月別: 2017年1月

[Published online Journal of Computer Chemistry, Japan Vol.15, 223-224, by J-STAGE]
<Title:> 電荷移動錯体の引力の原因:キノン類とベンゼンの分子間相互作用の解析
<Author(s):> 都築　誠二, 内丸　忠文, 小野　泰蔵
<Abstract:> Aromatic molecules form stable charge-transfer complexes with quinones, tetracyanoethylene or halogen molecules. The charge-transfer interaction (orbital-orbital interaction) was believed to be the source of the attraction in the complexes. However, the contributions of other intermolecular interactions (dispersion, electrostatic etc.) to the attraction in the complexes are not well understood. The total interaction energy and contributions of electrostatic, induction, dispersion and orbital-orbital (exchange-repulsion and charge-transfer) interactions in the benzene-p-benzoquinone complex were studied by ab initio molecular orbital calculations. The analysis shows that the dispersion interaction is the major source of the attraction in the complex and that the orbital-orbital interaction is not attractive but even repulsive.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0064/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 221-222, by J-STAGE]
<Title:> マルチスケール計算化学に基づく汚れ付着シミュレーション技術の開発
<Author(s):> 畠山　望, 長山　千恵子, 畑　北斗, 石澤　由紀江, 佐藤　亮, ボノー　パトリック, 三浦　隆治, 鈴木　愛, 宮本　明
<Corresponding author E-Mill:> hatakeyama(at)aki.niche.tohoku.ac.jp
<Abstract:> Plumbing stains grow up from invisible attachment of urea and urolith in the molecular level to biofilms in which bacteria adsorb such nutrients and secrete extracellular polymer substances. In order to understand and control such biofilm growth, we have developed a multiscale simulation that can analyze from adhesion of stains on the molecular scale to accumulation of biofilm on actual scale. In the present study, the biofilm growth and peeling by shear flow was successfully simulated for the condition of typical toilet use.
<Keywords:> Biofilm, Extracellular Polymer Substances (EPS), Ultra-Accelerated Quantum Chemical Molecular Dynamics (UA-QCMD), Kinetic Monte Carlo (KMC), Computational Fluid Dynamics (CFD)
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0060/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 219-220, by J-STAGE]
<Title:> 結晶軌道法によるDNAのHartree-Fock計算の試み
<Author(s):> 寺前　裕之, 青木　百合子
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> As an attempt at the electronic structure calculations of the B-type model-DNA, (poly-(guanine) poly-(cytosine)) model polymers is performed by means of ab initio crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and ions are included in the calculations. Energy band structures are calculated at 3-21G and 6-31G levels. The effective mass of hole shows a relatively large value while that of electron shows a smaller value which suggests electron conduction in the DNA backbones.
<Keywords:> Crystal orbital method, Screw-axis symmetry, B-type DNA, Parallel processing, Energy band structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0057/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 225-226, by J-STAGE]
<Title:> 転がりにおける面との摩擦
<Author(s):> 夏目　雄平
<Abstract:> The mechanism of rolling frictions of wheel is discussed in relation with movement of Reuleaux-pentagons. In fact, driving and braking processes lead us to the suggestion that hysteresis-energy loss model is naturally obtained. In addition to this, the combined model of hysteresis-energy loss and differential-slip mechanisms is proposed so as to promote the computational investigations for rolling frictions of wheel.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0066/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 217-218, by J-STAGE]
<Title:> 分子動力学法を用いた4-n-alkyl-4′-cyanobiphenyl (nCB) の熱伝導率シミュレーション
<Author(s):> 高橋　祐貴, 石川　良, 大木　竜勝, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Thermal conductivity of 4-n-alkyl-4′-cyanobiphenyl (nCB) simulated by using molecular dynamics method. We modified the dihedral angle parameter and the LJ parameters of the original AMBER Force Field for nCB. The dihedral angle parameter was corrected by using quantum chemical calculation, and the LJ parameters were fitted to reproduce the experimental data. Thermal conductivity was calculated by Green-Kubo Method. MD calculation using the corrected force field gave good thermal conductivity close to experimental value and successfully reproduced the anisotropy of thermal conductivity in the liquid crystal phase.
<Keywords:> Thermal conductivity, Molecular Dynamics, Corrected force field, Anisotropy of thermal conductivity, Green-Kubo Method
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0054/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 215-216, by J-STAGE]
<Title:> Ru(0)触媒による共役ジエンとヘテロ環状化合物のクロスカップリング反応機構の理論的解明
<Author(s):> 出口　光, 西久保　椋, 大槻　恒太, 駒崎　弘樹, 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 2,5-dihydrofuran by a Ru(0) complex, Ru(η⁶-naphthalene) (η⁴ 1,5-COD), were performed computationally. The rate-determining steps of main and side reactions are different mechanisms, and correspond to the reductive elimination step and the oxidative coupling step, respectively. This suggests that the yield of the main product may be improved by modification of the heterocyclic compound or catalyst structure. In addition, the computational studies predicted that cross-dimerization between 2,3-dimethylbuta-1,3-diene and 2,5-dihydropyrrole may occur via a similar reaction mechanism.
<Keywords:> oxidative coupling, reductive elimination, cross-dimerization, Ru(0) complex, DFT calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0055/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 213-214, by J-STAGE]
<Title:> [M(ABC)₆]錯体の配座解析
<Author(s):> 山　博史, 安孫子　誉晃, 伊藤　美咲, 脇　克志, 　了爾, 御厨　正博
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> Enumeration of the conformers and conformational analysis were successfully conducted for an octahedral [M(ABC)₆] complex. In this report the methods and results were briefly described. In the enumeration, 7173 conformers were found by the computational group theory method, and among them, 130 conformers were found to have stable M(AB)₆ cores of S₆ symmetry. The structures of the 130 conformers of [Zn(DMSO)₆]²⁺ (DMSO: dimethylsulfoxide) were optimized by the DFT method, and the most stable conformer was obtained.
<Keywords:> 配座解析, 配座異性体, 数え上げ, 正八面体型錯体, 密度汎関数法
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0067/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 211-212, by J-STAGE]
<Title:> ケイ酸塩鉱物の電子状態及びXANES計算
<Author(s):> 高橋　修, 末永　太河
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp
<Abstract:> We estimated surface energies of all flat surfaces of forsterite within the framework of density functional theory. We found that surface energy of (120) surface is the lowest and those of (010), (130) and (112) surfaces are followed subsequently. Morphology of forsterite at 0 K is predicted. Calculated Si K-edge XANES spectra of silicon in forsterite are consistent with experiments.
<Keywords:> Soft X-ray absorption spectroscopy, silicate compounds, surface energy, DFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0058/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, A55-A55, by J-STAGE]
<Title:> 2016年秋季年会を終えて，・・異次元の世界で!
<Author(s):> 半田　真
<Abstract:>
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<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_foreword_15_6/_article/-char/ja/