月別: 2017年10月

[Published online Journal of Computer Chemistry, Japan Vol.16, 102-105, by J-STAGE]
<Title:> ポドフィリックアルデヒドの全合成における中間体の反応性の計算化学的考察
<Author(s):> 三原　陽子, 森川　大, 野村　泰志, 西井　良典
<Corresponding author E-Mill:> dmorikawa(at)shinshu-u.ac.jp
<Abstract:> The (-)-podophyllic aldehydes (Figure 1) exhibit notable antineoplastic cytotoxicity by apoptosis-inducing activities. In this study, we analyzed the selectivity mechanisms of some important reactions in the asymmetric total synthesis of (+)-podophyllic aldehydes which are enantiomers of the (-)-podophyllic aldehydes, by the molecular orbital method. As a result, it was shown that the selectivity of the Grignard reaction in compound 1 (Figure 2) is caused by steric hindrance. Furthermore, it was also indicated that the selectivity of the reduction in compound 2 1 is caused by the localization of LUMO at the reactive site, and the reduction in compounds 2 2 and 2 3 Scheme 2) does not proceed due to the steric hindrance by the trimethoxyphenyl group.
<Keywords:> Podophyllic aldehydes, Selectivity mechanism, Asymmetric total synthesis, Nucleophilic addiction, MO method
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0030/_article/-char/ja/

[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/