arXiv subjects

Leif D. Jacobson

Publications and source records attributed to Leif D. Jacobson.

3 recordsLinked to original sources

arXiv2026

Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential

Electronic rearrangements associated with bond forming/breaking in catalytic enzymes require quantum mechanical (QM) treatment beyond classical molecular mechanics (MM). Hybrid QM/MM methods enable tractable simulations but require system-specific setup and are sensitive to the QM region choice and treatment of the QM/MM interface. We demonstrate quantum-accurate treatment of all-atom, complete enzymes in explicit solvent comprising up to 54k atoms and 1 microsecond of total simulation time using the machine-learned interatomic potential (MLIP) eSEN-omol. We reproduce experimental barrier trends for Claisen rearrangement in chorismate mutase, resolve critical intermediate states in PETase catalyzed polymer depolymerization, and distinguish mechanistic alternatives for metal-activated phosphoryl transfer in nucleoside diphosphate kinase. We realize 1000x speedups relative to typical QM/MM calculations without system-specific tuning. These results establish MLIPs as a practical route to QM-accurate simulations of enzyme catalysis.

physics.chem-ph↗

arXiv2025

Efficient Long-Range Machine Learning Force Fields for Liquid and Materials Properties

Machine learning force fields (MLFFs) have emerged as a sophisticated tool for cost-efficient atomistic simulations approaching DFT accuracy, with recent message passing MLFFs able to cover the entire periodic table. We present an invariant message passing MLFF architecture (MPNICE) which iteratively predicts atomic partial charges, including long-range interactions, enabling the prediction of charge-dependent properties while achieving 5-20x faster inference versus models with comparable accuracy. We train direct and delta-learned MPNICE models for organic systems, and benchmark against experimental properties of liquid and solid systems. We also benchmark the energetics of finite systems, contributing a new set of torsion scans with charged species and a new set of DLPNO-CCSD(T) references for the TorsionNet500 benchmark. We additionally train and benchmark MPNICE models for bulk inorganic crystals, focusing on structural ranking and mechanical properties. Finally, we explore multi-task models for both inorganic and organic systems, which exhibit slightly decreased performance on domain-specific tasks but surprising generalization, stably predicting the gas phase structure of $\simeq500$ Pt/Ir organometallic complexes despite never training to organometallic complexes of any kind.

physics.chem-ph↗

arXiv2019

Schrödinger-ANI: An Eight-Element Neural Network Interaction Potential with Greatly Expanded Coverage of Druglike Chemical Space

We have developed a neural network potential energy function for use in drug discovery, with chemical element support extended from 41% to 94% of druglike molecules based on ChEMBL. We expand on the work of Smith et al., with their highly accurate network for the elements H, C, N, O, creating a network for H, C, N, O, S, F, Cl, P. We focus particularly on the calculation of relative conformer energies, for which we show that our new potential energy function has an RMSE of 0.70 kcal/mol for prospective druglike molecule conformers, substantially better than the previous state of the art. The speed and accuracy of this model could greatly accelerate the parameterization of protein-ligand binding free energy calculations for novel druglike molecules.

physics.chem-ph↗