月別: 2020年3月

[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/