Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
Volume 10 , Issue 1
Showing 1-8 articles out of 8 articles from the selected issue
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  • Hideo SEKIYAMA
    2011 Volume 10 Issue 1 Pages 1-10
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 02, 2011
    JOURNALS FREE ACCESS
    Intermolecular interactions play a significant roles in the fields of physics, chemistry and biology. The study of intermolecular interactions is a useful step toward gaining a basic understanding of the dynamic behavior of molecules in various environments. Today's quantum chemical calculations are very powerful tools to investigate intermolecular interactions. In the present study, we first investigated the effect of the method of quantum chemical calculations, the selection of basis set and the BSSE (Basis set superposition error) on calculated interaction energies of Ar2 and Ar-NH3 Van der Waals dimers. Second, we carried out quantum chemical calculations to study the structure and stability of Ar2-NH3 Van der Waals trimer and to clarify the nature of molecular interactions. The most stable structure of Ar2-NH3 was found; it can be described by assuming the pairwise additivity of the interaction energies.
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  • Takayuki MATSUOKA, Shusuke SOMENO, Masahiko HADA
    2011 Volume 10 Issue 1 Pages 11-17
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 02, 2011
    JOURNALS FREE ACCESS
    We examined an equation-of-motion coupled-cluster (EOM-CC) method, which is basically equivalent to the SAC-CI method, starting from the generalized unrestricted Hartree-Fock (GUHF) wave function incorporated with a spin-dependent relativistic Hamiltonian. Demonstrations of the present method were carried out for the spin-orbit (SO) splitting energies of 3P and 2P states of relatively light atoms (Be - Ar). Although we considered only the lowest-order (c-2) Breit-Pauli one- and two-electron SO terms, it was found that the SO splitting energies calculated by the present method agree well with experimental ones, and are almost equivalent to those obtained by some conventional higher-order relativistic and electron-correlated methods.
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  • Hiroshi SAKIYAMA, Keisuke SUZUKI, Ryo YAMAGUCHI
    2011 Volume 10 Issue 1 Pages 18-24
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 23, 2011
    JOURNALS FREE ACCESS
    Conformational analysis was conducted for a dizinc(II) complex cation [Zn2(bomp)(OCOMe)2]+ based on the DFT method, where bomp- represents a dinucleating ligand: 2,6-bis[bis(2-methoxyethyl) aminomethyl]-4-methylphenolate anion. The complex cation is enantiomeric, and when the twisted angle-an angle between a phenolate plane and a plane including two zinc(II) ions and a phenolic oxygen atom-is positive, the most stable conformation of the chelating rings is (+, δ, δ), where the first symbol represents the sign of the twisted angle and the second and third symbols represent the conformations of equatorial and axial chelating rings, respectively. Computational modeling was also conducted to construct the most stable structure of the complex cation without referring to the crystal structure. The model was constructed step by step using molecular mechanics and DFT methods. Ultimately, the most stable structure was successfully obtained.
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  • Kentaro KAWAI, Kazutaka YOSHIMARU, Yoshimasa TAKAHASHI
    2011 Volume 10 Issue 1 Pages 25-31
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 23, 2011
    JOURNALS FREE ACCESS
    This paper describes an approach to candidate structure generation for drug design and discovery. The method is based on an evolutionary algorithm. Initially, a seed structure is submitted and is used for producing an initial set of individuals. For the initial set, the individual structures are randomly generated by adding substituent fragments to the seed structure. Then they are handled and evolved in accordance with evolutional operations such as crossover, mutation and selection. The algorithm was implemented. In the work a chemical structure was coded with an atomic connection table. To verify the method, a couple of computational trials were carried out in which we tried to reproduce a target structure from a simple seed using a fitness of structural similarity. Those results suggested that the present approach may successfully control the direction of structure evolution and works well for finding candidate structures that have the higher fitness.
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Technical Paper
  • Norio YOSHIMURA, Koji FUKUHARA, Kenichiro MITSUKI, Masao TAKAYANAGI
    2011 Volume 10 Issue 1 Pages 32-43
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 23, 2011
    JOURNALS FREE ACCESS
    Although chemometrics has become widely used recently for analyzing experimental chemical data, there exist only a few instructions for the proper usage of chemometrics other than those in some introductory books. As the fourth step of chemometrics calculations with Microsoft Excel (Excel), the principal component regression is performed on worksheets. Three worksheets were constructed for generating the spectra of model calibration samples and unknown samples, solving principal component analysis by NIPALS algorithm and calculating principal component regression. The quantitative performance of principal component regression was compared with that of multiple linear regression or the analysis based on Lambert-Beer law. Principal component regression was found to be superior to the other two methods.
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Note
  • Amih SAGAN, Umpei NAGASHIMA
    2011 Volume 10 Issue 1 Pages 44-47
    Published: 2011
    Released: April 05, 2011
    [Advance publication] Released: March 02, 2011
    JOURNALS FREE ACCESS
    It is well known that UHF, UMP2, UMP3 and UMP4SDTQ can properly reproduce the potential surface of H2 dissociation (H2®H + H) whereas RHF, RMP2, RMP3, RMP4SDTQ do not easily reproduce the proper potential surface. In this note, we demonstrate this fact because there are few textbook qualitatively representing both of them. The difference of RHF and UHF is very small in region RH-H<1.2Å and increases along with the increasing of RH-H>1.2Å. Corresponding to this trend, the electron correlation is large in the region RH-H<1.2Å but rapidly decreases along with increasing of RH-H. Finally the electron correlation is almost 0 in region RH-H>2.0Å.
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