カテゴリー: 未分類

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 散逸粒子動力学におけるシリカ−脂質膜界面付近の水の取扱い
<Author(s):> 土居　英男, 奥脇　弘次, 望月　祐志, 小沢　拓
<Corresponding author E-Mill:> hideo-doi(at)rikkyo.ac.jp
<Abstract:> 散逸粒子動力学(DPD: Dissipative Particle Dynamics)法を用いたシミュレーションは生体膜などの幅広い分野で用いられている．従来，このようなDPD シミュレーションでは，バルクの水と界面付近の水を同じように扱う場合がほとんどであった．しかし，こうしたやり方では系の性質を必ずしも忠実に再現して いるとはいえない．界面付近の水分子の性質とバルクの水分子の性質がかなり異なったものであるという実験的，あるいは理論的な研究がなされている からである．そこで，我々はこの問題を解決すべく，バルク水と界面水を区別して取り扱うアプローチを提案する．このアプローチを，脂質膜−シリカ −水の系のDPDシミュレーションに対して適用したところ，シリカに脂質膜が吸着する現象をうまくモデル化することができた．
<Keywords:> Dissipative particle dynamics, DPD, interface, water, lipid membrane
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0003/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> DFT法による塩化鉄(III)錯体の鉄−配位子間相互作用の解析
<Author(s):> 陳　奕廷, 陳　皇州, 福田　光完
<Corresponding author E-Mill:> mifukuda(at)hyogo-u.ac.jp
<Abstract:> 八面体構造から四面体構造まで塩素数に応じて構造が変化する塩化鉄(III)錯体に対してDFT法を用いて理論計算を行った．使用した汎関数は BHandHLYP，wB97XD，CAM-B3LYP，LC-wPBEの4種である．基底関数には6-311+G(d,p)あるいは 6-311+G(3df,2pd)を用い，PCM法による水媒体中で計算を行った．4種の汎関数を用いたDFT法は概ね錯体構造をよく再現し た．2原子の塩素が配位した八面体型[Fe(III)Cl₂(H₂O)₄]⁺のcis型 とtrans型の安定性，及び3原子の塩素が配位した三方両錐型の[Fe(III)Cl₃(H₂O)₂] と四面体型の[Fe(III)Cl₃(H₂O)] の安定性をエネルギー的に比較した．振動計算から得られる配位水分子の伸縮振動の波数の変化を[Fe(III)(H₂O)₆]³⁺か ら[Fe(III)Cl₃(H₂O)]まで調査したところ，八面体型では水分子の減少とともに伸縮 振動は高波数側へシフトし，フリーの単独水分子の伸縮振動に近づく．八面体型では塩素原子の鉄への配位は鉄の極性を低下させ，その結果として水分 子との相互作用を弱めると考えられる．しかし，三方両錐型([Fe(III)Cl₃(H₂O)₂]) から四面体型([Fe(III)Cl₃(H₂O)])になるにつれ再び伸縮振動はやや低波数側へシ フトした．配位する塩素原子数が同じ3であっても，水分子数が少ないほど鉄との相互作用は強められる．鉄−酸素間距離についても同じ傾向を示し た．
<Keywords:> DFT method, iron(III) chloride complex, infrared stretching frequency, interaction between metal and ligand
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0049/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> WinmostarのMOPAC計算による分子軌道モデルの3Dプリンタ用STLファイルの作成
<Author(s):> 吉村　忠与志, 八木　徹, 千田　範夫
<Corresponding author E-Mill:> tadayosi2438(at)yahoo.co.jp
<Abstract:> 分子モデリングソフトウェアには3Dプリンタ用STLファイルを創出するものが開発されていない．そのため，いろいろな機能を付加した研究が進む中 で，Winmostarで作成できるVRML形式ファイルをBlenderでSTLファイルに変換して分子軌道モデルを3Dプリンタで作成するこ とができた．これによって，分子軌道の3Dモデルを簡単に作成できることから，この方面でのますますの利用を期待できる．
<Keywords:> STL conversion from VRML file, Winmostar, Blender, 3D printer, Chemical education, Molecular orbital
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0046/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 244-245, by J-STAGE]
<Title:> 分子動力学シミュレーションによる基板の極性がZnO結晶成長プロセスに与える影響の解明
<Author(s):> 川岸　俊介, 許　競翔, 大谷　優介, 西松　毅, 樋口　祐次, 尾澤　伸樹, 久保　百司
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp
<Abstract:> We examine the effect of polarity of a ZnO substrate on the crystal growth process in physical vapor deposition via molecular dynamics simulation. First, we irradiate ZnO molecules at a velocity of 900 m/s on O-polar, Zn-polar, and nonpolar ZnO substrates and evaluate the crystallinity of the formed ZnO thin film. In the formed thin films on the O-polar and Zn-polar substrates, 8-membered rings are partly observed, while a normal ZnO crystal consists of only 6-membered rings. Thus, the formed thin films on the O-polar and Zn-polar substrates have O and Zn atomic defects. On the other hand, the formed thin film on the nonpolar substrate consists of only 6-membered rings and does not have the atomic defects. We reveal the crystal growth process of ZnO thin films at atomic scale and find that high-quality thin film is formed on the nonpolar substrate.
<Keywords:> Keywords Crystal growth, ZnO, Atomic defect, Polar substrate, Nonpolar substrate, Molecular dynamics simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0056/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 239-241, by J-STAGE]
<Title:> Electronic Similarity among Protein-Ligand Complexes: Development of the Interaction-Energy Projection Method
<Author(s):> Manabu SUGIMOTO, Takafumi INOUE
<Corresponding author E-Mill:> sugimoto(at)kumamoto-u.ac.jp
<Abstract:> A numerical model, called the interaction energy projection method (IEPM), is suggested to evaluate electronic similarity among protein-ligand complexes. Herein we apply the method by referring to the “inter-fragment interaction energy (IFIE),” calculated using the fragment molecular orbital (FMO) method, in two human estrogen receptor complexes.
<Keywords:> Electronic similarity, Protein-ligand docking, Fragment molecular orbital method, Inter-fragment interaction energy, Estrogen receptor, Interaction energy projection method
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0061/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 242-244, by J-STAGE]
<Title:> What Activates the Nitrogen Molecule in Ammonia Synthesis Using Supported Metal Catalysts ? A Quantum-Chemical Model Study
<Author(s):> Manabu SUGIMOTO
<Corresponding author E-Mill:> sugimoto(at)kumamoto-u.ac.jp
<Abstract:> The N-N bond breaking of the N₂ molecule on a metal surface is the key process in the ammonia synthesis using heterogeneous catalysts. Herein we discuss electronic factors in the bond cleavage on the basis of electronic-structure calculations. It is shown that the hydrogenation of the end-on coordinated N₂ molecule may play an important role, which may be accompanied by electron transfer from the catalyst to N₂.
<Keywords:> Electronic-structure calculations, Ammonia synthesis, Catalysis, Supported metal catalyst, Surface adsorption
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0062/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 235-238, by J-STAGE]
<Title:> フタロシアニン フラーレン系における電子物性評価
<Author(s):> 光井　和輝, 池永　祐乙, 成島　和男, 高　緑
<Corresponding author E-Mill:> narushim(at)ube-k.ac.jp
<Abstract:> Recently, studies of solar cells have been conducted actively. Especially, organic thin film solar cells are attracting attention for use as a next-generation flexible substrate material. The reasons include the recent advent of bulk heterojunction structures. Nevertheless, bulk heterojunction solar cells exhibit only about 10% conversion efficiency. They have remained in the study phase. One reason for their low conversion efficiency is that a bulk heterojunction conductive mechanism is so complicated that its fundamental electronic properties have not been elucidated well. This letter describes an examination of the excited state of the bulk heterojunction structure and evaluates its electronic properties. Charge densities are computed for excited and ground states. Then absorbance is computed and examined. Results suggest that the electronically excited state might come to differ from the electronic ground state in a phthalocyanine fullerene bimolecular system. Moreover, we infer that this behavior brings about energy level change and subsequent variation in absorbance.
<Keywords:> Bulk Hetero Junction, Organic thin Film Solar Cell, Molecular Orbital Method, Density Functional Method, Charge Density, Absorbance
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0065/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, A52-A54, by J-STAGE]
<Title:> Special Contribution to The Quantum Hydrogen Issue of Journal of Computer Chemistry, Japan
<Author(s):> Yasuyuki ISHIKAWA
<Corresponding author E-Mill:> yasuyukiishikawa1(at)gmail.com
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/5/15_Special_Contribution_15_5/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 229-231, by J-STAGE]
<Title:> Investigation of a Virtual Nested Two-dimensional Lattice Model for Representing the Diffusive Motion of a Transmembrane Protein in Cell Membrane
<Author(s):> Atsushi OKUMOTO, Tomonari SUMI, Hideo SEKINO, Hitoshi GOTO
<Corresponding author E-Mill:> gotoh(at)tut.jp
<Abstract:> As a refinement of the fluid mosaic model for explaining cell membrane functions, membrane-skeleton fence model and anchored membrane protein picket model have been proposed according to the tracing experiment of a single molecule in plasma membrane. In addition, the experimental observation that the diffusive motion of a transmembrane protein in plasma membrane leads to a normal diffusion through two-step relaxation has suggested that there are two types of nested compartments, large and small. In this paper, we propose a virtual nested two-dimensional lattice model that can express a nested compartment structure of plasma membrane using three parameters in order to represent such a single molecule diffusion movement. Using this 2D lattice model, various diffusive motion simulations of one particle random walks were performed and their trajectories were analyzed by Detrended fluctuation analysis. As a result, we have confirmed that both plasma membrane models, “fence” and “picket,” can be represented by our virtual nested 2D lattice model.
<Keywords:> Transmembrane protein, Plasma membrane, Diffusion movement, Random walk, Detrended fluctuation analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0069/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 232-233, by J-STAGE]
<Title:> 計算化学による生体分子の結合，運搬，代謝の機構解明
<Author(s):> 河野　雅弘, 畠山　望, 蒲池　利章, 宮本　明
<Corresponding author E-Mill:> kohno.m.aa(at)m.titech.ac.jp
<Abstract:> The existence of an energy field that dominates the physiological mechanism of incorporating O₂ in the atmosphere into the human body and excreting it outside the body as CO₂ was investigated using computational chemistry techniques based on quantum theory. As a result, it was revealed that the binding, transportation, and metabolism of gas molecules depend on the weak magnetic energy induced by the earth’s magnetic field (H₀ = 4.5 × 10^-5 T). Finally, it was concluded that the mechanism of oxygen transport and Christian Bohr’s proposed”Bohr effect” depend on magnetic coupling between biomolecules.
<Keywords:> Magnetic resonance, Hemoglobin, Myoglobin, Oxygen, Carbon dioxide
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0059/_article/-char/ja/