1
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Gałyńska M, de Moraes MMF, Tecmer P, Boguslawski K. Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study. Phys Chem Chem Phys 2024; 26:18918-18929. [PMID: 38952220 DOI: 10.1039/d4cp01500b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO3- substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo-O bond formation using orbital-based quantum information measures, which highlight the flow of σM-O bond formation and σN/S-O bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants.
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Affiliation(s)
- Marta Gałyńska
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Matheus Morato F de Moraes
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
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2
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Oxygen atom transfer catalysis by dioxidomolybdenum(VI) complexes of pyridyl aminophenolate ligands. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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3
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Synthesis, structural insights and catalytic activity of a dioxidomolybdenum(VI) complex chelated with N4-(3-methoxyphenyl) thiosemicarbazone. TRANSIT METAL CHEM 2020. [DOI: 10.1007/s11243-020-00398-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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4
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The oxygen-atom transfer reactions of Mo-diselenolene biomimetic complexes: A computational investigation. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Dong G, Ryde U. Effect of the protein ligand in DMSO reductase studied by computational methods. J Inorg Biochem 2017; 171:45-51. [DOI: 10.1016/j.jinorgbio.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/07/2017] [Accepted: 03/19/2017] [Indexed: 11/27/2022]
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6
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Bushnell EA. A computational investigation into the catalytic activity of a diselenolene sulfite oxidase biomimetic complex. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molybdenum is the only 4d metal found in almost all life. One such molybdenum-containing enzyme is sulfite oxidase, which also contains the dithiolene-molybdopterin ligand. Sulfite oxidase is essential in the degradation of sulfur-containing compounds such as cysteine and methionine. Past work has shown parallels in the chemistry of dithiolene–metal and diselenolene–metal complexes. Thus, in this present work, the oxygen atom transfer mechanism for a diselenolene sulfite oxidase biomimetic complex was investigated using computational tools, the results of which were compared to the analogous dithiolene biomimetic complex. From the results obtained, the molybdenum-diselenolene sulfite oxidase biomimetic complex is able to catalyse the oxygen atom transfer and does so with a marginally lower value of ΔrG‡ than that for the analogous dithiolene complex. In particular, it was found that on average, the diselenolene complex had an activation energy 1.2 kJ mol–1 lower in energy than the analogous dithiolene complex. However, the calculated value of ΔrG suggests that the oxidation of sulfite is more favourable for the dithiolene complex where the average difference in reaction aqueous Gibbs reaction energy was –9.4 kJ mol–1 relative to the diselenolene complex. It is noted that with the use of D3 and D3BJ corrections in combination with the B3LYP functional, the barrier for oxygen atom transfer is lowered by more than 30.0 kJ mol–1 for both the diselenolene and dithiolene complexes. Such results suggest that to study such oxo-transfer reactions, the proper treatment of dispersion interaction is necessary.
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Affiliation(s)
- Eric A.C. Bushnell
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, MB R7A 6A9, Canada
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, MB R7A 6A9, Canada
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7
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Hu L, Chen H. Assessment of DFT Methods for Computing Activation Energies of Mo/W-Mediated Reactions. J Chem Theory Comput 2015; 11:4601-14. [DOI: 10.1021/acs.jctc.5b00373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lianrui Hu
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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8
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Li J, Andrejić M, Mata RA, Ryde U. A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500209] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Duman S, Kizilcikli İ, Ülküseven B. Dioxomolybdenum(VI) Complexes of 5-Bromo/3,5-Dibromo-Salicylaldehyde 4-(H/C6H5)-S-Propyl-Thiosemicarbazones. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2014.947406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Songül Duman
- Department of Chemistry, Istanbul University, 34320 Avcılar, Istanbul, Turkey
| | - İrfan Kizilcikli
- Department of Chemistry, Istanbul University, 34320 Avcılar, Istanbul, Turkey
| | - Bahri Ülküseven
- Department of Chemistry, Istanbul University, 34320 Avcılar, Istanbul, Turkey
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10
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Andrejić M, Mata RA. Local Hybrid QM/QM Calculations of Reaction Pathways in Metallobiosites. J Chem Theory Comput 2014; 10:5397-404. [DOI: 10.1021/ct5008313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milica Andrejić
- Institut
für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institut
für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077 Göttingen, Germany
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11
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Li J, Ryde U. Comparison of the Active-Site Design of Molybdenum Oxo-Transfer Enzymes by Quantum Mechanical Calculations. Inorg Chem 2014; 53:11913-24. [DOI: 10.1021/ic5010837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jilai Li
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical and
Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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12
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DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme. J Inorg Biochem 2014; 142:84-91. [PMID: 25450022 DOI: 10.1016/j.jinorgbio.2014.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.
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13
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Ha Y, Tenderholt AL, Holm RH, Hedman B, Hodgson KO, Solomon EI. Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on monooxo Mo(IV) and bisoxo Mo(VI) bis-dithiolenes: insights into the mechanism of oxo transfer in sulfite oxidase and its relation to the mechanism of DMSO reductase. J Am Chem Soc 2014; 136:9094-105. [PMID: 24884723 PMCID: PMC4073832 DOI: 10.1021/ja503316p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 12/25/2022]
Abstract
Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [Mo(IV)O(bdt)2](2-) and [Mo(VI)O2(bdt)2](2-) (bdt = benzene-1,2-dithiolate(2-)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P-S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal-oxo and substrate-oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover.
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Affiliation(s)
- Yang Ha
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Adam L. Tenderholt
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Richard H. Holm
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Britt Hedman
- Stanford
Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford
Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, United States
| | - Edward I. Solomon
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford
Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, United States
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14
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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15
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de Visser SP, Quesne MG, Martin B, Comba P, Ryde U. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. Chem Commun (Camb) 2014; 50:262-82. [DOI: 10.1039/c3cc47148a] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Moula G, Bose M, Sarkar S. Replica of a Fishy Enzyme: Structure–Function Analogue of Trimethylamine-N-Oxide Reductase. Inorg Chem 2013; 52:5316-27. [DOI: 10.1021/ic4002576] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Golam Moula
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur-208016,
Uttar Pradesh, India
| | - Moumita Bose
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur-208016,
Uttar Pradesh, India
| | - Sabyasachi Sarkar
- Department
of Chemistry, Bengal Engineering and Science University, Shibpur,
Botanic Garden, Howrah 711103, West Bengal, India
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17
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Li JL, Mata RA, Ryde U. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction. J Chem Theory Comput 2013; 9:1799-807. [DOI: 10.1021/ct301094r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ji-Lai Li
- Department of Theoretical Chemistry,
Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin
University, Changchun 130023, People’s Republic of China
| | - Ricardo A. Mata
- Institut für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077, Göttingen, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry,
Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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18
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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19
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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20
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Tenderholt AL, Hodgson KO, Hedman B, Holm RH, Solomon EI. Substrate and metal control of barrier heights for oxo transfer to Mo and W bis-dithiolene sites. Inorg Chem 2012; 51:3436-42. [PMID: 22372518 DOI: 10.1021/ic2020397] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reaction coordinates for oxo transfer from the substrates Me(3)NO, Me(2)SO, and Me(3)PO to the biologically relevant Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)(2)](-) where mdt = 1,2-dimethyl-ethene-1,2-dithiolate(2-), and from Me(2)SO to the analogous W(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X-O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction.
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Affiliation(s)
- Adam L Tenderholt
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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21
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Recent Developments in Computational Bioinorganic Chemistry. STRUCTURE AND BONDING 2012. [DOI: 10.1007/b97941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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22
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Arumuganathan T, Volpe M, Harum B, Wurm D, Belaj F, Mösch-Zanetti NC. Unusual Nonoctahedral Geometry with Molybdenum Oxoimido Complexes Containing η2-Pyrazolate Ligands. Inorg Chem 2011; 51:150-6. [DOI: 10.1021/ic201308g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- T. Arumuganathan
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
| | - Manuel Volpe
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
| | - Bastian Harum
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
| | - Dietmar Wurm
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
| | - Ferdinand Belaj
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
| | - Nadia C. Mösch-Zanetti
- Institut für Chemie, Anorganische
Chemie, Karl-Franzens-Universität Graz, Stremayrgasse
16, A-8010 Graz, Austria
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23
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Mtei RP, Lyashenko G, Stein B, Rubie N, Hille R, Kirk ML. Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity. J Am Chem Soc 2011; 133:9762-74. [PMID: 21648481 PMCID: PMC3142581 DOI: 10.1021/ja109178q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.
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Affiliation(s)
- Regina P Mtei
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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24
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25
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Affiliation(s)
- Carola Schulzke
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
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26
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Tenderholt AL, Wang JJ, Szilagyi RK, Holm RH, Hodgson KO, Hedman B, Solomon EI. Sulfur K-edge X-ray absorption spectroscopy and density functional calculations on Mo(IV) and Mo(VI)=O bis-dithiolenes: insights into the mechanism of oxo transfer in DMSO reductase and related functional analogues. J Am Chem Soc 2010; 132:8359-71. [PMID: 20499905 DOI: 10.1021/ja910369c] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two Mo bis-dithiolene complexes, [Mo(OSi)(bdt)(2)](1-) and [MoO(OSi)(bdt)(2)](1-), where OSi = [OSiPh(2)(t)Bu](1-) and bdt = benzene-1,2-dithiolate(2-), that model the Mo(IV) and Mo(VI)=O states of the DMSO reductase family of molybdenum enzymes. These results show that the Mo(IV) complex undergoes metal-based oxidation unlike Mo tris-dithiolene complexes, indicating that the dithiolene ligands are behaving innocently. Experimentally validated calculations have been extended to model the oxo transfer reaction coordinate using dimethylsulfoxide (DMSO) as a substrate. The reaction proceeds through a transition state (TS1) to an intermediate with DMSO weakly bound, followed by a subsequent transition state (TS2) which is the largest barrier of the reaction. The factors that control the energies of these transition states, the nature of the oxo transfer process, and the role of the dithiolene ligand are discussed.
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Affiliation(s)
- Adam L Tenderholt
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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27
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Hernandez-Marin E, Ziegler T. A kinetic study of dimethyl sulfoxide reductase based on density functional theory. CAN J CHEM 2010. [DOI: 10.1139/v09-136] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present a density functional theory study on the oxygen atom transfer (OAT) reaction of dimethyl sulfoxide (DMSO) with model complexes resembling a functional synthetic analogue of the molybdoenzyme DMSO reductase. The good agreement between our calculated Gibbs free energy profile and data derived from experimental kinetic parameters supports the reaction mechanisms of the oxygen atom transfer proposed in this study. When the mechanism involves the formation of a DMSO-bound intermediate, the calculations on the free energy surface provide valuable information that explains the origin of the apparent contradiction between the experimental findings and previous theoretical calculations with respect to the rate-limiting step of the reaction mechanism. The enzymatic mechanism of the OAT reaction is more complex than the mechanism of any synthetic analogue, mainly due to the formation of an enzyme-substrate adduct prior to the appearance of the substrate-bound intermediate. This study also presents a possible mechanism for the formation of such an adduct and the subsequent oxygen atom transfer. The mechanism involves a proton transfer to and from the substrate.
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Affiliation(s)
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary, AB T2N 1N4, Canada
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Szaleniec M, Borowski T, Schühle K, Witko M, Heider J. Ab Inito Modeling of Ethylbenzene Dehydrogenase Reaction Mechanism. J Am Chem Soc 2010; 132:6014-24. [DOI: 10.1021/ja907208k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Szaleniec
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Karola Schühle
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Malgorzata Witko
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Johann Heider
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
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29
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Ryde U, Schulzke C, Starke K. Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study. J Biol Inorg Chem 2009; 14:1053-64. [PMID: 19479286 PMCID: PMC3085732 DOI: 10.1007/s00775-009-0548-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 05/01/2009] [Indexed: 11/29/2022]
Abstract
A density functional theory study of the influence of the various functional groups of the molybdopterin ligand on electronic and geometric properties of active-site models for the molybdenum and tungsten cofactors has been undertaken. We used analogous molybdenum and tungsten complexes with increasingly accurate representation of the molybdopterin ligands and compared bond lengths, angles, charge distribution, composition of the binding orbitals, as well as the redox potentials in relation to each other. On the basis of our findings, we suggest using ligand systems including the pyrane and the pyrazine rings, besides the dithiolene function, to obtain sufficiently reliable computational, but also synthetic, models for the molybdenum and tungsten cofactors, whereas the second ring of the pterin might be neglected for efficiency reasons.
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Affiliation(s)
- Ulf Ryde
- Department of Theoretical Chemistry, Chemical Center, Lund University, 124, 221 00 Lund, Sweden
| | - Carola Schulzke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
| | - Kerstin Starke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
- Department of Chemical Physics, Chemical Center, Lund University, 124, 221 00 Lund, Sweden
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30
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Antony S, Bayse CA. Theoretical Studies of Models of the Active Site of the Tungstoenzyme Acetylene Hydratase. Organometallics 2009. [DOI: 10.1021/om900230x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonia Antony
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529
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31
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Nomura M, Kanamori M, Yamaguchi Y, Tateno N, Fujita-Takayama C, Sugiyama T, Kajitani M. Hydrogen bonding interaction of CpCo(Dithiolene) complex with monocyclic 2-pyridonyl substituent and unexpected formation of dithiolene-fused tricyclic pyridone derivative. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Ilhan Ceylan, B, Dasdemir Kurt, Y, Ulkuseven, B. Synthesis and Characterization of Dioxomolybdenum(VI) Chelates with Dibasic Form of 5-Bromo-2-Hydroxybenzophenone S-Methyl/Ethyl-4-Phenyl-Thiosemicarbazones. REV INORG CHEM 2009. [DOI: 10.1515/revic.2009.29.1.49] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Ceylan Bİ, Kurt YD, Ülküseven B. Synthesis and characterization of new dioxomolybdenum(VI) complexes derived from benzophenone-thiosemicarbazone (H2L). Crystal structure of [MoO2L(PrOH)]. J COORD CHEM 2009. [DOI: 10.1080/00958970802339669] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Berat İlhan Ceylan
- a Department of Chemistry , Istanbul University , 34320, Avcılar, Istanbul, Turkey
| | | | - Bahrı Ülküseven
- a Department of Chemistry , Istanbul University , 34320, Avcılar, Istanbul, Turkey
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34
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Hernandez-Marin E, Ziegler T. Theoretical Study of the Oxidation Reaction and Electron Spin Resonance Parameters Involving Sulfite Oxidase. Inorg Chem 2009; 48:1323-33. [DOI: 10.1021/ic801158t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth Hernandez-Marin
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
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35
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Lyashenko G, Saischek G, Judmaier ME, Volpe M, Baumgartner J, Belaj F, Jancik V, Herbst-Irmer R, Mösch-Zanetti NC. Oxo-molybdenum and oxo-tungsten complexes of Schiff bases relevant to molybdoenzymes. Dalton Trans 2009:5655-65. [DOI: 10.1039/b820629e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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Pal K, Sarkar S. The Role of Axial Ligation in Nitrate Reductase: A Model Study by DFT Calculations on the Mechanism of Nitrate Reduction. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Hofmann M. Electronic State of the Dimethyl Sulfoxide Reductase Active Site. Inorg Chem 2008; 47:5546-8. [DOI: 10.1021/ic800519d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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38
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Tenderholt AL, Szilagyi RK, Holm RH, Hodgson KO, Hedman B, Solomon EI. Electronic control of the "Bailar twist" in formally d0-d2 molybdenum tris(dithiolene) complexes: a sulfur K-edge X-ray absorption spectroscopy and density functional theory study. Inorg Chem 2008; 47:6382-92. [PMID: 18517189 DOI: 10.1021/ic800494h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of a series of Mo tris(dithiolene) complexes, [Mo(mdt)3](z) (where mdt = 1,2-dimethylethene-1,2-dithiolate(2-) and z = 2-, 1-, 0), with near trigonal-prismatic geometries (D3h symmetry). These results show that the formally Mo(IV), Mo(V), and Mo(VI) complexes actually have a (dz(2))(2) configuration, that is, remain effectively Mo(IV) despite oxidation. Comparisons with the XAS data of another set of Mo tris(dithiolene) complexes, [Mo(tbbdt)3](z) (where tbbdt = 3,5-ditert-butylbenzene-1,2-dithiolate(2-) and z = 1-, 0), show that both neutral complexes, [Mo(mdt)3] and [Mo(tbbdt)3], have similar electronic structures while the monoanions do not. Calculations reveal that the "Bailar twist" present in the crystal structure of [Mo(tbbdt)3](1-) (D3 symmetry) but not [Mo(mdt)3](1-) (D3h symmetry) is controlled by electronic factors which arise from bonding differences between the mdt and tbbdt ligands. In the former, configuration interaction between the Mo d(z(2)) and a deeper energy, occupied ligand orbital, which occurs in D3 symmetry, destabilizes the Mo d(z(2)) to above another ligand orbital which is half-occupied in the D3h [Mo(mdt)3](1-) complex. This leads to a metal d(1) configuration with no ligand holes (i.e., d(1)[L3](0h)) for [Mo(tbbdt)3](1-) rather than the metal d(2) configuration with one ligand hole (i.e., d(2)[L3](1h)) for [Mo(mdt)3](1-). Thus, the Bailar twist observed in some metal tris(dithiolene) complexes is the result of configuration interaction between metal and ligand orbitals and can be probed experimentally by S K-edge XAS.
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Affiliation(s)
- Adam L Tenderholt
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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39
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Lyashenko G, Herbst-Irmer R, Jancik V, Pal A, Mösch-Zanetti NC. Molybdenum oxo and imido complexes of beta-diketiminate ligands: synthesis and structural aspects. Inorg Chem 2008; 47:113-20. [PMID: 18072764 DOI: 10.1021/ic701534a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Treatment of [MoO2(eta2-Pz)2] (Pz = 3,5-di-tert-butylpyrazolate) with the diketiminate ligand NacNacH (NacNac = CH[C(Me)NAr]2-, Ar = 2,6-Me2C6H3) at 55 degrees C leads under reduction of the metal to the formation of the dimeric molybdenum(V) compound [{MoO2(NacNac)}2] (1). The compound was characterized by spectroscopic means and by X-ray crystal structure analysis. The dimer consists of a [Mo2O4]2+ core with a short Mo-Mo bond (2.5591(5) A) and one coordinated diketiminate ligand on each metal atom. The reaction of [MoO2(eta2-Pz)2] with NacNacH in benzene at room temperature leads to a mixture of 1 and the monomeric molybdenum(VI) compound [MoO2(NacNac)(eta2-Pz)] (2). From such solutions, yellow crystals of 2 suitable for X-ray structural analysis were obtained revealing the coordination of one bidentate NacNac and one eta2-coordinate Pz ligand. This renders the two oxo groups inequivalent. Further high oxidation state molybdenum compounds containing the NacNac ligand were obtained by the reaction of [Mo(NAr)2Cl2(dme)] (Ar = 2,6-Me2C6H3) and [Mo(N-t-Bu)2Cl2(dme)] (dme = dimethoxyethane) with 1 equiv of the potassium salt NacNacK forming [Mo(NAr)2Cl(NacNac)] (3) and [Mo(N-t-Bu)2Cl(NacNac)] (4), respectively, in good yields. The X-ray structure analysis of 3 revealed a penta-coordinate compound where the geometry is best described as trigonal-bipyramidal.
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Affiliation(s)
- Ganna Lyashenko
- Institut für Chemie, Karl-Franzens-Universität Graz, Schubertstrasse 1, A-8010, Graz, Austria
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40
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Kurt YD, Pozan GS, Kızılcıklı İ, Ülküseven B. Dioxomolybdenum(VI) complexes of 2-hydroxybenzaldehyde 4-phenyl-S-methylthiosemicarbazone. RUSS J COORD CHEM+ 2007. [DOI: 10.1134/s1070328407110097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Sugimoto H, Tarumizu M, Miyake H, Tsukube H. Synthesis and Characterization of Bis(dithiolene) Tungsten(VI), -(V), and -(IV) Complexes and Their Reactivities in Coupled Electron–Proton Transfer: A New Series of Active Site Models of Tungstoenzymes. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700602] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Pal K, Chaudhury PK, Sarkar S. Structure of the Michaelis Complex and Function of the Catalytic Center in the Reductive Half-Reaction of Computational and Synthetic Models of Sulfite Oxidase. Chem Asian J 2007; 2:956-64. [PMID: 17600788 DOI: 10.1002/asia.200700020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
By using frontier-molecular-orbital and electrostatic (nucleophilic) interactions as well as relaxed potential-energy surface scans, it is shown that the initial step in the oxygen-atom transfer (OAT) reaction of [Mo(VI)O2-(S2C2Me2)SMe](-1) (1) and [Mo(VI)O2-{(S2C2(CN)2}2]2- (2) with HSO3(-) takes place by oxoanionic binding of the substrate to the Mo(VI) center with the formation of a stable Michaelis complex. The gas-phase and solvent-corrected enthalpy profile with fully optimized minima and transition states for the OAT reaction of 1 and 2 with HSO3(-) showed the release of reaction energy for both complexes. The optimized geometries of 1 and 2 in the respective enzyme-substrate complexes showed a common feature with the participation of hydrogen bonding of the substrate with the axial (spectator) oxo group in the subsequent formation of the six-membered MoO2HOS transition state. The enzyme-substrate complex of 2 shows heptacoordination as proposed earlier, although the trans (to axial oxo)-Mo-S(dithiolene) bond is elongated to 2.948 A.
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Affiliation(s)
- Kuntal Pal
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur 208016, India
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43
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Hofmann M. Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites. J Biol Inorg Chem 2007; 12:989-1001. [PMID: 17636351 DOI: 10.1007/s00775-007-0271-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 06/11/2007] [Indexed: 11/25/2022]
Abstract
Molybdenum and tungsten complexes as models for the active sites of assimilatory or dissimilatory nitrate reductases (NR) were computed at the CPCM-B98/SDDp//B3LYP/Lanl2DZp* plus zero point energy level of density functional theory. The ligands were chosen on the basis of available experimental protein or small chemical model structures. A water molecule is found to bind to assimilatory NR models [(Me(2)C(2)S(2))MO(YMe)](-) (-11.5 kcal mol(-1) for M is Mo, Y is S) and may be replaced by nitrate (-4.5 kcal mol(-1)) (but a hydroxy group may not). Nature's choice of M is Mo and Y is S for NR has the largest activation energy for protein-free models (13.3 kcal mol(-1)) and the least exothermic reaction energy for the nitrate reduction (-14.9 kcal mol(-1)) compared with M is W and Y is O or Se alternatives. Water binding to dissimilatory NR model complexes [(Me(2)C(2)S(2))(2)M(YR)](-) is considerably endothermic (10.3 kcal mol(-1)); nitrate binding is only slightly so (1.5 kcal mol(-1) for RY(-) is MeS(-)). The exchange of an oxo ligand (assimilatory NR) for a dithiolato ligand (dissimilatory NR model) reduces the exothermicity (-8.6 kcal mol(-1) relative to the fivefold-coordinate reduced complex) and raises the barrier for oxygen atom transfer (OAT) in the nitrate complex (19.2 kcal mol(-1)). Not for the mono but only for the bisdithiolato complexes hydrogen bonding involving the coordinated substrate may significantly lower the OAT barrier as shown by explicitly adding water molecules. Substitution of tungsten for molybdenum generally lowers OAT activation energies and makes nitrate reduction reaction energies more negative. Bidentate carboxylato binding identified in Escherichia coli NarGHI is the preferred binding mode also for an acetato model. However, one dithiolato ligand folds when the Mo(VI) center is bare of a good pi-donor ligand, e.g., an oxo group. Computations on [(mnt)(2)Mo(IV)(YR)(PPh(3))](-) [mnt is (CN)(2)C(2)S(2) (2-)] gave a smaller nitrate reduction activation energy for RY(-) is Cl(-), compared with RY(-) is PhS(-), although experimentally only the phenyl thiolato complex and not the chloro complex was found to be a functional NR model.
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Affiliation(s)
- Matthias Hofmann
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.
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44
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The role of quantum chemistry in the elucidation of the elementary mechanisms of catalytic processes: from atoms, to surfaces, to enzymes. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0199-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Lyashenko G, Saischek G, Pal A, Herbst-Irmer R, Mösch-Zanetti NC. Molecular oxygen activation by a molybdenum(iv) monooxo bis(β-ketiminato) complex. Chem Commun (Camb) 2007:701-3. [PMID: 17392955 DOI: 10.1039/b617199k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molybdenum(IV) monooxo compound that contains bis(beta-ketiminato) ligands activates molecular oxygen forming a molybdenum(VI) monooxo peroxo compound, representing a new entry into molybdenum peroxo derivatives.
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Affiliation(s)
- Ganna Lyashenko
- Institut für Chemie, Karl-Franzens-Universität Graz, Schubertstr. 1, A-8010 Graz, Austria
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46
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47
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Kail BW, Pérez LM, Zarić SD, Millar AJ, Young CG, Hall MB, Basu P. Mechanistic Investigation of the Oxygen-Atom-Transfer Reactivity of Dioxo-molybdenum(VI) Complexes. Chemistry 2006; 12:7501-9. [PMID: 16865754 DOI: 10.1002/chem.200600269] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The oxygen-atom-transfer (OAT) reactivity of [LiPrMoO2(OPh)] (1, LiPr=hydrotris(3-isopropylpyrazol-1-yl)borate) with the tertiary phosphines PEt3 and PPh2Me in acetonitrile was investigated. The first step, [LiPrMoO2(OPh)]+PR3-->[LiPrMoO(OPh)(OPR3)], follows a second-order rate law with an associative transition state (PEt3, DeltaH not equal=48.4 (+/-1.9) kJ mol-1, DeltaS not equal=-149.2 (+/-6.4) J mol-1 K-1, DeltaG not equal=92.9 kJ mol-1; PPh2Me, DeltaH not equal=73.4 (+/-3.7) kJ mol-1, DeltaS not equal=-71.9 (+/-2.3) J mol-1 K-1, DeltaG not equal=94.8 kJ mol-1). With PMe3 as a model substrate, the geometry and the free energy of the transition state (TS) for the formation of the phosphine oxide-coordinated intermediate were calculated. The latter, 95 kJ mol-1, is in good agreement with the experimental values. An unexpectedly large O-P-C angle calculated for the TS suggests that there is significant O-nucleophilic attack on the P--C sigma* in addition to the expected nucleophilic attack of the P on the Mo==O pi*. The second step of the reaction, that is, the exchange of the coordinated phosphine oxide with acetonitrile, [LiPrMoO(OPh)(OPR3)]+MeCN-->[LiPrMoO(OPh)(MeCN)]+OPR3, follows a first-order rate law in MeCN. A dissociative interchange (Id) mechanism, with activation parameters of DeltaH not equal=93.5 (+/-0.9) kJ mol-1, DeltaS not equal=18.2 (+/-3.3) J mol-1 K-1, DeltaG not equal=88.1 kJ mol-1 and DeltaH not equal=97.9 (+/-3.4) kJ mol-1, DeltaS not equal=47.3 (+/-11.8) J mol-1 K-1, DeltaG not equal=83.8 kJ mol-1, for [LiPrMoO(OPh)(OPEt3)] (2 a) and [LiPrMoO(OPh)(OPPh2Me)] (2 b), respectively, is consistent with the experimental data. Although gas-phase calculations indicate that the Mo--OPMe3 bond is stronger than the Mo--NCMe bond, solvation provides the driving force for the release of the phosphine oxide and formation of [LiPrMoO(OPh)(MeCN)] (3).
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Affiliation(s)
- Brian W Kail
- Department of Chemistry and Biochemistry, Duquesne University, Mellon Hall, Pittsburgh, PA 15282, USA
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48
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Millar AJ, Doonan CJ, Smith PD, Nemykin VN, Basu P, Young CG. Oxygen atom transfer in models for molybdenum enzymes: isolation and structural, spectroscopic, and computational studies of intermediates in oxygen atom transfer from molybdenum(VI) to phosphorus(III). Chemistry 2006; 11:3255-67. [PMID: 15786505 DOI: 10.1002/chem.200401101] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Intermediates in the oxygen atom transfer from Mo(VI) to P(III), [Tp(iPr)MoOX(OPR3)] (Tp(iPr) = hydrotris(3-isopropylpyrazol-1-yl)borate; X = Cl-, phenolates, thiolates), have been isolated from the reactions of [Tp(iPr)MoO2X] with phosphines (PEt3, PMePh2, PPh3). The green, diamagnetic oxomolybdenum(IV) complexes possess local C(1) symmetry (by NMR spectroscopy) and exhibit IR bands assigned to nu(Mo==O) (approximately 950 cm(-1)) and nu(P==O) (1140-1083 cm(-1)) vibrations. The X-ray crystal structures of [Tp(iPr)MoOX(OPEt3)] (X = OC6H4-2-sBu, SnBu), [Tp(iPr)MoO(OPh)(OPMePh2)], and [Tp(iPr)MoOCl(OPPh3)] have been determined. The monomeric complexes exhibit distorted octahedral geometries, with coordination spheres composed of tridentate fac-Tp(iPr) and mutually cis monodentate terminal oxo, phosphoryl (phosphine oxide), and monoanionic X ligands. The electronic structures and stabilities of the complexes have been probed by computational methods, with the three-dimensional energy surfaces confirming the existence of a low-energy steric pocket that restricts the conformational freedom of the phosphoryl ligand and inhibits complete oxygen atom transfer. The reactivity of the complexes is also briefly described.
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Affiliation(s)
- Andrew J Millar
- School of Chemistry, University of Melbourne, Victoria, 3010, Australia
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49
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Leopoldini M, Russo N, Toscano M, Dulak M, Wesolowski TA. Mechanism of Nitrate Reduction byDesulfovibrio desulfuricans Nitrate Reductase—A Theoretical Investigation. Chemistry 2006; 12:2532-41. [PMID: 16411255 DOI: 10.1002/chem.200500790] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The oxidative half-reaction of oxygen atom transfer from nitrate to an Mo(IV) complex has been investigated at various levels of theory. Two models have been used to simulate the enzyme active site. In the second, more advanced model, additional amino acid residues capable of significantly affecting the catalytic efficiency of the enzyme were included. B3LYP/6-31+G*, ONIOM, and orbital-free embedding approaches have been used to construct the potential energy profile and to qualitatively compare the results of a QM/MM study with those obtained by a full quantum mechanical strategy. The study has confirmed the utility of the orbital-free embedding method in the description of enzymatic processes.
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Affiliation(s)
- Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite, Centro d'Eccellenza MIUR, Università della Calabria, 87030 Arcavacata di Rende (CS), Italy
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