投稿者: 博佐藤

[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/

[Published online Journal of Computer Chemistry, Japan Vol.17, 235-236, by J-STAGE]
<Title:> 計算機化学を用いた天然ゴムの生合成過程解析
<Author(s):> 慶野　達也, 内田　希, 河原　成元, 秋山　和輝
<Corresponding author E-Mill:> tatsuya_keino(at)mst.nagaokaut.ac.jp
<Abstract:> Natural rubber is an excellent material in elasticity and abrasion resistance. However, the detailed structure and the reason for excellent physical properties of natural rubber are still unclear. We aimed to conduct a conformational search and structural analysis using computational chemistry and to elucidate the biosynthetic process of natural rubber. From the calculation results, as long as the catalyst (enzyme) required for each stage of the biosynthesis process exists, it turned out that the biosynthesis of natural rubber proceeded spontaneously.
<Keywords:> Natural rubber, Biosynthesis mechanism, MOPAC, PM7, COSMO method, Phosphate group
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0048/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 225-227, by J-STAGE]
<Title:> 赤外分光法と新規判別分析によるセルロース繊維種の判別
<Author(s):> 坂本　幸祐, 菅野　麻奈美, 吉村　季織, 高柳　正夫
<Corresponding author E-Mill:> s187475q(at)st.go.tuat.ac.jp
<Abstract:> As a new method for discrimination analysis applicable to data containing a large number of variables such as spectra, FDOD (Fisher’s Discriminant Orthogonal Decomposition) was developed by incorporating regularization and orthogonal decomposition into ordinary FDA (Fisher’s Discriminant Analysis). Here, FDOD was applied to distinguish infrared absorption (IR) spectra of rayon and modal. Since rayon and modal are very similar recycled fibers, their IR spectra cannot be discriminated by score plots based on principle component analysis (PCA). By using FDOD, their discrimination with a correct answer rate of 94% has been achieved.
<Keywords:> 判別分析, 正則化, 直交分解, 赤外分光法, 再生繊維
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0058/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 228-231, by J-STAGE]
<Title:> 特徴ベクトルから分子構造を生成するアルゴリズム
<Author(s):> 陸　明浩, 安田　耕二
<Corresponding author E-Mill:> yasudak(at)imass.nagoya-u.ac.jp
<Abstract:> Machine learning for predicting properties of molecules and designing molecules with desired properties requires suitable numerical representation of molecular structure. In this study we propose to represent a molecular graph as a high dimensional feature vector by counting the number of substructures of a molecule, and report conditions that these vectors should satisfy. The vectors are expanded by the lattice basis extracted from the feature vectors of a large molecular dataset. In addition, an efficient algorithm to reconstruct molecular structures from the feature vector is presented. The latent space provides a continuous and concise representation of molecular graphs, and the representation allows smooth interpolation between two molecules. The proposed method has wide application to studies of quantitative structure activity relationships and machine learning of molecules.
<Keywords:> KEYWORDS Machine learning, Feature vector, Molecular graph reconstruction, De Bruijn graph, Lattice basis
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0056/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.5, -, by J-STAGE]
<Title:> Revisiting the Nature of Si-O-Si Bridging
<Author(s):> Fumiya NORITAKE
<Corresponding author E-Mill:> fnoritake(at)yamanashi.ac.jp
<Abstract:> Non-empirical calculation based on the Schr dinger equation is an appropriate tool for investigating the relationship among Si-O-Si angle, Si-O bond length, Si-O bond strength, and electronic structure. However, past studies could not reach a consensus about the equilibrium structure of the C_2v pyrosilisic acid molecule. Moreover, the structure of disiloxane, the simplest siloxane molecule, could not be reproduced using non-empirical molecular orbital calculations. In this study, I checked the reproducibility of various model chemistries and basis sets, and found that employing the post-Hartree-Fock method and a larger basis set (at least, aug-cc-pVTZ) is necessary for accurate calculation of the disiloxane molecule. In contrast to past studies on molecular orbitals, the present study reveals no significant occupancy in the Si 3d orbitals. The total energy landscape of the C_2v pyrosilisic acid molecule is calculated by using the coupled cluster method concerning three excited electrons and the aug-cc-pVTZ basis set. The stable bond length for Si-O_br is 1.604 , and the stable Si-O-Si angle is 159.449°. There are gentle curves around the stable angles for each bond length comparing with bond length direction. The stable angle for each bond length decreased with increasing Si-O_br bond length. The weakening of the Si-O_br bond with decreasing Si-O-Si bond angle can be explained by the decrease in the bond index and the increase in the orbital energy for Si-O_br σ-bond. Consequently, hybridization of the valence electrons of the bridging oxygen with decreasing Si-O-Si angle weakens the Si-O_br σ-bond. Electrostatic potential favors a straight configuration because of the repulsion between the SiO₄ tetrahedra, while the valence electrons of the bridging oxygen favor a bent configuration. These two competing behaviors can explain the bent configuration of pyrosilisic acid without considering d-p π bonding.
<Keywords:> SIlicate, Pyrosilisic Acid, Disiloxane, Benchmark, Molecular Orbital Calculations
<URL:> https://www.jstage.jst.go.jp/article/jccjie/5/0/5_2018-0016/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.5, -, by J-STAGE]
<Title:> Development of PolyParGen Software to Facilitate the Determination of Molecular Dynamics Simulation Parameters for Polymers
<Author(s):> Makoto YABE, Kazuki MORI, Kazuyoshi UEDA, Minoru TAKEDA
<Corresponding author E-Mill:> kazuki.mori.013(at)ctc-g.co.jp
<Abstract:> In the case that the parameters to describe the force field, such as bond angles and charges, cannot be added to the library of a molecular dynamics (MD) simulation, self-development of the force field should be considered by performing quantum mechanics calculations and/or utilizing an automatic parameter generation tool. However, these techniques are not suitable for macromolecules with a large number of atoms. Typically, the force field of an oligomer containing three unit structures (a unit at both ends and a repeating unit at the center) is calculated and converted to polymer form (both ends + central part × n). Considering this, we recently developed the program o2p, which is a semi-automated program designed to set up the force field for polymers with repeating structures. However, it is difficult to apply this method to macromolecules with complex repeating structures. Thus, in this project, we developed PolyParGen, a new open-source automatic force field generation program for Gromacs that can relatively easily and reliably simulate the MD of complex macromolecules. The proposed program (1) divides the structure of the polymer into substructures with a number of atoms within the limit of the handling size for the automatic parameter generation tool program; then, (2) acquire the parameters for each divided substructure, and finally, (3) combine the parameters of these substructures to obtain the parameters for the whole polymer. By automating these processes, it is possible to acquire a parameter of a polymer having complicated structures. This program was evaluated by simulating the polymers P3EHT and F-P3EHT in chloroform. In agreement with previous reports, fluorination was found to cause F-P3EHT to adopt an extended structure, thereby indicating the effectiveness of the proposed program.
<Keywords:> Molecular dynamics simulation, Macromolecules, Parameters, Gromacs, Polymer
<URL:> https://www.jstage.jst.go.jp/article/jccjie/5/0/5_2018-0034/_html

[Published online Journal of Computer Chemistry, Japan Vol.17, 215-216, by J-STAGE]
<Title:> 分子軌道法を用いた多層グラフェン間への水素吸蔵特性の研究
<Author(s):> 菅谷　大智, 斎藤　秀俊, 内田　希
<Corresponding author E-Mill:> sugaya(at)stn.nagaokaut.ac.jp
<Abstract:> The activated carbon synthesized from rice husks has high hydrogen storage on 77K. It is inferred that activated carbon has a lot of defect on the surface compared with graphene. However, the actual structure and hydrogen storage mechanism have unknown by experiments. The purpose of this study is to clarify the hydrogen storage mechanism for multilayered graphene. The sp² hybrid system carbon structure that introduced a defect was prepared and set a hydrogen molecule between the layers. MOPAC PM7 involving the dispersion term for semiempirical MO was used for calculating heat of formation. From the potential curve between graphene layer where hydrogen was inserted, it is suggested that when a defect made on the edge, the structure becomes more stable.
<Keywords:> graphene layer, Carbon defect, Hydrogen storage, Semiempirical MO, Dispersion force
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0047/_article/-char/ja/