Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA

Hiroyuki Teramae, Yuriko Aoki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish
Title of host publicationInternational Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018
EditorsTheodore E. Simos, Zacharoula Kalogiratou, Theodore Monovasilis, Theodore E. Simos, Theodore E. Simos
PublisherAmerican Institute of Physics Inc.
Volume2040
ISBN (Electronic)9780735417663
DOIs
Publication statusPublished - Nov 30 2018
EventInternational Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018 - Thessaloniki, Greece
Duration: Mar 14 2018Mar 18 2018

Other

OtherInternational Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018
CountryGreece
CityThessaloniki
Period3/14/183/18/18

Fingerprint

helices
deoxyribonucleic acid
electronic structure
guanines
sodium
polymers
sugars
phosphates
screws
energy bands
counters
cations
orbitals
symmetry
crystals
atoms
ions

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)

Cite this

Teramae, H., & Aoki, Y. (2018). Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA. In T. E. Simos, Z. Kalogiratou, T. Monovasilis, T. E. Simos, & T. E. Simos (Eds.), International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018 (Vol. 2040). [020013] American Institute of Physics Inc.. https://doi.org/10.1063/1.5079055

Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA. / Teramae, Hiroyuki; Aoki, Yuriko.

International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. ed. / Theodore E. Simos; Zacharoula Kalogiratou; Theodore Monovasilis; Theodore E. Simos; Theodore E. Simos. Vol. 2040 American Institute of Physics Inc., 2018. 020013.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Teramae, H & Aoki, Y 2018, Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA. in TE Simos, Z Kalogiratou, T Monovasilis, TE Simos & TE Simos (eds), International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. vol. 2040, 020013, American Institute of Physics Inc., International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018, Thessaloniki, Greece, 3/14/18. https://doi.org/10.1063/1.5079055
Teramae H, Aoki Y. Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA. In Simos TE, Kalogiratou Z, Monovasilis T, Simos TE, Simos TE, editors, International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. Vol. 2040. American Institute of Physics Inc. 2018. 020013 https://doi.org/10.1063/1.5079055
Teramae, Hiroyuki ; Aoki, Yuriko. / Ab initio electronic structure calculation of polymononucleotide, a model of B-type DNA. International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. editor / Theodore E. Simos ; Zacharoula Kalogiratou ; Theodore Monovasilis ; Theodore E. Simos ; Theodore E. Simos. Vol. 2040 American Institute of Physics Inc., 2018.
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