月別: 2016年1月

[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/

[Published online Journal of Computer Chemistry, Japan Vol.14, 196-198, by J-STAGE]
<Title:> スマートフォン対応のAR分子グラフィックス表示アプリケーションの開発
<Author(s):> 宇野　健, 佐々　和洋, 林　治尚, 中野　英彦
<Corresponding author E-Mill:> uno(at)pu-hiroshima.ac.jp
<Abstract:> We developed an AR molecular graphics application for chemical education at secondary level. Flash which can execute on all platforms is used as a programming language for software development for smartphone, which the possession rate of which in junior and senior high school students is high. By developing and mounting the AR function, students can examine molecular graphics in 3D or when they look at a marker printed in a text or a handout just to read. To develop the web interface for making molecular data, the teacher can use molecular graphics in 3D easily when necessary.
<Keywords:> Chemical Education, Secondary education, Molecular Graphics, Augmented Reality, Smartphone
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0068/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 177-178, by J-STAGE]
<Title:> 共役ポリエンの家系図についての検討
<Author(s):> 細矢　治夫
<Abstract:> For all the isomers of conjugated polyenes C_2nH_2n+2 (n = 1 6) total π-electron energy Eπ, topological index Z, mean length of conjugation L were calculated, and their correlations were analyzed to get their genealogy. These Eπ values can be estimated fairly well from Z, moderately from L, and roughly from the number of tertiary carbon atoms. The Eπ change caused by the attachment of one C=C unit to a given polyene can be classified into elongation, outer branching, inner branching, and horn growing, by the site of the attached C atom. The genealogy of conjugated acyclic polyenes can thus be understood and interpreted even by chemistry beginners. By extending this analysis one can obtain mathematical proof and its limitation of the “organic electron theory.”
<Keywords:> Genealogy of conjugated polyene, HMO, Total π-electron energy, Topological indexZ, Mean length of conjugation, Elongation, Branching, Horn growing, Organic electron theory.
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0062/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 179-180, by J-STAGE]
<Title:> ある荷電空間について
<Author(s):> 鳴海　英之
<Corresponding author E-Mill:> nrhd2357(at)gray.plala.or.jp
<Abstract:> Electric charges are expressed by democratic matrices and unit matrices on the basis of Hueckel MO method.
<Keywords:> Hueckel MO Method, Electric Charges, Preons, Unit and Democratic Matrices
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0063/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 181-183, by J-STAGE]
<Title:> 分子動力学法を用いたナトリウムケイ酸塩ガラスの修飾イオンとネットワーク構造の関係
<Author(s):> 山本　優也, 澤口　直哉, 佐々木　眞
<Corresponding author E-Mill:> 14042074(at)mmm.muroran-it.ac.jp
<Abstract:> Network structure of sodium silicate glasses was investigated by molecular dynamics simulation. The simulations were performed that determined using the first-principles calculation. Variation of SiO₄ units and bond angles for alkali content were consistent with experimental results. It was also suggested that sodium ion and calcium ion give different effect to glass structure each other.
<Keywords:> Molecular dynamics, Interatomic potential, Sodium silicate glasses, Si-O-Si bond angle, Network-modifying ion
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0069/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 184-185, by J-STAGE]
<Title:> 生分解性キレート剤が作る鉄(III)錯体の構造予測
<Author(s):> 大友　秀一, 崎山　博史
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> The structures of iron(III) complexes with biodegradative chelating agent, methylglycinediacetic acid [H₃(mgda)], were computationally predicted based on the DFT method. The structures of dinuclear iron(III) complexes, [Fe₂O(mgda)₂(CO₃)]⁴ and [Fe₂O(mgda)₂(H₂O)₄]² , were predicted, and the structures were thought to be similar to those of related dinuclear iron(III) complexes with nitrilotriacetate (nta³ ), [Fe₂O(nta)₂(CO₃)]⁴ and [Fe₂O(nta)₂(H₂O)₄]² , respectively. The mgda complex, [Fe₂O(mgda)₂(H₂O)₄]² , is thought to interact with hydrogen peroxide like the nta complex [Fe₂O(nta)₂(H₂O)₄]² .
<Keywords:> 生分解性キレート剤, 鉄(III)錯体, 構造予測, 異性体, 密度汎関数法
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0070/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 186-188, by J-STAGE]
<Title:> Reduced HOMO-LUMO Gapを用いたCNTの電子構造の炭素数依存性の解析
<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 carbon number dependences of the chemical stabilities the several kinds of carbon nanotubes (CNTs) with unique Clar formula were examined by means of reduced HOMO-LUMO gap. It was found that the distributions of reduced HOMO-LUMO gaps of CNTs are divided into two regions with a border line of reduced HOMO-LUMO gap = about 3.0 and that the dependences on the tube length have distinct characters in the two regions. The difference in the dependences on the tube length is characterized by the existence of the 4n-conjugated circuit and by the existence of the fully-benzenoid structure. It was also indicated that the existence of the fully-benzenoid structure generates chemical instability in CNTs.
<Keywords:> Reduced HOMO-LUMO gap, Clar structure, Fully-benzenoid, Conjugated circuit, Carbon nanotube
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0071/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.14, 189-192, by J-STAGE]
<Title:> Fluorescence via Reverse Intersystem Crossing from Higher Triplet States
<Author(s):> Tohru SATO
<Corresponding author E-Mill:> tsato(at)moleng.kyoto-u.ac.jp
<Abstract:> A high external quantum efficiency observed for organic light-emitting diodes using PTZ-BZP (PTZ: 10-hexyl-phenothiazin, and BZP:4-phenyl-2,1,3-benzothiadiazole) is attributed to fluorescence from S₁ via reverse intersystem crossing from the T₃ or T₂ state under electrical excitation. The radiative and non-radiative transitions from these higher triplet states to the lower triplet states are suppressed because of their small overlap densities. In this study, a principle to design such an electronic structure is proposed.
<Keywords:> organic light-emitting diode (OLED), vibronic coupling, thermally activated delayed fluorescence (TADF), non-radiative transition, overlap density
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/6/14_2015-0072/_article/-char/ja/