Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 6, Issue 1
Displaying 1-7 of 7 articles from this issue
General papers
  • Junko KAMBE, Tomoo AOYAMA, Aiko YAMAUCHI, Umpei NAGASHIMA
    2007 Volume 6 Issue 1 Pages 1-18
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    Principal component analysis, cluster analysis and neural network were applied to assess the pollution levels along the Yoshinogawa River in Tokushima, Japan, by using water quality data (Dissolved Oxygen (DO), Biochemical Oxygen Demand (BOD), Chemical Oxygen Demand (COD),and Total Phosphorus (TP)) measured in 2002. Because there are a few defects in the data, we estimated them by linear equation and neural network to avoid information loss.
    In the Yoshinogawa River, there are four branching bays (Figure 1). Though it is usually difficult to find the relationships between the water quality of the Yoshinogawa River and the distances from their estuaries, the first principal components consisting of five parameters explained the nature of the river well.
    The water quality at Heiwabashi of the Shinmachigawa River was the most contaminated in the Yoshinogawa River (Figure 6, Table 12). This suggests that there is a source of water pollution in the upper region of Heiwabashi and that there is a source to improve water quality in the lower region of Heiwabashi.
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  • Junko KAMBE, Tomoo AOYAMA, Aiko YAMAUCHI, Umpei NAGASHIMA
    2007 Volume 6 Issue 1 Pages 19-26
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    Parameters as an index to efficiently assess the pollution level of the upper, middle, and lower streams of the Tamagawa (Tokyo, Japan) based on measured water quality were determined by using multivariate analysis, principal component analysis (PCA), and cluster analysis (CA) for data measured from 1994 to 2002. Missing data during 2000-2002 were estimated using a perceptron type neural network and arithmetic progression. The combination of scores for the first and second principal components obtained by PCA enabled classification of the upper, middle, and lower streams of the Tamagawa. The CA results corresponded well with the PCA results.
    Based on the score of the first principal compornent determined here, contributions to the water pollution of the middle and lower streams should be decreased to improve the water quality of the Tamagawa.
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  • Takeo KONAKAHARA, Harunobu KOMATSU, Norio SAKAI, Barry GOLD
    2007 Volume 6 Issue 1 Pages 27-32
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    Computational analysis of minor and major groove methidium-DNA complexes in B-form DNA 5'-d(CATCCCGGGATG) is performed for intercalation at each base pair. The most stable structure based on stabilization energies was calculated by a combination of molecular mechanics (augmented MM2) and molecular dynamics (MD) methods. When methidium intercalates from the minor groove, the phenanthridine ring is parallel to the nucleobase pairs, and the excluded site size is 6.4 Å. The stabilization is maximal when the methidium intercalates between 5'-d(CG) from the minor groove (-28.3 kcal·mol-1). Calculations using MD showed that the complex was considerably less stable when the methidium intercalated from the major groove. This result is consistent with experimental results demonstrating that the intercalation of methidium occurs from the minor groove. A plot of the calculated stabilization energy vs. the logarithm of the binding constant of ethidium bromide with each dinucleotide affords a linear relationship.
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  • Kousuke MAEDA, Alexander SCHUG, Hirofumi WATANABE, Kaori FUKUZAWA, Yuj ...
    2007 Volume 6 Issue 1 Pages 33-46
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    We have studied the molecular mechanism for the binding between estrogen receptor and estradiol using ab initio methods. To examine the validity of in silico analysis of mutation effects, we made point mutations of receptor employed in experiments, and compared the calculated results for the binding energies with experimental data. We performed the calculations at the HF/STO-3G and MP2/STO-3G levels by using the Fragment Molecular Orbital (FMO) method. The calculated results for three of six mutants qualitatively agreed with experimental data. However, the other three examples failed to reproduce the experimental data. We discussed the reasons for these discrepancies.
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  • Tatsuo TOIDA, Katsumi UCHIDA, Tadahiro ISHII, Hirofumi YAJIMA
    2007 Volume 6 Issue 1 Pages 47-58
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    This work describes a computer aided search program for multi-adduct fullerene C60 Rn structures by tracing the family tree of precursors and derivatives of all physically possible multi-adductions (Geometrical Evolution Graph). We developed a new searching algorithm, named Cones Product Strategy (Figure 2), based on the multi-dimensional network pathways. When applied to the highly symmetrical hexa-adduct C60 we obtained 3 possible pathways to hexa-adduct descendants. Th symmetrical hexa-adduct is the only hexa-adduct that is able to be derived from e and trans-1 bis-adduct isomers (Figures 3, 4). D3 symmetrical hexa-adduct is the only hexa-adduct that is able to be derived from the tris-adduct 0x0200 0081 that is the only tris-adduct able to be derived from e, trans-3 and trans-2 bis-adduct (Figures 5, 6). D3d symmetrical hexa-adduct is the only hexa-adduct that is able to be derived from the tris-adduct 0x0001 2001 whose structure has a very simple biconical zone (Figures 7, 8). This algorithm could facilitate the development of new complex chemical structures.
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  • Shinsaku FUJITA
    2007 Volume 6 Issue 1 Pages 59-72
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    Monosubstituted alkanes as stereoisomers, not as constitutional isomers, are regarded as planted three-dimensional (3D) trees, which are defined as a 3D extension of planted trees (graphs). They are thus recognized as 3D-objects (planted promolecules) and enumerated by Fujita's proligand method (Fujita S (2005) Theor. Chem. Acc. 113:73–79, 113:80–86, Fujita S (2006) Theor. Chem. Acc. 115:37–53). By starting from three kinds of sphericity indices, i.e., ad for homospheric cycles, cd for enantiospheric cycles, and bd for hemispheric cycles, cycle indices with chirality fittingness (CI-CFs) are obtained to enumerate planted 3D-trees or equivalently monosubstituted alkanes as stereoisomers. Functional equations a(x), c(x2), and b(x) for recursive calculations are derived from the CI-CFs and programmed in three ways by means of the Maple programming language. The three recursive procedures for calculating the numbers of planted 3D-trees are executed to give identical results, which are collected up to 100 carbon content in a tabular form. The results are compared with the enumeration of planted trees (as graphs).
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  • Shinsaku FUJITA
    2007 Volume 6 Issue 1 Pages 73-90
    Published: 2007
    Released on J-STAGE: April 09, 2007
    JOURNAL FREE ACCESS
    Monosubstituted alkanes are counted as stereoisomers by means of Fujita's proligand method (Fujita S (2005) Theor. Chem. Acc. 113:73-79, 113:80-86, Fujita S (2006) Theor. Chem. Acc. 115:37-53), where the numbers of primary, secondary, and tertiary ones are calculated after deriving respective functional equations. The procedures of counting are programmed by means of the Maple programming language. They are executed and the results collected up to carbon content 100 in a tabular form. By omitting the sphericities of the recursive functions a(x), c(x2), and b(x) so as to give a single dummy variable r(x), such functional equations with sphericity are transformed into Pólya's functional equations without sphericity, which are applied to the enumeration of primary, secondary, and tertiary monosubstituted alkanes as graphs (chemically, constitutional isomers). The results of Fujita's proligand method are compared with those based on Pólya's theorem in connection with several cases of pseudoasymmetry.
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