Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 3, Issue 4
Displaying 1-6 of 6 articles from this issue
General Papers
  • Tomoya TAKADA, Yuri KITAJIMA
    2004 Volume 3 Issue 4 Pages 121-128
    Published: 2004
    Released on J-STAGE: December 25, 2004
    JOURNAL FREE ACCESS
    The adsorption structure and hyperfine coupling constant of methyl radical CH3 on a boron-containing oxide surface have been studied by means of density functional theory (DFT) calculations. As models for CH3 adsorbed on boron oxide surface, Model-I in which CH3 interacts with a surface B atom and Model-II in which CH3 interacts with a surface B-OH group have been chosen. On the basis of the calculation results, Model-II is found to be a more favorable adsorption site. The proton hyperfine coupling constant of Model-II is calculated to be smaller than that of Model-I; the proton hyperfine coupling constant of Model-I is almost equal to that of free CH3. The reason for the difference between the proton hyperfine coupling constants of Model-I and Model-II has been discussed on the basis of the calculation results. The difference in the proton hyperfine coupling constants can be explained by the spin-polarization mechanism.
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  • Tadashi ANDO, Toshiyuki MEGURO, Ichiro YAMATO
    2004 Volume 3 Issue 4 Pages 129-136
    Published: 2004
    Released on J-STAGE: December 25, 2004
    JOURNAL FREE ACCESS
    A new simple implicit solvent model, effective charge (EC) model, was introduced into the Brownian dynamics algorithm based on AMBER united-atom force field. In the EC model, an atomic charge was decreased as a function of solvent-accessible surface area of the atom. We carried out the Brownian dynamics simulations of a 28-mer ββα fold peptide using four implicit solvent models: a generalized Born/solvent-accessible surface area (GB/SA) model, a solvent-accessible surface area (SA) based solvent model, a SA in combination with distance-dependent dielectric (DD/SA) and the EC combined with DD/SA (DD/SA/EC) model; and the calculated results on structure and dynamics of the peptide were compared with those of molecular dynamics simulation using explicit solvent model. Several artifacts were observed in the simulation using the GB/SA model. On the other hand, simulation using the DD/SA and DD/SA/EC implicit solvent models were free from such artifacts. Especially BD with the DD/SA/EC model gave the most stable trajectory as judged by root mean square deviations from the initial structure without large computational cost.
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  • Hiroaki KATO, Hiroyuki MIYATA, Naohiro UCHIMURA, Yoshimasa TAKAHASHI, ...
    2004 Volume 3 Issue 4 Pages 137-144
    Published: 2004
    Released on J-STAGE: December 25, 2004
    JOURNAL FREE ACCESS
    This paper describes a three-dimensional (3D) protein motif dictionary system that is closely related to the PROSITE sequence motifs. Because there were many different 3D motif patterns but having a particular PROSITE sequence pattern, we have investigated the approaches for quantitative comparison and clustering of such 3D structure segments. For a pair of 3D structure segments, the dissimilarity value was defined with the root mean squares of inter-residue distances. A conformational pattern clustering was employed for grouping the 3D patterns on the basis of the dissimilarity matrix. Some additional knowledge information described in PROSITE was also used to refine the clustering results. A 3D motif dictionary was constructed using all the data set of the Protein Data Bank. A graphical user interface for using the dictionary was also developed.
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  • Ayumu SAITO, Koichi NISHIGAKI
    2004 Volume 3 Issue 4 Pages 145-152
    Published: 2004
    Released on J-STAGE: December 25, 2004
    JOURNAL FREE ACCESS
    Genomic DNA contains sequences that are relics of evolution together with functional protein sequences and regulatory operands. The mutual relationship of chromosomes that constitute the genome is of interest from the viewpoint of evolution as well as from that of systems biology. Chromosome origin, the frequency of chromosomal alteration, and the nature of these alterations can be addressed by analyzing oligostickiness, which is highly informative of the hidden properties of genome sequences. Oligostickiness analysis is an oligonucleotide-affinity test performed along the genome sequence. This analysis revealed that frequent recombination events occur during the course of evolution, which is a phenomenon inherent to chromosomes. This was further supported by the finding of chromosome homogeneity in the nucleus and by the assimilation of oligostickiness for pairs of complementary oligonucleotides. Genomes consisting of multiple chromosomes possess a common property where all chromosomes share the same tendency of oligostickiness for any kind of probe (oligonucleotide), indicating that these chromosomes all experienced random-mode frequent inter-/intra-recombinations. The phenomenon observed here, namely the homogeneity of chromosomes, was novel but it could be interpreted in terms of random-mode frequent recombination of chromosomes with a considerable contribution of repeated sequences. Therefore, oligostickiness is useful for analyzing the similarity of chromosomes.
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  • Hirotaka TANIMURA, Masahiko HADA
    2004 Volume 3 Issue 4 Pages 153-158
    Published: 2004
    Released on J-STAGE: December 25, 2004
    JOURNAL FREE ACCESS
    A series of calculations of halogen nuclear magnetic shielding constants and chemical shifts in X- and XO4- (X = F, Cl, Br, I) were carried out to discuss the relativistic and electron-correlation effects and, especially, the non-additivity of both effects. The second-order Douglas-Kroll-Hess method was used as a relativistic method, and the Moller-Plesset method was applied to the generalized UHF wave function. The calculated chemical shifts in ClO4- and IO4- agree reasonably well with the observed ones, though there are no experimental values in FO4- and BrO4-. The relativistic effect was quite large especially in IO4- as reported previously, while the electron-correlation effect is significant in both FO4- and IO4-. The non-additivity of the relativistic and the electron-correlation effects in magnetic shielding constants is unexpectedly large in IO4-, and therefore a relativistic electron-correlated method is crucial for describing accurate heavy-element nuclear magnetic shielding constants and chemical shifts.
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