Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan14, 85-87, by J-STAGE]
<Title:> ジグザグ型CNTの電子構造のチューブ長依存性とチューブ径依存性
<Author(s):> 森川　大, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> 13st309e(at)shinshu-u.ac.jp

<Abstract:> 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 Kekule structure count or not.
<Keywords:> Zigzag CNT, Topological resonance energy, Algebraic structure count, Aromaticity, Clar structure.
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 83-84, by J-STAGE]
<Title:> Ni-Ptナノ粒子におけるPt拡散特性の分子動力学的解析
<Author(s):> 長尾　歩, 石元　孝佳, 古山　通久, 宮村　弘, ジョン　クヤ, バラチャンドラン　ジャヤデワン
<Corresponding author E-Mill:> jeyadevan.b(at)mat.usp.ac.jp

<Abstract:> 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.
<Keywords:> Nanoparticles, Diffusion, Molecular dynamics, Cage structure, Catalyst
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 88-89, by J-STAGE]
<Title:> 分子軌道法を用いたチタニア共析めっき機構の研究
<Author(s):> 宮井　菜月, 島崎　峻州, 内田　希
<Corresponding author E-Mill:> solgel2(at)vos.nagaokaut.ac.jp

<Abstract:> 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 (ΔE_ad) under acidic condition has lowest value within last step of the eutectoid.
<Keywords:> Composite plating, Molecular Orbital method, TiO2, Ni plating, PH
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0035/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Interatomic Potential Model for Molecular Dynamics Simulation of Lithium Borate Melts/Glasses
<Author(s):> Naoya SAWAGUCHI, Kakeru YAMAGUCHI, Makoto SASAKI, Katsuyuki KAWAMURA
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp

<Abstract:> An improved interatomic potential model was proposed for molecular dynamics simulations of lithium borate melt/glass systems. Charge of ion was reconsidered and a new composition dependent ionic charge model was suggested. A new three-body potential model controlling B-O-B angles was also proposed. The three-body term functioned to avoid square network ring consisted of B-O bonds, without preventing the change of boron coordination number between three and four. The edge-shared tetrahedra of four-coordination boron observed in the previous simulation were cleared by applying this three-body potential model.
<Keywords:> Molecular dynamics, Lithium borate, Glass, Three-body potential, Partial ionic charge model
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0017/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Frenkel Defects and Interstitial Atoms in Periclase (MgO) at High Temperature by Molecular Dynamics Simulation
<Author(s):> Yasuhiro UEDA, Akira MIYAKE
<Corresponding author E-Mill:> miya(at)kueps.kyoto-u.ac.jp

<Abstract:> An analysis program was newly developed to explore the vacancies and interstitial atoms and to determine atomic migration, i.e., atomic diffusion. We applied this program to the results calculated by the molecular dynamics (MD) simulation of periclase (MgO) in which Schottky defects (vacancies) were not initially introduced. Generation, migration and extinction of Frenkel defects and interstitial atoms for only magnesium ion were first observed at high temperature in this MD system and they strongly corresponded to the change of the mean square distance (MSD) of magnesium ion in MD system. On the other hand, we could not observe Frenkel defects and interstitial atoms for oxygen ion and MSD value of oxygen ion had almost constant value. Generation, migration and extinction of Frenkel defects and interstitial atoms cannot be ignored for the diffusion process at high temperature.
<Keywords:> Keyword Periclase (MgO), Molecular dynamics simulation, Frenkel defect, Interstitial atom, Diffusion
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 71-73, by J-STAGE]
<Title:> 最大エントロピー法による発光吸収スペクトルの解析
<Author(s):> 遠越　光輝, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> 14t0007(at)cis.k.hosei.ac.jp

<Abstract:> 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.
<Keywords:> Real-time, Time-dependent density functional theory, Maximum entropy method, Fourier transform, Dipole moment
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 80-82, by J-STAGE]
<Title:> 複数結合ポーズ系の標準自由エネルギー計算
<Author(s):> 谷田　義明, 松浦　東

<Abstract:> 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.
<Keywords:> 結合自由エネルギー, 標準状態, フラグメント, 創薬, アルケミカル変換法
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0029/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0048] Published online by J-STAGE
<Title:> “Maizo”-chemistry Project: toward Molecular- and Reaction Discovery from Quantum Mechanical Global Reaction Route Mappings
<Author(s):> Hiroko Satoh, Tomohiro Oda, Kumiyo Nakakoji, Takeaki Uno, Satoru Iwata, Koichi Ohno
<Corresponding author E-Mill:> hsatoh(at)nii.ac.jp<Abstract:> 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.
<Keywords:> Maizo-chemistry project, Global reaction route mapping (GRRM), Database, Quantum chemical calculation, RMapViewer, Minimum energy path
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0048/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0041] Published online by J-STAGE
<Title:> OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
<Author(s):> 梅田　宏明, 塙　敏博, 庄司　光男, 朴　泰祐, 重田　育照
<Corresponding author E-Mill:> umeda(at)ccs.tsukuba.ac.jp<Abstract:> 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.
<Keywords:> GPGPU, FMO, Inter-fragment Coulomb interaction, Molecular orbital calculation, Performance benchmark
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0041/_article/-char/ja/