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JCCJ Editorial Office, 日本コンピュータ化学会 JCCJ 編集室：埼玉県さいたま市桜区下大久保255 埼玉大学理工学研究科　太刀川研究室, Saitama-shi (2024)

12/01/2024

量子多体系ダイナミクスシミュレータの構築戸畑　海研, 石田　邦夫 ishd_kn(at)cc.utsunomiya-u.ac.jp We propose a quantum dynamics simulator for light-irradiated matter. As the coherent control of the quantum states of matter is an intriguing problem in realizing quantum technology, the quantum properties of light-matter complexes have attracted much attention. Theoretical calculations corresponding to individual experimental configurations are required to understand these properties, and simulation methods that flexibly adapt to various experimental configurations are required....

http://jccj.sakura.ne.jp/wordpress/archives/1240

[Published online Journal of Computer Chemistry, Japan …

21/12/2023

Theoretical Analysis of the Aggregation-Inhibition Effect of Arginine on Polyglutamine Protein by the Generalized-Ensemble Method Shoichi TANIMOTO, Hisashi OKUMURA sktanimoto(at)ims.ac.jp The aggregation of polyglutamine (polyQ) proteins, which have the abnormal expansion of glutamine repeats, is a critical pathological hallmark of polyQ diseases. Experimental studies have shown an amino acid arginine uniquely inhibits the polyQ-protein aggregation....

http://jccj.sakura.ne.jp/wordpress/archives/1235

[Published online Journal of Computer Chemistry, Japan …

21/12/2023

化学系特許中の表及びテキストからの材料知識データ抽出我妻　正太郎, 竹内　理 shotaro.agatsuma.hd(at)hitachi.com Material Informatics (MI) needs large amount of data about materials. However, the cost of data extraction is very high. Therefore, chemical researchers are interested in technology to automatically extract the data from published documents such as patents. Previous technologies can extract the data from text in patents, but not tables....

http://jccj.sakura.ne.jp/wordpress/archives/1233

[Published online Journal of Computer Chemistry, Japan …

21/12/2023

電子状態インフォマティクスによるα-glucosidase阻害剤の探索立石　優輔, 杉本　学 The molecular descriptor set suggested in electronic-structure informatics (ESI) was applied to predict activity of potential candidates of α-glucosidase inhibitors. In this study, we constructed a regression model for predicting the pIC50 values of the known inhibitors registered in the ChEMBL database. The obtained regression model reasonably reproduced the experimental values. After refinement of the model, we conducted in silico screening to search for active inhibitors drugs from a natural product database, called KampoDB, for traditional Japanese medicine....

[Published online Journal of Computer Chemistry, Japan …

08/12/2023

量子化学計算と各種スペクトル情報を用いた化合物の自動同定手法の開発熊谷　拓海, 中嶋　裕也, 清野　淳司 j-seino(at)aoni.waseda.jp Recent practical application of automated experiments using robotics, high-throughput experiments, and artificial intelligence technology has been progressing rapidly. In automated experiments, molecular identification is an important process for obtaining structural information on synthesized compounds and understanding their reactivity and chemical properties. In this study, we developed a system for automated molecular identification....

http://jccj.sakura.ne.jp/wordpress/archives/1229

[Published online Journal of Computer Chemistry, Japan …

08/12/2023

タンパク質に関する FMO-DPD シミュレーション用パラメータ算定と試行太刀野　雄介, 土居　英男, 奥脇　弘次, 平野　秀典, 望月　祐志 fullmoon(at)rikkyo.ac.jp We have been promoting a project to evaluate the set of effective interaction parameters used in dissipative particle dynamics (DPD) simulations for all amino acid residues covering various proteins, based on fragment molecular orbital (FMO) calculations. This simulation protocol has been termed FMO-DPD....

http://jccj.sakura.ne.jp/wordpress/archives/1227

[Published online Journal of Computer Chemistry, Japan …

28/11/2023

光活性イエロータンパク質の光反応サイクルにおけるtrans-cis光異性化過程の量子的分子動力学シミュレーション解析石田　賢亮, 西村　好史, 中井　浩巳 nakai(at)waseda.jp This study focused on the trans-cis photoisomerization process of p-coumaric acid (pCA) in photoactive yellow protein (PYP), which is an initial step of the photocycle. Quantum molecular dynamics simulations for the whole PYP system were performed using the divide-and-conquer density functional tight-binding method. The hydrogen bond between Glu46 and pCA was clarified to be shorter than that of the initial structure, which hinders the hula-twist isomerization process for structures after passing through the conical intersection....

http://jccj.sakura.ne.jp/wordpress/archives/1225

[Published online Journal of Computer Chemistry, Japan …

12/10/2023

Improvement of Blood-Brain Barrier Permeability Prediction Using Cosine Similarity Hiroshi SAKIYAMA, Ryushi MOTOKI, Takashi OKUNO, Jian-Qiang LIU saki(at)sci.kj.yamagata-u.ac.jp Prediction of blood-brain barrier permeability for chemicals is one of the key issues in brain drug development. In this study, the effect of using training data relatively similar to the test data was investigated in order to improve the performance of machine learning methods in predicting blood-brain barrier permeability....

http://jccj.sakura.ne.jp/wordpress/archives/1223

[Published online Journal of Computer Chemistry, Japan …

20/08/2023

電子を描く(12) ― 炭素原子のsp3, sp2, sp混成軌道時田　澄男 sumio.tokita(at)gmail.com 炭素原子をはじめとする多電子原子を原子価結合法で取り扱い，原子価状態の軌道関数を表す方法である混成軌道が，原子軌道の線形結合によってどのような数式で表され，それらの数式を可視化するいろいろな方法によってどのように描かれるかを紹介した． many electron atom, atomic orbital, covalent bond, valence state, valence bond theory, molecular orbital method, valence state electron pair repulsion

http://jccj.sakura.ne.jp/wordpress/archives/1221

[Published online Journal of Computer Chemistry, Japan …

20/08/2023

電子を描く(13) ― 混成軌道による分子の組立，σ結合とπ結合時田　澄男 sumio.tokita(at)gmail.com 混成軌道を用いて，ルイスの電子対共有結合の概念にどのようにして同等性(等価性)や方向性を加味できるかを，簡単な分子を例にとって示す．σ電子とπ電子のちがい，π電子が核磁気共鳴スペクトルのケミカルシフトに及ぼす影響についても解説した． covalent bond, valence state, valence bond theory, molecular orbital method, hybrid orbital, resonance, difference electron density, NMR spectroscopy, ring current.

http://jccj.sakura.ne.jp/wordpress/archives/1219

[Published online Journal of Computer Chemistry, Japan …

20/08/2023

環状メタノール4分子クラスターの配座異性体大古　善久, 長嶋　雲兵 y-ohko(at)aist.go.jp 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． methanol, cyclic cluster, starting structure, hydrogen-bonding, conformers

http://jccj.sakura.ne.jp/wordpress/archives/1217

[Published online Journal of Computer Chemistry, Japan …

20/08/2023

水酸基末端チタン二量体構造の電子状態大古　善久, 長嶋　雲兵 y-ohko(at)aist.go.jp 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． TiO2 photocatalysis, Ti2O6H4, surface model, frequency, B3LYP/6-311G

http://jccj.sakura.ne.jp/wordpress/archives/1215

[Published online Journal of Computer Chemistry, Japan …

08/08/2023

電子を描く(12) ― 炭素原子のsp3, sp2, sp混成軌道時田　澄男 sumio.tokita(at)gmail.com 炭素原子をはじめとする多電子原子を原子価結合法で取り扱い，原子価状態の軌道関数を表す方法である混成軌道が，原子軌道の線形結合によってどのような数式で表され，それらの数式を可視化するいろいろな方法によってどのように描かれるかを紹介した． Keywords many electron atom, atomic orbital, covalent bond, valence state, valence bond theory, molecular orbital method, valence state electron pair repulsion

http://jccj.sakura.ne.jp/wordpress/archives/1213

[Advanced Published online Journal of Computer Chemistr…

08/08/2023

電子を描く(13) ― 混成軌道による分子の組立，σ結合とπ結合時田　澄男 sumio.tokita(at)gmail.com 混成軌道を用いて，ルイスの電子対共有結合の概念にどのようにして同等性(等価性)や方向性を加味できるかを，簡単な分子を例にとって示す．σ電子とπ電子のちがい，π電子が核磁気共鳴スペクトルのケミカルシフトに及ぼす影響についても解説した． covalent bond, valence state, valence bond theory, molecular orbital method, hybrid orbital, resonance, difference electron density, NMR spectroscopy, ring current.

http://jccj.sakura.ne.jp/wordpress/archives/1211

[Advanced Published online Journal of Computer Chemistr…

19/07/2023

Implementation of Wang-Landau Algorithm for Probing Thermodynamic Stable Configuration of Multi-Element Materials and Application to Multinary Alloy Nanoparticles Yusuke NANBA, Michihisa KOYAMA nanba(at)shinshu-u.ac.jp With an increase in an element, the configurational entropy effect stabilizes the multi-element materials. However, the expansion of configuration space and heterogeneous surfaces such as nanoparticles preclude the analytical evaluation of configurational entropy....

http://jccj.sakura.ne.jp/wordpress/archives/1209

[Published online Journal of Computer Chemistry, Japan …