Journal of Computer Chemistry, Japan
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Volume 11 , Issue 2
Showing 1-9 articles out of 9 articles from the selected issue
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  • Yosuke KATAOKA, Yuri YAMADA
    Volume 11 (2012) Issue 2 Pages 81-88
    Released: August 10, 2012
    [Advance publication] Released: June 06, 2012
    JOURNALS FREE ACCESS
    Three-phase equilibrium in argon was obtained based on the thermodynamics of a perfect solid and liquid. The equation of state (EOS) for a perfect solid was previously obtained from the study of a pure substance with spherical molecules. The EOS for a perfect liquid is a van der Waals EOS with suitable coefficients to explain 3-phase equilibrium. The Lennard-Jones parameters for argon are applied to these EOSs. Thep-V-Trelations on the equilibrium lines are comparable with experimental and molecular simulation results. The calculated values of the average potential energy and entropy are also consistent with the simulations.
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  • Amih SAGAN, Shin-ich NAGAOKA, Hiroyuki TERAMAE, Umpei NAGASHIMA
    Volume 11 (2012) Issue 2 Pages 89-92
    Released: August 10, 2012
    [Advance publication] Released: June 06, 2012
    JOURNALS FREE ACCESS
    The nitrogen molecule N2has been regarded as a triple-bonded homonuclear diatomic molecule in many textbooks of physical chemistry. However, the character of the highest occupied molecular orbital HOMO (σ type or π type) is controversial in those textbooks. In this note, using RHF/6–311++G** calculation we show that the HOMO of N2is π type in the region close to the equilibrium (1.0703 Å ). In the region where the bond length is larger than 1.045 Å , the HOMO of N2is not σ type but π type.
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  • Toru YAGI, Junko KAMBE, Umpei NAGASHIMA, Tomoo AOYAMA
    Volume 11 (2012) Issue 2 Pages 93-97
    Released: August 10, 2012
    [Advance publication] Released: June 06, 2012
    JOURNALS FREE ACCESS
    We observed multi rainbows in the sky of Kihanadai, Miyazaki from E building of the Faculty of Technology, Miyazaki University at 16:18, September 22, 2010. Analyzing digital photos of the multi rainbow, the complicated structure of the multiple primary rainbow was clearly shown with surplus rainbows. The rainbow lays at the edge of the fog in the sky.
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  • Kazuki MORI, Tomohiro KABASHIMA, Satoshi MINAMOTO, Teppei TAMAKI, Kazu ...
    Volume 11 (2012) Issue 2 Pages 98-103
    Released: August 10, 2012
    [Advance publication] Released: June 30, 2012
    JOURNALS FREE ACCESS
    We have developed a supporting program for the molecular dynamics (MD) simulation program, Gromacs. This program, named GISP (Gromacs Input-file Supporting Programs), allows us to make gromacs's input files and to run MD simulation using not command lines but graphical user interface (GUI). In addition, the GISP program can easily analyze the resulting output files after MD simulation. GISP has a good scalability because it is coded by python. We think that GISP is useful for the beginner of MD to start their simulation, and will be good for teachers who want to teach MD simulation in universities or education institutions. The GISP program package will be provided free of charge.
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  • Motoki SHIGA, Yoshimasa TAKAHASHI
    Volume 11 (2012) Issue 2 Pages 104-111
    Released: August 10, 2012
    [Advance publication] Released: June 30, 2012
    JOURNALS FREE ACCESS
    The chemical space of drug candidates is vast, and data volume in chemical databases is still getting larger. For mining such vast chemical data, accelerating data analysis is an essential issue. This paper validates an approach for improving computational cost by compressing topological fragment spectra (TFS) which is a descriptor of chemical graphs proposed by Takahashi et al.. First we show that TFS is a periodic signal whose cycle length is around 12 (mass number of carbon). And then we apply compression methods for periodic signals: Fourier transform and Wavelet transform. Experimental results on structural similarity searches and pharmaceutical activity predictions show that Wavelet transform gives more effective compression than Fourier transform.
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  • Taehyung KIM, Hiromasa KANEKO, Naoya YAMASHIRO, Kimito FUNATSU
    Volume 11 (2012) Issue 2 Pages 112-120
    Released: August 10, 2012
    [Advance publication] Released: July 15, 2012
    JOURNALS FREE ACCESS
    Distillation is one of the dominating separation processes, but there are some problems. One of those problems is that inseparable mixtures are formed in some cases. This phenomenon is called azeotropy. It is essential to understand azeotropy in any distillation processes since azeotropes, i.e., inseparable mixtures, cannot be separated by ordinary distillation. In this study, to construct a model which predicts the azeotropic formation at any pressure, a novel approach is presented with support vector machine (SVM). The SVM method is used to classify data in the two classes, that is, azeotropes and nonazeotropes. 13 variables including pressure were used as explanatory variables. From the result of comparing the SVM models which were constructed with data measured at 1 atm and data measured at any pressure, the 1 atm model shows a higher prediction performance to the data measured at 1 atm than any pressure model does. Thus, for improving the performance of the any pressure model, we focused on intermolecular forces of solvents. The SVM models were constructed with only data of the solvents having the same subgroups. The accuracy of the model increased and the model predicted change of the presence of azeotrope according to pressure. It is expected that this proposed method will be used to predict azeotropic formation at any pressure with high accuracy.
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