カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.19, 161-163, by J-STAGE]
<Title:> 分子動力学シミュレーションによる嗅覚受容体タンパク質mOR-EGと香り分子オイゲノールの結合解析
<Author(s):> 岡本　千怜, 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> Molecular dynamics (MD) simulations were used to analyze the effect of the odorant molecule eugenol on the olfactory receptor protein mOR-EG and the dynamic correlation between amino acid residues around the binding site due to ligand binding. When eugenol hydrogen-bonded with Ser 113 of mOR-EG, the dynamic correlation with amino acid residues 213-218 on the adjacent α-helix increased within 10 ps. In particular, the correlation between Ser 113 and Leu 217 showed characteristic oscillations between 10 ps and 30 ps. The correlation with Leu 217 shifted toward residues closer to the G protein over time. Correlation with amino acids on the other side of the membrane was also observed, suggesting the contribution of collective protein motion
<Keywords:> Molecular dynamics simulation, Olfactory receptor, Membrane protein, Dynamical cross correlation
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 133-135, by J-STAGE]
<Title:> 計算化学を用いた新規メタン水酸化触媒の提案
<Author(s):> 池田　京, Mahyuddin　Muhammad Haris, 塩田　淑仁, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> Motivated by a recent study on light-induced solar cell that Iridium-oxo complex over WO₃ electrode catalyze water oxidation reaction, we investigated the methane hydroxylation reaction by the same complex. Herein we focused on the closed-shell singlet state reaction due to the no-radical intermediate mechanism although this reaction is energetically unfavored reaction. Using intrinsic bond orbital analysis, we found that the C H bond cleavage reaction proceed via the hydride transfer mechanism. From the view point of orbital interaction between σ orbital (C H bond in methane) and π* orbital (Ir=O bond in Ir complex), we demonstrated that the reactivity of the methane hydroxylation reaction in the closed shell singlet state depends on the energy level of π* orbital.
<Keywords:> DFT calculation, Methane hydroxylation, Iridium-oxo complex, IBO analysis, Orbital interaction
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 139-141, by J-STAGE]
<Title:> Reactive Molecular Dynamics Simulation on Friction-induced Chemical Reactions of SiC in Water Environments
<Author(s):> Masayuki KAWAURA, Yang WANG, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp
<Abstract:> Silicon carbide (SiC) exhibits super low friction in water environments. It has been well noticed that this super low friction property is caused by the generated lubricating layers through friction-induced chemical reactions. However, the chemical reactions at the friction interface have not been well clarified because it is difficult to observe the tribological processes at the friction interface in experiments. In the present study, we simulated the friction processes of SiC/SiC in water environments using reactive molecular dynamics simulations. It is interesting to observe that the hydrolysis reactions of Si-C and Si-Si bonds occurred, and however, the chemical reactions of C-C bonds hardly occur, indicating that Si atoms are preferentially oxidized and C atoms are not. The oxidation of Si atoms in SiC generates colloidal silica lubricating layers at the friction interface, being responsible for the super low friction of SiC.
<Keywords:> Molecular Dynamics, Friction, Wear, Silicon Carbide, Water Lubrication
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0010/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 146-148, by J-STAGE]
<Title:> β-LiAlSiO₄結晶の温度変化シミュレーション
<Author(s):> 藤田　和希, 澤口　直哉
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp
<Abstract:> Anisotropic low-thermal expansion of β-LiAlSiO₄ crystal was reproduced by MD calculation applying a potential model of a spherically symmetric two-body interatomic interaction. From the correlation between the Si-O-Al angle and the Si-Al distance in the c-axis direction, the expansion of a-axis and the contract of c-axis brings the split of Si-O-Al angle distribution. At the same time, the stable position of Li⁺ ion sites also changed. This suggests the cation position also important in the mechanism of low-thermal expansion observed in silicate materials.
<Keywords:> Molecular dynamics, Beta-eucryptite, Thermal expansion, Bonding angle distribution
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 136-138, by J-STAGE]
<Title:> ミクロ相分離構造の最大連結成分と自由エネルギー
<Author(s):> 川口　裕靖, 伊藤　真利子, 山中　貞人, 青柳　岳司, 大西　立顕
<Corresponding author E-Mill:> 20vr029p(at)rikkyo.ac.jp
<Abstract:> In this study, we attempted to quantify the shape of various metastable structures of microphase separation of ABA triblock copolymers that can be observed in a computer simulation. For the quantification, we focused on the domains where the volume fraction of B (or A) is greater than a preset threshold, and defined a measure that indicates how the size of the largest connected component of such domains decreases as the threshold increases. The value of the measure was strongly correlated with the free energy of the metastable structures.
<Keywords:> Block copolymers, Microphase separation, Largest connected component, Metastable structures, Free energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0001/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 142-145, by J-STAGE]
<Title:> FMOプログラムABINIT-MPの整備状況2020
<Author(s):> 望月　祐志, 坂倉　耕太, 渡邊　啓正, 奥脇　弘次, 加藤　幸一郎, 渡辺　尚貴, 沖山　佳生, 福澤　薫, 中野　達也
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing the ABINIT-MP program for fragment molecular orbital (FMO) calculations. In this report, improvements in the latest release Ver. 1 Rev. 22 and demonstrative applications on the Fugaku and ITO supercomputers are summarized.
<Keywords:> Fragment molecular orbital, FMO, ABINIT-MP, Supercomputer
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0015/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 149-150, by J-STAGE]
<Title:> アミノ酸間相互作用ポテンシャルにおける光学異性体の影響
<Author(s):> 寺島　千絵子, 谷田　義明, 佐藤　博之
<Corresponding author E-Mill:> c.terashima(at)jp.fujitsu.com
<Abstract:> In order to accelerate the conformational search of peptides, a coarse-grained model in which amino acid residues were treated with an amino acid pair interaction potential was investigated. To treat both natural and artificial types of amino acids and staples, new interaction potentials were developed by umbrella sampling. For the new potential, the effect of optical isomer was investigated with the threonine potential. As a result, the potential of allo-threonine was different from that of L-threonine.
<Keywords:> amino-acid, Peptide, Coarse-grained model, Interaction potential, Molecular dynamics
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0006/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 128-130, by J-STAGE]
<Title:> Implementation of Picture Change Corrected Density Functional Theory Based on Infinite-Order Two-Component Method to GAMESS Program
<Author(s):> Chinami TAKASHIMA, Junji SEINO, Hiromi NAKAI
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We implemented the picture change correction method for two-electron Coulomb interaction and density operator, which was based on the infinite-order two-component method with the local unitary transformation, to the GAMESS program. Numerical assessments for molecules containing heavy element confirmed the accuracies and efficiencies of the implementation. Furthermore, the comparison with several types of treatments indicated that whole picture change corrections of one- and two-electron operators and the density operator are necessary for accurate two-component density functional theory calculations.
<Keywords:> Relativistic effect, Infinite-order two-component theory, Local unitary transformation, Picture change, DFT
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0002/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 125-127, by J-STAGE]
<Title:> 環状ペプチドの膜透過における溶媒和自由エネルギー計算
<Author(s):> 栁　昂輝, 原田　隆平, 満田　祐樹, 重田　育照
<Corresponding author E-Mill:> shigeta(at)ccs.tsukuba.ac.jp
<Abstract:> The solvation free energies of cyclic dipeptides (CDPs) for a membrane were calculated to evaluate their membrane permeabilities. As a result, there were energy barriers between the membrane center and interface for each CDP. Furthermore, the profiles of solvation free energy depended on the amino acids that construct each CDP. These results indicate that each CDP changes its membrane permeability. Our results will be useful for designing cyclic peptides in the field of medium-molecular-weight drugs.
<Keywords:> MD, Cyclic Dipeptide (CDP), Solvation Free Energy, Energy Representation, Membrane Permeation Process
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0008/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 131-132, by J-STAGE]
<Title:> プロトン伝導性PVPA-xIm複合体のプロトン伝導機構の理論的解明
<Author(s):> 堀　太, 末武　鋭也, 井田　朋智, 水野　元博, 重田　育照
<Corresponding author E-Mill:> hori(at)ccs.tsukuba.ac.jp
<Abstract:> This paper overviews the local structures and dynamics of imidazole (Im) in proton-conducting poly (vinylphosphonic acid)-Im (PVPA-xIm) composites investigated by density functional theory calculations and molecular dynamics simulations. These calculations propose the proton conduction mechanism of PVPA-xIm based on Grotthuss-type mechanism consisting the following processes: proton transfers from PVPA to Im and between Im, and the reorientation of Im in the hydrogen-bond Im cluster.
<Keywords:> Imidazole, Proton conduction mechanism, Molecular dynamics simulation, Density functional theory, Grotthuss-type mechanism
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2020-0028/_article/-char/ja/