Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA
Autor(a) principal: | |
---|---|
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.jctc.2c00756 http://hdl.handle.net/11449/246262 |
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. |
id |
UNSP_17295b1564f380cc405455e67f5dc416 |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/246262 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
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.Instituto de Física Gleb Wataghin Universidade Estadual de Campinas, SPDept. of Mech. Eng. Chem. Eng. Eng. Sci. and Mechanics Chem. Materials Science and Engineering Penn State University, University ParkInstituto de Geociências e Ciências Exatas de Rio Claro Universidade Estadual Paulista Júlio de Mesquita Filho, SPInstituto de Geociências e Ciências Exatas de Rio Claro Universidade Estadual Paulista Júlio de Mesquita Filho, SPUniversidade Estadual de Campinas (UNICAMP)Penn State UniversityUniversidade Estadual Paulista (UNESP)De Faria, Jhaison C.Paupitz, Ricardo [UNESP]Van Duin, Adri C. T.Bernal, Mario A.2023-07-29T12:36:04Z2023-07-29T12:36:04Z2022-11-08info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article6463-6471http://dx.doi.org/10.1021/acs.jctc.2c00756Journal of Chemical Theory and Computation, v. 18, n. 11, p. 6463-6471, 2022.1549-96261549-9618http://hdl.handle.net/11449/24626210.1021/acs.jctc.2c007562-s2.0-85141596303Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Chemical Theory and Computationinfo:eu-repo/semantics/openAccess2023-07-29T12:36:04Zoai:repositorio.unesp.br:11449/246262Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:58:14.575797Repositório 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 De Faria, Jhaison C. |
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 |
De Faria, Jhaison C. |
author_facet |
De Faria, Jhaison C. 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) Penn State University Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
De Faria, Jhaison C. 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 |
2022-11-08 2023-07-29T12:36:04Z 2023-07-29T12:36:04Z |
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.jctc.2c00756 Journal of Chemical Theory and Computation, v. 18, n. 11, p. 6463-6471, 2022. 1549-9626 1549-9618 http://hdl.handle.net/11449/246262 10.1021/acs.jctc.2c00756 2-s2.0-85141596303 |
url |
http://dx.doi.org/10.1021/acs.jctc.2c00756 http://hdl.handle.net/11449/246262 |
identifier_str_mv |
Journal of Chemical Theory and Computation, v. 18, n. 11, p. 6463-6471, 2022. 1549-9626 1549-9618 10.1021/acs.jctc.2c00756 2-s2.0-85141596303 |
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 |
6463-6471 |
dc.source.none.fl_str_mv |
Scopus 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_ |
1808128879886336000 |