カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.18, 239-240, by J-STAGE]
<Title:> [2Fe-2S]フェレドキシン活性中心周囲の環境がイオン化ポテンシャルに与える影響に関する理論研究
<Author(s):> 江良　伊織, 北河　康隆, 多田　隼人, 藤井　琢也, 池永　和輝, 中野　雅由
<Corresponding author E-Mill:> kitagawa(at)cheng.es.osaka-u.ac.jp
<Abstract:> Iron Sulfur clusters are often found in active sites of electron transfer proteins. Their redox potentials are well controlled; however, its mechanism has not been understood well. In this study, therefore, we elucidate the effects of the protein-field, especially hydrogen bonds around the active site on the redox potential by using density functional theory (DFT) calculations. The results indicate that the ionization potentials are in proportion to the number of hydrogen bonds around the active site.
<Keywords:> 2Fe-2S Ferredoxin, Redox potential, Ionization potential, Hydrogen bond, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 230-232, by J-STAGE]
<Title:> 塩基性条件下におけるニトリルオキシドからイソシアネートへの異性化反応機構の理論的解明
<Author(s):> 石山　裕輝, 林　慶浩, 高田　十志和, 川内　進
<Corresponding author E-Mill:> kawauchi.s.aa(at)m.titech.ac.jp
<Abstract:> Reaction mechanisms for the isomerization of nitrile N-oxide to isocyanate catalyzed by hydroxide ion were investigated by density functional theory calculations. In this mechanism, nitrile N-oxide first dimerizes to a six-membered ring intermediate, and then undergoes two rearrangement reactions to isomerize into two isocyanate molecules. The process with the highest activation energy as an elementary reaction was the second rearrangement reaction, with an activation free energy of 31.1 kcal/mol, which is reasonable for a reaction proceeding slowly at room temperature. This mechanism can also explain the experimental results that the oxygen atom exchanges between nitrile N-oxide molecules during the isomerization reaction.
<Keywords:> reaction mechanism, Nitrile ??i??N??/i??-oxide, Isomerization, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 236-238, by J-STAGE]
<Title:> 非平衡分子動力学法によるシアノビフェニル液晶の熱伝導機構の解明
<Author(s):> 佐々木　遼馬, 林　慶浩, 川内　進
<Corresponding author E-Mill:> kawauchi.s.aa(at)m.titech.ac.jp
<Abstract:> All-atom molecular dynamics were performed on 4-heptyl-4’-cyanobiphenyl (7CB) to study the mechanism of heat conduction in the nematic liquid crystal. The non-equilibrium molecular dynamics simulation using our amended force field for 7CB has reproduced the anisotropy of the thermal conductivity in the nematic phase of 7CB. Furthermore, the calculated Phonon density of state shows that the higher thermal conductivity parallel to the director than that perpendicular to the director is due to the heat conduction derived from the stretching vibration of the well-oriented covalent bonds.
<Keywords:> Liquid crystal, Molecular dynamics, Thermal conductivity, Phonon, Phonon density of state
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 233-235, by J-STAGE]
<Title:> アシルピリジニウムカチオンの安定性および反応性の評価
<Author(s):> 柴田　裕介, 林　慶浩, 川内　進
<Corresponding author E-Mill:> kawauchi.s.aa(at)m.titech.ac.jp
<Abstract:> Among ester synthesis methods, there is a method using a pyridine derivative as a catalyst, and the esterification reaction rate may be increased through a highly active acylpyridinium cation intermediate. It has been reported that the stability of acylpyridinium cations correlates with the reaction rate of esterification. In this study, we try to clarify the reason for the correlation between the reaction rate and the stability, then we investigate the relationship between the stability and structures of acylpyridinium cations. As a result, we found that the stability largely depends on the electronic donor property of the substituents, and acylpyridinium cation may act as an effective catalyst for esterification when the substituents have strong donor property at positions 3, 4, 5 of the pyridine ring.
<Keywords:> DFT, NBO deletion, esterification, pyridine derivatives, acylpyridinium cations
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0049/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 224-226, by J-STAGE]
<Title:> 芳香族・キノイド性およびドナー・アクセプター性を用いた狭バンドギャップπ共役系高分子予測モデルの構築
<Author(s):> 林　慶浩, 川内　進
<Corresponding author E-Mill:> hayashi.y.ah(at)m.titech.ac.jp
<Abstract:> A band gap prediction model of π-conjugated polymers was constructed using aromatic/quinoid, donor/acceptor, and torsion properties to predict quantitatively the band gap of π-conjugated polymers from properties of monomers. Quinoid stabilization energy (QSE), energy difference between HOMO of donor and LUMO of acceptor, torsion angle in homo-dimer of monomers were used as descriptors of aromatic/quinoid, donor/acceptor, and torsion properties. The neural network, which was constructed by 2 hidden layers with 5 neurons per layer, quantitatively predicts (RMSD = 0.207 eV, R² = 0.885) the band gap of the π-conjugated polymers from descriptors of monomers.
<Keywords:> 高分子, バンドギャップ, 設計指標, DFT計算, 機械学習
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 227-229, by J-STAGE]
<Title:> 芳香族単分子並列回路の電気伝導度とフロンティア軌道の関係
<Author(s):> 岡澤　一樹, 辻　雄太, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> According to the current superposition law in nanoscale, the conductance gets more than doubled when the number of paths is doubled. The superposition law can be applied to the molecular graph, which is a discrete mathematical expression for a structure consisting of nodes and edges. We previously revealed that the aromatic parallel circuit i.e. benzene molecule breaks the superposition law. In this paper, we show that [4n+2] annulenes also break the current superposition law from the viewpoint of orbital interaction between two fragments in the parallel circuit.
<Keywords:> Single-molecular electronics, π-conjugated system, Graph theory, H ckel method, Frontier orbital
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 211-213, by J-STAGE]
<Title:> 分子軌道計算と機械学習によるフェルラ酸の抗酸化作用の研究
<Author(s):> 寺前　裕之, 玄　美燕, 山下　司, 高山　淳, 岡﨑　真理, 坂本　武史
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> Ferulic acid is known to have strong antioxidant properties. In the present study, we investigate the electronic structures of ferulic acid and its radical species extracting the hydrogen atom from its phenolic hydroxyl group. The relation of the results by several machine learning models using R/caret package, such as partial least squares, random forest, radial basis function kernel regularized least squares, and baysian regularized neural network, with the radical scavenging activity with the DPPH reagent, IC₅₀, measured by Sakamoto et al. is discussed. We found all four methods gave reasonable correlation coefficients which means the possible prediction of the IC₅₀ values with the results of the molecular orbital calculations only.
<Keywords:> Ferulic acid, Radical scavenging activity, Hamiltonian algorithm, Molecular orbital method, Machine learning, Random forest model
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 214-216, by J-STAGE]
<Title:> ブロック共重合体のミクロ相分離構造に対するマルチフラクタル解析
<Author(s):> 伊藤　真利子, 山中　貞人, 青柳　岳司, 大西　立顕
<Corresponding author E-Mill:> marikoito.rnu1(at)gmail.com
<Abstract:> In this study, we attempted to quantify the shape of various metastable morphologies of microphase separation in block copolymers that can be observed in a computer simulation under the same condition as that for double gyroid (stable state). For the quantification, we used multifractal analysis, which is a tool to evaluate the shape having heterogeneous density inside it. Our analysis showed that the indicators relating to the multifractal analysis of metastable structures are distributed far from that of double gyroid.
<Keywords:> Block copolymers, Microphase separation, Double gyroid, Multifractal analysis, Fractal dimension
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 217-220, by J-STAGE]
<Title:> ガス分離可能なイオン液体探索のためのデータベース構築
<Author(s):> 増田　千夏, 黒木　菜保子
<Corresponding author E-Mill:> kuroki.91d(at)g.chuo-u.ac.jp
<Abstract:> Ionic liquids (ILs) are non-volatile and highly stable solvents, which consist of organic/inorganic cations and anions. ILs are attractive since they can be utilized as gas-separating materials. Using a conductor-like screening model for realistic solvation (COSMO-RS) method, in this study, Henry’s law constants of 15 gases (HCN, SO₂, H₂O, NH₃, H₂S, NO₂, NO, CO, N₂O, CO₂, C₂H₆, C₂H₄, CH₄, N₂, H₂) in 68,775 ILs were calculated to construct an ab initio database to search for ILs which are suitable for gas separation. Based on the database, it was numerically confirmed that not only the ions’ geometric structures but also electronic structures are important to predict ILs’ gas absorption abilities with high accuracy.
<Keywords:> Ionic liquid, Gas absorption and separation, Fragmentation, Statistical thermodynamics, Database
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0046/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 208-210, by J-STAGE]
<Title:> 分子動力学計算によるRNAアプタマーとヒト抗体の複合体形成におけるCa²⁺の役割の解析
<Author(s):> 石井　清一郎, 関口　真裕, 吉田　尚恵, 増川　恵介, 石川　岳志, 坂本　泰一, 山岸　賢司
<Corresponding author E-Mill:> yamagishi.kenji(at)nihon-u.ac.jp
<Abstract:> An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca²⁺ ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca²⁺ ions. To elucidate the role of Ca²⁺ ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca²⁺ ions in a solvent. In the presence of Ca²⁺ ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca²⁺ ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca²⁺ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
<Keywords:> RNA aptamer, Human immunoglobulin G, Calcium ion, Molecular dynamics, Structural analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0051/_article/-char/ja/