月別: 2018年7月

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 天然有機化合物にもとづくNTG-活性辞書システムの開発
<Author(s):> 桂樹　哲雄, 金谷　重彦, 高橋　由雅
<Corresponding author E-Mill:> katsuragi(at)cs.tut.ac.jp
<Abstract:> 本研究では，天然有機化合物を対象とした，環系骨格構造とその関連する生理活性を相互に検索することができる辞書システムNTGdic/BOC (NTG dictionary for Bioactive Organic Compounds)を開発した．NTG (Non-Terminal vertex Graph)として表される環系骨格構造に注目し，天然有機化合物データベースKNApSAcK familyに収録されている51247件の化合物の化学構造式を対象に，単純グラフ，頂点重み付きグラフなど5種類の異なるグラフ表現を用いて，延べ57867件のNTGを抽出するとともに，既知の140種類の生理活性との関連付けを行った．これらの結果は関係データベース(関係辞書)としてシステムに実装した．NTGdic/BOCでは，構造エディタを用いて作画入力したクエリ化合物の化学構造式から，利用者が指定するグラフ表現レベルでのNTGを自動的に抽出し，NTG-活性辞書を用いて，関連する生理活性を参照することができる．一方，生理活性からNTG骨格構造を検索することや，各々のNTGの由来化合物を参照することもできる．また，類似構造(または類似NTG)検索も利用可能である．
<Keywords:> Molecular framework, Structure similarity, Biological activity, NTG, Natural organic compound
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0049/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.4, -, by J-STAGE]
<Title:> Determining the Three-phase Equilibrium Diagrams for Water, Oxygen, Propane and Lithium Using van der Waals Equations of State
<Author(s):> Yosuke KATAOKA
<Abstract:> In the present work, phase diagrams in (pressure, temperature) space were calculated for water, oxygen, propane and lithium, employing van der Waals (vdW) equations of state, similar to an approach previously employed for argon. These calculations allowed the triple point temperatures to be obtained. The experimentally-determined triple point pressure values (p3) normalized by the critical point pressure (pc) (that is, p3/pc) are known to exhibit a significant correlation with the normalized triple point temperature (T3/Tc), and the present results reproduce this correlation qualitatively. This work also demonstrated that the low-density solid, high-density solid, liquid and gas-phases of water produce a phase diagram similar to that of the ice-water system.
<Keywords:> Three-phase equilibrium, Van der Waals equation of state, Vapor pressure, Sublimation pressure, Melting curve, Water, Oxygen, Propane, Lithium
<URL:> https://www.jstage.jst.go.jp/article/jccjie/4/0/4_2017-0042/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.4, -, by J-STAGE]
<Title:> Extension of a van der Waals Equation of State to the Solid-liquid-vapor Phases of a Lennard-Jones System
<Author(s):> Yosuke KATAOKA
<Corresponding author E-Mill:> yosuke.kataoka(at)koganei-md.com
<Abstract:> An existing van der Waals (vdW) equation of state (EOS) based on hard-sphere repulsions during intermolecular interactions was extended to a Lennard-Jones (LJ) system. Specifically, an EOS for a perfect solid and liquid v5 (Y. Kataoka and Y. Yamada, J. Comput. Chem. Jpn.,12, 181 189 (2013)) was simplified to satisfy the Rigby conditions for a generalized vdW EOS. The phase diagram of argon was reproduced in pressure-temperature space using this extended EOS, and a phase diagram in temperature-density space was also generated and found to be qualitatively consistent with the LJ system.
<Keywords:> Van der Waals equation of state, Phase diagram, Critical point, Triple point, Perfect solid, Perfect liquid, Melting curve, Boiling pressure, Sublimation pressure
<URL:> https://www.jstage.jst.go.jp/article/jccjie/4/0/4_2017-0043/_html