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

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Quantum Mechanics

Background:

• Quantum mechanics/molecular mechanics (QM/MM) is standard for chemical reactivity but computationally expensive for large systems.
• Classical molecular mechanics (MM) force fields struggle with complex dynamics in large-scale simulations.

Purpose of the Study:

• To develop a computationally efficient alternative to QM/MM simulations for modeling chemical reactivity.
• To introduce a multiscale reactive molecular dynamics/coarse-grained molecular mechanics (MS-RMD/CG-MM) approach.

Main Methods:

• Developed a multiscale reactive molecular dynamics (MS-RMD) model for reactive centers.
• Embedded the MS-RMD model within a coarse-grained (CG) molecular mechanics (MM) environment.
• Derived CG force fields using the multiscale coarse-graining (MS-CG) method.
• Parametrized the all-atom reactive MD model using constrained DFT calculations.

Main Results:

• The MS-RMD/CG-MM method significantly reduces computational cost compared to traditional QM/MM.
• Successfully applied the scheme to model organic S_N2 reactions in a coarse-grained polar solvent (acetone).

Conclusions:

• MS-RMD/CG-MM provides a viable and efficient approach for simulating chemical reactivity in complex environments.
• This method holds promise for studying various reactions, including proton transport.