Modelling chemical processes in explicit solvents with machine learning potentials

H Zhang, V Juraskova, F Duarte - Nature Communications, 2024 - nature.com
Solvent effects influence all stages of the chemical processes, modulating the stability of
intermediates and transition states, as well as altering reaction rates and product ratios …

Kinetic solvent effects in organic reactions

BL Slakman, RH West - Journal of Physical Organic Chemistry, 2019 - Wiley Online Library
This article reviews prior work studying reaction kinetics in solution, with the goal of using
this information to improve detailed kinetic modeling in the solvent phase. Both experimental …

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 …

Revisiting the Enhanced Chemical Reactivity in Water Microdroplets: The Case of a Diels–Alder Reaction

K Gong, A Nandy, Z Song, QS Li… - Journal of the …, 2024 - ACS Publications
Often, chemical reactions are markedly accelerated in microdroplets compared with the
corresponding bulk phase. While identifying the precise causative factors remains …

Diels–Alder reactions in water are determined by microsolvation

LR Pestana, H Hao, T Head-Gordon - Nano letters, 2019 - ACS Publications
Nanoconfined aqueous environments and the recent advent of accelerated chemistry in
microdroplets are increasingly being investigated for catalysis. The mechanisms underlying …

Design and SAR analysis of covalent inhibitors driven by hybrid QM/MM simulations

A Lodola, D Callegari, L Scalvini, S Rivara… - Quantum Mechanics in …, 2020 - Springer
Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a
reliable computational method to investigate and characterize chemical reactions occurring …

Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels–Alder Reaction

X Han, J Zhang, YI Yang, Z Zhang… - Journal of Chemical …, 2022 - ACS Publications
The timescale involved in chemical reactions is quite often beyond that of normal molecular
dynamics simulations. Here, we combine metadynamics with selective integrated tempering …

Mechanistic insights into the reaction of chlorination of tryptophan catalyzed by tryptophan 7-halogenase

TG Karabencheva-Christova, J Torras, AJ Mulholland… - Scientific reports, 2017 - nature.com
Tryptophan 7-halogenase catalyzes chlorination of free tryptophan to 7-chlorotryptophan,
which is the first step in the antibiotic pyrrolnitrin biosynthesis. Many biologically and …

Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations

U Rivero, OT Unke, M Meuwly… - The Journal of chemical …, 2019 - pubs.aip.org
The Diels-Alder reaction between 2, 3-dibromo-1, 3-butadiene and maleic anhydride has
been studied by means of multisurface adiabatic reactive molecular dynamics and the …

About underappreciated yet active conformations of thiourea organocatalysts

A Supady, S Hecht, C Baldauf - Organic letters, 2017 - ACS Publications
Conformational dynamics can define the function of organocatalysts. While the accepted
mechanism of Schreiner's catalyst features a double hydrogen bond to the substrate that …