Journal of Computer Chemistry, Japan
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Volume 11 , Issue 3
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Foreword
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General Papers
  • Masato OSHIMA, Masaharu ITO, Shin-ya SUZUKI, Kazuhide MATSUMURA, Hiroh ...
    Volume 11 (2012) Issue 3 Pages 125-130
    Released: October 25, 2012
    [Advance publication] Released: August 10, 2012
    JOURNALS FREE ACCESS
    The calculations of a C–H bond activation were carried out with a two-layer ONIOM (MO:MM) method using DREIDING for the low layer and density functional theory (DFT) at the B3LYP level for the high layer. One of the calculated elementary reactions was that from (C5Me5)Ru(μ-CH2=CH2)(μ-H)2Ru(C5Me5) (4) to (C5Me5)Ru(μ-CH=CH2)(H)(μ-H)2Ru(C5Me5) (5) (eq 2) and the other was that from (C5Me5)Ru(C2H5)(μ-CH2=CH2)(μ-H)Ru (C5Me5) (6) to (C5Me5)Ru(C2H5)(μ-CH=CH2)(H)(μ-H)Ru(C5Me5) (7) (eq 3). All the optimized geometries were consistent with the intermediates in keeping with the phenomenon of "bimetallic activation" reaction where the two metal centers work concertedly in a reaction. The activation free energies of eqs 2 and 3 were 18.8 and 6.9 kcal/mol, respectively. The calculations of two types of C–H bond activation pathways that respectively contain eqs 2 and 3 were carried out. These results suggested that the pathway containing eq 3 was suitable.
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  • Shinsaku FUJITA
    Volume 11 (2012) Issue 3 Pages 131-139
    Released: October 25, 2012
    [Advance publication] Released: September 25, 2012
    JOURNALS FREE ACCESS
    On the basis of restricted subduced cycle indices with chirality fittingness (RSCI-CFs), the restricted-fixed-point-matrix (RFPM) method has been developed as a new method for the combinatorial enumeration of sterically hindered derivatives of a given skeleton. Such RSCI-CFs are derived from subduced cycle indices with chirality fittingness (SCI-CFs) defined in the unit-subduced-cycle-index (USCI) approach (S. Fujita, "Symmetry and Combinatorial Enumeration in Chemistry," Springer-Verlag (1991)). Thus, the SCI-CFs are combined with territory indicators to give territory discriminants, which are treated by considering a restriction condition that rejects the occupation of any adjacent sites, so as to generate RSCI-CFs. The resulting RSCI-CFs are used to evaluate marks (the numbers of fixed points) in place of the original SCI-CFs and combined with the fixed-point-matrix (FPM) method of the USCI approach to develop the RFPM method. The RFPV method based on RSCI-CFs is applied to enumeration of sterically hindered derivatives of dodecahedrane.
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  • Shinsaku FUJITA
    Volume 11 (2012) Issue 3 Pages 140-148
    Released: October 25, 2012
    [Advance publication] Released: September 25, 2012
    JOURNALS FREE ACCESS
    The restricted-partial-cycle-index (RPCI) method for combinatorial enumeration under the restriction of no adjacency of ligands has been developed as a restricted version of the partial-cycle-index (PCI) method of the unit-subduced-cycle-index (USCI) approach (S. Fujita, "Symmetry and Combinatorial Enumeration in Chemistry," Springer-Verlag (1991)). To take account of the restriction condition, (unrestricted) subduced cycle indices with chirality fittingness (SCI-CFs) of the USCI approach are converted into restricted subduced cycle indices with chirality fittingness (RSCI-CFs). Then, restricted partial cycle indices with chirality fittingness (RPCI-CFs) are derived from the RSCI-CFs, just as partial cycle indices with chirality fittingness (PCI-CFs) are derived from the SCI-CFs in the USCI approach. The resulting RPCI-CFs provide generating functions for restricted enumerations. The RPCI method using such RPCI-CFs is applied to enumeration of dodecahedrane derivatives under the restriction of no adjacency of ligands. Several enumerated derivatives are depicted and their symmetries are discussed to comprehend stereochemical properties such as pseudoasymmetry, sphericity, and prochirality.
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Technical Paper
  • Norio YOSHIMURA, Masao TAKAYANAGI
    Volume 11 (2012) Issue 3 Pages 149-158
    Released: October 25, 2012
    [Advance publication] Released: October 16, 2012
    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 fifth step of chemometrics calculations with Microsoft Excel (Excel), the smoothing and the numerical differentiation of data, which are used for pretreatment of signal and spectra, are performed on worksheets. One of the most famous methods of smoothing and numerical differentiation is the Savitzky Golay method (SG method), which is based on the least-squares method. We developed a smoothing and numerical differentiation method on Excel worksheet. Two worksheets were constructed in this method. One worksheet was for obtaining the smoothing and the numerical differentiation coefficients, which correspond to the convolution coefficients of the SG method. Another worksheet was for the smoothing and the numerical differentiation. In this worksheet, the Gauss function is used as an example. The smoothed and the numerical differentiated data obtained from our method almost agreed with the Gauss function and its derivatives. It was confirmed that the smoothing and the differentiation coefficients obtained from our method are the same as the convolution coefficients of the SG method. Additionally, we found an error in the table of the convolution coefficients of the SG method. These results revealed that our method is practical for the smoothing and the numerical differentiation.
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Note
  • Yoshimitsu YAMAZAKI, Yasuhiro KAWANO, Umpei NAGASHIMA
    Volume 11 (2012) Issue 3 Pages 159-163
    Released: October 25, 2012
    [Advance publication] Released: September 25, 2012
    JOURNALS FREE ACCESS
    Chalcones and the related α,β-unsaturated ketones were studied to discover their inhibitory activities for tumor necrosis factor-α (TNF-α) and nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW264 macrophages and their molecular orbital energies. The simple α,β-enone, 1-penten-3-one (6), showed the activities stronger than or comparable to those of the phenyl-conjugated α,β-enones including natural chalcones, suggesting that the α,β-enone structure in 6 is enough to induce the above inhibition. The correlation between the inhibitory activities and the frontier molecular orbital energies suggests that (1) the enones primarily act as Michael acceptors in the inhibition with high susceptibility to the steric hindrance from their molecular structures, and (2) a possibility remains that the phenyl-conjugated enones and those with phenolic hydroxy groups act as electron-donating agents in the inflammatory process. Thus, the α,β-enone core singly suppresses the TNF-α and NO production in LPS-stimulated macrophages, but the conjugated hydroxyphenyl rings in chalcones are also important for their pharmacological activity.
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