Journal of Computer Chemistry, Japan

[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/

[Published online Journal of Computer Chemistry, Japan Vol.15, 227-228, by J-STAGE]
<Title:> スマートフォンを用いたSPM可視化アプリケーションの開発
<Author(s):> 八木　徹, 神部　順子, 長嶋　雲兵, 青山　智夫
<Abstract:> A smartphone application for observating atmospheric state and visualizing suspended particle matter (SPM) was developed. By using the ratio of B/R, G/R and B/G, it was confirmed that the nonlinearity in the developed image can be canceled and the distribution of scattered light in the atmosphere can be observed.
<Keywords:> SPM, Smartphone application, Visualization, Scattered light, Air polution
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0063/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 223-224, by J-STAGE]
<Title:> 電荷移動錯体の引力の原因:キノン類とベンゼンの分子間相互作用の解析
<Author(s):> 都築　誠二, 内丸　忠文, 小野　泰蔵
<Abstract:> Aromatic molecules form stable charge-transfer complexes with quinones, tetracyanoethylene or halogen molecules. The charge-transfer interaction (orbital-orbital interaction) was believed to be the source of the attraction in the complexes. However, the contributions of other intermolecular interactions (dispersion, electrostatic etc.) to the attraction in the complexes are not well understood. The total interaction energy and contributions of electrostatic, induction, dispersion and orbital-orbital (exchange-repulsion and charge-transfer) interactions in the benzene-p-benzoquinone complex were studied by ab initio molecular orbital calculations. The analysis shows that the dispersion interaction is the major source of the attraction in the complex and that the orbital-orbital interaction is not attractive but even repulsive.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0064/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 221-222, by J-STAGE]
<Title:> マルチスケール計算化学に基づく汚れ付着シミュレーション技術の開発
<Author(s):> 畠山　望, 長山　千恵子, 畑　北斗, 石澤　由紀江, 佐藤　亮, ボノー　パトリック, 三浦　隆治, 鈴木　愛, 宮本　明
<Corresponding author E-Mill:> hatakeyama(at)aki.niche.tohoku.ac.jp
<Abstract:> Plumbing stains grow up from invisible attachment of urea and urolith in the molecular level to biofilms in which bacteria adsorb such nutrients and secrete extracellular polymer substances. In order to understand and control such biofilm growth, we have developed a multiscale simulation that can analyze from adhesion of stains on the molecular scale to accumulation of biofilm on actual scale. In the present study, the biofilm growth and peeling by shear flow was successfully simulated for the condition of typical toilet use.
<Keywords:> Biofilm, Extracellular Polymer Substances (EPS), Ultra-Accelerated Quantum Chemical Molecular Dynamics (UA-QCMD), Kinetic Monte Carlo (KMC), Computational Fluid Dynamics (CFD)
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0060/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 219-220, by J-STAGE]
<Title:> 結晶軌道法によるDNAのHartree-Fock計算の試み
<Author(s):> 寺前　裕之, 青木　百合子
<Corresponding author E-Mill:> teramae(at)gmail.com
<Abstract:> As an attempt at the electronic structure calculations of the B-type model-DNA, (poly-(guanine) poly-(cytosine)) model polymers is performed by means of ab initio crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and ions are included in the calculations. Energy band structures are calculated at 3-21G and 6-31G levels. The effective mass of hole shows a relatively large value while that of electron shows a smaller value which suggests electron conduction in the DNA backbones.
<Keywords:> Crystal orbital method, Screw-axis symmetry, B-type DNA, Parallel processing, Energy band structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0057/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 225-226, by J-STAGE]
<Title:> 転がりにおける面との摩擦
<Author(s):> 夏目　雄平
<Abstract:> The mechanism of rolling frictions of wheel is discussed in relation with movement of Reuleaux-pentagons. In fact, driving and braking processes lead us to the suggestion that hysteresis-energy loss model is naturally obtained. In addition to this, the combined model of hysteresis-energy loss and differential-slip mechanisms is proposed so as to promote the computational investigations for rolling frictions of wheel.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0066/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 217-218, by J-STAGE]
<Title:> 分子動力学法を用いた4-n-alkyl-4′-cyanobiphenyl (nCB) の熱伝導率シミュレーション
<Author(s):> 高橋　祐貴, 石川　良, 大木　竜勝, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Thermal conductivity of 4-n-alkyl-4′-cyanobiphenyl (nCB) simulated by using molecular dynamics method. We modified the dihedral angle parameter and the LJ parameters of the original AMBER Force Field for nCB. The dihedral angle parameter was corrected by using quantum chemical calculation, and the LJ parameters were fitted to reproduce the experimental data. Thermal conductivity was calculated by Green-Kubo Method. MD calculation using the corrected force field gave good thermal conductivity close to experimental value and successfully reproduced the anisotropy of thermal conductivity in the liquid crystal phase.
<Keywords:> Thermal conductivity, Molecular Dynamics, Corrected force field, Anisotropy of thermal conductivity, Green-Kubo Method
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0054/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 215-216, by J-STAGE]
<Title:> Ru(0)触媒による共役ジエンとヘテロ環状化合物のクロスカップリング反応機構の理論的解明
<Author(s):> 出口　光, 西久保　椋, 大槻　恒太, 駒崎　弘樹, 川内　進
<Corresponding author E-Mill:> skawauch(at)polymer.titech.ac.jp
<Abstract:> Mechanistic studies for linear cross-dimerization between 2,3-dimethylbuta-1,3-diene and 2,5-dihydrofuran by a Ru(0) complex, Ru(η⁶-naphthalene) (η⁴ 1,5-COD), were performed computationally. The rate-determining steps of main and side reactions are different mechanisms, and correspond to the reductive elimination step and the oxidative coupling step, respectively. This suggests that the yield of the main product may be improved by modification of the heterocyclic compound or catalyst structure. In addition, the computational studies predicted that cross-dimerization between 2,3-dimethylbuta-1,3-diene and 2,5-dihydropyrrole may occur via a similar reaction mechanism.
<Keywords:> oxidative coupling, reductive elimination, cross-dimerization, Ru(0) complex, DFT calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0055/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 213-214, by J-STAGE]
<Title:> [M(ABC)₆]錯体の配座解析
<Author(s):> 山　博史, 安孫子　誉晃, 伊藤　美咲, 脇　克志, 　了爾, 御厨　正博
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> Enumeration of the conformers and conformational analysis were successfully conducted for an octahedral [M(ABC)₆] complex. In this report the methods and results were briefly described. In the enumeration, 7173 conformers were found by the computational group theory method, and among them, 130 conformers were found to have stable M(AB)₆ cores of S₆ symmetry. The structures of the 130 conformers of [Zn(DMSO)₆]²⁺ (DMSO: dimethylsulfoxide) were optimized by the DFT method, and the most stable conformer was obtained.
<Keywords:> 配座解析, 配座異性体, 数え上げ, 正八面体型錯体, 密度汎関数法
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/6/15_2016-0067/_article/-char/ja/