TY - GEN
T1 - Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA
AU - Teramae, Hiroyuki
AU - Aoki, Yuriko
N1 - Funding Information:
This work was supported by JSPS KAKENHI Grant Number 16K05666.
PY - 2018/11/30
Y1 - 2018/11/30
N2 - As an attempt at the electronic structure calculations of the B-type model-DNA, (poly-(guanine) poly-(cytosine)) double helix including sodium atoms as counter cations, hereafter referred as (poly-(dG)poly-(dC), double helix model polymer is performed by means of ab initio Hartree-Fock crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and ions are included in the calculations. At the level of 6-31G basis sets, energy band structures were calculated for the polymers with and without sugar and sodium phosphate and found that the difference is very large when excluding the sodium phosphate. We also calculated the four single helix polymers in order to compare these band structures with the double helix polymononucleotide. The difference is not small especially for the guanine-citosine polymer.
AB - As an attempt at the electronic structure calculations of the B-type model-DNA, (poly-(guanine) poly-(cytosine)) double helix including sodium atoms as counter cations, hereafter referred as (poly-(dG)poly-(dC), double helix model polymer is performed by means of ab initio Hartree-Fock crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and ions are included in the calculations. At the level of 6-31G basis sets, energy band structures were calculated for the polymers with and without sugar and sodium phosphate and found that the difference is very large when excluding the sodium phosphate. We also calculated the four single helix polymers in order to compare these band structures with the double helix polymononucleotide. The difference is not small especially for the guanine-citosine polymer.
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U2 - 10.1063/1.5079055
DO - 10.1063/1.5079055
M3 - Conference contribution
AN - SCOPUS:85058657053
T3 - AIP Conference Proceedings
BT - International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018
A2 - Simos, Theodore E.
A2 - Kalogiratou, Zacharoula
A2 - Monovasilis, Theodore
A2 - Simos, Theodore E.
A2 - Simos, Theodore E.
PB - American Institute of Physics Inc.
T2 - International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018
Y2 - 13 March 2018 through 17 March 2018
ER -