カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.24, 39-45, by J-STAGE]
<Title:> 直線分子の計算分子分光学: パラダイムシフトへの挑戦
<Author(s):> 平野　恒夫, 長嶋　雲兵, 馬場　正昭
<Corresponding author E-Mill:> hirano(at)nccsk.com
<Abstract:> [Abstract] In conventional molecular spectroscopy, the viewpoint of how Nature (the world of Schr dinger equation) is observed has been lacking. We have asserted a new paradigm: In Nature the vibrationally averaged structure of a linear molecule is linear, but on observation, it is recognized as being bent. This new paradigm is substantiated by 1) the theoretically-derived expectation value for the deviation-angle from linearity, and the r₀ structure derived from the experimental rotational constant B_0,eff, 2) the non-zero b-axis component of dipole moment, 3) the elucidation of the so-called shrinkage effect in electron diffraction, 4) the too-short C≡N bond lengths in FeNC, CoCN, and NiCN, 5) the unusual relation r_0,eff < r_e for some linear molecules showing large amplitude bending motion, and 6) the vibrationally averaged structure of benzene (explanation of the unexpected relation r_0,eff(C H) r_0,eff(C D) and prediction of the planar but non-flat r₀ structure). Hence, a paradigm shift is requested.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/2/24_2021-0049/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 58-67, by J-STAGE]
<Title:> 化学勾配の緩和過程に基づくゾウリムシの長距離後退遊泳行動モデリング
<Author(s):> 宇座　恩, 砂川　泰也, 國田　樹
<Corresponding author E-Mill:> kunita(at)ie.u-ryukyu.ac.jp
<Abstract:> 本研究は，ゾウリムシの空間適応行動を化学勾配の緩和過程に基づいて数理モデルで再現することを目的とした．ゾウリムシは，細長い空間内で障害物に衝突した際，短距離の後退遊泳を繰り返しながら徐々に後退距離を伸ばし，最終的に3-4 mmの長距離後退遊泳を発現する．この行動は細胞内外の化学勾配が膜電位を変化させ，繊毛運動の方向と頻度を制御することで生じる．そこで，膜電位動態と繊毛運動の関係を定式化した運動モデルを膜電位モデルに統合した数理モデルを構成した．数値シミュレーションにより，カルシウムイオンチャネルの遅い応答に加えて，後退遊泳を引き起こすカルシウム電流の閾値が動的に変化する仕組みを導入することで，短距離後退遊泳から1 mm程度までの長距離後退遊泳への移行過程の一部を再現できた．これにより，ゾウリムシは単に化学勾配に受動的に応答するだけでなく，膜電位と繊毛運動のダイナミクスを通じた内因的な制御メカニズムを備えた適応能を備えていることが示唆された．
<Keywords:> chemical gradients, membrane potential, Paramecium, ciliary reversal, Hodgkin Huxley model
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/2/24_2024-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 46-57, by J-STAGE]
<Title:> 化学勾配に駆動される膜興奮動態による単細胞生物ゾウリムシの障害物衝突に対する行動応答モデル
<Author(s):> 大嶺　志歩, 國田　樹
<Corresponding author E-Mill:> kunita(at)ie.u-ryukyu
<Abstract:> 本研究は，生物の柔軟な行動を生み出す情報処理システムの本質的原理を化学勾配に基づく数理モデルで表現することを目的とした．単細胞生物の繊毛虫ゾウリムシが障害物に衝突した際の行動応答を生物実験により調べた結果，ゾウリムシは衝突後すぐに方向転換する行動と，障害物に沿って移動した後に方向転換する行動を示した．これらの行動を生じた時の衝突時の角度や速度は同じであったが，直前の角度変化の符号が異なっていた．ゾウリムシの行動は，体表に生えた繊毛運動によって制御され，それは細胞内外の化学勾配に従って生じる膜興奮動態によって調整される．この膜興奮動態と行動とを対応づける数理モデルを構成し，数値シミュレーション実験を行った．その結果，実験結果と同様にゾウリムシが障害物に衝突する前の角度変化の符号の違いで2つの行動を再現できた．つまり，ゾウリムシは同じ化学勾配状態でも，直前の角度変化という運動履歴の違いによって異なる行動を生じる柔軟性を有していた．
<Keywords:> membrane excitation dynamics, chemical gradients, Paramecium, ciliary movement, FitzHugh-Nagumo model
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/2/24_2024-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.11, -, by J-STAGE]
<Title:> Accuracy of Hartree Fock Energies and Physical Properties Calculated Using Lambda Functions for Helium, Lithium, and Beryllium Atoms
<Author(s):> Yasuyo HATANO, Shigeyoshi YAMAMOTO
<Corresponding author E-Mill:> syamamot(at)lets.chukyo-u.ac.jp
<Abstract:> Multiple-precision Hartree Fock equations are solved for the ground states of the He, Li, and Be atoms and highly accurate wave functions are determined. The numbers of significant figures of the total energies are 66 for He, 43 for Li, and 43 for Be. The Lambda function, which is a Laguerre-type basis and can be used to construct a complete orthonormal system, acts as the basis function. Using the resulting Hartree Fock wave functions, nucleus-electron cusp conditions are also calculated. Their significant figures are 30 for He, 19 for Li, and 19 for Be, in close proportion to the numbers of significant figures for the total energies. In fact, the ratios are 0.45, 0.44, and 0.44, respectively. The radial expectation values, < rⁱ > (i = -2, -1, 1, … 9), are also investigated. It is verified that the computational accuracy varies depending on the physical property.
<Keywords:> Number of significant figures, Arbitrary precision package, Hartree Fock limit, Cusp condition, Complete orthonormal system, Laguerre-type basis function
<URL:> https://www.jstage.jst.go.jp/article/jccjie/11/0/11_2024-0032/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.11, -, by J-STAGE]
<Title:> Development of Coarse-Grained Molecular Dynamics Simulation Model to Elucidate the Wear Behavior of Concentrated Polymer Brushs
<Author(s):> Yukihi HARA, Yusuke OOTANI, Shuichi UEHARA, Arisa CHIBA, Shogo FUKUSHIMA, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> yusuke.ootani.e1(at)tohoku.ac.jp
<Abstract:> To elucidate the micro-scale wear mechanisms of concentrated polymer brushes (CPB), we developed a coarse-grained molecular dynamics (CGMD) model of CPB-against-slider sliding simulation with an explicit solvent. Under good solvent conditions, the CPB swelled. The thickness of the swollen CPB reached approximately 77% of the fully stretched length, which is in close agreement with the experimentally determined range for swollen film thicknesses of CPB. The validity of the developed model was evaluated through a sliding simulation. The simulation analysis showed that the wear of the CPB can involve multiple factors, such as contact with the slider, solvent flow, and interactions between polymer chains. This indicates that the simulation model allows us to analyze not only the wear caused by direct contact with the slider but also the wear caused by solvent flow.
<Keywords:> Concentrated Polymer Brushs, Wear, Coarse-Grained Molecular Dynamics, Tribology, Polymer
<URL:> https://www.jstage.jst.go.jp/article/jccjie/11/0/11_2024-0036/_html

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 化学勾配に駆動される膜興奮動態による単細胞生物ゾウリムシの障害物衝突に対する行動応答モデル
<Author(s):> 大嶺　志歩, 國田　樹
<Corresponding author E-Mill:> kunita(at)ie.u-ryukyu
<Abstract:> 　本研究は，生物の柔軟な行動を生み出す情報処理システムの本質的原理を化学勾配に基づく数理モデルで表現することを目的とした．単細胞生物の繊毛虫ゾウリムシが障害物に衝突した際の行動応答を生物実験により調べた結果，ゾウリムシは衝突後すぐに方向転換する行動と，障害物に沿って移動した後に方向転換する行動を示した．これらの行動を生じた時の衝突時の角度や速度は同じであったが，直前の角度変化の符号が異なっていた．ゾウリムシの行動は，体表に生えた繊毛運動によって制御され，それは細胞内外の化学勾配に従って生じる膜興奮動態によって調整される．この膜興奮動態と行動とを対応づける数理モデルを構成し，数値シミュレーション実験を行った．その結果，実験結果と同様にゾウリムシが障害物に衝突する前の角度変化の符号の違いで2つの行動を再現できた．つまり，ゾウリムシは同じ化学勾配状態でも，直前の角度変化という運動履歴の違いによって異なる行動を生じる柔軟性を有していた．
<Keywords:> membrane excitation dynamics, chemical gradients, Paramecium, ciliary movement, FitzHugh-Nagumo model
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2024-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 36-38, by J-STAGE]
<Title:> Givens回転と誤差逆伝播法を組み合わせた自己無撞着場計算の高効率収束法の開発
<Author(s):> 大島　玲生, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We have recently proposed a highly efficient convergence method for self-consistent (SCF) calculations combining Givens rotation and error back-propagation (EBP) algorithms, referred to as direct Givens rotation (DGR) method [J. Chem. Phys. 162, 014108 (2025)]. The Givens rotation corresponds to unitary transformations that guarantee the orthogonality of molecular orbitals. Complicated gradients constructed through sequential Givens rotations were computed using the EBP technique without deriving explicit forms. This article reviews the proposed DGR method and compares it with conventional methods such as the standard SCF procedure, the second-order SCF method, and the direct inversion in iterative subspace technique for H₂O molecule. The DGR method exhibited a convergence speed comparable to that of the SOSCF method while achieving a lower and more reliable energy.
<Keywords:> キーワード self-consistent field, direct minimization, Givens rotation, error back-propagation, Hartree-Fock, Kohn-Sham density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2025-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 18-24, by J-STAGE]
<Title:> 立体電子状態の定量評価による求核反応の面選択性の起源の解明
<Author(s):> 坂口　大門, 五東　弘昭
<Corresponding author E-Mill:> gotoh-hiroaki-yw(at)ynu.ac.jp
<Abstract:> 化学反応の反応性や選択性の起源の解明は学術的に興味深いだけでなく，反応を制御するうえでも重要である．我々は最近，環状ケトンの立体的な電子状態を定量評価して求核反応の面選択性を定量的に説明し解釈する新しい方法を提案した [1]．本稿では日本コンピュータ化学会2024年秋季年会での口頭発表の内容 [2] に基づき，化学反応と立体電子状態に関するこれまでの研究と，我々が開発した新しい方法について紹介する．
<Keywords:> Keywords ketone, nucleophilic addition, π-facial selectivity, QSSR, data-driven chemistry
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 27-29, by J-STAGE]
<Title:> PdおよびAgRh合金ナノクラスターへの水素吸収と拡散に関する相対論的量子化学計算分子動力学シミュレーション
<Author(s):> 木村　愛花, 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> Molecular dynamics simulations of hydrogen absorption and diffusion in Pd and AgRh alloy nanoclusters were performed. Parameters for atomic interaction potentials were determined from relativistic quantum chemical calculations. Although Rh is known not to absorb hydrogen in bulk, the Rh-H interaction strength obtained from the calculations was about 80% of that of the Pd-H. Using the parameters obtained, molecular dynamics simulations were performed. Molecular dynamics simulations of AgRh clusters with different Ag:Rh ratio have shown no significant difference in the Rh-Rh distance distribution at the nearest neighbor except for Ag₇₀Rh₃₀. However, at the second nearest neighbor the distance increased as the Ag fraction increased.
<Keywords:> Keywords Molecular dynamics simulation, Relativistic Quantum Chemical Calculations, Hydrogen-absorbing metal nanoclusters
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 30-35, by J-STAGE]
<Title:> Predicting CO Adsorption on Multi-elemental Alloy through Machine Learning Analysis of Ternary Components
<Author(s):> Susan Menez ASPERA, Gerardo ALADEZ HUERTA, Yusuke NANBA, Kaoru HISAMA, Michihisa KOYAMA
<Corresponding author E-Mill:> aspera_susan(at)shinshu-u.ac.jp
<Abstract:> Surface-molecule interaction has always been an integral part in the analysis of reactions and surface reactivity in heterogenous catalysis. With the advent of computational resource advancement, the search for the next generation catalysts explores the combination of several metal elements in the multi-elemental nanoparticles (NP). However, with the complexity of the catalysts’ surface comes the difficulty of understanding surface-molecule interaction and methods to overcome this should be considered. In our previous study, we used metal-coordination to predict CO adsorption on the ternary alloy combinations. This method describes the adsorption site by the network of metal elements interacting with the site that contributes to the change in its electronic properties. Since this network considers up to the neighbor of the first nearest neighbor of the adsorption site, in this study, we considered to use the dataset of regression coefficient of ternary alloy combinations to predict molecular adsorption on a multi-elemental NP. We tested the method on CO molecular adsorption on the quaternary RuRhIrPt NP and used the regression coefficient obtained from RuRhPt, RhIrPt, RuIrPt and RuRhIr ternary alloy. Results show that the predicted values of CO adsorption energy on the RuRhIrPt NP have comparable values of coefficient of determination (R²) and mean absolute error (MAE) with the prediction of CO adsorption on ternary alloy. Thus, this method could pave the way for predicting molecular adsorption on multi-elemental NP using only the dataset of regression coefficient from ternary alloy combinations and the atomic configurational structure of the multi-elemental NP.
<Keywords:> Multi-elemental nanoparticle alloy, Machine learning, Generalized coordination number, Adsorption prediction
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2025-0002/_article/-char/ja/