Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 6 , Issue 2
Showing 1-6 articles out of 6 articles from the selected issue
  • Junko KAMBE, Umpei NAGASHIMA, Aiko YAMAUCHI, Tomoo AOYAMA
    2007 Volume 6 Issue 2 Pages 91-102
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    We researched the water quality of the Donau based on OECD reports. Observations in the reports have defects that make evaluation of environmental situations difficult. By using interpolations in the compensation quantitative structure-activity relationships (CQSAR), we complement the defects in the water quality of the rivers. Thus, we get a complete data set for dissolved oxygen, biochemical oxygen demand, and total phosphorus. Using the data set, we examine re-naturalization of the Donau. We investigate the effect of dams between Slovakia and Hungary, by using reconstructions of neural networks in CQSAR.
    The water quality of the Donau has been improved as to DO and BOD. The rivers have been re-naturalized. We believe that the effect is found in these indexes; however, not so much for the T-P.
    We find a negative effect of the dam construction on changes of DO in the Hungary Donau.
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  • Tomoo AOYAMA, Takatoshi HIGUCHI, Umpei NAGASHIMA
    2007 Volume 6 Issue 2 Pages 103-108
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    An approximate orthogonalization method called "pseudo-orthogonalization" was derived here from the Schmidt orthogonalization in a partial space. Precision of the orthogonalization is decimal 2 digits when the partial space of 1/3 of the Schmidt orthogonalization is used. The speed-up ratio is 3.3 with 1000 vectors of 1500th dimension. Although the pseudo-orthogonalization is high-speed, the precision is inadequate for general numerical calculations. Two possible approaches to improve this precision were considered: (a) introducing a band structure in the vectors, and (b) restricting the sign of the vector elements. These approaches improved the precision by a factor of 2.1 and 1.5, respectively, without increasing the CPU time.
    To demonstrate the applicability of this high-speed pseudo-orthogonalization for large-scale calculations, we coded a complex-form of it into the SCF part of the Car-Parrinello method. In calculations of the total energy for bulk-silicon, the difference in total energy calculated using the pseudo-orthogonalization and that using the Schmidt orthogonalization was less than O(-5) [a.u.]. Based on this accuracy, this pseudo-orthogonalization can be used to speed-up the Car-Parrinello method when it is applied to large-scale calculations.
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  • Yoshiya KOGO, Sumio TOKITA, Kichisuke NISHIMOTO
    2007 Volume 6 Issue 2 Pages 109-116
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    The bathochromicity of thiophene and thiazole azo dyes was studied by using quantum chemical calculations on azo compounds consisting of benzene, thiophene, furan, pyrrole, cyclopentadiene and their aza substituted rings. Conformational analyses at AM1, PM3 and B3LYP/6-31G* level of theory were performed to estimate the stable conformers of these compounds. The CNDO/S calculations including and excluding 3d-AOs on the sulfur atom confirmed that the 3d-AOs do not contribute to the bathochromicity of thiophene and thiazole azo dyes. The results of CNDO/S and TD-B3LYP/6-31+G* calculations on absorption spectra suggested that azo compounds with a 5-membered ring commonly absorb at longer wavelengths relative to the corresponding azobenzenes.
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  • Kumiko SAKAMOTO, Aiko YAMAUCHI, Mikio SASAKI, Hiroshi CHUMAN
    2007 Volume 6 Issue 2 Pages 117-122
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    Many efforts have been devoted to the development of computer-aided prediction of drug toxicity over the decades, but at present, systems and programs available for predicting teratogenicity from chemical structures do not always give satisfactory answers yet, mainly because of the complex and unknown mechanism of reproductive and developmental toxicity. We developed a novel algorithm and implemented in the program "SimScore" to evaluate quantitatively the structural similarity score of a target compound with the teratogenic drugs which are defined as serious human teratogens by the United States Food and Drug Administration. In SimScore, a molecular structure is divided into its skeletal and substituent parts in order to perform similarity comparison for these parts independently. This idea is based on that compounds with the same or similar skeleton show a similar biological activity, but their activity strengths depend on the variation of substituents. We demonstrated the usefulness of SimScore by applying it to an example.
    SimScore will be used in our web-based information system about teratogenicity to predict the potential risk of query compounds.
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  • Hiroshi SAKIYAMA
    2007 Volume 6 Issue 2 Pages 123-134
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    MagSaki(A) software was developed for the magnetic analysis of dinuclear high-spin cobalt(II) complexes. This software performs magnetic analysis to determine magnetic parameters using five types of theoretical susceptibility equations. A characteristic feature of the software is that the exchange interaction can be treated anisotropically whereas the previous MagSaki software treats the exchange interaction isotropically.
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  • Tomoo AOYAMA, Junko KAMBE, Aiko YAMAUCHI, Umpei NAGASHIMA
    2007 Volume 6 Issue 2 Pages 135-144
    Published: 2007
    Released: August 28, 2007
    JOURNALS FREE ACCESS
    A model for purification mechanisms in a river was proposed to express changes in the values of BOD (Biochemical Oxygen Demand), COD (Chemical Oxygen Demand), T-N (Total Nitrogen), and T-P (Total Phosphorous) as the combination of inflows, streams, and weirs. Because expressions for these functions are unknown, the model first constructs multi-layer neural-network functions based on observations, and then uses the derivatives to evaluate the cause and effect of pollution.
    For data of the Tamagawa through Tokyo, Japan in 2002, the model suggested that the cause of pollution is inflows from sewage, the stream of the Tamagawa has purification functions for COD and T-P, but has little ability for T-N, and the weirs have purification for COD, but have no purification for T-N and T-P. The results from the model were consistent with common sense for the water quality, and thus, there was no failure in the model.
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