投稿者: 博佐藤

[Published online Journal of Computer Chemistry, Japan Vol.16, 96-97, by J-STAGE]
<Title:> The Koide’s Equation for the Sums of Masses in the Same Sectors
<Author(s):> Hideyuki NARUMI
<Corresponding author E-Mill:> nrhd2357(at)gray.plala.or.jp
<Abstract:> Koide’s equation was discovered for masses in the same sectors.
<Keywords:> Koide’s Equation, the Masses of the Same Sector, Brannen, Fermion Particles, Gluons
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0025/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 98-101, by J-STAGE]
<Title:> Na₂O-K₂O-SiO₂ 系ガラスにおける混合アルカリ効果の考察
<Author(s):> 山本　優也, 澤口　直哉, 佐々木　眞
<Corresponding author E-Mill:> 16096004(at)mmm.muroran-it.ac.jp
<Abstract:> The mechanism of the mixed alkali effect of 0.25{xK₂O-(1-x) Na₂O}-0.75SiO₂ glasses was studied by using the molecular dynamics (MD) simulation. MD simulations of this work reproduced the mixed alkali effect. In addition, the tendency of molar volume with temperature change by this work was reproduced in the experimental tendency. The mixing of alkali was independent to the network structure of Si and O. The free volume in the glass systems indicated that high condensed packing occurred by alkali mixing. The results of ³⁹K¹³³KSi₃O₇ glass showed that the mass difference from one alkali metal ion decreased the diffusion of the other alkali metal ion. The mixed alkali effect was considered to relate to both the size- and the mass-differences of the coexisting alkali metal ions.
<Keywords:> Molecular dynamics simulation, Mixed alkali effect, Silicate glass, Self-diffusion, Mechanism
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0032/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 89-90, by J-STAGE]
<Title:> プローブ分子によるタンパク質の結合サイト探索
<Author(s):> 佐藤　博之, 松浦　東
<Corresponding author E-Mill:> shryk(at)jp.fujitsu.com
<Abstract:> A new and efficient approach for analyzing protein-ligand binding sites is proposed using a large number of properly interacting probe molecules with human coagulation factor Xa (fXa). Firstly, the probe molecules are set up to mimic the functional groups of the known ligand RRR, and cover the fXa surface by molecular dynamics (MD) simulation without water. Then, the unit cell is filled with water for following MD simulation to replace weakly binding probe molecules with water. The analyzed probe density explains well the experimental crystal structure of RRR whose terminal pyridine group is placed in the unexpected S4 pocket. This result indicates that the probe density evaluated from this approach has the ability to explain the binding orientation of a ligand.
<Keywords:> Protein-ligand binding site, Probe molecule, Molecular dynamics, Density, Binding orientation
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0028/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 81-82, by J-STAGE]
<Title:> 4成分相対論における超微細結合定数の定式化に関する考察
<Author(s):> 砂賀　彩光, 阿部　穣里, 波田　雅彦
<Corresponding author E-Mill:> sunaga-ayaki(at)ed.tmu.ac.jp
<Abstract:> We analyze the relativistic effects of the hyperfine coupling constant (HFCC) by using the solutions of the Dirac and Schr dinger equations of Hydrogen-like atoms. We find that the relativistic effects of HFCC of the ground states of the Hydrogen-like atoms (Z = 30, 40) are about 8% and 15%, respectively.
<Keywords:> Hyperfine coupling constant, Dirac equation, Hydrogen-like atom, Hydrogen atom, Relativistic effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 83-88, by J-STAGE]
<Title:> 調和溶媒和モデル(HSM)を用いた 凝縮系の自由エネルギー計算
<Author(s):> 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We have proposed a novel quantum chemical model to evaluate condensed-phase thermodynamic properties, that is, the harmonic solvation model (HSM). This paper explains the theoretical background of HSM and the practical procedure to use for the HSM with some sample inputs. Illustrative applications demonstrate the usefulness and accuracy of HSM.
<Keywords:> Condensed-phase thermodynamic property, Quantum chemical calculation, Solvation effect, Rotational and translational entropies, Molecular partition function
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 91-92, by J-STAGE]
<Title:> 閉殻重原子系における外部静磁場によって誘起される電子スピン密度の解析
<Author(s):> 宮本　優弥, 小山　裕貴, 波田　雅彦
<Corresponding author E-Mill:> hada(at)tmu.ac.jp
<Abstract:> We present a clear equation and a simple display method to analyze theoretically the spin density induced by an external static magnetic field in closed-shell molecules containing heavy atoms (Xe and HI). We showed that the magnitude of the spin density in a heavy-atom-light-atom (HALA) system is proportional to the mixing of the opposite spin orbital caused by the spin-orbit interaction.
<Keywords:> Heavy atom NMR chemical shift, Spin density map, Spin-orbit interaction, Zeeman interaction, Spin polarization
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0031/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 93-95, by J-STAGE]
<Title:> Quantum Chemical Study on the Multi-Electron Transfer of Keggin-Type Polyoxotungstate Anions: The Relation of Redox Potentials to the Bond Valence of ₄-O-W
<Author(s):> Aki TAKAZAKI, Kazuo EDA, Toshiyuki OSAKAI, Takahito NAKAJIMA
<Corresponding author E-Mill:> 148s231s(at)stu.kobe-u.ac.jp
<Abstract:> By selectively investigating the effect of the bond valence using the hypothetical [(PO₄)W₁₂O₃₆]³ species having various bond valences, we could clearly reveal the origin of the linear dependence of the LUMO energy (or the redox potential) on the bond valence. The LUMO of the Keggin-type polyoxotungstates mainly consists of W 5d. The energy of W 5d as well as of the LUMO goes down as the bond valence becomes large (i.e., as the net electron population on W decreases due to the electron-withdrawing effect of the μ₄-O atoms). This is the origin of the linear dependence of LUMO energy on the bond valence.
<Keywords:> Multi-electron transfer, Polyoxometalate, Polyoxotungstate, DFT, LUMO
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, A23-A26, by J-STAGE]
<Title:> 電子を描く(8) 球形彫刻とその特徴
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> tokita(at)apc.saitama-u.ac.jp
<Abstract:> 水素原子の波動方程式を解いて得られる極座標(動径波動関数と球面調和関数の積)で表される原子軌道を実軌道関数化し，球殻状の節面を持たない1s – 6h軌道の平方を，球形のガラスブロック内に実3次元で彫刻した．球形彫刻をZ 軸まわりに連続して回転すると，複素軌道関数(極座標で表される軌道)の確率密度が観察できた．
<Keywords:> Keywords electron, visualization, hydrogen atom, atomic orbital, imaginary wave function, real wave function, real 3-dimensional representation of an electron
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/3/16_2017-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 63-69, by J-STAGE]
<Title:> 反復構造を持つ高分子に対する分子動力学計算のためのパラメータ設定支援プログラムo2pの開発
<Author(s):> 矢部　誠, 園部　智彩, 上田　一義, 武田　穣
<Corresponding author E-Mill:> takeda-minoru-bd(at)ynu.ac.jp
<Abstract:> Molecular dynamics (MD)の実行に必須の結合角や電荷などのパラメータセット(力場)がライブラリに存在しない場合，力場の量子力学計算による算出やパラメータ自動生成 ツールの活用という手法が用いられる．しかし，これらの手法は原子数の多い高分子の場合には適していない．そこで，3つの単位構造(両末端の単位 と中央部の繰り返し単位)を含むオリゴマーの力場を算出し，それらをポリマー形式(両末端部+中央部 × n)に変換し対処することがよく行われる．しかしながら，変換は手作業にならざるを得ず，非効率的でヒューマンエラーの恐れもある．そこで，反復構造を持 つ高分子に対するMDを簡便かつ確実に実行すべく，分子動力学ソフトとして汎用されているGromacs用の力場変換半自動化プログラムo2pを 開発した．開発にあたっては，作業負荷の低減と時間短縮を意図してGUIを積極的に取り入れた．また，複雑なファイル変換過程を自動化することに よってヒューマンエラーの一掃を目指した．本プログラムにより変換したファイルを用いてノナン中のアミロース分子を想定した系でMDを実行したと ころ，実験による報告と同じく左巻きの一重らせん構造が形成され，プログラムが有効に動作していることを確認した．
<Keywords:> Molecular dynamics simulation, Macromolecules, Parameters, Gromacs, Polymer, Repeating unit
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/3/16_2017-0013/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 70-76, by J-STAGE]
<Title:> 線形変換と交差検証法による空間線量率予測
<Author(s):> 青山　智夫, 八木　徹, 神部　順子
<Abstract:> 環境中のγ線線量値を長期にわたり予測するため，放射性核種の物性と担体の拡散を考慮した空間線量値の時間変化を直線化する方法を提示した．現象の変化が 直線化できると予測は線形補外となる．交差検証法で過去のデータの一部を用いて予測を行い実測との対応から予測精度を見積る．将来の予測計算も， 過去の処理と同一である．方法自体の精度のオーダは同じである．本処理の可能性を示す指標も示した．福島県伊達市下小国集会所のモニタリング・ポ ストのデータでテストすると，線量予測式と実測値の決定係数は0.9以上，1年先の予測値では0.7であった．観測点の気象的擾乱，周辺環境の変 化は決定係数の低下として現れる．我々は，福島原子力発電所事故により他の市町村に避難し，帰宅時期を考慮している人を想定した．
<Keywords:> Gamma-ray ambient dose rate, Flux prediction, Forest fire, Soil flow, Radioactive cesium
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/3/16_2016-0070/_article/-char/ja/