Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics

Jonathan A. Semelak

doi:10.1021/acs.jctc.4c01792

Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics

2025-03-01

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AI

Juan Santiago Grassano

Mariano C. González Lebrero

DOI：10.1021/acs.jctc.4c01792

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We introduce an innovative machine learning (ML)-based framework for multiscale molecular modeling in which the ML subsystem is treated as an electrostatic entity interacting with its molecular mechanics (MM) environment through classical electrostatics. The integration of ML accuracy with multiscale modeling is accomplished by leveraging the capabilities of the ANI neural networks to predict geometry-dependent atomic partial charges at the minimal basis iterative stockholder (MBIS) level, going beyond static mechanical embedding. This ML/MM approach can closely approximate state-of-the-art multiscale quantum-classical (QM/MM) methods while significantly lowering computational requirements, thereby facilitating more efficient and precise simulations in computational chemistry. The method requires no additional training beyond the initial model setup and is integrated into Amber, one of the most widely used software suites for molecular modeling, ensuring accessibility to the broader community. We validate its performance across a variety of challenging applications, including the solvation structure, vibrational spectra, torsion free energy profiles, and protein-ligand interactions, achieving excellent agreement with QM/MM benchmarks. This framework not only advances the frontiers of multiscale modeling but also showcases the potential of machine learning to achieve quantum-level accuracy with exceptional efficiency for complex chemical systems.

Keyword:

DYNAMICS SIMULATIONS

QM/MM METHODS

ATOMIC CHARGES

BINDING

COMPLEXES

CHEMISTRY

QUALITY

DESIGN

BIOTIN

ION

Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics

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