投稿者: 博佐藤

[Published online Journal of Computer Chemistry, Japan Vol.21, 55-57, by J-STAGE]
<Title:> Structural Symmetry and Spin Multiplicity of Sumanene Derivative Radical Molecules
<Author(s):> Yuika BABA, Hidehiro SAKURAI, Azusa MURAOKA
<Corresponding author E-Mill:> muraokaa(at)fc.jwu.ac.jp
<Abstract:> π-conjugated carbon molecules such as fullerenes and carbon nanotubes have attracted great interest because of their potential applications as electronic materials and catalysts. Among these molecular frameworks, fullerene substructures of sumanene molecules with C_3v symmetry are expected to form vertical columnar crystal structures and exhibit a range of conduction properties. Various syntheses of molecules with extended π-conjugation at the benzyl position of sumanene have now been reported. However, there are no examples of open-shell systems with extended sumanene features. In this study, we use the results of DFT calculations to discuss the relationship between molecular conformational symmetry and spin multiplicity in a new, extended open-shell system of sumanenes by adding a phenyl group at the benzyl position.
<Keywords:> Sumanene derivatives, Radical molecules, Molecular symmetry, Spin multiplicity, DFT calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 58-60, by J-STAGE]
<Title:> 化学実験画像データセットの作成と物体検出の数値検証
<Author(s):> 佐々木　良輔, 藤波　美起登, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> In recent years, the remarkable advances in artificial intelligence technology have led to digital transformation (DX) in various fields. The automated construction of laboratory notebook through filming experiments is a promising application of image recognition for chemistry． In this study, we created an image dataset of chemical experiment, which contains 2376 images and consists of 7 classes of objects. Object detection methods and a multiple object tracking method were implemented and assessed using the dataset toward to develop automated laboratory notebook system.
<Keywords:> Machine learning, Object detection, Multiple object tracking, Laboratory notebook, Chemical experiment
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/2/21_2022-0025/_article/-char/ja/

[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/