Journal of Computer Chemistry, Japan -International Edition
Online ISSN : 2189-048X
ISSN-L : 2189-048X
Volume 5
Displaying 1-4 of 4 articles from this issue
General Paper
  • Fumiya NORITAKE
    2019 Volume 5 Article ID: 2018-0016
    Published: 2019
    Released on J-STAGE: March 14, 2019

    Non-empirical calculation based on the Schrödinger equation is an appropriate tool for investigating the relationship among Si-O-Si angle, Si-O bond length, Si-O bond strength, and electronic structure. However, past studies could not reach a consensus about the equilibrium structure of the C2v pyrosilisic acid molecule. Moreover, the structure of disiloxane, the simplest siloxane molecule, could not be reproduced using non-empirical molecular orbital calculations. In this study, I checked the reproducibility of various model chemistries and basis sets, and found that employing the post-Hartree-Fock method and a larger basis set (at least, aug-cc-pVTZ) is necessary for accurate calculation of the disiloxane molecule. In contrast to past studies on molecular orbitals, the present study reveals no significant occupancy in the Si 3d orbitals. The total energy landscape of the C2v pyrosilisic acid molecule is calculated by using the coupled cluster method concerning three excited electrons and the aug-cc-pVTZ basis set. The stable bond length for Si-Obr is 1.604 Å, and the stable Si-O-Si angle is 159.449°. There are gentle curves around the stable angles for each bond length comparing with bond length direction. The stable angle for each bond length decreased with increasing Si-Obr bond length. The weakening of the Si-Obr bond with decreasing Si-O-Si bond angle can be explained by the decrease in the bond index and the increase in the orbital energy for Si-Obr σ-bond. Consequently, hybridization of the valence electrons of the bridging oxygen with decreasing Si-O-Si angle weakens the Si-Obr σ-bond. Electrostatic potential favors a straight configuration because of the repulsion between the SiO4 tetrahedra, while the valence electrons of the bridging oxygen favor a bent configuration. These two competing behaviors can explain the bent configuration of pyrosilisic acid without considering d-p π bonding.

  • Makoto YABE, Kazuki MORI, Kazuyoshi UEDA, Minoru TAKEDA
    2019 Volume 5 Article ID: 2018-0034
    Published: 2019
    Released on J-STAGE: March 14, 2019

    In the case that the parameters to describe the force field, such as bond angles and charges, cannot be added to the library of a molecular dynamics (MD) simulation, self-development of the force field should be considered by performing quantum mechanics calculations and/or utilizing an automatic parameter generation tool. However, these techniques are not suitable for macromolecules with a large number of atoms. Typically, the force field of an oligomer containing three unit structures (a unit at both ends and a repeating unit at the center) is calculated and converted to polymer form (both ends + central part × n). Considering this, we recently developed the program o2p, which is a semi-automated program designed to set up the force field for polymers with repeating structures. However, it is difficult to apply this method to macromolecules with complex repeating structures. Thus, in this project, we developed PolyParGen, a new open-source automatic force field generation program for Gromacs that can relatively easily and reliably simulate the MD of complex macromolecules. The proposed program (1) divides the structure of the polymer into substructures with a number of atoms within the limit of the handling size for the automatic parameter generation tool program; then, (2) acquire the parameters for each divided substructure, and finally, (3) combine the parameters of these substructures to obtain the parameters for the whole polymer. By automating these processes, it is possible to acquire a parameter of a polymer having complicated structures. This program was evaluated by simulating the polymers P3EHT and F-P3EHT in chloroform. In agreement with previous reports, fluorination was found to cause F-P3EHT to adopt an extended structure, thereby indicating the effectiveness of the proposed program.

  • Takashi FUJII, Mikio KAWAHARA, Akihiro TSUYADA, Manabu SUGIYAMA, Masak ...
    2019 Volume 5 Article ID: 2017-0044
    Published: 2019
    Released on J-STAGE: April 18, 2019
    Supplementary material

    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.