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Volume 13 , Issue 3
Special Issue: Selected Papers from the Annual Spring Meeting 2014
Showing 1-21 articles out of 21 articles from the selected issue
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Foreword
Announcement
Letters (Selected Paper)
  • Shinsaku FUJITA
    Volume 13 (2014) Issue 3 Pages 155-156
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    The RS-stereoisomeric group T d σ ˜ I ˆ for characterizing stereoisograms based on a tetrahedral skeleton is formulated by starting from the point group T d Each stereoisogram consists of a quadruplet of promolecules, which is governed by the RS-stereoisomeric group. The number of quadruplets with a given set of proligands is calculated by the extended unit-subduced-cycle-index (USCI) approach. The representative promoleucles of the resulting quadruplets are depicted in a tabular form.
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  • Shintaro ISHIYAMA, Chikara KANEDA, Jun SHIBAYAMA, Keisuke SUZUKI, Ryo ...
    Volume 13 (2014) Issue 3 Pages 157-158
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    Dinuclear zinc complexes showed aminopeptidase activity, while dinuclear magnesium complexes did not. The reason for the difference is discussed based on the Density Functional Theory (DFT). In the zinc complex, a chelating arm is expected to work as a general base catalyst, while in the magnesium complex, the arm cannot work as a general base catalyst.
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  • Teppei TAMAKI, Tomohiro KABASHIMA, Kazuki MORI, Satoshi MINAMOTO, Kazu ...
    Volume 13 (2014) Issue 3 Pages 159-160
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We have been developing a supporting program named GISP for the molecular dynamics (MD) simulation program, Gromacs. The program is designed for the researchers who are not experts of molecular modeling and for the students who want to start to learn MD simulation. We added some new features to the old version of GISP, such as, reformation of basic design of graphical user interface and advanced function for MD simulation of protein in solvent.
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  • Kimichika FUKUSHIMA
    Volume 13 (2014) Issue 3 Pages 161-162
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    For proper anion description, the author 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). In the DV method, a relatively deep (such as −1 Eh) well potential is added to the potential for electrons to generate stable atomic orbital basis functions, where the depth and radius of the well are not definitely determined. Meanwhile, the SIWB method uniquely determines the well radius and the well depth, which is relatively shallow (such as −0.34 Eh). In this article, calculations of the one-electron wave function for a molecule containing an anion were performed using the finite element method (FEM). The FEM results were compared not only to results from the usual LCAO method with a relatively deep well, but also to those from the improved LCAO method with the SIWB scheme (denoted as LCAO−SIWB). It was shown that the FEM results for the anion are consistent with the LCAO−SIWB results.
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  • Shota UEHARA, Kazuhiro FUJIMOTO, Shigenori TANAKA
    Volume 13 (2014) Issue 3 Pages 163-164
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    Protein-ligand docking is one of the most significant issues in structure-based drug design (SBDD). Generally, this docking is considered as an optimization problem which specifies the energetically stable conformation of the ligand at the binding site. However, it is very difficult to identify the correct pose because of many optimization parameters with high correlation. In previous studies, it has been reported that popular docking programs can identify the correct docking pose with an accuracy of only about 60%. In this work, we attempted to apply the Artificial Bee Colony (ABC) algorithm to docking. ABC is an optimization algorithm based on the intelligent behavior of a honey bee swarm, which has higher global search ability than other algorithms. The performance of the ABC for docking was evaluated for 85 protein-ligand complexes of Astex diverse set using AutoDock Energy Function 4.2 as a scoring function. In comparison with three novel docking algorithms, namely SODOCK, PSO@AutoDock and AutoDock default (LGA; Lamarckian Genetic Algorithm), ABC provides the highest success rate of 72.9% (Table 1). The results reveal that the ABC might be more suitable for docking than others in particular for dealing with highly flexible ligands (Figure 1).
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  • Haruo HOSOYA
    Volume 13 (2014) Issue 3 Pages 165-166
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    The main purpose of this series of research is to reconstruct theoretically the "Organic Electron Theory," which was established by Robinson and Ingold in the 1920s without any quantum-theoretical and mathematical basis but still used by organic chemists of the 21st century. The main strategy is graph-theoretical molecular orbital method (GTMO) using topological index Z and supplemented by the perturbation treatment by Coulson and Longuet-Higgins. In this paper the mean length of conjugation L is proposed to be defined for a conjugated hydrocarbon molecule with only one Kekulé structure. With this L the relative stability of isomers of conjugated hydrocarbons can be well predicted, and the extent and stability of heterosubsituted conjugated hydrocarbons can also be explained, which can be diagrammatically obtained by using the "curly arrow" but with no logical support. Thus verification and limitation of the conventional organic electron theory are gradually being accumulated and clarified.
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  • Kasumi UKAJI, Minori ABE, Masahiko HADA, Hiroshi FUJII
    Volume 13 (2014) Issue 3 Pages 167-168
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    High-valent iron (IV)-oxo porphyrin π-cation radical species (P+・) FeIV = O are known as an active intermediate in various enzymatic reactions of cytochrome P450s. In epoxidation reactions catalyzed by these species, potential surfaces between reactant and product are connected by the intersystem crossing. In this report, CASPT2, SO-CASPT2 and SAC-CI calculations were carried out to analyze low-lying doublet, quartet, and sextet electronic ground and excited states in an expoxidation reaction of olefin catalyzed by Cl(P+・) FeIV = O. In both CASPT2 and SAC-CI calculations, we obtained the quartet and sextet ground states of Cl(P+・) FeIV = O and Cl (P) FeIII respectively as suggested experimentally.
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  • Moe SAKURAI, Hiroshi SAKUMA, Noriyoshi TSUJINO, Eiichi TAKAHASHI, Kats ...
    Volume 13 (2014) Issue 3 Pages 169-170
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We have calculated the electronic state in enstatite (En, MgSiO3) using the DFT to understand the hydrous mechanism. Stable positions of hydrogen in En were estimated from the direct comparison of the vibrational frequencies obtained by the experimental FT-IR method and by the first-principles methods. The calculated wavenumber for the structures of conf. Si-1, 2 and Mg-M1, M2 (Figure 2) indicated good agreement to experimental En band. Especially, high wavenumber bands are better reproduced by the structures of conf. Si-1, 2.
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  • Takayoshi ISHIMOTO, Michihisa KOYAMA
    Volume 13 (2014) Issue 3 Pages 171-172
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We analyzed the interaction energy between water molecule and graphene model compounds by using density functional theory (DFT) under the PW91 or PBE functionals with 6-31G** basis set for understanding the relation between electronic structure and the wettability of interface. Four kinds of compounds, benzene (C6H6), coronene (C24H12), circumcoronene (C54H18), and circumcircumcoronene (C96H24), are prepared as graphene models. We found that the interaction energy becomes small when the size of the graphene model compound becomes large.
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  • Yuya YAMAMOTO, Naoya SAWAGUCHI, Makoto SASAKI
    Volume 13 (2014) Issue 3 Pages 173-174
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    Ionic charges of lithium silicates for molecular dynamics simulations were calculated by using density functional theory calculations. The reproducibility of simulated crystal structures were improved compared to that of previous works. The results suggest that the alkali ionic charge should be according to the A2O/SiO2 ratio because of difference of the bond nature.
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  • Takahiro SUZUKI, Hitoshi GOTO
    Volume 13 (2014) Issue 3 Pages 175-176
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We have developed a new molecular visualization tool "TUTmol" as an Android application for mobile terminal devices. Various drawing models; dot, wireframe, stick, ball and stick, space fill, and CPK for general small molecules, and also ribbon and tube models for easier recognition of the secondary structure of protein. Visualization for protein-ligand complex displayed by combining many kinds of drawing models can be supported well for drug and material design purpose.
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  • Hiroki MURABAYASHI, Takeshi TSURUDA, Yang WANG, Yoshihiko KOBAYASHI, S ...
    Volume 13 (2014) Issue 3 Pages 177-178
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We investigated a tribo-chemical reaction between molybdenum dithiocarbamate (MoDTC) and diamond-like carbon (DLC) films using tight-binding quantum chemical molecular dynamics method. First, we perform compression simulation for DLC films with linkage isomer of MoDTC (LI-MoDTC). Then, we observe the LI-MoDTC molecule adsorption on DLC surface with electron transfer from the LI-MoDTC molecule to the DLC surface. Next, we perform the friction simulation on the LI-MoDTC sandwiched between DLC films. S-Mo bond in the adsorbed LI-MoDTC molecule is dissociated during the sliding, which corresponds to the early reaction of the decomposition of LI-MoDTC. We propose that the electron transfer from LI-MoDTC to DLC films weakens the S-Mo bond and the mechanical force dissociates the weakened S-Mo bond during the decomposition of LI-MoDTC on the DLC surface.
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  • Kazuhiro SASA, Tadayosi YOSHIMURA, Hitoshi GOTO
    Volume 13 (2014) Issue 3 Pages 179-180
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We carried out a questionnaire research to develop a "model-core" curriculum for chemical technical colleges, and education for first level simulation engineering in chemistry. Based on the results, we propose educational core-contents in three sections: basic knowledge, computer techniques, and numerical and statistical analysis.
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  • Akinobu SHIGA
    Volume 13 (2014) Issue 3 Pages 181-183
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    A practical method for determining the cluster model size and the estimation of the energy barrier on heterogeneous catalyst, In2O3(111) cluster, on which acetaldehyde is successively converted acetic acid and acetoacetic acid, has been proposed. The cluster size determination is executed as follows; 1) we determine the optimized adsorption structure of reactant, 2) we divide the structure into the reactant fragment and the cluster fragment, and calculate "Paired interacting orbitals (PIO)," 3) we determine the cluster size by using the atomic composition of the PIO of cluster fragment. The estimation of energy barrier is executed as follows; 1) we suppose a transition state, and assume a reactant side intermediate state (RTint), and a product side intermediate state (PDint), 2) we calculate PIOs of the RTint and those of the PDint and compare them, 3) we change the structures of RTint and PDint until the similarities of the PIOs are almost equal, 4) we calculate the total energies of both final intermediates, then, 5) we define an estimated barrier (Ebarriar) according to the following equation;Ebarrier = (ERTint.final +EPDint.final)/2 –Ereactant.
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  • Tomoko AKAMA, Kiho SATO, Shinkoh NANBU
    Volume 13 (2014) Issue 3 Pages 184-186
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    The real-time propagation (RT) of time-dependent Hartree-Fock (TDHF) method and time-dependent density functional theory (TDDFT) have been applied to describing electron dynamics. However, RT-TDHF/TDDFT calculations are computationally demanding. We have developed and implemented RT-TDHF/TDDFT based on the three-term recurrence relation (3TRR) to accelerate time-evolution procedure. 3TRR achieved an efficient time-evolution of electron dynamics.
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  • Souichiro SUGIMOTO, Yasunari ZEMPO
    Volume 13 (2014) Issue 3 Pages 187-189
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    We present a meshfree particle method for real-space electronic structure calculations based on symmetric smoothed particle hydrodynamics (SSPH). As a simple example, we applied SSPH to the HEMT device simulation and the electronic simulation for a simple atom such as H, He and Li. The results calculated using SSPH are in good agreement with those of the finite difference method. Our results indicate that SSPH can be applied to real-space electronic structure calculations that require high accuracy.
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  • Mitsuki TOOGOSHI, Mai KATO, Satoru S. KANO, Yasunari ZEMPO
    Volume 13 (2014) Issue 3 Pages 190-192
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    Maximum entropy method (MEM) is one of the key techniques for spectral analysis. The main feature is improving spectral resolution with short time-series data. We adopt MEM to the calculation of time-dependent density functional theory (TDDFT) in real time, which is intensively studied and applied to computing optical properties. Usually, the spectrum is obtained from Fourier transform (FT) of the time evolution of the dipole moment. In the spectrum comparison of MEM and FT calculations for several molecules, we realize that MEM provides a similar spectrum to that of FT with almost half of the time evolution. In the MEM analysis, not only the total number of time-series data, but also the length of the autocorrelation has an important role to obtain the high resolution spectrum. In this paper, we present the effectiveness and characteristic features of MEM, comparing with those of the FT technique in TDDFT.
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  • Yoshiaki TANIDA, Takashi MITSUI, Azuma MATSUURA
    Volume 13 (2014) Issue 3 Pages 193-195
    Released: September 30, 2014
    JOURNALS FREE ACCESS
    An alchemical free energy method along a thermodynamic pathway was applied to calculate the binding free energy of theophylline (or caffeine) with an RNA aptamer. To keep the ligand at the binding site during the decoupling of the ligand from the surrounding environment, a distant restraining potential between the ligand's center of mass and the binding site was used. The calculated”absolute” binding affinities are in good agreement with the experimental values. We show that the alchemical free energy calculation is a powerful tool in the realm of rational computational drug design and lead optimization.
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  • Suguru UEMURA, Atsushi ODERA, Shohji TSUSHIMA, Katsuyuki KAWAMURA, Shu ...
    Volume 13 (2014) Issue 3 Pages 196-198
    Released: September 30, 2014
    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 comparison 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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