Theoretical modeling of the hydroxylation of methane as mediated by the particulate methane monooxygenase

Chen, Peter P.‐Y.; Chan, Sunney I.

doi:10.1016/j.jinorgbio.2005.12.014

Cited by 59 publications

(51 citation statements)

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“…Analysis by density functional theory of various mechanistic scenarios by Peter Chen confirmed that the proposed direct singlet oxene insertion mediated by the trinuclear copper cluster offered the most facile pathway for the alkane hydroxylation (29), and this mechanism yielded catalytic turnover rates and 1 H/ 2 H kinetic isotope effect values in close agreement with experiment.…”

Section: Particulate Methane Monooxygenase: a Membrane-bound Enzyme Tmentioning

confidence: 61%

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Chan

2009

Annu. Rev. Biophys.

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NMR of base-stacking interactions in nucleic acids in solution, dynamic structure of bilayer membranes, membrane biophysics, metal cofactor structure and function, redox linkage and proton pumping in cytochrome c oxidase, methane hydroxylation by the particulate methane monooxygenase, early kinetic events in protein folding AbstractDespite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

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Section: Particulate Methane Monooxygenase: a Membrane-bound Enzyme Tmentioning

confidence: 61%

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Chan

2009

Annu. Rev. Biophys.

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“…Experimentally, only (2R)-pentan-2-ol and (2S)-pentan-2-ol are observed (ee%80 %). [23] The tricopper cluster harnesses a "singlet oxene [9,10,35] In the activated tricopper cluster, the ligands on Cu1 are PmoA His38 and PmoC Glu154, the ligands on Cu2 are PmoA Asp47 and Met42, and the ligands on Cu3 are PmoA Asp49 and Glu100, aside from the bridging m-oxos. Cu3 has the hardest ligands, with one Asp ligand and one Glu ligand, and, hence, is more likely to be formally Cu III .…”

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“…[35] In these simulations, two neutral ammonia molecules were adopted as ligands for each of the copper ions in the tricopper complex. We compared three models of the putative active intermediate: 1) the above- ) and the frequency of the imaginary mode in the optimized structure of the transition state is much lower for the tricopper species than for the dicopper species (593i cm À1 versus 799i cm…”

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“…2 Cu III ] dicopper species at 300 K in the transient binary complexes that were formed between CH 4 and the corresponding catalytic copper intermediate. [35] Copper species complex shows a triad of copper ions that are arranged in an isosceles triangle and an oxo group that bridges the two basal copper ions (Figure 7). [36] The first prototype of the biomimetic tricopper models were constructed with L = 7-Me and 7-Et, with six neutral amines and two hydroxy groups.…”

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Development of the Tricopper Cluster as a Catalyst for the Efficient Conversion of Methane into MeOH

Chen

Nagababu

et al. 2013

ChemCatChem

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Following recent progress towards understanding the structure of the particulate methane monooxygenase in methanotrophic bacteria, it is now possible to attempt the development of laboratory catalysts for the conversion of methane into MeOH under ambient conditions. To this end, a class of tricopper complexes that are capable of efficiently oxidizing small hydrocarbon substrates at room temperature has recently been developed. In this Minireview, we describe the development of a tricopper cluster to accomplish the catalytic conversion of methane into MeOH, as well as a number of small n‐alkanes into their corresponding alcohols and ketones, with high efficiencies. The properties of this robust catalytic system are discussed.

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“…Although only two of the three reducing equivalents are required for hydroxylation chemistry, we have proposed that the third reducing equivalent in the hydroxylation cluster is required for efficient O-atom transfer based on the concerted singlet oxene insertion across the COH bond (3,13). Analysis of this process by density functional theory (DFT) has ensured that the oxo-transfer chemistry proceeds on a ''singlet'' reaction potential surface without spin crossover (13). This analysis also indicates that the putative trinuclear copper cluster offers a significantly more facile pathway for alkane hydroxylation compared with the traditional dinuclear copper cluster.…”

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Facile O-atom insertion into CC and CH bonds by a trinuclear copper complex designed to harness a singlet oxene

Chen

Yang

Lee

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Two trinuclear copper [Cu I Cu I Cu I (L)] 1؉ complexes have been prepared with the multidentate ligands (L) 3,3 -(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-Me) and (3,3 -(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-Et) as models for the active site of the particulate methane monooxygenase (pMMO). The ligands were designed to form the proper spatial and electronic geometry to harness a ''singlet oxene,'' according to the mechanism previously suggested by our laboratory. Consistent with the design strategy, both [Cu I Cu I Cu I (L)] 1؉ reacted with dioxygen to form a putative bis( 3-oxo)Cu II Cu II Cu III species, capable of facile O-atom insertion across the central COC bond of benzil and 2,3-butanedione at ambient temperature and pressure. These complexes also catalyze facile O-atom transfer to the COH bond of CH 3CN to form glycolonitrile. These results, together with our recent biochemical studies on pMMO, provide support for our hypothesis that the hydroxylation site of pMMO contains a trinuclear copper cluster that mediates COH bond activation by a singlet oxene mechanism. density functional theory ͉ methane monooxygenase ͉ membrane-bound or particulate methane monooxygenase ͉ soluble methane monooxygenase ͉ mass spectroscopy T here presently is considerable interest in the development of efficient catalysts for the facile conversion of methane to methanol (1). Industrially, this is a difficult process. However, two methane monooxygenases (MMO) are known to mediate this process in methanotrophic bacteria: a membrane-bound MMO called particulate MMO (pMMO) and a water-soluble form referred to as soluble MMO (sMMO) (2). pMMO is a multicopper protein (3), and sMMO is a nonheme diiron protein (4, 5). Both systems exploit metal clusters to catalyze this difficult chemistry.The pMMO is found in all methanotrophs; in contrast, the sMMO has only been isolated from certain strains of methanotrophic bacteria. As an MMO, the oxidation of the COH bond often is described by the chemical equationSeveral possible mechanisms for the catalytic function of MMO have been considered. One involves a radical mechanism, wherein an activated ''oxygen'' species abstracts a hydrogen atom from the hydrocarbon substrate, followed by radical-rebound chemistry of the alkyl radical with the ''hot'' hydroxyl radical to form product. This mechanism has been implicated for the nonheme diiron cluster at the active site of sMMO (6-8). The other mechanism suggested by our laboratory invokes oxenoid or ''singlet oxene'' insertion across the COH bond (3). Evidence for a direct insertion mechanism has been provided by the turnover chemistry mediated by pMMO (9-12). Direct insertion of a singlet oxene across a COH bond should result in facile bond closure of the COO bond after formation of the OOH bond, and the process should proceed with full retention of configuration at the carbon center oxidized.Indeed, the hydroxylation of small straight-chain alkanes (C1-C5) me...

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Theoretical modeling of the hydroxylation of methane as mediated by the particulate methane monooxygenase

Cited by 59 publications

References 31 publications

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Development of the Tricopper Cluster as a Catalyst for the Efficient Conversion of Methane into MeOH

Facile O-atom insertion into CC and CH bonds by a trinuclear copper complex designed to harness a singlet oxene

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