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Implementing reactivity in molecular dynamics simulations with harmonic force fields

Author

Listed:
  • Jordan J. Winetrout

    (University of Colorado at Boulder
    University of Colorado at Boulder)

  • Krishan Kanhaiya

    (University of Colorado at Boulder
    University of Colorado at Boulder
    Universitätstrasse 150)

  • Joshua Kemppainen

    (Michigan Technological University)

  • Pieter J. in ‘t Veld

    (Molecular Modeling & Drug Discovery)

  • Geeta Sachdeva

    (Michigan Technological University)

  • Ravindra Pandey

    (Michigan Technological University)

  • Behzad Damirchi

    (Pennsylvania State University)

  • Adri Duin

    (Pennsylvania State University)

  • Gregory M. Odegard

    (Michigan Technological University)

  • Hendrik Heinz

    (University of Colorado at Boulder
    University of Colorado at Boulder)

Abstract

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

Suggested Citation

  • Jordan J. Winetrout & Krishan Kanhaiya & Joshua Kemppainen & Pieter J. in ‘t Veld & Geeta Sachdeva & Ravindra Pandey & Behzad Damirchi & Adri Duin & Gregory M. Odegard & Hendrik Heinz, 2024. "Implementing reactivity in molecular dynamics simulations with harmonic force fields," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50793-0
    DOI: 10.1038/s41467-024-50793-0
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    References listed on IDEAS

    as
    1. Isidro Lorenzo Geada & Hadi Ramezani-Dakhel & Tariq Jamil & Marialore Sulpizi & Hendrik Heinz, 2018. "Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    2. Peter C. St. John & Yanfei Guan & Yeonjoon Kim & Seonah Kim & Robert S. Paton, 2020. "Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. Peter C. John & Yanfei Guan & Yeonjoon Kim & Seonah Kim & Robert S. Paton, 2020. "Publisher Correction: Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost," Nature Communications, Nature, vol. 11(1), pages 1-3, December.
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