月別: 2016年11月

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> C₅Ch₅およびC₆Ch₆ (Ch = S, Se, Te)の分子構造と芳香族性の評価
<Author(s):> 川田　修太郎, 望月　祐志, 中野　克洋
<Corresponding author E-Mill:> kawada(at)rikkyo.ac.jp
<Abstract:> (CO)_nで記されるCO単位の環状重合体であるオキソカーボンは長 年関心を集めてきた．しかし，Oをカルコゲン原子Ch = (S, Se, Te)で置換した擬オキソカーボン類については，これまで系統的に理論計算による検討はなされてはいない．そこで今回，(CCh)_n (n = 5,6)についてDFT計算による分子構造の最適化とNICS値の算定を試みた．最適化計算からは，カルコゲンが高周期になるにつれて構造の平面性が増す ことが分かった．NICS値からは，(CTe)₆でベンゼンに匹敵する芳香族性が示唆された．
<Keywords:> Oxocarbon, Chalcogen, DFT calculation, NICS evaluation, Aromaticity
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0042/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Intel Xeon Phi上でのSMASHによる並列化DFT計算の性能評価
<Author(s):> 齊藤　天菜, 望月　祐志, 山崎　大, 石村　和也
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> Intel Xeon Phiプロセッサが科学技術計算用のメニーコアプロセッサとして注目を集めている．私たちは，高い並列性能を持つ分子軌道計算プログラムSMASHを用 い，DFT計算に関して第一世代Phi (Knights Corner)上のネィティブモードで性能評価を行った．その結果，実60コアから論理120コアへ増分したマルチスレッディングの領域でも1.4倍程の 加速が得られることが分かった．これは，第二世代Phi (Knights Landing)でも好ましい性能が得られると期待させるものである．
<Keywords:> Intel Xeon Phi, Many-core, Multi-threads, Parallelized DFT calculations, SMASH program
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0047/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 固体表面に存在する水素原子が示す量子効果
<Author(s):> 奥山　弘
<Abstract:> Quantum effect is manifest for hydrogen atoms on surfaces as well as for those in solution and solids. The excited states of a hydrogen atom directly adsorbed on metal surfaces are beyond the diffusion barrier, thus being delocalized to the next sites, and even spread over the entire surface in the low-coverage limit. In addition, water and hydroxyl group on the surfaces show significant quantum effect, due to tunneling and zero-point motion of the hydrogen atom. We briefly review some experimental and theoretical studies that revealed the quantum effect of the hydrogen atom on the surfaces.
<Keywords:> Hydrogen atom, Metal surface, Quantum delocalization
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0013/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 3Dプリンターによる分子キャビティーの構造解析
<Author(s):> 戸澤　理詞, 玉井　良則
<Corresponding author E-Mill:> tamai(at)u-fukui.ac.jp
<Abstract:> 立体規則性高分子の単結晶において，分子鎖間に「分子キャビティー」と呼ばれる空孔が生成する系があり，その構造を制御することにより，特定の分子を分 離・回収する高性能な分離膜としての利用が期待されている．分子キャビティーの構造を解明するために様々な研究が行われているが，複雑なキャビ ティーの構造を立体的・直観的に把握することは困難である．そこで，本研究では，3Dプリンターを用いてキャビティーの立体モデルを作成すること で，構造の理解を深めることを目的とする．分子キャビティーを持つシンジオタクチックポリスチレン(s-PS)のδ_e型，ε型 及びS-I型を対象として，分子動力学(MD)シミュレーションを行い，分子キャビティーの構造を再現した．得られたデータを3Dプリンターで利 用可能な構造データに変換し，分子キャビティーの立体造形モデルを作成した．δ_e型について，b軸 方向及びac軸方向につながるチャネルを再現したところ，気体分子が拡散しやすいac軸方向につながるチャネルの方 が太くて短い様子が十分に再現されていた．一方ε型とS-I型については，それぞれ，円筒型とジグザグ状のチャネルが得られた．さ らに，これらのモデルに気体分子を挿入した系について解析を行い，気体分子が跳躍運動をしている瞬間を3Dモデル化することにより，結晶構造と気 体の拡散様式の関係を直観的にとらえることに成功した．
<Keywords:> Molecular cavity, Syndiotactic polystyrene, 3D printer, Diffusion, Gas separation
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 83-84, by J-STAGE]
<Title:> XyMT_EX/L_AT_EXに よる学際的書籍「Mathematical Stereochemistry」の出版
<Author(s):> 藤田　眞作
<Corresponding author E-Mill:> shinsaku_fujita(at)nifty.com
<Abstract:> An interdisciplinary book entitled “Mathematical Stereochemistry” has been published by means of the combination of freely-available computer systems, i.e., the L_AT_EX system for typesetting mathematical formulas and the XyMT_EX system for drawing chemical structural formulas.
<Keywords:> Structural formula, Mathematical formula, Typesetting, Book publication
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 85-86, by J-STAGE]
<Title:> Theoretical Study of Hydrogen Bonds in Water Nanodroplet on Graphene
<Author(s):> Takayoshi ISHIMOTO, Michihisa KOYAMA
<Corresponding author E-Mill:> ishimoto(at)ifrc.kyushu-u.ac.jp
<Abstract:> We analyzed the structural differences of H₂O molecules in water nanodroplet on graphene ((H₂O)₉₈ on graphene) model by using the density functional theory. 98 H₂O molecules on graphene were classified into four groups based on the surrounding condition (bulk region, water-gas interface, water-graphene interface, and water-graphene-gas interface). The O H distances and vibrational frequencies of H₂O molecules near the gas region were wider distributions compared with the H₂O molecules in the bulk region, whereas narrower distributions were obtained near the graphene interface.
<Keywords:> Wettability, Water nanodroplet, Hydrogen bond, Inhomogeneity, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0048/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 81-82, by J-STAGE]
<Title:> 第一原理計算による水分解用光カソード材料La₅Ti₂CuS₅O₇の 解析
<Author(s):> 阪田　薫穂, 久富　隆史, 後藤　陽介, Magyari-K pe　Blanka, De k　Peter, 山田　太郎, 堂免　一成
<Corresponding author E-Mill:> k_sakata(at)arpchem.t.u-tokyo.ac.jp
<Abstract:> La₅Ti₂Cu_1-xAg_xS₅O₇, the solid solution of La₅Ti₂CuS₅O₇ and La₅Ti₂AgS₅O₇, is a candidate of photocatalysts for sunlight-driven water splitting. It is known that La₅Ti₂Cu_0.9Ag_0.1S₅O₇ has a narrower band gap than La₅Ti₂CuS₅O₇ and La₅Ti₂AgS₅O₇. In this study, density functional theory (DFT) calculation was performed to analyze the band structure and effective mass of La₅Ti₂Cu_1-xAg_xS₅O₇ solid solutions. The band gap of La₅Ti₂Cu_0.75Ag_0.25S₅O₇ was calculated to be narrower than those of La₅Ti₂CuS₅O₇ and La₅Ti₂AgS₅O₇, which was qualitatively consistent with the experimental observation. The effective mass for electron was also estimated from the band structure to be smaller in the b-axis direction than in the other directions.
<Keywords:> DFT calculation, Band structure, Effective mass, Solid solution, Photocatalyst
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 77-78, by J-STAGE]
<Title:> N3系色素の近赤外線光吸収の理論的設計:スピン禁制励起
<Author(s):> 菅野　翔平, 今村　穣, 波田　雅彦
<Corresponding author E-Mill:> yimamura(at)tmu.ac.jp
<Abstract:> We theoretically examine spin-forbidden excitations for an N3-skeleton Ru dye with a thienyl group and iodine anion by time-dependent density functional theory with spin-orbit coupling. We found that the oscillator strength in the near-infrared region and spin-orbit coupling are enhanced by introducing the thienyl group into bipirydyl ligands.
<Keywords:> Dye sensitizer, Time-dependent density functional theory, Spin-orbit coupling, Spin-forbidden excitation, Oscillator strength
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0031/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 79-80, by J-STAGE]
<Title:> 交差共役系での置換基効果
<Author(s):> 藤山　亮治, 日高　りさ子
<Corresponding author E-Mill:> fujiyama(at)kochi-u.ac.jp
<Abstract:> Substituent effects in cross-conjugated systems were carried out on a series of substituted 3-methylenepenta- 1,4-diynes with primary carbocation CH₂⁺. Their optimized energies were calculated at the B3LYP/6-31G (d) level. The substituent effects were expressed in terms of isodesmic reactions and were analyzed by LSFE equation. The analysis results show that the substituent effect is inversely proportional to the stability of the whole molecule. In other words, the more stable the cross-conjugated molecule is, the smaller it’s substituent effect become.
<Keywords:> Cross-conjugation, Substituent effect, LSFE equation, Resonance effect, 3-Methylenepenta-1, 4-diyne
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0036/_article/-char/ja/