Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 7 , Issue 1
Showing 1-5 articles out of 5 articles from the selected issue
General Papers
  • Yusuke ASAKUMA, Kouji MAEDA, Keisuke FUKUI
    2008 Volume 7 Issue 1 Pages 1-8
    Published: March 15, 2008
    Released: March 15, 2008
    [Advance publication] Released: January 18, 2008
    JOURNALS FREE ACCESS
    Impurity effect of KDP(KH2PO4 crystal growth by trivalent metal ion in solution is reasonably well documented. If the metal ion is adsorbed onto the crystal surface, it prevents the step propagation relevant to the crystal growth rate. Although a recovery effect of the metal ion adsorption was discovered in our recent work on the addition of chelate agents, the impurity effect and recovery mechanisms are not clearly understood both theoretically and phenomenally. Moreover, the dye compound in solution can colour the KDP crystal. However, dyes are segregated in specific growth sectors due to crystal anisotropy. The mechanism of the dye selectivity and the orientation of the adsorbed dye are also not clear. Accordingly, the impurity effect by metal ion, recovery effect by chelate and colouring mechanism by dye about the KDP crystal were investigated by computational chemistry in this study. It was found that these behaviors could be explained by electrostatic potential (ESP) distribution.
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  • Isao ETO, Hideo FUJIWARA, Miyako AKIYOSHI, Takehiro MATSUNAGA
    2008 Volume 7 Issue 1 Pages 9-20
    Published: March 15, 2008
    Released: March 15, 2008
    [Advance publication] Released: February 20, 2008
    JOURNALS FREE ACCESS
    A DFT study of hydrogen peroxide (H2O2)-metal ion (M) complexes has been carried out, in order to explain a runaway reaction of hydrogen peroxide initiated by addition of metal ion. Basis sets considered are LANL2DZ for metal atom, and D95V, D95V+*, and 6-311+G* for H and O atoms. The B3LYP method is used. Hydrogen peroxide-metal ion (K+, Ni2+, Cu+, Cu2+, Fe2+, Fe3+) complexes (1:1), K+, Cu+, and Fe2+ complexes have been optimized. However, no stable structures have been found for Ni2+, Cu2+ and Fe3+ complexes, because the excess charge transfer from the metal ion to H2O2 causes Coulomb repulsion. Multi-molecular complexes containing water molecules have been converged to stationary points, because the positive charges of metal atom properly disperse. The interaction of metal hydrated ions and hydrogen peroxide changed with charge distribution, hydrogen bond and coordination state of the complexes.
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  • Yoshio HONMA
    2008 Volume 7 Issue 1 Pages 21-26
    Published: March 15, 2008
    Released: March 15, 2008
    [Advance publication] Released: February 26, 2008
    JOURNALS FREE ACCESS
    Using Jmol, a free molecule viewer that operates on the Java applet, a collection of web educational materials on biological macromolecules that allow three-dimensional structures on the browser was prepared and released. It processes structural data included in the Protein Data Bank (PDB) as needed, using the Jmol script to enable various display alignments according to each datum, which can be utilized for learning and education of life sciences.
    This is a successive conversion of materials that had been released using Chime at our laboratory, modified for easier use by classification of types such as membrane proteins, cytochrome P450s and glycoproteins, and allowing each structure's characteristics to be highlighted.
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  • Hiroshi SAKIYAMA, Akito KAZAMA, Satoshi SUZUKI, Yuzo NISHIDA
    2008 Volume 7 Issue 1 Pages 27-32
    Published: March 15, 2008
    Released: March 15, 2008
    [Advance publication] Released: February 26, 2008
    JOURNALS FREE ACCESS
    The molecular structure of a dinuclear zinc(II) complex was optimized by several computational methods, including ab initio methods, a DFT method, semi-empirical methods, and molecular mechanics methods. The computed structures were compared with a crystallographically obtained structure. The B3LYP/LANL2DZ method could reproduce the crystal structure well, and an axial-elongation tendency around the zinc(II) ion was also reproduced. The resulting structure could be improved by the MP2/3-21G method, indicating the importance of the configuration interaction. Among the semi-empirical methods, only the PM5 and the PM6 could reproduce the crystal structure. For molecular mechanics methods, applicable parameter sets could be determined to reproduce the crystal structure.
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  • Masahiko SUENAGA
    2008 Volume 7 Issue 1 Pages 33-54
    Published: March 15, 2008
    Released: March 15, 2008
    JOURNALS FREE ACCESS
    A GUI (Graphic User Interface) for GAMESS / FMO (Fragment MO method) calculation was developed and implemented on Facio, the pre/post-processor for computational chemistry. By using this GUI, one can easily make FMO fragments for a given protein or nucleic acid and generate FMO input files.
    Besides automatic fragmentation, one can manually define additional FMO fractioning points to non-peptide moiety of conjugated protein. For manual definition, a novel local structure viewer was also developed. The desired local structure is defined by an atom number or by a fragment number. Using this local structure viewer, one can check the structural validity of each FMO fragment and perform manual definition of additional fractioning points on the fragment. Manually defined fractioning points can be saved as "fragment definition file", which can be loaded later to set the predefined fractioning points.
    For the optimization of hydrogen atoms automatically added to the PDB file of a protein or nucleic acid which lacks hydrogen atoms, a fragment optimization function was implemented for the GUI. While a molecular dynamics method or molecular mechanics method is usually used for this purpose, the new optimization method utilizes a molecular orbital method, such as PM3 or STO-3G of GAMESS.
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