Mechanism of Nitrate Reduction by <i>Desulfovibrio desulfuricans</i> Nitrate Reductase—A Theoretical Investigation

Leopoldini, Monica; Russo, Nino; Toscano, Marirosa; Dułak, Marcin; Wesołowski, Tomasz Adam

doi:10.1002/chem.200500790

Cited by 73 publications

(88 citation statements)

References 77 publications

(91 reference statements)

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“…The former is in line with previous experimental 8,9 and theoretical 29,30 mechanistic suggestions, but requires a conformational rearrangement of the pseudo-dithiolene ligand to facilitate the access of the nitrate molecule to the molybdenum center.…”

Section: The Catalytic Reduction Mechanism Of Nitrate Into Nitritesupporting

confidence: 73%

The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase

et al. 2009

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The catalytic mechanism of nitrate reduction by periplasmic nitrate reductases has been investigated using theoretical and computational means. We have found that the nitrate molecule binds to the active site with the Mo ion in the +6 oxidation state. Electron transfer to the active site occurs only in the proton-electron transfer stage, where the Mo(V) species plays an important role in catalysis. The presence of the sulfur atom in the molybdenum coordination sphere creates a pseudo-dithiolene ligand that protects it from any direct attack from the solvent. Upon the nitrate binding there is a conformational rearrangement of this ring that allows the direct contact of the nitrate with Mo(VI) ion. This rearrangement is stabilized by the conserved methionines Met141 and Met308. The reduction of nitrate into nitrite occurs in the second step of the mechanism where the two dimethyl-dithiolene ligands have a key role in spreading the excess of negative charge near the Mo atom to make it available for the chemical reaction. The reaction involves the oxidation of the sulfur atoms and not of the molybdenum as previously suggested. The mechanism involves a molybdenum and sulfur-based redox chemistry instead of the currently accepted redox chemistry based only on the Mo ion. The second part of the mechanism involves two protonation steps that are promoted by the presence of Mo(V) species. Mo(VI) intermediates might also be present in this stage depending on the availability of protons and electrons. Once the water molecule is generated only the Mo(VI) species allow water molecule dissociation, and, the concomitant enzymatic turnover.

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Section: The Catalytic Reduction Mechanism Of Nitrate Into Nitritesupporting

confidence: 73%

The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase

et al. 2009

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“…[17] As shown in Figure S11 and S12, protonation occurs preferentially at one of the Natoms of the ligand with respect to the oxo group (À27.32 kcal mol À1 versus À12.61 kcal mol À1 ). This reaction facilitates the first oneelectron reduction (À16.49 kcal mol À1 versus 5.26 kcal mol À1 ).…”

Section: à019mentioning

confidence: 96%

A Bioinspired Molybdenum Complex as a Catalyst for the Photo‐ and Electroreduction of Protons

et al. 2015

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A molybdenum-dithiolene-oxo complex was prepared as a model of some active sites of Mo/W-dependent enzymes. The ligand, a quinoxaline-pyran-fused dithiolene, mimics molybdopterin present in these active sites. For the first time, this type of complex was shown to be active as a catalyst for the photoreduction of protons with excellent turnover numbers (500) and good stability in aqueous/organic media and for the electroreduction of protons in acetonitrile with remarkable rate constants (1030 s(-1) at -1.3 V versus Ag/AgCl). DFT calculations provided insight into the catalytic cycle of the reaction, suggesting that the oxo ligand plays a key role in proton exchange. These results provide a basis to optimize this new class of H2 -evolving catalysts.

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“…Only singlet reaction pathways were considered in the model, because in the previous studies on Desulfovibrio desulfuricans nitrate reductase (NAP) [12], a reaction pathway on the singlet potential energy surface was found to be energetically preferred over a mechanistically similar triplet pathway. This conclusion was also confirmed for EBDH in our preliminary studies [13].…”

Section: Computational Proceduresmentioning

confidence: 99%

Quantum chemical modeling studies of ethylbenzene dehydrogenase activity

Szaleniec

Salwiński

Borowski

et al. 2011

Int J of Quantum Chemistry

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Quantum chemical modeling is used to predict the reactivity of ethylbenzene dehydrogenase (EBDH), a molybdenum enzyme that catalyzes the stereoselective oxidation of alkylaromatic and alkylheterocyclic hydrocarbons to the (S)-enantiomers of secondary alcohols. The reaction mechanism is studied for four different substrates: ethylbenzene, 4-ethylphenol, allylbenzene, and 4-ethylpyridine with a cluster model of the active site. The modeling predicts radical CAH activation followed by the formation of a radical intermediate product. Then another electron is transferred to form a carbocation species in TS2, followed by a tightly associated OH rebound step. The modeling study allows qualitative correlation of energy barriers with the results of kinetic assays and identifies factors influencing the chemical reactivity of EBDH with different substrates.

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Mechanism of Nitrate Reduction by Desulfovibrio desulfuricans Nitrate Reductase—A Theoretical Investigation

Cited by 73 publications

References 77 publications

The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase

The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase

A Bioinspired Molybdenum Complex as a Catalyst for the Photo‐ and Electroreduction of Protons

Quantum chemical modeling studies of ethylbenzene dehydrogenase activity

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