Reaction coordinates and transition states in enzymatic catalysis

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Kirill Zinovjev ◽  
Iñaki Tuñón
Keyword(s):  
Enzymatic Catalysis ◽  
Transition States ◽  
Reaction Coordinates

scholarly journals Introductory remarks to the second session

1981 ◽  
Vol 293 (1063) ◽  
pp. 63-64
Keyword(s):  
Steady State ◽  
Enzymatic Catalysis ◽  
Transition States ◽  
Phosphoglycerate Kinase ◽  
Reaction Rates ◽  
Steady State Rate ◽  
And Function ◽  
Enzyme Structure And Function ◽  
And Control

The four presentations in this session cover studies on different aspects of enzyme structure and function. They effectively illustrate how one has to combine different approaches to arrive at an understanding of enzymatic catalysis and control. Nowadays, the molecular description of an enzyme is hardly credible without detailed crystallographic information. Thus, Dr Blake’s paper on the structure of phosphoglycerate kinase is particularly relevant to our understanding of phosphate-transfer mechanisms. The question of the relation between structure in the solid and solution is still with us and n.m.r. has proved to be the best way to study the differences and similarities. M any enzyme substrate complexes have been ‘mapped’ in solution, by using the perturbation of the n.m.r. spectra by param agnetic centres as a measure of interatomic distances. How such results can lead to both structural and mechanistic information will be discussed by Dr Mildvan. To understand mechanisms we must also get some information about the nature of transition states. Here, stereochemical observations play an important role and Dr Lowe will describe some elegant work on the use of chiral phosphates in approaching this problem. Finally, it is important to describe structures, intermediates and transition states in terms of the kinetic behaviour of the enzyme and Dr Dalziel will give us an example of both steady-state and pre-steady-state rate studies. Measurements of reaction rates ultimately link studies on the isolated enzyme to their behaviour in vivo . As this last step in the sequence is not covered by the formal presentations at this meeting I should like to show briefly how n.m.r. can now be used to obtain fluxes of enzyme catalysed reactions in vivo both in the steady state and at equilibrium.

Pattern of Intrinsic Reaction Coordinates and Separatrices for a Symmetry-Forbidden Reaction

1986 ◽  
Vol 41 (3) ◽  
pp. 529-531 ◽  
Author(s):  
Ariel Fernández
Keyword(s):  
Structural Stability ◽  
Transition States ◽  
Chemical Species ◽  
Basins Of Attraction ◽  
Thermal Isomerization ◽  
Relative Distribution ◽  
Reaction Coordinates ◽  
Jahn Teller ◽  
Stability Principle ◽  
Good Agreement

The relative distribution of the basins of attraction of the chemical species and of the transition states is derived for the thermal isomerization of cyclobutene to butadiene.It is shown that the transition states for the symmetry-allowed and symmetry-forbidden pathways are lumomers of one another. Use is made of the structural stability principle of Ariel Fernández and Oktay Sinanoglu to show that these transition states are respectively the conrotatory and disrotatory Jahn-Teller distortions of the 2-butene diradical.The results exhibit good agreement with J. A. Berson’s conclusions in the sense that even the forbidden pathway is concerted.

The Decomposition Pathways of CH2SiCl3, CH3SiCl2 and CH2SiCl2 in CVD of SiC from MTS/H2 System

2013 ◽  
Vol 699 ◽  
pp. 378-382
Author(s):  
Xin Wang ◽  
Ke He Su ◽  
Yan Li Wang ◽  
Juan Li Deng
Keyword(s):  
Radical Reaction ◽  
Transition States ◽  
Heat Capacities ◽  
Free Radical Reaction ◽  
Electronic Correlation ◽  
Free Energies ◽  
Elementary Reactions ◽  
Reaction Coordinates ◽  
Reaction Energies ◽  
Accurate Model Chemistry

The decomposition pathways in CVD preparing SiC with CH3SiCl3-H2 precursors was searched theoretically, which involves 54 well-defined transition states. The geometries of the species were optimized by employing the B3PW91/6-311G(d,p) method. The transition states as well as their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The energy barriers and the reaction energies were evaluated with the accurate model chemistry method at G3(MP2) level after a non-dynamical electronic correlation detection. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K and 1200 K for all of the reactions were reported. The energies at any temperature could be derived classically by using the analytical heat capacities. All the possible elementary reactions, including both direct decomposition and the radical attacking dissociations for CH2SiCl3, CH3SiCl2 and CH2SiCl2 were examined. A free radical reaction mechanism was proposed.

1994 R.U. Lemieux Award Lecture Hydrolysis of acetals and ketals. Position of transition states along the reaction coordinates, and stereoelectronic effects

1994 ◽  
Vol 72 (10) ◽  
pp. 2021-2027 ◽  
Author(s):  
Pierre Deslongchamps ◽  
Yves L. Dory ◽  
Shigui Li
Keyword(s):  
Ab Initio ◽  
Reaction Pathway ◽  
Transition States ◽  
Experimental Results ◽  
Reaction Coordinates ◽  
Stereoelectronic Effects ◽  
Theoretical Support ◽  
Semi Empirical ◽  
Hydrolysis Of ◽  
Support Evidence

Past and recent experimental results on the formation or hydrolysis (or isomerization) of various acetals and ketals including α-and β-glycoside models are presented. Ab initio investigations of simple acetals are also briefly reviewed as well as recent experimental and theoretical support evidence for a synperiplanar effect. A detailed study using the semi-empirical Hamiltonian AM1 defining the reaction pathway in the hydrolysis of various acetals and ketals is reported. This overall study shows that the hydrolysis of acetals and ketals is controlled by powerful stereoelectronic effects.

scholarly journals Quantifying the limits of transition state theory in enzymatic catalysis

2017 ◽  
Vol 114 (47) ◽  
pp. 12390-12395 ◽  
Author(s):  
Kirill Zinovjev ◽  
Iñaki Tuñón
Keyword(s):  
Transition State ◽  
Degrees Of Freedom ◽  
Transition State Theory ◽  
Enzymatic Catalysis ◽  
State Theory ◽  
Enzymatic Reactions ◽  
Reaction Coordinates ◽  
Dividing Surface ◽  
Human Dihydrofolate Reductase ◽  
Computational Strategy

While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis.

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