Journal of Computer Chemistry, Japan

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 反復構造を持つ高分子に対する分子動力学計算のためのパラメータ設定支援プログラムo2pの開発
<Author(s):> 矢部　誠, 園部　智彩, 上田　一義, 武田　穣
<Corresponding author E-Mill:> takeda-minoru-bd(at)ynu.ac.jp
<Abstract:> Molecular dynamics (MD)の実行に必須の結合角や電荷などのパラメータセット(力場)がライブラリに存在しない場合，力場の量子力学計算による算出やパラメータ自動生成 ツールの活用という手法が用いられる．しかし，これらの手法は原子数の多い高分子の場合には適していない．そこで，3つの単位構造(両末端の単位 と中央部の繰り返し単位)を含むオリゴマーの力場を算出し，それらをポリマー形式(両末端部+中央部 × n)に変換し対処することがよく行われる．しかしながら，変換は手作業にならざるを得ず，非効率的でヒューマンエラーの恐れもある．そこで，反復構造を持 つ高分子に対するMDを簡便かつ確実に実行すべく，分子動力学ソフトとして汎用されているGromacs用の力場変換半自動化プログラムo2pを 開発した．開発にあたっては，作業負荷の低減と時間短縮を意図してGUIを積極的に取り入れた．また，複雑なファイル変換過程を自動化することに よってヒューマンエラーの一掃を目指した．本プログラムにより変換したファイルを用いてノナン中のアミロース分子を想定した系でMDを実行したと ころ，実験による報告と同じく左巻きの一重らせん構造が形成され，プログラムが有効に動作していることを確認した．
<Keywords:> Molecular dynamics simulation, Macromolecules, Parameters, Gromacs, Polymer, Repeating unit
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2017-0013/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.3, -, by J-STAGE]
<Title:> Analysis of Time Series of the Ambient Dose Rates
<Author(s):> Tomoo AOYAMA, Jun ASANUMA
<Abstract:> Radioactive substances are diffused by meteorological effects and soil property or underground water. The movements affect the ambient dose rate slowly and with smoothing in the long term. We detect the phenomena at monitoring posts in Fukushima. The monitoring post measures the flux from radionuclides; therefore, we discuss relations between the flux and mass density. Time-decreasing of the flux is a function of convection-diffusion of carriers of the nuclides. At the same time, it is also a decay function of radionuclides. We discuss product of the two functions, and get an expression for the time series of radioactive contaminated grounds. By using the expressions, we research changes of typical contaminants in Fukushima. This indicates movements of radionuclides.
<Keywords:> Radioactive cesium, Re-diffusion, Radioactive substance, Ambient dose rate, Forest fire
<URL:> https://www.jstage.jst.go.jp/article/jccjie/3/0/3_2016-0053/_html

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.3, -, by J-STAGE]
<Title:> Practical Training on Adding Polarization Function to Basis Set for Molecular Orbital Calculation of Ethylene
<Author(s):> Shin-ichi NAGAOKA, Hiroyuki TERAMAE, Umpei NAGASHIMA
<Corresponding author E-Mill:> nagaoka(at)ehime-u.ac.jp
<Abstract:> Adding a polarization function to a basis set for molecular orbital calculation is frequently useful for producing accurate representations of chemical bonding. This article explains practical training that could greatly promote intuitive understanding of the general idea of adding a 3d-type polarization function in a π-type molecular-orbital function. In the training, by using Microsoft Excel, students draw contour plots of the molecular orbitals supplemented with and without the polarization function in ethylene (CH₂ = CH₂), and visualize the effect of the addition.
<Keywords:> Orbital contour plot, Polarization function, Ethylene, C2H4, Chemical Education
<URL:> https://www.jstage.jst.go.jp/article/jccjie/3/0/3_2016-0068/_html

[Published online Journal of Computer Chemistry, Japan Vol.16, 52-57, by J-STAGE]
<Title:> Mathematical Stereochemistry as the Theoretical Foundations of Organic and Inorganic Chemistry
<Author(s):> Shinsaku FUJITA
<Corresponding author E-Mill:> shinsaku_fujita(at)nifty.com
<Abstract:> Mathematical stereochemistry is discussed by surveying books written on Fujita’s USCI (unit-subduced-cycle-index) approach, Fujita’s proligand method, Fujita’s stereoisogram approach, and related matters from a viewpoint of developing an interdisciplinary chemistry/mathematics field.
<Keywords:> Stereochemistry, Sphericity, Enumeration, USCI, Stereoisogram
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0002/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 47-51, by J-STAGE]
<Title:> The Bright Side of Mathematical Chemistry
<Author(s):> Haruo HOSOYA
<Corresponding author E-Mill:> hosoya.haruo(at)ocha.ac.jp
<Abstract:> The personal history of the present author’s research career of almost forty-five years in the application of graph theory to chemistry is briefly described in an essay with particular reference to the author’s “bright side of mathematical chemistry.” The chosen topics are as follows: two seminal papers by the present author, more than 1500 citations of his topological index, Z, Hosoya polynomial, Hosoya items, more than 200 papers carrying “Hosoya” in the title, Erd s number, etc.
<Keywords:> Topological index, Hosoya index, Hosoya polynomial, Hosoya items, Mathematical chemistry, Conjecture
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 58-64, by J-STAGE]
<Title:> LadderグラフのAlgebraic Structure CountとHOMO-LUMO ギャップの周期性
<Author(s):> 溝口　則幸, 野村　泰志, 森川　大
<Corresponding author E-Mill:> nori(at)ksj.biglobe.ne.jp
<Abstract:> ladderグラフのalgebraic structure count (ASC)のサイズ依存性を調べた．ladderグラフのASCの漸化式を導出し，ASC の長さ依存性に周期3の周期性があることを見出した．このASC の周期性を用いて，ladderグラフのnon-bonding MO (NBMO) やHOMO-LUMO ギャップの長さ依存性に同じ周期性があることを明らかにした．
<Keywords:> Ladder graph, Algebraic structure count, Periodicity, Non-bonding molecular orbital, HOMO-LUMO gap
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 38-41, by J-STAGE]
<Title:> Use of Mathematical Chemodescriptors and Biodescriptors for New Drug Discovery, Environmental Protection, and Surveillance of Emerging Global Pathogens
<Author(s):> Subhash C. BASAK
<Corresponding author E-Mill:> sbasak(at)nrri.umn.edu
<Abstract:> This article reviews results of research on the development of graph theoretical chemodescriptors, topological indices in particular, and proteomics as well as DNA/RNA sequence based biodescriptors and their applications in predicting property/bioactivity of chemicals as well as viruses. Use of biodescriptors in the characterization of emerging pathogens like the Zika virus (ZIKV) has been discussed. The use of proper statistical methods in model building is emphasized with special reference to research carried out by the author of this review.
<Keywords:> Mathematical chemodescriptors, Biodescriptors, New drug discovery, Environmental protection, Emerging global pathogens, Graph invariants, Topological index, Quantitative structure-activity/property relationship (QSAR/QSPR)
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 33-37, by J-STAGE]
<Title:> Chemistry-Mathematics-Philosophy Brew: a Personal Approach
<Author(s):> Alexandru T. BALABAN
<Abstract:> Chemical applications of discrete mathematics and graph theory are briefly reviewed, including philosophical implications. Using the concept of dualist (inner graph-theoretical duals) it was possible to classify (cata-peri-corona classes) and enumerate benzenoid and diamondoid hydrocarbons. By associating numbers with molecular graphs, one can use these numbers (topological indices) for correlations with properties of chemical compounds – an early, simple, and rapid approach to drug design. The two types of atoms (metals and non-metals), are connected by three types pf chemical bonds (ionic, metallic, and covalent) that lead to four types pf lattices (ionic, metallic, atomic and molecular), allowing quick “2-3-4 grasp” of chemistry. The Periodic System of Elements, which is the cornerstone of chemistry and atomic physics, is in danger of being presented wrongly, devoid of the symmetry based on electronic s, p, d, and f shells; several possibilities for showing correctly these shells are discussed.
<Keywords:> Chemical graphs; Dualists of benzenoids and diamondoids; Classification, codification, and enumeration of benzenoids and diamondoids; Topological indices; 2-3-4 Types of atoms-bonds-lattices; Periodic System of Elements; Electronic s, p, d, and f shells
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0023/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 42-46, by J-STAGE]
<Title:> On Solved and Unsolved Problems in Chemistry
<Author(s):> Milan RANDI
<Abstract:> In this article we have illustrated one solved problem in chemistry, which left room for improvements. This instance is raising an issue when a solved problem is to be considered solved. As we will see by using novel tools, not known at the time of solving a problem, one can arrived at additional unknown information on the problem. We will consider several problems of chemistry, some even considered as having no exact solution, which have been solved by using previously unknown concepts in chemistry. The last problem which we consider has been solved, but the problem is still open, as it might have additional solutions.
<Keywords:> Conjugated Circuits, Aromaticity, “QSAR nightmare”, Young diagrams, Graphical Bioinformatics
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/2/16_2017-0024/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.16, 1-16, by J-STAGE]
<Title:> DFT法による塩化鉄(III)錯体の鉄−配位子間相互作用の解析
<Author(s):> 陳　奕廷, 陳　皇州, 福田　光完
<Corresponding author E-Mill:> mifukuda(at)hyogo-u.ac.jp
<Abstract:> 八面体構造から四面体構造まで塩素数に応じて構造が変化する塩化鉄(III)錯体に対してDFT法を用いて理論計算を行った．使用した汎関数は BHandHLYP，wB97XD，CAM-B3LYP，LC-wPBEの4種である．基底関数には6-311+G(d,p)あるいは 6-311+G(3df,2pd)を用い，PCM法による水媒体中で計算を行った．4種の汎関数を用いたDFT法は概ね錯体構造をよく再現し た．2原子の塩素が配位した八面体型[Fe(III)Cl₂(H₂O)₄]⁺のcis型 とtrans型の安定性，及び3原子の塩素が配位した三方両錐型の[Fe(III)Cl₃(H₂O)₂] と四面体型の[Fe(III)Cl₃(H₂O)] の安定性をエネルギー的に比較した．振動計算から得られる配位水分子の伸縮振動の波数の変化を[Fe(III)(H₂O)₆]³⁺か ら[Fe(III)Cl₃(H₂O)]まで調査したところ，八面体型では水分子の減少とともに伸縮 振動は高波数側へシフトし，フリーの単独水分子の伸縮振動に近づく．八面体型では塩素原子の鉄への配位は鉄の極性を低下させ，その結果として水分 子との相互作用を弱めると考えられる．しかし，三方両錐型([Fe(III)Cl₃(H₂O)₂]) から四面体型([Fe(III)Cl₃(H₂O)])になるにつれ再び伸縮振動はやや低波数側へシ フトした．配位する塩素原子数が同じ3であっても，水分子数が少ないほど鉄との相互作用は強められる．鉄−酸素間距離についても同じ傾向を示し た．
<Keywords:> DFT method, iron(III) chloride complex, infrared stretching frequency, interaction between metal and ligand
<URL:> https://www.jstage.jst.go.jp/article/jccj/16/1/16_2016-0049/_article/-char/ja/