Journal of Computer Chemistry, Japan
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13 巻 , 2 号
選択された号の論文の6件中1~6を表示しています
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研究論文
  • Yosuke KATAOKA, Yuri YAMADA
    13 巻 (2014) 2 号 p. 115-123
    公開日: 2014/06/30
    [早期公開] 公開日: 2014/04/08
    ジャーナル フリー
    The phase diagram of a Lennard-Jones system was estimated using conventional NPT molecular dynamics (MD) simulations. The standard cyclic boundaries were assumed. An elongated unit cell with both solid and fluid sections was found to be suitable as a model during the NPT MD simulations when calculating both the melting and vapor pressure curves. This unit cell contained 1000 molecules, of which, in the initial state, half were assigned to an FCC structure while the remainder had a density close to that of the critical state. The results of these simulations were compared with those of phase-1/phase-2 coexistence simulations and also with reported experimental data. The triple point was obtained by NVE MD calculations based on a unit cell containing both solid and gaseous sections, while the critical point was estimated by NVE MD using an elongated unit cell with a density near the critical value. Sublimation pressure was calculated by NVT MD with a unit cell again containing both solid and gaseous sections.
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  • Hiroshi SAKIYAMA, Shintaro ISHIYAMA, Keisuke SUZUKI, Ryo YAMAGUCHI
    13 巻 (2014) 2 号 p. 124-129
    公開日: 2014/06/30
    [早期公開] 公開日: 2014/06/04
    ジャーナル フリー
    Aminopeptidases remove the N-terminal amino acids from proteins by hydrolysis. Previously we synthesized an aminopeptidase mimic [Zn2(bomp)(OCOCH3)2]BPh4 [bomp = 2,6-bis[bis(2-methoxyethyl)aminomethyl]-4-methylphenolate] and reported that the aminopeptidase mimic hydrolyzed L-leucine-p-nitroanilide as a substrate. Although the structure of the aminopeptidase mimic was determined by single-crystal X-ray diffraction method, the structure of the substrate incorporation mode (how the substrate was incorporated) was not clarified. Therefore, in this study, we investigate the substrate incorporation mode using the technique of conformational analysis based on the Density Functional Theory (DFT). We have found an efficient incorporation mode for the aminopeptidase-like reaction. In the structure the substrate is incorporated in its best conformation, and the Zn-OH nucleophile is very close to the substrate. Moreover, one of the chelating arms of the ligand (bomp) is hydrogen-bonded to the Zn-OH nucleophile, so the arm is expected to work as a general base catalyst capable of enhancing the Zn-OH nucleophile. Furthermore, the other zinc(II)ion is expected to work as a general acid catalyst capable of enhancing the electrophilicity of the carbonyl carbon on the substrate. We have concluded that the aminopeptidase activity is expected to be increased if the ratio of the efficient substrate incorporation mode is increased.
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  • Yosuke KATAOKA, Yuri YAMADA
    13 巻 (2014) 2 号 p. 130-138
    公開日: 2014/06/30
    [早期公開] 公開日: 2014/06/21
    ジャーナル フリー
    Equations of state (EOSs) are proposed for a system consisting of a perfect solid and a perfect liquid made up of single spherical molecules. The Lennard-Jones interaction is assumed for this system. Molecular dynamics simulations are performed in order to determine the temperature and density dependences of the internal energy and pressure. The supercooled liquid state is also examined. The internal energy term in the EOSs is the sum of the average kinetic and potential energies at 0 K and the temperature-dependent potential energy. The temperature-dependent term of the average potential energy is assumed to be a linear function of temperature, and its coefficient is expressed as a polynomial function of the number density. The pressure is expressed in a similar manner, where the pressure satisfies the thermodynamic EOS. The equilibrium condition is solved numerically for the phase equilibrium of argon. The Gibbs energy provides a reasonable transition pressure for three-phase equilibrium in argon. The thermodynamic properties at low pressures have significant temperature dependences. The linear character of the pressure and internal energy as functions of temperature in the condensed phases is discussed based on the short-term vibration motion.
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技術論文
  • 吉村 季織, 高柳 正夫
    13 巻 (2014) 2 号 p. 139-154
    公開日: 2014/06/30
    [早期公開] 公開日: 2014/05/17
    ジャーナル フリー
    近年,化学データを数学的・統計的手法により解析する「ケモメトリクス」が頻繁に用いられるようになってきた.しかし,日本の大学の化学教育の場ではほとんど取り上げられていない.ケモメトリクスや数値計算の専用ソフトウェアを使うことなく,現在最も普及しているソフトウェアのひとつであるMicrosoft Excel (Excel)の基本機能を用いてケモメトリクス計算を行うことができれば,多くの教育・研究機関で役立つものと思われる.シリーズ6回目は,ケモメトリクスの多変量による定量モデル作成において,最も頻繁に用いられるPLS (partial least squares) 回帰 (PLSR)を取り扱った.これまでと同様に,スペクトルの解析を例に挙げた.モデル構成試料および未知試料のスペクトルの生成,潜在変量を抽出するPLS1 (1化学種の場合) とPLS2 (多化学種の場合) の実行,PLSRによる濃度定量モデル作成を行うワークシートを作成した.生成したスペクトルを使いPLSRとPCRの定量性能について比較を行った.その結果,PLS1によるPLSRでは特定の化学種の濃度データを用いるため,目的とする化学種に関して少ない因子数で良好なモデルが得られた.一方PLS2によるPLSRでは,複数の化学種に対して安定して濃度予測できるモデルが得られることが分かった.少ない因子数においてPLSRがPCRと比較して優位であることは示されたが,最適なモデルが得られるとは限らなかった.モデル化手法と因子数を変えて予測性能を比較しながら最適なモデルを得る必要があることが示唆された.
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