Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
Volume 5 , Issue 4
Showing 1-4 articles out of 4 articles from the selected issue
  • Kayoko HAYASHI, Shiori FUKUDA, Umpei NAGASHIMA, Haruo HOSOYA
    1999 Volume 5 Issue 4 Pages 137-146
    Published: December 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    We have developed and opened Graphical Characteristics Data Base (GCDB) at Ochanomizu University (http://www.sap.is.ocha.ac.jp/~hayasi/cgi-bin/gcdb.cgi). 16 kinds of graphical characteristics of 330 multi-layered cyclic fence graphs are included in this version of GCDB.Details of graphical characteristics, system configuration and some examples are described in this paper.
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  • Eiichi AKAHO, Chikako FUJIKAWA, Howell I. RUNION, Craig R. HILL, Hideh ...
    1999 Volume 5 Issue 4 Pages 147-162
    Published: December 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    Nonsteroidal anti-inflammatory drugs (NSAIDs) which selectively inhibit COX2 without affecting an enzyme activity of COX 1 would be an ideal anti-inflammatory drug. Thus an attempt was made to examine those binding modes of NSAIDs against COX1 and COX2 in terms of hydrogen bond and binding energy by utilizing Dock4.0. It was shown that binding mode to COX2 selective NSAIDs coincided with the result reported in the in vitro study by R.S. Spangler (Seminars in Arthritis and Rheumatism, 26, 435-446 (1996)). Thus, it can be said that there is a fairly good correlation between the Dock4.0 results and those reported in the in vitro study. As far as the binding mode of COX1 selective NSAIDs is concerned one corresponded to the in vitro study reported by R.S. Spangler, another did not and a third presented a mediocre conformity. It was also shown that there existed one to three H-bonds with the net total being at least twelve when NSAIDs such as nabumetone, meclofenamate, niflumic acid, indomethacin, sulindac, and flurbiprofen were bound to COX2. Amino acid residues involved in such hydrogen bonds were Phe A518, Arg A120, Tyr A385, His A90, Tyr A355. Met A522, Ser A353, Gln A192, Leu A352, and Arg A513. Phe A518 and His A90 were reported by R. G. Kurumbail et al. (Nature, 384, 644-648 (1996)) but the rest of the amino acid residues were not.
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  • Hiroyuki MIURA, Takeshi KIKUCHI
    1999 Volume 5 Issue 4 Pages 163-172
    Published: December 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    This paper describes a computer program which constructs crystal structure models using the Monte Carlo and the R-factor method from powder X-ray diffraction data. In order to study an unknown crystal structure by the Rietveld method, a correct structure model must be prepared in advance. This is usually very difficult when no information is available about the structure. A program which automatically constructs a crystal structure model of the object material would simplify the task of solving the structure of the powdered material by the Rietveld method. This program, which sets atomic positions by the Monte Carlo method, requires XRD data, cell constants, a space group, a chemical formula, and a Z-number (the number of the formula in a unit cell). Wyckoff positions and coordinates of independent atoms in a unit cell are selected by random numbers, and theoretical XRD data are calculated. The R-factor of the model is calculated from theoretical and observed XRD data. Hundreds of models of a low R value are selected and stored. As atoms of the stored model concentrate in a particular area, search areas are restricted to the vicinity of these atoms, a process which minimizes the total calculation time. Using this program and a personal computer (Pentium 166), the structure of brookite (TiO2, Z=8) and forsterite (Mg2SiO4, Z=4) could be solved within one or two days, which demonstrates that this method is a powerful tool to solve the structure of powder materials.
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  • Hiroshi SAKIYAMA
    1999 Volume 5 Issue 4 Pages 173-180
    Published: December 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    A new software, which is named ‘KINE', was developed for the time course analysis of chemical reactions. It runs on the Macintosh computer (system 7 or higher). It calculates the time courses for 25 kinds of reactions containing side reactions such as parallel and sequential reactions (Table 1). Deviations of the data obtained by KINE from theoretical values were within 1% (Figs. 1 and 2). KINE also obtains the rate constants automatically, and errors in the constants were within 2% (). As an example use of KINE, the kinetics of aminopeptidase reaction by a synthetic aminopeptidase mimic were analyzed (Schemes 1 and 2). Time courses were well simulated (example in Fig. 4), and rate constants were determined.
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