Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.15, 13-21, by J-STAGE]
<Title:> Quantitative Evaluation of Dissociation Mechanisms in Phenolphthalein and the Related Compounds
<Author(s):> Toshihiko HANAI
<Corresponding author E-Mill:> thanai(at)kf7.so-net.ne.jp
<Abstract:> Computational chemistry programs were evaluated as aids to teaching qualitative analytical chemistry. Computational chemical calculations can predict absorption spectra, thus enabling the modeling of indicator dissociation mechanisms by different computational chemical programs using a personal computer. An updated MNDO program among 51 programs was found to be the best predictor to explain the dissociation mechanisms of isobenzofuranones and sulfonephthaleins. Unknown dissociation constants were predicted from atomic partial charges instead of Hammett’s constants.
<Keywords:> Quantitative analysis of dissociation mechanisms, Isobenzofuranone, Sulfonephthalein, Computational chemistry
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/1/15_2015-0055/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, A3-A6, by J-STAGE]
<Title:> SCCJ Cafe Season 5 生命現象の分子科学 (1) 「黎明期の生体分子科学」
<Author(s):> 高妻　孝光
<Corresponding author E-Mill:> takamitsu.kohzuma.qbs(at)vc.ibaraki.ac.jp
<Abstract:> 20世紀は，生命現象をつかさどる物質の理解が進んだ時代である．量子力学の発展とともに，複雑な化合物の量子化学的理解が進んだ．そして，分子生物学， 構造生物学，生物無機化学が誕生し，今や，生命現象を分子レベル，原子レベルで理解し，大規模な計算によって，その詳細を知る時代となっている． 本稿では，19世紀後半から20世紀中期までの科学とともに成長してきた黎明期の生体分子科学について概観する．
<Keywords:> Biomolecule, Quantum Beam, Quantum Mechanics, X-ray Crystallographic Structure Analysis, Molecular Biology
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/1/15_2016-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 1-6, by J-STAGE]
<Title:> Calculation of Potential Energy Concerning “H + Cl₂ → HCl + Cl” and Production of CG Movie for Learner to Acquire Its Image with Structures of Reactants and Reaction Profile
<Author(s):> Akira IKUO, Yosuke KOJIMA, Yusuke YOSHINAGA, Haruo OGAWA
<Corresponding author E-Mill:> ikuo(at)u-gakugei.ac.jp
<Abstract:> Geometries and potential energies for reactants of “H-Cl-Cl” around the transition state in the reaction of H + Cl₂ → HCl + Cl were calculated. The reactant on the transition state was formed at incident angle of 180°. This reactant was supported by the method of the intrinsic reaction coordinate (IRC). We produced a movie, which displays CGs of potential energy surfaces in 2-D and 3-D for reactants on the way of the reaction. The reaction profile with potential energy and structures of the reactants are also displayed. The profile was synchronized with the structures. The CG movie was tried, and it was improved through the application to student’s learning on the Web. It was effective for students to acquire images of the reaction from the standpoint of its potential energy and molecular structure.
<Keywords:> Potential energy surface, HCl formation, Incident angle, Visualization, CG movie
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/1/15_2015-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 7-12, by J-STAGE]
<Title:> 3Dプリンタ用ファイル作成のためのWinmostar機能の付加
<Author(s):> 吉村　忠与志, 千田　範夫
<Corresponding author E-Mill:> tadayosi(at)fukui-nct.ac.jp
<Abstract:> 3Dプリンタで分子モデルを作成するためにSTLファイルを創出できるCADを探したが見つけることができなかったので，分子モデリングソフトで分子デー タ(原子の位置x,y,zデータ)を作成し，それをSTLファイルに変換できるOpenSCAD言語でプログラミングすることで分子モデルの3D プリンタ用ファイルを作成してきた．その一連の作業を分子モデリングソフトWinmostar (V6.003)で実現したことを報告する．これによって，OpenSCAD言語を理解することなく，分子モデルの3Dプリンタ用ファイルを作成すること ができる．
<Keywords:> Creating of STL file, Winmostar (V6.003), OpenSCAD, 3D molecular modeling
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/1/15_2015-0074/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, A7-A12, by J-STAGE]
<Title:> 電子を描く(5) — 3d_zx軌道, 3d_yz軌 道, 3d_x2–y2軌 道, 3d_xy軌道
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> tokita(at)apc.saitama-u.ac.jp
<Abstract:> 水素原子の波動方程式を解くと，無数の原子軌道が導出される．磁気量子数が0でない軌道は複素関数で表される．複素関数の軌道を組み合わせて実関数に変換 する手続きを，3d軌道を例にとって説明した．これらの軌道を，ガラスブロック内に実3次元で彫刻し，変換の過程でZ軸を含む平面節面がどのよう に増加するかを調べた．
<Keywords:> Electron, Visualization, Hydrogen atom, Atomic orbital, Imaginary wave function, Real wave function, 3dzxorbital, 3dyzorbital, 3dx2-y2orbital, 3dxyorbital, Planar node containing z axis, Isosurface, Real 3-dimensional representation of an electron
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/1/15_2016-0002/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Calculation of Potential Energy Concerning “H + Cl₂ → HCl + Cl” and Production of CG Movie for Learner to Acquire Its Image with Structures of Reactants and Reaction Profile
<Author(s):> Akira IKUO, Yosuke KOJIMA, Yusuke YOSHINAGA, Haruo OGAWA
<Corresponding author E-Mill:> ikuo(at)u-gakugei.ac.jp
<Abstract:> Geometries and potential energies for reactants of “H-Cl-Cl” around the transition state in the reaction of H + Cl₂ → HCl + Cl were calculated. The reactant on the transition state was formed at incident angle of 180°. This reactant was supported by the method of the intrinsic reaction coordinate (IRC). We produced a movie, which displays CGs of potential energy surfaces in 2-D and 3-D for reactants on the way of the reaction. The reaction profile with potential energy and structures of the reactants are also displayed. The profile was synchronized with the structures. The CG movie was tried, and it was improved through the application to student’s learning on the Web. It was effective for students to acquire images of the reaction from the standpoint of its potential energy and molecular structure.
<Keywords:> Potential energy surface, HCl formation, Incident angle, Visualization, CG movie
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0005/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 3Dプリンタ用ファイル作成のためのWinmostar機能の付加
<Author(s):> 吉村　忠与志, 千田　範夫
<Corresponding author E-Mill:> tadayosi(at)fukui-nct.ac.jp
<Abstract:> 3Dプリンタで分子モデルを作成するためにSTLファイルを創出できるCADを探したが見つけることができなかったので，分子モデリングソフトで分子デー タ(原子の位置x,y,zデータ)を作成し，それをSTLファイルに変換できるOpenSCAD言語でプログラミングすることで分子モデルの3D プリンタ用ファイルを作成してきた．その一連の作業を分子モデリングソフトWinmostar (V6.003)で実現したことを報告する．これによって，OpenSCAD言語を理解することなく，分子モデルの3Dプリンタ用ファイルを作成すること ができる．
<Keywords:> Creating of STL file, Winmostar (V6.003), OpenSCAD, 3D molecular modeling
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0074/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 213-214, by J-STAGE]
<Title:> 2 アザスピロ環化合物における閉環反応の理論的研究
<Author(s):> 寺前　裕之, 須田　岬, 湯川　満, 林　浩輔, 高山　淳, 坂本　武史
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> The geometric structures of the phenoxenium cation which is a cation intermediate of 2-azaspiro ring compounds (2-azaspiro[4.5]decane) from N-methoxy-N-prenylbenzamide are studied by means of the Hamiltonian algorithm with ab intio molecular orbital calculations at HF/3-21G level. The geometries are further refined with MP2/6-311G** level. We tried four substituted compounds with the methyl group. Among them only one compound with two methyl groups gives a ring-closure intermediate, which agrees well with the experimental results.
<Keywords:> Hamiltonian algorithm, Phenoxenium cation, 2-azaspiro[4.5]decane, Optimized structure, Substituent effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0060/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 215-216, by J-STAGE]
<Title:> Ru(0)触媒による共役ジエンとスチレンのクロスカップリング反応における置換基効果の理論的解明
<Author(s):> 出口　光, 大槻　恒太, 中村　沙季, 平野　雅文, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Mechanistic studies for linear cross-dimerization between 2,3-dimethylbuta-1,3-diene and para-substituted styrenes by a Ru(0) complex, Ru(η⁶-naphthalene) (η⁴ 1,5-COD), were performed computationally. The COD ligand is actually not a simple spectator ligand, it engages to assist the hydrogen migration steps. The computational studies verified the oxidative coupling step to govern the overall reaction as a rate-determining step. The reaction rate was found to be correlated well with the electronegativity of styrenes.
<Keywords:> oxidative coupling, cross-dimerization, Ru(0) complex, DFT calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0065/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 211-212, by J-STAGE]
<Title:> 全原子モデルを用いた4-n-alkyl-4′-cyanobiphenyl (nCB)の分子動力学シミュレーション
<Author(s):> 高橋　祐貴, 石川　良, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Molecular dynamics simulation of 4-n-alkyl-4′-cyanobiphenyl series (nCB) using the full-atom model was carried out. We used a force field that was fitting the dihedral angle parameter and the LJ parameters of the AMBER Force Field against nCB. The dihedral angle parameter is set to reference the quantum chemical calculation, and the LJ parameters were fitted to reproduce the experimental data. By using the modified force field, experimental data such as isotropic-nematic phase transition temperature and density were reproduced.
<Keywords:> Molecular dynamics simulation, Full-atom model, Dihedral angle parameter, LJ parameter, Phase transition
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0064/_article/-char/ja/