Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
Volume 10 , Issue 2
Showing 1-7 articles out of 7 articles from the selected issue
Foreword
Commentary
  • Tomoo AOYAMA, Toru YAGI, Junko KAMBE, Eiko NAKAYAMA
    2011 Volume 10 Issue 2 Pages A7-A12
    Published: 2011
    Released: September 05, 2011
    [Advance publication] Released: May 28, 2011
    JOURNALS FREE ACCESS
    The 2011 off the Pacific coast of Tohoku Earthquake occurred Friday 11 March, 14:46 (Japan Standard Time, JST). The earthquake and tsunami inflicted serious damages on the Fukushima 1 nuclear power plant, especially the cooling functions. On 15 March, radioactive dust was escaping from the power plant. For serious situation on 14 April, we summarize the diffusion of radioactive matter and impacts against the environment. We point out the following: (1) The diffusing distances are different according to the direction. Such facts show that the radiation exposure is caused by radioactive dust, which is moved and sunk by wind and rain. (2) The ambient dose rates in Fukushima prefecture are accumulated during 737 h and they are compared with those of 2010. There is a village where the rate is 7.6 mSv. We optimize an expression of the ambient dose rate for the village, and integrate it. We get 41.1 mSv/year. The village is 40 km NW from the nuclear power plant. By using the same way, we predict the accumulated rate of Fukushima city, and get 16.2 mSv/year. (3) The soil of the village radiates 1.63 × 105 or 2.2 × 105 Bq/kg from 137Cs. The values are detected on 20 March and 26 March. The residence half-time for 131I is 9.6 d. We calculate the half-time of the water in a pond, and get 11 d and 7.2 d for 137Cs and 131I. (4) We find two monitoring points of 162 and 293 mSv/year, which are 30 km and 20 km in NW direction.
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General Paper
  • Takatoshi NAKA, Shinya MIYAZAKI, Yasuyo HATANO, Shigeyoshi YAMAMOTO
    2011 Volume 10 Issue 2 Pages 49-58
    Published: 2011
    Released: September 05, 2011
    [Advance publication] Released: August 06, 2011
    JOURNALS FREE ACCESS
    A computer program for 3D visualization of atomic orbitals (AOs) has been developed. Information on the spatial extents or shapes of AOs in a molecular orbital (MO) is important to gain an understanding of the bonding mechanism of a molecule. It also serves to provide a rough image of MOs before actual MO calculations. The extents of AOs are illustrated as isosurfaces of electron density with this program. This isosurface is defined so that a given percentage (e.g., 90%) of an electron is contained inside it. An algorithm for calculating the density value of the isosurface is presented. Isosurfaces can be drawn by arbitrarily specifying the quantum numbers and the positions of AOs. The program is named "EDENSAS" (atomic orbital electron density isosurface assembly) and is integrated as a module in the MOOTIC program system that has been developed by the authors, aiming at 3D visualization of MOs. With 3D CG of AOs, the electronic structure of Cu atom in inert gas matrices is discussed (Figure 9). The bonding characteristics of three transition metal dimers (Mn2, Fe2 and Zn2) are drawn out by applying this module (Figure 10,11).
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Technical Paper
  • Takahide NAKAMURA, Takahisa KOUNO, Ryo KOBAYASHI, Shuji OGATA
    2011 Volume 10 Issue 2 Pages 59-68
    Published: 2011
    Released: September 05, 2011
    [Advance publication] Released: August 20, 2011
    JOURNALS FREE ACCESS
    The concurrent-type hybrid simulation scheme, in which a total system is divided into sub-systems and a proper numerical method is applied to each of them, has attracted much attention in recent years. We have developed a visu alization package "Akira" to be applicable directly to analyses of various hybrid simulation results composed usually of both atomic (particle) and volume data. Akira can display the simulation results in impressive manners, for example, by showing both atomic and volume data with colors relating to the values of physical quantities, and by showing the traces of selected atoms. A user can easily create sequential image-files for the time-evolution. Akira is written in Java with OpenGL; hence, it is executable on various platforms. The source code of Akira is open for the public along with its developing documents. The characteristic functions of Akira are explained with demonstrations.
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Notes
  • Satoshi YANASE, Takao OI
    2011 Volume 10 Issue 2 Pages 69-74
    Published: 2011
    Released: September 05, 2011
    [Advance publication] Released: June 25, 2011
    JOURNALS FREE ACCESS
    H/D isotope effects accompanying the electrolysis of liquid water based on the evaluation of the RPFRs of involved hydrogen species were studied using molecular orbital (MO) methods at the B3LYP/6-31G (d, p) level of theory. Our purpose is understanding the isotope effects; thus, taking into consideration the H/D isotope exchange equilibriums between the hydrogen species absorbed on surfaces of electrodes and H2O or H3O+ seems a better approach than simply considering the equilibrium between H2 and H2O.
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  • Amih SAGAN, Umpei NAGASHIMA, Hiroyuki TERAMAE, Shin-ichi NAGAOKA
    2011 Volume 10 Issue 2 Pages 75-77
    Published: 2011
    Released: September 05, 2011
    JOURNALS FREE ACCESS
    The molecular orbital energy level diagram of LiH in conventional textbooks for quantum chemistry is incorrect from viewpoint of ab initio Hartree-Fock SCF-MO calculation, because the 2σlevel of LiH is drawn at a lower position than the 1s orbital of H. It means that the 1s electron of H is stabilized by forming LiH. We show an molecular orbital energy level diagram of LiH obtained by ab initio Hartree-Fock SCF-MO calculation with 6-311++G** basis set in this note. The 2σlevel of LiH is drawn at a higher position than the 1s of H in this diagram. The 1s electron of H is thus destabilized in LiH. Since the 2s electron of Li comes close to the H atom, the 1s electrons of H in 2σorbital are destabilized by electron repulsion.
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