投稿者: 博佐藤

[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/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.2, -, by J-STAGE]
<Title:> Development of a Software to Analyze the Dispersion State of Particles on a Flat Substrate
<Author(s):> Kayato OOYA, Hidenobu SHIROISHI, Yuya HARADA
<Corresponding author E-Mill:> h-shiroishi(at)tokyo-ct.ac.jp
<Abstract:> A program called “Roughness Analyzer,” has been developed with Visual Basic Language, and it can analyze the dispersion state of particles on a flat substrate from a three dimensional profile obtained by surface roughness meters. This software enables us to separate secondary particles agglomerated on the substrate to calculate the area, the volume and the average height of each secondary particle. Further, the surface of the substrate can be divided into any number from the center of the substrate in a radial direction and an angular direction, and then it is possible to calculate the area, the volume and the area occupied by the particles in each section. In addition, this software has functions such as the correction of only the shape of the substrate by a spline interpolation method and the conversion of any range on the substrate surface to DXF format.
<Keywords:> Roughness Analyzer, Dispersion state, Secondary particles, Cluster analysis, Height data
<URL:> https://www.jstage.jst.go.jp/article/jccjie/2/0/2_2016-0009/_article

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.2, -, by J-STAGE]
<Title:> A Program for Single-center Expansion in Laguerre-type Orbitals for the Hydrogen Molecular Ion
<Author(s):> Yasuyo HATANO, Shigeyoshi YAMAMOTO
<Corresponding author E-Mill:> hatano(at)sist.chukyo-u.ac.jp
<Abstract:> A Fortran program is given for calculating wave functions of the molecular hydrogen ion, expanded in terms of single-center Laguerre-type orbitals. Using this program, the radial quantum number has been extended to 203, and accuracy has been attained in energy of the order of 10^-6 a.u. The electron-nucleus Coulomb integrals are evaluated numerically by applying Gaussian quadratures.
<Keywords:> Associated Laguerre polynomials, Gaussian quadratures, Hydrogen molecular ion, Complete orthonormal basis set, Single-center expansion
<URL:> https://www.jstage.jst.go.jp/article/jccjie/2/0/2_2016-0003/_article

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.2, -, by J-STAGE]
<Title:> Photographic Detection of Scattering Light of Suspended Solids in the Sea
<Author(s):> Umpei NAGASHIMA, Junko KAMBE, Toru YAGI, Tomoo AOYAMA
<Corresponding author E-Mill:> aoyama.tomoo3(at)gmail.com
<Abstract:> An imaging tool is proposed to research marine environment in science teaching. It is for usage of digital cameras in housing underwater. Analyzed format is JPEG, in which RGB intensity is digitized in 8 bits. The intensity relates wavelength dependence in the bandwidth of RGB. We extract information from the dependence, and investigate absorption, scattering, and reflection in the water. Ratio index for wavelength dependence is discussed, which is easy for students to understand. Next, using the idea of the index, Ratio-RGB image is defined and discussed. The image is introduced for visualizing suspended solids in the sea. The environment in the sea is displayed using the Ratio-RGB images. Turbulence of scattering light layers, distribution of fishes, and small marine biology are detected clearly. The approach enables understanding of conditions in the sea visually.
<Keywords:> Science teaching, Sea contamination, Suspended solid, Underwater camera, Scattering
<URL:> https://www.jstage.jst.go.jp/article/jccjie/2/0/2_2015-0054/_article

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.2, -, by J-STAGE]
<Title:> Join Us and Help JCCJIE Make an Impact
<Author(s):> Tadayosi YOSHIMURA
<URL:> https://www.jstage.jst.go.jp/article/jccjie/2/0/2_Foreword_2/_article

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.2, -, by J-STAGE]
<Title:> Development of MagSaki(Tetra) Software for the Magnetic Analysis of Tetranuclear High-spin Cobalt(II) Complexes
<Author(s):> Hiroshi SAKIYAMA
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> MagSaki(Tetra) software was developed for the purpose of analyzing the magnetic susceptibility data of tetranuclear octahedral high-spin cobalt(II) complexes. The software enables the analyses six types of tetranuclear cobalt(II) structures, including cubane and defect dicubane structures, to obtain magnetic parameters: the interaction parameters, J, J’, 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, Tetranuclear cobalt(II) complex, MagSaki software series
<URL:> https://www.jstage.jst.go.jp/article/jccjie/2/0/2_2016-0001/_article

[Published online Journal of Computer Chemistry, Japan Vol.15, 32-40, by J-STAGE]
<Title:> イソシアナートのウレタン化反応過程におけるエネルギー，立体変化および置換基効果の分子シミュレーション
<Author(s):> 染川　賢一, 満塩　勝, 上田　岳彦
<Corresponding author E-Mill:> somekw(at)voice.ocn.ne.jp
<Abstract:> ウレタン樹脂の製造と物性に関する基本的情報である，イソシアナートのウレタン化反応性と触媒作用，生成するカルバミン酸とそのエステルの脱炭酸と安定性 および副生物の挙動について，計算化学を用いて検 討した．その際各節に示す基本的な実験結果につき，反応過程のエネルギーと立体化学変化をMOPAC-PM6 法 でシミュレーションして解析した．置換フェニルイソシアナートとアルコールとのウレタン化反応性が，フロンティア軌道HOMOとLUMOのエネルギーを利 用する置換基分子のMullikenの電気陰性度値((IP + EA)/2)，と大きい相関係数で表されること を示す．そのウレタン化反応は，1：2モル比の6員環錯体を経て，遷移状態の活性化エネルギー(Ea)は4 13 kcal mol^-1 と検証された．メチルアミンとのウレア化は反応性が高いが，それは会合体を形成し易く，Ea が小さいためと判断された．遷移状態構造の結果からは，3分子間の水素結合とその役割が理解される．第3級アミンの触媒作用は，上記1：2 錯体中のプロトンの捕捉促進とNCOへの受け渡しで，Eaを低下させると解析された．イソシアナートと水の反応で生成するカルバミ ン酸の不安定で発泡の事実等に関しては，分解の素過程の Ea が11 kcal mol^-1と低く，ア ミンと CO₂ に分解すると検証された．
<Keywords:> Urethane, Isocyanate, Carbamic acid, PM6, Activation energy, Six-membered 12 complex
<URL:> https://www.jstage.jst.go.jp/article/jccj/15/2/15_2015-0073/_article/-char/ja/