カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.24, 80-82, by J-STAGE]
<Title:> SVDを用いた実時間TDDFTのスペクトル解析
<Author(s):> 谷　直樹, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> naoki.tani.7x(at)stu.hosei.ac.jp
<Abstract:> Optical spectrum prediction based on first-principles calculations is important for the development of optical materials. In particular, Time Dependent Density Functional Theory (TDDFT) in real-time is one of the most widely used calculation methods. In real-time TDDFT, the dynamic dipole moment is used to obtain the polarizability by Fourier transform (FT). The optical spectrum can be obtained from this polarizability. However, if the time length is not sufficient, the spectrum resolution depends on the length and becomes ambiguous. To solve this problem, we introduced Dynamic Mode Decomposition (DMD). This spectral analysis technique uses both Singular Value Decomposition and Proper Orthogonal Decomposition to obtain frequencies and intensities of spectrum. The signal frequency and the intensity are directly obtained. This method was applied to TDDFT time series data for ethylene and small molecules of benzene, naphthalene, anthracene, and tetracene. Compared to conventional FT, clear spectra were obtained from a short time series data.
<Keywords:> Keywords TDDFT, Dynamic Mode Decomposition (DMD), Fourier Transform (FT), Singular Value Decomposition (SVD), Real-time TDDFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0010/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 86-89, by J-STAGE]
<Title:> 親水性カーボンナノオニオンの溶媒抽出法に対する分子動力学計算による検討
<Author(s):> 守屋　祐輝, YEH　Jungwen, 内田　正哉
<Corresponding author E-Mill:> f5005ddf(at)sit.ac.jp
<Abstract:> Carbon nano-onions (CNOs) are concentric fullerene-like shells recognized for stability and versatility. We evaluated the liquid liquid extraction of hydroxylated CNOs in a toluene water system using molecular dynamics simulations. The analysis of trajectories, radial distribution functions (RDFs), and spatial distribution functions (SDFs) revealed that increasing the surface OH density decreases the coordination number of toluene, redistributes toluene molecules to non-functionalized patches, and alters their spatial distribution. Highly hydroxylated CNOs tended to reside in the water phase or at the interface. Collectively, these results identify surface OH density as the key determinant of solvent selectivity and phase distribution, enabling practical control of CNO partitioning during liquid liquid extraction.
<Keywords:> キーワード molecular dynamics, carbon nano-onions, hydroxylation, toluene water extraction, RDF, SDF.
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0019/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 83-85, by J-STAGE]
<Title:> Physics-Based Docking Complements AlphaFold-Multimer Based Selection in de novo Binder Design: A HER2 Affibody Case Study
<Author(s):> Masatomo GO, Motoki INOUE, Takefumi YAMASHITA
<Corresponding author E-Mill:> yamashita.takefumi(at)hoshi.ac.jp
<Abstract:> Accurate antigen binder interfaces are critical for de novo campaigns that use AlphaFold-Multimer (AFM) in selection. In the HER2 ZHER2 affibody case, AFM produced correct monomer folds but placed the binder at a non-native site. Inter-chain Predicted Aligned Error indicated low interface confidence for the AFM complexes. By contrast, a physics-based workflow combining ZDOCK, RMSD-based clustering, and HADDOCK refinement recovered near-native interfaces. These observations indicate that physics-based docking may serve as a complementary approach to AFM-based selection.
<Keywords:> De novo binder design, AlphaFold-Multimer, Docking, Affibody, HER2
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0013/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 零磁場分裂を考慮した軸対称スピン四重項状態における角度依存磁化の厳密解
<Author(s):> 細川　恵美, 大宮　陽斗, 藤井　翔, 金井塚　勝彦, 三橋　了爾, Muddassir　Mohd, Liu　Jianqiang, 﨑山　博史
<Corresponding author E-Mill:> jianqiangliu2010(at)126.com
<Abstract:> In paramagnetic materials with multiple unpaired electrons per magnetic center, even when the ground state has no first-order orbital angular momentum, structural anisotropy around the magnetic center gives rise to zero-field splitting and g-factor anisotropy, resulting in magnetic anisotropy. This paper presents an exact algebraic expression for the angle-dependent magnetization in the axially symmetric spin-quartet (S = 3/2) ground state without first-order orbital angular momentum, taking into account zero-field splitting and g-factor anisotropy. The use of this angle-dependent expression enables accurate and rapid simulations of magnetic anisotropy, particularly for powder averaging of magnetization. The study also includes simulations of anisotropic saturation magnetization curves, cross-sectional views of angle-dependent magnetization, and three-dimensional representations of magnetization. Furthermore, the powder average and arithmetic average of anisotropic magnetization have been compared, and the circumstances under which powder average calculations are necessary have been discussed.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2025-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 77-79, by J-STAGE]
<Title:> Nonlocal Modulation of Antigen Antibody Interactions Underlying A107R-Mediated Affinity Gain in VHH D2-L29: MD Simulations with MM-PBSA Based Thermodynamic Analysis
<Author(s):> Rika MUNAKATA, Motoki INOUE, Takefumi YAMASHITA
<Corresponding author E-Mill:> yamashita.takefumi(at)hoshi.ac.jp
<Abstract:> Single-domain VHH antibodies offer attractive developability, but rational affinity improvement requires atomistic insight into how sequence changes reshape binding. We investigated the A107R substitution in VHH D2-L29 bound to hen egg-white lysozyme using long-timescale molecular dynamics simulations with MM-PBSA based thermodynamic analysis. Computed binding free energies recapitulated the experimentally observed increase in affinity. Per-residue decomposition of the change in binding free energy indicated that residue 107 (A107R) and Tyr100 had the largest favorable changes, whereas Asn102 had the largest unfavorable change. Together, the results indicate that molecularly detailed, interface-wide analysis of nonlocal interaction changes is essential for rationally engineering VHH variants with enhanced affinity.
<Keywords:> VHH, nanobodies, Molecular dynamics simulations, MM-PBSA, Affinity enhancement
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/3/24_2025-0015/_article/-char/ja/

[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/