カテゴリー: 未分類

[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/

[Published online Journal of Computer Chemistry, Japan Vol.14, 203-205, by J-STAGE]
<Title:> 実空間実時間のTDDFTによる11-cis型レチナールの光吸収スペクトルの解析
<Author(s):> 田中　志歩, 遠越　光輝, 善甫　康成
<Corresponding author E-Mill:> shiho.tanaka.2a(at)stu.hosei.ac.jp
<Abstract:> We have applied time-dependent density functional theory (TDDFT) in real-time and real-space to 11-cis retinal to investigate the optical absorption. As the exchange-correlation functional, we use the usual LDA and B88, which is the simplest GGA to describe the correct asymptotic behavior. The calculated result of B88 is closer to that of experiment, compared to that of LDA. Our results indicate that, if the functional to express the correct asymptotic form is selected, more accurate results can be obtained. In our TDDFT calculation, the peak position is confirmed by the maximum entropy method, which is applied to the spectrum analysis to find the peak related to the optical absorption effectively.
<Keywords:> Real-time and real-space, Time-dependent density functional theory, 11-cisretinal, Density functionals, Correct asymptotic behavior, Maximum Entropy Method
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0075/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 206-208, by J-STAGE]
<Title:> 比較的大きな分子に対する内殻二重正孔分光
<Author(s):> 高橋　修
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp
<Abstract:> The ionization energies of single, double, and triple core-hole (SCH, DCH, and TCH) states were calculated for three isomers of aminophenol with the framework of density functional theory. Our calculated single core-hole ionization potentials were consistent with experiment and the previous theoretical values. Core-ionization energies via complex processes were also estimated. The difference of relaxation energy of two-site DCH (tsDCH) states can be visualized using Wagner plots. We found that the electron density of π orbitals on benzene ring are relaxed to core-vacancy sites at N,O tsDCH state.
<Keywords:> oft X-ray spectroscopy, double-core-hole state, X-ray free electron laser, DFT, Wagner plot
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0057/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 209-210, by J-STAGE]
<Title:> TD DFT法によるOHBAの吸光・発光スペクトルの理論的研究
<Author(s):> 新井　健文, 長岡　伸一, 長嶋　 雲兵, 寺前　裕之
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> We have studied the first excited state of o-hydoroxybenzaldehyde with TD DFT calculations. We have attempted systematic calculations to select a proper functional to describe the correlation between the absorption and emission spectra and the Hammett’s σ values. The results with XAB95 functional are considered to be near the experimental results of the emission spectra.
<Keywords:> o-hydroxybenzaldehyde, OHBA, Time-dependent density functional theory, TDDFT, Proton transfer
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0061/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 199-200, by J-STAGE]
<Title:> SbおよびTe化合物のリガンド交換・リガンドカップリング反応メカニズム
<Author(s):> 小林　正人, 黒田　悠介, 秋葉　欣哉, 武次　徹也
<Corresponding author E-Mill:> k-masato(at)mail.sci.hokudai.ac.
<Abstract:> Theoretical and computational studies on the mechanisms of ligand exchange reaction (LER) and ligand coupling reaction (LCR) of hypervalent pentacoordinate Sb and tetracoordinate Te compounds were carried out. Contrary to the previous suggestion from experimentalists, the lone pair electrons of Te do not participate in LER. Also, LER of R₅Sb proceeds via a similar mechanism to that of R₄Te. As for the LCR of R₅Sb, the apical-equatorial coupling mechanism was suggested.
<Keywords:> Hypervalent compounds, Three-center four-electron bond, Natural bond orbital, Dispersion corrected DFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0058/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 201-202, by J-STAGE]
<Title:> 並列分子科学計算プログラムの電力制約下における性能最適化
<Author(s):> 稲富　雄一, 井上　弘士
<Corresponding author E-Mill:> yuichi.inadomi(at)cpc.ait.kyushu-u.ac.jp
<Abstract:> Power is the most important resource on the next-generation supercomputers, and they will be operated under power constraint. Therefore, there is a need to maximize performance of HPC application under power constraint. To do such optimization, we’ve developed and reported a method to improve performance by power allocation for each processor, which is called the variation-aware power budgeting. In this study, we carried out large-scale performance evaluation of a proposed method for two mini-applications related to molecular science, Modylas-mini and NTChem-mini. As a result, our method can improve their performance under power constraint up to 1.99 times speedup compared to conventional power constraint.
<Keywords:> Power-constrained supercomputing, Variation-aware power budgeting
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0066/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 193-195, by J-STAGE]
<Title:> Handling of Highly Symmetric Molecules for Chemical Structure Elucidation in a CAST/CNMR System
<Author(s):> Shungo KOICHI, Hiroyuki KOSHINO, Hiroko SATOH
<Corresponding author E-Mill:> shungo(at)nanzan-u.ac.jp
<Abstract:> In chemical structure elucidation, symmetric structures sometimes need careful handling. In the course of the development of a system for NMR-based structure elucidation, we have developed a method for processing chemical structures with high symmetry by applying an efficient algorithm for graph inference. In the present letter, we describe the outline of the algorithm by taking bibenzyl as an example. The method has been implemented to CAST/CNMR, a system for NMR-based structure/chemical shift prediction.
<Keywords:> Chemical structure elucidation, Highly symmetric chemical graphs, Graph inference, NMR chemical shift data, CAST/CNMR.
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0067/_article/-char/ja/