投稿者: 博佐藤

[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/

[Published online Journal of Computer Chemistry, Japan Vol.15, 49-50, by J-STAGE]
<Title:> [Mg(DMF)₆]²⁺の構造に及ぼす結晶中の陰 イオンの効果
<Author(s):> 山　博史, 伊藤　美咲, 三橋　了爾, 御厨　正博
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> In a crystal, an octahedral magnesium(II) complex cation, [Mg(DMF)₆]²⁺ (DMF: N,N-dimethylformamide), was found to exist as a C₂ conformer, which was thought to be energetically unfavorable. In order to find the reason for this, structural analysis was conducted on the basis of semi-empirical PM6 method and density functional theory method. The C₂ conformer was not found to be stable in a vacuum; however, it was found to be stabilized when surrounded by four tetraphenyl borate anions like the crystal structure.
<Keywords:> マグネシウム錯体, DMF錯体, 結晶構造, 配座異性体, 密度汎関数法
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 51-52, by J-STAGE]
<Title:> ペプトイド類のフラグメント分子軌道計算
<Author(s):> 川田　修太郎, 坂口　正貴, 米倉　伊吹, 奥脇　弘次, 望月　祐志, 福澤　薫
<Corresponding author E-Mill:> kawada(at)rikkyo.ac.jp
<Abstract:> Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.
<Keywords:> Peptoid, Fragment Molecular Orbital Method, Nanobiotechnology, Self-assembling, Crystallization
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0032/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 53-54, by J-STAGE]
<Title:> 軟X線分光法による炭酸水溶液の電子状態と構造
<Author(s):> 西田　尚大, 堀川　裕加, 徳島　高, 高橋　修
<Corresponding author E-Mill:> shu(at)hiroshima-u.ac.jp
<Abstract:> We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of carbonate in the liquid phase at the oxygen K-edge. Structure sampling as a cluster model was performed from a snapshot of the first principles molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. Theoretical XES spectra for CO₃^2- and HCO₃^– were well reproduced experimentally and that for H₂CO₃ was predicted.
<Keywords:> Soft X-ray absorption spectroscopy, soft X-ray emission spectroscopy, carbonate, DFT, meta-dynamics method
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.15, 55-56, by J-STAGE]
<Title:> 世代の起源 Heisenberg方程式からSchrodinger方程式へ
<Author(s):> 鳴海　英之
<Abstract:> We changed a mass formula obtained by the Heisenburg Method into one expressed in Schroedinger style and tried to clarify its physical meanings including of the origin of generations.
<Keywords:> KEY WORDS Heisenberg Equation, Schroedinger Equation, Kinetic and Potential Energy, Generations
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/3/15_2016-0028/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> ミュオニウム化学反応の新展開
<Author(s):> 高柳　敏幸, 吉田　崇彦
<Corresponding author E-Mill:> tako(at)mail.saitama-u.ac.jp
<Abstract:> 正または負電荷を有するミューオン粒子を用いて，ミュオニウム(0.114 amu) およびミュオニックヘリウム(4.11 amu)と呼ばれる水素原子の同位体をつくりだすことができる．これを利用することによって，H/D/Tを超えた質量比の同位体効果を観測することができ る．ミュオニウムはその小さな質量のため，化学反応系の水素原子がミュオニウムに置換されると，ゼロ点振動エネルギーやトンネル効果による大きな 量子効果を示す．また，反応経路そのものが変化する例や，遷移状態が安定化する特異な現象も存在する．
<Keywords:> Muon, Muonium, Muonic helium, Isotope effect, Nuclear quantum effect, Vibrational bonding
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2016-0006/_article/-char/ja/