A Theoretical Study on the Reaction Pathways of Peroxynitrite Formation and Decay at Nonheme Iron Centers Amr Ali Attia and Radu Silaghi-Dumitrescu* A computational study based on density functional theory was undertaken to identify possible reaction pathways for the for- mation and decomposition of peroxynitrite at models of the active sites of the nonheme superoxide scavenging enzymes superoxide reductase (SOR) and iron superoxide dismutase (FeSOD). Two peroxynitrite isomers and their possible proto- nated states were investigated, namely FeAOONO 2 , FeAN(O)OO 2 , FeAOONOH, and FeAN(O)OOH. Peroxynitrite formation at the active sites was assumed by either the inter- action of a peroxynitrite cis/trans anion with the pentacoordi- nated iron active site or the interaction between a nitric oxide bound adduct and superoxide; both scenarios were found to be facile for all models investigated. The ferrous adducts of the FeAOONO 2 isomer were found to undergo instant hetero- lytic cleavage of the OAONO bond to yield nitrite, whereas for the ferric adducts, the homolytic cleavage of the OAONO bond to yield nitrogen dioxide was found to be energetically facile. For the FeAN(O)OO 2 isomer, the active site models of FeSOD and SOR were only able to accommodate the cis iso- mer of peroxynitrite. Ferric adducts of the cis FeAOONO 2 iso- mer were found to be energetically more stable than their trans counterparts and were also more stable than the cis adducts of the FeAN(O)OO 2 isomer; conversely, the proto- nated forms of all adducts of the FeAOONOH isomer were found to be lower in energy than their equivalent FeAN(O)OOH adducts. Multiple reaction pathways for the decomposition of the formed peroxynitrite adducts (whether the anions or the protonated forms) were proposed and explored. The energy requirements for the decomposition processes ranged from exothermic to highly demanding depending on the peroxynitrite isomer, the type of model (whether an SOR or FeSOD active site), and the oxidation state of iron. VC 2014 Wiley Periodicals, Inc. DOI: 10.1002/qua.24650 Introduction Peroxynitrite, the anion with the chemical formula ONOO 2 , is an oxidant and nitrating agent capable of causing drastic dam- age to a wide range of molecules in the cell including DNA and proteins. [1–5] The formation of peroxynitrite is achieved in vivo by the reaction between the free radicals superoxide and nitric oxide [6] or, to a lesser extent, via the reaction of nitroxyl anion with molecular oxygen. [7] Superoxide reductases (SORs) and superoxide dismutases (SODs) are nonheme superoxide scavenging enzymes that cat- alyze the reduction and disproportionation of superoxide radi- cals, respectively. [8] In mononuclear iron SODs (FeSODs), two molecules of superoxide are converted to molecular oxygen and hydrogen peroxide via a mechanism that involves two half-reactions with the Fe ion cycling between the 13 and 12 formal oxidation state. [9,10] The active site of FeSOD consists of the Fe ion, three histidine residues (one axial and two equato- rial), and one equatorial aspartate residue. A water molecule occupies the axial position opposite to one of the histidines and completes the trigonal bipyramidal structure. The exact protonation states of the metal-bound water molecule were assigned by means of X-ray refinement to be a hydroxide ion in the oxidized state (Fe 31 ) and a water molecule in the reduced state (Fe 21 ). The superoxide molecule is said to bind associatively to the active site to form a six-coordinate octahedral intermediate as evidence from crystal structures and spectroscopic studies. [10–12] SORs, conversely, operate exclusively in anaerobic organisms where they efficiently reduce superoxide to hydrogen peroxide without the formation of oxygen as a byproduct. [13] The active site of mononuclear iron SOR consists of four equatorial histi- dine ligands alongside a cysteine thiolate ligated axially to an empty coordination position where binding of the substrate takes place. [13] The proposed catalytic cycle of SOR involves the binding of superoxide to the ferrous form of the active site, the formation of a ferric-hydroperoxo intermediate via the protonation of the distal oxygen atom, the protonation of the proximal oxygen, and the release of hydrogen peroxide then takes place after which the metal is reduced to its ferrous rest- ing state. [13] The interaction between peroxynitrite and heme active sites has gained much attention and is well-documented. [14–25] Pre- viously, we reported a density functional theory (DFT) study A. A. Attia, R. Silaghi-Dumitrescu Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, 11 Arany Janos Street, Cluj-Napoca RO-400028, Romania E-mail: rsilaghi@chem.ubbcluj.ro Contract grant sponsor: Romanian Ministry of Education and Research; contract grant number: PCCE 488/2012. VC 2014 Wiley Periodicals, Inc. 652 International Journal of Quantum Chemistry 2014, 114, 652–665 WWW.CHEMISTRYVIEWS.ORG FULL PAPER WWW.Q-CHEM.ORG