Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.3, -, by J-STAGE]
<Title:> Thermodynamics of Three-phase Equilibrium by Van Der Waals Equation of State
<Author(s):> Yosuke KATAOKA
<Abstract:> The phase diagram for a three-phase equilibrium was derived using van der Waals (vdW) equation of state (EOS) with respect to pressure. Aside from the typical liquid-gas vdW EOS, a new solid-gas vdW EOS was introduced. The new vdW EOS had the same functional form as the original equation of state and only the van der Waals coefficients were different. The thermodynamic EOSs were integrated to obtain the internal energy and the integral constants were given explicitly. The calculated phase diagram was consistent with that for argon and the Lennard-Jones system.
<Keywords:> Three-phase equilibrium, Van der Waals equation of state, Argon, Lennard-Jones system, Thermodynamics
<URL:> https://www.jstage.jst.go.jp/article/jccjie/3/0/3_2017-0026/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.3, -, by J-STAGE]
<Title:> Calculation of the Melting Entropy of Argon at Constant Volume Using Molecular Dynamics
<Author(s):> Yosuke KATAOKA
<Abstract:> The melting entropy values of argon at constant volume (Δ_vS) as a function of density were calculated using molecular dynamics simulations. These calculations employed cells with N = 864 molecules. The resulting entropy of melting per particle, Δ_vS/N, was found to be essentially constant (with some slight effect of the crystal form) and nearly equal to 0.5 k, where k is the Boltzmann constant. The melting entropy values at constant pressure (Δ_pS) were also determined and it was observed that Δ_pS > Δ_vS. In addition, variations in the vibrational frequency in the liquid were compared with fluctuations in the solid near the melting point as a means of further investigating the melting entropy.
<Keywords:> Melting entropy at constant volume, Argon, Molecular dynamics, Fluctuation of vibrational frequency
<URL:> https://www.jstage.jst.go.jp/article/jccjie/3/0/3_2017-0021/_html

[Published online Journal of Computer Chemistry, Japan Vol.16, 110-111, by J-STAGE]
<Title:> Parameterization of Reactive Force Field for Iron Water System
<Author(s):> Qian CHEN, Jingxiang XU, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp
<Abstract:> Reactive force field parameters are re-optimized for simulating the stress corrosion cracking (SCC) of iron-based material in a supercritical water environment. The parameters for molecular dynamics (MD) simulation are determined by fitting the adsorption energies of H, OH, and H₂O on an Fe(110) surface obtained by reactive force field to the density functional theory (DFT) calculations. The errors of adsorption energies for the most stable positions are less than 5%, and our parameters are in good agreement with the DFT calculations. The development of Fe/O/H parameters is expected to contribute to SCC simulation of iron-based materials in supercritical water environments.
<Keywords:> Molecular dynamics simulation, Reactive force field, DFT calculation, Iron-based material
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 108-109, by J-STAGE]
<Title:> スペクトル解析法による固体有機結晶の振動スペクトル計算法
<Author(s):> 末永　太河, 高橋　修
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp
<Abstract:> We performed MD calculations on chloroform and 1,3,5-triamino-2,4,6-trinitrobebzene (TATB) and further frequency analysis under high pressure. Peaks around 3000 cm^-1 of chloroform uniformly blue shifted, but ones around 3000 cm^-1 of TATB were red shifted. It was concluded that whether hydrogen bonds are formed or not greatly influences the shift of the peaks of the two stretching vibrations.
<Keywords:> Solid organic crystal, Spectral analysis, Chloroform, TATB
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0027/_article/-char/ja/

[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/