Journal of Computer Chemistry, Japan
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Volume 12 , Issue 1
Special Issue in Honor of Professor Miyamoto′s Retirement
Showing 1-12 articles out of 12 articles from the selected issue
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Foreword
Commentary
  • Momoji KUBO
    Volume 12 (2013) Issue 1 Pages A3-A13
    Released: April 10, 2013
    [Advance publication] Released: March 30, 2013
    JOURNALS FREE ACCESS
    The low friction mechanism of diamond-like carbon (DLC) was investigated by first-principles molecular dynamics and tight-binding quantum chemical molecular dynamics methods. We found that under a load of 1 GPa low friction of H-terminated DLC is realized by hydrogen-hydrogen repulsion. Furthermore, H2 formation reaction occurs at the friction interface and it leads to the further decrement of the friction coefficient. On the other hand, we found that under a high load of 7 GPa C–C bond formation reaction occurs and it significantly increases the friction coefficient. A text book of mechanical engineering states that the friction coefficient does not depend on the load. However, our simulation results show that when chemical reactions occur at the friction interface the friction coefficient depends on the load. This means that our present outcomes rewrite the textbook of mechanical engineering. Furthermore, we also propose that OH-termination of the DLC surface can solve the increment of the friction coefficient under a high load of 7 GPa and it can be realized by tribochemical reactions under methanol environments.
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Accounts
  • Michihisa KOYAMA, Haruhiko KOHNO, Teppei OGURA, Takayoshi ISHIMOTO
    Volume 12 (2013) Issue 1 Pages 1-7
    Released: April 10, 2013
    [Advance publication] Released: February 14, 2013
    JOURNALS FREE ACCESS
    Our recent applications of computational chemistry methods to practical issues in fuel cell technologies are reviewed in the manuscript; i.e., degradation of polymer electrolyte and platinum catalyst in a polymer electrolyte fuel cell (PEFC), development of platinum alternative catalyst for low temperature fuel cells, sulfur poisoning and microstructure optimization of solid oxide fuel cell anode. As degradation issues in PEFC, degradation mechanisms of polymer electrolyte from side chain and platinum dissolution from catalyst surface are clarified by using a density functional method. A novel metal-organic framework as a potential platinum alternative catalyst is studied and the ethanol oxidation pathway over the catalyst is clarified. Then the importance of subsurface sulfur to understand the experimentally-observed cell performance decrease by the sulfur impurity is pointed out. Finally, a microstructure-based index for designing microstructure with better overpotential characteristics is discussed on the basis of simulation data obtained for a number of different microstructures.
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  • Takashi TOKUMASU, Akinori FUKUSHIMA, Takuya MABUCHI, Yuta SUGAYA
    Volume 12 (2013) Issue 1 Pages 8-15
    Released: April 10, 2013
    [Advance publication] Released: March 12, 2013
    JOURNALS FREE ACCESS
    Computer simulation is a very powerful tool to analyze transport phenomena in the membrane electrode assembly (MEA) of polymer electrolyte fuel cells (PEFCs). In particular, there are many nanoscale structures in this flow field, and therefore the phenomena should be analyzed from the microscopic point of view rather than computational fluid dynamics. In this paper, we report large-scale molecular dynamics (MD) simulations to analyze these flows. In particular, dissociation phenomena of a hydrogen molecule on a Pt catalyst, transport phenomena of proton and water in a polymer electrolyte membrane (PEM), oxygen permeability of ionomers in a catalyst layer (CL), and transport phenomena of a water droplet in a nanopore were simulated, and their characteristics are discussed. In the analysis of the dissociation phenomena of the hydrogen molecule, it was found that the trend of dissociation probability as a function of impinging energy considering the motion of the molecule differs from that without considering the motion of the molecule. In the analysis of proton transfer in a PEM, the diffusion coefficients obtained by this simulation were consistent with the experimental data. In the analysis of oxygen permeability of ionomers, the dependence of water content on the permeability was estimated and the difference between ionomer on catalyst layer and that in bulk state was clarified. In the analysis of transport phenomena of a water droplet in a nanopore, we compared the results of our simulation with the macroscopic governing equation.
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Review
  • Abhijit CHATTERJEE
    Volume 12 (2013) Issue 1 Pages 16-29
    Released: April 10, 2013
    [Advance publication] Released: March 09, 2013
    JOURNALS FREE ACCESS
    Reactivity index is that theory which was developed at the right time to rational chemical bonding. Density Functional theory (DFT) has given precision to chemical concepts such as electro negativity, hardness, and softness and has embedded them in a perturbational approach to chemical reactivity. Since the majority of the reactions can be analyzed through the electrophilicity/nucleophilicity of various species involved, a proper understanding of these properties becomes essential. The hard soft acid-base (HSAB) principles classify the interaction between acids and bases in terms of global softness. In last few years the reactivity index methodology is well established and had found its application in a wide variety of systems. This study is to revisit the definition of reactivity index using density functional theory, within the domain of hard soft acid base (HSAB) principle and then to discuss its application in industrial applications; in combination with intra and intermolecular reactivity in materials.
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General Papers
  • Paweł KOZYRA, Małgorzata ŚWIĘTEK, Jerzy DATKA, Ewa BROCŁAWIK
    Volume 12 (2013) Issue 1 Pages 30-37
    Released: April 10, 2013
    [Advance publication] Released: March 14, 2013
    JOURNALS FREE ACCESS
    Adsorption and activation of molecular hydrogen on cationic sites in zeolites was studied by performing theoretical analysis. of charge-transfer between various parts of a three-component complex system (H2, silver or copper cation and a zeolite treated as a generalized ligand). ETS-NOCV analysis resolved electron density redistribution accompanying complex formation into independent electron transfer channels: electron donation from σ(H-H) to 4s (Cu) or 5s (Ag) orbitals, backdonation from 3dπ (for Cu) or 4dπ (for Ag) to σ*(H-H) antibonding orbital and electron transfer into the bonding region between hydrogen and cation. All three electron transfer channels strengthen the bonding of hydrogen molecule while the first two are responsible for H-H bond activation. By embedding in zeolite framework donation of electrons from hydrogen bonding orbital is reduced and backdonation to hydrogen antibonding orbital is enhanced compared to free cations, stronger for Cu+ than for Ag+. This result rationalizes why copper sites in zeolites are exceptionally good absorbers and activators for hydrogen.
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  • András STIRLING
    Volume 12 (2013) Issue 1 Pages 38-42
    Released: April 10, 2013
    [Advance publication] Released: February 20, 2013
    JOURNALS FREE ACCESS
    Ab initio molecular dynamics simulations have been performed to study the dissolution of SO2 in water. It has been obtained that the hydrated SO2 is surrounded by the water molecules without any S-H hydrogen bond, restraining the sulfonate anion formation but allowing the bisulfite isomer formation. The metadynamics method has been employed to explore the free energy surface of the SO2 + H2O reaction. The simulations revealed that the hydrated SO2 forms bisulfite anion and hydronium cation after overcoming a ca. 17 kcal/mol free energy barrier. Direct, one-step H2SO3 formation could not been observed, in sharp contrast with earlier cluster calculations. These findings indicate a step-wise H2SO3 formation in water. The presence of the sulfur lone pair represents an important constraint on the mechanism: the nucleophilic H2O attack can occur only from certain angles as shown by the reactive trajectories.
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  • Hiromitsu TAKABA, Huifeng ZHONG, Hideyuki TSUBOI, Momoji KUBO, Akira M ...
    Volume 12 (2013) Issue 1 Pages 43-51
    Released: April 10, 2013
    JOURNALS FREE ACCESS
    This paper presents an efficient method to integrate chemical reactions into molecular dynamics. The methodology requires no more than the knowledge of the empirical intermolecular potentials for the species at play as well as the elementary reaction path among them. We have applied the method to evaluate the reaction rate of copolymerization of ethylene and 1-butene using C5(CH3)4-Si-(CH3)2-N-C5(CH3)3-C-(CH3)3-Ti-Cl2)/methylaluminoxane catalyst, and have successfully demonstrated the propagation dynamics under the same conditions as in the experiment. The reaction rate was estimated from the calculated amount of the polymerized monomers by introducing principles of transition state theory. The calculated reaction rates are comparable with experiment, which illustrates the validity of the method. The simplicity of the RTAMD scheme enables the simulation of large scale systems involving large numbers of simultaneous chemical reactions and the evaluation of the reaction rate.
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  • Ken SUZUKI, Hideo MIURA
    Volume 12 (2013) Issue 1 Pages 52-60
    Released: April 10, 2013
    [Advance publication] Released: March 12, 2013
    JOURNALS FREE ACCESS
    Highly reliable gate stack systems using a high-k dielectric thin film such as a hafnium dioxide film are indispensable for the development of ULSI (Ultra-Large-Scale Integration) devices. In this study, the degradation mechanisms of the electronic reliability of hafnium dioxide dielectric film caused by point defects such as oxygen vacancies and carbon interstitials was investigated by using quantum chemical molecular dynamics method. The magnitude of the band gap of the HfO2-x, which is hafnium dioxide with oxygen vacancies, decreased drastically from 5.7 eV to about 1.0 eV due to the generation of donor states within the band gap of hafnium dioxide. When a carbon atom as the impurity was introduced in HfO2 film, carbon impurity states (donor and acceptor) formed in the band gap of hafnium dioxide. The band gap calculated from the energy difference between the donor and acceptor decreases to 1.6 eV. The estimated changes of the magnitude of the band gap due to the point defects were validated by experiments using synchrotron radiation photoemission spectroscopy. We conclude therefore, it is very important to minimize point defects in the hafnium dioxide dielectric film in order to ensure the electronic performance and reliability of MOS transistors.
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  • Ai SUZUKI, Marc C. WILLIAMS, Kenji INABA, Ryo SATO, Kotaro OKUSHI, Ryu ...
    Volume 12 (2013) Issue 1 Pages 61-70
    Released: April 10, 2013
    [Advance publication] Released: November 10, 2012
    JOURNALS FREE ACCESS
    The electronic configuration between the interface of supported Rh and CeO2 (111) surface was investigated by Tight Binding based Ultra Accelerated Quantum Chemical Molecular Dynamics method (TB-UAQCMD) at 1073 K. Time courses of bond energies of Rh-O (-Ce) plots for 5000 fs showed gradual increases of bond strength between oxygen and rhodium atoms in the uppersurface of the CeO2 (111). This caused the anchoring effect of Rh-O (-Ce) bonds in the form of Rh-O (-Ce). Therefore total energies of the Ce-O bonds in the Rh/CeO2 were found to become more stable than that in the pure CeO2. The activation energy of grain growth of Rh/CeO2 nanoparticles was estimated by this deviation in these Ce-O bond energies. Experimentally observed suppression in the grain growth of Rh/CeO2 nanoparticles relative to those without Rh was quantitatively reproduced by three dimensional Kinetic Monte Carlo method (3D-KMC).
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  • Hiroaki MUNAKATA, Rado RAHARINTSALAMA, Akira MIYAMOTO
    Volume 12 (2013) Issue 1 Pages 71-85
    Released: April 10, 2013
    JOURNALS FREE ACCESS
    Density functional theory calculations are applied to investigate roles of cationic and neutral intermediate species in palladium catalyzed reactions of interest, including solvent effects. We have developed a catalyst model to investigate both cationic and neutral intermediate species in the same model system, which made it possible to evaluate the energy difference between cationic and neutral intermediate systems. Solvent effects on homogeneous catalytic reactions are very important. To model such systems, discrete solvent molecules are introduced to accommodate coordination of a solvent molecule to central palladium atom and further COSMO method is applied to whole molecular system to include solvent screening effect. Using this methodology, decomposition of mono-ethyl-palladium(II) complex, bis-trimethylphosphine-ethyl-Pd(II) Br·(Solv.)2, Solv. = acetonitrile, to produce ethene and hydrido-Pd(II) complex was examined. In this process, β-hydrogen elimination of ethyl group plays an important role. The cationic agostic Pd(II) complex is well stabilized and is obtained at an equilibrium state. Substitution of Br ligand of the bis-trimethylphosphine-ethyl-Pd(II) Br complex by AgBF4 forms the cationic Pd(II) species, and ethene formation from the cationic bis-trimethlphosphine-ethyl-PdII complex having BF4 anion was also examined.
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