Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 15, Issue 4
Displaying 1-7 of 7 articles from this issue
Foreword
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General Paper
  • Syuutaro KAWADA, Yuji MOCHIZUKI, Katsuhiro NAKANO
    2016 Volume 15 Issue 4 Pages 87-91
    Published: 2016
    Released on J-STAGE: December 18, 2016
    Advance online publication: November 30, 2016
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    The so-called oxocarbons, with cyclic polymer form of CO unit as (CO)n, have attracted considerable interest for many years. However, pseudo-oxocarbons of chalcogen substitutions, (CCh)n (Ch=S, Se, Te) have not yet been investigated by theoretical calculations in a systematic way. In this contribution, we report the DFT-based evaluations of molecular structures and NICS values for (CCh)5 and (CCh)6. It is shown that the planarity of molecules is enhanced for heavier chalcogens. Additionally, the NICS evaluation indicates that (CTe)6 has an aromaticity comparable to that of benzene as a reference.

  • Sona SAITOU, Yuji MOCHIZUKI, Yutaka YAMAZAKI, Kazuya ISHIMURA
    2016 Volume 15 Issue 4 Pages 92-96
    Published: 2016
    Released on J-STAGE: December 18, 2016
    Advance online publication: November 30, 2016
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    Intel's Xeon Phi processors have attracted considerable attention as promising many-core processors for scientific computing and simulation. We report the performance results of parallelized DFT calculations with the SMASH program on a first-generation chip (Knights Corner) in a native mode of executions. As a result, an acceleration of 1.4 was observed for a multi-threading increment from 60 cores to 120 cores. This fact implies a preferable performance on the second-generation Phi (Knights Landing) processors.

Technical Paper
  • Masashi TOZAWA, Yoshinori TAMAI
    2016 Volume 15 Issue 4 Pages 97-104
    Published: 2016
    Released on J-STAGE: December 18, 2016
    Advance online publication: November 25, 2016
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    Supplementary material

    A single crystal of a tactic polymer can be utilized as a high-performance separation membrane (smart membrane) for separating and recovering a target substance, by controlling the structure of the pore, the so-called a "molecular cavity," between the polymer chains. Although various studies have been carried out to elucidate the structure of the molecular cavity, it is difficult to intuitively understand the complex three-dimensional cavity structure. In this study, for a better understanding of these structures, a three-dimensional model of the cavity was created by using a 3D printer. The molecular cavities of the δe, ε, and S-I form of syndiotactic polystyrene (s-PS) were reproduced by molecular dynamics (MD) simulation. The obtained structural data were converted into 3D printable STL data, and solid models of the molecular cavities were fabricated by the 3D printer. For the δe form, two types of channel structures along the b axis and ac-axis directions were reproduced. The channel along the ac-axis direction, along which the gas molecules are likely to diffuse, was demonstrated to be shorter and thicker than that along the b axis. On the other hand, cylindrical and zigzag channels were obtained for the ε and S-I forms, respectively. An analysis of the system of cavities associated with diffusing gas molecules was carried out by fabricating 3D models at the moment the gas molecule jumps between cavities. The relationship between the crystal structures and the diffusion pattern of gases could be intuitively understood.

  • Yasuyo HATANO, Shigeyoshi YAMAMOTO, Hiroshi TATEWAKI
    2016 Volume 15 Issue 4 Pages 105-117
    Published: 2016
    Released on J-STAGE: December 18, 2016
    Advance online publication: December 08, 2016
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    Supplementary material

    The exact solution of Dirac equation is schematically shown for the hydrogen atom. It is important to have images of the spinors to study the relativistic effects in molecules containing heavy metals such as lanthanoids. The s, p, d, and f spinors have characteristic shapes. The main purpose of this paper is to make it possible to view them all at once by presenting an illustrated book of their 3D density plots. We have also given the 3D density plots of the Schrödinger orbitals. One can easily observe that most of the nodes observed in the nonrelativistic orbitals vanish by comparing the spinors and the corresponding Schrödinger orbitals. We have calculated the mean value of r(< r > ) for Z = 100. It is well known that <r > is reduced by the relativistic effects, however, we have found that their effects are not uniform. Their effects are largest for spinors of j = 1/2, i.e., s1/2 and p1/2. With this paper, we present Mathematica notebooks for plotting and computation, which would be useful also as teaching materials.

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