投稿者: 博佐藤

Journal of Computer Chemistry, Japan [No.2015-0038] Published online by J-STAGE
<Title:> 積分で定義される関数の高精度数値計算法：量子力学の数値解析から数学・数値解析へのフィードバック
<Author(s):> 石川　英明
<Corresponding author E-Mill:> UHI91261(at)nifty.com<Abstract:> We applied a method for calculating indefinite integrals developed for atomic structure calculations to mathematical functions defined by integrals and obtained highly accurate results. The method is simple and has wide applicability. Examples of application are, elementary transcendental functions such as exponential, logarithmic, and arctangent functions, then error function, Fresnel integrals, exponential, cosine, and sine integrals, and incomplete gamma functions.
<Keywords:> method, numerical calculation, integral, mathematical functions, high accuracy
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0038/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0036] Published online by J-STAGE
<Title:> xNa2O-(1-x) SiO2 ガラスに適用する原子間相互作用の考察
<Author(s):> 山本　優也, 澤口　, 佐々木　眞
<Corresponding author E-Mill:> 14042074(at)mmm.muroran-it.ac.jp<Abstract:> The interatomic potential for a wide composition range of sodium silicate glasses was proposed by first-principles calculation. Point charge was set for each glass composition on the basis of population analysis of the alkali silicate crystals by using the density functional theory. The potential parameters were obtained from the energy surface of the SiO2+ model by using the molecular orbital method. The molecular dynamics simulation using the new interatomic potential showed improved structures of sodium silicate glasses.
<Keywords:> Molecular dynamics, Interatomic potential, First-principles calculation, Sodium silicate glasses, Glass structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0036/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0032] Published online by J-STAGE
<Title:> 放射性plume 軌跡のためのシミュレータ開発
<Author(s):> 青山　智夫, 若月　泰孝
<Corresponding author E-Mill:> aoyama.tomoo(at)gmail.com<Abstract:> Under nuclear power plant accident, by the ventilation of containment vessel, suspended particulate matter (SPM) is emitted; it attracts radioactive compounds, and the plume diffuses in air. It soaks into the human body. We are required to run away from the invisible plumes. The routes do not exist at any time. We recognize status soon, and should select priority persons to escape from there. We code a real-time plume tracer, which reads 4D-winds of Meso Scale Model (MSM), calculates time-development of plumes. The precision for reach time of plumes is 3?5 min, inner 8 km points from emission.
<Keywords:> radioactive substance, movement of SPM, accident prediction, air contamination
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0032/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0034] Published online by J-STAGE
<Title:> 分子動力学法理解のためのExcelを用いた授業実践と量子力学への応用
<Author(s):> 成島　和男, 岩武　澄, 川上　侑作
<Corresponding author E-Mill:> narushim(at)ube-k.ac.jp<Abstract:> The author is confident that knowledge of electronic materials and molecular simulation will become indispensable for future students of electrical and electronic engineering majors.This paper presents an approach for an introductory lesson on molecular simulation just inaugurated by the author. Specifically, the first step of molecular simulation was incorporated into the lecture “The Basic Theory of Optical Property.” This lesson was taught using spreadsheets (Excel; Microsoft Corp.), which are familiar and easily used software for students. Comments by students after the lesson included the following; “Abstract contents were well understood through exercises,” and “The significance of simulations was abundantly clear.” Consequently, the author believes that effects anticipated from this lesson (the objective of this lesson) were attained to a good degree.
<Keywords:> Molecular Simulation Education, Oligomer, Photoirradiation, Compton effect, Tunnel Effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0034/_article/-char/ja/

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.
<Keywords:>
<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/