月別: 2020年3月

[Published online Journal of Computer Chemistry, Japan Vol.18, 248-250, by J-STAGE]
<Title:> 粒子法とBohm形式による量子波束の電子状態計算
<Author(s):> 廣野　史明, 岩沢　美佐子, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> 18t0014(at)cis.k.hosei.ac.jp
<Abstract:> In order to describe the time evolution of the electronic state, we have developed a new method, using the particle method with the Bohmian, to solve the time-dependent Schr dinger equation. The method has been applied to the time-dependent coherent state for a harmonic potential, whose analytical solutions are well-known. To evaluate this method, the ground state is evolved to estimate the excited state, and we follow the dynamic dipole moment as the linear responses of the system under externally applied perturbations in real time. From the polarizability obtained as the Fourier transform of the dipole moment, we calculate the optical strength function. As a result, a single peak is observed, which was exactly expected from the analytical solution. We recognize that the method is quite valid for the time dependent electronic structure calculation.
<Keywords:> Symmetric smoothed particle hydrodynamics, Bohmian, Harmonic potential, Wave packet, Dipole moment, Optical strength function
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0048/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 251-253, by J-STAGE]
<Title:> Surface Adsorption Model Calculation Database and Its Application to Activity Prediction of Heterogeneous Catalysts
<Author(s):> Masato KOBAYASHI, Haruka ONODA, Yusuke KURODA, Tetsuya TAKETSUGU
<Corresponding author E-Mill:> k-masato(at)sci.hokudai.ac.
<Abstract:> The surface adsorption model calculation database, which we are constructing from systematic quantum chemical calculations, is reported. The database can be utilized to analyze heterogeneous catalytic reactions. As an application, we predicted the experimental catalytic activity for the methane steam reforming reaction with this database by using the sparse modeling techniques.
<Keywords:> Calculation database, Catalytic reaction, Methane steam reforming, Conversion rate, Sparse modeling
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0053/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.6, -, by J-STAGE]
<Title:> QM- and ONIOM-Molecular Dynamics Studies of the S_N2 Reaction. How Does the Rare Event Take Place?
<Author(s):> Toshiaki MATSUBARA
<Corresponding author E-Mill:> matsubara(at)kanagawa-u.ac.jp
<Abstract:> A model S_N2 reaction of 2-chlorobutane with OH^– is examined from the dynamical point of view by means of the molecular dynamics (MD) methods. The reactions are simulated in both the gas phase and the water solvent by the QM- and the ONIOM-MD methods, respectively. The MD simulations show that a migration of the kinetic energy between the atoms generated by the fluctuation of the kinetic energy of the atoms triggers the reaction. When some requirements of the velocity vector with a certain direction of the specific atoms participating in the reaction are satisfied by the migration of the kinetic energy, the substrate is led to the transition state and then to the product in turn. The time required to pass the transition state becomes shorter in the water solvent compared to the case of the gas phase, which shows that the reaction proceeds more quickly in the water solvent. Another pattern of the requirement of the velocity vector with a certain direction of the specific atoms for the reaction, which makes the reaction rate faster, is also found at a higher temperature in the water solvent.
<Keywords:> Molecular dynamics simulation, SN2 reaction, Requirement for the reaction, Solvent effect
<URL:> https://www.jstage.jst.go.jp/article/jccjie/6/0/6_2019-0006/_html

[Published online Journal of Computer Chemistry, Japan Vol.18, 244-247, by J-STAGE]
<Title:> 分子動力学法を用いた水/xNa₂O-(1-x)SiO₂ (x=0~0.5)ガラス界面の構造解析
<Author(s):> 星野　圭祐, 澤口　直哉
<Corresponding author E-Mill:> 18042073(at)mmm.muroran-it.ac.jp
<Abstract:> Weathering of glass is a problem because it degrades the optical performance of the glass. The weathering occurs when the glass has been contacted with water in the long-term. In this work, a water/glass interface model was prepared and molecular dynamics simulation was performed to investigate the structure and properties near the water/glass interface. The broken surface of the glass network at near the interface was confirmed by the distribution change of the Qⁿ species, and it suggests that the sodium ions are trapped by the destabilized glass surface structure.
<Keywords:> Molecular dynamics, Sodium silicate glasses, Water, Glass structure, Interface structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0052/_article/-char/ja/

[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/