Extended transition‐state theory and constant‐energy chemical‐reaction molecular‐dynamics method for liquid‐phase chemical reactions

1992 ◽  
Vol 97 (11) ◽  
pp. 8143-8155 ◽  
Author(s):  
Masataka Nagaoka ◽  
Yoshishige Okuno ◽  
Tokio Yamabe
Keyword(s):  
Molecular Dynamics ◽  
Liquid Phase ◽  
Transition State ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Transition State Theory ◽  
State Theory ◽  
Constant Energy ◽  
Dynamics Method ◽  
Phase Chemical

scholarly journals Protein dynamics and catalysis: the problems of transition state theory and the subtlety of dynamic control

2006 ◽  
Vol 361 (1472) ◽  
pp. 1433-1438 ◽  
Author(s):  
J.R.E.T Pineda ◽  
S.D Schwartz
Keyword(s):  
Lactate Dehydrogenase ◽  
Transition State ◽  
Protein Dynamics ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Condensed Phase ◽  
Transition State Theory ◽  
State Theory ◽  
Ongoing Research ◽  
Chemical Catalysis

This manuscript describes ongoing research on the nature of chemical reactions in enzymes. We will investigate how protein dynamics can couple to chemical reaction in an enzyme. We first investigate in some detail why transition state theory cannot fully describe the dynamics of chemical reactions catalysed by enzymes. We describe quantum theories of chemical reaction in condensed phase including studies of how the symmetry of coupled vibrational modes differentially affects reaction dynamics. We make reference to previous work in our group on a variety of condensed phase chemical reactions (liquid and crystalline) and a variety of enzymatically catalysed reactions including the reactions of lactate dehydrogenase and purine nucleoside phosphorylase. All the protein motions we have studied have been quite rapid. We will propose methods to find motions over a broad range of time-scales in enzymes that couple to chemical catalysis. We report recent findings which show that conformational fluctuations in lactate dehydrogenase can strongly affect its ability to catalyse reactions through protein motion, and that only a tiny minority of conformations appear to be catalytically competent.

On the Calculation of Transition State Activity Coefficient and Solvent Effects on Chemical Reactions

1998 ◽  
Vol 63 (12) ◽  
pp. 1969-1976 ◽  
Author(s):  
Alvaro Domínguez ◽  
Rafael Jimenez ◽  
Pilar López-Cornejo ◽  
Pilar Pérez ◽  
Francisco Sánchez
Keyword(s):  
Activity Coefficient ◽  
Transition State ◽  
Chemical Reactions ◽  
Solvent Effects ◽  
Transition State Theory ◽  
Reaction Medium ◽  
State Theory ◽  
Precursor Complex ◽  
State Activity ◽  
Classical Transition

Solvent effects, when the classical transition state theory (TST) holds, can be interpreted following the Brønsted equation. However, when calculating the activity coefficient of the transition state, γ# it is important to take into account that this coefficient is different from that of the precursor complex, γPC. The activity coefficient of the latter is, in fact, that calculated in classical treatments of salt and solvent effects. In this paper it is shown how the quotients γ#/γPC change when the reaction medium changes. Therefore, the conclusions taken on the basis of classical treatments may be erroneous.

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