Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1021/acs.jctc2c00756 http://hdl.handle.net/11449/245121 |
Resumo: | The early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine- guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process. |
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Repositório Institucional da UNESP |
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spelling |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNAThe early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine- guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process.Coordena��o de Aperfei�oamento de Pessoal de N�vel Superior (CAPES)Funda��o de Amparo � Pesquisa do Estado de S�o Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cient�fico e Tecnol�gico (CNPq)Univ Estadual Campinas, Inst Fis Gleb Wataghin, BR-13083859 Campinas, SP, BrazilUniv Estadual Paulista, Inst Geociencias & Ciencias Exatas Rio Claro, BR-13506900 Rio Claro, SP, BrazilPenn State Univ, Dept Mech Engn Chem Engn Engn Sci & Mech Chem Mat, State Coll, PA 16802 USAUniv Estadual Paulista, Inst Geociencias & Ciencias Exatas Rio Claro, BR-13506900 Rio Claro, SP, BrazilCAPES: 001FAPESP: 2011/51594-2FAPESP: 2015/21873-8FAPESP: 2018/15316-7FAPESP: 2020/08647-7CNPq: 306775/2015-8CNPq: 306298/2018-0CNPq: 312807/2021-0Amer Chemical SocUniversidade Estadual de Campinas (UNICAMP)Universidade Estadual Paulista (UNESP)Penn State UnivFaria, Jhaison C. dePaupitz, Ricardo [UNESP]van Duin, Adri C. T.Bernal, Mario A.2023-07-29T11:37:50Z2023-07-29T11:37:50Z2022-10-28info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article9http://dx.doi.org/10.1021/acs.jctc2c00756Journal of Chemical Theory and Computation. Washington: Amer Chemical Soc, 9 p., 2022.1549-9618http://hdl.handle.net/11449/24512110.1021/acs.jctc2c00756WOS:000878995300001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal Of Chemical Theory And Computationinfo:eu-repo/semantics/openAccess2023-07-29T11:37:50Zoai:repositorio.unesp.br:11449/245121Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T18:52:49.070593Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
title |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
spellingShingle |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA Faria, Jhaison C. de |
title_short |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
title_full |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
title_fullStr |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
title_full_unstemmed |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
title_sort |
Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA |
author |
Faria, Jhaison C. de |
author_facet |
Faria, Jhaison C. de Paupitz, Ricardo [UNESP] van Duin, Adri C. T. Bernal, Mario A. |
author_role |
author |
author2 |
Paupitz, Ricardo [UNESP] van Duin, Adri C. T. Bernal, Mario A. |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual de Campinas (UNICAMP) Universidade Estadual Paulista (UNESP) Penn State Univ |
dc.contributor.author.fl_str_mv |
Faria, Jhaison C. de Paupitz, Ricardo [UNESP] van Duin, Adri C. T. Bernal, Mario A. |
description |
The early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine- guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-10-28 2023-07-29T11:37:50Z 2023-07-29T11:37:50Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1021/acs.jctc2c00756 Journal of Chemical Theory and Computation. Washington: Amer Chemical Soc, 9 p., 2022. 1549-9618 http://hdl.handle.net/11449/245121 10.1021/acs.jctc2c00756 WOS:000878995300001 |
url |
http://dx.doi.org/10.1021/acs.jctc2c00756 http://hdl.handle.net/11449/245121 |
identifier_str_mv |
Journal of Chemical Theory and Computation. Washington: Amer Chemical Soc, 9 p., 2022. 1549-9618 10.1021/acs.jctc2c00756 WOS:000878995300001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal Of Chemical Theory And Computation |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
9 |
dc.publisher.none.fl_str_mv |
Amer Chemical Soc |
publisher.none.fl_str_mv |
Amer Chemical Soc |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128993772175360 |