Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 3, Issue 1
Displaying 1-5 of 5 articles from this issue
General Papers
  • Yuji MOCHIZUKI, Umpei NAGASHIMA
    2004 Volume 3 Issue 1 Pages 1-12
    Published: 2004
    Released on J-STAGE: March 31, 2004
    JOURNAL FREE ACCESS
    Integral transformation from basis functions to molecular orbitals is necessary in configuration-based correlation treatments of molecular orbital calculations. In particular, the processing of two-electron integrals having fourth power dependence of the number of basis functions can be costly, thus care should be taken to reduce the operation counts as far as possible. In this contribution, we report a development of integral transformation modules, based on Yamamoto-Nagashima's algorithm (J. Comp. Chem., 9, 627 (1988)) by which only non-zero integrals within threshold are efficiently processed. The BLAS routines, DAXPY and DDOT are used in the innermost part of the transformation step.
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  • Mitsuhiro FUKUDA, Yoshinori TAMAI, Satoru KUWAJIMA
    2004 Volume 3 Issue 1 Pages 13-20
    Published: 2004
    Released on J-STAGE: March 31, 2004
    JOURNAL FREE ACCESS
    The layered structure of rigid-rod polyesters with flexible alkyl side chains has been constructed by a molecular dynamics (MD) simulation. Two kinds of polyesters from 1,4-dialkylesters of pyromellitic acid with 4,4'-biphenol with hexyl (n = 6) and tetradecyl group (n = 14) as the side chain were used. The obtained structure at 298 K showed that 1) the aromatic main chains highly extended to the fiber axis (z-axis), 2) the main chains packed laterally (y-axis) to form the layer structure, and 3) the flexible side chain favouring the liquid state occupied the space between the layers. The layer distance, the lateral spacing of the main chain, and the bulk density obtained by the MD simulation showed good correspondence to the experimental results.
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  • Masaki FUJITA, Hirohide NAKAMATSU, Sunao SUGIHARA, Jun-ichi AIHARA, Ri ...
    2004 Volume 3 Issue 1 Pages 21-26
    Published: 2004
    Released on J-STAGE: March 31, 2004
    JOURNAL FREE ACCESS
    Low-energy parts of the Ti-K XANES spectra for SrTiO3 and CaTiO3 consist of a main peak and pre-edge peaks B and C. We made a characterization of these peaks using the DV Xα cluster model combined with L2 continuum wave functions. This approach with a [TiO6M8(TiO5)6M24]20+ model cluster (M=Sr or Ca) was successful in reproducing the relative positions and intensities of the low-energy peaks. It was found that transitions of the titanium 1s electron to p-type atomic orbitals (AOs) of the same atom are responsible for all these peaks. In general, p-type atomic orbitals (AOs) of the central titanium atom are mixed with various AOs of nearby atoms in the model cluster. Thus, the origin of main and pre-edge peaks for typical perovskite-type titanates has been elucidated consistently within a single theoretical framework.
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  • Masahiko SUENAGA
    2004 Volume 3 Issue 1 Pages 27-34
    Published: 2004
    Released on J-STAGE: March 31, 2004
    JOURNAL FREE ACCESS
    The molecule given in Figure 2 shows dodecahedral symmetry. It is constructed with a symmetrically unique structure (Figure 3) which resides on the edge of the virtual dodecahedral skeleton. In order to generate all the coordinates, a symmetrically unique fragment structure is rotationally transformed in three ways : (1) 72 degree about z-axis, (2) 180 degree about y-axis and (3) 2φ about y-axis, where 2φ is the angle between two normals which run through the center of the two juxtaposing faces. In order to generate all the connectivity from the fragment structure, the numbering of the whole molecule should be expressed with a parameter related to the number of atoms in the fragment structure. In general, the fragment structure can be expressed as in Figure 4 and the numbering of all the atoms can be expressed with a parameter n (= k-2). This parametrization of the numbering made it possible to generate all the connectivity required for the construction of the dodecahedral structure.
    A newly developed program was written in a script language, Perl. It takes the structural data of a fragment as an input and generates the structural data of the corresponding dodecahedronic molecule. This program is useful especially when the fragment structure contains a hydrogen bond or coordination bond. For such a molecule, molecular mechanics or the molecular orbital method cannot be fully utilized for the construction of the model.
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  • Tadayosi YOSHIMURA, Yuusuke NAKAYAMA, Akinori UEJIMA
    2004 Volume 3 Issue 1 Pages 35-40
    Published: 2004
    Released on J-STAGE: March 31, 2004
    JOURNAL FREE ACCESS
    Despite their amazing profusion, mobile phones have not been a part of school education and there have been no reports on testing for their active use in this arena. We have thus developed chemistry resources via the Internet that allow mobile phones to be used as mobile computer terminals for educational purposes. Because mobile phone displays are extremely small, they are not suitable for viewing lengthy texts or large images over the Internet. In consideration of this limitation, we have developed chemistry resources that prioritize the greater convenience offered by mobile phones over desktop computers. We revised the "Physical Chemistry Experiment" preparation system, which was already available on the Internet, so that it could be accessed using a mobile telephone. The Physical Chemistry Experiment comprises 18 topics. Testing use of these resources began during student experiments in April, 2003, and this paper reports the results of our development efforts and the results of implementing these developments in the educational environment.
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