Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 5, Issue 1
Displaying 1-7 of 7 articles from this issue
Technical Paper
  • Takayuki OHMAE
    2006 Volume 5 Issue 1 Pages 1-6
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    A computer program which used Excel/VBA was made so that the student who did not major in chemistry could learn concepts about similarity of molecular structure easily. By this program, it is possible to calculate Pearson correlation coefficient (rP) and Tanimoto coefficient (rT). From the point of view of education, both programs were done in a convenient way which plural comparison molecule cannot handle. We kept the function which changed reference value into the program which calculated rT. The possibility that there was a concept of resolving power in similarity was suggested by the results of calculation with this function. We calculated rP and rT of Dioxin isomers for 2,3,7,8-PCDD with this program. It was suggested that there was good correlation between calculated indexes and TEF.
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General Papers
  • Hiromi NAKAI, Jochen HEYD, Gustavo E. SCUSERIA
    2006 Volume 5 Issue 1 Pages 7-18
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    Periodic boundary condition (PBC) calculations using the Heyd-Scuseria-Ernzerhof screened Coulomb hybrid functional (HSE03) have been carried out to investigate the electronic structure of the anatase and rutile TiO2 bulk solids. As a comparison, we have performed the investigation using local density approximation (LDA), generalized gradient approximation (GGA), and conventional hybrid functionals. It is proved that the truncation of the Hartree-Fock (HF) exchange terms, whose evaluation is the bottleneck of the PBC calculations, is much accelerated in the HSE03 model when compared to the conventional hybrid model. Cohesive energies for anatase and rutile calculated by HSE03, as well as the GGA and conventional hybrid functionals, are shown to be in a good agreement with the experimental values. As is well known, band gaps obtained by LDA and GGA are underestimated by 40 % in comparison with the experimental values. Usage of a hybrid functional significantly improved the evaluation of the band gaps. Actually, the absolute errors calculated with HSE03 are about 0.3 eV for both anatase and rutile. Geometric parameters obtained by HSE03, which are between LDA and GGA values, reasonably agree with experiment. As for bulk moduli, HSE03 gives values close to LDA rather than GGA. As a consequence, the present study confirms that the new type of hybrid functional HSE03 brings about reasonable computational cost and achieves high accuracy comparable with or superior to the conventional hybrid functionals.
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  • Ryo MIYAMOTO, Jun KAWAKAMI, Shuko TAKAHASHI, Shunji ITO, Masahiko NAGA ...
    2006 Volume 5 Issue 1 Pages 19-22
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    8-Hydroxyquinoline derivatives (BQOH and BQClOH) were synthesized as fluorescent chemosensors for metal ions. BQOH and BQClOH hardly show fluorescence themselves, but they showed strong fluorescence with the addition of zinc or cadmium ions. The order of the maximum values of fluorescence intensity (If,max) was BQClOH-Zn2+ > BQClOH-Cd2+ >> BQOH-Cd2+ > BQOH-Zn2+. Therefore, the ab initio calculations (by Gaussian 98) using the time-dependent density functional method with 6-31+G(d) basis set were carried out on the Zn2+ complexes of quinoline chromophore, BQOH and BQClOH, in order to investigate the cause of the difference in the fluorescent intensity (BQClOH-M2+ >> BQOH-M2+, M2+ = Zn2+ or Cd2+). The results of the calculations showed that the T2 state of the [ZnBQO]+ lay just below its S1 state, while that was not the case for [ZnBQClO]+.
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  • Sumie TAJIMA, Tohru YAGI, Tomoko FUKUDA, Umpei NAGASHIMA
    2006 Volume 5 Issue 1 Pages 23-28
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    We have started to develop Computed Property Data Base: CPDB. A part of the CPDB has been opened to the public at RIO-DB (Research Information Database) of the National Institute of Advanced Industrial Science and Technology, Tsukuba from January 2005.
    (http://www.aist.go.jp/RIODB/hrmsdb/index.html)
    Thirteen molecular properties (Table 1) of 258,907 molecules were stored in CPDB. All of the properties are estimated using mainly the Joback method which is implemented in an Integrated Software Tool for Molecular Design: MolWorks. It is possible to retrieve not only molecular property of input but also molecules which have inputted properties.
    CPDB is an attempt to develop a system for efficient molecular screening using estimated molecular property.
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  • Norio YOSHIMURA
    2006 Volume 5 Issue 1 Pages 29-38
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    A simulation method for acid – base titration was developed by using not VBA programming but fundamental functions of Microsoft Excel. For calculating a pH value corresponding to a given titration volume, an approximation is need. In this study, the approximation was computed on a worksheet of Excel. Moreover, for simulating a titration curve, the pH value must be calculated for every dropping of titrant. The simulations were performed by using "table" which is one of the fundamental functions of Excel.
    Using this method, not only weak acid (base) – strong base (acid) titrations such as citric acid – sodium hydroxide and ammonium hydroxide – hydrochloric acid, but also weak acid – weak base titrations such as citric acid – ammonium hydroxide were simulated. The effect of errors, which arise from carbonic acid contamination and the round-off operations of titration volumes and pH values, on titration curves were discussed.
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  • Oleg URSU, Mircea V. DIUDEA, Shin-ichi NAKAYAMA
    2006 Volume 5 Issue 1 Pages 39-46
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    This study presents a method and algorithms for calculation of 3D similarity between pairs of chemical structures represented as 3D molecular graphs. Similarity searching in chemical databases is widely used for virtual screening, lead discovery and optimization, and most recently protein amino-acid sequences studies to discover and determine the functionality of a new isolated protein. This method has obvious advantages over other known methods due to the following: (i) the superposition method does not depend on the preliminary alignments of the chemical structures; (ii) entire conformational space is searched without generation of each conformer; (iii) excellent discrimination between geometrical isomers. Although it is a computationally demanding method, recent implementation of maximum clique algorithm and bound smoothing algorithm made possible the optimization of this method and application to similarity searching in chemical databases of non trivial size.
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  • Yosuke KATAOKA, Yuri YAMADA
    2006 Volume 5 Issue 1 Pages 47-52
    Published: 2006
    Released on J-STAGE: May 01, 2006
    JOURNAL FREE ACCESS
    The canonical ensemble partition function is obtained for a two-molecule system with the repulsive step function outside the hard sphere wall in a spherical cell. Fluid-fluid phase transition-like behavior is evident at low temperatures. The spinodal line is obtained in the (V, T) domain and a negative expansion coefficient is found in the stable state. The theoretical pVT relationship is confirmed through Monte Carlo simulations. The periodic 108-molecule system examined by Monte Carlo simulations also provides a qualitatively similar pVT relationship to the two-molecule system.
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