投稿者: 博佐藤

[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/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Quantum Molecular Dynamics Simulation of Condensed Hydrogens by Nuclear and Electron Wave Packet Approach
<Author(s):> Kim HYEON-DEUK
<Corresponding author E-Mill:> kim(at)kuchem.kyoto-u.ac.jp
<Abstract:> We recently proposed a real-time simulation method of nuclear and electron wave packet molecular dynamics (NEWPMD) based on wave functions of hydrogen molecules composed of nuclear and electron WPs. Non-empirical intra- and intermolecular interactions of non-spherical hydrogen molecules were explicitly derived and a long-range dispersion force between hydrogen molecules was successfully derived. Nuclear quantum effects (NQEs) such as nuclear delocalization and zero-point energy were non-perturbatively taken into account. The developed NEWPMD method can be applied to various condensed hydrogen systems from a gas-phase to a high-pressure solid phase at feasible computational cost, providing intuitive understandings of real-time dynamics of each hydrogen molecule including H-H bond vibration, molecular orientations and librational motions. We will report the demonstrations not only in liquid hydrogens but also in solid and supercooled hydrogens which exhibited strong NQEs and thus anomalous static and dynamic properties.
<Keywords:> Quantum molecular dynamics simulation, Nuclear wave packet, Electron wave packet, Nuclear quantum effect, Liquid/solid/supeercooled hydrogen
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0020/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 核・電子軌道法における原子核軌道エネルギーとプロトン束縛エネルギー計算
<Author(s):> 五十幡　康弘, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> 核・電子軌道 (NOMO) 法は，原子核に対して軌道の概念を導入した量子化学理論である．NOMO法におけるHartree-Fock (HF)方程式の解として得られる原子核軌道エネルギーは，全エネルギーや軌道そのものと比較して注目されていない．本論文では，NOMO法における原子 核軌道エネルギーの物理的意味とpost-HF理論への応用を述べる．特に，最近開発されたプロトンプロパゲーター法による束縛エネルギーの見積 りについて，計算例を含めて紹介する．
<Keywords:> Nuclear orbital plus molecular orbital method, Nuclear orbital energy, Proton propagator method, Proton binding energy, Divide-and-conquer method
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 71-73, by J-STAGE]
<Title:> 古典ポテンシャル系のメタダイナミクスによる準安定構造探索
<Author(s):> 谷田　義明, 松浦　東
<Abstract:> We have performed metadynamics to explore the ligand docking poses with an RNA aptamer in three collective variables (CVs) space, one distance and two dihedral angles. We showed that the free energy surface (FES) of the ligand binding has several local minima. Furthermore, we also demonstrate that each metastable structure can be deduced from CVs of each free energy minimum.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 74-76, by J-STAGE]
<Title:> Grid Inhomogeneous Solvation Theoryを用いた血液凝固因子Xaの水和サイト解析
<Author(s):> 佐藤　博之, 松浦　東
<Corresponding author E-Mill:> shryk(at)jp.fujitsu.com
<Abstract:> The hydration structure in the active site of human coagulation factor Xa (fXa) was investigated from the viewpoint of excess free energy. Water distribution in the active site of fXa was calculated using partly constrained molecular dynamics (MD) simulation. Then the free energy of the distribution was evaluated using grid inhomogeneous solvation theory (GIST). The analyzed excess free energy shows excellent correlation to the experimental binding affinity of known ligands only if the side chain fluctuation of the active site of fXa was taken into account. This result indicates that the side chain fluctuation generated by partly constrained MD has an important role for identifying the appropriate hydration structure, and that GIST in combination with partly constrained MD provides useful information for assessing the protein-ligand binding affinity.
<Keywords:> Hydration structure, Partly constraind MD, GIST, Binding affinity, Excess free energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 57-59, by J-STAGE]
<Title:> Armchair α-Graphyne NanotubeのHOMO-LUMO Gapのチューブ長依存性
<Author(s):> 森川　大, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> 13st309e(at)shinshu-u.ac.jp
<Abstract:> Graphyne nanotubes (GNTs) are new carbon-based nanotubes and have a structure similar to the carbon nanotubes (CNTs). In the GNTs, armchair α-GNT is the highest resemblance to armchair CNT, and algebraic structure counts (ASC) are equal. This correspondence suggests that the HOMO-LUMO gaps in the finite-length armchair α-GNT oscillate with the increase of the tube length in the same fashion as the oscillation of HOMO-LUMO gaps in finite-length armchair CNT. In this work, the tube length dependences of the HOMO-LUMO gaps in the finite-length armchair α-GNT were examined by means of the H ckel method and density functional theory (DFT). It was found that the HOMO-LUMO gaps in armchair α-GNT oscillate as functions of the tube length with the period of 3.
<Keywords:> Graphyne nanotube, Carbon nanotube, Algebraic structure count, Kekul structure, HOMO-LUMO gap
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0038/_article/-char/ja/