Journal of Computer Chemistry, Japan

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 分子動力学プログラムMXDORTO用可視化ソフトウェアMDVISの開発
<Author(s):> 大石　駿介, 大川　政志
<Corresponding author E-Mill:> mokawa(at)numazu-ct.ac.jp

<Abstract:> 酸化物のシミュレーションに有用である分子動力学(MD)シミュレーションプログラムMXDORTO用の結果を可視化するソフトワエア Visualizer for Molecular Dynamics Simulation (MDVIS)を開発した． MDVISは，メイン，データ，オペレーション，チャートの4つのフォームで構成されている．メインフォームには3次元コンピュータグラフィックス (3DCG)によりMDシミュレーションで記録されている原子座標を連続的に表示する． オペレーションフォームの設定により特定の場所のみを表示したり，周期境界条件を考慮した拡張ができる．さらに選択した原子の軌跡を表示させる機能や選択 した2原子間の原子間距離を計算する機能を備えた．3DCGの画面に同期している温度，圧力，格子定数，密度，内部エネルギーなどのデータを数値 で表示するデータフォームとシミュレーション時間全般での変化を表示させるチャートフォームを実装した．
<Keywords:> Molecular dynamics simulation, Visualization software
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0010/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 分子動力学法によるSiO₂組成フォージャサイトの熱膨張変化の研究
<Author(s):> 大川　政志, 堤　涼, 大石　駿介, 松本　泰誠, 山口　力
<Corresponding author E-Mill:> mokawa(at)numazu-ct.ac.jp

<Abstract:> マイクロ孔を有するゼオライトは，相転移や負の熱膨張など興味深い熱的挙動を示すことが知られている．様々な温度での三次元細孔の挙動を知ることは触媒反 応の点から重要である．そこで本研究では立方晶のフォージャサイト(FAU)の構造を有するSiO₂組成ゼオライトを分子 動力学法により100 Kから1100 Kの範囲で計算を行い，格子定数および細孔に相当するスーパーケージのリング構造の変化を検討した．この温度領域において立方晶の構造は維持され格子定数 aは温度上昇とともに減少し，負の熱膨張を示した．二体相関関数からは第一近接のSiとSiの原子間距離は2種類ありそれらの温度に対する挙動が 異なり高温での負の熱膨張はSi-Si距離が減少することにより引き起こされていることが分かった．スーパーケージの12員環のリング径の平均値 は温度に対してほとんど変化しなかったが，温度上昇に伴い振幅は大きくなり600 K以上では10％以上変化することが分かった．
<Keywords:> molecular dynamics simulation, zeolite, faujasite, negative thermal expansion, ring structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 94-95, by J-STAGE]
<Title:> 粗視化分子動力学法におけるダブルネットワークゲルのモデリング手法の開発と破壊プロセスへの応用
<Author(s):> 斎藤　圭祐, 樋口　祐次, 尾澤　伸樹, 久保　百司
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp

<Abstract:> We examine the mechanism of fracture processes in a double-network (DN) gel model by using a coarse-grained molecular dynamics simulation. Initially, we develop a modeling method for DN gel containing both slightly and highly cross-linked networks, and then stretch the DN gel model. During stretching, the highly cross-linked network begins to dissociate at a strain of 1.0, increasing the stress. At strains from 4.0 to 5.0, the slightly and highly cross-linked networks simultaneously dissociate and the stress decreases. Then, the dissociation of the highly cross-linked network stops and only the slightly cross-linked network dissociates at a strain of 12.0, while the stress remains almost the same. We reveal that characteristics of each type of network gradually appear in the DN gel. Next, we change the polymer chain length to reveal its influence on the mechanical properties of the gel. An increase in the length of the slightly cross-linked network chains improves the strength of the DN gel, whereas that of the highly cross-linked network chains does not affect its strength. An increase in the slightly cross-linked network chain length increases the number of entanglements, leading to the increase in strength.
<Keywords:> Polymer, Double-network gel, Fracture process, Mechanical strength, Coarse-grained molecular dynamics
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0053/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> The Nature of Si-O-Si Bonding via Molecular Orbital Calculations
<Author(s):> Fumiya NORITAKE, Katsuyuki KAWAMURA
<Corresponding author E-Mill:> noritake(at)eqchem.s.u-tokyo.ac.jp

<Abstract:> The nature of Si-O bonding and Si-O-Si bridging is discussed using molecular orbital calculations. We found the equilibrium geometries for two pyrosilisic acid molecules (C_2V and 60° torsion) using Moller-Plesset perturbation theory and 6-311G (d,p) split valence basis set. The bent configuration of the Si-O-Si angle in equilibrium geometries can be explained by the balance of Coulombic repulsion between SiO₄ tetrahedra and the energy of lone pair orbitals belonging to bridging oxygen atom without concerning the contribution of d-p π-bonding from the results of natural bonding orbital analysis. The energy surfaces of two pyrosilisic acid molecules with varying Si-O length to the bridging oxygen and Si-O-Si angle were calculated and we found the relationship between Si-O length to the bridging and Si-O-Si bridging angle. The Si-O bonding strengthens with increasing Si-O-Si angle because of stabilization in energy of Si-O bonding orbital with decreasing the hybridization index λ in sp^λ orbital of bridging oxygen and increase of Coulombic interaction between Si and bridging oxygen atom.
<Keywords:> Keyword Siloxanes, Silicates, Molecular Orbital Calculation, Natural Bonding Orbital Analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0009/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 92-93, by J-STAGE]
<Title:> 固体酸化物形燃料電池の電解質におけるカチオンの拡散経路の理論解析
<Author(s):> 林　敬堂, 石元　孝佳, 古山　通久
<Corresponding author E-Mill:> koyama(at)ifrc.kyushu-u.ac.jp

<Abstract:> Cation diffusions at materials interfaces in solid oxide fuel cell (SOFC) potentially cause degradations of cell performance during long-term operation. We investigate the cation diffusion mechanism in yttria stabilized zirconia (YSZ), as a first step to clarify the cation diffusion mechanism at SOFC interface. Molecular dynamics simulation combined with the metadynamics method are used to simulate cation jumps in this study. Y³⁺ and Sr²⁺ migration mechanisms in YSZ are discussed on the basis of cation jumps observed by using the metadyanamics method.
<Keywords:> Molecular dynamics, Metadynamics, Cation diffusion
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 90-91, by J-STAGE]
<Title:> 天然ゴムの配座探索と構造解析
<Author(s):> 秋山　和輝, 河原　成元, 内田　希
<Corresponding author E-Mill:> s133183(at)stn.nagaokaut.ac.jp

<Abstract:> Natural rubber is an excellent material in elasticity and abrasion resistance, so that it is used for tires of airplanes and heavy automobiles, such as a bus. It is impossible to make a synthetic rubber having the same physical properties as the natural rubber, even with the latest synthesis technology. However, the detailed structure of a natural rubber is still unclear. The aim of this study is to clarify the conformation and the thermochemical properties of a natural rubber. The conformational search and calculation of thermodynamic variables were performed with the computer chemistry program CONFLEX. In the calculation, we used two models; one with phosphate group and the with no phosphate group. The model having a phosphate group has a linear stable conformation, while the other has a coiled coherent one. As a result, we found that the end group of natural rubber has a significant effect on its stable structure. Moreover, natural rubber with a linear structure had relatively lower energy.
<Keywords:> Natural rubber, Molecular mechanics, Conformation search, CONFLEX, Phosphate group
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0045/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 85-87, by J-STAGE]
<Title:> ジグザグ型CNTの電子構造のチューブ長依存性とチューブ径依存性
<Author(s):> 森川　大, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> 13st309e(at)shinshu-u.ac.jp

<Abstract:> The effects of the tube length and diameter on the thermodynamic stability and chemical reactivity of zigzag carbon nanotubes (CNTs) with finite-length Clar cell (FLCC) were examined by means of topological resonance energy (TRE) and algebraic structure count (ASC), respectively. It was found that TRE and HOMO-LUMO gap in FLCC-(3,0) CNT with fully-benzenoid oscillate as functions of the tube length with the period of 2. In contrast, FLCC-(4,0) and (5,0) CNTs were found to have the tube length dependence different from that of FLCC-(3,0) CNT. This difference in tube diameter (chiral-index) dependence was found to be characterized by whether ASC is equal to Kekule structure count or not.
<Keywords:> Zigzag CNT, Topological resonance energy, Algebraic structure count, Aromaticity, Clar structure.
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 83-84, by J-STAGE]
<Title:> Ni-Ptナノ粒子におけるPt拡散特性の分子動力学的解析
<Author(s):> 長尾　歩, 石元　孝佳, 古山　通久, 宮村　弘, ジョン　クヤ, バラチャンドラン　ジャヤデワン
<Corresponding author E-Mill:> jeyadevan.b(at)mat.usp.ac.jp

<Abstract:> Pt decorated cubic Ni nanoparticles exhibited high catalytic activity in spite of the fact that they contained only a few at.% of Pt. The unusual catalytic property was believed due to the unique arrangement of Pt on the edges and corners of the Ni cube, which was experimentally confirmed to be the consequence of the diffusion of Pt atoms from the core of the particle at the initial stages of the reaction. Thus an explanation for diffusion property of the Pt atoms in the particle was attempted by performing molecular dynamics calculation by constructing models based on experimental findings.
<Keywords:> Nanoparticles, Diffusion, Molecular dynamics, Cage structure, Catalyst
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 88-89, by J-STAGE]
<Title:> 分子軌道法を用いたチタニア共析めっき機構の研究
<Author(s):> 宮井　菜月, 島崎　峻州, 内田　希
<Corresponding author E-Mill:> solgel2(at)vos.nagaokaut.ac.jp

<Abstract:> Composite plating of TiO2 nanoparticle with electrolessly plated nickel films was developed by Matsubara. Although, it is assumed that the eutectoid mechanism is divided into four steps of adsorption, it is not elucidated. So elucidating the eutectoid mechanism at the molecular level provides valuable information about not only this composite plating but also other type of plating. It should be noted that TiO2 surface charge is changed by pH of plating bath. As we conduct a study on the interaction of TiO2 with reactant, it is important to consider the TiO2 surface state i.e., TiO2 surface charge. In this study, we aim to reveal the eutectoid mechanism at molecular level and the influence of TiO2 surface charge in eutectoid by using molecular orbital calculation. For theoretical chemical calculations, we used the publicly available semi-empirical calculation software MOPAC2012. The Hamiltonian PM7 to be used for molecular orbital calculation semi-empirical. We used the citric acid as organic acid, and Ti2O2 is adopted as TiO2.The result shows that the adsorption energy (ΔE_ad) under acidic condition has lowest value within last step of the eutectoid.
<Keywords:> Composite plating, Molecular Orbital method, TiO2, Ni plating, PH
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0035/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Interatomic Potential Model for Molecular Dynamics Simulation of Lithium Borate Melts/Glasses
<Author(s):> Naoya SAWAGUCHI, Kakeru YAMAGUCHI, Makoto SASAKI, Katsuyuki KAWAMURA
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp

<Abstract:> An improved interatomic potential model was proposed for molecular dynamics simulations of lithium borate melt/glass systems. Charge of ion was reconsidered and a new composition dependent ionic charge model was suggested. A new three-body potential model controlling B-O-B angles was also proposed. The three-body term functioned to avoid square network ring consisted of B-O bonds, without preventing the change of boron coordination number between three and four. The edge-shared tetrahedra of four-coordination boron observed in the previous simulation were cleared by applying this three-body potential model.
<Keywords:> Molecular dynamics, Lithium borate, Glass, Three-body potential, Partial ionic charge model
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0017/_article/-char/ja/