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Schulz C, Castillo RG, Pantazis DA, DeBeer S, Neese F. Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations. J Am Chem Soc 2021; 143:6560-6577. [PMID: 33884874 PMCID: PMC8154522 DOI: 10.1021/jacs.1c01180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/22/2022]
Abstract
The determination of the diiron core intermediate structures involved in the catalytic cycle of soluble methane monooxygenase (sMMO), the enzyme that selectively catalyzes the conversion of methane to methanol, has been a subject of intense interest within the bioinorganic scientific community. Particularly, the specific geometry and electronic structure of the intermediate that precedes methane binding, known as intermediate Q (or MMOHQ), has been debated for over 30 years. Some reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer Fe-Fe distance. The lack of consensus calls for a thorough re-examination and reinterpretation of the spectroscopic data available on the MMOHQ intermediate. Herein, we report extensive simulations based on a hybrid quantum mechanics/molecular mechanics approach (QM/MM) approach that takes into account the complete enzyme to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum chemical approaches are used to correlate specific structural motifs with geometric parameters for comparison with crystallographic and EXAFS data, as well as with spectroscopic data from Mössbauer spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy (HERFD XAS), and resonance Raman 16O-18O difference spectroscopy. The results provide strong support for an open-core-type configuration in MMOHQ, with the most likely topology involving mono-oxo-bridged Fe ions and alternate terminal Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen bonding. The implications of an open-core intermediate Q on the reaction mechanism of sMMO are discussed.
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Affiliation(s)
- Christine
E. Schulz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G. Castillo
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Ansari A, Ansari M, Singha A, Rajaraman G. Interplay of Electronic Cooperativity and Exchange Coupling in Regulating the Reactivity of Diiron(IV)-oxo Complexes towards C−H and O−H Bond Activation. Chemistry 2017; 23:10110-10125. [DOI: 10.1002/chem.201701059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Azaj Ansari
- Department of Chemistry; CUH Haryana; Haryana 123031 India
| | | | - Asmita Singha
- Department of Chemistry; IIT Bombay; Mumbai 400076 India
| | - Gopalan Rajaraman
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai, Maharashtra 400076 India
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3
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Janssen FFBJ, Peters LCJM, Schlebos PPJ, Smits JMM, de Gelder R, Rowan AE. Uncorrelated Dynamical Processes in Tetranuclear Carboxylate Clusters Studied by Variable-Temperature 1H NMR Spectroscopy. Inorg Chem 2013; 52:13004-13. [DOI: 10.1021/ic401522v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Femke F. B. J. Janssen
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Laurens C. J. M. Peters
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul P. J. Schlebos
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jan M. M. Smits
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - René de Gelder
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alan E. Rowan
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Yoshizawa K. Quantum Chemical Studies on Dioxygen Activation and Methane Hydroxylation by Diiron and Dicopper Species as well as Related Metal–Oxo Species. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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5
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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6
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Pérez LM, Webster CE, Low AA, Hall MB. Theoretical study of the biologically important dioxo diiron diamond core structures. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0438-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rinaldo D, Philipp DM, Lippard SJ, Friesner RA. Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. J Am Chem Soc 2007; 129:3135-47. [PMID: 17326634 PMCID: PMC2517126 DOI: 10.1021/ja0654074] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein effects in the activation of dioxygen by methane monooxygenase (MMO) were investigated by using combined QM/MM and broken-symmetry Density Functional Theory (DFT) methods. The effects of a novel empirical scheme recently developed by our group on the relative DFT energies of the various intermediates in the catalytic cycle are investigated. Inclusion of the protein leads to much better agreement between the experimental and computed geometric structures for the reduced form (MMOH(red)). Analysis of the electronic structure of MMOH(red) reveals that the two iron atoms have distinct environments. Different coordination geometries tested for the MMOH(peroxo) intermediate reveal that, in the protein environment, the mu-eta2,eta2 structure is more stable than the others. Our analysis also shows that the protein helps to drive reactants toward products along the reaction path. Furthermore, these results demonstrate the importance of including the protein environment in our models and the usefulness of the QM/MM approach for accurate modeling of enzymatic reactions. A discrepancy remains in our calculation of the Fe-Fe distance in our model of HQ as compared to EXAFS data obtained several years ago, for which we currently do not have an explanation.
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Noodleman L, Lovell T, Han WG, Li J, Himo F. Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 2004; 104:459-508. [PMID: 14871132 DOI: 10.1021/cr020625a] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Yumura T, Yoshizawa K. A Vibrational Analysis on Possible Peroxo Forms of Soluble Methane Monooxygenase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.1305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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Hudáky P, Perczel A. Conformation Dependence of pKa: Ab Initio and DFT Investigation of Histidine. J Phys Chem A 2004. [DOI: 10.1021/jp048964q] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ito M, Re S, Tokiwa H. Ab Initio Molecular Orbital Investigation of a Precursor in Ethylene Biosynthesis: Proton Transfer in a Cluster of 1-Aminocyclopropane-1-carboxylic Acid and Water. J Phys Chem A 2004. [DOI: 10.1021/jp031146y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mika Ito
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
| | - Suyong Re
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
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Noradoun C, Engelmann MD, McLaughlin M, Hutcheson R, Breen K, Paszczynski A, Cheng IF. Destruction of Chlorinated Phenols by Dioxygen Activation under Aqueous Room Temperature and Pressure Conditions. Ind Eng Chem Res 2003. [DOI: 10.1021/ie030076e] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Baik MH, Newcomb M, Friesner RA, Lippard SJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev 2003; 103:2385-419. [PMID: 12797835 DOI: 10.1021/cr950244f] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Baik MH, Gherman BF, Friesner RA, Lippard SJ. Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q. J Am Chem Soc 2002; 124:14608-15. [PMID: 12465971 DOI: 10.1021/ja026794u] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The electronic structures of key species involved in methane hydroxylation performed by the hydroxylase component of soluble methane monooxygenase (sMMO), as proposed previously on the basis of high-level density functional theory, were investigated. The reaction starts with initial approach of methane at one of the bridging oxo atoms in intermediate Q, a di(mu-oxo)diiron(IV) unit. This step is accompanied by a proton-coupled outer-sphere transfer of the first electron from a C-H sigma-bond in methane to one of the metal centers. The second electron transfer, also an outer-sphere electron transfer process, occurs along a two-component reaction pathway. Both redox reactions are strongly coupled to structural distortions of the diiron core. The electronic consequence and driving force of these distortions are intuitively explained by using the computed Kohn-Sham orbitals in the broken-symmetry framework to incorporate the experimentally observed antiferromagnetic coupling of the unpaired electrons at the metal centers. The broken-symmetry orbital scheme is essential for describing the C-H bond activation process in a consistent and complete manner, enabling derivation of both an intuitive and quantitative understanding of the most salient electronic features that govern the details of the hydroxylation.
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Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Musaev DG, Basch H, Morokuma K. Theoretical study of the mechanism of alkane hydroxylation and ethylene epoxidation reactions catalyzed by diiron bis-oxo complexes. The effect of substrate molecules. J Am Chem Soc 2002; 124:4135-48. [PMID: 11942853 DOI: 10.1021/ja0176393] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The hybrid density functional method B3LYP was used to study the mechanism of the hydrocarbon (methane, ethane, methyl fluoride, and ethylene) oxidation reaction catalyzed by the complexes cis-(H(2)O)(NH(2))Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(NH(2))(H(2)O), I, and cis-(HCOO)(Imd)Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(Imd)(HCOO) (Imd = Imidazole), I_m, the "small" and "medium" model of compound Q of the methane monooxygenase (MMO). The improvement of the model from "small" to "medium" did not change the qualitative conclusions but significantly changed the calculated energetics. As in the case of methane oxidation reported by the authors previously, the reaction of all the substrates studied here is shown to start by coordination of the substrate molecule to the bridging oxygen atom, O(1) of I, an Fe(IV)-Fe(IV) complex, followed by the H-atom abstraction at the transition state III leading to the bound hydroxy alkyl intermediate IV of Fe(III)-Fe(IV) core. IV undergoes a very exothermic coupling of alkyl and hydroxy groups to give the alcohol complex VI of Fe(III)-Fe(III) core, from which alcohol dissociates. The H(b)-atom abstraction (or C-H bond activation) barrier at transition state III is found to be a few kcal/mol lower for C(2)H(6) and CH(3)F than for CH(4). The calculated trend in the H(b)-abstraction barrier, CH(4) (21.8 kcal/mol) > CH(3)F (18.8 kcal/mol) > or = C(2)H(6) (18.5 kcal/mol), is consistent with the C-H(b) bond strength in these substrates. Thus, the weaker the C-H(b) bond, the lower is the H(b)-abstraction barrier. It was shown that the replacement of a H-atom in a methane molecule with a more electronegative group tends to make the H(b)-abstraction transition state less "reactant-like". In contrast, the replacement of the H-atom in CH(4) with a less electronegative group makes the H(b)-abstraction transition state more "reactant-like". The epoxidation of ethylene by complex I is found to proceed without barrier and is a highly exothermic process. Thus, in the reaction of ethylene with complex I the only product is expected to be ethylene oxide, which is consistent with the experiment.
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Affiliation(s)
- Djamaladdin G Musaev
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Torrent M, Musaev DG, Basch H, Morokuma K. Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase. J Comput Chem 2002; 23:59-76. [PMID: 11913390 DOI: 10.1002/jcc.1157] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An overview of the computational efforts made by our group during the last few years in the field of nonheme diiron proteins is presented. Through application of ab initio methodology to a reasonable set of molecular models, significant progress is made in understanding how the soluble Methane Monooxygenase system achieves the hydroxylation of methane and how the catalytic cycle of Ribonucleotide Reductase is initiated. In particular, the current studies reveal in more detail (1) the nature of key intermediates in the reaction cycles of these two metalloenzymes, (2) details of how the iron centers regulate the systems, and (3) important aspects of how the carboxylate ligands in the active sites may tailor the enzymatic needs of the metalloprotein. This knowledge also leads to novel connections between the two enzymes. The coordinative unsaturation and carboxylate shifts investigated herein are two properties that are likely to be of more general impact in nonheme proteins. The control of the redox chemistry of the enzyme by the binuclear metal center, also analyzed here, should find common ground among other bimetallic systems as well.
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Affiliation(s)
- Maricel Torrent
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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