月別: 2018年10月

[Published online Journal of Computer Chemistry, Japan Vol.17, 142-143, by J-STAGE]
<Title:> GAPシステムを用いるベンゼン異性体の数え上げの簡略化
<Author(s):> 藤田　眞作
<Corresponding author E-Mill:> shinsaku_fujita(at)nifty.com
<Abstract:> After the development of a GAP command for calculating cycle indices with chirality fittingness (CICFs), benzene derivatives have been enumerated as 3D molecular entities.
<Keywords:> benzene derivatives, enumeration, proligand method, GAP syste
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0015/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 144-146, by J-STAGE]
<Title:> FMO計算-粗視化シミュレーション連携手法の開発と応用
<Author(s):> 奥脇　弘次, 土居　英男, 望月　祐志, 小沢　拓, 泰岡　顕治, 福澤　薫
<Corresponding author E-Mill:> okuwaki(at)rikkyo.ac.jp
<Abstract:> We have been developing a combination scheme of fragment molecular orbital (FMO) calculations and dissipative particle dynamics (DPD) simulations in order to predict the structure of functional materials. FMO-DPD simulations for polymer electrolyte membrane, lipid membrane, and protein model were conducted using in-house automatic parameter determination software.
<Keywords:> FMO-DPD Simulation, Fragment Molecular Orbital Method, Polymer Electrolyte Membrane, Lipid Membrane
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 138-141, by J-STAGE]
<Title:> Regioselectivity of H₂ Adsorption on Ga₂O₃ Surface Based on Vibronic Coupling Density Analysis
<Author(s):> Wataru OTA, Kentaro TERAMURA, Saburo HOSOKAWA, Tsunehiro TANAKA, Tohru SATO
<Corresponding author E-Mill:> tsato(at)scl.kyoto-u.ac.jp
<Abstract:> Regioselectivity of H₂ adsorption on the Ga₂O₃ surface is investigated using the vibronic coupling density (VCD) as a reactivity index. The cluster model of Ga₂O₃ surface obtained by Step-by-Step Hydrogen-Terminated (SSHT) approach is employed. The VCD analysis shows that H₂ is dissociatively adsorbed as H⁺ on the Lewis basic O atoms and as H^– on the adjacent Ga atoms. The heterolytic dissociation implies that the H^– atom bonded to the Ga atom is a reductant responsible for photocatalytic reduction of CO₂ to CO.
<Keywords:> Regioselectivity, Cluster model, Vibronic coupling density
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 124-126, by J-STAGE]
<Title:> ポテンシャルエネルギー曲面の交差構造に関する理論的研究
<Author(s):> 稲森　真由, 五十幡　康弘, 王　祺, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> The crossing of potential energy surfaces plays an important role in photo-decay processes and photochemical reactions. The energies and geometries of the crossing points have been reported for various molecules using quantum chemical calculations. In this research, excitation energy components of uracil are investigated to understand the characteristics of the crossing points. We revealed that the HOMO-LUMO exchange integral becomes approximately zero at the minimum energy conical intersection between S₀ and S₁ states. Furthermore, it was found that the HOMO-LUMO gap is close to the HOMO-LUMO Coulomb integral at the crossing structures.
<Keywords:> Conical intersection, Intersystem crossing, Frozen orbital analysis, Excitation energy component, Exchange integral
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 120-121, by J-STAGE]
<Title:> ラジカル共重合の理論的意義付け
<Author(s):> 西久保　椋, 林　慶浩, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Radical copolymerization was theoretically investigated by using correlations between Q-e values and properties of monomers and terminal radical models. As a result, it was found that same e value used for monomers and radicals is reasonable. In addition, it was found that Q value is mainly related in reaction kinetics but not reaction thermodynamics.
<Keywords:> Polymer, Radical Copolymerization, Q-e Scheme
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0024/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 122-123, by J-STAGE]
<Title:> 双安定性ロタキサンのスイッチングシミュレーション
<Author(s):> 林　慶浩, 大木　竜勝, 檜脇　悠輔, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Molecular dynamics simulation was performed on the switching behavior of bistable rotaxane having two interaction points on axial components. The switching behavior was reproduced in the case of the rotaxane composed of amine-ester type axial and DB24C8 crown ether ring. In this system, switching was completed in subnano seconds. It is suggested that DB24C8 is more suitable for switching as a ring component than 24C8, which is analog of DB24C8 having no benzene rings.
<Keywords:> ロタキサン, シャトリング, 分子スイッチ, MDシミュレーション
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0025/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 130-132, by J-STAGE]
<Title:> CD44におけるヒアルロン酸結合機構の解明
<Author(s):> リントゥルオト　正美, 堀岡　洋太, 本郷　紗記, リントゥルオト　ユハミカエル
<Corresponding author E-Mill:> masami(at)kpu.ac.jp
<Abstract:> The hyaluronan (HA) binding mechanism on CD44 was investigated by using molecular dynamics simulation. The Ordered (O) and partially disordered (PD) structures have been reported for CD44 HA binding domain (HABD). Two binding forms were investigated for the HA binding for O and PD structures in this study. O and PD structures show different HA binding structures, and the HA binding affinity on the PD structure was larger than that on O structure. The mobility of HA molecule on CD44 was high, especially for O structure. High affinity of HA binding on PD structure is suggested to regulate the rate of cell rolling under blood flow.
<Keywords:> Keywords CD44, Hyaluronan, Cell rolling, Molecular dynamics, Protein
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0027/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 133-137, by J-STAGE]
<Title:> GW近似を超えた電子系の自由エネルギー
<Author(s):> 中村　賢
<Corresponding author E-Mill:> s.nakamura(at)rist.or.jp
<Abstract:> We propose a scheme based on a kind of self-consistent perturbation theory, where both the one-particle Green’s function and the screened Coulomb interaction are determined self-consistently. To describe the screened Coulomb interaction dynamics, we use a functional-integral representation of the free energy. Our main approximation is to replace the exact free energy functional by a variationally chosen quadratic form in the fluctuating field. This procedure leads to the inclusion of electron correlation beyond the GW approximation. As an illustration, the scheme is used to calculate the potential surface of hydrogen fluoride molecule.
<Keywords:> Green’s function, Screened Coulomb interaction, GW approximation, Variational principle, Functional-integral method, Many-body perturbation theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 127-129, by J-STAGE]
<Title:> 光受容タンパク質の機構解明に向けた分割統治型時間依存密度汎関数強束縛法の開発
<Author(s):> 河本　奈々, 吉川　武司, 小野　純一, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> The divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems, as denoted by DC-TDDFTB. In this article, the implementation of TDDFTB and DC-TDDFTB methods into our in-house program, DC-DFTB-K, is explained. Dependence of CPU time on system-size for the DC-TDDFTB calculations indicates significant reduction of computational cost by adopting the DC method. Owing to the feature, excited-state calculations for whole photoactive yellow protein (PYP) surrounded by 4684 water molecules could be carried out in order to examine the hydrogen bond between p-coumaric acid and Glu46 in PYP.
<Keywords:> Divide-and-conquer method, Time-dependent density-functional tight-binding method, Photoactive yellow protein, Excited state, ??i??p??/i??-Coumaric acid.
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0032/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 117-119, by J-STAGE]
<Title:> グラフ理論と分子力場法によるNaクラスター全異性体の安定性の解析
<Author(s):> 関根　理香, 室野　あゆみ, 岡倉　雅弥, 小林　陽介, 仲上　祐斗
<Corresponding author E-Mill:> sekine.rika(at)shizuoka.ac.jp
<Abstract:> All isomers for sodium clusters up to Na₉ were investigated by graph theory where a vertex and an edge correspond to atom and bond between adjacent atoms, respectively. All isomers, more than 10 million, for Na₁₀ were listed. Structural features for sodium clusters up to Na₉ were elucidated by using graph theory. Furthermore, geometrically forbidden graphs were excluded by using molecular mechanics.
<Keywords:> Keywords Graph theory, Molecular mechanics, Sodium cluster, H ckel Method, Metal cluster, Isomer, Connected simple graph
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0026/_article/-char/ja/