Friction for the oxygen-containing MoS(2) sheets was influenced by not only the Coulomb repulsive interaction but also the atomic-scale roughness of the MoS(2)/MoS(2) sliding interface.

Grand canonical Monte Carlo simulation of the adsorption of CO2 on silicalite and NaZSM-5

The adsorption of carbon dioxide in silicalite and NaZSM-5 zeolite has been studied using new Monte Carlo software. In this program, sodium cations and framework are movable during the simulation. The calculated adsorption isotherms are in good agreement with the experimental results. The energy distribution of carbon dioxide over silicalite and NaZSM-5 shows that the increase of the adsorption energy for NaZSM-5 is mainly due the electric field generated by sodium cations.

A Computational Chemistry Study on Friction of h-MoS2. Part II. Friction Anisotropy

In this work, the friction anisotropy of hexagonal MoS(2) (a well-known lamellar compound) was theoretically investigated. A molecular dynamics method was adopted to study the dynamical friction of two-layered MoS(2) sheets at atomistic level. Rotational disorder was depicted by rotating one layer and was changed from 0° to 60°, in 5° intervals. The superimposed structures with misfit angle of 0° and 60° are commensurate, and others are incommensurate. Friction dynamics was simulated by applying an external pressure and a sliding speed to the model. During friction simulation, the incommensurate structures showed extremely low friction due to cancellation of the atomic force in the sliding direction, leading to smooth motion. On the other hand, in commensurate situations, all the atoms in the sliding part were overcoming the atoms in counterpart at the same time while the atomic forces were acted in the same direction, leading to 100 times larger friction than incommensurate situation. Thus, lubrication by MoS(2) strongly depended on its interlayer contacts in the atomic scale. According to part I of this paper [Onodera, T., et al. J. Phys. Chem. B 2009, 113, 16526-16536], interlayer sliding was source of friction reduction by MoS(2) and was originally derived by its material property (interlayer Coulombic interaction). In addition to this interlayer sliding, the rotational disorder was also important to achieve low friction state.

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Ligand–protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme–ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligand–protein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate reductase (DHFR)–methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date.

Molecular dynamics simulation of enhanced oxygen ion diffusion in strained yttria-stabilized zirconia

The application of strain to yttria-stabilized zirconia (YSZ), which can be realized by sandwiching a thin YSZ film epitaxially between layers of a material with larger lattice constants, is proposed as a means to enhance oxygen ion mobility. The possible mechanism of such an enhancement was investigated by molecular dynamics using a CeO2–YSZ superlattice. The calculated diffusion coefficient of oxygen ions in the superlattice is some 1.7 times higher than in YSZ alone due to a decreased activation barrier from the strain of the YSZ structure.

Molecular simulation of pressure-driven fluid flow in nanoporous membranes

An extended nonequilibrium molecular dynamics technique has been developed to investigate the transport properties of pressure-driven fluid flow in thin nanoporous membranes. Our simulation technique allows the simulation of the pressure-driven permeation of liquids through membranes while keeping a constant driving pressure using fluctuating walls. The flow of argon in the liquid state was simulated on applying an external pressure difference of 2.4x10(6) Pa through the slitlike and cylindrical pores. The volume flux and velocity distribution in the membrane pores were examined as a function of pore size, along with the interaction with the pore walls, and these were compared with values estimated using the Hagen-Poiseuille flow. The calculated velocity strongly depends on the strength of the interaction between the fluid and the atoms in the wall when the pore size is approximately<20sigma. The calculated volume flux also shows a dependence on the interaction between the fluid and the atoms in the wall. The Hagen-Poiseuille law overestimates or underestimates the flux depending on the interaction. From the analysis of calculated results, a good linear correlation between the density of the fluid in the membrane pores and the deviation of the flux estimated from the Hagen-Poiseuille flow was found. This suggests that the flux deviation in nanopore from the Hagen-Poiseuille flow can be predicted based on the fluid density in the pores.

Molecular dynamics simulation of iso- and n-butane permeations through a ZSM-5 type silicalite membrane

Molecular dynamics simulation of the permeation processes of single and mixed gases of iso- and n-butane through a ZSM-5 type silicalite membrane are presented. After 200 ps of simulation time the permeation of n-butane is observed whereas the permeation of iso-butane is not observed. The permeation of n-butane at 373 K takes place after the saturation of the zeolite pores, whereas at higher temperature, 773 K, it occurs without significant pores saturation. The calculated permeability of n-butane is close to experimental data. The permeation of the gas mixture shows that the membrane can separate the two isomers, n-butane permeates whereas iso-butane does not.

Estimation of inorganic gas permeability through an MFI-type silicalite membrane by a molecular simulation technique combined with permeation theory

Abstract A methodology based on a molecular simulation technique and permeation theory was applied to the systematic estimation of permeabilities of inorganic gases (Ar, He, Ne, N 2 , O 2 ) through an MFI-type silicalite membrane. The estimated inorganic gas permeabilities were in qualitative agreement with available experimental data. The estimated permeabilities decrease in the order N 2 >O 2 >Ar>Ne>He. This result means that their permeation mechanism is significantly influenced by their adsorption properties rather than by their kinetic properties, and can be described by the adsorption model. The qualitative agreement of the calculated permeability with experiment suggests that the method used is a leading candidate for the theoretical approach to the prediction of the performance of zeolite membranes.

The effect of gas molecule affinities on CO2 separation from the CO2/N2 gas mixture using inorganic membranes as investigated by molecular dynamics simulation

Applying molecular dynamics simulation and computer graphics methods we have investigated the dynamic behavior of the separation process of CO2 from the CO2/N2 gas mixture in inorganic membranes at high temperatures. We have demonstrated that the permeation dynamics follows the Knudsen diffusion mechanism in our model system that has a slit-like pore of 6.3 A. We have analyzed the effect of affinities of gas molecules for the membrane wall on the permeation to predict the optimal affinity strength for high selectivity of CO2. Our results indicate that in the model with the 600 K and 200 K affinities for CO2 and N2, respectively, we can obtain a high selectivity of CO2 even if the temperature is 1073 K. It is also shown that there is an optimal range for the CO2 affinity for the membrane wall to achieve good separation, which was estimated as the range of 400–600 K in our system, if the affinity of N2 is always weaker than that of CO2.

Molecular design of carbon nanotubes for the separation of molecules

Studies on the molecular dynamics (MD) simulation of the structure of a carbon nanotube and the dynamic behavior of benzene, alkylated benzenes and alkylated naphthalenes are reported. The results of our calculations indicate the possibility of the development of a carbon nanotube as potential material for selective adsorption and shape-selective separation. The carbon nanotubes behave as flexible porous material towards organic molecules. The carbon nanotubes can be useful in the separation of molecules with different sizes (isomers of monomethylnaphthalenes) and with different shapes (isomers of dimethylnaphthalenes) as demonstrated with a tube of 0.73 nm I.D.