Hydrogen tunneling in enzymes and biomimetic models

JP Layfield, S Hammes-Schiffer - Chemical reviews, 2014 - ACS Publications
Hydrogen transfer reactions play an important role throughout chemistry and biology. In
general, hydrogen transfer reactions encompass proton and hydride transfer, which are …

Theoretical methods of potential use for studies of inorganic reaction mechanisms

T Ziegler, J Autschbach - Chemical reviews, 2005 - ACS Publications
It is customary1 to analyze a chemical process as a series of several elementary reaction
steps. In every elementary step, a transformation takes place from one minimum on the …

Simulation of activation free energies in molecular systems

E Neria, S Fischer, M Karplus - The Journal of chemical physics, 1996 - pubs.aip.org
A method is presented for determining activation free energies in complex molecular
systems. The method relies on knowledge of the minimum energy path and bases the …

Free energy from constrained molecular dynamics

M Sprik, G Ciccotti - The Journal of chemical physics, 1998 - pubs.aip.org
Activated processes can be studied in the molecular dynamics (MD) approach by imposing
a mechanical constraint on the corresponding reaction coordinate and by performing a kind …

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

E Paci, M Karplus - Journal of molecular biology, 1999 - Elsevier
Titin, an important constituent of vertebrate muscles, is a protein of the order of a micrometer
in length in the folded state. Atomic force microscopy and laser tweezer experiments have …

A comparison of methods to compute the potential of mean force

D Trzesniak, APE Kunz, WF van Gunsteren - ChemPhysChem, 2007 - Wiley Online Library
Most processes occurring in a system are determined by the relative free energy between
two or more states because the free energy is a measure of the probability of finding the …

The calculation of free-energy differences by constrained molecular-dynamics simulations

WK den Otter, WJ Briels - The Journal of chemical physics, 1998 - pubs.aip.org
In reaction rate theory one is interested in the free energy, A, of a reacting system as a
function of some internal coordinate of the system, the reaction coordinate (xi), which …

Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics

T Ikeda, M Boero, K Terakura - The Journal of chemical physics, 2007 - pubs.aip.org
We studied the solvation structures of the divalent metal cations Mg 2+ and Ca 2+ in ambient
water by applying a Car-Parrinello-based constrained molecular dynamics method. By …

First Principles Molecular Dynamics Study of Ziegler− Natta Heterogeneous Catalysis

M Boero, M Parrinello, K Terakura - Journal of the American …, 1998 - ACS Publications
We present a first principles study of the Ziegler− Natta MgCl2-supported polymerization of
ethylene in the framework of the Car-Parrinello approach. In particular we investigate the …

A quantum molecular‐dynamics study of proton‐transfer reactions along asymmetrical H bonds in solution

H Azzouz, D Borgis - The Journal of chemical physics, 1993 - pubs.aip.org
A molecular‐dynamics study of a model for AH− B⇄ A−− H+ B reactions in liquid
chloromethane is presented. The parameters of the model are fitted to those of typical OH–N …