scholarly journals Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site

2016 ◽  
Vol 138 (23) ◽  
pp. 7386-7394 ◽  
Author(s):  
Daniel Roston ◽  
Darren Demapan ◽  
Qiang Cui
Keyword(s):  
Transition State ◽  
Active Site ◽  
State Structure ◽  
Transition State Structure ◽  
Enzyme Active Site ◽  
Leaving Group ◽  
Leaving Group Ability ◽  
Single Enzyme

Solvent effects on the structure of SN2 transition states

1978 ◽  
Vol 56 (20) ◽  
pp. 2691-2699 ◽  
Author(s):  
Kenneth Charles Westaway
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Solvent Effects ◽  
Kinetic Isotope Effect ◽  
Transition States ◽  
State Structure ◽  
Transition State Structure ◽  
Kinetic Isotope ◽  
Wide Range ◽  
Leaving Group

Two research groups have used heavy atom leaving group kinetic isotope effects to determine how the structure of an SN2 transition state is affected by a change in solvent. Two completely different types of behaviour were observed in these studies. In one case, the leaving group kinetic isotope effect, and thus the transition state structure, changed markedly when the solvent was varied over a reasonably narrow range. In the other study, the leaving group kinetic isotope effect (transition state structure) remained constant over a wide range of solvents. A model describing the interaction between solvent molecules and SN2 transition states is developed and a SolvationruleforSN2reactions which rationalizes the different experimental results is explained and justified. Finally, predictions based on the solvation rule are shown to be in agreement with the results of theoretical calculations of solvent effects on SN2 transition states and secondary α deuterium kinetic isotope effect measurements.

scholarly journals Modeling the Transition State Structures of the Reductive-Half Reaction Active Site of Xanthine Oxidase Bound to Guanine Analogues: A Density Functional Theory Approach

2018 ◽  
Vol 10 (1) ◽  
pp. 137
Author(s):  
Mamaru Bitew Alem ◽  
Yilkal Bezie Ayele
Keyword(s):  
Transition State ◽  
Xanthine Oxidase ◽  
Active Site ◽  
Bond Order ◽  
Density Functional ◽  
Basis Set ◽  
Theory Approach ◽  
State Structure ◽  
Transition State Structure ◽  
Xanthine Oxidase Inhibitor

Modeling and characterization the transition state structure of enzyme catalyzed reactions is essential. A DFT method employing B3LYP level of theory with 6-31G (d',p') basis set for non-metals and LanL2DZ basis set for molybdenum have been used. The bond orders of chemical fragments were calculated using AOmix softaware. The effect of chalcogen replacement, amine group and methyl group in the parent structure of xanthine bound to xanthine oxidase active site were compared. The transition state structure of model substrates (2AX, 2A6TP, 2A6SP and 2A6MP) bound to the truncated form of XO active site has been confirmed by the presence of one negative imaginary frequencies (s-1) (-60), (-140), (-230) and (-270), respectively. The corresponding normalized energy barriers (kcal/mol) from pre-transition state to the transition state, respectively, are (13.869), (21.753), (23.109) and (0.212). In this work, 2A6SP and 2A6TP substrates were found to be potential xanthine oxidase inhibitors. The large bond distances and minimum bond order for CRH-HRH bond, and small bond distances and maximum bond order for SMo-HRH bond at the transition state for chalcogen replaced 2AX confirms early transition state structure. Methyl substituted 2AX analog found to have post transition state structure. A potential xanthine oxidase inhibitor can be designed from purine family enzymes using DFT approach.

Rearrangement of chorismate to prephenate. Use of chorismate mutase inhibitors to define the transition state structure

Biochemistry ◽  
1977 ◽  
Vol 16 (22) ◽  
pp. 4848-4852 ◽  
Author(s):  
P. R. Andrews ◽  
E. N. Cain ◽  
E. Rizzardo ◽  
G. D. Smith
Keyword(s):  
Transition State ◽  
Chorismate Mutase ◽  
State Structure ◽  
Transition State Structure

Conservation of Transition State Structure in Fast Folding Peripheral Subunit-Binding Domains

2008 ◽  
Vol 383 (1) ◽  
pp. 224-237 ◽  
Author(s):  
Timothy D. Sharpe ◽  
Neil Ferguson ◽  
Christopher M. Johnson ◽  
Alan R. Fersht
Keyword(s):  
Transition State ◽  
State Structure ◽  
Transition State Structure ◽  
Binding Domains
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