月別: 2019年2月

[Published online Journal of Computer Chemistry, Japan Vol.18, 18-28, by J-STAGE]
<Title:> リチウムイオン電池Solid Electrolyte Interphase (SEI)に関する第一原理計算研究
<Author(s):> 館山　佳尚
<Corresponding author E-Mill:> TATEYAMA.Yoshitaka(at)nims.go.jp
<Abstract:> リチウムイオン電池(LIB)中の負極と電解液の界面に主に充電時に形成される被膜をSolid Electrolyte Interphase (SEI)と呼ぶ．このSEIの性質によってLIBの性能や安全性が大きく変化する．しかし，この界面過程のその場観察・オペランド観察実験はいまだに困難が多く，高精度な理論計算による微視的機構の解明に大きな期待が寄せられている．本稿では，特に密度汎関数理論をベースにした第一原理計算によるSEI研究の現状を，著者らの研究も含めて，概観し今後について展望する．
<Keywords:> Keywords Lithium ion battery, Solid electrolyte Interphase, first-principles calculation, redox reactions, interface
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/1/18_2018-0046/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 84-94, by J-STAGE]
<Title:> Li and Na Interaction with Ti₂C-MXene: A First-Principles Calculation
<Author(s):> Shunsuke KURAHASHI, Saeid ARABNEJAD, Hiroshi USHIYAMA, Koichi YAMASHITA
<Corresponding author E-Mill:> yamasita(at)chemsys.t.u-tokyo.ac.jp
<Abstract:> This article presents a density functional theory (DFT) study that explores the chemical interactions and mechanisms in Li/Na-MXene systems with the aim of improving the performance of rechargeable batteries. Experimental studies indicate the presence of chemical and physical adsorption mechanisms in these systems. To understand the interaction mechanisms in the charging/discharging process, we investigated the ion intercalation/adsorption process and the induced chemical shielding. Different possible surface terminations have been investigated to determine which type of interaction is more likely to exist at the interlayer surfaces. The DFT results obtained in this study suggested the use of various methods, such as surface modification and expansion of the interlayer distance, to enhance the energy storage performance; nuclear magnetic resonance measurements can be used to check whether the ideal surface modifications have been experimentally achieved.
<Keywords:> Rechargeable battery, Ti2C-MXene, Density functional theory (DFT), Energy storage, Charging/discharging process
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/1/18_2018-0050/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 189-192, by J-STAGE]
<Title:> 棄却法を用いたタンパク質分子軌道の雲状可視化法の研究
<Author(s):> 江口　晴輝, 平野　敏行, 佐藤　文俊
<Corresponding author E-Mill:> satofumi(at)iis.u-tokyo.ac.jp
<Abstract:> The new visualization technique of canonical molecule orbitals (MOs) was developed with the cloud-like model. The random position points according with MO distribution were generated by the rejection method. Quasi-isosurface indication was proposed and succeeded in representation of internal structure containing inclusion-type isosurface. Because this method also displays a wide range of MO values simultaneously, MO distribution can be observed with little loss of information. This method is useful for analyses in the complicated protein MOs.
<Keywords:> Keywords Molecular orbital, Protein, Scientific visualization, Rejection method, Cloud-like model
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0062/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 193-195, by J-STAGE]
<Title:> 正規表現拡張SMILESを用いた化学構造検索の提案
<Author(s):> 坂本　雅志, 藤芳　明生
<Corresponding author E-Mill:> akio.fujiyoshi.cs(at)vc.ibaraki.ac.jp
<Abstract:> This paper proposes the use of regular expressions for chemical structure search. As regular expressions dramatically improve the convenience of string search, a regular expression extension for SMILES can improve the convenience of chemical structure search．The regular expression extension for SMILES is obtained from the existing SMILES notation by adding the curly brackets “{” and “}” for range specifications, the vertical bar “|” for enumerations of choices, the asterisk “*” for repetitions of 0 or more times, and the plus“+” for repetitions of 1 or more times. Software for chemical structure search using the extended SMILES was implemented and released.
<Keywords:> キーワード：Chemical structure search, Regular expression, SMILES, Graph automaton
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0051/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 196-198, by J-STAGE]
<Title:> Principal Component Analysis for Molecular Dynamics Simulation of the Crystal Phase Transition
<Author(s):> Takako MASHIKO
<Corresponding author E-Mill:> takako.mashiko.zs(at)kyocera.jp
<Abstract:> Principal component analysis (PCA) which is one of the dimensionality reduction techniques is adapted to find the common or major factors from sampling big data. In order to be clear the trigger motion of phase transition/change, PCA performed the MD sampling coordinates of crystal structure around phase transition temperature. In this paper, we especially focus on the α – β transition using the PCA analysis to the MD trajectories. The first principal component of PCA can be approximated as a mixed motion of the rotational mode of one SiO₃-OSiO₃ bond and the bending mode of Si-O-Si angle. The result indicated that the PCA can show the trigger motion of phase transition/change as found in previous studies. We could suggest that the PCA is useful tool to understand the importance information of phase transfer/change of crystal structure.
<Keywords:> MD simulation, Principal component analysis, Phase transition
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0066/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 199-201, by J-STAGE]
<Title:> 正規表現拡張SMILESが示す化合物集合に対する部分構造探索
<Author(s):> 藤芳　明生, 坂本　雅志
<Corresponding author E-Mill:> akio.fujiyoshi.cs(at)vc.ibaraki.ac.jp
<Abstract:> This paper proposes a substructure search method for finding an element of a set of chemical structures represented by a SMILES string with regular expression extension. It is known that substructure search is an NP-hard problem in general. However, by taking advantage of a graph-theoretical characterization of chemical compounds, the proposed method runs fast enough. Software for substructure search using the proposed method was implemented and released.
<Keywords:> Substructure search, Regular expression, SMILES, Graph automaton, Treewidth
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0053/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 第一原理計算を用いた硫化スズ電極のNaイオン電池性能評価と放電機構解明
<Author(s):> 小鷹　浩毅, 籾田　浩義, 喜多條　鮎子, 岡田　重人, 小口　多美夫
<Corresponding author E-Mill:> kotaka(at)esicb.kyoto-u.ac.jp
<Abstract:> スズ化合物は安価かつ大きな理論容量が期待されることから，Naイオン二次電池の負極材料候補として研究される物質の一つである．本研究では，Naイオン二次電池の負極材料となりうるコンバージョン系負極材料として硫化スズに着目し，その電池特性を第一原理計算を用いて調べた．負極材料とキャリアであるNaが反応した場合に生成すると予想されるNa-Sn-S系化合物を計算し，生成エネルギー解析に基づいて評価した3元系相図から充放電反応過程の生成物を明らかにした．計算から得た充放電反応式をもとに電圧容量曲線を作成し，Na / SnSハーフセル実験にて測定された充放電曲線との比較を行ったところ，実験結果をよく再現する結果を得た．さらに，充放電反応過程の生成物を特定するために，硫黄 K端のX線吸収スペクトルを計算し，実測結果と比較した．放電時にNa₂S由来のスペクトル形状変化が現れ，それが充電時に再びSnS由来のスペクトル形状に戻ることを確認した．
<Keywords:> Na-ion battery, Electrode, First-principles calculation, Battery performance, X-ray absorption spectrum.
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0041/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 金・銀・銅クラスターの安定構造，異性化反応経路，およびNO解離反応経路の探索とその電子物性
<Author(s):> 近藤　有輔, 高原　里奈, 毛利　広野, 高木　牧人, 前田　理, 岩佐　豪, 武次　徹也
<Corresponding author E-Mill:> tiwasa(at)sci.hokudai.ac.jp
<Abstract:> 原子クラスターは自由度が高いために多くの構造異性体を持つ．通常の理論研究では，その最安定構造の探索と続く電子物性解析が主であったが，近年の理論化学的手法の発展により，安定構造間の異性化反応や，異性体を含めた触媒活性の研究が可能になってきた．本研究では，金，銀，銅のクラスターを対象として安定構造および異性化反応経路，およびNO解離の触媒反応経路の探索を行いその比較を行った．異性化反応の計算からは，金と銀に比べると銅は異性化反応の障壁が高く，これはバルクのモース硬度と同様の傾向を示していた．NO解離反応の触媒作用に関しては，金と銀は障壁が高い一方で，銅は障壁が低く，安価で豊富な元素による触媒の可能性があることが分かった．
<Keywords:> Keywords AFIR, metal cluster, isomerization, NO dissociation, cluster catalyst, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0044/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 金属電極電解液界面の古典動力学シミュレーション
<Author(s):> 中農　浩史, 佐藤　啓文
<Corresponding author E-Mill:> hnaka(at)moleng.kyoto-u.ac.jp
<Abstract:> 電極電解液界面ではバルクの溶液とは大きく異なる特異な溶媒構造のもとで多彩かつ重要な反応が進行する．古典動力学シミュレーションは反応場としての電極電解液界面に対する微視的な理解を得ることが出来る有効なアプローチの一つである．本稿では，金属電極電解質水溶液系の古典動力学シミュレーションを行うにあたり注意すべき三点: 相互作用ポテンシャルの選択，電極の分極と定電位条件の記述，長距離静電相互作用の評価 について述べる．
<Keywords:> Battery, Interface, Molecular dynamics, Simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0040/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Li and Na Interaction with Ti₂C-MXene: A First-Principles Calculation
<Author(s):> Shunsuke KURAHASHI, Saeid ARABNEJAD, Hiroshi USHIYAMA, Koichi YAMASHITA
<Corresponding author E-Mill:> yamasita(at)chemsys.t.u-tokyo.ac.jp
<Abstract:> This article presents a density functional theory (DFT) study that explores the chemical interactions and mechanisms in Li/Na-MXene systems with the aim of improving the performance of rechargeable batteries. Experimental studies indicate the presence of chemical and physical adsorption mechanisms in these systems. To understand the interaction mechanisms in the charging/discharging process, we investigated the ion intercalation/adsorption process and the induced chemical shielding. Different possible surface terminations have been investigated to determine which type of interaction is more likely to exist at the interlayer surfaces. The DFT results obtained in this study suggested the use of various methods, such as surface modification and expansion of the interlayer distance, to enhance the energy storage performance; nuclear magnetic resonance measurements can be used to check whether the ideal surface modifications have been experimentally achieved.
<Keywords:> Rechargeable battery, Ti2C-MXene, Density functional theory (DFT), Energy storage, Charging/discharging process
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0050/_article/-char/ja/