Journal of Computer Chemistry, Japan
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Volume 13 , Issue 4
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  • Takahiro KUDOU
    Volume 13 (2014) Issue 4 Pages A14-A17
    Released: October 12, 2014
    JOURNALS FREE ACCESS
    The information on protein molecule structure at atomic resolution is useful for various purposes such as understanding the mechanism of chemical reaction and developing medicines for therapy. We manage Protein Data Bank (PDB), the archive of such data. We receive the deposition of structural data determined by experimental method, and provide the archive which is accessible with no charge. PDB was established in 1971 with seven structures. Recently the number of entries increased dramatically by developing the experimental method and now we keep more than 100,000 PDB entries. PDB includes various structures such as myoglobin (PDB entry 1mbn (Figure 1), which is the first structure of the protein) and hemoglobin, which is composed of four myoglobin-like chains. We also provide interactive interface "Yorodumi"(Figure 2), which enables the operation of molecules by mouse action. Another feature of our site is a Japanese keyword search (Figure 3).
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General Papers
  • Toru YAGI, Junko KAMBE, Eiko NAKAYAMA, Umpei NAGASHIMA, Tomoo AOYAMA
    Volume 13 (2014) Issue 4 Pages 199-209
    Released: October 12, 2014
    [Advance publication] Released: July 19, 2014
    JOURNALS FREE ACCESS
    It is well known that there is a radioactive hot spot in south Kanto. The map is published by Japan Atomic Energy Agency. We research environmental dynamics of the hot spot. We select representative 26 points and plot the ambient dose rate. Many defects are found, which are interpolated. The graphs have vibrations even if smoothing is done. Using the least-squares method, the residence half-life is 2.3y at Toride city near the center of the hot spot. Radioactive substances in there are Cs-134 and Cs-137.To research the vibrations, we use Fourier transformations, and split the change of ambient dose rate into slow and rapid phenomena. The boundary is 48 h on Nyquist frequency. On the slow phenomenon, the vibrations are not found at all points. Thus, we calculate half-lifes and accumulated dose rates in a year for all points in Kanto.The Fourier spectrum of rapid phenomenon shows there is a wave of 24 h and the harmonics. To investigate the shape of the wave of 24h, we draw ambient dose rates at instants for 4, 12, 20 h per every day. That is to find daily waves at 3 phases.In the phase investigations, we find that ambient dose rate of 12 h is about −0.02 μSv/h smaller than those of others at Toride city. Considering the circulation of the atmosphere, the phenomenon relates with suspended particulate matter of radioactive Cs. We measure the intensity by using a technique for Lock-in amplifier, and get −0.005μSv/h. The rate is negligible in the case of external exposure. However; considering of small particles of Cs, it is rejected. We believe watchful waiting for 2 years is appropriate.
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  • Masaaki HONDA, Kazuo NARUSHIMA
    Volume 13 (2014) Issue 4 Pages 210-222
    Released: October 12, 2014
    [Advance publication] Released: July 26, 2014
    JOURNALS FREE ACCESS
    Recently, the photoelectric conversion characteristics of the organic semiconductor have improved considerably, but they remain inferior to those of inorganic semiconductors. The enhanced performance of the organic semiconductor is mainly attributed to a bulk heterojunction. However, the conductive mechanism of this structure is complicated. Its details have not been clarified to date. Therefore, we investigated electron transfer and charge density change and estimated the carrier density when phthalocyanine and fullerene, a p-type and n-type organic semiconductor, respectively, are brought close. Results demonstrate the possibility of carrier generation in each molecule using the molecular orbital method.
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  • Hiroshi SAKIYAMA, Katsushi WAKI
    Volume 13 (2014) Issue 4 Pages 223-228
    Released: October 12, 2014
    [Advance publication] Released: August 23, 2014
    JOURNALS FREE ACCESS
    Computational group theory (CGT) method investigations have been conducted for a hexakis-methylamine nickel(II) complex cation [Ni(CH3NH2)6]2+ [hexakis(methylamine-κN)nickel(II) dication] to find 54 possible conformers. Considering all the conformers, six conformers have been finally obtained after optimization based on the Density Functional Theory (DFT) computations. The most stable conformer has been found to be a helical conformer (C1 symmetry), which is suitable for avoiding steric repulsion between adjacent ligands. A related zinc(II) complex ([Zn(CH3NH2)6]2+) has also been investigated, and the same conformer was found to be the most stable. Since the energy differences among the conformers have been found to be very small, the conformers are thought to be mixed at room temperature, and the dominant species are thought to be changeable by environment for both complexes.
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  • Yuji IMAFUKU, Minori ABE, Michael W. SCHMIDT, Masahiko HADA
    Volume 13 (2014) Issue 4 Pages 229-232
    Released: October 12, 2014
    [Advance publication] Released: August 20, 2014
    JOURNALS FREE ACCESS
    Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Our work is the first development and application of the diagonal BO correction (DBOC) based on spin-free relativistic Hamiltonians. We used the second and infinite-order Douglas-Kroll-Hess Hamiltonians at their spin-free levels. Our test calculations of noble atoms (He – Xe) show that the DBOC energy (EDBOC) is approximately proportional to atomic number Z. Hence the BO correction generally increases when a molecule contains heavier atoms. We also computed the adiabatic corrections to the barrier heights for linearization of H2X molecules where X = O, S, Se, and Te, to discuss DBOC corrections for heavy elements.
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  • Kenichi SOMEKAWA
    Volume 13 (2014) Issue 4 Pages 233-241
    Released: October 12, 2014
    JOURNALS FREE ACCESS
    Photochromic dithienylethenes are among promising molecular switching systems for future molecular electronics. Experimental data of potential energies and substituent effects in the photochromic cyclization/cycloreversion reactions of three kinds of dithienylethenes were simulated by MOPAC-PM6 methods. The 6π open-ring isomers are types 1, 3(3h and 3m) and 5, and the closed-ring isomers are 2, 4 and 6. The simulations were also compared with them by B3LYP/6-31G and CASSCF (10,10)/6-31G methods.The photocyclization quantum yields (φOC) depending on the distance (RCC) between the reactive carbon atoms in the crystals are close to unity when RCC of 3h(4'-H) and 5 are less than 4 Å. Their dynamic simulations of the ground state and singlet excited state from the stable anti-parallel conformers made the behaviors clear. Frontier orbital interactions of higher singly occupied molecular orbital (HSOMO) etc. of the 6π open-ring systems of the RCC less than 4 Å are inferred to be effective to go to the singlet excited states (3h* and 5*: Rcc ≒ 2.1 Å) for the cyclizations. Photocyclizations of 1 and 3m(4'-Me) of Rcc larger than 4 Å in solution were also rationalized from the easy change of the 6π faces.Cycloreversions from 2 and 4 via their singlet excited states (2*, 4*: Rcc ≒ 1.6 Å) were cleared. The singlet excited state 6* from 6 was not observed except 5*. The phenomenon is inferred to be one evidence of relative high φCO of 6→5 photoreaction.Some better PM6 calculations comparing with B3LYP/6-31G etc. and one correction for the PM6 are also shown.
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  • Yuta TAKADA, Masaki OKOSHI, Minoru HOSHINO, Atsushi ISHIKAWA, Makoto I ...
    Volume 13 (2014) Issue 4 Pages 242-249
    Released: October 12, 2014
    JOURNALS FREE ACCESS
    DNAs, which have charge transport abilities, are expected to apply to advanced materials in nanotechnology as conducting nano-wires. While the hole-transfer in DNA has been extensively investigated in many experimental and theoretical studies, the knowledge on the transfer of a negative charge, i.e., the excess-electron transfer (EET), is limited so far. In the present study, we evaluated the rate constants of EET in DNA, using the Marcus theory with density functional theory (DFT) calculations. The computed rate constant of EET between thymine bases, 2.31 − 3.49 × 1010 s−1, showed good agreement with the experimental value, 4.4 ± 0.3 × 1010 s−1. Furthermore, the mechanism of the decrease of EET rates due to miss-match base pairs was elucidated.
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Note
  • Amih SAGAN, Sumie TAJIMA, Naofumi NAKAYAMA, Umpei NAGASHIMA, Hiroyuki ...
    Volume 13 (2014) Issue 4 Pages 250-256
    Released: October 12, 2014
    [Advance publication] Released: September 08, 2014
    JOURNALS FREE ACCESS
    H3+, H3 and H3 are the simplest homo nucleus three atomic molecules and examples of three center two/three/four electron bond respectively. The structure of H3+ takes the equilateral triangle that three H atomic nuclei become equivalent, because two electrons of H3+ occupy the first node-less σorbital. In the case of H3 and H3, an electron (or two electrons) occupies the second σorbital which has a node through an H atom and a center of H-H bond of the equilateral triangle of H3+. Thus, the structures of H3 and H3 become linear. In this note, we show the angular dependence of molecular structure, orbital energy, total energy and Mulliken charge of H3+, H3 and H3 using HF/6–311++G**.
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