カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.20, 97-99, by J-STAGE]
<Title:> ヘモグロビンのアロステリック制御に関するデータ科学的研究
<Author(s):> 田中　美帆, 高橋　由芽, 高見　慧, 北村　勇吉, 長岡　正隆
<Corresponding author E-Mill:> kitamura.yuhkichi(at)shizuoka.ac.jp
<Abstract:> In this letter, we investigated the contribution of bridging hydrogen bonds (BHB) via Cl^– on the T-R transition of human adult hemoglobin (HbA). We applied the time-series clustering method to time-series data of the αβ dimer rotation angle φ and the total number of the BHBs. Compared with the above two results, we have concluded that Cl^–-BHBs do not significantly contribute to the structural regulation of HbA.
<Keywords:> Keyword Hemoglobin, Allostery regulation, Chloride ion, Bridging hydrogen bond, Time-series clustering method
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0045/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 92-93, by J-STAGE]
<Title:> FMO結晶エネルギーを用いた結晶構造予測の高精度化
<Author(s):> 内海　洋平, 梅田　大貴, 奥脇　弘次, 小畑　繁昭, 中山　尚史, 後藤　仁志, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> k-fukuzawa(at)hoshi.ac.jp
<Abstract:> The aim of this study is to improve the accuracy of crystal structure prediction for Target XXIII, which was the target of the 6th Crystal Structure Prediction Blind Test (CSP6), by using the fragment molecular orbital (FMO) method. The intermolecular interaction analysis revealed that the dispersion interaction is stronger than the electrostatic interaction in all crystal polymorphs. In our method, the three correct structures included in the predicted structures were located within the top five. Furthermore, it was possible to evaluate the stability of polymorphs by the difference of intramolecular hydrogen bonds.
<Keywords:> Polymorphism, Crystal structure prediction, CONFLEX, Fragment molecular orbital method, ABINI-MP
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.7, -, by J-STAGE]
<Title:> Development of a Protein-Gene Motif Dictionary System for One-Stop Motif Analysis
<Author(s):> Masahiro OHTOMO, Hiroaki KATO
<Corresponding author E-Mill:> ohtomo(at)kuicr.kyoto-u.ac.jp
<Abstract:> The amino acid sequence of a protein is closely related to its structure and function. This is especially true for particular structural features called motifs, which are well-reserved sites in genome sequences. Biological data, such as the data for biopolymers, are rapidly increasing. Constructing a database for efficient analysis is important for identifying the structure and function of unknown biological data. Here, we constructed a protein-gene motif dictionary system for several model species using NoSQL, a database management system. This dictionary stored protein sequence motifs based on PROSITE, along with their corresponding mRNA sequences. Additionally, the database stored 3D structural information of the corresponding protein sequence motifs. The protein-gene dictionary has 49,265 registered entries, 120,047 sequence motifs, and 57,452 3D structural motifs from 7 model species. Software tools with graphical user interface were also developed to assist with intuitive search and analysis using the system. As a result, we discovered that zinc protease motif had co-occurrence with the cysteine switch motif. It was followed by the cysteine switch motif with a gap of 117 to 293 amino acids, however, its 3D Euclidean distance was preserved at around 12 .
<Keywords:> Protein motif, Nucleotide motif, Protein-gene motif dictionary, 3D structural motif, PROSITE, Co-occurrence motif analysis
<URL:> https://www.jstage.jst.go.jp/article/jccjie/7/0/7_2020-0008/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.7, -, by J-STAGE]
<Title:> Effect of meso-Substitution on the Selectivity of the Propene Reaction by Fe(IV)OCl Porphyrin: a Density Functional Theory Mechanistic Study
<Author(s):> Zhifeng MA, Masahiko HADA
<Corresponding author E-Mill:> hada(at)tmu.ac.jp
<Abstract:> We have performed density functional theory (DFT) calculations of C=C epoxidation and C-H hydroxylation of propene using a model of Fe(IV)OCl porphyrin cation radical complexes with fluorine and methyl groups as meso-substituents of the porphyrin ring. By gas-phase DFT calculations, it is found that fluorine substitution enhances the reactivity. According to detailed electronic feature analysis of the reactant complexes and transition states, electron-withdrawing groups at the meso-position stabilize the electron acceptor orbital of the complex more than the electron donation orbital of the substrate, leading to a decrease in the energy gap between these orbitals, and a lower energy barrier. More importantly, fluorine substitution for the pull effect makes hydroxylation favorable, whereas methyl substitution makes epoxidation preferable. The selective oxidation reactivity of Fe(IV)OCl porphyrin is largely ascribed to the effect of meso-substitution on the amount of electron transfer from propene to Fe(IV)OCl porphyrin. Additionally, we analyzed intersystem crossing between the quartet and sextet spin states using the potential energy surfaces (PESs), and the crossing seam between the quartet and sextet PESs occurs at around transition state TS1.
<Keywords:> Density functional theory, meso-substitution effect, Oxoiron(IV) porphyrin, Electronic structure, Molecular orbital
<URL:> https://www.jstage.jst.go.jp/article/jccjie/7/0/7_2020-0011/_html

[Published online Journal of Computer Chemistry, Japan Vol.20, A12-A15, by J-STAGE]
<Title:> 進化する社会と学問:コンピュータ化学との出会いと未来に生きる世代への期待
<Author(s):> 宮本　明
<Abstract:> 新しい日本国憲法施行の日にうまれてから73年，大学卒業からでも50年，大学での教員・研究者として過ごしてきたが，その間の研究の展開について，「進化する社会と学問」の観点で纏めた．特に，コンピュータ化学に出会ってからは，「進化する社会と学問」を強く意識することにより，研究推進に力を得ることが多かった．未来に生きる世代には，それに加え，「自分の飯のタネは自分で考える」ことの大切さを強調した．
<Keywords:> Catalyst, Environment technology, Computational chemistry, iIndustry-academy collaboration, Research development, Research philosophy
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2020-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, A17-A19, by J-STAGE]
<Title:> 計算カガクをネットでツタエル
<Author(s):> 本間　善夫
<Corresponding author E-Mill:> ecosci.honma(at)gmail.com
<Abstract:> 新型コロナウイルスの影響で全国の科学イベントが制限されたりオンライン開催になるなどしている．日本コンピュータ化学会の公開イベント等も影響を受けていることを紹介し，計算科学の役割を知ってもらう上でも，オンラインコンテンツの公開やソーシャルメディア活用による連携の必要性を述べる．
<Keywords:> Science communication, Chemical education, Internet, Online contents, Social media
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2021-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, A20-A20, by J-STAGE]
<Title:> 私と日本コンピュータ化学会
<Author(s):> 志穂 曽々木
<Corresponding author E-Mill:> shiho(at)hpc-sol.co.jp
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2021-0046/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, A21-A26, by J-STAGE]
<Title:> 電子を描く(11) ― 電子の波が分子をつくる
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> tokita(at)apc.saitama-u.ac.jp
<Abstract:> 水素原子がふたつ集まって水素分子をつくる過程を原子価結合法や分子軌道法で取り扱うと，分子を形成した方が安定になることを説明できる．このとき，分子軌道における原子軌道の波の重なり方が同じ位相のときは安定な結合性分子軌道が出来，異なる位相のときは不安定な反結合性分子軌道が出来る．
<Keywords:> Keywords hydrogen atom, atomic orbital, hydrogen molecule, molecular orbital (MO), electron, wave, interference, in-phase, out-of-phase, bonding, antibonding, highest occupied MO (HOMO), lowest unoccupied MO (LUMO), difference electron densit
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2021-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, A27-A41, by J-STAGE]
<Title:> 日本コンピュータ化学会20周年に寄せて
<Author(s):> 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> 日本コンピュータ化学会（SCCJ）は，日本化学プログラム交換機構（JCPE）と化学ソフトウェア学会（CSSJ）が合併して2002年1月1日に設立され，まもなく創立20周年を迎える．この記事では，コンピュータ化学に関連する文献を紹介することにより，SCCJの過去20年間を振り返りる．まず，化学，物理学，工学，材料科学，生化学などの研究分野ごとに文献数を比較する．次に，引用数の多い上位100位の文献のいくつかを，方法論，ソフトウェア，データベース，およびトピックに分類して説明する．
<Keywords:> Computational chemistry, Quantum chemistry, Molecular simulation, Machine learning, Quantum simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2021-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, A42-A49, by J-STAGE]
<Title:> Support Vector Machineを用いた国内の新型コロナウイルス(COVID-19)死亡率の分析
<Author(s):> 田辺　和俊, 鈴木　孝弘
<Corresponding author E-Mill:> kazutoshitanabe(at)jcom.home.ne.jp
<Abstract:> 全世界に蔓延している新型コロナウイルス(COVID-19)の日本における死亡要因を探るために，都道府県別の死亡率を目的変数とし，生活や健康，社会経済的要因など各種の指標を説明変数として重回帰分析による実証研究を試みた.目的変数と説明変数との非線形関係に対処するためにSupport Vector Machineを適用し，感度分析により要因を探索した.その結果，死亡率を上げる危険要因として生活保護，都市化，貧困率，サービス業，性比の5種，死亡率を下げる防御要因として単独世帯，食事，睡眠の3要因，併せて計8種の要因が得られた.特に，いわゆる「三密」に関連する都市化，サービス業，単独世帯の3要因の寄与がもっとも大きいこと，次いで貧困層の実態を反映する生活保護と貧困率の寄与が大きいことなど，新型コロナウイルスの予防対策に関して新規かつ有用な知見が得られた.
<Keywords:> COVID-19 Mortality, Socio-economic Factor, Support Vector Machine
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/2/20_2020-0030/_article/-char/ja/