Journal of Computer Chemistry, Japan

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> フラグメント分子軌道(FMO)法を用いた散逸粒子動力学シミュレーションのための有効相互作用パラメータ算出の自動化フレームワーク
<Author(s):> 奥脇　弘次, 土居　英男, 望月　祐志
<Corresponding author E-Mill:> okuwaki(at)rikkyo.ac.jp
<Abstract:> 近年，用途に応じて目的の機能を有した材料開発の要求が高まっており，大規模な構造予測のためのシミュレーションが注目を浴びている．私達は，今回，散逸 粒子動力学(DPD: Dissipative Particle Dynamics)シミュレーションを例に，有効相互作用パラメータ(χパラメータと呼ばれる) をフラグメント分子軌道(FMO)法から算定するためのフレームワークとワークフローシステムを開発した．FMO計算は非経験的であるため，高分子系素材 に関わるほとんどの有機化合物に対して使うことが可能であり，χパラメータの算定に対して汎用性を持つと考えられる．この報告では，本システム (FCEWS: FMO-based Chi-parameter Evaluation Workflow System)の開発の目的，理論的な背景，ならびにソフトウェアについて解説する．
<Keywords:> Dissipative particle dynamics, DPD, fragment molecular orbital, FMO, chi-parameter
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0048/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 133-134, by J-STAGE]
<Title:> 原子価結合局在電子波束による分子内電子励起ダイナミクス
<Author(s):> 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> A simple model of localized electron wave packets, floating and breathing Gaussians with non-orthogonal valence-bond spin-coupling, is demonstrated to produce an accurate high-harmonic generation (HHG) spectrum from an LiH molecule induced by an intense laser pulse. In contrast with the conventional molecular orbital picture in which the Li 2s and H 1s atomic orbitals are strongly mixed in the valence σ bonding orbital, the present calculation indicates that a superposition of independent responses of the electrons reproduces the spectrum in which the contribution of the H 1s electron dominates the characteristic plateau and cut-off of HHG.
<Keywords:> Electron dynamics, Localized wave-packets, Valence-bond theory, High-harmonic generation
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0056/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 131-132, by J-STAGE]
<Title:> 計算化学手法によるフラーレンの位置選択的反応の解析
<Author(s):> 伊熊　直彦
<Corresponding author E-Mill:> ikuma(at)chem.eng.osaka-u.ac.jp
<Abstract:> Organic reactions with fullerene realize functional nanomaterials, although selective functionalization is still challenging because of many equivalent olefins causing various regioisomers. Thus, the improvement of reactivity and regioselectivity of C₆₀ reaction has been realized by structural organic chemistry such as enhancement of strain, introduction of heteroatom, and nucleophilic additoin via single eletron transfer (Figure 1 Figure 1. Concept of the activation of C₆₀ to obtain regioselective adducts. ). This paper presents the theoretical clarification for the reactivity and selectivity of these activated reaction conditions.
<Keywords:> Fullerene, Regioselectivity, Strain energy, Ambident basicity, Single elecron transfer
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0054/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 126-128, by J-STAGE]
<Title:> 散逸粒子動力学(DPD)プログラムCAMUSの新規開発と性能評価
<Author(s):> 土居　英男, 齊藤　天菜, 奥脇　弘次, 内藤　貴充, 望月　祐志
<Corresponding author E-Mill:> hideo-doi(at)rikkyo.ac.jp
<Abstract:> Recently, simulations with coarse-graining models, such as coarse-grained molecular dynamics (CG-MD) and dissipative particle dynamics (DPD), have attracted practical interest. We have developed a portable code CAMUS for DPD simulations. Performance evaluations of CAMUS (Code for dissipative particle dynAMics simUlationS) have been made by comparison with COGNAC (Coarse-Grained molecular dynamics program by Nagoya Cooperation) as a standard DPD code, in 5,000 – 100,000 particles systems.
<Keywords:> Dissipative particle dynamics, DPD, Software development, Performance evaluation, Benchmark
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0050/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 119-122, by J-STAGE]
<Title:> FMOプログラムABINIT-MPの開発状況と機械学習との連携
<Author(s):> 望月　祐志, 坂倉　耕太, 秋永　宜伸, 加藤　幸一郎, 渡邊　啓正, 沖山　佳生, 中野　達也, 古明地　勇人, 奥沢　明, 福澤　薫, 田中　成典
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing the ABINIT-MP program for the fragment molecular orbital (FMO) method. The list of inter-fragment interaction energies (IFIEs) is available from FMO calculations and is useful in analyzing the nature of interactions in a given target system. In this Letter, we summarize the current status of ABINIT-MP and also the machine-learning assisted analyses of IFIE data.
<Keywords:> キーワード：Fragment molecular orbital, FMO, ABINIT-MP, Interaction energy, Machine learning
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/5/16_2017-0051/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 112-115, by J-STAGE]
<Title:> 分子動力学法による水系電解液電気二重層キャパシタの界面特性の解析
<Author(s):> 矢野　振一郎, 古山　通久
<Corresponding author E-Mill:> koyama(at)ifrc.kyushu-u.ac.jp
<Abstract:> Electric double layer capacitor (EDLC) is a storage device based on the interfacial interaction between electrode and electrolyte. We have conducted molecular dynamics simulations to study the atomistic origin of storage capacity. Electric double layer structures are studied by changing the electric field applied to the electrolyte. Charge density distribution in the electrolyte phase derived on the basis of molecular dynamics simulation is used to discuss the capacitance-voltage characteristics for different electrolyte species.
<Keywords:> キーワード：Electric double layer capacitor, Interfacial interaction, Molecular dynamics, Charge density distribution, Capacitance-voltage characteristics
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/4/16_2017-0033/_html/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> ケクレ構造数え上げのアルゴリズムを用いたASC及びConjugated Circuitの計算プログラムの開発
<Author(s):> 森川　, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> dmorikawa(at)shinshu-u.ac.jp
<Abstract:> 成田らのケクレ構造の数え上げアルゴリズムを改良する事によって，各種共役分子のalgebraic structure count (ASC)を求める計算プログラムを開発した．さらに，この計算はケクレ構造の重ね合わせを利用する事から，全てのconjugated circuitの数え上げも可能となった．これによりASCとconjugated circuitを一度に求める事が可能となった．また，ASCを決定できない非交互共役系についても議論を行った．
<Keywords:> Algebraic structure count, Kekul structure, Conjugated circuit, Sachs graph, Resonance energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0036/_html/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.3, -, by J-STAGE]
<Title:> Thermodynamics of Three-phase Equilibrium by Van Der Waals Equation of State
<Author(s):> Yosuke KATAOKA
<Abstract:> The phase diagram for a three-phase equilibrium was derived using van der Waals (vdW) equation of state (EOS) with respect to pressure. Aside from the typical liquid-gas vdW EOS, a new solid-gas vdW EOS was introduced. The new vdW EOS had the same functional form as the original equation of state and only the van der Waals coefficients were different. The thermodynamic EOSs were integrated to obtain the internal energy and the integral constants were given explicitly. The calculated phase diagram was consistent with that for argon and the Lennard-Jones system.
<Keywords:> Three-phase equilibrium, Van der Waals equation of state, Argon, Lennard-Jones system, Thermodynamics
<URL:> https://www.jstage.jst.go.jp/article/jccjie/3/0/3_2017-0026/_html