Systematic Embedding of All-Atom Reactive Molecular Dynamics into a Coarse-Grained Environment.

Quantum mechanics/molecular mechanics (QM/MM) simulations are widely used for modeling chemical reactivity in complex environments. In the QM/MM method, the reactive center under study is typically treated using explicit quantum chemical calculations, while the nonreactive environment is treated using classical molecular mechanics. However, for large systems, even with the use of classical force fields for the MM part, QM/MM simulations are very computationally costly, particularly for systems with complex MM dynamics. In this work, we propose a much faster alternative method for studying reactivity denoted by multiscale reactive molecular dynamics/coarse-grained molecular mechanics (MS-RMD/CG-MM). MS-RMD has been shown to be a powerful method for modeling reactions involving proton transport and in principle other reactions. This all-atom reactive MD model, systematically parametrized from constrained DFT calculations, is embedded in a CG environment in this work, where the CG force fields are derived using the multiscale coarse-graining (MS-CG) method. We apply this scheme to organic SN2 reactions in a CG polar solvent (acetone) as examples.

• Publication year

  2025

• Venue

  Journal of Chemical Theory and Computation

• Publication date

  2025-08-19

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1021/acs.jctc.5c00930PMID 40828679
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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