1
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Dias AHS, Cao Y, Skaf MS, de Visser SP. Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments. Phys Chem Chem Phys 2024; 26:17577-17587. [PMID: 38884162 DOI: 10.1039/d4cp01282h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.
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Affiliation(s)
- Artur Hermano Sampaio Dias
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Yuanxin Cao
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Munir S Skaf
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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2
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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3
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Katoch A, Mandal D. High-valent nonheme Fe(IV)O/Ru(IV)O complexes catalyze C-H activation reactivity and hydrogen tunneling: a comparative DFT investigation. Dalton Trans 2024; 53:2386-2394. [PMID: 38214597 DOI: 10.1039/d3dt03155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
A comprehensive density functional theory investigation has been presented towards the comparison of the C-H activation reactivity between high-valent iron-oxo and ruthenium-oxo complexes. A total of four compounds, e.g., [Ru(IV)O(tpy-dcbpy)] (1), [Fe(IV)O(tpy-dcbpy)] (1'), [Ru(IV)O(TMCS)] (2), and [Fe(IV)O(TMCS)] (2'), have been considered for this investigation. The macrocyclic ligand framework tpy(dcbpy) implies tpy = 2,2':6',2''-terpyridine, dcbpy = 5,5'-dicarboxy-2,2'-bipyridine, and TMCS is TMC with an axially tethered -SCH2CH2 group. Compounds 1 and 2' are experimentally synthesized standard complexes with Ru and Fe, whereas compounds 1' and 2 were considered to keep the macrocycle intact when switching the central metal atom. Three reactants including benzyl alcohol, ethyl benzene, and dihydroanthracene were selected as substrates for C-H activation. It is noteworthy to mention that Fe(IV)O complexes exhibit higher reactivity than those of their Ru(IV)O counterparts. Furthermore, regardless of the central metal, the complex featuring a tpy-dcbpy macrocycle demonstrates higher reactivity than that of TMCS. Here, a thorough analysis of the reactivity-controlling characteristics-such as spin state, steric factor, distortion energy, energy of the electron acceptor orbital, and quantum mechanical tunneling-was conducted. Fe(IV)O exhibits the exchanged enhanced two-state-reactivity with the quintet reactive state, whereas Ru(IV)O has only a triplet reactive state. Both the distortion energy and acceptor orbital energy are low in the case of Fe(IV)O supporting its higher reactivity. All the investigated C-H activation processes involve a significant contribution from hydrogen tunneling, which is more pronounced in the case of Ru, although it cannot alter the reactivity pattern. Furthermore, it has also been found that, independent of the central metal, aliphatic hydroxylation is always preferable to aromatic hydroxylation. Overall, this work is successful in establishing and investigating the cause of enzymes' natural preference for Fe over Ru as a cofactor for C-H activation enzymes.
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Affiliation(s)
- Akanksha Katoch
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
| | - Debasish Mandal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
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4
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Lakk-Bogáth D, Pintarics D, Török P, Kaizer J. Influence of Equatorial Co-Ligands on the Reactivity of LFe IIIOIPh. Molecules 2023; 29:58. [PMID: 38202641 PMCID: PMC10779584 DOI: 10.3390/molecules29010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Previous biomimetic studies clearly proved that equatorial ligands significantly influence the redox potential and thus the stability/reactivity of biologically important oxoiron intermediates; however, no such studies were performed on FeIIIOIPh species. In this study, the influence of substituted pyridine co-ligands on the reactivity of iron(III)-iodosylbenzene adduct has been investigated in sulfoxidation and epoxidation reactions. Selective oxidation of thioanisole, cis-cyclooctene, and cis- and trans-stilbene in the presence of a catalytic amount of [FeII(PBI)3](OTf)2 with PhI(OAc)2 provide products in good to excellent yields through an FeIIIOIPh intermediate depending on the co-ligand (4R-Py) used. Several mechanistic studies were performed to gain more insight into the mechanism of oxygen atom transfer (OAT) reactions to support the reactive intermediate and investigate the effect of the equatorial co-ligands. Based on competitive experiments, including a linear free-energy relationship between the relative reaction rates (logkrel) and the σp (4R-Py) parameters, strong evidence has been observed for the electrophilic character of the reactive species. The presence of the [(PBI)2(4R-Py)FeIIIOIPh]3+ intermediates and the effect of the co-ligands was also supported by UV-visible measurements, including the color change from red to green and the hypsochromic shifts in the presence of co-ligands. This is another indication that the title iron(III)-iodosylbenzene adduct is able to oxygenate sulfides and alkenes before it is transformed into the oxoiron form by cleavage of the O-I bond.
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Affiliation(s)
| | | | | | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, H-8201 Veszprém, Hungary; (D.L.-B.); (D.P.); (P.T.)
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5
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Jóźwik IK, Bombino E, Abdulmughni A, Hartz P, Rozeboom HJ, Wijma HJ, Kappl R, Janssen DB, Bernhardt R, Thunnissen AMWH. Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling. FEBS J 2023; 290:5016-5035. [PMID: 37453052 DOI: 10.1111/febs.16906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/31/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The P450 monooxygenase CYP109A2 from Bacillus megaterium DSM319 was previously found to convert vitamin D3 (VD3) to 25-hydroxyvitamin D3. Here, we show that this enzyme is also able to convert testosterone in a highly regio- and stereoselective manner to 16β-hydroxytestosterone. To reveal the structural determinants governing the regio- and stereoselective steroid hydroxylation reactions catalyzed by CYP109A2, two crystal structures of CYP109A2 were solved in similar closed conformations, one revealing a bound testosterone in the active site pocket, albeit at a nonproductive site away from the heme-iron. To examine whether the closed crystal structures nevertheless correspond to a reactive conformation of CYP109A2, docking and molecular dynamics (MD) simulations were performed with testosterone and vitamin D3 (VD3) present in the active site. These MD simulations were analyzed for catalytically productive conformations, the relative occurrences of which were in agreement with the experimentally determined stereoselectivities if the predicted stability of each carbon-hydrogen bond was taken into account. Overall, the first-time determination and analysis of the catalytically relevant 3D conformation of CYP109A2 will allow for future small molecule ligand screening in silico, as well as enabling site-directed mutagenesis toward improved enzymatic properties of this enzyme.
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Affiliation(s)
- Ilona K Jóźwik
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Ammar Abdulmughni
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Philip Hartz
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Henriette J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Reinhard Kappl
- Department of Biophysics, CIPMM, School of Medicine, Saarland University, Saarbrücken, Germany
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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6
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Cao YC, Liao RZ. QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase. Inorg Chem 2023; 62:4066-4075. [PMID: 36857027 DOI: 10.1021/acs.inorgchem.2c03742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b595. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b595 to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b595 to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.
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Affiliation(s)
- Yu-Chen Cao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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7
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Awasthi N, Yadav R, Kumar D. Revealing metabolic path of Ketamine catalyzed by CYP450 via quantum mechanical approach. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Wang Y, Wang J, Wei J, Wang C, Wang H, Yang X. Catalytic Mechanisms and Active Species of Benzene Hydroxylation Reaction System Based on Fe-Based Enzyme-Mimetic Structure. Catal Letters 2022. [DOI: 10.1007/s10562-022-04238-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Ashworth MA, Bombino E, de Jong RM, Wijma HJ, Janssen DB, McLean KJ, Munro AW. Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin. ACS Catal 2022; 12:15028-15044. [PMID: 36570080 PMCID: PMC9764288 DOI: 10.1021/acscatal.2c03974] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/22/2022] [Indexed: 11/29/2022]
Abstract
CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.
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Affiliation(s)
- Mark A. Ashworth
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Elvira Bombino
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - René M. de Jong
- DSM
Food & Beverage, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Hein J. Wijma
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands,
| | - Kirsty J. McLean
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom,Department
of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom
| | - Andrew W. Munro
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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10
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Mokkawes T, Lim ZQ, de Visser SP. Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation? J Phys Chem B 2022; 126:9591-9606. [PMID: 36380557 PMCID: PMC9706573 DOI: 10.1021/acs.jpcb.2c07200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C6-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C6-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Ze Qing Lim
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.,
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11
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Mai BK, Neris NM, Yang Y, Liu P. C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp 3)-H Amination: A Combined Computational and Experimental Investigation. J Am Chem Soc 2022; 144:11215-11225. [PMID: 35583461 DOI: 10.1021/jacs.2c02283] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.
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Affiliation(s)
- Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Zhang H, Wang C, Guo F, Jin L, Song R, Yang F, Ji L, Yu H. In Silico simulation of Cytochrome P450-Mediated metabolism of aromatic amines: A case study of N-Hydroxylation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113544. [PMID: 35483145 DOI: 10.1016/j.ecoenv.2022.113544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Aromatic amines, the widely used raw materials in industry, cause long-term exposure to human bodies. They can be metabolized by cytochrome P450 enzymes to form active electrophilic compounds, which will potentially react with nucleophilic DNA to exert carcinogenesis. The short lifetime and versatility of the oxidant (a high-valent iron (IV)-oxo species, compound I) of P450 enzymes prompts us to use theoretical methods to investigate the metabolism of aromatic amines. In this work, the density functional theory (DFT) has been employed to simulate the hydroxylation metabolism through H-abstraction and to calculate the activation energy of this reaction for 28 aromatic amines. The results indicate that the steric effects, inductive effects and conjugative effects greatly contribute to the metabolism activity of the chemicals. The further correlation reveals that the dissociation energy of -NH2 (BDEN-H) can successfully predict the time-consuming calculated activation energy (R2 for aromatic and heteroaromatic amines are 0.93 and 0.86, respectively), so BDEN-H can be taken as a key parameter to characterize the relative stability of aromatic amines in P450 enzymes and further to quickly assess their potential toxicity. The validation results prove such relationship has good statistical performance (qcv2 for aromatic and heteroaromatic amines are 0.95 and 0.90, respectively) and can be used to other aromatic amines in the application domain, greatly reducing computational cost and providing useful support for experimental research.
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Affiliation(s)
- Huanni Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangjie Guo
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Quality and Safety Engineering Institute of Food and Drug, School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, China
| | - Lingmin Jin
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangxing Yang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China.
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13
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Seeman JI. The Many Chemists Who Could Have Proposed the Woodward-Hoffmann Rules (Including Roald Hoffmann) But Didn't: The Theoretical and Physical Chemists †. CHEM REC 2022; 22:e202200052. [PMID: 35561024 DOI: 10.1002/tcr.202200052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/24/2022] [Indexed: 11/11/2022]
Abstract
It is a reasonable question to ask, why, as of 1965 when the five Woodward-Hoffmann communication appeared, did no other physical chemist or chemical physicist or theoretical chemist discover the orbital symmetry rules for all pericyclic reactions? Two theoretical chemists - Luitzen Oosterhoff (in 1961) and Kenichi Fukui (in 1964) had discovered portions of the orbital symmetry rules; their stories appear in the papers immediately preceding this paper which is Paper 5 in a 27-paper series on the history of Woodward-Hoffmann rules. Concise yet telling stories of 19 other chemists who could have, might have, perhaps even should have discovered the Woodward-Hoffmann rules are presented with explanations as to why they did not do so. Social, political, and scientific explanations will summarize the analyses.
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Affiliation(s)
- Jeffrey I Seeman
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
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14
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Metabolism of 8-aminoquinoline (8AQ) primaquine via aromatic hydroxylation step mediated by cytochrome P450 enzyme using density functional theory. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2021.122154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Awasthi N, Yadav R, Shukla A, Kumar D. Interplay between two degenerate spin state determines the hydroxylation of 4-nitrophenol catalyzed via Cytochrome P450. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.108857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Lan Z, Mallikarjun Sharada S. A framework for constructing linear free energy relationships to design molecular transition metal catalysts. Phys Chem Chem Phys 2021; 23:15543-15556. [PMID: 34254089 DOI: 10.1039/d1cp02278d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A computational framework for ligand-driven design of transition metal complexes is presented in this work. We propose a general procedure for the construction of active site-specific linear free energy relationships (LFERs), which are inspired from Hammett and Taft correlations in organic chemistry and grounded in the activation strain model (ASM). Ligand effects are isolated and quantified in terms of their contribution to interaction and strain energy components of ASM. Scalar descriptors that are easily obtainable are then employed to construct the complete LFER. We successfully demonstrate proof-of-concept by constructing and applying an LFER to CH activation with enzyme-inspired [Cu2O2]2+ complexes. The key benefit of using ASM is a built-in compensation or error cancellation between LFER prediction of interaction and strain terms, resulting in accurate barrier predictions for 37 of the 47 catalysts examined in this study. The LFER is also transferable with respect to level of theory and flexible towards the choice of reference system. The absence of interaction-strain compensation or poor model performance for the remaining systems is a consequence of the approximate nature of the chosen interaction energy descriptor and LFER construction of the strain term, which focuses largely on trends in substrate and not catalyst strain.
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Affiliation(s)
- Zhenzhuo Lan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA.
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA. and Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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17
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Roach S, Faponle AS, Satpathy JK, Sastri CV, de Visser SP. Substrate sulfoxidation by a biomimetic cytochrome P450 Compound I mimic: How do porphyrin and phthalocyanine equatorial ligands compare? J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01917-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Monika, Yadav O, Chauhan H, Ansari A. Electronic structures, bonding, and spin state energetics of biomimetic mononuclear and bridged dinuclear iron complexes: a computational examination. Struct Chem 2021. [DOI: 10.1007/s11224-020-01690-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Bracco P, Wijma HJ, Nicolai B, Buitrago JAR, Klünemann T, Vila A, Schrepfer P, Blankenfeldt W, Janssen DB, Schallmey A. CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering*. Chembiochem 2020; 22:1099-1110. [PMID: 33145893 PMCID: PMC8048783 DOI: 10.1002/cbic.202000735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/03/2020] [Indexed: 12/27/2022]
Abstract
CYP154C5 from Nocardia farcinica is a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein engineering and substrate modifications based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation had been achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternative binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that the entrance of water to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure-function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.
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Affiliation(s)
- Paula Bracco
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Hein J Wijma
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Bastian Nicolai
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Jhon Alexander Rodriguez Buitrago
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Agustina Vila
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Patrick Schrepfer
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Dick B Janssen
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
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20
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Kumar R, Pandey B, Sen A, Ansari M, Sharma S, Rajaraman G. Role of oxidation state, ferryl-oxygen, and ligand architecture on the reactivity of popular high-valent FeIV=O species: A theoretical perspective. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Sen A, Vyas N, Pandey B, Jaccob M, Rajaraman G. Mechanistic Insights on the Formation of High‐Valent Mn
III/IV
=O Species Using Oxygen as Oxidant: A Theoretical Perspective. Isr J Chem 2020. [DOI: 10.1002/ijch.201900142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Asmita Sen
- Department of Chemistry Indian Institute of Technology Bombay Mumbai 400076 India
| | - Nidhi Vyas
- Department of Chemistry Indian Institute of Technology Bombay Mumbai 400076 India
- School of Biotechnology Jawaharlal Nehru University New Delhi 110067 India
| | - Bhawana Pandey
- Department of Chemistry Indian Institute of Technology Bombay Mumbai 400076 India
| | - Madhavan Jaccob
- Department of Chemistry Indian Institute of Technology Bombay Mumbai 400076 India
- Department of chemistry Loyola College Chennai 600 034
| | - Gopalan Rajaraman
- Department of Chemistry Indian Institute of Technology Bombay Mumbai 400076 India
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22
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Hussain R, Yadav R, Ahmed M, Khan TA, Kumar D, Akhter Y. Interplay between two spin states determines the hydroxylation catalyzed by P
450
monooxygenase from
Trichoderma brevicompactum. J Comput Chem 2020; 41:1330-1336. [DOI: 10.1002/jcc.26177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Razak Hussain
- Department of BotanyAligarh Muslim University Aligarh Uttar Pradesh India
| | - Rolly Yadav
- Department of Applied PhysicsSchool for Physical Sciences, Babasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
| | - Mushtaq Ahmed
- Centre for Molecular BiologySchool of Life Sciences, Central University of Jammu Bagla Jammu and Kashmir India
| | - Tabreiz A. Khan
- Department of BotanyAligarh Muslim University Aligarh Uttar Pradesh India
| | - Devesh Kumar
- Department of Applied PhysicsSchool for Physical Sciences, Babasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
| | - Yusuf Akhter
- Department of BiotechnologyBabasaheb Bhimrao Ambedkar University Lucknow Uttar Pradesh India
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23
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Mubarak MQE, de Visser SP. Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study. Dalton Trans 2019; 48:16899-16910. [PMID: 31670737 DOI: 10.1039/c9dt03048d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.
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Affiliation(s)
- M Qadri E Mubarak
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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24
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Takayanagi T, Saito K, Suzuki H, Watabe Y, Fujihara T. Computational Analysis of Two-State Reactivity in β-Hydride Elimination Mechanisms of Fe(II)– and Co(II)–Alkyl Complexes Supported by β-Diketiminate Ligand. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Haruya Suzuki
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yuya Watabe
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Takashi Fujihara
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
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25
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Bietti M, Cucinotta E, DiLabio GA, Lanzalunga O, Lapi A, Mazzonna M, Romero-Montalvo E, Salamone M. Evaluation of Polar Effects in Hydrogen Atom Transfer Reactions from Activated Phenols. J Org Chem 2019; 84:1778-1786. [DOI: 10.1021/acs.joc.8b02571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università “Tor Vergata”, Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
| | - Erica Cucinotta
- Dipartimento di Chimica, Sapienza Università di Roma and Sezione Meccanismi di Reazione, Istituto CNR per i Sistemi Biologici (ISB-CNR), Sapienza Università di Roma, P.le A. Moro, 5 I-00185 Rome, Italy
| | - Gino A. DiLabio
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
- Faculty of Management, University of British Columbia, 1137 Alumni Avenue Kelowna, British Columbia V1V 1V7, Canada
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica, Sapienza Università di Roma and Sezione Meccanismi di Reazione, Istituto CNR per i Sistemi Biologici (ISB-CNR), Sapienza Università di Roma, P.le A. Moro, 5 I-00185 Rome, Italy
| | - Andrea Lapi
- Dipartimento di Chimica, Sapienza Università di Roma and Sezione Meccanismi di Reazione, Istituto CNR per i Sistemi Biologici (ISB-CNR), Sapienza Università di Roma, P.le A. Moro, 5 I-00185 Rome, Italy
| | - Marco Mazzonna
- Dipartimento di Chimica, Sapienza Università di Roma and Sezione Meccanismi di Reazione, Istituto CNR per i Sistemi Biologici (ISB-CNR), Sapienza Università di Roma, P.le A. Moro, 5 I-00185 Rome, Italy
| | - Eduardo Romero-Montalvo
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Michela Salamone
- Dipartimento di Scienze e Tecnologie Chimiche, Università “Tor Vergata”, Via della Ricerca Scientifica, 1 I-00133 Rome, Italy
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26
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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27
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Mukherjee A, Pattanayak S, Sen Gupta S, Vanka K. What drives the H-abstraction reaction in bio-mimetic oxoiron-bTAML complexes? A computational investigation. Phys Chem Chem Phys 2018; 20:13845-13850. [PMID: 29717729 DOI: 10.1039/c8cp01333k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monomeric iron-oxo units have been confirmed as intermediates involved in the C-H bond activation in various metallo-enzymes. Biomimetic oxoiron complexes of the biuret modified tetra-amido macrocyclic ligand (bTAML) have been demonstrated to oxidize a wide variety of unactivated C-H bonds. In the current work, density functional theory (DFT) has been employed to investigate the hydrogen abstraction (HAT) reactivity differences across a series of bTAML complexes. The cause for the differences in the HAT energy barriers has been found to be the relative changes in the energy of the frontier molecular orbitals (FMOs) induced by electronic perturbation.
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Affiliation(s)
- Anagh Mukherjee
- Physical and Material Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India.
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28
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Leipzig BK, Rees JA, Kowalska JK, Theisen RM, Kavčič M, Poon PCY, Kaminsky W, DeBeer S, Bill E, Kovacs JA. How Do Ring Size and π-Donating Thiolate Ligands Affect Redox-Active, α-Imino-N-heterocycle Ligand Activation? Inorg Chem 2018; 57:1935-1949. [PMID: 29411979 DOI: 10.1021/acs.inorgchem.7b02748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L•-), initially suggested that the electron-donating thiolate had reduced the N-heterocycle. Sulfur K-edge X-ray absorption spectroscopic (XAS) data, however, provides evidence for direct communication, via backbonding, between the thiolate sulfur and the formally orthogonal (α-imino)-N-heterocycle ligand π*-orbitals. DFT calculations provide evidence for extensive delocalization of bonds over the sulfur, iron, and (α-imino)-N-heterocycle, and TD-DFT shows that the intense optical CT bands involve transitions between a mixed Fe/S donor, and (α-imino)-N-heterocycle π*-acceptor orbital. The energies and intensities of the optical and S K-edge pre-edge XAS transitions are shown to correlate with N-heterocycle ring size, as do the redox potentials. When the thiolate is replaced with a thioether, or when the low-spin S = 0 Fe(II) is replaced with a high-spin S = 3/2 Co(II), the N-heterocycle ligand metrical parameters and electronic structure do not change relative to the neutral L0 ligand. With respect to the development of future catalysts containing redox-active ligands, the energy cost of storing reducing equivalents is shown to be lowest when a quinoline, as opposed to imidazole or pyridine, is incorporated into the ligand backbone of the corresponding Fe complex.
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Affiliation(s)
- Benjamin K Leipzig
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A Rees
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Joanna K Kowalska
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Roslyn M Theisen
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | | | | | - Werner Kaminsky
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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29
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Hu L, Chen H. Substrate-Dependent Two-State Reactivity in Iron-Catalyzed Alkene [2+2] Cycloaddition Reactions. J Am Chem Soc 2017; 139:15564-15567. [DOI: 10.1021/jacs.7b06086] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lianrui Hu
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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30
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31
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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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32
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Dai W, Shang S, Lv Y, Li G, Li C, Gao S. Highly Chemoselective and Enantioselective Catalytic Oxidation of Heteroaromatic Sulfides via High-Valent Manganese(IV)–Oxo Cation Radical Oxidizing Intermediates. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00968] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Wen Dai
- Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Sensen Shang
- Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Ying Lv
- Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Guosong Li
- Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Chunsen Li
- State Key Laboratory of Structural
Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, People’s Republic of China
| | - Shuang Gao
- Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
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33
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Bigelow JO, England J, Klein JEMN, Farquhar ER, Frisch JR, Martinho M, Mandal D, Münck E, Shaik S, Que L. Oxoiron(IV) Tetramethylcyclam Complexes with Axial Carboxylate Ligands: Effect of Tethering the Carboxylate on Reactivity. Inorg Chem 2017; 56:3287-3301. [DOI: 10.1021/acs.inorgchem.6b02659] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer O. Bigelow
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason England
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Johannes E. M. N. Klein
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erik R. Farquhar
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jonathan R. Frisch
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Marlène Martinho
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Debasish Mandal
- Institute of Chemistry and the Lise Meitner-Minerva
Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva
Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lawrence Que
- Department of Chemistry
and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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34
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Peters GM, Winegrad JB, Gau MR, Imler GH, Xu B, Ren S, Wayland BB, Zdilla MJ. Synthesis and Structure of 2,5-Bis[N-(2,6-mesityl)iminomethyl]pyrrolylcobalt(II): Evidence for One-Electron-Oxidized, Redox Noninnocent Ligand Behavior. Inorg Chem 2017; 56:3377-3385. [DOI: 10.1021/acs.inorgchem.6b02898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Garvin M. Peters
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Jacob B. Winegrad
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Michael R. Gau
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Gregory H. Imler
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Beibei Xu
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Shenqiang Ren
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Bradford B. Wayland
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Michael J. Zdilla
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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35
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Strengths, Weaknesses, Opportunities and Threats: Computational Studies of Mn- and Fe-Catalyzed Epoxidations. Catalysts 2016. [DOI: 10.3390/catal7010002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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36
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Yang CL, Lin CH, Luo WI, Lee TL, Ramu R, Ng KY, Tsai YF, Wei GT, Yu SSF. Mechanistic Study of the Stereoselective Hydroxylation of [2-2
H1
,3-2
H1
]Butanes Catalyzed by Cytochrome P450 BM3 Variants. Chemistry 2016; 23:2571-2582. [DOI: 10.1002/chem.201603956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Chung-Ling Yang
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Cheng-Hung Lin
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Wen-I Luo
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Tsu-Lin Lee
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Ravirala Ramu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Kok Yaoh Ng
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Yi-Fang Tsai
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Guor-Tzo Wei
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
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37
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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38
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Shaik S, Mandal D, Ramanan R. Oriented electric fields as future smart reagents in chemistry. Nat Chem 2016; 8:1091-1098. [DOI: 10.1038/nchem.2651] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
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39
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Barman P, Faponle AS, Vardhaman AK, Angelone D, Löhr AM, Browne WR, Comba P, Sastri CV, de Visser SP. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes. Inorg Chem 2016; 55:10170-10181. [PMID: 27704794 DOI: 10.1021/acs.inorgchem.6b01384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClOx- in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO2- into either ClO2 or ClO3¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO2 and ClO3- products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.
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Affiliation(s)
- Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Anil Kumar Vardhaman
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Davide Angelone
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna-Maria Löhr
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati , Guwahati 781 039, Assam, India
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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Attia AAA, Silaghi-Dumitrescu R. A mononuclear non-heme-iron dioxygen-carrying protein? J Mol Graph Model 2016; 69:103-10. [PMID: 27607306 DOI: 10.1016/j.jmgm.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
Abstract
The ability of mononuclear non-heme iron complexes to function as molecular oxygen transporters is investigated by density functional theory. The factors governing the efficiency of the reversible binding of dioxygen at the active site of the dinuclear non-heme iron enzyme hemerythrin, including antiferromagnetic coupling and the conversion of dioxygen to hydroperoxo by a proton coupled 2-electron transfer mechanism, are revisited and considered as possible tools in mononuclear non-heme complexes. Several mononuclear non-heme model complexes, including active sites of enzymes already known to interact with dioxgenic ligands, are constructed and the molecular oxygen transportation capabilities of these complexes are examined computationally. The high-spin nature of the ground state of these complexes implies an intrinsic kinetic lability of the oxy structures, as also evident from potential energy surface calculations towards iron-dioxygen cleavage. Proton affinities as calibrated with reference compounds showed that these complexes are highly unlikely to undergo protonation to form hydroperoxo-like adducts. Mixed superoxo descriptions of the dissociated dioxygenic ligands in all complexes add to the overall conclusion that these model structures are significantly disadvantaged in any attempt to be employed for molecular oxygen transportation.
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Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
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41
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Sharon DA, Mallick D, Wang B, Shaik S. Computation Sheds Insight into Iron Porphyrin Carbenes' Electronic Structure, Formation, and N-H Insertion Reactivity. J Am Chem Soc 2016; 138:9597-610. [PMID: 27347808 DOI: 10.1021/jacs.6b04636] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Iron porphyrin carbenes constitute a new frontier of species with considerable synthetic potential. Exquisitely engineered myoglobin and cytochrome P450 enzymes can generate these complexes and facilitate the transformations they mediate. The current work harnesses density functional theoretical methods to provide insight into the electronic structure, formation, and N-H insertion reactivity of an iron porphyrin carbene, [Fe(Por)(SCH3)(CHCO2Et)](-), a model of a complex believed to exist in an experimentally studied artificial metalloenzyme. The ground state electronic structure of the terminal form of this complex is an open-shell singlet, with two antiferromagnetically coupled electrons residing on the iron center and carbene ligand. As we shall reveal, the bonding properties of [Fe(Por)(SCH3)(CHCO2Et)](-) are remarkably analogous to those of ferric heme superoxide complexes. The carbene forms by dinitrogen loss from ethyl diazoacetate. This reaction occurs preferentially through an open-shell singlet transition state: iron donates electron density to weaken the C-N bond undergoing cleavage. Once formed, the iron porphyrin carbene accomplishes N-H insertion via nucleophilic attack. The resulting ylide then rearranges, using an internal carbonyl base, to form an enol that leads to the product. The findings rationalize experimentally observed reactivity trends reported in artificial metalloenzymes employing iron porphyrin carbenes. Furthermore, these results suggest a possible expansion of enzymatic substrate scope, to include aliphatic amines. Thus, this work, among the first several computational explorations of these species, contributes insights and predictions to the surging interest in iron porphyrin carbenes and their synthetic potential.
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Affiliation(s)
- Dina A Sharon
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904, Jerusalem, Israel
| | - Dibyendu Mallick
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904, Jerusalem, Israel
| | - Binju Wang
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904, Jerusalem, Israel
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42
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Catalytic oxidation of cyclohexane to KA oil by zinc oxide supported manganese 5,10,15,20-tetrakis(4-nitrophenyl)porphyrin. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2015.09.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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43
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Seeman JI. Woodward–Hoffmann’s Stereochemistry of Electrocyclic Reactions: From Day 1 to the JACS Receipt Date (May 5, 1964 to November 30, 1964). J Org Chem 2015; 80:11632-71. [DOI: 10.1021/acs.joc.5b01792] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeffrey I. Seeman
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
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44
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Salamone M, Bietti M. Tuning reactivity and selectivity in hydrogen atom transfer from aliphatic C-H bonds to alkoxyl radicals: role of structural and medium effects. Acc Chem Res 2015; 48:2895-903. [PMID: 26545103 DOI: 10.1021/acs.accounts.5b00348] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydrogen atom transfer (HAT) is a fundamental reaction that takes part in a wide variety of chemical and biological processes, with relevant examples that include the action of antioxidants, damage to biomolecules and polymers, and enzymatic and biomimetic reactions. Moreover, great attention is currently devoted to the selective functionalization of unactivated aliphatic C-H bonds, where HAT based procedures have been shown to play an important role. In this Account, we describe the results of our recent studies on the role of structural and medium effects on HAT from aliphatic C-H bonds to the cumyloxyl radical (CumO(•)). Quantitative information on the reactivity and selectivity patterns observed in these reactions has been obtained by time-resolved kinetic studies, providing a deeper understanding of the factors that govern HAT from carbon and leading to the definition of useful guidelines for the activation or deactivation of aliphatic C-H bonds toward HAT. In keeping with the electrophilic character of alkoxyl radicals, polar effects can play an important role in the reactions of CumO(•). Electron-rich C-H bonds are activated whereas those that are α to electron withdrawing groups are deactivated toward HAT, with these effects being able to override the thermodynamic preference for HAT from the weakest C-H bond. Stereoelectronic effects can also influence the reactivity of the C-H bonds of ethers, amines, and amides. HAT is most rapid when these bonds can be eclipsed with a lone pair on an adjacent heteroatom or with the π-system of an amide functionality, thus allowing for optimal orbital overlap. In HAT from cyclohexane derivatives, tertiary axial C-H bond deactivation and tertiary equatorial C-H bond activation have been observed. These effects have been explained on the basis of an increase in torsional strain or a release in 1,3-diaxial strain in the HAT transition states, with kH(eq)/kH(ax) ratios that have been shown to exceed one order of magnitude. Medium effects on HAT from aliphatic C-H bonds to CumO(•) have been also investigated. With basic substrates, from large to very large decreases in kH have been measured with increasing solvent hydrogen bond donor (HBD) ability or after addition of protic acids or alkali and alkaline earth metal ions, with kinetic effects that exceed 2 orders of magnitude in the reactions of tertiary alkylamines and alkanamides. Solvent hydrogen bonding, protonation, and metal ion binding increase the electron deficiency and the strength of the C-H bonds of these substrates deactivating these bonds toward HAT, with the extent of this deactivation being modulated by varying the nature of the substrate, solvent, protic acid, and metal ion. These results indicate that through these interactions careful control over the HAT reactivity of basic substrates toward CumO(•) and other electrophilic radicals can be achieved, suggesting moreover that these effects can be exploited in an orthogonal fashion for selective C-H bond functionalization of substrates bearing different basic functionalities.
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Affiliation(s)
- Michela Salamone
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Massimo Bietti
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica, 1, I-00133 Rome, Italy
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Liu S, Jung J, Ohkubo K, Hicks SD, Bougher CJ, Abu-Omar MM, Fukuzumi S. Activationless Electron Self-Exchange of High-Valent Oxo and Imido Complexes of Chromium Corroles. Inorg Chem 2015; 54:9223-8. [DOI: 10.1021/acs.inorgchem.5b01777] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuo Liu
- Brown Laboratory and Department of Chemistry, Purdue University, 560
Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jieun Jung
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Kei Ohkubo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, ALCA and SENTAN, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871, Japan
| | - Scott D. Hicks
- Brown Laboratory and Department of Chemistry, Purdue University, 560
Oval Drive, West Lafayette, Indiana 47907, United States
| | - Curt J. Bougher
- Brown Laboratory and Department of Chemistry, Purdue University, 560
Oval Drive, West Lafayette, Indiana 47907, United States
| | - Mahdi M. Abu-Omar
- Brown Laboratory and Department of Chemistry, Purdue University, 560
Oval Drive, West Lafayette, Indiana 47907, United States
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, ALCA and SENTAN, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871, Japan
- Faculty of Science and Engineering, Meijo University, ALCA and SENTAN, Japan Science and Technology Agency (JST), Nagoya, Aichi 468-0073, Japan
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Mitra M, Nimir H, Demeshko S, Bhat SS, Malinkin SO, Haukka M, Lloret-Fillol J, Lisensky GC, Meyer F, Shteinman AA, Browne WR, Hrovat DA, Richmond MG, Costas M, Nordlander E. Nonheme Fe(IV) Oxo Complexes of Two New Pentadentate Ligands and Their Hydrogen-Atom and Oxygen-Atom Transfer Reactions. Inorg Chem 2015. [PMID: 26198840 DOI: 10.1021/ic5029564] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two new pentadentate {N5} donor ligands based on the N4Py (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) framework have been synthesized, viz. [N-(1-methyl-2-benzimidazolyl)methyl-N-(2-pyridyl)methyl-N-(bis-2-pyridyl methyl)amine] (L(1)) and [N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine] (L(2)), where one or two pyridyl arms of N4Py have been replaced by corresponding (N-methyl)benzimidazolyl-containing arms. The complexes [Fe(II)(CH3CN)(L)](2+) (L = L(1) (1); L(2) (2)) were synthesized, and reaction of these ferrous complexes with iodosylbenzene led to the formation of the ferryl complexes [Fe(IV)(O)(L)](2+) (L = L(1) (3); L(2) (4)), which were characterized by UV-vis spectroscopy, high resolution mass spectrometry, and Mössbauer spectroscopy. Complexes 3 and 4 are relatively stable with half-lives at room temperature of 40 h (L = L(1)) and 2.5 h (L = L(2)). The redox potentials of 1 and 2, as well as the visible spectra of 3 and 4, indicate that the ligand field weakens as ligand pyridyl substituents are progressively substituted by (N-methyl)benzimidazolyl moieties. The reactivities of 3 and 4 in hydrogen-atom transfer (HAT) and oxygen-atom transfer (OAT) reactions show that both complexes exhibit enhanced reactivities when compared to the analogous N4Py complex ([Fe(IV)(O)(N4Py)](2+)), and that the normalized HAT rates increase by approximately 1 order of magnitude for each replacement of a pyridyl moiety; i.e., [Fe(IV)(O)(L(2))](2+) exhibits the highest rates. The second-order HAT rate constants can be directly related to the substrate C-H bond dissociation energies. Computational modeling of the HAT reactions indicates that the reaction proceeds via a high spin transition state.
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Affiliation(s)
- Mainak Mitra
- †Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Hassan Nimir
- ‡Department of Chemistry and Earth Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, State of Qatar
| | - Serhiy Demeshko
- §Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammanstrasse 4, D-37077 Göttingen, Germany
| | - Satish S Bhat
- †Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Sergey O Malinkin
- †Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Matti Haukka
- ⊥Department of Chemistry, University of Jyväskylä, P.O. Box-35, Jyväskylä, FI-40014, Finland
| | - Julio Lloret-Fillol
- ¶QBIS, Department of Chemistry, University de Girona, Campus Montilivi, E-17071 Girona, Spain
| | - George C Lisensky
- ∥Department of Chemistry, Beloit College, 700 College Street, Beloit, Wisconsin 53511, United States
| | - Franc Meyer
- §Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammanstrasse 4, D-37077 Göttingen, Germany
| | - Albert A Shteinman
- #Institute of Problems of Chemical Physics, Chernogolovka, Moscow District, 142432, Russian Federation
| | - Wesley R Browne
- ∇Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - David A Hrovat
- ○Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203, United States.,◆Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - Michael G Richmond
- ◆Department of Chemistry, University of North Texas, Denton, Texas 76203, United States
| | - Miquel Costas
- ¶QBIS, Department of Chemistry, University de Girona, Campus Montilivi, E-17071 Girona, Spain
| | - Ebbe Nordlander
- †Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
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48
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Ye S, Xue G, Krivokapic I, Petrenko T, Bill E, Que Jr L, Neese F. Magnetic circular dichroism and computational study of mononuclear and dinuclear iron(IV) complexes. Chem Sci 2015; 6:2909-2921. [PMID: 26417426 PMCID: PMC4583211 DOI: 10.1039/c4sc03268c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
High-valent iron(IV)-oxo species are key intermediates in the catalytic cycles of a range of O2-activating iron enzymes. This work presents a detailed study of the electronic structures of mononuclear ([FeIV(O)(L)(NCMe)]2+, 1, L = tris(3,5-dimethyl-4-methoxylpyridyl-2-methyl)amine) and dinuclear ([(L)FeIV(O)(μ-O)FeIV(OH)(L)]3+, 2) iron(IV) complexes using absorption (ABS), magnetic circular dichroism (MCD) spectroscopy and wave-function-based quantum chemical calculations. For complex 1, the experimental MCD spectra at 2-10 K are dominated by a broad positive C-term band between 12000 and 18000 cm-1. As the temperature increases up to ~20 K, this feature is gradually replaced by a derivative-shaped signal. The computed MCD spectra are in excellent agreement with experiment, which reproduce not only the excitation energies and the MCD signs of key transitions but also their temperature-dependent intensity variations. To further corroborate the assignments suggested by the calculations, the individual MCD sign for each transition is independently determined from the corresponding electron donating and accepting orbitals. Thus, unambiguous assignments can be made for the observed transitions in 1. The ABS/MCD data of complex 2 exhibit ten features that are assigned as ligand-field transitions or oxo- or hydroxo-to-metal charge transfer bands, based on MCD/ABS intensity ratios, calculated excitation energies, polarizations, and MCD signs. In comparison with complex 1, the electronic structure of the FeIV=O site is not significantly perturbed by the binding to another iron(IV) center. This may explain the experimental finding that complexes 1 and 2 have similar reactivities toward C-H bond activation and O-atom transfer.
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Affiliation(s)
- Shengfa Ye
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Genqiang Xue
- Department of Chemistry , Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant St. SE , Minneapolis , Minnesota 55455 , USA .
| | - Itana Krivokapic
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Taras Petrenko
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Eckhard Bill
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Lawrence Que Jr
- Department of Chemistry , Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant St. SE , Minneapolis , Minnesota 55455 , USA .
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
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Knizia G, Klein JEMN. Electron Flow in Reaction Mechanisms-Revealed from First Principles. Angew Chem Int Ed Engl 2015; 54:5518-22. [DOI: 10.1002/anie.201410637] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/14/2014] [Indexed: 11/11/2022]
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Knizia G, Klein JEMN. Elektronenfluss in Reaktionsmechanismen - enthüllt aus quantenmechanischen Grundprinzipien. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410637] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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