Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.24, 69-71, by J-STAGE]
<Title:> クロメン誘導体の異性化反応に対する遷移パスサンプリング解析
<Author(s):> 重光　保博, 大賀　恭
<Corresponding author E-Mill:> yshige(at)nagasaki-u.ac.jp
<Abstract:> Chemical reactions with many degrees of freedom are governed by dynamic coupling between fast reaction modes and slow fluctuation ones, particularly in condensed phases. Although this coupling effect is absent when the system maintains chemical equilibrium throughout the reaction, the dynamic effect in solution can be clearly observed under extremely high-pressure conditions where the disparity in intrinsic timescales becomes large enough to disrupt chemical equilibrium between the solute and solvent. In the present study, we computationally investigate the dynamic coupling effect in the ring-closing reaction of chromene (naphtho[2,1-b]pyran), employing a simulation-based approach (Transition Path Sampling: TPS) combined with non-equilibrium reaction theory.
<Keywords:> キーワード Reaction Rate Theory, Non-Equilibrium, Transition Path Sampling, Reaction Coordinate, Committor
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0009/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 74-76, by J-STAGE]
<Title:> 味覚受容体タンパク質―アミノ酸リガンド複合体における構造変化とゆらぎの分子動力学シミュレーション解析
<Author(s):> 荒木　貴絵, 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> Molecular dynamics simulations were performed on the ligand-bound taste receptor proteins T1r2a-T1r3, followed by principal component analysis (PCA). PCA confirmed that ligand binding induces opening and closing motion of the lower part of the protein (the part closer to the cell membrane), with significant movement particularly in T1r3. The free energy landscape revealed features of metastable states reflecting this movement. These results suggest that the movement of T1r3 induced by ligand binding may play an important role in triggering signal transmission to the transmembrane region of the taste receptor.
<Keywords:> Keywords Molecular dynamics simulation, Taste receptor protein, Principal component analysis, Free energy landscape
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 72-73, by J-STAGE]
<Title:> PIMD法によるBiuretおよびBiguanideの分子内水素結合構造に対する原子核量子効果の解析
<Author(s):> 西川　琴美, 田中　輝, 桑畑　和明, 立川　仁典, 宇田川　太郎
<Corresponding author E-Mill:> udagawa.taro.f1(at)f.gifu-u.ac.jp
<Abstract:> We focus on the specific features of biuret and biguanide, which adopt a six-membered ring structure via intramolecular hydrogen bonds. The proton donor and acceptor atoms differ between the two molecules, leading to distinct energy barrier heights for proton transfer. To investigate the relationship between proton transfer and the π-electron delocalization within the six-membered ring framework, we performed path integral molecular dynamics (PIMD) simulations. The results show that the π-electrons in the framework are delocalized regardless of the ease of intramolecular proton transfer.
<Keywords:> Keywords Path integral molecular dynamics, Nuclear quantum effects, Intramolecular proton transfer
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0011/_article/-char/ja/

[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/