Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.22, 28-30, by J-STAGE]
<Title:> 量子多体系ダイナミクスシミュレータの構築
<Author(s):> 戸畑　海研, 石田　邦夫
<Corresponding author E-Mill:> ishd_kn(at)cc.utsunomiya-u.ac.jp
<Abstract:> 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. In this paper, we propose a quantum dynamics simulation method that encompasses program modules corresponding to light sources, optical components, material systems, and the evaluation of physical properties. We demonstrate the entanglement generation dynamics between two spin-chains via irradiated photons and show that a flexible and expandable quantum dynamics simulator can be constructed.
<Keywords:> Quantum many-body system simulator, Quantum dynamics calculation, Modularized simulator
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0024/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 18-20, by J-STAGE]
<Title:> Theoretical Analysis of the Aggregation-Inhibition Effect of Arginine on Polyglutamine Protein by the Generalized-Ensemble Method
<Author(s):> Shoichi TANIMOTO, Hisashi OKUMURA
<Corresponding author E-Mill:> sktanimoto(at)ims.ac.jp
<Abstract:> 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. We performed replica-permutation molecular dynamics simulations to clarify the inhibitory effects of arginine on the polyQ-protein aggregation. We found arginine makes more contact with the polyQ protein than lysine, and this tendency of arginine likely inhibits the polyQ-protein aggregation.
<Keywords:> Molecular dynamics simulation, Generalized-ensemble algorithm, Polyglutamine, Protein-aggregation inhibition, Amyloid
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 21-23, by J-STAGE]
<Title:> 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
<Author(s):> 我妻　正太郎, 竹内　理
<Corresponding author E-Mill:> shotaro.agatsuma.hd(at)hitachi.com
<Abstract:> 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. Therefore, we develop the data for MI extraction method from texts and tables in patents. In our evaluation, our method can reduce the time of data extraction by one-half. In the results, it can be expected that the new method can sufficiently reduce the cost of data extraction.
<Keywords:> Materials informatics, Machine learning, Natural Language Processing, Data Extraction
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 12-14, by J-STAGE]
<Title:> 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
<Author(s):> 熊谷　拓海, 中嶋　裕也, 清野　淳司
<Corresponding author E-Mill:> j-seino(at)aoni.waseda.jp
<Abstract:> 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. The system uses spectral information and quantum chemical calculations, which provide no fluctuating data and have a potential to explore a wide range of chemical space. Numerical validation results suggested that the system is capable of efficient and accurate automated molecular identification in organic compounds with low molecular weight.
<Keywords:> Molecular identification; Quantum chemical calculation; Spectral data; Molecular generator; Organic compound
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 15-17, by J-STAGE]
<Title:> 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
<Author(s):> 太刀野　雄介, 土居　英男, 奥脇　弘次, 平野　秀典, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> 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. Here we report a test application to the folding problem of Chignolin and Superchignolin with hairpin structures, where 7 amino acid residues were considered.
<Keywords:> Fragment Molecular Orbital, FMO, Dissipative Particle Dynamics, DPD, Protein Folding, Chignolin
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0019/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 9-11, by J-STAGE]
<Title:> 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
<Author(s):> 石田　賢亮, 西村　好史, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> 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.
<Keywords:> Photoactive yellow protein, p-Coumaric acid, Bicycle-Pedal, Hula-Twist, Quantum molecular dynamics simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.9, -, by J-STAGE]
<Title:> Improvement of Blood-Brain Barrier Permeability Prediction Using Cosine Similarity
<Author(s):> Hiroshi SAKIYAMA, Ryushi MOTOKI, Takashi OKUNO, Jian-Qiang LIU
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> 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. The results showed that selecting training data with high cosine similarity to the test data improved prediction performance with a smaller number of training data. The best model in this study also showed improved scores on two external test sets to examine generalization performance, outperforming excellent existing models. The cosine similarity method is expected to be effective for predicting the properties of compounds with large diversity and a small number of data.
<Keywords:> Blood-brain barrier permeability, Prediction, Cosine similarity, Machine learning, Chemicals
<URL:> https://www.jstage.jst.go.jp/article/jccjie/9/0/9_2023-0017/_html

[Published online Journal of Computer Chemistry, Japan Vol.22, A2-A7, by J-STAGE]
<Title:> 電子を描く(12) ― 炭素原子のsp³, sp², sp混成軌道
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> sumio.tokita(at)gmail.com
<Abstract:> 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
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/1/22_2022-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, A8-A15, by J-STAGE]
<Title:> 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
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> sumio.tokita(at)gmail.com
<Abstract:> 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．
<Keywords:> covalent bond, valence state, valence bond theory, molecular orbital method, hybrid orbital, resonance, difference electron density, NMR spectroscopy, ring current.
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/1/22_2022-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 1-4, 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/22/1/22_2022-0031/_article/-char/ja/