Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 14 , Issue 3
Special Issue: Selected Papers from the Annual Spring Meeting 2015
Showing 1-21 articles out of 21 articles from the selected issue
Foreword
Letters (Selected Paper)
  • Yoshifumi NISHIMURA, Takeaki KAIHO, Hiromi NAKAI
    2015 Volume 14 Issue 3 Pages 43-46
    Published: 2015
    Released: September 25, 2015
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    The authors' group has developed the program named DC-DFTB-K for the on-the-fly quantum mechanical molecular dynamics (MD) simulation of huge systems using the density-functional tight binding (DFTB) method. The combination with the divide-and-conquer (DC) method enables linear-scaling calculation of DFTB energy and its derivatives. Due to the massively parallel implementation, the program can treat systems containing one million atoms on the K computer. In this paper, the recent extension of DC-DFTB-MD technique is outlined together with the illustrative application to chemical reaction dynamics in lithium-ion device.
  • Hideaki ISHIKAWA
    2015 Volume 14 Issue 3 Pages 47-49
    Published: 2015
    Released: September 25, 2015
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    We applied a method for calculating indefinite integrals developed for atomic structure calculations to mathematical functions defined by integrals and obtained highly accurate results. The method is simple and has wide applicability. Examples of application are, elementary transcendental functions such as exponential, logarithmic, and arctangent functions, then error function, Fresnel integrals, exponential, cosine, and sine integrals, and incomplete gamma functions.
  • Katsumi NAKAGAWA
    2015 Volume 14 Issue 3 Pages 50-51
    Published: 2015
    Released: September 25, 2015
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    Isotropic NMR shielding constants σiso were calculated for hydrogen, carbon, nitrogen, oxygen, fluorine and phosphorous atoms in small molecules by using numerical basis functions, which were based on AOs of Discrete Variational Xα (DV-Xα) method and were modified to London atomic orbitals to avoid the gauge-origin-dependence when magnetic field exists. In DV-Xα method AOs are prepared by solving the Hartree-Fock-Slater (HFS) equation substantially equivalent to that used to calculate MOs and are very accurate around each nucleus. However, σisos calculated in the default condition of DV-Xα method don't agree well to experimental ones. By optimizing AOs in a reasonable way, σisos were highly improved and agreed with experimental ones far better than results by Hartree-Fock (HF) method having conventional basis functions. The usefulness of MOs constructed with optimized numerical basis functions was clearly demonstrated.
  • Takayoshi ISHIMOTO, Yuichi INADOMI, Hiroaki HONDA, Michihisa KOYAMA
    2015 Volume 14 Issue 3 Pages 52-53
    Published: 2015
    Released: September 25, 2015
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    Electronic structure calculation is necessary for metal nanoparticles composed of more than 1000 atoms to understand the intrinsic physical and chemical properties of nanoparticles. In this study, we analyzed the parallel performance of electronic structure calculation for metal nanoparticles by using the Vienna Ab-initio Simulation Package (VASP) program with large-scale computational resources. We found that VASP is suitable for the large-scale electronic structure calculation because the parallelization efficiency improved with increasing metal nanoparticle size (Pd405, Pd807, and Pd1289).
  • Hiroyuki SATO, Azuma MATSUURA
    2015 Volume 14 Issue 3 Pages 54-56
    Published: 2015
    Released: September 25, 2015
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    The role of water in the protein-ligand binding site was investigated from the viewpoint of enthalpic bridging between human coagulation factor Xa (fXa) and four ligands. Ligand-constrained MD simulation was done for identifying hydration sites and representative water molecules were arranged at the sites. The calculated fXa-ligand interaction energy while considering these explicit water molecules as parts of fXa shows excellent correlation to the experimental binding affinity, while the energy with considering them as implicit solvent does not correlate. This result indicates that the representative water molecules at the hydration sites should be explicitly considered when protein-ligand interaction energy is analyzed, and ligand-constrained MD simulation is a powerful tool to identify these hydration sites.
  • Kazuo NARUSHIMA, Toru IWATAKE, Yusaku KAWAKAMI
    2015 Volume 14 Issue 3 Pages 57-59
    Published: 2015
    Released: September 25, 2015
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    The author is confident that knowledge of electronic materials and molecular simulation will become indispensable for future students of electrical and electronic engineering majors.This paper presents an approach for an introductory lesson on molecular simulation just inaugurated by the author. Specifically, the first step of molecular simulation was incorporated into the lecture "The Basic Theory of Optical Property." This lesson was taught using spreadsheets (Excel; Microsoft Corp.), which are familiar and easily used software for students. Comments by students after the lesson included the following; "Abstract contents were well understood through exercises," and "The significance of simulations was abundantly clear." Consequently, the author believes that effects anticipated from this lesson (the objective of this lesson) were attained to a good degree.
  • Naohiro NISHIDA, Seiji KANAI, Takashi TOKUSHIMA, Yuka HORIKAWA, Osamu ...
    2015 Volume 14 Issue 3 Pages 60-62
    Published: 2015
    Released: September 25, 2015
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    We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of acetic acid and methyl formate in the liquid phase at two oxygen K-edge (OC=O and OOH,OCH3) to observe the intermolecular interaction dependence of XES spectra. Structure sampling as a cluster model was performed from a snapshot of molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. We found that theoretical XES spectra were well reproduced experimentally.
  • Yuya YAMAMOTO, Naoya SAWAGUCHI, Makoto SASAKI
    2015 Volume 14 Issue 3 Pages 63-66
    Published: 2015
    Released: September 25, 2015
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    The interatomic potential for a wide composition range of sodium silicate glasses was proposed by first-principles calculation. Point charge was set for each glass composition on the basis of population analysis of the alkali silicate crystals by using the density functional theory. The potential parameters were obtained from the energy surface of the SiO2+ model by using the molecular orbital method. The molecular dynamics simulation using the new interatomic potential showed improved structures of sodium silicate glasses.
  • Hiroshi SAKIYAMA
    2015 Volume 14 Issue 3 Pages 67-68
    Published: 2015
    Released: September 25, 2015
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    Chiral dinuclear zinc(II) complexes [Zn2(R-bppmp)(MeCO2)2]BPh4 (1R) and [Zn2(S-bppmp)(MeCO2)2]BPh4 (1S) were previously reported to hydrolyze peptide bonds, and the activity of 1S was two times larger than that of 1R. In order to clarify the reason for the difference in activity, substrate incorporation modes were investigated on the basis of Density Functional Theory (DFT) method. Consequently, in the case of 1S, the most stable isomer was found to be suitable in incorporating the substrate in a stable form. As for the case of 1R, the most stable isomer was found to be not suitable, whereas the second most stable isomer was found to be suitable in incorporating the substrate in a stable form.
  • Hiroaki UMEDA, Toshihiro HANAWA, Mitsuo SHOJI, Taisuke BOKU, Yasuteru ...
    2015 Volume 14 Issue 3 Pages 69-70
    Published: 2015
    Released: September 25, 2015
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    GPU acceleration of four-center (4C) inter-fragment Coulomb interaction term (IFC) for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. FMO calculation has two time-consuming steps: Fock matrix construction and IFC calculation, and in our previous letter, it was reported that the former is successfully accelerated with our GPU-enable code. The 4C-IFC calculation is the core part of the latter and its code is similar to that of Fock matrix construction. In this letter, we briefly describe the GPU-accelerated 4C-IFC calculation routine, and report a performance benchmark for GPU-accelerated FMO calculation. The GPU-accelerated program shows 3.3× speedups from CPU only FMO-HF/6-31G (d) calculation for 642 atomic protein on 8 nodes of HA-PACS base cluster.
  • Mitsuki TOOGOSHI, Satoru S. KANO, Yasunari ZEMPO
    2015 Volume 14 Issue 3 Pages 71-73
    Published: 2015
    Released: September 30, 2015
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    The maximum entropy method (MEM) is one of the key techniques for spectral analysis. The main feature is to describe spectra in low frequency with short time-series data. We adopted MEM to analyze the spectrum from the dipole moment obtained by the time-dependent density functional theory (TDDFT) calculation in real time, which is intensively studied and applied to computing optical properties. In the MEM analysis, we proposed that we use the concatenated data set made from several-times repeated raw data and the phase shift. We have applied this technique to the spectral analysis of the TDDFT dipole moment of oligo-fluorene with n=8. As a result, higher resolution can be obtained without any peak shift due to the phase jump. The peak position is in good agreement with that of FT with just raw data. The efficiency and the characteristic feature of this technique are presented in this paper.
  • Tomoo AOYAMA, Yasutaka WAKAZUKI
    2015 Volume 14 Issue 3 Pages 74-76
    Published: 2015
    Released: September 25, 2015
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    Under nuclear power plant accident, by the ventilation of containment vessel, suspended particulate matter (SPM) is emitted; it attracts radioactive compounds, and the plume diffuses in air. It soaks into the human body. We are required to run away from the invisible plumes. The routes do not exist at any time. We recognize status soon, and should select priority persons to escape from there. We code a real-time plume tracer, which reads 4D-winds of Meso Scale Model (MSM), calculates time-development of plumes. The precision for reach time of plumes is 3–5 min, inner 8 km points from emission.
  • Hiroko SATOH, Tomohiro ODA, Kumiyo NAKAKOJI, Takeaki UNO, Satoru IWATA ...
    2015 Volume 14 Issue 3 Pages 77-79
    Published: 2015
    Released: September 25, 2015
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    We have launched a project called "Maizo"-chemistry, which is aimed toward molecular- and reaction discovery based on big data of quantum mechanical global reaction route mappings. The global reaction data includes equilibrium structures (EQs), dissociation channels (DCs), and transition structures (TSs), which are automatically calculated by a global search on a potential energy surface using the GRRM (global reaction route mapping) method. Applications to molecular- and synthesis design are an important part of the project. Machine learning and visualization techniques as well as chemoinformatics methods are essential to acquire useful information from the large reaction data space. We describe here a software system, RMapViewer, which we have developed to visualize and analyze the GRRM outputs.
  • Yoshiaki TANIDA, Azuma MATSUURA
    2015 Volume 14 Issue 3 Pages 80-82
    Published: 2015
    Released: September 30, 2015
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    We have applied alchemical free energy calculation of theophylline with an RNA aptamer with one or more ligand docking poses. We find that the predicted binding affinity strongly depends on the anchor's position at the receptor using only distance restraints; it means that a ligand is trapped at the other metastable states during the decoupling process. We also demonstrate that the binding affinity of a fragment-like molecule such as theophylline to the receptor is obtained by phase space decomposition with orientational restraints.
  • Ayumu NAGAO, Takayoshi ISHIMOTO, Michihisa KOYAMA, Hiroshi MIYAMURA, J ...
    2015 Volume 14 Issue 3 Pages 83-84
    Published: 2015
    Released: October 17, 2015
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    Pt decorated cubic Ni nanoparticles exhibited high catalytic activity in spite of the fact that they contained only a few at.% of Pt. The unusual catalytic property was believed due to the unique arrangement of Pt on the edges and corners of the Ni cube, which was experimentally confirmed to be the consequence of the diffusion of Pt atoms from the core of the particle at the initial stages of the reaction. Thus an explanation for diffusion property of the Pt atoms in the particle was attempted by performing molecular dynamics calculation by constructing models based on experimental findings.
  • Dai MORIKAWA, Yasushi NOMURA, Noriyuki MIZOGUCHI
    2015 Volume 14 Issue 3 Pages 85-87
    Published: 2015
    Released: October 17, 2015
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    The effects of the tube length and diameter on the thermodynamic stability and chemical reactivity of zigzag carbon nanotubes (CNTs) with finite-length Clar cell (FLCC) were examined by means of topological resonance energy (TRE) and algebraic structure count (ASC), respectively. It was found that TRE and HOMO-LUMO gap in FLCC-(3,0) CNT with fully-benzenoid oscillate as functions of the tube length with the period of 2. In contrast, FLCC-(4,0) and (5,0) CNTs were found to have the tube length dependence different from that of FLCC-(3,0) CNT. This difference in tube diameter (chiral-index) dependence was found to be characterized by whether ASC is equal to Kekulé structure count or not.
  • Natsuki MIYAI, Takakuni SHIMAZAKI, Nozomu UCHIDA
    2015 Volume 14 Issue 3 Pages 88-89
    Published: 2015
    Released: October 17, 2015
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    Composite plating of TiO2 nanoparticle with electrolessly plated nickel films was developed by Matsubara. Although, it is assumed that the eutectoid mechanism is divided into four steps of adsorption, it is not elucidated. So elucidating the eutectoid mechanism at the molecular level provides valuable information about not only this composite plating but also other type of plating. It should be noted that TiO2 surface charge is changed by pH of plating bath. As we conduct a study on the interaction of TiO2 with reactant, it is important to consider the TiO2 surface state i.e., TiO2 surface charge. In this study, we aim to reveal the eutectoid mechanism at molecular level and the influence of TiO2 surface charge in eutectoid by using molecular orbital calculation. For theoretical chemical calculations, we used the publicly available semi-empirical calculation software MOPAC2012. The Hamiltonian PM7 to be used for molecular orbital calculation semi-empirical. We used the citric acid as organic acid, and Ti2O2 is adopted as TiO2.The result shows that the adsorption energy (ΔEad) under acidic condition has lowest value within last step of the eutectoid.
  • Kazuki AKIYAMA, Seiichi KAWAHARA, Nozomu UCHIDA
    2015 Volume 14 Issue 3 Pages 90-91
    Published: 2015
    Released: October 24, 2015
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    Natural rubber is an excellent material in elasticity and abrasion resistance, so that it is used for tires of airplanes and heavy automobiles, such as a bus. It is impossible to make a synthetic rubber having the same physical properties as the natural rubber, even with the latest synthesis technology. However, the detailed structure of a natural rubber is still unclear. The aim of this study is to clarify the conformation and the thermochemical properties of a natural rubber. The conformational search and calculation of thermodynamic variables were performed with the computer chemistry program CONFLEX. In the calculation, we used two models; one with phosphate group and the with no phosphate group. The model having a phosphate group has a linear stable conformation, while the other has a coiled coherent one. As a result, we found that the end group of natural rubber has a significant effect on its stable structure. Moreover, natural rubber with a linear structure had relatively lower energy.
  • ChingTang LIN, Takayoshi ISHIMOTO, Michihisa KOYAMA
    2015 Volume 14 Issue 3 Pages 92-93
    Published: 2015
    Released: October 24, 2015
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    Cation diffusions at materials interfaces in solid oxide fuel cell (SOFC) potentially cause degradations of cell performance during long-term operation. We investigate the cation diffusion mechanism in yttria stabilized zirconia (YSZ), as a first step to clarify the cation diffusion mechanism at SOFC interface. Molecular dynamics simulation combined with the metadynamics method are used to simulate cation jumps in this study. Y3+ and Sr2+ migration mechanisms in YSZ are discussed on the basis of cation jumps observed by using the metadyanamics method.
  • Keisuke SAITO, Yuji HIGUCHI, Nobuki OZAWA, Momoji KUBO
    2015 Volume 14 Issue 3 Pages 94-95
    Published: 2015
    Released: October 30, 2015
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    We examine the mechanism of fracture processes in a double-network (DN) gel model by using a coarse-grained molecular dynamics simulation. Initially, we develop a modeling method for DN gel containing both slightly and highly cross-linked networks, and then stretch the DN gel model. During stretching, the highly cross-linked network begins to dissociate at a strain of 1.0, increasing the stress. At strains from 4.0 to 5.0, the slightly and highly cross-linked networks simultaneously dissociate and the stress decreases. Then, the dissociation of the highly cross-linked network stops and only the slightly cross-linked network dissociates at a strain of 12.0, while the stress remains almost the same. We reveal that characteristics of each type of network gradually appear in the DN gel. Next, we change the polymer chain length to reveal its influence on the mechanical properties of the gel. An increase in the length of the slightly cross-linked network chains improves the strength of the DN gel, whereas that of the highly cross-linked network chains does not affect its strength. An increase in the slightly cross-linked network chain length increases the number of entanglements, leading to the increase in strength.
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