月別: 2016年10月

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> Quantum Molecular Dynamics Simulation of Condensed Hydrogens by Nuclear and Electron Wave Packet Approach
<Author(s):> Kim HYEON-DEUK
<Corresponding author E-Mill:> kim(at)kuchem.kyoto-u.ac.jp
<Abstract:> We recently proposed a real-time simulation method of nuclear and electron wave packet molecular dynamics (NEWPMD) based on wave functions of hydrogen molecules composed of nuclear and electron WPs. Non-empirical intra- and intermolecular interactions of non-spherical hydrogen molecules were explicitly derived and a long-range dispersion force between hydrogen molecules was successfully derived. Nuclear quantum effects (NQEs) such as nuclear delocalization and zero-point energy were non-perturbatively taken into account. The developed NEWPMD method can be applied to various condensed hydrogen systems from a gas-phase to a high-pressure solid phase at feasible computational cost, providing intuitive understandings of real-time dynamics of each hydrogen molecule including H-H bond vibration, molecular orientations and librational motions. We will report the demonstrations not only in liquid hydrogens but also in solid and supercooled hydrogens which exhibited strong NQEs and thus anomalous static and dynamic properties.
<Keywords:> Quantum molecular dynamics simulation, Nuclear wave packet, Electron wave packet, Nuclear quantum effect, Liquid/solid/supeercooled hydrogen
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0020/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 核・電子軌道法における原子核軌道エネルギーとプロトン束縛エネルギー計算
<Author(s):> 五十幡　康弘, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> 核・電子軌道 (NOMO) 法は，原子核に対して軌道の概念を導入した量子化学理論である．NOMO法におけるHartree-Fock (HF)方程式の解として得られる原子核軌道エネルギーは，全エネルギーや軌道そのものと比較して注目されていない．本論文では，NOMO法における原子 核軌道エネルギーの物理的意味とpost-HF理論への応用を述べる．特に，最近開発されたプロトンプロパゲーター法による束縛エネルギーの見積 りについて，計算例を含めて紹介する．
<Keywords:> Nuclear orbital plus molecular orbital method, Nuclear orbital energy, Proton propagator method, Proton binding energy, Divide-and-conquer method
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 71-73, by J-STAGE]
<Title:> 古典ポテンシャル系のメタダイナミクスによる準安定構造探索
<Author(s):> 谷田　義明, 松浦　東
<Abstract:> We have performed metadynamics to explore the ligand docking poses with an RNA aptamer in three collective variables (CVs) space, one distance and two dihedral angles. We showed that the free energy surface (FES) of the ligand binding has several local minima. Furthermore, we also demonstrate that each metastable structure can be deduced from CVs of each free energy minimum.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 74-76, by J-STAGE]
<Title:> Grid Inhomogeneous Solvation Theoryを用いた血液凝固因子Xaの水和サイト解析
<Author(s):> 佐藤　博之, 松浦　東
<Corresponding author E-Mill:> shryk(at)jp.fujitsu.com
<Abstract:> The hydration structure in the active site of human coagulation factor Xa (fXa) was investigated from the viewpoint of excess free energy. Water distribution in the active site of fXa was calculated using partly constrained molecular dynamics (MD) simulation. Then the free energy of the distribution was evaluated using grid inhomogeneous solvation theory (GIST). The analyzed excess free energy shows excellent correlation to the experimental binding affinity of known ligands only if the side chain fluctuation of the active site of fXa was taken into account. This result indicates that the side chain fluctuation generated by partly constrained MD has an important role for identifying the appropriate hydration structure, and that GIST in combination with partly constrained MD provides useful information for assessing the protein-ligand binding affinity.
<Keywords:> Hydration structure, Partly constraind MD, GIST, Binding affinity, Excess free energy
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 57-59, by J-STAGE]
<Title:> Armchair α-Graphyne NanotubeのHOMO-LUMO Gapのチューブ長依存性
<Author(s):> 森川　大, 野村　泰志, 溝口　則幸
<Corresponding author E-Mill:> 13st309e(at)shinshu-u.ac.jp
<Abstract:> Graphyne nanotubes (GNTs) are new carbon-based nanotubes and have a structure similar to the carbon nanotubes (CNTs). In the GNTs, armchair α-GNT is the highest resemblance to armchair CNT, and algebraic structure counts (ASC) are equal. This correspondence suggests that the HOMO-LUMO gaps in the finite-length armchair α-GNT oscillate with the increase of the tube length in the same fashion as the oscillation of HOMO-LUMO gaps in finite-length armchair CNT. In this work, the tube length dependences of the HOMO-LUMO gaps in the finite-length armchair α-GNT were examined by means of the H ckel method and density functional theory (DFT). It was found that the HOMO-LUMO gaps in armchair α-GNT oscillate as functions of the tube length with the period of 3.
<Keywords:> Graphyne nanotube, Carbon nanotube, Algebraic structure count, Kekul structure, HOMO-LUMO gap
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 60-62, by J-STAGE]
<Title:> ホモ/ヘテロダイマー系分子間振動の粗視化による分子間/分子内剛性の定量化
<Author(s):> 磯貝　実, 北條　博彦
<Corresponding author E-Mill:> houjou(at)iis.u-tokyo.ac.jp
<Abstract:> We have developed a method for quantifying the intermolecular forces in supramolecular systems by modifying our original method of coarse-graining intermolecular vibrations. We evaluated the true and apparent intermolecular stiffness constants for 21 dimers composed of formic acid-, acetic acid-, trichloroacetic acid-, formamide-, formamidine- or urea-monomer. In this method, the atomic displacement vectors of a dimer were projected onto a subspace spanned by bases corresponding to 12 relative translational and rotational motions and several intramolecular vibrations that are coupled with intermolecular vibrations. The intermolecular stiffness constants showed moderate linearity with the corresponding dimerization energies. The apparent stiffness constant can be explained by a mechanical model using inter- and intramolecular stiffness constants of the constituent monomers.
<Keywords:> Intermolecular forces, Normal mode analysis, Coarse graining, Principal component analysis, Hydrogen bond, Terahertz spectroscopy
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0039/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 63-65, by J-STAGE]
<Title:> 量子化学計算情報を記述子とした機械学習に基づく反応予測手法の開発
<Author(s):> 藤波　美起登, 清野　淳司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We have developed a novel reaction prediction system, which uses machine learning with quantum chemical descriptors. Numerical assessments of the system were performed on basic polar and radical organic chemical reactions. The accuracy of the present system was close to that of a previous system having machine learning with topological information, which is termed ReactionPredictor.
<Keywords:> Reaction prediction system, Quantum chemical descriptor, Machine learning, Neural network, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 66-67, by J-STAGE]
<Title:> 化学・生命科学系の理学教育における3Dプリンタの活用事例
<Author(s):> 望月　祐志, 中村　昇太, 山中　正浩, 山田　康之, 工藤　光子, 常盤　広明, 川上　勝, 北本　俊二
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> Recently, technologies and applications of 3D-printers have attracted practical interests in the contexts of manufacturing and research developments. In contrast, the educational usages have still been underway. In this Letter, we report a variety of demonstrative 3D-printed molecular models used for education of chemistry and biology in our faculty of Science.
<Keywords:> Science Education, 3D-printers, On-demand molecular models, DNA, Proteins, Catalysts, Orbital lobes
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 68-70, by J-STAGE]
<Title:> Implementation of Efficient Two-component Relativistic Method Using Local Unitary Transformation to GAMESS Program
<Author(s):> Yuya NAKAJIMA, Junji SEINO, Michael W. SCHMIDT, Hiromi NAKAI
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> This Letter provides an implementation of an efficient and accurate relativistic method based on the infinite-order two-component scheme with the local unitary transformation (LUT-IOTC) to the GAMESS program. The sample input and major capabilities in GAMESS are shown as well as the accuracies and efficiencies in energy and analytical energy gradient calculations. The scheme realizes calculations of molecules containing heavy elements with four-component relativistic accuracy and the non-relativistic computational cost.
<Keywords:> Relativistic effect, Linear-scaling, Infinite order Douglas Kroll Hess transformation, Divide-and-conquer method, Local unitary transformation
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 15-15, by J-STAGE]
<Title:> 計算化学連携講座 於:都立戸山高等学校
<Author(s):> 内田　希
<Abstract:>
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_foreword_15_3/_article/-char/ja/