Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 8, Issue 2
Displaying 1-5 of 5 articles from this issue
General Papers
  • Shamoon Ahmad SIDDIQUI, Apoorva DWIVEDI, Anoop PANDEY, P. K. SINGH, Ta ...
    2009 Volume 8 Issue 2 Pages 59-72
    Published: June 15, 2009
    Released on J-STAGE: June 15, 2009
    Advance online publication: April 03, 2009
    JOURNAL FREE ACCESS
    (Note:Author for Correspondence: Neeraj Misra, B-981, sector-A, Mahanagar, Lucknow 226006, India) This work deals with a theoretical study of the molecular structure of colchicine. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by the ab initio Hartree-Fock method and the Density Functional B3LYP method employing 6-31G(d) as the basis set, and the vibrational studies were interpreted in terms of the potential energy distribution (P.E.D.). The internal coordinates were optimized repeatedly to maximize the P.E.D. contributions. A detailed interpretation of the infrared and Raman spectra of colchicine is reported. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The FT-IR spectra of colchicine was recorded in solid phase, and the FT-Raman spectra of colchicine have been taken from the literature.
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  • Masato OSHIMA, Noriko INOUE
    2009 Volume 8 Issue 2 Pages 73-80
    Published: June 15, 2009
    Released on J-STAGE: June 15, 2009
    Advance online publication: June 02, 2009
    JOURNAL FREE ACCESS
    To analyze the mechanism of the β-hydrogen elimination process of η3-1,1-dimethylallylpalladium compounds, we assumed the plausible intermediates and transition states for composing the possible pathways. Their geometry optimization, and vibrational frequencies and energy calculations were carried out with density functional theory (DFT) at the B3LYP level. The most suitable pathway was that in which the allylic ligand transformed from η3- to η1-allyl form having agnostic interaction between β-hydrogen and palladium atoms, and succeeding elimination of β-hydrogen gave 2-methyl-1,3-butadiene moiety with low activation energy (9.76 kcal/mol).
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  • Junko KAMBE, Eiko NAKAYAMA, Umpei NAGASHIMA, Tomoo AOYAMA
    2009 Volume 8 Issue 2 Pages 81-86
    Published: June 15, 2009
    Released on J-STAGE: June 15, 2009
    Advance online publication: June 06, 2009
    JOURNAL FREE ACCESS
    In this note, we present a method to draw a distribution map of materials observed at a few, sparse and localized data points, such situations frequently appear in the problems of chemistry and environmental science. In these situations, it is usually difficult to draw a distribution map because data on triangular or square lattice are required for drawing. We generate additional points where the amount of materials is estimated by CQSAR: Compensation Quantitative Structure-Activity Relationships based on perceptron type neural network after learning of 31 observation data taken at Seoul, Korea on April 13-14, 2008. Then the generated data were used for drawing a distribution map. The distribution map using the additional points generated by CQSAR is useful to understanding the overview of material distributions.
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  • Hiroshi SAKIYAMA, Masato OSHIMA, Satoshi SUZUKI, Yuzo NISHIDA
    2009 Volume 8 Issue 2 Pages 87-92
    Published: June 15, 2009
    Released on J-STAGE: June 15, 2009
    JOURNAL FREE ACCESS
    The molecular structure of a dinuclear nickel(II) complex was optimized by several computational methods, including ab initio, DFT, and semi-empirical methods. The computed structures were compared with crystallographically obtained structures. All the DFT methods reproduced the crystal structures well, and the B3LYP and LC-BLYP methods were better than the others. None of the semi-empirical methods gave a reasonable structure. All the reasonable structures were obtained by assuming the quintet state, which was consistent with the ferromagnetic exchange interaction.
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