Theoretical Study of the Oxidation Reaction and Electron Spin Resonance Parameters Involving Sulfite Oxidase

Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase

We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.

QM/MM study of the reaction mechanism of sulfite oxidase

Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39–49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.

Acid-facilitated product release from a Mo(IV) center: relevance to oxygen atom transfer reactivity of molybdenum oxotransferases

We report that pyridinium ions (HPyr⁺) accelerate the conversion of [Tp*Mo^IVOCl(OPMe₃)] (1) to [Tp*Mo^IVOCl(NCCH₃)] (2) by 10³-fold, affording 2 in near-quantitative yield; Tp* = hydrotris(3,5-dimethyl-1-pyrazolyl)borate. This novel reactivity and the mechanism of this reaction were investigated in detail. The formation of 2 followed pseudo-first-order kinetics, with the observed pseudo-first-order rate constant (k _obs) linearly correlated with [HPyr⁺]. An Eyring plot revealed that this HPyr⁺-facilitated reaction has a small positive value of ∆S ^‡ indicative of a dissociative interchange (I_d) mechanism, different from the slower associative interchange (I_a) mechanism in the absence of HPyr⁺ marked with a negative ∆S ^‡. Interestingly, log(k _obs) was found to be linearly correlated to the acidity of substituted pyridinium ions. This novel reactivity is further investigated using combined DFT and ab initio coupled cluster methods. Different reaction pathways, including I_d, I_a, and possible alternative routes in the absence or presence of HPyr⁺, were considered, and enthalpy and free energies were calculated for each pathway. Our computational results further underscored that the I_d route is energetically favored in the presence of HPyr⁺, in contrast with the preferred I_a-NNO pathway in the absence of HPyr⁺. Our computational results also revealed molecular-level details for the HPyr⁺-facilitated I_d route. Specifically, HPyr⁺ initially becomes hydrogen-bonded to the oxygen atom of the Mo(IV)-OPMe₃ moiety, which lowers the activation barrier for the Mo-OPMe₃ bond cleavage in a rate-limiting step to dissociate the OPMe₃ product. The implications of our results were discussed in the context of molybdoenzymes, particularly the reductive half-reaction of sulfite oxidase.

Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes

The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.

A quantum-mechanical study of the reaction mechanism of sulfite oxidase

The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2.

Comparative calculation of EPR spectral parameters in [Mo(V)OX4]-, [Mo(V)OX5]2-, and [Mo(V)OX4(H2O)]- complexes

The EPR spectral parameters, i.e. g-tensors and molybdenum hyperfine couplings, for several d(1) systems of the general formula [Mo(V)EX(4)](n-), [Mo(V)OX(5)](2-), and [Mo(V)OX(4)(H(2)O)](-) (E = O, N; X = F, Cl, Br; n = 1 or 2) were calculated using Density Functional Theory. The influence of basis sets, their contraction scheme, the type of exchange-correlation functional, the amount of Hartree-Fock exchange, molecular geometry, and relativistic effects on the calculated EPR spectra parameters have been discussed. The g-tensors and molybdenum hyperfine coupling parameters were calculated using a relativistic Hamiltonian coupled with several LDA, GGA, and 'hybrid' exchange-correlation functionals and uncontracted full-electron DGauss DZVP basis sets. The calculated EPR parameters are found to be sensitive to the Mo=E distance and E=Mo-Cl angle, and thus the choice of starting molecular geometry should be considered as an important factor in predicting the g-tensors and hyperfine coupling constants in oxo-molybdenum compounds. In the present case, the GGA exchange-correlation functionals provide a better agreement between the theory and the experiment.