月別: 2015年12月

[Published online Journal of Computer Chemistry, Japan -International Edition1, 1-4, by J-STAGE]
<Title:> Cage-Shaped Molecules Derived by Applying the Edge Strategy to a Cubane Skeleton
<Author(s):> Shinsaku FUJITA
<Abstract:> The edge strategy of Fujita’s unit-subduced-cycle-index (USCI) approach (S. Fujita, “Symmetry and Combinatorial Enumeration in Chemistry,” Springer, 1991) is shown to be effective for derivation based on a cubane skeleton, where twelve edges accommodate a set of methano-bridges and/or ethano-bridges.
<Keywords:> cubane, symmetry, enumeration, edge strategy, cage molecule
<URL:> https://www.jstage.jst.go.jp/article/jccjie/1/0/1_2015-0046/_article

[Published online Journal of Computer Chemistry, Japan -International Edition1, 5-8, by J-STAGE]
<Title:> Conformational Analysis of Hexakis-N-Methylformamide Nickel(II) Complex on the Basis of Computational Group Theory and Density Functional Theory
<Author(s):> Hiroshi SAKIYAMA, Katsushi WAKI
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> Conformational analysis was conducted for a hexakis-N-methylformamide nickel(II) complex cation, [Ni- (NMF)₆]²⁺ [hexakis(N-methylformamide-κO)nickel(II) dication], by the semi-empirical PM6 method and the Density Functional Theory (DFT) method, using 54 possible conformers obtained by the Computational Group Theory (CGT) method as initial structures. In the preliminary structural optimization by the PM6, all of the initial structures converted to only two conformers, pseudo–S₆ and pseudo–D₃ conformers. Subsequently, the structures of the two conformers were optimized by the DFT method, and the pseudo–S₆ conformer was found to be more stable than the pseudo–D₃ conformer by 1.8 ~ 2.2 kcal mol ¹. From the energy difference, the pseudo–S₆ conformer was found to be practically the only species at room temperature. This result is consistent with the crystal structure.
<Keywords:> Conformational analysis, Hexakis-N-methylformamide complex, Nickel(II) complex, Computational group theory (CGT) method, Density Functional Theory (DFT) method
<URL:> https://www.jstage.jst.go.jp/article/jccjie/1/0/1_2015-0047/_article

[Published online Journal of Computer Chemistry, Japan -International Edition1, 9-13, by J-STAGE]
<Title:> Development of MagSaki(Tri) Software for the Magnetic Analysis of Trinuclear High-spin Cobalt(II) Complexes
<Author(s):> Hiroshi SAKIYAMA
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> MagSaki(Tri) software was developed for the purpose of analyzing the magnetic data of trinuclear octahedral high-spin cobalt(II) complexes. The software enables analyses for five types of trinuclear cobalt(II) structures, including equilateral triangle shapes, isosceles triangle shapes, and linear shapes, to obtain magnetic parameters: the interaction parameters, J and J’, the spin-orbit coupling parameter, λ, the orbital reduction factor, κ, and the axial splitting parameter, Δ.
<Keywords:> Magnetic analysis, Octahedral high-spin cobalt(II) complex, Spin-orbit coupling, Ligand field, Trinuclear cobalt(II) complex
<URL:> https://www.jstage.jst.go.jp/article/jccjie/1/0/1_2015-0050/_article

[Published online Journal of Computer Chemistry, Japan14, A34-A37, by J-STAGE]
<Title:> SCCJ Cafe Season 4 分子のかたち(5)「分子閲覧ソフト」
<Author(s):> 工藤　高裕
<Corresponding author E-Mill:> t-kudou(at)protein.osaka-u.ac.jp
<Abstract:>
<Keywords:> molecular viewer, Java, JavaScript, WebGL, mobile, jV
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/5/14_2015-0059/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, A38-A41, by J-STAGE]
<Title:> 電子を描く(4) — p_z軌道，d_3z2–r2軌 道，f_5z3-3zr2軌道
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> tokita(at)apc.saitama-u.ac.jp
<Abstract:> 水素原子の波動方程式を解くと，無数の原子軌道が導出される．これらのうち，z軸方向に伸びる p, d, および，f軌道をガラスブロック内に実3次元で彫刻し，球殻状節面や円錐面節面の描かれ方を調べた．
<Keywords:> electron, visualization, hydrogen atom, carbon atom, radial distribution function, spherical harmonics, p orbital, d orbital, f orbital, spherical node, planar and conical node symmetrical about z axis, isosurface, real 3-dimentional representation of electron cloud
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/5/14_2015-0049/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Mathematicaによる分子動力学
<Author(s):> 山田　祐理, 片岡　洋右
<Corresponding author E-Mill:> yuri(at)mail.dendai.ac.jp
<Abstract:> 分子動力学(MD)法の初学者への入門のために，Wolfram Mathematicaに よるMDのプログラムを開発した．MD計算やその結果を解析するアルゴリズムを理解し易いように，扱う分子間相互作用はLennard- Jones 12 6ポテンシャル，MDセルは立方体，アンサンブルはNEVまたはNVTアンサンブルのみとした．Mathematicaの ノートブックファイル内で，粒子数，数密度，温度などの計算条件を設定する．計算結果は，熱力学量のほかに粒子の軌跡，粒子配置，二体相関関数， 速度自己相関関数，平均自乗変位および自己拡散係数が出力される．
<Keywords:> Mathematica, Molecular dynamics, Lennard-Jones system, Pair correlation function, Self-diffusion coef cient
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0027/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 赤色蛍光タンパク質 DsRed の色素部周辺における水分子ならびに隣接アミノ酸残基の構造の励起エネルギーへの影響評価
<Author(s):> 坂口　正貴, 望月　祐志, 渡邉　千鶴, 福澤　薫
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> DsRedはDiscosoma種サンゴから単離された赤色蛍光タンパク質 (RFP)の一種である．私たちのグループでは，多層フラグメント分子軌道(MFMO)スキームの下，クロモフォアにCIS (D)系の励起状態計算法を用いてDsRedの励起エネルギー・発光エネルギーを算定し，実験のスペクトルの極大値との良好な対応を報告している [Mochizuki et al., Chem. Phys. Lett., 433, 360 (2007) & Taguchi et al., J. Phys. Chem. B, 113, 1153 (2009)]．しかし，色素部近傍の水分子，隣接アミノ酸残基の側鎖の配向や構造緩和についての検討は必ずしも明示的になされてはいなかった．そこで今 回，励起エネルギーを指標としてこれらの影響を系統的に検証した．その結果，前者では色素部CRQ66や周辺アミノ酸残基と水素結合ネットワーク を形成している水2分子の存在，および色素に隣接するSer69の側鎖のOH基の配向，さらに隣接する荷電性のLys163とGlu215の構造 の緩和が重要であることが確認された．これらは，結果として既報でのタンパク質構造のモデリングの妥当性を支持するものとなった．
<Keywords:> DsRed, FMO method, Fluorescent protein, Excitation energy, Protein structure modeling, Hydrogen-bond
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2015-0033/_article/-char/ja/