Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization
Abstract We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis – i.e. at close to ambient temperatures and over a wide range...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-03-01
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| Series: | npj Computational Materials |
| Online Access: | https://doi.org/10.1038/s41524-022-00722-w |
| _version_ | 1818356808442445824 |
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| author | André P. Carvalho Sérgio M. Santos Germán Pérez-Sánchez José D. Gouveia José R. B. Gomes Miguel Jorge |
| author_facet | André P. Carvalho Sérgio M. Santos Germán Pérez-Sánchez José D. Gouveia José R. B. Gomes Miguel Jorge |
| author_sort | André P. Carvalho |
| collection | DOAJ |
| description | Abstract We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis – i.e. at close to ambient temperatures and over a wide range of pH. The key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky particles. The simplicity of the model, its applicability in standard parallelized molecular dynamics codes, and its compatibility with the widely used MARTINI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time scales. The model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point, and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle. |
| first_indexed | 2024-12-13T20:03:06Z |
| format | Article |
| id | doaj.art-8089db451c7447e0a92d320dc553623d |
| institution | Directory Open Access Journal |
| issn | 2057-3960 |
| language | English |
| last_indexed | 2024-12-13T20:03:06Z |
| publishDate | 2022-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Computational Materials |
| spelling | doaj.art-8089db451c7447e0a92d320dc553623d2022-12-21T23:33:06ZengNature Portfolionpj Computational Materials2057-39602022-03-018111310.1038/s41524-022-00722-wSticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerizationAndré P. Carvalho0Sérgio M. Santos1Germán Pérez-Sánchez2José D. Gouveia3José R. B. Gomes4Miguel Jorge5CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de SantiagoCICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de SantiagoCICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de SantiagoCICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de SantiagoCICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de SantiagoDepartment of Chemical and Process Engineering, University of StrathclydeAbstract We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis – i.e. at close to ambient temperatures and over a wide range of pH. The key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky particles. The simplicity of the model, its applicability in standard parallelized molecular dynamics codes, and its compatibility with the widely used MARTINI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time scales. The model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point, and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle.https://doi.org/10.1038/s41524-022-00722-w |
| spellingShingle | André P. Carvalho Sérgio M. Santos Germán Pérez-Sánchez José D. Gouveia José R. B. Gomes Miguel Jorge Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization npj Computational Materials |
| title | Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization |
| title_full | Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization |
| title_fullStr | Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization |
| title_full_unstemmed | Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization |
| title_short | Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization |
| title_sort | sticky martini as a reactive coarse grained model for molecular dynamics simulations of silica polymerization |
| url | https://doi.org/10.1038/s41524-022-00722-w |
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