The oxygen vacancy in bulk MgO and at its ͑001͒ surface have been studied by means of the EMBED program which adopts an embedded-cluster approach in the frame of the Hartree-Fock ͑HF͒ approximation ͓Comp. Phys. Comm. 82, 139 ͑1994͒; 96, 152 ͑1996͔͒: A spin restricted ͑RHF͒ or unrestricted ͑UHF͒ method has been used according to whether the vacancy contains an even number ͑F and F 2ϩ centers͒ or an odd number ͑F ϩ center͒ of electrons. The semi-infinite crystal has been simulated with a three-layer slab. Particular attention has been given to the optimization of the basis functions which serve to describe the trapped electron͑s͒ in the vacancy. The correlation energy was estimated using second order Mo "ller-Plesset theory. The three electronic configurations have been studied by allowing for relaxation of all neighboring ions. For the paramagnetic center, spin density data are provided and discussed with reference to results from EPR experiments and molecular cluster calculations.

The reduction of nitrite to nitric oxide in respiratory denitrification is catalyzed by a cytochrome cd(1) nitrite reductase in Paracoccus pantotrophus (formerly known as Thiosphaera pantotropha LMD 92.63). High-resolution structures are available for the fully oxidized [Fülöp, V., Moir, J. W., Ferguson, S. J., and Hajdu, J. (1995) Cell 81, 369-377; Baker, S. C., Saunders, N. F., Willis, A. C., Ferguson, S. J., Hajdu, J., and Fülöp, V. (1997) J. Mol. Biol. 269, 440-455] and fully reduced forms of this enzyme, as well as for various intermediates in its catalytic cycle [Williams, P. A., Fülöp, V., Garman, E. F., Saunders, N. F., Ferguson, S. J., and Hajdu, J. (1997) Nature 389, 406-412]. On the basis of these structures, quantum mechanical techniques (QM), including density functional methods (DFT), were combined with simulated annealing (SA) and molecular mechanics techniques (MM) to calculate the electronic distribution of molecular orbitals in the active site during catalysis. The results show likely trajectories for electrons, protons, substrates, and products in the process of nitrite reduction, and offer an interpretation of the reaction mechanism. The calculations indicate that the redox state of the d(1) heme and charges on two histidines in the active site orchestrate catalysis locally. Binding of nitrite to the reduced iron is followed by proton transfer from His345 and His388 to one of the oxygens of nitrite, creating a water molecule and an [Fe(II)-NO(+)] complex. Valence isomerization within this complex gives [Fe(III)-NO]. The release of NO from the ferric iron is influenced by the protonation state of His345 and His388, and by the orientation of NO on the d(1) heme. Return of Tyr25 to a hydrogen-bonding position between His345 and His388 facilitates product release, but a rebinding of Tyr25 to the oxidized iron may be bypassed in steady-state catalysis.

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