Journal of Computer Chemistry, Japan
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Volume 13 , Issue 5
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Foreword
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  • Takahiro KUDO
    Volume 13 (2014) Issue 5 Pages A21-A24
    Released: December 25, 2014
    JOURNALS FREE ACCESS
    When you search "hemoglobin" at PDBj site, you will find various types of molecule shapes in the search result list (Figure 1). The variety means the molecule may be folded into different form for each situation as well as the included atomic coordinates (asymmetric unit, AU) don't always equal to the biological functional unit (biological unit, BU) (Figure 2). Then I illustrated some examples of hemoglobin molecules. The Figure 3 shows two states of hemoglobin molecules from human: one is oxidized form, and the other is reduced form. Figure 4 shows two types: one is normal type, and the other is hemoglobin S which causes sickle-cell anemia. Finally I introduce another feature of PDBj search that the search target includes not only PDB entries but also PDBj websites, such as news, help and Molecule of the Month articles (Figure 5).
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  • Sumio TOKITA
    Volume 13 (2014) Issue 5 Pages A25-A28
    Released: December 25, 2014
    [Advance publication] Released: November 29, 2014
    JOURNALS FREE ACCESS
    A three dimensional representation of the probability density of a hydrogen 1s orbital in a spherical glass block was developed. It was compared with a two dimensional hydrogen atomic orbit proposed by E. Rutherford. In 1897, J. J. Thomson discovered the electron. The atomic nucleus was discovered by E. Rutherford in 1911. These epoch-making findings in the history of chemistry and physics lead to an atomic orbit model as a planet around the sun (Figure 1(a)). This orbit model had a problem in that the line spectrum (Figure 2 (b)) emitted from excited hydrogen atoms could not be explained. N. Bohr solved the problem assuming that the energies of the electron in a hydrogen atom are quantized, but the atomic orbit model was incorrect because it was based on classical mechanics. In 1924, L. de Broglie proposed that all moving particles such as electrons exhibit wave behavior. E. Schrödinger's equation, published in 1926, describes an electron as a wavefunction. Although this concept was mathematically convenient, it was difficult to visualize. M. Born proposed that Schrödinger's wavefunction could be used to calculate the probability of finding an electron at any given location around the nucleus. A three dimensional representation of Born's probability density of a hydrogen 1s orbital in a spherical glass block was developed (Figure 1(b)). This model allows that the electron may exhibit the properties of both a wave and a particle. The concept of "electron cloud" is frequently used, however, it leads to misunderstanding about an electron, because the observation of an electron gave always a point image of a particle, as was shown on the experiment of the interference of the electron beam using a biprism. The two slit interference experiment with electrons was performed by A. Tonomura [9]. The wave-particle duality of electrons was demonstrated in this experiment using an electron microscope equipped with an electron biprism and a position sensitive electron-counting system. Electrons incident on a wall with two slits pass through the slits and are detected one by one on a screen behind them. The electron is detected as a particle at a point somewhere on the screen according to the probability distribution of the interference pattern (Figure 3). In Figure 1(b), an electron can potentially be found at any distance from the nucleus, but, depending on the square of hydrogen 1s wavefunction, exists more frequently in certain regions around the nucleus than others.
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General Paper
  • Yosuke KATAOKA, Yuri YAMADA
    Volume 13 (2014) Issue 5 Pages 257-262
    Released: December 25, 2014
    [Advance publication] Released: December 06, 2014
    JOURNALS FREE ACCESS
    The phase diagram for a Lennard-Jones system was estimated using conventional NPH molecular dynamics (MD) simulations. Standard periodic boundaries were assumed for unit cells containing 1000 molecules. An elongated unit cell with both solid and vacuum sections was found to be suitable for the NPH MD simulations when calculating both the melting and vapor pressure curves under pressures lower than the critical one. Under high pressures, a unit cell with both solid and liquid sections was used as the initial configuration to obtain the melting temperature. The results of these simulations were compared with the phase transition point given by the reported equations of state.
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  • Masaaki MATSUBARA, Hitoshi GOTO
    Volume 13 (2014) Issue 5 Pages 263-267
    Released: December 25, 2014
    JOURNALS FREE ACCESS
    Conformations and their behaviors of saccharide and glycan take a part of the essential functions in intravital molecular recognition mechanism. Due to the detailed conformational analysis has been made possible by the development of the experimental measurements and computational simulation technology, uniform nomenclature system for saccharide conformations including hydroxyl groups on the pyranose ring is needed rather than usage of conventional descriptions depending on the past researches. In this work, new nomenclature system for aldohexopyranose conformation, which is the unified nomenclature of both the legal IUPAC rule for describing aldohexopyranose ring conformations and our original definition of the notations for rotational isomers of hydroxyl groups on the ring, have been proposed. To describing their orientation of hydroxyl groups on pyranose ring, that is "clockwise" or "reverse clockwise" along the ring, and "inside" or "outside" of the ring, four types of notation; "c" or "r," and "i," or "o," respectively, have been introduced. We applied this method to all stable conformers of α/β-D-glucopyranose, α/β-D-galactopyranose, α/β-D-mannopyranose, and confirmed that almost all conformers can distinguish uniquely.
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  • Yasutaka WAKAZUKI, Tomoo AOYAMA, Masayuki TAKIGAWA
    Volume 13 (2014) Issue 5 Pages 268-277
    Released: December 25, 2014
    JOURNALS FREE ACCESS
    We discuss mass deposition equations of radionuclides diffused by the Fukushima Daiichi nuclear disaster. The empirical equations of physical dry and moist depositions are constructed by using numerical atmospheric model simulation results including diffused radioactive substances and precipitation. The gamma-ray fluxes from radionuclides in the tracer are evaluated and the ambient dose rate is calculated. The rates are fitted to observations, and four parameters of the deposition equations are optimized. The equation is not only for empirical and statistical correction of numerical atmospheric model simulation results but also for understanding physical deposition processes.Using the optimized equation, we calculate ambient dose rates from March 15 to 16 in 2011, as for 32 points along R114, R399, and Ban-Etsu highway in Fukushima prefecture. They are measured by teams of MEXT, KEK, and Fukushima prefecture. 71% of the calculation errors are under the ratio 3.1. The error level is remarkably smaller than that of no-optimization.
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  • Yasuhiro MATSUURA, Ichiro YAMATO, Tadashi ANDO, Atsushi SUENAGA
    Volume 13 (2014) Issue 5 Pages 278-291
    Released: December 30, 2014
    JOURNALS FREE ACCESS
    OmpF porin is one of the major components of the outer membrane proteins in Escherichia coli, and it facilitates the transport of small hydrophilic molecules across the outer membrane. The conductance values of various alkali metal ions for OmpF porin show a trend of Li+ < Na+ < K+ < Rb+ ~ Cs+ (C. Danelon, A. Suenaga, M. Winterhalter, and I. Yamato, Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation. Biophysical chemistry 104 (2003) 591–603.) On the other hand, permeability ratios of the alkali metal ions to chloride anions, estimated by zero-current membrane potential measurements, show an opposite trend at low salt concentrations, that is, Li+ > Na+ > K+ > Rb+ > Cs+, meaning that the protein has a small cation selectivity. In order to elucidate the physico-chemical mechanisms responsible for the conductance and selectivity of OmpF porin, we performed all-atom molecular dynamics (MD)/free energy calculations of the protein. In MD simulations at low salt concentrations under an electric field; simultaneous binding of two Na+ ions to Asp113 in the constriction zone of OmpF porin was observed in the Na+ permeation processes, which is consistent with a previous simulation study (A. Suenega, Y. Komeiji, M. Uebayasi, T. Meguro, M. Saito, and I. Yamato, Computational observation of an ion permeation through a channel protein. Bioscience reports 18 (1998) 39–48.) Then, we hypothesized that the stability of the two-cation bound states plays an important role in determining the conductance sequence of monovalent cations. Driven by this idea, we estimated the binding affinities of two Li+, Na+, and K+ ions to Asp113 in the bound state by a free energy calculation technique, showing that the affinity decreases with their atomic radii, that is, Li+ > Na+ >> K+. This result is qualitatively consistent with the experimental observation of the protein under the electric field and offers new insights into understanding the ion permeation mechanism of OmpF porin.
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