ArticleJournal of chemical theory and computation2023
Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Modeling Targeted Mechanochemistry in Polymeric Solids.Chemical reviews · 2026Review
- KIMMDY: a biomolecular reaction emulator.Nature communications · 2026Article
- Coarse-Grained Model of the Sodium Dodecyl Sulfate Anionic Surfactant Based on the MDPD-Martini Force Field.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
- Determining the Role of Electrostatics in the Making and Breaking of the Caprin1-ATP Nanocondensate.The journal of physical chemistry. B · 2025Article
- Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations.Communications chemistry · 2024Article
- Block Chemistry for Accurate Modeling of Epoxy Resins.The journal of physical chemistry. B · 2023Article
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Authors and funding
2 authors.
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Abstract
Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.
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