月別: 2019年4月

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.5, -, by J-STAGE]
<Title:> Analysis Method for Digital PCR Data on Two Dimensional Orthogonal Coordinate (x, y) by Converting to Two Dimensional Polar Coordinate (r, θ) Using EXCEL Macro
<Author(s):> Takashi FUJII, Mikio KAWAHARA, Akihiro TSUYADA, Manabu SUGIYAMA, Masakazu AKAHORI
<Corresponding author E-Mill:> takashi.fujii(at)rikengenesis.jp
<Abstract:> An absolute quantitative analysis method has been recently developed as a third generation polymerase chain reaction method “PCR” for fractionated DNA. The method is designed to determine the number of DNA molecules in target DNA samples by counting the number of PCR products obtained from fractionated DNA. We applied EXCEL Macro to perform the conversion of two dimensional orthogonal coordinate (x, y) fluorescent signal plot data obtained by digital PCR device to two dimensional polar coordinate (r, θ) fluorescent signal plot data, followed by analyzing the angle (θ) histogram of plot data without overlapping of plot data occurring by two dimensional orthogonal coordinate (x, y) histogram. The analysis made it possible to identify gene mutation and count the number of DNA molecules with mutation faster and easier.
<Keywords:> Digital PCR, DNA, Polar coordinate, EXCEL
<URL:> https://www.jstage.jst.go.jp/article/jccjie/5/0/5_2017-0044/_html

[Published online Journal of Computer Chemistry, Japan Vol.17, 232-234, by J-STAGE]
<Title:> ロタキサン構造により緩やかに束縛された高分子鎖の配座解析
<Author(s):> 渡邊　寿雄, 川内　進
<Abstract:> Conformational analysis of the reactant, product, and complex of the polymer and macrocyclic catalyst (PdMC) was carried out in order to investigate the reaction mechanism of the intramolecular cyclization reaction of the polymer chain having a Rotaxane structure. Focusing on the N-C distance of the intramolecular cyclization reaction coordinate, a group of stable conformers with short N-C distances for the reaction was found. By forming a complex with PdMC, the conformations of the reactant with a short N-C distance were stabilized and the intramolecular cyclization reaction was promoted.
<Keywords:> 高分子反応, 配座探索, ロタキサン構造, DFT計算
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0065/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, A28-A33, by J-STAGE]
<Title:> IV族ホモ六員環から成るナノリボン，ナノリング，ナノチューブの基底状態におけるスピン多重度安定性
<Author(s):> 松永　雄樹, 武田　京三郎
<Abstract:> We systematically investigate the molecular and electronic structures of the group-IV (C, Si, Ge) nano-systems such as nanoribbons (NRBs), nanorings (NRGs) and nanotubes (NTBs). The present calculation reveals that C nano-system has a planar structure whereas Si and Ge ones have a non-planar structure. Focusing on the electron correlation, we further investigate the planarity/non-planarity of these nano-systems, and study the energetics of the singlet-triplet (ST) crossover in the ground state. We then extend our study to the infinite NRB and NTB systems and find that these nano-systems have the ground-state spin singlet.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0060/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.17, 235-236, by J-STAGE]
<Title:> 計算機化学を用いた天然ゴムの生合成過程解析
<Author(s):> 慶野　達也, 内田　希, 河原　成元, 秋山　和輝
<Corresponding author E-Mill:> tatsuya_keino(at)mst.nagaokaut.ac.jp
<Abstract:> Natural rubber is an excellent material in elasticity and abrasion resistance. However, the detailed structure and the reason for excellent physical properties of natural rubber are still unclear. We aimed to conduct a conformational search and structural analysis using computational chemistry and to elucidate the biosynthetic process of natural rubber. From the calculation results, as long as the catalyst (enzyme) required for each stage of the biosynthesis process exists, it turned out that the biosynthesis of natural rubber proceeded spontaneously.
<Keywords:> Natural rubber, Biosynthesis mechanism, MOPAC, PM7, COSMO method, Phosphate group
<URL:> https://www.jstage.jst.go.jp/article/jccj/17/5/17_2018-0048/_article/-char/ja/