Metadynamics

A Barducci, M Bonomi… - Wiley Interdisciplinary …, 2011 - Wiley Online Library
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition

X Huang, J Feng, J Cui, G Jiang, W Harrison, X Zang… - Nature Catalysis, 2022 - nature.com
Exploiting nature's catalysts for non-natural transformations that are inaccessible to
chemocatalysis is highly desirable but challenging. On the one hand, the widespread …

Full atomistic reaction mechanism with kinetics for CO reduction on Cu (100) from ab initio molecular dynamics free-energy calculations at 298 K

T Cheng, H Xiao… - Proceedings of the …, 2017 - National Acad Sciences
A critical step toward the rational design of new catalysts that achieve selective and efficient
reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed …

Reaction Mechanisms for the Electrochemical Reduction of CO2 to CO and Formate on the Cu(100) Surface at 298 K from Quantum Mechanics Free Energy …

T Cheng, H Xiao, WA Goddard III - Journal of the American …, 2016 - ACS Publications
Copper is the only elemental metal that reduces a significant fraction of CO2 to
hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product …

Electrochemical CO reduction builds solvent water into oxygenate products

Y Lum, T Cheng, WA Goddard III… - Journal of the American …, 2018 - ACS Publications
Numerous studies have examined the electrochemical reduction of CO (COR) to oxygenates
(eg, ethanol). None have considered the possibility that oxygen in the product might arise …

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

A Laio, FL Gervasio - Reports on Progress in Physics, 2008 - iopscience.iop.org
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …

Covalent mechanochemistry: theoretical concepts and computational tools with applications to molecular nanomechanics

J Ribas-Arino, D Marx - Chemical reviews, 2012 - ACS Publications
In the following section, we will recapitulate selected experimental milestones through the
eyes of the theoretician, which, in our opinion, significantly advanced the field of covalent …

Operando modeling of zeolite-catalyzed reactions using first-principles molecular dynamics simulations

V Van Speybroeck, M Bocus, P Cnudde… - ACS …, 2023 - ACS Publications
Within this Perspective, we critically reflect on the role of first-principles molecular dynamics
(MD) simulations in unraveling the catalytic function within zeolites under operating …

The molecular mechanism of the catalase reaction

M Alfonso-Prieto, X Biarnés, P Vidossich… - Journal of the …, 2009 - ACS Publications
Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading
hydrogen peroxide to water and oxygen (2H2O2→ 2 H2O+ O2) with high efficiency. The …