投稿者: 博佐藤

[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/

[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/