Journal of Computer Chemistry, Japan
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Volume 12 , Issue 4
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  • Kimichika FUKUSHIMA, Hikaru SATO
    Volume 12 (2013) Issue 4 Pages 197-203
    Released: December 25, 2013
    [Advance publication] Released: October 18, 2013
    JOURNALS FREE ACCESS
    An anion (negative ion) such as O2−, which is stable in a molecule/solid, sometimes cannot bind an attached electron in a vacuum and emits an electron. To describe an anion, the author previously developed the SIWB (surrounding or solid Coulomb-potential-induced well for basis set) method for a linear combination of atomic orbitals (LCAO) calculated numerically in a discrete variational (DV) density functional theory (DFT). For the generation of basis atomic orbitals, the DV method usually adds a well potential to the potential for electrons to stabilize the electrons. There was no reasonable method for determining the depth and radius of the well and the usual well depth has a relatively deep value of about −1 Eh independent of electron attachment tendency. In contrast, the SIWB method adds a well potential solely for generating and improving anion basis atomic orbital functions and uniquely determines the depth and radius of the well, which is relatively shallow, considering the Coulomb potential arising from the surrounding nuclei and electron cloud in a molecule/solid. This article aims to attempt calculations for the one-electron wave function of a molecule including an anion using the finite element method, which adopts a basis set localized in a small region on a space lattice that is suitable for the wave function behavior of an anion. The finite element results were compared not only to results from the usual LCAO method with a relatively deep well (denoted as LCAO−N), but also to those from the improved LCAO method with the SIWB scheme (denoted as LCAO−SIWB). It emerged from the present study that the finite element results for the anion are consistent with the LCAO−SIWB results.
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  • Tadashi ANDO, Seigo ITOH, Ichiro YAMATO
    Volume 12 (2013) Issue 4 Pages 204-214
    Released: December 25, 2013
    [Advance publication] Released: December 10, 2013
    JOURNALS FREE ACCESS
    Simulating a whole cell system based on the data obtained from various 'omics' researches is getting a practical aspect. In this study, we developed a software for simulating dynamical behaviors of a cell system in terms of individual enzymatic reactions. Basic concepts in developing the simulator are as follows: 1. Parameters are obtained from experimental data as far as possible for direct comparison of simulation and experimental results. 2. Various types of reactions are integrated into the simulator in order to simulate a whole cell without other programs. As a first step toward whole cell simulations, we try to simulate "diauxie" of E. coli in the medium containing two carbon sources, glucose and lactose, in which the bacteria show two separate growth phases; they consume glucose first and then switch to use lactose. The simulation model consists of a gene regulation system (lactose operon, lacI gene, crp gene), metabolic pathway (glycolytic and lactose-utilizing pathways), and phospho-transferase system, PTS (Figures. 1–3). Parameters required for cell systems simulation such as Km, kcat, Ka, etc, were collected from experimental reports and a simulation of gene regulation. In our cell simulation, ATP was produced in two phase manner similar to the diauxie growth phenomenon (Figure 4). Even when the concentration of the cAMP:CRP (cAMP receptor protein) complex was fixed at a basal expression level 1 μM throughout the simulation, the diauxie-like phenomenon was observed. This result strongly supports the experimental findings of Inada et al. that the cAMP and CRP concentration was not very different in the presence of glucose and lactose and that the activation of lactose repressor by inhibition of lactose permease (inducer exclusion) would be a main factor for diauxie.
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  • Katsuyuki SHIZU, Tohru SATO, Kazuyoshi TANAKA
    Volume 12 (2013) Issue 4 Pages 215-221
    Released: December 25, 2013
    [Advance publication] Released: December 18, 2013
    JOURNALS FREE ACCESS
    The 1/Nπ relationship states that the reorganization energy λ of a molecule associated with charge transport is inversely proportional to the number Nπ of sites or π electrons involved in a π state of the molecule: λ∝1/Nπ. We investigated the fundamental question of how λ is influenced by Nπ, from the perspective of the vibronic coupling density. Vibronic coupling density analysis showed that symmetric distribution of the electron-density difference Δρ is essential for this relationship. The relationship can be more precisely rephrased as the size of the vibronic coupling constant is inversely proportional to the square-root of the number of sites over which Δρ is delocalized. Our findings provide not only a fundamental understanding of the 1/Nπ relationship, but also a practical approach to the molecular design of functional materials through controlling Δρ and vibronic couplings.
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  • Suguru UEMURA, Atsushi ODERA, Shohji TSUSHIMA, Katsuyuki KAWAMURA, Shu ...
    Volume 12 (2013) Issue 4 Pages 222-229
    Released: December 25, 2013
    JOURNALS FREE ACCESS
    Carbon dioxide enhanced oil recovery (CO2-EOR) is a technique to recover the residual oil from oil reservoirs by injection of CO2. CO2 dissolution causes changes in the physical-chemical properties of oil, resulting in improvement in the oil recovery efficiency. However, the fundamental dissolution mechanism is not clear. To clarify it, we have investigated CO2 dissolution phenomena in cyclohexane (C6H12) using molecular dynamics simulations. The results show that CO2 dissolves in C6H12 by forming a cluster structure. The dissolution state of CO2 in C6H12 is discussed by comparing with the dissolution state of H2O in C6H12, and the electric fields around CO2, H2O, and C6H12 are analyzed from the viewpoint of molecular polarity and coulomb interactions. As a result, the CO2 dissolution state with cluster formation is considered to be strongly dominated by the similarity of the shape and size of the electric fields around CO2 and C6H12.
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Note
  • Amih SAGAN, Sumie TAJIMA, Umpei NAGASHIMA, Hiroyuki TERAMAE, Shin-ichi ...
    Volume 12 (2013) Issue 4 Pages 230-234
    Released: December 25, 2013
    JOURNALS FREE ACCESS
    We discuss a half bond and a single bond formed from 1s electron of H2+, H2, HeH+, He2+,and He22+ using UMP2 with 6–311++G** basis set. Equilibrium nuclear distances of H2+, H2, HeH+, He2+,and He22+ are 1.050, 0.738, 0.785, 1.086, 0.712 Å (1 Å =1−10m) respectively The difference of the nuclear distances is explained by electron repulsion and orbital correlation. The nuclear distance of He2+ is shorter than that of H2+ but longer than that of He22+. As to the possible cause it is possible to consider that the 1s orbital radius of He2+ is shorter than that of H2+ or that a 3rd electron occupied the anti-bonding orbital of He22+.
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