Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 5, Issue 4
Displaying 1-8 of 8 articles from this issue
General Papers
  • Katsuhiko SATOH
    2006 Volume 5 Issue 4 Pages 165-170
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    The end-over-end rotational motion of nematic-phase molecules was examined by an isobaric-isothermal molecular-dynamics simulation for a Gay-Berne mesogenic system. The result was compared with the Meier-Saupe theory and the previous result obtained from a molecular-dynamics simulation for the same Gay-Berne model at constant volume in order to examine the influence of volume fluctuation on nematic-phase dynamics. The results from the simulation at constant pressure were closer to the theoretical value the retardation factor g||, which is the concept used to interpret reduction of the relaxation time for end-over-end rotational molecular motion, throughout the entire range of the second-rank orientational order parameter <P2> and the strength parameter of Maier-Saupe form σ than were those values for constant volume. Volume fluctuation is important in evaluating the retardation factor g||. This finding significantly increases our understanding of the role of pressure control in the simulation of slow dynamics in the liquid crystalline phase.
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  • Masashi HATANAKA, Ryuichi SHIBA
    2006 Volume 5 Issue 4 Pages 171-176
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    High-spin stability of non-Kekulé-type molecule triiminiummethane ion (TIM3+) is discussed using the semiempirical molecular orbital method. The triplet ground state 3A2' with a D3h geometry is predicted to lie below the Jahn-Teller distorted singlet states similar to trimethylenemethane (TMM). The lowest singlet states 1B1, 1B2 and 1A1 with C2v geometries are nearly degenerate. The spin-density distribution of the 3A2' state is calculated and the origin of the spin alignment is discussed relating to the spin-polarization rule characteristic of high-spin organic molecules. The valence bond analysis on the spin states of TIM3+ is also carried out.
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  • Tatsuo TOIDA, Katsumi UCHIDA, Tadahiro ISHII, Hirofumi YAJIMA
    2006 Volume 5 Issue 4 Pages 177-184
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    The structure ID that is 8 digits hexadecimal index (30 bits width) corresponding to any adduct patterns on 30 kinds of hex-hex double bond of C60 fullerene is classified to the Minor structure ID which is impossible to distinguish and the Major structure ID which is representative for the Minor structure IDs. The Major structure ID is the index without duplications of structural isomers and is able to compare any two adduct patterns directly. In this study the software tools to visualize the structure ID for the Schlegel diagram (SVG 1.1) or 3-dimensional geometry (PDB) are developed and the hyperlinks to these graphics for all structures are provided. The tools are able to input any adduct patterns in graphical user interface and immediately output the Major structure ID and its enantiomeric Major structure ID. It is also possible to display the adductable sites under steric hindrance and to rotate the Schlegel diagram while sustaining its network topology.
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  • Tatsuo TOIDA, Katsumi UCHIDA, Tadahiro ISHII, Hirofumi YAJIMA
    2006 Volume 5 Issue 4 Pages 185-200
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    In this study, we report the development of a program tool for 1H- and 13C-NMR peak prediction of C60Rn(n=0-30) compounds. This tool is able to count up the NMR peak and its intensity for any multi-adduct C60 fullerene in the case where addend is bonding on one of the 30 hex-hex double bonds of fullerene and its monoadduct has C2 or C2v symmetry. The model is in good agreement with the experimental data for bis-adduct methano[60]fullerene. Using this tool, an exhaustive list of peak counts and intensities for all possible multi-adducts was calculated under the restrictive condition that any two addends cannot be in the range of cis-1. The NMR patterns were investigated for each adduct number using simple proportions of the calculated intensities.
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  • Junko KAMBE, Yuan YAN, Umpei NAGASHIMA, Tomoo AOYAMA
    2006 Volume 5 Issue 4 Pages 201-212
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    We attempted to extract chemical parameters characterizing the upper, middle and lower stream of the Tamagawa River in Tokyo, Japan, by Compensation Quantitative Structure-Activity Relationships (CQSAR) method [11, 12] for analysis of incomplete data by perceptron type neural network with three layers.
    Dissolved Oxygen (DO) and Total Phosphorus (T-P) were extracted from 12 chemical parameters (Table 2) at 17 points (Table 1) along the main stream of the Tamagawa River (Figure 1) in Tokyo, Japan, for 1997-2001 [10].
    DO indicated that water pollution became worse at all points of the Tamagawa River (Figure 4) but T-P shows that water pollution is changed for the better in the middle and the lower stream (Figure 5).
    This result suggests that the water pollution is more drastic in the middle stream of the Tamagawa River than the lower stream. The water pollution in the middle stream should be decreased for keeping the Tamagawa River clean.
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  • Shinichi MURAYAMA, Chuya YOSHIDA, Takashi AOYAMA, Satoshi URATA, Koich ...
    2006 Volume 5 Issue 4 Pages 213-218
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    Nano-second (ns) MD simulations of peptides, which are known to be insufficient to obtain stable structures, were confirmed to provide faint secondary structure (especially, α-helix) images through a novel approach termed triangle map representation of %stickiness (TMR-%σ). %stickiness is a measure formerly introduced to describe dynamic conformation changes of biopolymers. In TMR-%σ representation, the α-helix forming propensity of a peptide was expressed as an off-diagonal dotted line, indicating α-helix intrinsic interactions. The coordinate information derived from %σ and radius of gyration (Rg) of a peptide calculated from ns-MD results could be converted to a probability matrix of secondary peptide structure formation.
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  • Tsutomu YONEZAWA
    2006 Volume 5 Issue 4 Pages 219-226
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    In the infrared region, an expression for the mean absorption intensity has been obtained using the Elsasser model based only on the assumption of pressure broadening. Around atmospheric pressure, however, a better interpretation of the empirical results has been found by introducing a new effect of splitting due to the pressure of the degenerate vibrational-rotational levels.
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  • Tadayosi YOSHIMURA, Yoshitaka SAKASHITA
    2006 Volume 5 Issue 4 Pages 227-230
    Published: 2006
    Released on J-STAGE: January 09, 2007
    JOURNAL FREE ACCESS
    Much information in today's information society goes through the Internet. On five senses smell information, DigiScent Inc. reported the development of the scent generator "iSmell" in 1999. But, it was never available and closed down in April 2001. We thought that the cause of the bankruptcy was smell blending. The smells are not blended in our policy. We developed a smell emitter which stored some element of the perfume. Ethanol and a cooling gel material were used in order to enable the emission of long term perfume. Using this device, we succeeded in transmitting/receiving the perfume mail. The result of this research indicates the future application of a smell emitter system via Internet.
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