A comparative DFT study of substrates and products of industrial enzyme nitrile hydratase

Abstract

ABSTRACT:Nitrile hydratase (NHase) is a metalloenzyme used in industrial biotechnology for a large scale production of common chemicals. NHases convert nitriles to the corresponding amides. Although the structures of some forms of NHases containing nonheme low spin Fe(III) or low spin noncorrinoid Co(III) are known, neither a catalytic mechanism nor the reasons of high selectivity towards aromatic ligands are recognized. Optimized geometries, molecular electrostatic potential maps and infrared spectra of commercially important aromatic substrates of the NHase (nicotinonitrile, o-, m-, p-methylbenzonitrile) and the corresponding products (nicotinamide, o-, m-, p-methylbenzamid) were investigated using the density functional theory method with the B3LYP functional and the 6-31G(d,p) basis set. Calculated hypothetical intrinsic reaction paths indicate that benzimidic acids may be involved as intermediates. This study elucidates differences in the electronic properties of substrates and products of NHases, provides an insight into the molecular basis of the catalytic reaction and helps to explain varying enzymatic activities of microbial NHases.

Molecular Dynamics Simulations of the Photoactive Protein Nitrile Hydratase

“…Our data on the water dynamics further support this hypothesis. However, the presence of an imidate intermediate is suggested by recent quantum chemical DFT calculations of reaction paths (7,86).…”

Controlled Sulfur Oxygenation of the Ruthenium Dithiolate (4,7-Bis-(2′-methyl-2′-mercaptopropyl)-1-thia-4,7-diazacyclononane)RuPPh3 under Limiting O2 Conditions Yields Thiolato/Sulfinato, Sulfenato/Sulfinato, and Bis-Sulfinato Derivatives

“…Geometry optimization and subsequent molecular orbital (MO) analysis of complexes 1 − 4 were performed using the Gaussian 03 suite of programs. Density functional theory (DFT) calculations employed the BP86 , and B3LYP − functionals. For these calculations, the LANL2DZ basis set was used for the Ru atom while the 6-31G(d) basis set was applied for all other atoms.…”