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  TDDFT-Based Study on the Proton-DNA Collision

Seraide, R., Bernal, M. A., Brunetto, G., de Giovannini, U., & Rubio, A. (2017). TDDFT-Based Study on the Proton-DNA Collision. The Journal of Physical Chemistry B, 121(30), 7276-7283. doi:10.1021/acs.jpcb.7b04934.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0001-75DF-1 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-AA6E-2
Genre: Journal Article

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https://dx.doi.org/10.1021/acs.jpcb.7b04934 (Publisher version)
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https://arxiv.org/abs/1905.03575 (Preprint)
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 Creators:
Seraide, R.1, Author
Bernal, M. A.1, Author
Brunetto, G.1, Author
de Giovannini, U.2, 3, Author              
Rubio, A.2, 4, 5, Author              
Affiliations:
1Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, ou_persistent22              
2Theory Group, Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society, ou_2266715              
3Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, ou_persistent22              
4Center for Free-Electron Laser Science and Department of Physics, University of Hamburg, ou_persistent22              
5Nano-Bio Spectroscopy Group and ETSF, Dpto. Física de Materiales, Universidad del País Vasco UPV/EHU, ou_persistent22              

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 Abstract: The interaction of heavy charged particles with DNA is of interest for hadrontherapy and the aerospace industry. Here, a time-dependent density functional theory study on the interaction of a 4 keV proton with an isolated DNA base pair (bp) was carried out. Ehrenfest dynamics was used to study the evolution of the system up to about 193 fs. It was observed that the dissociation of the target occurs between 80 and 100 fs. The effect of bp linking to the DNA double helix was emulated by fixing the four O3′ atoms responsible for the attachment. The bp tends to dissociate into its main components, namely, the phosphate groups, sugars, and nitrogenous bases. A central impact with an energy transfer of 17.9 eV only produces a base damage while keeping the backbone intact. An impact on a phosphate group with an energy transfer of about 60 eV leads to a backbone break at that site together with a base damage, and the opposite backbone site integrity is kept. As the whole system is perturbed during this collision, no atom remains passive. These results suggest that base damage accompanies all backbone breaks as the hydrogen bonds that keep bases together are much weaker that those between the other components of the DNA.

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Language(s): eng - English
 Dates: 2017-07-042017-05-222017-07-062017-07-06
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1021/acs.jpcb.7b04934
arXiv: 1905.03575
 Degree: -

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Project name : M.A.B. thanks the Conselho Nacional para o Desenvolvimento Científico e Tecnológico (CNPq), Brazil, for financing his research activities through the project 306775/2015-8. A.R. and U.d.G. acknowledge financial support from the European Research Council (ERC-2015-AdG-694097), Grupos Consolidados (IT578-13), H2020-NMP-2014 project MOSTOPHOS (GA no. 646259), European Union’s H2020 programme under GA no. 676580 (NOMAD), and COST Action MP1306 (EUSpec). The images in this work were made with VMD software support. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.
Grant ID : 646259
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : M.A.B. thanks the Conselho Nacional para o Desenvolvimento Científico e Tecnológico (CNPq), Brazil, for financing his research activities through the project 306775/2015-8. A.R. and U.d.G. acknowledge financial support from the European Research Council (ERC-2015-AdG-694097), Grupos Consolidados (IT578-13), H2020-NMP-2014 project MOSTOPHOS (GA no. 646259), European Union’s H2020 programme under GA no. 676580 (NOMAD), and COST Action MP1306 (EUSpec). The images in this work were made with VMD software support. VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign.
Grant ID : 676580
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

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Title: The Journal of Physical Chemistry B
  Other : J. Phys. Chem. B
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: 8 Volume / Issue: 121 (30) Sequence Number: - Start / End Page: 7276 - 7283 Identifier: ISSN: 1520-6106
CoNE: /journals/resource/1000000000293370_1