カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.18, 227-229, by J-STAGE]
<Title:> 芳香族単分子並列回路の電気伝導度とフロンティア軌道の関係
<Author(s):> 岡澤　一樹, 辻　雄太, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> According to the current superposition law in nanoscale, the conductance gets more than doubled when the number of paths is doubled. The superposition law can be applied to the molecular graph, which is a discrete mathematical expression for a structure consisting of nodes and edges. We previously revealed that the aromatic parallel circuit i.e. benzene molecule breaks the superposition law. In this paper, we show that [4n+2] annulenes also break the current superposition law from the viewpoint of orbital interaction between two fragments in the parallel circuit.
<Keywords:> Single-molecular electronics, π-conjugated system, Graph theory, H ckel method, Frontier orbital
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 211-213, by J-STAGE]
<Title:> 分子軌道計算と機械学習によるフェルラ酸の抗酸化作用の研究
<Author(s):> 寺前　裕之, 玄　美燕, 山下　司, 高山　淳, 岡﨑　真理, 坂本　武史
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> Ferulic acid is known to have strong antioxidant properties. In the present study, we investigate the electronic structures of ferulic acid and its radical species extracting the hydrogen atom from its phenolic hydroxyl group. The relation of the results by several machine learning models using R/caret package, such as partial least squares, random forest, radial basis function kernel regularized least squares, and baysian regularized neural network, with the radical scavenging activity with the DPPH reagent, IC₅₀, measured by Sakamoto et al. is discussed. We found all four methods gave reasonable correlation coefficients which means the possible prediction of the IC₅₀ values with the results of the molecular orbital calculations only.
<Keywords:> Ferulic acid, Radical scavenging activity, Hamiltonian algorithm, Molecular orbital method, Machine learning, Random forest model
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 214-216, by J-STAGE]
<Title:> ブロック共重合体のミクロ相分離構造に対するマルチフラクタル解析
<Author(s):> 伊藤　真利子, 山中　貞人, 青柳　岳司, 大西　立顕
<Corresponding author E-Mill:> marikoito.rnu1(at)gmail.com
<Abstract:> In this study, we attempted to quantify the shape of various metastable morphologies of microphase separation in block copolymers that can be observed in a computer simulation under the same condition as that for double gyroid (stable state). For the quantification, we used multifractal analysis, which is a tool to evaluate the shape having heterogeneous density inside it. Our analysis showed that the indicators relating to the multifractal analysis of metastable structures are distributed far from that of double gyroid.
<Keywords:> Block copolymers, Microphase separation, Double gyroid, Multifractal analysis, Fractal dimension
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 217-220, by J-STAGE]
<Title:> ガス分離可能なイオン液体探索のためのデータベース構築
<Author(s):> 増田　千夏, 黒木　菜保子
<Corresponding author E-Mill:> kuroki.91d(at)g.chuo-u.ac.jp
<Abstract:> Ionic liquids (ILs) are non-volatile and highly stable solvents, which consist of organic/inorganic cations and anions. ILs are attractive since they can be utilized as gas-separating materials. Using a conductor-like screening model for realistic solvation (COSMO-RS) method, in this study, Henry’s law constants of 15 gases (HCN, SO₂, H₂O, NH₃, H₂S, NO₂, NO, CO, N₂O, CO₂, C₂H₆, C₂H₄, CH₄, N₂, H₂) in 68,775 ILs were calculated to construct an ab initio database to search for ILs which are suitable for gas separation. Based on the database, it was numerically confirmed that not only the ions’ geometric structures but also electronic structures are important to predict ILs’ gas absorption abilities with high accuracy.
<Keywords:> Ionic liquid, Gas absorption and separation, Fragmentation, Statistical thermodynamics, Database
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0046/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 208-210, by J-STAGE]
<Title:> 分子動力学計算によるRNAアプタマーとヒト抗体の複合体形成におけるCa²⁺の役割の解析
<Author(s):> 石井　清一郎, 関口　真裕, 吉田　尚恵, 増川　恵介, 石川　岳志, 坂本　泰一, 山岸　賢司
<Corresponding author E-Mill:> yamagishi.kenji(at)nihon-u.ac.jp
<Abstract:> An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca²⁺ ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca²⁺ ions. To elucidate the role of Ca²⁺ ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca²⁺ ions in a solvent. In the presence of Ca²⁺ ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca²⁺ ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca²⁺ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
<Keywords:> RNA aptamer, Human immunoglobulin G, Calcium ion, Molecular dynamics, Structural analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0051/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 221-223, by J-STAGE]
<Title:> 自由エネルギー反応経路探索法による水中アラニンペプチドの自由エネルギーネットワーク計算
<Author(s):> 満田　祐樹, 重田　育照
<Corresponding author E-Mill:> mitsutay(at)ccs.tsukuba.ac.jp
<Abstract:> Umbrella sampling is a method to calculate free energy by using molecular dynamics simulation. In the previous study, Free Energy Reaction Route Mapping Method (FERRMap) [5,6] is proposed, which is the method to calculate free energy reaction networks by using the umbrella integration method [1,2] and scaled hypersphere searching method [3,4]. In this study, we calculated FERNs of alanine octapeptide (Ala8) in water by using the FERRMap method on the dihedral of the Ramachandran plot, which is 12 dimensional. We found 613 equation structures and 835 transition structures on the FERN of Ala8. This FERN is too complicated to explain the folding of Ala8, we propose an effective flow analysis method. By using this method, we found the representative paths connecting the beta-strand and alpha-helix structure.
<Keywords:> Molecular Dynamics Simulation, Umbrella Sampling, Free Energy Reaction Network
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0045/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 199-201, by J-STAGE]
<Title:> レアイベントサンプリング法の開発と応用研究
<Author(s):> 原田　隆平, Vladimir　Sladek, 重田　育照
<Corresponding author E-Mill:> ryuhei(at)ccs.tsukuba.ac.jp
<Abstract:> Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a rare event sampling method of proteins, which does not rely on knowledge of the target structure. nt-PaCS-MD is an extension of targeted PaCS-MD (t-PaCS-MD). In nt-PaCS-MD, it makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. Reliable identification of these initial structures is the key to using nt-PaCS-MD. In the present study, we introduce the moving root-mean-square deviation (mRMSD) as a metric for identification of these statistical conformation outliers. mRMSD can be calculated for any ith geometry in the trajectory generated by short MD runs. The reference to which the mRMSD relates is the close surrounding of the ith conformation, often the (i-1) st one. Based on mRMSD, we show that it increases its effectiveness compared to the conventional MD.
<Keywords:> Protein, Molecular Dynamics Simulation, Conformational Sampling, Biologically Relevant Rare Event
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0036/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 202-204, by J-STAGE]
<Title:> フォルステライト表面における水分子の分解とプロトン拡散
<Author(s):> 久保　文音, 西澤　隼哉, 深澤　倫子
<Corresponding author E-Mill:> fukazawa(at)meiji.ac.jp
<Abstract:> To investigate the effects of forsterite structure on processes of H₂O decomposition and proton diffusion, we performed molecular dynamics calculations on forsterites in glassy and crystalline states. The result shows that the decomposition rate of H₂O on forsterite in the glassy state is higher than that in crystalline state in a temperature range of 200 to 400 K. Furthermore, the decomposed proton permeates into the internal part of glassy forsterite through hopping, whereas no permeation was observed for the crystalline state. These results suggest that the glassy structure of forsterite is an important factor for chemical evolution processes in interstellar spaces.
<Keywords:> Molecular dynamics calculation, Forsterite glass, Forsterite crystal, Amorphous ice, Surface
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 205-207, by J-STAGE]
<Title:> Geometric and Electronic Structures of Acene Crystals: A van der Waals Density Functional Theory Study
<Author(s):> Ryota MIYAZAKI, Ikutaro HAMADA
<Corresponding author E-Mill:> ihamada(at)prec.eng.osaka-u.ac.jp
<Abstract:> We demonstrate that accurate prediction of the crystal structures of anthracene and its derivatives is possible with the van der Waals density functional. Based on the calculated crystal structures, we investigate their electronic structures and discuss the correlation between crystal structure/molecular configuration and the electronic structure, in particular, the dispersion of the bands composed of the highest occupied molecular orbitals, which are important to discuss the charge carrier transport property.
<Keywords:> Organic semiconductor, Molecular crystal, Acene, Density functional theory, Van der Waals density functional
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 194-197, by J-STAGE]
<Title:> GaussianとGAMESSが内蔵している基底関数の違い
<Author(s):> 竹内　宗孝, 吉田　真史, 長嶋　雲兵
<Corresponding author E-Mill:> myoshida(at)tcu.ac.jp
<Abstract:> 非経験的分子軌道法の計算コードであるGaussianとGAMESSはSTO-3G等の基底の名称を指定するだけで使用できるが，同一名称の基底であっても同一のパラメータセットではない場合は，両者の答えに違いが生じる．本稿では2つのプログラムを使って研究を行っているユーザに注意を喚起するために，第三周期元素の水素化物(NaH，MgH₂，AlH₃，SiH₄，PH₃，H₂S，HCl) についてSTO-3Gを用いた計算をGaussianとGAMESSとで実行し計算結果を比較した．その結果，HClを除き全エネルギーとHOMOのエネルギーはGaussianよりGAMESSのほうが低くなった．これは第三周期元素の原子基底の3s軌道と3p軌道の空間的広がりの違いに起因する．またMulliken電荷は，GaussianよりGAMESSのほうが小さくなった．いくつかの別のプログラムを使用するとき，入力データが利用者が意図した電子状態を記述できうるかを吟味することは大切なことである．
<Keywords:> basis set, Gaussian, GAMESS, STO-3G, total energy, HOMO energy, Mulliken charge
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/4/18_2019-0007/_article/-char/ja/