投稿者: 博佐藤

[Published online Journal of Computer Chemistry, Japan Vol.17, 172-179, by J-STAGE]
<Title:> X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明
<Author(s):> 新庄　永治, 奥脇　弘次, 土居　英男, 望月　祐志, 古石　誉之, 福澤　薫, 米持　悦生
<Abstract:> ドラッグ・デリバリー・システムにおけるナノ微粒子設計の効率化のために，分子シミュレーションによる物性予測や原子分解能のメカニズム解明が望まれている．本研究では，散逸粒子動力学 (DPD) 法とX線小角散乱を用いて，脂質二重膜および混合脂質のベシクル形成の分子メカニズムを明らかにすることを目的として検討を行った．DPDシミュレーションに用いる相互作用パラメータは，フラグメント分子軌道 (FMO) 法を用いて高精度に算定した(FMO-DPD法)．脂質二重膜形成の結果から，飽和結合のみをもつリン脂質 (DPPC) よりも不飽和結合をもつリン脂質 (DOPC) の方が，膜流動性が高いことが分かった．さらに，リン脂質と正電荷脂質を混合したベシクルの形成では，正電荷脂質の比率が増えるにつれて膜の流動性が高くなり，球から扁平球へと形状が変化することが明らかとなった．
<Keywords:> Lipid bilayer, vesicle, Dissipative particle dynamics (DPD), Fragment molecular orbital (FMO) method, SAXS
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/4/17_2018-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 180-187, by J-STAGE]
<Title:> 可視光の衛星画像の海面の色相変化を用いた広域海洋汚染の調査方法の開発
<Author(s):> 神部　順子, 小原　裕二, 青山　智夫, 長嶋　雲兵
<Corresponding author E-Mill:> nagashima(at)j-focus.or.jp
<Abstract:> 可視光の衛星画像を新たな環境科学の研究資料及び教材とするための解析手法を開発した．環境の異変は特に微細な色相の変化に現れるので，色相とコントラストの強調法を新たに開発し, その手法を用いて2018年1月のタンカーSanchi号の沈没事故後のひまわり8号撮影の衛星写真を解析したところ，海中に投棄された凝縮物(Condensate)の影響は見いだせなかったが，重油と考えられる海面の黒色帯が存在することが分かった．また東シナ海の富栄養化が日本の排他的経済水域(Exclusive Economic Zone: EEZ)近くまで及んでいること，時にはその海水の一部が九州西岸に到達することが分かった．
<Keywords:> satellite image, sea hue, marine pollution, marine eutrophication, tanker accident
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/4/17_2018-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.4, -, by J-STAGE]
<Title:> Development of ConfDatMaker Software for Generating the Conformers of Metal Complexes
<Author(s):> Hiroshi SAKIYAMA
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> ConfDatMaker software was developed for the purpose of generating the conformers of metal complexes. The software builds structures by symmetry operation of the inputted ligand coordinates, on the basis of the prepared enumeration results. A series of generated structures are useful for the conformational analysis.
<Keywords:> Conformer, Metal complex, Symmetry operation, Enumeration, ConfDatMaker software
<URL:> https://www.jstage.jst.go.jp/article/jccjie/4/0/4_2018-0013/_html

[Published online Journal of Computer Chemistry, Japan Vol.17, 160-162, by J-STAGE]
<Title:> FMO法によるエストロゲン受容体のリガンド結合特異性解析
<Author(s):> 関　祐哉, 加藤　司, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> k-fukuzawa(at)hoshi.ac.jp
<Abstract:> There are two subtypes (α, β) in the estrogen receptor (ER), and ERβ has binding selectivity for phytoestrogens. It is known that only two hydrophobic amino acid residues (Met336Leu and Ile373Met) differ in ligand binding pocket between subtypes. However, the mechanisms of its binding properties and subtype selectivity have not been fully understood. We evaluated the subtype selectivity by comprehensively analyzing the complex of ERβ and ligands based on the fragment molecular orbital (FMO) method. By comparing the interaction between ligand and amino acid residues of ER, it was revealed that both hydrogen bond with Glu305 and CH/π interaction with Phe356 were essential for ligand binding of ERβ, and stable interaction with Met336 and His475 would be related to β selectivity.
<Keywords:> Estrogen Receptor β, Fragment Molecular Orbital Method, PIEDA, Protein-Ligand Interaction, Subtype Selectivity
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0028/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 可視光の衛星画像の海面の色相変化を用いた広域海洋汚染の調査方法の開発
<Author(s):> 神部　順子, 小原　裕二, 青山　智夫, 長嶋　雲兵
<Corresponding author E-Mill:> nagashima(at)j-focus.or.jp
<Abstract:> 可視光の衛星画像を新たな環境科学の研究資料及び教材とするための解析手法を開発した．環境の異変は特に微細な色相の変化に現れるので，色相とコントラストの強調法を新たに開発し, その手法を用いて2018年1月のタンカーSanchi号の沈没事故後のひまわり8号撮影の衛星写真を解析したところ，海中に投棄された凝縮物(Condensate)の影響は見いだせなかったが，重油と考えられる海面の黒色帯が存在することが分かった．また東シナ海の富栄養化が日本の排他的経済水域(Exclusive Economic Zone: EEZ)近くまで及んでいること，時にはその海水の一部が九州西岸に到達することが分かった．
<Keywords:> satellite image, sea hue, marine pollution, marine eutrophication, tanker accident
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2018-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 158-159, by J-STAGE]
<Title:> 計算機化学を用いたムライト結晶の構造異常の研究2
<Author(s):> 鈴木　泰地, 長島　啓, 中嶋　義晴, 内田　希
<Corresponding author E-Mill:> s153242(at)stn.nagaokaut.ac.jp
<Abstract:> The purpose of this study is to clarify the regularity of occupancy hidden in the bi-occupied site by Al or Si of mullite crystal．Many mullite models with different atom arrangement were prepared and their stability was examined after performed structural relaxation calculations．The peak intensities of pair correlation function for metal atoms changed with the composition．From the three-view drawings of oxygen vacancy sites，it is suggested that when the oxygen vacancies aligned on the c axis, the crystal structure becomes unstable．
<Keywords:> mullite, crystal structure, structural relaxation calculation, distribution of oxygen vacancy, random arrangement
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0017/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 153-154, by J-STAGE]
<Title:> [M(dmso)₆][BPh₄]₂錯体[M=Co(II), Zn(II)]の結晶相転移と配座解析
<Author(s):> 崎山　博史, 三橋　了爾, 御厨　正博, 脇　克志
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> Based on the conformational analysis for an octahedral zinc(II) complex cation, [Zn(dmso)₆]²⁺ (dmso: dimethylsulfoxide), the crystal-to-crystal phase transition behavior of [Co(dmso)₆][BPh₄]₂ and [Zn(dmso)₆][BPh₄]₂ was discussed.
<Keywords:> コバルト(II)錯体, 亜鉛(II)錯体, 結晶相転移, 配座解析, 配座異性体
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0019/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 150-152, by J-STAGE]
<Title:> フェルラ酸のフリーラジカル消去能に関する理論的研究
<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 have investigated the electronic structures of Ferulic acid and its radical extracting the hydrogen atom from its phenolic hydroxyl group. We have discussed the relation of the results with the radical scavenging activity using the DPPH reagent measured by Xuan et al. We have found that the total energies of Ferulic acid derivatives and its radical species made from removing the hydrogen radical from the phenolic hydroxy group have the relation with the IC₅₀ values. The orbital energies of the radical species also have the relation with the IC₅₀ values. The deep learning study with the random forest model suggests that the contribution from α-SOMO and α-LUMO energies is important.
<Keywords:> KeywordsFerulic acid, Radical scavenging activity, Hamiltonian algorithm, Molecular orbital method, Machine learning, Random forest model
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0018/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 155-157, by J-STAGE]
<Title:> Soft Crystal Force Field for Reproducing the Crystal Structures of Aryl Gold Isocyanide Complexes
<Author(s):> Naofumi NAKAYAMA, Shigeaki OBATA, Yoshikazu HORI, Hitoshi GOTO, Tomohiro SEKI, Hajime ITO
<Corresponding author E-Mill:> gotoh(at)tut.jp
<Abstract:> Force field parameters around Au atom that have been lacking in standard parameter set of the MMFF94s were temporarily determined to reproduce the molecular crystal structure of phenyl(phenylisocyanide)gold(I) complex by classical force field calculations. It was confirmed that two polymorphic forms optimized by CONFLEX software with these parameters are in good agreement with the experimental structures. Application of the parameters to other derivatives also gives good results but the Au..Au distances in some crystal structures are longer than those of the experimental. Therefore, further optimization of these parameters will be required.
<Keywords:> Soft crystal, Aryl gold isocyanide complex, Force field, Crystal structure optimization, Root-mean-square deviation
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0031/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 147-149, by J-STAGE]
<Title:> FMOプログラムABINIT-MPのOakforest-PACS上での多層並列化と性能評価
<Author(s):> 渡邊　啓正, 佐藤　伸哉, 坂倉　耕太, 齊藤　天菜, 望月　祐志
<Corresponding author E-Mill:> hi-watanabe(at)hpc.co.jp
<Abstract:> The Oakforest-PACS (OFP) system is a many-core type supercomputer with Intel’s Knights Landing (KNL) processors. In this paper, we report the performance of fragment molecular orbital (FMO) calculations with the ABINIT-MP program (to which a three-layer parallelization was made recently) on the OFP system. The effect of hyper-threading in KNL is addressed as well.
<Keywords:> Fragment molecular orbital, FMO, ABINIT-MP, Many-core, Parallelization, Performance benchmark
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/3/17_2018-0023/_article/-char/ja/