カテゴリー: 未分類

[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/

[Published online Journal of Computer Chemistry, Japan Vol.17, 113-116, by J-STAGE]
<Title:> 分子動力学シミュレーションを用いたナトリウムホウ酸塩ガラスにおけるホウ酸異常現象の考察
<Author(s):> 山本　優也, 澤口　 直哉, 佐々木　眞
<Corresponding author E-Mill:> 16096004(at)mmm.muroran-it.ac.jp
<Abstract:> We investigated the structural units of xNa₂O-(1 – x) B₂O₃ glasses using molecular dynamics (MD) simulation with the interatomic potential provided by first-principles calculations. The results are consistent with experimental trends in interatomic distance, linear thermal expansion coefficient and BO₄ units. The amount of 5- to 8-membered rings at x = 0.2 is larger than the other composition range. This suggests that the structural unit constructed by a few rings is related to suppression of thermal expansion.
<Keywords:> Molecular dynamics simulation, Borate glasses, Boron oxide anomaly, Oxide glasses
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 111-112, by J-STAGE]
<Title:> 大学初年度向け化学教育のためのScratchプログラムの開発
<Author(s):> 満野　仁美, 中川　知樹, 土居　英男, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have developed several Scratch-based educational programs for the students in a first-year university chemistry course. Demonstrative programs were made for chemical bonding and chemical thermodynamics. Making of such programs could be easy even for students without coding skills and be valuable for self-education as well.
<Keywords:> キーワード：Scratch, Educational program, Chemistry course, Self-education
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0022/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明
<Author(s):> 新庄　永治, 奥脇　弘次, 土居　英男, 望月　祐志, 古石　誉之, 福澤　薫, 米持　悦生
<Abstract:> ドラッグ・デリバリー・システムにおけるナノ微粒子設計の効率化のために，分子シミュレーションによる物性予測や原子分解能のメカニズム解明が望まれている．本研究では，散逸粒子動力学 (DPD) 法とX線小角散乱を用いて，脂質二重膜および混合脂質のベシクル形成の分子メカニズムを明らかにすることを目的として検討を行った．DPDシミュレーションに用いる相互作用パラメータは，フラグメント分子軌道 (FMO) 法を用いて高精度に算定した(FMO-DPD法)．脂質二重膜形成の結果から，飽和結合のみをもつリン脂質 (DPPC) よりも不飽和結合をもつリン脂質 (DOPC) の方が，膜流動性が高いことが分かった．さらに，リン脂質と正電荷脂質を混合したベシクルの形成では，正電荷脂質の比率が増えるにつれて膜の流動性が高くなり，球から扁平球へと形状が変化することが明らかとなった．
<Keywords:> Lipid bilayer, vesicle, Dissipative particle dynamics (DPD), Fragment molecular orbital (FMO) method, SAXS
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0012/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 天然有機化合物にもとづくNTG-活性辞書システムの開発
<Author(s):> 桂樹　哲雄, 金谷　重彦, 高橋　由雅
<Corresponding author E-Mill:> katsuragi(at)cs.tut.ac.jp
<Abstract:> 本研究では，天然有機化合物を対象とした，環系骨格構造とその関連する生理活性を相互に検索することができる辞書システムNTGdic/BOC (NTG dictionary for Bioactive Organic Compounds)を開発した．NTG (Non-Terminal vertex Graph)として表される環系骨格構造に注目し，天然有機化合物データベースKNApSAcK familyに収録されている51247件の化合物の化学構造式を対象に，単純グラフ，頂点重み付きグラフなど5種類の異なるグラフ表現を用いて，延べ57867件のNTGを抽出するとともに，既知の140種類の生理活性との関連付けを行った．これらの結果は関係データベース(関係辞書)としてシステムに実装した．NTGdic/BOCでは，構造エディタを用いて作画入力したクエリ化合物の化学構造式から，利用者が指定するグラフ表現レベルでのNTGを自動的に抽出し，NTG-活性辞書を用いて，関連する生理活性を参照することができる．一方，生理活性からNTG骨格構造を検索することや，各々のNTGの由来化合物を参照することもできる．また，類似構造(または類似NTG)検索も利用可能である．
<Keywords:> Molecular framework, Structure similarity, Biological activity, NTG, Natural organic compound
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0049/_article/-char/ja/