An elongation method for large systems toward bio-systems

Physical Chemistry Chemical Physics : PCCP
Yuriko Aoki, Feng Long Gu

Abstract

The elongation method, proposed in the early 1990s, originally for theoretical synthesis of aperiodic polymers, has been reviewed. The details of derivation of the localization scheme adopted by the elongation method are described along with the elongation processes. The reliability and efficiency of the elongation method have been proven by applying it to various models of bio-systems, such as gramicidin A, collagen, DNA, etc. By means of orbital shift, the elongation method has been successfully applied to delocalized π-conjugated systems. The so-called orbital shift works in such a way that during the elongation process, some strongly delocalized frozen orbitals are assigned as active orbitals and joined with the interaction of the attacking monomer. By this treatment, it has been demonstrated that the total energies and non-linear optical properties determined by the elongation method are more accurate even for bio-systems and delocalized systems like fused porphyrin wires. The elongation method has been further developed for treating any three-dimensional (3D) systems and its applicability is confirmed by applying it to entangled insulin models whose terminal is capped by both neutral and zwitterionic sequences.

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Citations

Apr 18, 2014·Physical Chemistry Chemical Physics : PCCP·Shigenori TanakaKaori Fukuzawa
Feb 8, 2013·The Journal of Chemical Physics·Masato Kobayashi, Hiromi Nakai
May 3, 2013·The Journal of Chemical Physics·Hiroya NakataShinichiro Nakamura
Jun 1, 2014·Journal of Molecular Modeling·Piotr KuźniarowiczJacek Korchowiec
Mar 17, 2015·The Journal of Chemical Physics·Yuuichi OrimotoYuriko Aoki
Nov 20, 2015·Journal of Chemical Theory and Computation·Kurt R BrorsenMark S Gordon
May 25, 2016·Physical Chemistry Chemical Physics : PCCP·Yoshio Nishimoto, Dmitri G Fedorov
Jul 31, 2020·Journal of Computational Chemistry·Denis MashkovtsevYuriko Aoki
Apr 24, 2015·Journal of Computational Chemistry·Xun Zhu, Yuriko Aoki
Sep 5, 2015·Journal of Computational Chemistry·Yuuichi OrimotoYuriko Aoki
Mar 15, 2015·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Kai LiuYuriko Aoki
Mar 6, 2021·The Journal of Physical Chemistry. a·Giovanni MacettiAlessandro Genoni
Jul 10, 2021·Journal of Chemical Theory and Computation·Zikuan Wang, Wenjian Liu
Jul 16, 2014·Accounts of Chemical Research·Zhendong LiWenjian Liu

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