Machine learning for chemical reactions

M Meuwly - Chemical Reviews, 2021 - ACS Publications
Machine learning (ML) techniques applied to chemical reactions have a long history. The
present contribution discusses applications ranging from small molecule reaction dynamics …

CHARMM at 45: Enhancements in accessibility, functionality, and speed

W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

IS Gutiérrez, FY Lin, K Vanommeslaeghe… - Bioorganic & medicinal …, 2016 - Elsevier
A halogen bond is a highly directional, non-covalent interaction between a halogen atom
and another electronegative atom. It arises due to the formation of a small region of positive …

[HTML][HTML] Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

T Bereau, RA DiStasio, A Tkatchenko… - The Journal of …, 2018 - pubs.aip.org
Classical intermolecular potentials typically require an extensive parametrization procedure
for any new compound considered. To do away with prior parametrization, we propose a …

Structure, organization, and heterogeneity of water-containing deep eutectic solvents

K Töpfer, A Pasti, A Das, SM Salehi… - Journal of the …, 2022 - ACS Publications
The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with
varying water content is investigated from 2D IR (with the C–N stretch vibration of the SCN …

Transferable atomic multipole machine learning models for small organic molecules

T Bereau, D Andrienko… - Journal of chemical …, 2015 - ACS Publications
Accurate representation of the molecular electrostatic potential, which is often expanded in
distributed multipole moments, is crucial for an efficient evaluation of intermolecular …

High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning

OT Unke, D Koner, S Patra, S Käser… - … Learning: Science and …, 2020 - iopscience.iop.org
An overview of computational methods to describe high-dimensional potential energy
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …

Permutationally invariant, reproducing kernel-based potential energy surfaces for polyatomic molecules: From formaldehyde to acetone

D Koner, M Meuwly - Journal of chemical theory and computation, 2020 - ACS Publications
Constructing accurate, high-dimensional molecular potential energy surfaces (PESs) for
polyatomic molecules is challenging. Reproducing kernel Hilbert space (RKHS) …

Charge anisotropy: where atomic multipoles matter most

C Kramer, A Spinn, KR Liedl - Journal of chemical theory and …, 2014 - ACS Publications
Specific intermolecular interactions are largely guided by electrostatics. However, the most
common model for electrostatic interactions atomic point charges fails to reproduce …

Topology automated force-field interactions (TAFFI): a framework for developing transferable force fields

B Seo, ZY Lin, Q Zhao, MA Webb… - Journal of Chemical …, 2021 - ACS Publications
Force-field development has undergone a revolution in the past decade with the
proliferation of quantum chemistry based parametrizations and the introduction of machine …