カテゴリー: 未分類

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 環状メタノール4分子クラスターの配座異性体
<Author(s):> 大古　善久, 長嶋　雲兵
<Corresponding author E-Mill:> y-ohko(at)aist.go.jp
<Abstract:> メタノール4分子の環状クラスター(CH₃OH)₄のOH基とCを同一面内に配置した初期構造から構造最適化計算を行った．HF/STO-3Gでは，初期構造のO-O間距離が2.7 以上の場合に最安定構造が高い頻度で得られる．O-O間距離が短い場合には他の安定な配座異性体が2種類得られる．この約2.7 の距離はOH基の水素結合力の範囲を示唆する．HF/6-31G (d)では，虚振動を持つ平面構造で収束する．B3LYP/6-31G (d)では，メチル基が環面外の同じ側に向いた構造で収束する．これらの結果は，酸素の非共有電子対の軌道の広がりによる安定化とメチル基の反発力の均衡から説明でき，配座異性体同士の変換傾向を反映する．計算過程で力定数を計算(calcall)すると初期O-O間距離に関わらず最安定構造が得られる．
<Keywords:> methanol, cyclic cluster, starting structure, hydrogen-bonding, conformers
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2022-0031/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 水酸基末端チタン二量体構造の電子状態
<Author(s):> 大古　善久, 長嶋　雲兵
<Corresponding author E-Mill:> y-ohko(at)aist.go.jp
<Abstract:> 酸化チタン光触媒の表面反応を理論計算で考察する時に，従来から用いられている平面型チタン二量体モデルの電子状態を調べた．用いた計算方法はB3LYP/6-311Gで，末端を水酸基化した初期構造(Ti₂O₆H₄)を最適化計算した．水酸基の初期の配向によって結果が異なり，非平面構造を取り易いことがわかった．また，HOMOとLUMOのエネルギー準位の比較から，光触媒反応の酸化力と還元力に水素の位置が重要であることがわかった．チタン二量体モデルのみでは電子状態の記述に無理があり，周辺構造を含めた新しい表面モデルの構築が必要であることが示唆された．
<Keywords:> TiO2 photocatalysis, Ti2O6H4, surface model, frequency, B3LYP/6-311G
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2022-0032/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> ケイ酸塩溶融体/ガラスのMD計算について- 無機物の分子シミュレーション-
<Author(s):> 河村　雄行
<Corresponding author E-Mill:> kawamura.k.ah(at)m.titech.ac.jp
<Abstract:> 無機化合物のMD計算を念頭において，高分子様の構造を持つ無機凝集体について構造などの概要を示し，古典分子動力学法による2元系ケイ酸塩溶融体/ガラスの計算における構造緩和の問題を述べる．また無機凝集体のMD計算の困難さ，意義，および必要性について述べる．
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2022-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 61-62, by J-STAGE]
<Title:> Na冷却高速炉におけるNa中での水素の存在形態に着目した挙動推定
<Author(s):> 畠山　望, 三浦　隆治, 宮本　直人, 宮本　明, 荒　邦章, 下山　一仁, 加藤　篤志, 山本　智彦
<Corresponding author E-Mill:> hatakeyama(at)aki.niche.tohoku.ac.jp
<Abstract:> In the cooling system of sodium-cooled fast reactors, it is required to identify and rapidly detect hydrogen explosively produced by the sodium-water reaction when a water leak occurs due to damage of a heat exchanger tube in a steam generator (SG), in contrast to low-concentration background hydrogen permeating through SG tubes during normal operation. In the present study, we focus on the difference between the background hydrogen and the hydrogen generated by the sodium-water reaction, and theoretically estimate the hydrogen behavior in liquid sodium by using computational chemistry methods. We find that dissolved H or NaH, rather than H₂, is the predominant form of the background hydrogen in liquid sodium, and that hydrogen produced in large amounts by the sodium-water reaction can exist stably as fine bubbles with a NaH layer on their surface.
<Keywords:> Sodium-cooled fast reactor (SFR), Steam generator (SG), Sodium-water reaction, Hydrogen detection, Ultra-accelerated quantum chemical molecular dynamics (UA-QCMD)
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 55-57, by J-STAGE]
<Title:> Structural Symmetry and Spin Multiplicity of Sumanene Derivative Radical Molecules
<Author(s):> Yuika BABA, Hidehiro SAKURAI, Azusa MURAOKA
<Corresponding author E-Mill:> muraokaa(at)fc.jwu.ac.jp
<Abstract:> π-conjugated carbon molecules such as fullerenes and carbon nanotubes have attracted great interest because of their potential applications as electronic materials and catalysts. Among these molecular frameworks, fullerene substructures of sumanene molecules with C_3v symmetry are expected to form vertical columnar crystal structures and exhibit a range of conduction properties. Various syntheses of molecules with extended π-conjugation at the benzyl position of sumanene have now been reported. However, there are no examples of open-shell systems with extended sumanene features. In this study, we use the results of DFT calculations to discuss the relationship between molecular conformational symmetry and spin multiplicity in a new, extended open-shell system of sumanenes by adding a phenyl group at the benzyl position.
<Keywords:> Sumanene derivatives, Radical molecules, Molecular symmetry, Spin multiplicity, DFT calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 58-60, by J-STAGE]
<Title:> 化学実験画像データセットの作成と物体検出の数値検証
<Author(s):> 佐々木　良輔, 藤波　美起登, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> In recent years, the remarkable advances in artificial intelligence technology have led to digital transformation (DX) in various fields. The automated construction of laboratory notebook through filming experiments is a promising application of image recognition for chemistry． In this study, we created an image dataset of chemical experiment, which contains 2376 images and consists of 7 classes of objects. Object detection methods and a multiple object tracking method were implemented and assessed using the dataset toward to develop automated laboratory notebook system.
<Keywords:> Machine learning, Object detection, Multiple object tracking, Laboratory notebook, Chemical experiment
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0025/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 52-54, by J-STAGE]
<Title:> 密度汎関数法におけるSCF計算条件の最適化による高速化
<Author(s):> 大田　栄二, 白幡　晃一, 石川　敦之
<Corresponding author E-Mill:> eiji(at)fujitsu.com
<Abstract:> Density functional theory (DFT) is a successful theory for calculating the electronic structure of atoms, molecules, and solids. However, in modern computing environments is difficult significantly improve the computational efficiency of DFT. Acceleration of DFT requires optimization of the computational algorithms. We demonstrate two acceleration methods by optimization of the computational algorithms that optimize parallel parameters for eigenvalue calculations and optimization of convergence conditions for the self-consistent field (SCF) calculation.
<Keywords:> Density functional theory, Self-consistent field, Eigenvalue calculation, Convergence conditions, Optimization
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0027/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> A Tautomerization Software Based on Lewis Structures and Reaction Mechanisms
<Author(s):> Ming YU
<Corresponding author E-Mill:> yuming086(at)gmail.com
<Abstract:> A new method is proposed to translate molecule Lewis structures to machine-readable format data and a software based on Lewis structures has been developed to simulate the practice of chemists writing tautomerization mechanisms. For a tautomeric compound, from one Lewis formula entered by users, the software can generate its other equivalent tautomer (s), which share a common tautomerization intermediate stabilized by resonance. Not only atom balance but also electron balance are guaranteed in the tautomerism representation. The stereochemistry changes caused by tautomeric equilibrium can be tracked too. All the stereoisomers for the compounds containing tetrahedral carbon stereocenters and double bond stereocenters can be identified.
<Keywords:> Tautomerization, Software, Stereochemistry, Lewis structure, Mechanism
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0050/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Calculus of Several Harmonic Functions
<Author(s):> Kazuhiro ISHIDA
<Corresponding author E-Mill:> k-ishida(at)fancy.ocn.ne.jp
<Abstract:> Abstract: We describe several harmonic functions; the solid harmonics (SH), the mixed SH, the reducing SH and the reducing mixed SH. We do the solid harmonic gradient (SHG) operator. Using the SHG, we derive a new Gauss-transform and a new Fourier-transform for real-type general Slater-type orbitals (STO). Several formulas can be derived for the calculus of harmonic functions. They will be useful especially for evaluating the angular part of molecular integrals over STOs and over Gaussian-type orbitals with higher-angular-momenta.Keywords: Several harmonic functions; Molecular integrals; Solid harmonics; Higher-angular-momenta; Slater-type orbital; Solid harmonic gradient.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0029/_html

[Published online Journal of Computer Chemistry, Japan Vol.21, 48-51, by J-STAGE]
<Title:> COVID-19の経口治療薬開発に向けたハイブリッド型in Silico創薬
<Author(s):> 小清水　初花, 小野　純一, 福西　快文, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Hybrid in silico drug discovery was performed by combining large-scale quantum molecular dynamics (QMD) simulations with the conventional in silico drug discovery, focusing on developing covalent inhibitors against the main protease (M^pro) of SARS-CoV-2, the virus responsible for ongoing COVID-19 pandemic. The crystal structures and instantaneous structures obtained from the large-scale QMD simulations for M^pro were used as receptors in ensemble docking to estimate the binding affinities of the four ligands: the natural substrate recognized by M^pro, that recognized by the other enzyme of SARS-CoV-2, approved covalent inhibitor (PF-07321332), and the new candidate compound X determined from virtual screening. The present result shows that the binding affinity of X was comparable to that of PF-07321332, demonstrating the potency of our drug discovery.
<Keywords:> COVID-19, In silico drug discovery, Quantum molecular dynamics, Main protease, Covalent drug
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0029/_article/-char/ja/