Journal of Computer Chemistry, Japan
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Volume 12 , Issue 3
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  • Hiroshi SAKIYAMA, Syoji MIYAZATO, Satoshi TAKARA, Eiji ASATO
    Volume 12 (2013) Issue 3 Pages 157-161
    Released: September 30, 2013
    [Advance publication] Released: June 26, 2013
    JOURNALS FREE ACCESS
    The electronic spectra of dinuclear zinc (II) complexes were simulated for [Zn2(μ-H2THBQ)(TPA)2](ClO4)2 (1) and [Zn2(μ-RHOD)(TPA)2](ClO4)2 (2) [H2THBQ2–: 2,3,5,6-tetrahydroxy-1,4-benzoquinonate, TPA: tris (2-pyridylmethyl) amine, RHOD2–: rhodizonate] using the methods of density functional theory (DFT). A band at 361 nm for 1 was assigned to a (2nd HOMO)-LUMO transition, which originates from a bridging benzoquinonate moiety; a band at 502 nm and a band at 449 nm for 2 were assigned to a HOMO-LUMO transition and a HOMO-(2nd LUMO) transition, respectively, and both are originated from a bridging rhodizonate moiety.
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  • Yoshihisa OHKO, Shiori KUBO, Umpei NAGASHIMA
    Volume 12 (2013) Issue 3 Pages 162-167
    Released: September 30, 2013
    [Advance publication] Released: June 26, 2013
    JOURNALS FREE ACCESS
    Electron impact ionization mass spectrometry enables detection of cluster ions from a water-alcohol binary mixture, by which it was previously reported that a pure alcohol solution gave only small cluster ions, while the addition of water in a small amount (ca. 20wt%) resulted in the appearance of much larger cluster ions. We have theoretically examined the effect of existing water on the formation of alcohol clusters, by taking a typical cyclic cluster composed of three ethanol and one water molecules. The calculations were carried out with the Hartree-Fock method with 6-31G** basis set. As a result, we showed that the ionization of alcohols is followed by proton (H+) donation by the water close to the ionized alcohol via energy transfer. The excess ionization energy is taken by the dissociation of the water molecule so that the alcohol-rich cluster ions will be stabilized. In the absence of water, the excess energy is distributed throughout the cluster, so that large cluster ions, not possible to observe, will be fragmented into small pieces in a vacuum.
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  • Keita ABE, Yukako CHIBA, Ryo YAMAGUCHI, Hiroshi SAKIYAMA
    Volume 12 (2013) Issue 3 Pages 168-171
    Released: September 30, 2013
    [Advance publication] Released: July 17, 2013
    JOURNALS FREE ACCESS
    Density Functional Theory (DFT) investigations have been conducted for a hexakis-DMF nickel(II) complex cation [Ni(DMF)6]2+ [hexakis(N,N-dimethylformamide-κO)nickel(II)dication] for the purpose of revealing the reasons for the structural features − an S6 symmetry and a trigonal compression − observed by the single-crystal X-ray diffraction experiment, where DMF is an N,N-dimethylformamide molecule as a ligand. The DFT investigations have shown that there are only two conformers − S6 and D3 − for the complex cation [Ni(DMF)6]2+, and the most stable conformer has been found to be the S6 conformer, which is consistent with the crystal structure. In addition, the trigonal compression is reproduced by the DFT computation, indicating that the trigonal compression is the nature of the complex cation but not due to crystal packing. Moreover, inter-ligand hydrogen-bonds have been found to play important roles in determining the structure.
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  • Makoto YABE, Teppei TAMAKI, Minoru TAKEDA, Junichi KOIZUMI, Kazuyoshi ...
    Volume 12 (2013) Issue 3 Pages 172-180
    Released: September 30, 2013
    [Advance publication] Released: July 25, 2013
    JOURNALS FREE ACCESS
    With the rapid expansion of multi-core computing, the parallel processing platform such as MPI and OpenMP becomes popular as a way to improve the efficiency of computation. These techniques can increase the speed of calculation of software after compiled source codes, with revision using parallel programming rules, through parallel libraries. However, parallel programming is generally difficult for effective speeding-up in the search of finding all solution, because parallel processing is usually repeated each time in the calculation of the energy and structure optimization. To solve these problems, we developed a system based on the distributed processing method, which consists of the procedures of the pretreatment of the division of input-file and distribution of divided processes to many slave machines. This system can divide the input-file into appropriate size of jobs and execute them without having to optimize the source code with parallel processing. It is expected to improve computing speed, reliability of result and data accessibility. To show the efficiency of this system, we applied it to make a conformational energy map of cellulose triacetate using the charmm molecular dynamics simulation program.
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  • Yosuke KATAOKA, Yuri YAMADA
    Volume 12 (2013) Issue 3 Pages 181-189
    Released: September 30, 2013
    [Advance publication] Released: August 28, 2013
    JOURNALS FREE ACCESS
    Equations of state (EOS) are proposed for a system involving argon and consisting of a perfect solid and a perfect liquid composed of single spherical molecules in which Lennard–Jones interactions are assumed. Molecular dynamics simulations of this system were performed to determine the temperature and density dependencies of the internal energy and pressure and the supercooled liquid state was also examined. The sum of the average kinetic and potential energies at 0 K and the temperature-dependent potential energy was applied as the internal energy term in the EOS, while the temperature-dependent term of the average potential energy was assumed to be a linear function of the temperature and its coefficient was expressed as a polynomial function of the number density. The pressure was expressed in a similar manner, such that it satisfied the thermodynamic EOS. Using this approach, the equilibrium condition was solved numerically for the phase equilibrium of argon. The Gibbs energy thus calculated gives a reasonable transition pressure for argon's three-phase equilibrium state. The thermodynamic properties at low pressures were found to exhibit significant temperature dependencies.
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Technical Paper
  • Amih SAGAN, Naofumi NAKAYAMA, Umpei NAGASHIMA, Hiroyuki TERAMAE, Shin- ...
    Volume 12 (2013) Issue 3 Pages 190-195
    Released: September 30, 2013
    [Advance publication] Released: September 17, 2013
    JOURNALS FREE ACCESS
    Strong basis set dependency of calculated molecular structure of H2 in the ground state 2Σu+ is shown using standard basis sets equipped on Gaussian03: 6-311G**, 6-311++G**, aug-cc-pVTZ, cc-pVTZ, D95, D95++. Calculation methods are HF, MP2 and Full CI. The bond lengths of H2 calculated using standard basis sets without diffuse function are almost twice as long as those of H2 because excess electron occupies anti-bonding orbital of H2. The bond lengths of H2 using standard basis sets with a diffuse function are almost the same as those of H2 because excess electron occupies anti-bonding but very diffuse orbital. The relation between the bond length and ζ of diffuse function is also demonstrated. When ζ is large: the expectation value <r> is small, the bond length of H2 is large. When ζ is small: the expectation value <r> is large, the bond length of H2 is close to that of H2.
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