カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.21, 52-54, by J-STAGE]
<Title:> 密度汎関数法におけるSCF計算条件の最適化による高速化
<Author(s):> 大田　栄二, 白幡　晃一, 石川　敦之
<Corresponding author E-Mill:> eiji(at)fujitsu.com
<Abstract:> Density functional theory (DFT) is a successful theory for calculating the electronic structure of atoms, molecules, and solids. However, in modern computing environments is difficult significantly improve the computational efficiency of DFT. Acceleration of DFT requires optimization of the computational algorithms. We demonstrate two acceleration methods by optimization of the computational algorithms that optimize parallel parameters for eigenvalue calculations and optimization of convergence conditions for the self-consistent field (SCF) calculation.
<Keywords:> Density functional theory, Self-consistent field, Eigenvalue calculation, Convergence conditions, Optimization
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0027/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> A Tautomerization Software Based on Lewis Structures and Reaction Mechanisms
<Author(s):> Ming YU
<Corresponding author E-Mill:> yuming086(at)gmail.com
<Abstract:> A new method is proposed to translate molecule Lewis structures to machine-readable format data and a software based on Lewis structures has been developed to simulate the practice of chemists writing tautomerization mechanisms. For a tautomeric compound, from one Lewis formula entered by users, the software can generate its other equivalent tautomer (s), which share a common tautomerization intermediate stabilized by resonance. Not only atom balance but also electron balance are guaranteed in the tautomerism representation. The stereochemistry changes caused by tautomeric equilibrium can be tracked too. All the stereoisomers for the compounds containing tetrahedral carbon stereocenters and double bond stereocenters can be identified.
<Keywords:> Tautomerization, Software, Stereochemistry, Lewis structure, Mechanism
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0050/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Calculus of Several Harmonic Functions
<Author(s):> Kazuhiro ISHIDA
<Corresponding author E-Mill:> k-ishida(at)fancy.ocn.ne.jp
<Abstract:> Abstract: We describe several harmonic functions; the solid harmonics (SH), the mixed SH, the reducing SH and the reducing mixed SH. We do the solid harmonic gradient (SHG) operator. Using the SHG, we derive a new Gauss-transform and a new Fourier-transform for real-type general Slater-type orbitals (STO). Several formulas can be derived for the calculus of harmonic functions. They will be useful especially for evaluating the angular part of molecular integrals over STOs and over Gaussian-type orbitals with higher-angular-momenta.Keywords: Several harmonic functions; Molecular integrals; Solid harmonics; Higher-angular-momenta; Slater-type orbital; Solid harmonic gradient.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0029/_html

[Published online Journal of Computer Chemistry, Japan Vol.21, 48-51, by J-STAGE]
<Title:> COVID-19の経口治療薬開発に向けたハイブリッド型in Silico創薬
<Author(s):> 小清水　初花, 小野　純一, 福西　快文, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Hybrid in silico drug discovery was performed by combining large-scale quantum molecular dynamics (QMD) simulations with the conventional in silico drug discovery, focusing on developing covalent inhibitors against the main protease (M^pro) of SARS-CoV-2, the virus responsible for ongoing COVID-19 pandemic. The crystal structures and instantaneous structures obtained from the large-scale QMD simulations for M^pro were used as receptors in ensemble docking to estimate the binding affinities of the four ligands: the natural substrate recognized by M^pro, that recognized by the other enzyme of SARS-CoV-2, approved covalent inhibitor (PF-07321332), and the new candidate compound X determined from virtual screening. The present result shows that the binding affinity of X was comparable to that of PF-07321332, demonstrating the potency of our drug discovery.
<Keywords:> COVID-19, In silico drug discovery, Quantum molecular dynamics, Main protease, Covalent drug
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0029/_article/-char/ja/

[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/