Machine learning of reactive potentials

Y Yang, S Zhang, KD Ranasinghe… - Annual Review of …, 2024 - annualreviews.org
In the past two decades, machine learning potentials (MLPs) have driven significant
developments in chemical, biological, and material sciences. The construction and training …

Modern alchemical free energy methods for drug discovery explained

DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines

T Kubař, M Elstner, Q Cui - Annual review of biophysics, 2023 - annualreviews.org
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …

Condensed matter systems exposed to radiation: multiscale theory, simulations, and experiment

AV Solov'yov, AV Verkhovtsev, NJ Mason… - Chemical …, 2024 - ACS Publications
This roadmap reviews the new, highly interdisciplinary research field studying the behavior
of condensed matter systems exposed to radiation. The Review highlights several recent …

QDπ: A quantum deep potential interaction model for drug discovery

J Zeng, Y Tao, TJ Giese, DM York - Journal of chemical theory …, 2023 - ACS Publications
We report QDπ-v1. 0 for modeling the internal energy of drug molecules containing H, C, N,
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …

Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions

TJ Giese, J Zeng, S Ekesan… - Journal of chemical theory …, 2022 - ACS Publications
We present a fast, accurate, and robust approach for determination of free energy profiles
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

J Zeng, Y Tao, TJ Giese, DM York - The Journal of chemical physics, 2023 - pubs.aip.org
Modern semiempirical electronic structure methods have considerable promise in drug
discovery as universal “force fields” that can reliably model biological and drug-like …

How Accurate Are QM/MM Models?

J Ho, H Yu, Y Shao, M Taylor… - The Journal of Physical …, 2024 - ACS Publications
Despite the success and widespread use of QM/MM methods in modeling (bio) chemically
important processes, their accuracy is still not well understood. A key reason is because …

Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates

Y Chung, WH Green - Chemical Science, 2024 - pubs.rsc.org
Fast and accurate prediction of solvent effects on reaction rates are crucial for kinetic
modeling, chemical process design, and high-throughput solvent screening. Despite the …

Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation

R Snyder, B Kim, X Pan, Y Shao, J Pu - The Journal of Chemical …, 2023 - pubs.aip.org
Free energy simulations that employ combined quantum mechanical and molecular
mechanical (QM/MM) potentials at ab initio QM (AI) levels are computationally highly …