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NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution

[Image: see text] Functionalized metal nanoparticles (NPs) are macromolecular assemblies with a tunable physicochemical profile that makes them interesting for biotechnology, materials science, and energy conversion. In this regard, molecular simulations offer a way to scrutinize the structural and...

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Autores principales: Franco-Ulloa, Sebastian, Riccardi, Laura, Rimembrana, Federico, Grottin, Edwin, Pini, Mattia, De Vivo, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10018737/
https://www.ncbi.nlm.nih.gov/pubmed/36795071
http://dx.doi.org/10.1021/acs.jctc.2c01029
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author Franco-Ulloa, Sebastian
Riccardi, Laura
Rimembrana, Federico
Grottin, Edwin
Pini, Mattia
De Vivo, Marco
author_facet Franco-Ulloa, Sebastian
Riccardi, Laura
Rimembrana, Federico
Grottin, Edwin
Pini, Mattia
De Vivo, Marco
author_sort Franco-Ulloa, Sebastian
collection PubMed
description [Image: see text] Functionalized metal nanoparticles (NPs) are macromolecular assemblies with a tunable physicochemical profile that makes them interesting for biotechnology, materials science, and energy conversion. In this regard, molecular simulations offer a way to scrutinize the structural and dynamical features of monolayer-protected NPs and their interactions with relevant matrices. Previously, we developed NanoModeler, a webserver that automates the preparation of functionalized gold NPs for atomistic molecular dynamics (MD) simulations. Here, we present NanoModeler CG (www.nanomodeler.it), a new release of NanoModeler that now also allows the building and parametrizing of monolayer-protected metal NPs at a coarse-grained (CG) resolution. This new version extends our original methodology to NPs of eight different core shapes, conformed by up to 800,000 beads and coated by eight different monolayer morphologies. The resulting topologies are compatible with the Martini force field but are easily extendable to any other set of parameters parsed by the user. Finally, we demonstrate NanoModeler CG’s capabilities by reproducing experimental structural features of alkylthiolated NPs and rationalizing the brush-to-mushroom phase transition of PEGylated anionic NPs. By automating the construction and parametrization of functionalized NPs, the NanoModeler series offers a standardized way to computationally model monolayer-protected nanosized systems.
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spelling pubmed-100187372023-03-17 NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution Franco-Ulloa, Sebastian Riccardi, Laura Rimembrana, Federico Grottin, Edwin Pini, Mattia De Vivo, Marco J Chem Theory Comput [Image: see text] Functionalized metal nanoparticles (NPs) are macromolecular assemblies with a tunable physicochemical profile that makes them interesting for biotechnology, materials science, and energy conversion. In this regard, molecular simulations offer a way to scrutinize the structural and dynamical features of monolayer-protected NPs and their interactions with relevant matrices. Previously, we developed NanoModeler, a webserver that automates the preparation of functionalized gold NPs for atomistic molecular dynamics (MD) simulations. Here, we present NanoModeler CG (www.nanomodeler.it), a new release of NanoModeler that now also allows the building and parametrizing of monolayer-protected metal NPs at a coarse-grained (CG) resolution. This new version extends our original methodology to NPs of eight different core shapes, conformed by up to 800,000 beads and coated by eight different monolayer morphologies. The resulting topologies are compatible with the Martini force field but are easily extendable to any other set of parameters parsed by the user. Finally, we demonstrate NanoModeler CG’s capabilities by reproducing experimental structural features of alkylthiolated NPs and rationalizing the brush-to-mushroom phase transition of PEGylated anionic NPs. By automating the construction and parametrization of functionalized NPs, the NanoModeler series offers a standardized way to computationally model monolayer-protected nanosized systems. American Chemical Society 2023-02-16 /pmc/articles/PMC10018737/ /pubmed/36795071 http://dx.doi.org/10.1021/acs.jctc.2c01029 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Franco-Ulloa, Sebastian
Riccardi, Laura
Rimembrana, Federico
Grottin, Edwin
Pini, Mattia
De Vivo, Marco
NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title_full NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title_fullStr NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title_full_unstemmed NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title_short NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
title_sort nanomodeler cg: a tool for modeling and engineering functional nanoparticles at a coarse-grained resolution
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10018737/
https://www.ncbi.nlm.nih.gov/pubmed/36795071
http://dx.doi.org/10.1021/acs.jctc.2c01029
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