scholarly journals Erratum: “Crossing the dividing surface of transition state theory. I. Underlying symmetries and motion coordination in multidimensional systems” [J. Chem. Phys. 140, 134303 (2014)]

2014 ◽  
Vol 140 (16) ◽  
pp. 169902 ◽  
Author(s):  
J. C. Lorquet
Keyword(s):  
Transition State ◽  
Transition State Theory ◽  
Chem Phys ◽  
State Theory ◽  
Multidimensional Systems ◽  
Motion Coordination ◽  
Dividing Surface

scholarly journals Simulations of long time scale dynamics using the dimer method

2001 ◽  
Vol 677 ◽  
Author(s):  
Graeme Henkelman ◽  
Hannes Jónsson
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Transition State ◽  
Time Scale ◽  
Transition State Theory ◽  
Kinetic Monte Carlo ◽  
Chem Phys ◽  
State Theory ◽  
Kinetic Monte Carlo Method ◽  
Long Time

We have carried out long time scale simulations where the “dimer method” [G. Henkelman and H. Jónsson, J. Chem. Phys. 111, 7010 (1999)] is used to find the mechanism and estimate the rate of transitions within harmonic transition state theory and time is evolved by using the kinetic Monte Carlo method. Unlike traditional applications of kinetic Monte Carlo, the atoms are not assigned to lattice sites and a list of all possible transitions does not need to be specified beforehand. Rather, the relevant transitions are found on the y during the simulation. An application to the diffusion and island formation of Al adatoms on an Al(100) surface is presented.

scholarly journals Communication: Transition state theory for dissipative systems without a dividing surface

2012 ◽  
Vol 136 (9) ◽  
pp. 091102 ◽  
Author(s):  
F. Revuelta ◽  
Thomas Bartsch ◽  
R. M. Benito ◽  
F. Borondo
Keyword(s):  
Transition State ◽  
Transition State Theory ◽  
State Theory ◽  
Dissipative Systems ◽  
Dividing Surface

scholarly journals Dynamic barriers and tunneling. New views of hydrogen transfer in enzyme reactions

2003 ◽  
Vol 75 (5) ◽  
pp. 601-608 ◽  
Author(s):  
J. P. Klinman
Keyword(s):  
Transition State ◽  
Transition State Theory ◽  
Hydrogen Transfer ◽  
Isotope Effects ◽  
Heavy Atom ◽  
Chem Phys ◽  
State Theory ◽  
Tunnel Effect ◽  
Tunneling Model ◽  
Wide Range

Hydrogen-transfer processes are expected to show appreciable quantum mechanical behavior. Intensive investigations of enzymes under their physiological conditions show this to be true in practically every example investigated. Initially, tunneling was treated either as a tunneling correction [cf. Bell, The Tunnel Effect in Chemistry, Chapman & Hall, New York, (l980)], or as corner-cutting [Truhlar et al., J. Chem. Phys. 100, 12771 (l996)]. This worked well as long as the observed properties could be explained by “corrections” to transition-state theory. However, over the past several years, enzymatic behaviors have been observed that are so deviant as to lie outside of transition-state theory. This phenomenon is discussed in the context of the enzyme, soybean lipoxygenase. An environmentally coupled hydrogen-tunneling model is presented that derives from the treatments of Kuznetsov and Ullstrup [Can. J. Chem. 77, 689 (l999)], and includes heavy-atom reorganization (temperature-dependent and largely isotope-independent), together with heavy-atom gating (temperature- and isotope-dependent). This treatment can explain a wide range of behaviors and leads to a new view of the origin of kinetic isotope effects in hydrogen-transfer reactions. These properties link enzyme fluctuations to the hydrogen-transfer reaction coordinate, making a quantum view of H-transfer necessarily a dynamic view of catalysis.

Transition-State Theory Rate Calculations with a Recrossing-Free Moving Dividing Surface†

2008 ◽  
Vol 112 (2) ◽  
pp. 206-212 ◽  
Author(s):  
Thomas Bartsch ◽  
T. Uzer ◽  
Jeremy M. Moix ◽  
Rigoberto Hernandez
Keyword(s):  
Transition State ◽  
Transition State Theory ◽  
State Theory ◽  
Dividing Surface
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