cp2k: atomistic simulations of condensed matter systems

J Hutter, M Iannuzzi, F Schiffmann… - Wiley Interdisciplinary …, 2014 - Wiley Online Library
cp2k has become a versatile open‐source tool for the simulation of complex systems on the
nanometer scale. It allows for sampling and exploring potential energy surfaces that can be …

Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation …

SCL Kamerlin, M Haranczyk… - The journal of physical …, 2009 - ACS Publications
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …

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 …

We Already Know Everything about Oxidative Addition to Pd (0): Do We?

J Rio, H Liang, MEL Perrin, LA Perego, L Grimaud… - ACS …, 2023 - ACS Publications
The oxidative addition (OA) of organic electrophiles to Pd (0) is a fundamental step in
organopalladium chemistry and plays a key role in palladium-catalyzed cross-coupling …

Reactivity of shape-controlled crystals and metadynamics simulations locate the weak spots of alumina in water

R Réocreux, É Girel, P Clabaut, A Tuel… - Nature …, 2019 - nature.com
The kinetic stability of any material in water relies on the presence of surface weak spots
responsible for chemical weathering by hydrolysis. Being able to identify the atomistic nature …

Real-world predictions from ab initio molecular dynamics simulations

B Kirchner, PJ di Dio, J Hutter - Multiscale Molecular Methods in Applied …, 2012 - Springer
In this review we present the techniques of ab initio molecular dynamics simulation
improved to its current stage where the analysis of existing processes and the prediction of …

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

NV Plotnikov, SCL Kamerlin… - The Journal of Physical …, 2011 - ACS Publications
Recent years have seen tremendous effort in the development of approaches with which to
obtain quantum mechanics/molecular mechanics (QM/MM) free energies for reactions in the …

Protein flexibility and ligand recognition: challenges for molecular modeling

F Spyrakis, A BidonChanal, X Barril… - Current topics in …, 2011 - ingentaconnect.com
The intrinsic dynamics of macromolecules is an essential property to relate the structure of
biomolecular systems with their function in the cell. In the field of ligand-receptor recognition …

Experimental and computational studies of high-valent nickel and palladium complexes

NM Camasso, AJ Canty, A Ariafard… - Organometallics, 2017 - ACS Publications
This article describes a detailed comparison of the organometallic chemistry of high-valent
nickel and palladium model complexes supported by tris (pyrazolyl) borate and …

Reductive elimination and dissociative β-hydride abstraction from Pt (IV) hydroxide and methoxide complexes

NA Smythe, KA Grice, BS Williams, KI Goldberg - Organometallics, 2009 - ACS Publications
The platinum (IV) hydroxide and methoxide complexes fac-(dppbz) PtMe3 (OR)(dppbz= o-
bis (diphenylphosphino) benzene; R= H (1), CH3 (2)) have been prepared and …