月別: 2023年3月

[Published online Journal of Computer Chemistry, Japan Vol.21, 80-81, by J-STAGE]
<Title:> 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
<Author(s):> 渡辺　七都稀, 庄司　光男, 堀　優太, 重田　育照
<Corresponding author E-Mill:> watanabe.natsuki.sm(at)alumni.tsukuba.ac.jp
<Abstract:> Racemization of amino acid catalyzed by aldehyde and carboxylic acid has been proposed and widely used. Herein, we investigated the detailed racemization mechanism of alanine catalyzed by salicylaldehyde and acetic acid. Quantum chemistry calculations based on the density functional theory demonstrated that the dehydration reaction is the rate-determining step, and this dehydration step is enhanced by surrounding water molecules. We also discussed the dependence of the reaction rates on the type of amino acid.
<Keywords:> Racemization reaction, Organocatalytic reaction, Amino acid, Alanine, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0004/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 77-79, by J-STAGE]
<Title:> Theoretical Characterization of the Electronic and Spin Structures for Iron Sulfur Cubane in Reduced High-Potential Iron Sulfur Proteins Using Density Functional Theory
<Author(s):> Yuta HORI, Ayaka SATO, Yasuteru SHIGETA
<Corresponding author E-Mill:> hori(at)ccs.tsukuba.ac.jp
<Abstract:> In this work, density functional theory and natural bond orbital analysis are used to investigate the electronic structures of the [4Fe-4S] cluster in reduced high-potential iron sulfur proteins. Calculated 3d-orbital occupancies of Fe atoms in the [4Fe-4S] cluster revealed a spin structure with two ferromagnetically coupled [2Fe-2S]⁺ subclusters that are antiferromagnetically coupled to each other. In addition, the chemical bonds between S Fe were found to form primarily through the donation of electrons from S to Fe atoms.
<Keywords:> [4Fe-4S] cluster, High-potential iron sulfur protein, Natural bond orbital, Density functional theory, Electronic structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 85-86, by J-STAGE]
<Title:> Keggin型ポリオキソタングステートの合成経路に関する研究
<Author(s):> 石上　快, 大堺　利行, 中嶋　隆人, 枝　和男
<Corresponding author E-Mill:> 212s203s(at)stu.kobe-u.ac.jp
<Abstract:> Synthetic pathways of Keggin-type polyoxotungstates (POTs), which are expected to catalyze multi-electron transfer reactions, were investigated by first-principles calculations. The reaction pathways for the formation of new Keggin-type POTs from existing ones via ion exchange were explored by the Nudged Elastic Band (NEB) method, and the effects of the kind of heteroatom and the relative permittivity of the solvent were discussed.
<Keywords:> Keggin, Polyoxometalates, Polyoxotungstates, First-principles calculations, NEB method
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 77-79, by J-STAGE]
<Title:> Theoretical Characterization of the Electronic and Spin Structures for Iron Sulfur Cubane in Reduced High-Potential Iron Sulfur Proteins Using Density Functional Theory
<Author(s):> Yuta HORI, Ayaka SATO, Yasuteru SHIGETA
<Corresponding author E-Mill:> hori(at)ccs.tsukuba.ac.jp
<Abstract:> In this work, density functional theory and natural bond orbital analysis are used to investigate the electronic structures of the [4Fe-4S] cluster in reduced high-potential iron sulfur proteins. Calculated 3d-orbital occupancies of Fe atoms in the [4Fe-4S] cluster revealed a spin structure with two ferromagnetically coupled [2Fe-2S]⁺ subclusters that are antiferromagnetically coupled to each other. In addition, the chemical bonds between S Fe were found to form primarily through the donation of electrons from S to Fe atoms.
<Keywords:> [4Fe-4S] cluster, High-potential iron sulfur protein, Natural bond orbital, Density functional theory, Electronic structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 82-84, by J-STAGE]
<Title:> 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
<Author(s):> 宗井　陽平, 堀　優太, Hengphasatporn　Kowit, 原田　隆平, 重田　育照
<Corresponding author E-Mill:> shigeta(at)ccs.tsukuba.ac.jp
<Abstract:> Metalloproteins such as 4-hydroxyphenylpyruvate dioxygenase (HPPD) and Cytochrome P450 are important for agrochemical research. In classical mechanics, to reproduce the metal-coordination environment of metalloproteins, various models (Nonbonded model, Bonded model, Nonbonded/Bonded Hybrid model etc.) for metal complexes have been developed. In this study, we built force field parameters for the molecular dynamics simulation of HPPD and evaluated the Fe²⁺-coordination environment. The result revealed that the hybrid model is suitable for the simulation of HPPD and able to simulate the metal-ligand (water) exchange process.
<Keywords:> Molecular dynamics, Metalloprotein, Force field, 4-Hydroxyphenylpyruvate dioxygenase, Agrochemical
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, A7-A12, by J-STAGE]
<Title:> Journal of Computer Chemistry, Japan の今までとこれから
<Author(s):> 中村　恵子
<Corresponding author E-Mill:> jccjoffice(at)sccj.net
<Abstract:> コンピュータ化学会創立ならびにJournal of Computer Chemistry, Japanの発行20周年を記念して，創設期の先生がたから受け継いだものと新しい時代の流れに即して変化を重ねてきた部分を振り返るとともに，ジャーナルの現状と未来についての私見を述べる．
<Keywords:> Keywords SCCJ, Journal of Computer Chemistry, Japan(JCCJ), Journal of Computer Chemistry, Japan -International Edition(JCCJIE), XML, Web of Science Emerging Source Citation Index (ESCI), Directory of Open Access Journals (DOAJ), Creative Commons License
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/3/21_2022-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, A13-A18, by J-STAGE]
<Title:> 憧れの千田範夫さん
<Author(s):> 薄井　玲子
<Corresponding author E-Mill:> usui(at)bri.or.jp
<Abstract:> 筆者が30年来憧れている千田範夫さんが亡くなってしまわれた．とても悲しく，寂しい．私が千田さんに憧れていることはご本人にもお伝えしているし，今までも方々で公言しているが，いま一度改めてお伝えするとともに，私が事務局を務めているCAMMフォーラムに千田さんがかつて寄稿された原稿をご紹介して，千田さんのご功績とお人柄を残したい．
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<URL:> https://www.jstage.jst.go.jp/article/jccj/21/3/21_2022-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, A19-A22, by J-STAGE]
<Title:> 千田顧問の遺したWinmostarとその思想
<Author(s):> 古賀　良太, 坂牧　隆司
<Corresponding author E-Mill:> rkoga(at)x-ability.jp
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/3/21_2022-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, A23-A24, by J-STAGE]
<Title:> Winmostar千田範夫さんの多大な貢献
<Author(s):> 本間　善夫
<Corresponding author E-Mill:> ecosci.honma(at)gmail.com
<Abstract:> 国内外で多くの方に利用されている原子・分子構造モデリング・可視化ソフトウェアWinmostar原作者の千田範夫さんが2021年に逝去された．独学でプログラミングを習得し，Winmostarを公開された業績は極めて大きなものがある．また全国各地で開催された公開イベントに出展され，分子の魅力を幅広くアピールし続けた一部を紹介したい．
<Keywords:> Computational chemistry, Molecular modeling and visualization software, Winmostar, Chemical education, Science communication
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/3/21_2022-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, A25-A25, by J-STAGE]
<Title:> 千田さんを偲んで
<Author(s):> 吉村　忠与志
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/3/21_2022-0017/_article/-char/ja/