Momoji Kubo

Atomic‐scale formation of ultrasmooth surfaces on sapphire substrates for high‐quality thin‐film fabrication

The atomically ultrasmooth surfaces with atomic steps of sapphire substrates were obtained by annealing in air at temperatures between 1000 and 1400 °C. The terrace width and atomic step height of the ultrasmooth surfaces were controlled on an atomic scale by changing the annealing conditions and the crystallographic surface of substrates. The obtained ultrasmooth surface was stable in air. The topmost atomic structure of the terrace was examined quantitatively by atomic force microscopy and ion scattering spectroscopy as well as a theoretical approach using molecular dynamics simulations.

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.

Density functional theory calculations of the reaction pathway for methane activation on a gallium site in metal exchanged ZSM‐5

Density functional theory is used to describe the reaction profile for methane dissociation on Ga‐exchanged ZSM‐5. Stable structures on the reaction pathway are characterized as weakly adsorbed methane molecule and the C–H dissociation product. The transition state is also explicitly defined and optimized. The nonlocal density functional approximation is invoked to calculate the energy parameters of the reaction. The activation barrier is estimated at about 120 kJ/mol, in excellent agreement with other similar reactions. From vibrational analysis the reaction coordinate is deduced and transformation of a methane molecule on adsorption is discussed.Density functional theory is used to describe the reaction profile for methane dissociation on Ga‐exchanged ZSM‐5. Stable structures on the reaction pathway are characterized as weakly adsorbed methane molecule and the C–H dissociation product. The transition state is also explicitly defined and optimized. The nonlocal density functional approximation is invoked to calculate the energy parameters of the reaction. The activation barrier is estimated at about 120 kJ/mol, in excellent agreement with other similar reactions. From vibrational analysis the reaction coordinate is deduced and transformation of a methane molecule on adsorption is discussed.

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.

Development of RYUGA for three-dimensional dynamic visualization of molecular dynamics results

Abstract We have developed a new computer graphics (CG) code RYUGA for three-dimensional dynamic visualization of molecular dynamics (MD) results. The applicability of RYUGA for visualizing and analyzing the dynamics of atomic motions in various materials was demonstrated. RYUGA supports various functions, such as solid-modeling CG pictures (called the CPK model), CG animation of the MD results, Miller plane cutting of crystal structures, building graphs, etc., similar to other CG codes for MD simulation. In addition, RYUGA has a number of advantages as follows: (i) a perspective is employed for drawing CG pictures, (ii) three-dimensional trajectories of atoms can be constructed, (iii) an operator can travel inside the materials, (iv) graphic speed and animation speed are enhanced because of the specific algorithms, and (v) it works on any workstations, moreover even personal computers with a UNIX operating system and an X window system are available.

ON THE ELECTRONIC STRUCTURE OF THE PALLADIUM MONOXIDE AND THE METHANE ADSORPTION : DENSITY FUNCTIONAL CALCULATIONS

Electronic structure of the palladium monoxide and its interaction with a methane molecule has been investigated by means of density functional theory. The two triplets, 3Π and 3Σ−, lie very close in energy, with the indication at the 3Π ground state of the oxide. A methane molecule interacts with the open shell PdO and forms two stable adsorption complexes: in collinear on palladium and bridging conformations. The scission of the C–H bond in adsorbed methane requires moderate activation energy of 24.5 kcal/mol and the dissociation product is very stable, however, the singlet–triplet crossing occurs at the transition state.

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.