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Lupp D, Christensen NJ, Fristrup P. Synergy between experimental and theoretical methods in the exploration of homogeneous transition metal catalysis. Dalton Trans 2014; 43:11093-105. [DOI: 10.1039/c4dt00342j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this Perspective, we will focus on the use of both experimental and theoretical methods in the exploration of reaction mechanisms in homogeneous transition metal catalysis. The current state-of-the-art is highlighted using examples from the literature with particular focus on the synergy between experiment and theory.
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Affiliation(s)
- D. Lupp
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby, Denmark
| | - N. J. Christensen
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby, Denmark
| | - P. Fristrup
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby, Denmark
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Hirao H, Chuanprasit P, Cheong YY, Wang X. How is a metabolic intermediate formed in the mechanism-based inactivation of cytochrome P450 by using 1,1-dimethylhydrazine: hydrogen abstraction or nitrogen oxidation? Chemistry 2013; 19:7361-9. [PMID: 23592585 DOI: 10.1002/chem.201300689] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Indexed: 11/10/2022]
Abstract
A precise understanding of the mechanism-based inactivation of cytochrome P450 enzymes (P450s) at the quantum mechanical level should allow more reliable predictions of drug-drug interactions than those currently available. Hydrazines are among the molecules that act as mechanism-based inactivators to terminate the function of P450s, which are essential heme enzymes responsible for drug metabolism in the human body. Despite its importance, the mechanism explaining how a metabolic intermediate (MI) is formed from hydrazine is not fully understood. We used density functional theory (DFT) calculations to compare four possible mechanisms underlying the reaction between 1,1-dimethylhydrazine (or unsymmetrical dimethylhydrazine, UDMH) and the reactive compound I (Cpd I) intermediate of P450. Our DFT calculations provided a clear view on how an aminonitrene-type MI is formed from UDMH. In the most favorable pathway, hydrogen is spontaneously abstracted from the N2 atom of UDMH by Cpd I, followed by a second hydrogen abstraction from the N2 atom by Cpd II. Nitrogen oxidation of nitrogen atoms and hydrogen abstraction from the C-H bond of the methyl group were found to be less favorable than the hydrogen abstraction from the N-H bond. We also found that the reaction of protonated UDMH with Cpd I is rather sluggish. The aminonitrene-type MI binds to the ferric heme more strongly than a water molecule. This is consistent with the notion that the catalytic cycle of P450 is impeded when such an MI is produced through the P450-catalyzed reaction.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.
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Pati SG, Shin K, Skarpeli-Liati M, Bolotin J, Eustis SN, Spain JC, Hofstetter TB. Carbon and nitrogen isotope effects associated with the dioxygenation of aniline and diphenylamine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:11844-11853. [PMID: 23017098 DOI: 10.1021/es303043t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dioxygenation of aromatic rings is frequently the initial step of biodegradation of organic subsurface pollutants. This process can be tracked by compound-specific isotope analysis to assess the extent of contaminant transformation, but the corresponding isotope effects, especially for dioxygenation of N-substituted, aromatic contaminants, are not well understood. We investigated the C and N isotope fractionation associated with the biodegradation of aniline and diphenylamine using pure cultures of Burkholderia sp. strain JS667, which can biodegrade both compounds, each by a distinct dioxygenase enzyme. For diphenylamine, the C and N isotope enrichment was normal with ε(C)- and ε(N)-values of -0.6 ± 0.1‰ and -1.0 ± 0.1‰, respectively. In contrast, N isotopes of aniline were subject to substantial inverse fractionation (ε(N) of +13 ± 0.5‰), whereas the ε(C)-value was identical to that of diphenylamine. A comparison of the apparent kinetic isotope effects for aniline and diphenylamine dioxygenation with those from abiotic oxidation by manganese oxide (MnO(2)) suggest that the oxidation of a diarylamine system leads to distinct C-N bonding changes compared to aniline regardless of reaction mechanism and oxidant involved. Combined evaluation of the C and N isotope signatures of the contaminants reveals characteristic Δδ(15)N/Δδ(13)C-trends for the identification of diphenylamine and aniline oxidation in contaminated subsurfaces and for the distinction of aniline oxidation from its formation by microbial and/or abiotic reduction of nitrobenzene.
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Affiliation(s)
- Sarah G Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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Skarpeli-Liati M, Pati SG, Bolotin J, Eustis SN, Hofstetter TB. Carbon, hydrogen, and nitrogen isotope fractionation associated with oxidative transformation of substituted aromatic N-alkyl amines. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:7189-7198. [PMID: 22681573 DOI: 10.1021/es300819v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigated the mechanisms and isotope effects associated with the N-dealkylation and N-atom oxidation of substituted N-methyl- and N,N-dimethylanilines to identify isotope fractionation trends for the assessment of oxidations of aromatic N-alkyl moieties by compound-specific isotope analysis (CSIA). In laboratory batch model systems, we determined the C, H, and N isotope enrichment factors for the oxidation by MnO(2) and horseradish peroxidase (HRP), derived apparent (13)C-, (2)H-, and (15)N-kinetic isotope effects (AKIEs), and characterized reaction products. The N-atom oxidation pathway leading to radical coupling products typically exhibited inverse (15)N-AKIEs (up to 0.991) and only minor (13)C- and (2)H-AKIEs. Oxidative N-dealkylation, in contrast, was subject to large normal (13)C- and (2)H-AKIEs (up to 1.019 and 3.1, respectively) and small (15)N-AKIEs. Subtle changes of the compound's electronic properties due to different types of aromatic and/or N-alkyl substituents resulted in changes of reaction mechanisms, rate-limiting step(s), and thus isotope fractionation trends. The complex sequence of electron and proton transfers during the oxidative transformation of substituted aromatic N-alkyl amines suggests highly compound- and mechanism-dependent isotope effects precluding extrapolations to other organic micropollutants reacting along the same degradation pathways.
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Affiliation(s)
- Marita Skarpeli-Liati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
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Kwiecień RA, Le Questel JY, Lebreton J, Delaforge M, André F, Pihan E, Roussel A, Fournial A, Paneth P, Robins RJ. Cytochrome P450-Catalyzed Degradation of Nicotine: Fundamental Parameters Determining Hydroxylation by Cytochrome P450 2A6 at the 5′-Carbon or the N-Methyl Carbon. J Phys Chem B 2012; 116:7827-40. [DOI: 10.1021/jp304276v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Renata A. Kwiecień
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jean-Yves Le Questel
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jacques Lebreton
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Marcel Delaforge
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Emilie Pihan
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Roussel
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Fournial
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Piotr Paneth
- Laboratory for Isotope Effects
Studies, Faculty of Chemistry, Institute
of Applied Radiation Chemistry, University of Technology Lodz, Zeromskiego 116, 90-924 Łodź, Poland
| | - Richard J. Robins
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
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