Journal of Computer Aided Chemistry
Online ISSN : 1345-8647
ISSN-L : 1345-8647
Volume 6
Showing 1-10 articles out of 10 articles from the selected issue
  • Tatsuo Toida, Yuki Hori, Katsumasa Nemoto, Katsumi Uchida, Tadahiro Is ...
    2005 Volume 6 Pages 1-11
    Published: 2005
    Released: February 22, 2005
    JOURNALS FREE ACCESS
    Maximum adduct number to hex-hex double bond on C60 was analyzed by computer simulation with eight kinds of steric hindrance. In the case of condition that any two addends cannot be in the range of cis-2, there are 136 kinds of derivatives and maximum number of adducts is at most 6. But in the case of condition that any two addends can be in the range of cis-2, there are 2017 kinds of derivatives and maximum number of adducts is up to 10. In the case of condition that any two addends can be in the range of cis-1, there are 17,912,448 kinds of derivative and the count of isomers versus adduct number is possible to approximate to binomial distribution. To derive for all k-adduct isomers all possible k+1 adduct isomers were traced, and their inheritance diagram “Geometrical Evolution Graph” were obtained. In this paper we propose a new strategy to analyze unknown structure by using this graph.
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  • Kenji Okada, Ploenpit Boochathum, Keiichi Noguchi, Kenji Okuyama, Yuki ...
    2005 Volume 6 Pages 12-22
    Published: 2005
    Released: March 09, 2005
    JOURNALS FREE ACCESS
    PreLALS workbench is designed to aid users in the task of visualizing chemical structures using three-dimensional models, editing and the data manipulation for WinLALS program that refines the internal coordinates based on linked-atom least-squares (LALS) method for helical polymers. It combines the views of model building (MB), analyses, and data preparation tools with easy-to-use graphical user interfaces. We describe the outline of the WinLALS program with mathematical expressions and explain the several functions of the PreLALS workbench using each menu of the data preparation and example dialogs. The PreLALS workbench runs on most IBM compatible Windows PCs having a minimum of Pentium and the operating system must be either Windows 2000, 98, Me or XP.
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  • Toshiyuki Mitsui, Shuji Okuyama
    2005 Volume 6 Pages 23-29
    Published: 2005
    Released: March 29, 2005
    JOURNALS FREE ACCESS
    The different calculation method of regression (DCR) is the new quantitative analysis method considered by the author. DCR is not needed a calibration curve for the quantitative analysis, but it is carried out from the coefficient of the multiple regression expression obtained from the measured data of known samples and an unknown sample. The determination of blend composition of kerosene and light oil was carried out from gas chromatogram using DCR Furthermore, removal of a sample unsuitable to quantitative analysis is possible for DCR.
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  • Application to Synthesis Routes for Substituted Fran-2,3-dione
    Kenzi Hori, Katsuhiko Okano, Kazuaki Yoshimura, Akiko Nishida, Hidetos ...
    2005 Volume 6 Pages 30-36
    Published: 2005
    Released: April 15, 2005
    JOURNALS FREE ACCESS
    Recently, several synthetic route design systems (SRDS) such as AIPHOS, TOSP and EROS have been available. However, it is very difficult to experimentally check all the routes that the systems offer. As computational chemistry is powerful to investigate the mechanisms of chemical reactions, we can use the method to examine whether or not synthesis routes from SRDS produce target compounds. In order to confirm possibility of theoretical calculations, mechanisms for three synthesis routes of substituted- furan- 2,3-dione, a literature method and two from the TOSP program, were investigated.
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  • H. Iwamoto, H. Sakamoto, K. Kimura
    2005 Volume 6 Pages 37-43
    Published: 2005
    Released: June 17, 2005
    JOURNALS FREE ACCESS
    The distribution of spirobenzopyran derivatives incorporating a crown ether moiety in water/1,2- dichloroethane two-phase system was simulated using a molecular dynamics method. Regardless of the size of crown ether moiety of the compounds, the steric energy was changed with the length of their alkyl chains. The steric energy in aqueous phase was increased with lengthening the alkyl chain, while the steric energy in the organic phase remained almost unchanged. As a result, these difference in the steric energy between the two phase were increased with the alkyl chain length and the compounds are, therefore, energetically stable in the organic phase. The snapshot obtained by the calculation showed that the compounds at the interface push their alkyl chain into the organic phase to stabilize them.
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  • Hidetoshi Maruyama, Kenji Kaijiri
    2005 Volume 6 Pages 44-56
    Published: 2005
    Released: August 26, 2005
    JOURNALS FREE ACCESS
    In the post-genome era, the number of registered 3D protein structures increases dramatically. BLAST homology search tool is widely used for finding homologues. However, there are many remote homologue proteins with 3D structural similarity that BLAST cannot detect. Accordingly 3D protein structural homology search is strongly required. We propose a novel 3D protein structural homology search algorithm based on the Triangle ID comparison method. We focused a triangle structure consisting of three amino acids and called it as Triangle ID. We considered 20 kinds of amino acids, so there are 8000 kinds of Triangle IDs. We assumed that proteins can be characterized by using these Triangle IDs. To prove the validness of this assumption, we developed the homology search tool and made several sample data sets that consist of serine protease family and different family from serine protease. Using these data, we did several search experiments and showed the validness of our assumption and the scalability of our method. Our method opens the possibility of the efficient 3D protein structural homology search.
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  • Katsuhiko Okano, Kouji Satoh, Hideo Takahasi, Kenzi Hori
    2005 Volume 6 Pages 57-66
    Published: 2005
    Released: October 28, 2005
    JOURNALS FREE ACCESS
    We have been constructing a database named Transition State Data Base (TSDB) in order to develop synthesis routes in silico. The ability to predict experimental yields for synthesis reactions is very important for determining which synthetic route is better than others. For this purpose, we have been investigating the fusion of computational and information chemistry. In the present study, we tried to predict yields using the statistical method with explanatory variables as reaction and activation energies, calculated from molecular orbital (MO) calculations. The analysis also used experimental parameters such as dielectric constants of solvents and reaction temperatures. The present study adopted these parameters and applied the GA-PLS method to aromatic nucleophilic substitution (SNAr) reactions producing a 1,4-dihydro- quinoline-3-carboxylic acid skeleton. It was confirmed that the GA-PLS analysis adopting the calculated values as well as the experimental conditions could expect the experimental yields. However, we have to divide experimental data into 3 categories depending on the isolated techniques such as crystallization, re-crystallization and column
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  • Haruhiko Nakamura, Ryo Usuki, Takayuki Natume, Noriyuki Kurita
    2005 Volume 6 Pages 67-82
    Published: 2005
    Released: October 28, 2005
    JOURNALS FREE ACCESS
    Stable structures for complexes between catabolite activator protein (CAP) or its mutated proteins and cyclic AMP (cAMP) were obtained by the AMBER force field. For these structures, the binding energies between CAP and cAMP were investigated by semiempirical molecular orbital method to elucidate how the interaction between CAP and cAMP is influenced by the amino acid mutations. The results clarify that the 82nd amino-acid Arg is indispensable for the binding between CAP and cAMP, which is consistent with the experimental results [1,3].
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  • Hisayuki Horai, Kouichi Doi, Hirofumi Doi
    2005 Volume 6 Pages 83-89
    Published: 2005
    Released: December 16, 2005
    JOURNALS FREE ACCESS
    We propose a new method for the prediction of protein function, especially enzyme activity, based on statistical characteristics of oligopeptides. A known function of a protein is regarded to be inherited to its oligopeptides, and the correspondence between oligopeptides and the function is calculated in the whole proteins. In our method, unknown functions of proteins are predicted by means of the correspondence automatically. We measured the prediction performance for several enzymes by recall, precision and maximum f-measure using 28,520 whole human proteins registered in RefSeq. This paper reports prediction of a specific enzyme 'protein-tyrosine kinase' (EC 2.7.1.112) and a large class of enzymes 'transferases' (EC 2.-.-.-). The former and the latter score maximum f-measure of 0.932 and 0.786, respectively. The results suggest that the proposed method is quite efficient in predicting enzyme activity.
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  • Masamoto Arakawa, Yoshiro Yamada, Kimito Funatsu
    2005 Volume 6 Pages 90-96
    Published: 2005
    Released: February 14, 2006
    JOURNALS FREE ACCESS
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