Constant-pH simulations of a coarse-grained model of polyfunctional weak charged biopolymers

A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, 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 influence of electrostat...

Descripción completa

Detalles Bibliográficos
Autores: Naranjo Tovar, David Alejandro, Blanco Andrés, Pablo M., Garcés Gonzalez, Josep Lluís, Madurga Diez, Sergio, Mas Pujadas, Francesc
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/418531
Acceso en línea:https://hdl.handle.net/2117/418531
https://dx.doi.org/10.3390/biophysica4010008
Access Level:acceso abierto
Palabra clave:Charged biopolymer
Polyelectrolyte
Proton binding
Constant pH
Langevin dynamics
ESPResSo
Coarse-grained
Humic acid
Frumkin isotherm
Àrees temàtiques de la UPC::Enginyeria química
id ES_8937f6c83ac68fefd2ffdf8780bc6554
oai_identifier_str oai:upcommons.upc.edu:2117/418531
network_acronym_str ES
network_name_str España
repository_id_str
spelling Constant-pH simulations of a coarse-grained model of polyfunctional weak charged biopolymersNaranjo Tovar, David AlejandroBlanco Andrés, Pablo M.Garcés Gonzalez, Josep LluísMadurga Diez, SergioMas Pujadas, FrancescCharged biopolymerPolyelectrolyteProton bindingConstant pHLangevin dynamicsESPResSoCoarse-grainedHumic acidFrumkin isothermÀrees temàtiques de la UPC::Enginyeria químicaA coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, 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 influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics 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.Peer ReviewedMultidisciplinary Digital Publishing Institute (MDPI)20242024-02-2820242024-11-21journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/418531https://dx.doi.org/10.3390/biophysica4010008reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/4185312026-05-27T15:37:01Z
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 Tovar, David Alejandro
Charged biopolymer
Polyelectrolyte
Proton binding
Constant pH
Langevin dynamics
ESPResSo
Coarse-grained
Humic acid
Frumkin isotherm
Àrees temàtiques de la UPC::Enginyeria química
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 Tovar, David Alejandro
Blanco Andrés, Pablo M.
Garcés Gonzalez, Josep Lluís
Madurga Diez, Sergio
Mas Pujadas, Francesc
author Naranjo Tovar, David Alejandro
author_facet Naranjo Tovar, David Alejandro
Blanco Andrés, Pablo M.
Garcés Gonzalez, Josep Lluís
Madurga Diez, Sergio
Mas Pujadas, Francesc
author_role author
author2 Blanco Andrés, Pablo M.
Garcés Gonzalez, Josep Lluís
Madurga Diez, Sergio
Mas Pujadas, Francesc
author2_role author
author
author
author
dc.subject.none.fl_str_mv Charged biopolymer
Polyelectrolyte
Proton binding
Constant pH
Langevin dynamics
ESPResSo
Coarse-grained
Humic acid
Frumkin isotherm
Àrees temàtiques de la UPC::Enginyeria química
topic Charged biopolymer
Polyelectrolyte
Proton binding
Constant pH
Langevin dynamics
ESPResSo
Coarse-grained
Humic acid
Frumkin isotherm
Àrees temàtiques de la UPC::Enginyeria química
description A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, 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 influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics 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
2024-02-28
2024
2024-11-21
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/418531
https://dx.doi.org/10.3390/biophysica4010008
url https://hdl.handle.net/2117/418531
https://dx.doi.org/10.3390/biophysica4010008
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute (MDPI)
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869412610353397760
score 15,811543

Similares en LA Referencia