月別: 2015年9月

Journal of Computer Chemistry, Japan [No.2015-0031] Published online by J-STAGE
<Title:> 分割統治型密度汎関数強束縛分子動力学 (DC-DFTB-MD)法の最近の展開
<Author(s):> 西村　好史, 海寳　丈彰, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp<Abstract:> The authors’ group has developed the program named DC-DFTB-K for the on-the-fly quantum mechanical molecular dynamics (MD) simulation of huge systems using the density-functional tight binding (DFTB) method. The combination with the divide-and-conquer (DC) method enables linear-scaling calculation of DFTB energy and its derivatives. Due to the massively parallel implementation, the program can treat systems containing one million atoms on the K computer. In this paper, the recent extension of DC-DFTB-MD technique is outlined together with the illustrative application to chemical reaction dynamics in lithium-ion device.
<Keywords:> Divide-and-conquer method, Density-functional tight-binding method, Linear-scaling calculation, Molecular dynamics, Chemical reaction simulation, Parallel quantum chemistry calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0031/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0030] Published online by J-STAGE
<Title:> 血液凝固因子XaとリガンドとのFMO相互作用解析
<Author(s):> 佐藤　博之, 松浦　東<Abstract:> The role of water in the protein-ligand binding site was investigated from the viewpoint of enthalpic bridging between human coagulation factor Xa (fXa) and four ligands. Ligand-constrained MD simulation was done for identifying hydration sites and representative water molecules were arranged at the sites. The calculated fXa-ligand interaction energy while considering these explicit water molecules as parts of fXa shows excellent correlation to the experimental binding affinity, while the energy with considering them as implicit solvent does not correlate. This result indicates that the representative water molecules at the hydration sites should be explicitly considered when protein-ligand interaction energy is analyzed, and ligand-constrained MD simulation is a powerful tool to identify these hydration sites.
<Keywords:> Hydration sites, Interaction energy, Binding affinity, Ligand-constrained MD, FMO
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0030/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0028] Published online by J-STAGE
<Title:> キラルな二核亜鉛錯体によるペプチド加水分解反応の立体選択性
<Author(s):> 崎山　博史
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp<Abstract:> Chiral dinuclear zinc(II) complexes [Zn2(R-bppmp)(MeCO2)2]BPh4 (1R) and [Zn2(S-bppmp)(MeCO2)2]BPh4 (1S) were previously reported to hydrolyze peptide bonds, and the activity of 1S was two times larger than that of 1R. In order to clarify the reason for the difference in activity, substrate incorporation modes were investigated on the basis of Density Functional Theory (DFT) method. Consequently, in the case of 1S, the most stable isomer was found to be suitable in incorporating the substrate in a stable form. As for the case of 1R, the most stable isomer was found to be not suitable, whereas the second most stable isomer was found to be suitable in incorporating the substrate in a stable form.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0028/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0026] Published online by J-STAGE
<Title:> 液体状態における酢酸，ギ酸メチルの分子間相互作用依存性
<Author(s):> 西田　尚大, 金井　清二, 徳島　高, 堀川　裕加, 高橋　修
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp<Abstract:> We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of acetic acid and methyl formate in the liquid phase at two oxygen K-edge (OC=O and OOH,OCH3) to observe the intermolecular interaction dependence of XES spectra. Structure sampling as a cluster model was performed from a snapshot of molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. We found that theoretical XES spectra were well reproduced experimentally.
<Keywords:> XES spectrum, site selectivity, core-hole excited state, intermolecular interaction, MD simulation, cluster sampling
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0026/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0025] Published online by J-STAGE
<Title:> Calculation of NMR Shielding Constants with Optimized Numerical Basis Function
<Author(s):> Katsumi Nakagawa
<Corresponding author E-Mill:> nakagawa.katsumi(at)nifty.com<Abstract:> Isotropic NMR shielding constants σiso were calculated for hydrogen, carbon, nitrogen, oxygen, fluorine and phosphorous atoms in small molecules by using numerical basis functions, which were based on AOs of Discrete Variational Xα (DV-Xα) method and were modified to London atomic orbitals to avoid the gauge-origin-dependence when magnetic field exists. In DV-Xα method AOs are prepared by solving the Hartree-Fock-Slater (HFS) equation substantially equivalent to that used to calculate MOs and are very accurate around each nucleus. However, σisos calculated in the default condition of DV-Xα method don’t agree well to experimental ones. By optimizing AOs in a reasonable way, σisos were highly improved and agreed with experimental ones far better than results by Hartree-Fock (HF) method having conventional basis functions. The usefulness of MOs constructed with optimized numerical basis functions was clearly demonstrated.
<Keywords:> NMR shielding constant, Chemical shift, Basis function, DV-Xα method, London atomic orbital
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0025/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0007] Published online in advanced by J-STAGE
<Title:> UO2-ZrO2固溶体の融点および熱伝導率の分子動力学解析
<Author(s):> 有馬　立身
<Corresponding author E-Mill:> arima(at)nucl.kyushu-u.ac.jp<Abstract:> 原子炉過酷事故の事象進展には溶融燃料の熱的物性が大きく影響する．溶融燃料の主な物質であるUO2-ZrO2固溶体の融点を古典分子動力学法を用いて組 成をパラメータとして，また熱伝導率を組成・温度を変えて固体から液体状態まで評価した．融点に関しては固液2相共存法が単相で評価するよりも実 験値に近い値を与えた．これは結晶性固体の単相に対して温度を上げても融解の核が生成しにくく，過加熱状態に陥りやすいことを意味している．ま た，UO2とZrO2を互いに固溶させることにより融点は低下し，それが融解エンタルピーの減少と相関することを明らかにした．熱伝導率は平衡分 子動力学法によりグリーン-久保の関係式から，エネルギーと電荷の流れの相互効果を考慮し，固体から液体状態までの格子振動の寄与を評価した．固 体の熱伝導率には，ウムクラップ散乱による温度上昇に伴う低下，低温の固溶体で見られるフォノンの不純物散乱による低下が確認できた．一方，超高 温の液体状態の熱伝導率は低く，温度および組成の依存性は小さいことが分かった．
<Keywords:> Molecular dynamics, Thermal conductivity, Melting point, UO2, ZrO2
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0007/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0016] Published online in advanced by J-STAGE
<Title:> Molecular Dynamics Simulation of the Behavior of Beryllium Diffusion in Corundum
<Author(s):> Jun Kawano, Muneyuki Okuyama, Takeshi Miyata<Abstract:> Molecular dynamics (MD) simulations are highly useful for analyzing atomic behavior during diffusion, especially in systems that are difficult to investigate experimentally. The focus of the present study was the diffusion behavior of Be in corundum, which was analyzed by MD calculations. First, we derived new potential parameter sets for O, Al, and Be. This parameter set was verified to well reproduce the structures and properties of corundum, bromellite, and chrysoberyl. Based on MD simulations of corundum containing Be as interstitial atoms, where the simulations were performed using the newly derived potential parameters, the diffusion coefficient was estimated to be approximately 10-7 cm2/s at around 2100 K. This is consistent with previously published experimental results, which confirms the validity of the MD simulation. The present calculations also reveal the detailed atomic movement, where Be atoms jump between Al sites and/or interstitial sites, and that the activation energy of this process is approximately 1.1 × 102 kJ/mol.
<Keywords:> Diffusion, Molecular dynamics simulation, Corundum, Beryllium, Gemology
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URL: https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0016/_article/-char/ja/
Corresponding author E-Mill: j-kawano(at)mail.sci.hokudai.ac.jp

Journal of Computer Chemistry, Japan [No.2015-0008] Published online in advanced by J-STAGE
Title: Interlayer Bonding Energy of Mg-Chlorite: A Density Functional Theory Study
Author(s): Hiroshi SakumaAbstract: Interlayer bonding energy (ILBE) of Mg-chlorite was calculated based on the density functional theory with dispersion force correction (DFT-D2). The calculated ILBE of Mg-chlorite was smaller than brucite, phlogopite, gibbsite, and muscovite and was comparable to talc, kaolinite, pyrophyllite, and lizardite. The attractive interaction between layers would be generated by the weak hydrogen bond between layers. The ILBE of Mg-chlorite should be the minimum ILBE in natural chlorite group, since the natural chlorite shows the isomorphic substitution which induces high layer charge resulting in stronger attractive interaction between layers like phlogopite and muscovite.
Keywords: Separation energy, Friction, Clay mineral, Chlorite, DFT
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URL: https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0008/_article/-char/ja/
Corresponding author E-Mill: SAKUMA.Hiroshi(at)nims.go.jp