月別: 2020年2月

[Published online Journal of Computer Chemistry, Japan Vol.18, 199-201, by J-STAGE]
<Title:> レアイベントサンプリング法の開発と応用研究
<Author(s):> 原田　隆平, Vladimir　Sladek, 重田　育照
<Corresponding author E-Mill:> ryuhei(at)ccs.tsukuba.ac.jp
<Abstract:> Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a rare event sampling method of proteins, which does not rely on knowledge of the target structure. nt-PaCS-MD is an extension of targeted PaCS-MD (t-PaCS-MD). In nt-PaCS-MD, it makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. Reliable identification of these initial structures is the key to using nt-PaCS-MD. In the present study, we introduce the moving root-mean-square deviation (mRMSD) as a metric for identification of these statistical conformation outliers. mRMSD can be calculated for any ith geometry in the trajectory generated by short MD runs. The reference to which the mRMSD relates is the close surrounding of the ith conformation, often the (i-1) st one. Based on mRMSD, we show that it increases its effectiveness compared to the conventional MD.
<Keywords:> Protein, Molecular Dynamics Simulation, Conformational Sampling, Biologically Relevant Rare Event
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0036/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 202-204, by J-STAGE]
<Title:> フォルステライト表面における水分子の分解とプロトン拡散
<Author(s):> 久保　文音, 西澤　隼哉, 深澤　倫子
<Corresponding author E-Mill:> fukazawa(at)meiji.ac.jp
<Abstract:> To investigate the effects of forsterite structure on processes of H₂O decomposition and proton diffusion, we performed molecular dynamics calculations on forsterites in glassy and crystalline states. The result shows that the decomposition rate of H₂O on forsterite in the glassy state is higher than that in crystalline state in a temperature range of 200 to 400 K. Furthermore, the decomposed proton permeates into the internal part of glassy forsterite through hopping, whereas no permeation was observed for the crystalline state. These results suggest that the glassy structure of forsterite is an important factor for chemical evolution processes in interstellar spaces.
<Keywords:> Molecular dynamics calculation, Forsterite glass, Forsterite crystal, Amorphous ice, Surface
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0041/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 205-207, by J-STAGE]
<Title:> Geometric and Electronic Structures of Acene Crystals: A van der Waals Density Functional Theory Study
<Author(s):> Ryota MIYAZAKI, Ikutaro HAMADA
<Corresponding author E-Mill:> ihamada(at)prec.eng.osaka-u.ac.jp
<Abstract:> We demonstrate that accurate prediction of the crystal structures of anthracene and its derivatives is possible with the van der Waals density functional. Based on the calculated crystal structures, we investigate their electronic structures and discuss the correlation between crystal structure/molecular configuration and the electronic structure, in particular, the dispersion of the bands composed of the highest occupied molecular orbitals, which are important to discuss the charge carrier transport property.
<Keywords:> Organic semiconductor, Molecular crystal, Acene, Density functional theory, Van der Waals density functional
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 194-197, by J-STAGE]
<Title:> GaussianとGAMESSが内蔵している基底関数の違い
<Author(s):> 竹内　宗孝, 吉田　真史, 長嶋　雲兵
<Corresponding author E-Mill:> myoshida(at)tcu.ac.jp
<Abstract:> 非経験的分子軌道法の計算コードであるGaussianとGAMESSはSTO-3G等の基底の名称を指定するだけで使用できるが，同一名称の基底であっても同一のパラメータセットではない場合は，両者の答えに違いが生じる．本稿では2つのプログラムを使って研究を行っているユーザに注意を喚起するために，第三周期元素の水素化物(NaH，MgH₂，AlH₃，SiH₄，PH₃，H₂S，HCl) についてSTO-3Gを用いた計算をGaussianとGAMESSとで実行し計算結果を比較した．その結果，HClを除き全エネルギーとHOMOのエネルギーはGaussianよりGAMESSのほうが低くなった．これは第三周期元素の原子基底の3s軌道と3p軌道の空間的広がりの違いに起因する．またMulliken電荷は，GaussianよりGAMESSのほうが小さくなった．いくつかの別のプログラムを使用するとき，入力データが利用者が意図した電子状態を記述できうるかを吟味することは大切なことである．
<Keywords:> basis set, Gaussian, GAMESS, STO-3G, total energy, HOMO energy, Mulliken charge
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/4/18_2019-0007/_article/-char/ja/