Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.18, A6-A11, by J-STAGE]
<Title:> 相対論的量子化学計算プログラムRAQETの公開
<Author(s):> 五十幡　康弘, 吉川　武司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> The “Relativistic And Quantum Electronic Theory (RAQET)” program was released for academic use. One-component (spin-free) and two-component (spin-dependent) relativistic calculations are possible based on the infinite-order Douglas-Kroll-Hess transformation and local unitary transformation. This review describes available features, registration/installation, and input/output of the RAQET program.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0022/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 123-125, by J-STAGE]
<Title:> 機械学習によるテキスト処理ツールの開発と応用
<Author(s):> 亘理　結香, 奥脇　弘次, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have developed a text processing tool consisting of several machine learning-related programs such as TreeTagger and Doc2Vec. This system was applied to a number of abstracts of a couple of physical chemistry journals (Chemical Physics Letters and American Journal of Physics). The degree of similarity of contents was then made evaluatable as a guide for papers to be checked for a certain topic.
<Keywords:> Text processing, Machine learning, Doc2Vec, Degree of similarity
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 129-131, by J-STAGE]
<Title:> ABINIT-MP Openシリーズの最新の開発状況について
<Author(s):> 望月　祐志, 秋永　宜伸, 坂倉　耕太, 渡邊　啓正, 加藤　幸一郎, 渡辺　尚貴, 奥脇　弘次, 中野　達也, 福澤　薫
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing an original program named ABINIT-MP for fragment molecular orbital (FMO) calculations. Various functionalities for interaction analyses, e.g. PIEDA (Pair Interaction Energy Decomposition Analysis), have been augmented in Revision 10 and Revision 15 of the ABINIT-MP Open Series Version 1. In this Letter, we briefly describe such new features.
<Keywords:> キーワード：Fragment molecular orbital, FMO, ABINIT-MP, Interaction analysis, Correlation energy correction
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 126-128, by J-STAGE]
<Title:> Scratchを経由する機械学習教材の開発の試み
<Author(s):> 満野　仁美, 奥脇　弘次, 伊藤　雅仁, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing a Scratch-based educational program for machine learning in the chemistry context. This system has an interface with the DeepChem library set of Python. The solubility prediction of several molecules with SMILES notation was demonstrated as a preliminary application.
<Keywords:> キーワード：Scratch, Educational program, Machine learning, DeepChem, Solubility prediction
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0013/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 132-135, by J-STAGE]
<Title:> 転移学習と生成ネットワークの試行事例
<Author(s):> 伊藤　雅仁, 篠嶋　友也, 望月　祐志, 秋永　宜伸, 小杉　範仁
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> Transfer learning has attracted interests because of the reduction of training costs. We applied this technique to the analyses for visualized results of computational fluid dynamics (CFD) simulations on 2-dimensional wing models. The accuracy and cost reduction were addressed. Preliminary studies of generative network have been made as well.
<Keywords:> Transfer learning, Generative network, Keras, 2-dimensional wing model, Computational fluid dynamics
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 136-138, by J-STAGE]
<Title:> カチオン性イリジウム触媒を用いた均一系触媒反応における相対論効果
<Author(s):> 髙島　千波, 五十幡　康弘, 栗田　久樹, 高野　秀明, 柴田　高範, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> A cationic Ir complex was reported to show specific catalytic activity in C-H bond activation reaction of benzanilides. The present study examined reaction energy profiles of the C-H bond activation with Ir and Rh catalysts based on non-relativistic and relativistic quantum chemical calculations. We found that the relativistic effect is essential to demonstrate the difference in the catalytic activity. In particular, the activation of the d orbital of Ir, which is caused by the s- and p- orbital contraction followed by the self-consistent d-orbital expansion, leads to stabilization of the transition state and product of the C-H bond activation.
<Keywords:> C-H Bond activation, Transition metal catalyst, Relativistic effect, Oxidative addition, Iridium
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 115-121, by J-STAGE]
<Title:> 高屈折率および高ガラス転移温度をもつ高分子材料のモノマー設計
<Author(s):> 高野　森乃介, 金子　弘昌
<Corresponding author E-Mill:> hkaneko(at)meiji.ac.jp
<Abstract:> 本研究ではポリマー物性として屈折率 (refractive index, RI) およびガラス転移温度 (glass transition temperature, Tg) を対象にして，モノマーの化学構造から計算される構造記述子 X とそのモノマーを重合して得られるポリマーの物性 y との間で，高分子データベースを用いて物性推定モデルを構築し，構築されたモデルを用いて高い RI かつ高い Tg をもつポリマーを重合できると考えられる新規モノマー構造の設計を行った．モノマー構造の前処理方法・構造記述子・回帰分析手法を検討したところ，RDKit で構造記述子を計算し，support vector regression で回帰モデルを構築したときに，推定性能の良好な RI および Tg 推定モデルが得られた．RI と Tg がともに高いポリマーを達成するモノマーを設計するため，breaking of retrosynthetically interesting chemical substructure (BRICS) により仮想的な化学構造を生成し，モデルの適用範囲により推定値の信頼性を評価した後に，モデルを用いて RI および Tg を推定した．その結果，多様な化学構造が得られ，中には良好な RI および Tg の推定値をもつ化学構造が存在することを確認した．提案手法により複数の目標物性のある高分子材料の開発が促進することを期待する．
<Keywords:> Molecular design, Polymer, Monomer, Refractive index, Glass transition temperature
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/2/18_2019-0004/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.5, -, by J-STAGE]
<Title:> Analysis Method for Digital PCR Data on Two Dimensional Orthogonal Coordinate (x, y) by Converting to Two Dimensional Polar Coordinate (r, θ) Using EXCEL Macro
<Author(s):> Takashi FUJII, Mikio KAWAHARA, Akihiro TSUYADA, Manabu SUGIYAMA, Masakazu AKAHORI
<Corresponding author E-Mill:> takashi.fujii(at)rikengenesis.jp
<Abstract:> An absolute quantitative analysis method has been recently developed as a third generation polymerase chain reaction method “PCR” for fractionated DNA. The method is designed to determine the number of DNA molecules in target DNA samples by counting the number of PCR products obtained from fractionated DNA. We applied EXCEL Macro to perform the conversion of two dimensional orthogonal coordinate (x, y) fluorescent signal plot data obtained by digital PCR device to two dimensional polar coordinate (r, θ) fluorescent signal plot data, followed by analyzing the angle (θ) histogram of plot data without overlapping of plot data occurring by two dimensional orthogonal coordinate (x, y) histogram. The analysis made it possible to identify gene mutation and count the number of DNA molecules with mutation faster and easier.
<Keywords:> Digital PCR, DNA, Polar coordinate, EXCEL
<URL:> https://www.jstage.jst.go.jp/article/jccjie/5/0/5_2017-0044/_html

[Published online Journal of Computer Chemistry, Japan Vol.17, 232-234, by J-STAGE]
<Title:> ロタキサン構造により緩やかに束縛された高分子鎖の配座解析
<Author(s):> 渡邊　寿雄, 川内　進
<Abstract:> Conformational analysis of the reactant, product, and complex of the polymer and macrocyclic catalyst (PdMC) was carried out in order to investigate the reaction mechanism of the intramolecular cyclization reaction of the polymer chain having a Rotaxane structure. Focusing on the N-C distance of the intramolecular cyclization reaction coordinate, a group of stable conformers with short N-C distances for the reaction was found. By forming a complex with PdMC, the conformations of the reactant with a short N-C distance were stabilized and the intramolecular cyclization reaction was promoted.
<Keywords:> 高分子反応, 配座探索, ロタキサン構造, DFT計算
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0065/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, A28-A33, by J-STAGE]
<Title:> IV族ホモ六員環から成るナノリボン，ナノリング，ナノチューブの基底状態におけるスピン多重度安定性
<Author(s):> 松永　雄樹, 武田　京三郎
<Abstract:> We systematically investigate the molecular and electronic structures of the group-IV (C, Si, Ge) nano-systems such as nanoribbons (NRBs), nanorings (NRGs) and nanotubes (NTBs). The present calculation reveals that C nano-system has a planar structure whereas Si and Ge ones have a non-planar structure. Focusing on the electron correlation, we further investigate the planarity/non-planarity of these nano-systems, and study the energetics of the singlet-triplet (ST) crossover in the ground state. We then extend our study to the infinite NRB and NTB systems and find that these nano-systems have the ground-state spin singlet.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0060/_article/-char/ja/