Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study.

The hydroxylase component (MMOH) of the multicomponent soluble methane monooxygenase (MMO) system catalyzes the oxidation of methane by dioxygen to form methanol and water at non-heme, dinuclear iron active sites. The catalytic cycle of MMOH is well established.1,2 Following reduction of the Fe(III)Fe(III) resting enzyme to the Fe(II)Fe(II) state, two spectroscopically observable intermediates, Hperoxo and Q, are formed upon reaction with dioxygen. Q is a high-valent Fe(IV)Fe(IV) species that oxidizes methane.3,4 Previously, we described the construction of a large-scale theoretical model (∼100 atoms) of the MMOH active site that energetically and structurally reproduced the species in the catalytic cycle.5 In the present paper, we use ab initio quantum chemical density functional (DFT) methods employing the B3LYP functional6,7 to examine the reaction by which intermediate Q converts methane to methanol. Computational methods and structural modeling strategies closely follow those of ref 5; computational details of the present work (e.g. basis sets) are given in Table S1. The theoretical structure determined previously for Q (Figure S1) resembles others in the literature in having a di-μ-oxo core with both iron atoms in the Fe(IV) oxidation state.3,8,9 Our Q structure differs from others in the literature, however, in that the water molecule bound to Fe1 is not displaced by Glu243,8,9 yielding a much lower energy than the alternatives. While modeling the reaction of Q with methane, we identified another structure for this intermediate that is 8.8 kcal/mol lower in energy than that reported previously.5 The new alternative Q structure, depicted in Figure 1, is nearly identical to the previous one except that the water molecule on Fe1 is hydrogen bonded to the other oxygen atom of Glu243. The new structure has key properties, including spin, charge, and Fe-Fe distance, that are comparable to those of the previous structure. Our investigation of the methane reaction reveals little difference when using either structure; below, we employ the structure in Figure 1 because it is lower in energy. The calculations began by first docking methane into the complex to form a transition state that would lead to methanol product. In contrast to earlier calculations,9 we considered only an approach to the core via a path opposite the two histidine residues, since a hydrophobic substrate binding cavity exists at this location in the full protein structure.10 After many alternatives failed to provide an energetically reasonable result, we concluded, as in refs 8 and 9, that the only way in which a reaction can take place is for methane to approach a bridging oxo atom in the core straight on. We rule out any possibility of direct involvement of the iron atoms in the catalytic process. The transition state is depicted in Figure 2. Our calculations predict an activation energy of 13.2 kcal/mole for the reaction, including an estimated zero point correction of 4.8 kcal/mole computed in ref 11. Over the past several years, a considerable amount of data have been accumulated concerning the kinetics of the methane reaction.2,4 A key issue, raised by the structure in Figure 2 as well as the experimental data and in previous theoretical modeling of MMO,8,9,11 is whether a radical rebound or a concerted mechanism is operative. Experiments with radical clock substrate probes employing MMOH from the M. capsulatus (Bath) system suggest that a radical rebound mechanism is not feasible, since the lifetime of the radical would have to be shorter than ∼150 fs to be consistent with the failure to observe radical-derived ring-opened products.12,13 Alternative experiments with ethane made chiral by virtue of the three isotopes of hydrogen yield a retention of configuration of ∼70%.14,15 Although the majority product argues † Columbia University. ‡ Massachusetts Institute of Technology. (1) Liu, K. E.; Lippard, S. J. AdV. Inorg. Chem. 1995, 42, 263-289. (2) Wallar, B. J.; Lipscomb, J. D. Chem. ReV. 1996, 96, 2625-2657. (3) Shu, L.; Nesheim, J. C.; Kauffmann, K.; Münck, E.; Lipscomb, J. D.; Que, L., Jr. Science 1997, 275, 515-517. (4) Valentine, A. M.; Stahl, S. S.; Lippard, S. J. J. Am. Chem. Soc. 1999, 121, 3876-3887. (5) Dunietz, B. D.; Beachy, M. D.; Cao, Y.; Whittington, D. A.; Lippard, S. J.; Friesner, R. A. J. Am. Chem. Soc. 2000, 122, 2828-2839. (6) Johnson, B. G.; Gill, P. M. W.; Pople, J. A. J. Chem. Phys. 1993, 98, 5612-5626. (7) Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377. (8) Siegbahn, P. E. M. Inorg. Chem. 1999, 38, 2880-2889. (9) Basch, H.; Mogi, K.; Musaev, D. G.; Morokuma, K. J. Am. Chem. Soc. 1999, 121, 7249-7256. (10) Rosenzweig, A. C.; Frederick, C. A.; Lippard, S. J.; Nordlund, P. Nature 1993, 366, 537-543. (11) Siegbahn, P. E. M.; Crabtree, R. H. J. Am. Chem. Soc. 1997, 119, 3103-3113. (12) Liu, K. E.; Johnson, C. C.; Newcomb, M.; Lippard, S. J. J. Am. Chem. Soc. 1993, 115, 939-947. (13) Choi, S.-Y.; Eaton, P. E.; Kopp, D. A.; Lippard, S. J.; Newcomb, M.; Shen, R. J. Am. Chem. Soc. 1999, 121, 12198-12199. (14) Priestley, N. D.; Floss, H. G.; Froland, W. A.; Lipscomb, J. D.; Williams, P. G.; Morimoto, H. J. Am. Chem. Soc. 1992, 114, 7561-7562. (15) Valentine, A. M.; Wilkinson, B.; Liu, K. E.; Komar-Panicucci, S.; Priestly, N. D.; Williams, P. G.; Morimoto, H.; Floss, H. G.; Lippard, S. J. J. Am. Chem. Soc. 1997, 119, 1818-1827. Figure 1. Core structure of the minimized lower energy, isomeric Q model. Numbers indicate bond distances (Å) and dashed lines indicate hydrogen bonding interactions. The Fe-Fe distance is 2.700 Å.