Picturing the Transition-State Region and Understanding Vibrational Enhancement for the Cl + CH4→ HCl + CH3Reaction

1996 ◽  
Vol 100 (19) ◽  
pp. 7938-7947 ◽  
Author(s):  
William R. Simpson ◽  
T. Peter Rakitzis ◽  
S. Alex Kandel ◽  
Topaz Lev-On ◽  
Richard N. Zare
Keyword(s):  
Transition State ◽  
State Region ◽  
Vibrational Enhancement

Study of the transition state region in the Cl+HCl reaction by photoelectron spectroscopy of ClHCl−

1988 ◽  
Vol 88 (2) ◽  
pp. 1463-1465 ◽  
Author(s):  
R. B. Metz ◽  
T. Kitsopoulos ◽  
A. Weaver ◽  
D. M. Neumark
Keyword(s):  
Transition State ◽  
Photoelectron Spectroscopy ◽  
State Region

scholarly journals Sampling the Folding Transition State Ensemble in a Tube-Like Model of Protein

10.29007/ml3c ◽  
2020 ◽  
Author(s):  
Ba Hung Nguyen ◽  
Hoang Trinh Xuan
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformational root-mean-square deviation (RMSD) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using the umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

Reaction path Hamiltonian for the association reactions CH3 + H and CH3 + D

1992 ◽  
Vol 70 (7) ◽  
pp. 1897-1904 ◽  
Author(s):  
David M. Wardlaw
Keyword(s):  
Transition State ◽  
Transition State Theory ◽  
Reaction Path ◽  
State Theory ◽  
Hydrogen Separation ◽  
Coupling Coefficients ◽  
Symmetry Coordinates ◽  
Different Types ◽  
State Region ◽  
Reaction Path Hamiltonian

Coupling coefficients and normal mode frequencies appearing in the reaction path Hamiltonian formulated by Miller, Handy, and Adams have been calculated for the title reactions as a function of distance along the reaction path. The calculation of the coupling coefficients requires the use of symmetry coordinates which are described herein. It is found that the carbon–hydrogen separation provides an excellent representation of the reaction path coordinate, being linearly related to it. The coupling coefficients for CH3 + H and CH3 + D are approximately the same in the region of variational transition states and do not support the suggestion that an apparent isotope anomaly in the experimentally derived rates of these reactions might be attributable to different dynamics along the reaction path. The relative magnitudes of coupling coefficients for CH3 + H are used to assess some of the usual assumptions in variational transition state theory concerning separability of different types of motion in the transition state region.

Threshold photodetachment spectroscopy of the iodine atom + hydrogen iodide transition-state region

1990 ◽  
Vol 94 (6) ◽  
pp. 2240-2242 ◽  
Author(s):  
I. M. Waller ◽  
T. N. Kitsopoulos ◽  
D. M. Neumark
Keyword(s):  
Transition State ◽  
Iodine Atom ◽  
Hydrogen Iodide ◽  
State Region

Spectroscopy of the iodine atom + hydrogen iodide transition-state region by photodetachment of IHI-

1988 ◽  
Vol 92 (20) ◽  
pp. 5558-5560 ◽  
Author(s):  
A. Weaver ◽  
R. B. Metz ◽  
S. E. Bradforth ◽  
D. M. Neumark
Keyword(s):  
Transition State ◽  
Iodine Atom ◽  
Hydrogen Iodide ◽  
State Region

scholarly journals Sampling the Folding Transition State Ensemble in a Tube-like Model of Protein

2019 ◽  
Vol 29 (2) ◽  
pp. 129
Author(s):  
Nguyen Ba Hung ◽  
Trinh Xuan Hoang
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformationalroot mean square deviation (rmsd) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

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