カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.21, 39-42, by J-STAGE]
<Title:> 量子コンピュータを利用したタンパク質の畳み込みモデル
<Author(s):> 齊藤　瑠偉, 奥脇　弘次, 望月　祐志, 永井　隆太郎, 加藤　拓己, 杉﨑　研司, 湊　雄一郎
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have performed a series of quantum computations for folding of the PSVKMA peptide by using the blueqat AutoQML simulator by which a given problem can be converted from QUBO (quadratic unconstrained binary optimization) of quantum annealing to QAOA (quantum approximate optimization algorithm) of VQE (variational quantum eigensolver). The IonQ quantum system of ion-trap type was utilized as well. A three qubit problem was successful by both. However, the situation became difficult for a five qubit case, especially for the IonQ having vulnerability to noises.
<Keywords:> Quantum computation, Protein folding, Lattice model, QUBO, QAOA
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0022/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 33-35, by J-STAGE]
<Title:> β-LiAlSiO₄結晶の分子動力学法に用いる原子間相互作用の改良
<Author(s):> 大垣　毅弥, 澤口　直哉
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp
<Abstract:> Thermal change of lattice parameters of β-LiAlSiO₄ crystal simulated by molecular dynamics simulation was improved by revision of the interatomic potential. The discontinuity of thermal change of c-axis lattice parameter observed in the previous work between 800 K and 900 K was dissolved, but the simulated linear thermal expansion of c-axis was smaller than the reference data. The visualized shift of relative coordinates of each atom with the temperature increase from 300 K to 1200 K showed the different variation between the two types of double helix structures that exist in the unit cell.
<Keywords:> Molecular dynamics, ??i??β??/i??-eucryptite, ??i??β??/i??-LiAlSiO4, Thermal expansion, Structure analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 36-38, by J-STAGE]
<Title:> 少数データを効率的に利用したデータ駆動型反応機構探索
<Author(s):> 塩谷　友希, 嶋田　五百里
<Corresponding author E-Mill:> iori(at)shinshu-u.ac.jp
<Abstract:> Chemical reaction neural network (CRNN) is a machine learning model that enables a data-driven search of chemical reaction mechanisms by incorporating reaction kinetics theory into the neural network architecture. Conventionally, 10³ order data were required for searching a simple reaction system, but the reduction in the number of data required for CRNN is expected to enable its application to various experimental systems. In this study, we investigated the number of data required for prediction in the CRNN. The result showed that prediction of the reaction is possible with as few as 180 data by avoiding falling into local optimal solutions. We also confirmed that incorporating the concept of material balance into loss function has effect of reducing the computational complexity.
<Keywords:> Reaction mechanism, Kinetics, Chemical reaction neural network, Physics-informed machine learning, Data-driven
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0024/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 43-44, by J-STAGE]
<Title:> VR-MD: スマホ VR で実施する分子動力学計算とその教育への適用
<Author(s):> 吉川　信明, 松田　健郎, 梶田　晴司, 佐藤　宗太, 谷川　智洋
<Corresponding author E-Mill:> kikkawa(at)mosk.tytlabs.co.jp
<Abstract:> An application for molecular dynamics (MD) simulations was implemented on a smartphone for utilizing virtual reality (VR) in chemistry education. This application consists only of a smartphone, a simple VR lens, and an on-board camera. The screen displays molecular motions equivalent to MD calculations in actual research. The molecules move synchronously with the six-dimensional movements of the user’s head. The on-board camera also recognizes hand coordinates, allowing the user to “touch” and “grab” the molecules through the hand model displayed in the VR space. This application enables users to intuitively understand molecular motion. A special lecture was held at high schools using this application, and survey results shows that students’ understanding of molecules improved.
<Keywords:> Chemical education, Virtual reality, Smartphone application, Molecular dynamics
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0028/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 45-47, by J-STAGE]
<Title:> Theoretical Study on the Reaction Mechanism of the Water-Splitting Process on Cobalt Oxide Catalysts
<Author(s):> Narumi FUJIWARA, Koichi YAMASHITA, Azusa MURAOKA
<Corresponding author E-Mill:> muraokaa(at)fc.jwu.ac.jp
<Abstract:> In recent years, artificial photosynthesis has attracted attention as a mechanism for generating fuel by sunlight irradiation of a photocatalyst to split water into O and H. Elucidation of the four-electron oxidation reaction mechanism of this split is essential for the development of highly active photocatalysts. A reaction mechanism has been proposed for Co₃O₄ catalysts using time-resolved Fourier transform infrared spectroscopy to identify the intermediates in the oxidation of water under reaction. In this study, density functional theory was used to examine the mechanism of the four-electron reaction of the Co₃O₄ photocatalysts.
<Keywords:> cobalt oxide, Photocatalyst, Four-electron oxidation reaction, DFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 1-9, by J-STAGE]
<Title:> 特許公開公報文章からの化学物質名の抽出
<Author(s):> 田中　るみ子, 中山　伸一
<Corresponding author E-Mill:> pbb00275(at)nifty.ne.jp
<Abstract:> 化学知識を有効活用するには，化学物質名とその構造，機能，製造方法，化学反応，用途などを効率よく抽出，整理，蓄積することが必要であるが，それには多大な時間と労力を伴う．英文からの化学物質名抽出については多くの研究が行われ，一定の成果が得られている．一方日本語文の場合，英文のように単語が空白や記号によって区切られていないため，化学物質名を単語として扱うには，最初に形態素解析を行って単語に区切り，細かく分離された単語をひとかたまりの単語として連結する必要がある．しかしながら，連結により，不要な部分が化学物質名についてしまう場合もある．本論文では，特許公開公報に化学物質名をタグ付けしたコーパスを作り，化学物質名の文字種，配置，前後の関係，文脈などに着目した単語切り出しとWord2Vecによるベクトル化を行い，コーパスを学習データとした機械学習モデルによる日本語文からの化学物質名抽出の可能性について検討する．
<Keywords:> chemical substance name, compound name, patent publication, machine learning, Word2Vec, binary classification
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/1/21_2021-0047/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 10-19, by J-STAGE]
<Title:> 準結晶ペンローズタイルクラスタにおける周辺構造修飾と中心局在相
<Author(s):> 金崎　翼, 石井 　楽士, 武田　京三郎
<Corresponding author E-Mill:> takeda(at)waseda.jp
<Abstract:> 準結晶格子は短距離秩序と長距離非周期性という新たな構造的特質を有する．本研究ではこの格子の幾何的特質に依って生じ得る電子構造の特徴の抽出を試みた．具体的には典型的準結晶二次元格子であるペンローズタイル(PT)模様を想定し，そのクラスター化により対象系の簡素化を図った．さらに1格子原子1電子近似を行い，Harrison法とSlater-Koster法を組み合わせた強結合近似を用いて，当該系の電子構造を算出し，その体系化を行った． その結果，PTが有する5回回転対称短距離秩序と長距離非周期性により，クラスタ中心部位に強く局在する準位が発現する可能性を見出した．この準位はその中心局在性により，PTC外周辺部位に対し”構造鈍感”である．従って5回対称性を保持するように当該PTC類の周辺構造修飾(原子団の除去及び付加)を行えば，其れに伴う電子数の可変により，同準位のSOMO化が可能となる．こうして，短距離秩序と長距離非周期性という準結晶の幾何的特徴により，中心部位に局在かつ露出化された電子スピン状態の創出が期待できる事が明らかとなった．
<Keywords:> Penrose tile, clusters, quasicrystal, peripheral modification, central localization
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/1/21_2022-0006/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 20-32, by J-STAGE]
<Title:> モチーフコドン縮約表現に基づいた動的計画 (DP) 法によるゲノム機能部位推定システムの開発
<Author(s):> 大友　将宏, 小林　貴史, 加藤　博明
<Corresponding author E-Mill:> ohtomo(at)kuicr.kyoto-u.ac.jp
<Abstract:> 高等生物のゲノム配列にはタンパク質に翻訳されるエクソン領域とそれ以外のイントロン領域が存在し，その複雑な構造の中から機能部位を推定するのは一つの大きな課題である．一方，タンパク質アミノ酸配列にはその機能と密接な関係がある特徴的な配列パターンであるモチーフが保存され，遺伝子配列にもよく保存されていると考えられる．本研究ではコドン縮約表現とその近似表現を用いた，動的計画 (DP) 法によるゲノム機能部位推定システムを開発した．さらに，公共データベースのモチーフ辞書PROSITEのアミノ酸配列モチーフに対応する遺伝子配列を定量的に表現したコドン重み行列を基にした，モチーフコドン縮約表現を提案した．はじめに，HumanのTNNC1ゲノム配列に対してタンパク質のコーディング配列 (CDS) の推定実験を行った．次に，Humanをはじめとするいくつかのモデル生物種のTNNC1とHPCAゲノム配列に対してEF-handモチーフの推定実験を行い，システムの有用性を示した．
<Keywords:> codon reduced representation, dynamic programming, functional site estimation, PROSITE, protein-gene motif
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/1/21_2022-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 150-154, by J-STAGE]
<Title:> Effect of Pore Size of Carbon Support on Electrode Reaction Activity of Catalyst Layer in Polymer Electrolyte Fuel Cell: Reactive Molecular Dynamics Simulations
<Author(s):> Tetsuya NAKAMURA, Riku OTSUKI, Shuichi UEHARA, Yuta ASANO, Qian CHEN, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)tohoku.ac.jp
<Abstract:> For large output of polymer electrolyte fuel cells (PEFCs), the electrode reaction activity of the catalyst layer (CL) consisting of carbon supports, Pt nanoparticles, Nafion chains, and water should be improved. Experimentally, it is reported that when Ketjen black (KB) with meso pores is used as the carbon support, the output of PEFC increases and that the pore size of the KB support affects the electrode reaction activity of the Pt nanoparticles. Therefore, in the present study, to clarify the effect of pore size on the electrode reaction activity of the Pt nanoparticles, we constructed catalyst particle (CP) models in which the Pt nanoparticles are supported and Nafion chains are coated on the KB model and investigated the CP structures with a different pore size of the KB support by reactive molecular dynamics method. Regardless of the pore size, the Pt nanoparticles on the exterior of the pore are fully covered with the Nafion chains and the Pt nanoparticles in the interior of the pore are not covered with the Nafion chains. This result suggests that the Pt nanoparticles in the interior of the pore show high oxygen transport property that does not depend on the pore size. Furthermore, we evaluated the connectivity of the Nafion chains to H₂O molecules absorbed on the Pt nanoparticles on the exterior and in the interior of the pores because the Nafion chains conduct the protons to the H₂O molecules on the Pt nanoparticles. As the pore size increases, more Nafion chains penetrate the interior of the pore and contact with H₂O molecules on the Pt nanoparticles, because more Nafion chains are vertically distributed above the larger pore. Finally, these results propose that both high oxygen transport property and high electrode reaction activity are achieved over the Pt nanoparticles in the interior of the large pore of the KB support because the oxygen diffusion in the pore is not blocked by the Nafion chains and the large pore size promotes the formation of a proton conducting path composed of the Nafion chains, H₂O, and Pt nanoparticles.
<Keywords:> Reactive Molecular Dynamics, Polymer Electrolyte Fuel Cell, Catalyst Layer, Ketjen Black, Reaction Activity
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/4/20_2022-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Relativistic DFT Calculations of Changes in NMR Chemical Shifts in Aqueous Solutions of Heavy-Metal Nitrates
<Author(s):> Yoshimitsu ASAKURA, Daisuke KUWAHARA, Naoya NAKAGAWA
<Corresponding author E-Mill:> kuwahara(at)uec.ac.jp
<Abstract:> The NMR chemical shifts for metal ions in aqueous solutions of inorganic salts often change with the solution concentration. These changes are referred to herein as dilution concentration (dc) shifts. For main-group elements, the dc shifts generally increase with increasing atomic number. We calculated the dc shifts for various metal and nonmetal ions in aqueous nitrate solutions of elements in periods 5 and 6 by the DFT method based on the spin orbit ZORA Hamiltonian. The calculation results revealed that the dc shifts of metal and nonmetal ions with the outermost shell electron configuration of 6s² are primarily determined by the changes in the spin orbit interaction terms of the shielding constants. Furthermore, the spin densities of the Pb(II) ions in aqueous lead nitrate solutions under an external magnetic field were calculated using the matrix/modified Dirac Kohn Sham Hamiltonian, which confirmed the presence of Fermi contacts between the spin-polarized electrons and the lead nucleus. When a suitable threshold for visualizing the spin density was set, there was no Fermi contact in the infinite dilution state, whereas the upward-spin electron was in Fermi contact with the lead nucleus in the saturation state. There have been few reports of the NMR chemical shifts of heavy atoms in terms of Fermi contacts with relativistically spin-polarized electrons. We succeeded in clarifying how the dc shifts occur on the hydrated ions of heavy atoms by visualizing the Fermi contact of spin-polarized electrons with heavy-metal nuclei.
<Keywords:> Spin orbit interaction, NMR, Density functional theory, Nitrates, Solvation, Hydration
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0048/_html