Density functional theory on the larger active site models for [NiFe] hydrogenases: Two-state reactivity?

2008 ◽  
Vol 11 (8) ◽  
pp. 790-804 ◽  
Author(s):  
Hong Wu ◽  
Michael B. Hall
Keyword(s):  
Density Functional Theory ◽  
Active Site ◽  
Density Functional ◽  
Functional Theory

Insights from the computational studies on the oxidized as-isolated state of [NiFeSe] hydrogenase from D. vulgaris Hildenborough

2015 ◽  
Vol 17 (32) ◽  
pp. 20677-20686 ◽  
Author(s):  
Swaminathan Angeline Vedha ◽  
Gunasekaran Velmurugan ◽  
Rajangam Jagadeesan ◽  
Ponnambalam Venuvanalingam
Keyword(s):  
Density Functional Theory ◽  
Active Site ◽  
Density Functional ◽  
Computational Studies ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Site Structure ◽  
Active Site Structure

A density functional theory study of the active site structure and features of the oxygen tolerant [NiFeSe] Hase in the oxidized as-isolated state of the enzyme D. vulgaris Hildenborough (DvH) is reported here.

Ni−Fe Hydrogenases:  A Density Functional Theory Study of Active Site Models

1999 ◽  
Vol 38 (11) ◽  
pp. 2658-2662 ◽  
Author(s):  
L. De Gioia ◽  
P. Fantucci ◽  
B. Guigliarelli ◽  
P. Bertrand
Keyword(s):  
Density Functional Theory ◽  
Active Site ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory

scholarly journals Determination of the Effect of Chalcogen Replacement on the Interaction Site and Transition State of the Substituted Analogues of Formaldehyde with Aldehyde Oxidase: A Density Functional Theory Approach

2019 ◽  
pp. 25-42
Author(s):  
Tadege Belay
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Active Site ◽  
Density Functional ◽  
Aldehyde Oxidase ◽  
Theory Approach ◽  
Functional Formalism ◽  
Functional Theory ◽  
Reported Data

Aldehyde oxidase (AO) enzyme is known to oxidize aldehydes. One of the aldehydes, formaldehyde, is known to inhibit xanthine oxidase as it turns over. However, there is no reported data whether it behaves the same when it reacts with aldehyde oxidase. Similarly, the effect of chalcogen replacement on nucleophilic reaction and charge density distribution on the substituted analogs of formaldehyde and their behavior during catalysis has never been studied. Therefore, the research is intended to probe the most tractable substrate that interacts to the reductive half-reaction active site of AO. Therefore, a density functional theory of the B3LYP correlation functional formalism (DFT-B3LYP) methods was used to generate several parameters from the electronic structure calculations. Accordingly, the higher percentage (%) contribution to HOMO and energy barrier (kcal/mol) (0.099, -7.185040E+04) makes formaldehyde as the favored substrate for aldehyde oxidase, compared to thioformaldehyde (-0.245, -2.745113E+05) and selenoformaldehyde (-0.175, -1.529992E+06), respectively. In addition, the transition state structures for the active site bound to formaldehyde (ACT-FA), thioformaldehyde (ACT-THIO FA), and selenoformaldehyde (ACT-SELENO FA), respectively, were confirmed by one imaginary negative frequency (S-1) (-328.44, -430.266, and -624.854).

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