Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers

A coarse-grained model of linear polyfunctional weak charged biopolymers was imple- mented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The in- fluence of electro...

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Autores: Naranjo, Daniel, Blanco Andrés, Pablo M., Garcés, Josep Lluís, Madurga Díez, Sergio, Mas i Pujadas, Francesc
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/218763
Acceso en línea:https://hdl.handle.net/2445/218763
Access Level:acceso abierto
Palabra clave:Biopolímers
Àcid húmic
Polielectròlits
Biopolymers
Humic acid
Polyelectrolytes
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spelling Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged BiopolymersNaranjo, DanielBlanco Andrés, Pablo M.Garcés, Josep LluísMadurga Díez, SergioMas i Pujadas, FrancescBiopolímersÀcid húmicPolielectròlitsBiopolymersHumic acidPolyelectrolytesA coarse-grained model of linear polyfunctional weak charged biopolymers was imple- mented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The in- fluence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynam- ics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.MDPI2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/218763Articles publicats en revistes (Ciència dels Materials i Química Física)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.3390/biophysica4010008Biophysica, 2024, vol. 4, p. 107-127https://doi.org/10.3390/biophysica4010008cc-by (c) Naranjo, D. et al., 2024http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2187632026-05-27T06:46:51Z
dc.title.none.fl_str_mv Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
title Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
spellingShingle Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
Naranjo, Daniel
Biopolímers
Àcid húmic
Polielectròlits
Biopolymers
Humic acid
Polyelectrolytes
title_short Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
title_full Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
title_fullStr Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
title_full_unstemmed Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
title_sort Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
dc.creator.none.fl_str_mv Naranjo, Daniel
Blanco Andrés, Pablo M.
Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author Naranjo, Daniel
author_facet Naranjo, Daniel
Blanco Andrés, Pablo M.
Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author_role author
author2 Blanco Andrés, Pablo M.
Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author2_role author
author
author
author
dc.subject.none.fl_str_mv Biopolímers
Àcid húmic
Polielectròlits
Biopolymers
Humic acid
Polyelectrolytes
topic Biopolímers
Àcid húmic
Polielectròlits
Biopolymers
Humic acid
Polyelectrolytes
description A coarse-grained model of linear polyfunctional weak charged biopolymers was imple- mented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The in- fluence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynam- ics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/218763
url https://hdl.handle.net/2445/218763
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.3390/biophysica4010008
Biophysica, 2024, vol. 4, p. 107-127
https://doi.org/10.3390/biophysica4010008
dc.rights.none.fl_str_mv cc-by (c) Naranjo, D. et al., 2024
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Naranjo, D. et al., 2024
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv Articles publicats en revistes (Ciència dels Materials i Química Física)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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