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Gong Z, Wang L, Xu Y, Xie D, Qi X, Nam W, Guo M. Enhanced Reactivities of Iron(IV)-Oxo Porphyrin Species in Oxidation Reactions Promoted by Intramolecular Hydrogen-Bonding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310333. [PMID: 38477431 PMCID: PMC11109629 DOI: 10.1002/advs.202310333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
High-valent iron-oxo species are one of the common intermediates in both biological and biomimetic catalytic oxidation reactions. Recently, hydrogen-bonding (H-bonding) has been proved to be critical in determining the selectivity and reactivity. However, few examples have been established for mechanistic insights into the H-bonding effect. Moreover, intramolecular H-bonding effect on both C-H activation and oxygen atom transfer (OAT) reactions in synthetic porphyrin model system has not been investigated yet. In this study, a series of heme-containing iron(IV)-oxo porphyrin species with or without intramolecular H-bonding are synthesized and characterized. Kinetic studies revealed that intramolecular H-bonding can significantly enhance the reactivity of iron(IV)-oxo species in OAT, C-H activation, and electron-transfer reactions. This unprecedented unified H-bonding effect is elucidated by theoretical calculations, which showed that intramolecular H-bonding interactions lower the energy of the anti-bonding orbital of iron(IV)-oxo porphyrin species, resulting in the enhanced reactivities in oxidation reactions irrespective of the reaction type. To the best of the knowledge, this is the first extensive investigation on the intramolecular H-bonding effect in heme system. The results show that H-bonding interactions have a unified effect with iron(IV)-oxo porphyrin species in all three investigated reactions.
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Affiliation(s)
- Zhe Gong
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Yiran Xu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Duanfeng Xie
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Xiaotian Qi
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
| | - Wonwoo Nam
- Department of Chemistry and Nano ScienceEwha Womans UniversitySeoul03760South Korea
| | - Mian Guo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhanHubei430072P. R. China
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2
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Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [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: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Kaur L, Mandal D. Role of "S" Substitution on C-H Activation Reactivity of Iron(IV)-Oxo Cyclam Complexes: a Computational Investigation. Inorg Chem 2022; 61:14582-14590. [PMID: 36069431 DOI: 10.1021/acs.inorgchem.2c01504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A comprehensive density functional theory (DFT) investigation has been presented in this article to address the role of equatorial sulfur ligation in C-H activation. A non-heme iron-oxo compound with four nitrogen atoms constituting the equatorially connected macrocyclic framework (represented as N4) [Fe(IV)═O(THC)(CH3CN)]2+(THC = 1,4,8,11-tetrahydro1,4,8,11-tetraazacyclotetradecane) has been considered as the base compound. Other complexes have been anticipated by the sequential replacement of this nitrogen by sulfur, that is, N4, N3S1, N2S2, N1S3, and S4. Counterions, as always, have been considered to avoid the self-interaction error in DFT. Generally, the anti-conformers (with respect to equatorial N-H and Fe═O) turned out to be the most stable. It was found that with the enrichment of the equatorial sulfur atom, reactivity increases successively, that is, we get the trend N4 < N3S1 < N2S2 < N1S3 < S4. Our investigations have also verified the available experimental results where it has been reported that N2S2 is more reactive than N4 in their mixed conformation. In search of insights into this typical pattern of reactivity, the interplay of several factors has been recognized, such as the distortion energy which decreases for the transition states with the addition of sulfur; the spin density on the oxygen atom which increases implying that the radical character of abstractor increases on sulfur ligation; the energy of the electron acceptor orbital (the lowest unoccupied molecular orbital (σz2*)) which decreases continuously with the sulfur substitution; and the triplet-quintet oxidant energy gap which decreases consistently with S enrichment in the equatorial position. The computational predictions reported here, if further validated by experiments, will definitely encourage the synthesis of sulfur-ligated bio-inspired complexes instead of the ones constituting nitrogen exclusively.
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Affiliation(s)
- Lovleen Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Debasish Mandal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
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4
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Rajeev A, Balamurugan M, Sankaralingam M. Rational Design of First-Row Transition Metal Complexes as the Catalysts for Oxidation of Arenes: A Homogeneous Approach. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anjana Rajeev
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Mani Balamurugan
- Department of Materials Science and Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
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5
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Sheng Y, Abelson CS, Prakash J, Draksharapu A, Young VG, Que L. Unmasking Steps in Intramolecular Aromatic Hydroxylation by a Synthetic Nonheme Oxoiron(IV) Complex. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuan Sheng
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | - Chase S. Abelson
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | - Jai Prakash
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | | | - Victor G. Young
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
| | - Lawrence Que
- Department of Chemistry University of Minnesota Minneapolis MN 55455 USA
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6
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Sheng Y, Abelson CS, Prakash J, Draksharapu A, Young VG, Que L. Unmasking Steps in Intramolecular Aromatic Hydroxylation by a Synthetic Nonheme Oxoiron(IV) Complex. Angew Chem Int Ed Engl 2021; 60:20991-20998. [PMID: 34292639 PMCID: PMC8429247 DOI: 10.1002/anie.202108309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 11/09/2022]
Abstract
In this study, a methyl group on the classic tetramethylcyclam (TMC) ligand framework is replaced with a benzylic group to form the metastable [FeIV (Osyn )(Bn3MC)]2+ (2-syn; Bn3MC=1-benzyl-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane) species at -40 °C. The decay of 2-syn with time at 25 °C allows the unprecedented monitoring of the steps involved in the intramolecular hydroxylation of the ligand phenyl ring to form the major FeIII -OAr product 3. At the same time, the FeII (Bn3MC)2+ (1) precursor to 2-syn is re-generated in a 1:2 molar ratio relative to 3, accounting for the first time for all the electrons involved and all the Fe species derived from 2-syn as shown in the following balanced equation: 3 [FeIV (O)(LPh )]2+ (2-syn)→2 [FeIII (LOAr )]2+ (3)+[FeII (LPh )]2+ (1)+H2 O. This system thus serves as a paradigm for aryl hydroxylation by FeIV =O oxidants described thus far. It is also observed that 2-syn can be intercepted by certain hydrocarbon substrates, thereby providing a means to assess the relative energetics of aliphatic and aromatic C-H hydroxylation in this system.
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Affiliation(s)
- Yuan Sheng
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Chase S Abelson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jai Prakash
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Apparao Draksharapu
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Victor G Young
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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7
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Latifi R, Palluccio TD, Ye W, Minnick JL, Glinton KS, Rybak-Akimova EV, de Visser SP, Tahsini L. pH Changes That Induce an Axial Ligand Effect on Nonheme Iron(IV) Oxo Complexes with an Appended Aminopropyl Functionality. Inorg Chem 2021; 60:13821-13832. [PMID: 34291939 DOI: 10.1021/acs.inorgchem.1c01312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonheme iron enzymes often utilize a high-valent iron(IV) oxo species for the biosynthesis of natural products, but their high reactivity often precludes structural and functional studies of these complexes. In this work, a combined experimental and computational study is presented on a biomimetic nonheme iron(IV) oxo complex bearing an aminopyridine macrocyclic ligand and its reactivity toward olefin epoxidation upon changes in the identity and coordination ability of the axial ligand. Herein, we show a dramatic effect of the pH on the oxygen-atom-transfer (OAT) reaction with substrates. In particular, these changes have occurred because of protonation of the axial-bound pendant amine group, where its coordination to iron is replaced by a solvent molecule or anionic ligand. This axial ligand effect influences the catalysis, and we observe enhanced cyclooctene epoxidation yields and turnover numbers in the presence of the unbound protonated pendant amine group. Density functional theory studies were performed to support the experiments and highlight that replacement of the pendant amine with a neutral or anionic ligand dramatically lowers the rate-determining barriers of cyclooctene epoxidation. The computational work further establishes that the change in OAT is due to electrostatic interactions of the pendant amine cation that favorably affect the barrier heights.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Taryn D Palluccio
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Wanhua Ye
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Kwame S Glinton
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Elena V Rybak-Akimova
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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8
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Jin L, Wang Q, Chen X, Liu N, Fang X, Yang YF, She YB. Computational Studies on the Mechanism and Origin of the Different Regioselectivities of Manganese Porphyrin-Catalyzed C-H Bond Hydroxylation and Amidation of Equilenin Acetate. J Org Chem 2020; 85:14879-14889. [PMID: 33225704 DOI: 10.1021/acs.joc.0c01444] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate developed by Breslow and his co-worker have been investigated with density functional theory (DFT) calculations. The hydroxylation of C(sp2)-H bond of equilenin acetate leading to the 6-hydroxylated product is more favorable than the hydroxylation of C(sp3)-H bond of equilenin acetate, leading to the 11β-hydroxylation product. The computational results suggest that the C(sp2)-H bond hydroxylation of equilenin acetate undergoes an oxygen-atom-transfer mechanism, which is more favorable than the C(sp3)-H bond hydroxylation undergoing the hydrogen-atom-abstraction/oxygen-rebound (HAA/OR) mechanism by 1.6 kcal/mol. That is why, the 6-hydroxylated product is the major product and the 11β-hydroxylated product is the minor product. In contrast, the 11β-amidated product is the only observed product in manganese porphyrin-catalyzed amidation reaction. The benzylic amidation undergoes a hydrogen-atom-abstraction/nitrogen-rebound (HAA/NR) mechanism, in which hydrogen atom abstraction is followed by nitrogen rebound, leading to the 11β-amidated product. The benzylic C(sp3)-H bond amidation at the C-11 position is more favorable than aromatic amidation at the C-6 position by 4.9 kcal/mol. Therefore, the DFT computational results are consistent with the experiments that manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate have different regioselectivities.
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Affiliation(s)
- Liyuan Jin
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Qunmin Wang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xiahe Chen
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Ning Liu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xiaoli Fang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yun-Fang Yang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yuan-Bin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
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9
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Maldonado-Domínguez M, Srnec M. Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis. J Am Chem Soc 2020; 142:3947-3958. [PMID: 32000494 DOI: 10.1021/jacs.9b12800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.
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Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
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10
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Zhang S, Liu Y. Mechanism of fatty acid decarboxylation catalyzed by a non-heme iron oxidase (UndA): a QM/MM study. Org Biomol Chem 2019; 17:9808-9818. [PMID: 31710061 DOI: 10.1039/c9ob02116g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UndA is a non-heme iron enzyme that was recognized to catalyze the decarboxylation of medium chain (C10-C14) fatty acids to produce trace amounts of 1-alkenes. Owing to the electron imbalance during the oxidative decarboxylation of the substrate and the reduction of O2, only single turnover reactions were obtained in UndA in vitro assays. Unlike the general non-heme iron enzymes, the catalytic efficiency of UndA is quite low. According to the previous proposal, both FeIII-OO˙- and FeIV[double bond, length as m-dash]O complexes may abstract the β-H of fatty acids to trigger the oxidative decarboxylation reaction. Herein, on the basis of the crystal structures of UndA in complex with the substrate analogues, we constructed a series of computational models and performed quantum mechanics/molecular mechanics (QM/MM) calculations to explore the UndA-catalyzed decarboxylation using lauric acid as the substrate. Our calculation results reveal that only the FeIII-OO˙- complex can initiate the decarboxylation, and the substrate (lauric acid) should monodentately coordinate to the Fe center to facilitate the β-H abstraction. In addition, the monodentate coordination corresponds to higher relative energy than the bidentate mode, which may explain the low efficiency of UndA. It is also revealed that as long as the β-H is extracted by the FeIII-OO˙-, the decarboxylation of the substrate radical is quite easy, and an electron transfer from the substrate to the iron center is the prerequisite. For the FeIV[double bond, length as m-dash]O complex, since the β-H is far from the OFe atom and the angle of ∠Fe-O-H is 53.1°, the H-abstraction is calculated to be difficult.
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Affiliation(s)
- Shiqing Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
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11
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Mukherjee M, Dey A. Electron Transfer Control of Reductase versus Monooxygenase: Catalytic C-H Bond Hydroxylation and Alkene Epoxidation by Molecular Oxygen. ACS CENTRAL SCIENCE 2019; 5:671-682. [PMID: 31041387 PMCID: PMC6487540 DOI: 10.1021/acscentsci.9b00046] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Indexed: 05/11/2023]
Abstract
Catalytic oxidation of organic substrates, using a green oxidant like O2, has been a long-term goal of the scientific community. In nature, these oxidations are performed by metalloenzymes that generate highly oxidizing species from O2, which, in turn, can oxidize very stable organic substrates, e.g., mono-/dioxygenases. The same oxidants are produced during O2 reduction/respiration in the mitochondria but are reduced by electron transfer, i.e., reductases. Iron porphyrin mimics of the active site of cytochrome P450 (Cyt P450) are created atop a self-assembled monolayer covered electrode. The rate of electron transfer from the electrode to the iron porphyrin site is attenuated to derive monooxygenase reactivity from these constructs that otherwise show O2 reductase activity. Catalytic hydroxylation of strong C-H bonds to alcohol and epoxidation of alkenes, using molecular O2 (with 18O2 incorporation), is demonstrated with turnover numbers >104. Uniquely, one of the two iron porphyrin catalysts used shows preferential oxidation of 2° C-H bonds of cycloalkanes to alcohols over 3° C-H bonds without overoxidation to ketones. Mechanistic investigations with labeled substrates indicate that a compound I (FeIV=O bound to a porphyrin cation radical) analogue, formed during O2 reduction, is the primary oxidant. The selectivity is determined by the shape of the distal pocket of the catalyst, which, in turn, is determined by the substituents on the periphery of the porphyrin macrocycle.
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Affiliation(s)
| | - Abhishek Dey
- Address:
Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, 2A&2B
Raja SC Mullick Road, Jadavpur, Kolkata, West Bengal, India 700032.
E-mail:
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12
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Lankelma M, Olivares AM, de Bruin B. [Co(TPP)]-Catalyzed Formation of Substituted Piperidines. Chemistry 2019; 25:5658-5663. [PMID: 30844097 PMCID: PMC6563703 DOI: 10.1002/chem.201900587] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Indexed: 01/12/2023]
Abstract
Radical cyclization via cobalt(III)-carbene radical intermediates is a powerful method for the synthesis of (hetero)cyclic structures. Building on the recently reported synthesis of five-membered N-heterocyclic pyrrolidines catalyzed by CoII porphyrins, the [Co(TPP)]-catalyzed formation of useful six-membered N-heterocyclic piperidines directly from linear aldehydes is presented herein. The piperidines were obtained in overall high yields, with linear alkenes being formed as side products in small amounts. A DFT study was performed to gain a deeper mechanistic understanding of the cobalt(II)-porphyrin-catalyzed formation of pyrrolidines, piperidines, and linear alkenes. The calculations showed that the alkenes are unlikely to be formed through an expected 1,2-hydrogen-atom transfer to the carbene carbon. Instead, the calculations were consistent with a pathway involving benzyl-radical formation followed by radical-rebound ring closure to form the piperidines. Competitive 1,5-hydrogen-atom transfer from the β-position to the benzyl radical explained the formation of linear alkenes as side products.
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Affiliation(s)
- Marianne Lankelma
- Van 't Hoff Institute for Molecular Sciences (HIMS)Homogeneous, Supramolecular & Bio-Inspired CatalysisUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Astrid M. Olivares
- Department of ChemistryUniversity of Rochester404 Hutchison HallRochesterNY14627-0216USA
| | - Bas de Bruin
- Van 't Hoff Institute for Molecular Sciences (HIMS)Homogeneous, Supramolecular & Bio-Inspired CatalysisUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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13
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Saito T, Fujiwara M, Takano Y. Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results. Molecules 2018; 23:E3332. [PMID: 30558286 PMCID: PMC6321459 DOI: 10.3390/molecules23123332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 11/17/2022] Open
Abstract
We report a reparameterization of PM6 parameters for fluorine and chlorine using our training set containing transition metal complexes. Spin unrestricted calculations with the resulting rPM6 (UrPM6) were examined quantitatively using two test sets: (i) the description of magnetic interactions in 25 dinuclear metal complexes and (ii) the prediction of barrier heights and reaction energies for epoxidation and fluorination reactions catalyzed by high-valent manganese-oxo species. The conventional UPM6 and UPM7 methods were also evaluated for comparison on the basis of either experimental or computational (the UB3LYP/SVP level) outcomes. The merits of UrPM6 are highlighted by both the test sets. As regards magnetic exchange coupling constants, the UrPM6 method had the smallest mean absolute errors from the experimental data (19 cm-1), followed by UPM7 (119 cm-1) and UPM6 (373 cm-1). For the epoxidation and fluorination reactions, all of the transition state searches were successful using UrPM6, while the success rates obtained by UPM6 and UPM7 were only 50%. The UrPM6-optimized stationary points also agreed well with the reference UB3LYP-optimized geometries. The accuracy for estimating reaction energies was also greatly remedied.
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Affiliation(s)
- Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan.
| | - Manami Fujiwara
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan.
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan.
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14
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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15
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Pandey B, Jaccob M, Rajaraman G. Mechanistic insights into intramolecular ortho-amination/hydroxylation by nonheme Fe IV[double bond, length as m-dash]NTs/Fe IV[double bond, length as m-dash]O species: the σ vs. the π channels. Chem Commun (Camb) 2018; 53:3193-3196. [PMID: 28220156 DOI: 10.1039/c6cc08761b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Comparative oxidative abilities of nonheme FeIV[double bond, length as m-dash]NTs and FeIV[double bond, length as m-dash]O species using DFT has been explored. Our calculations reveal that the FeIV[double bond, length as m-dash]NTs is found to be a stronger oxidant in two electron transfer reactions and react exclusively via π channels while the FeIV[double bond, length as m-dash]O species is found to be a stronger oxidant when the σ-pathway is activated such as in HAT reactions.
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Affiliation(s)
- Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India.
| | - Madhavan Jaccob
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India. and Department of Chemistry, Loyola College, Chennai 600 034, Tamil Nadu, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India.
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16
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Cantú Reinhard FG, Faponle AS, de Visser SP. Substrate Sulfoxidation by an Iron(IV)-Oxo Complex: Benchmarking Computationally Calculated Barrier Heights to Experiment. J Phys Chem A 2016; 120:9805-9814. [PMID: 27973805 DOI: 10.1021/acs.jpca.6b09765] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
High-valent metal-oxo oxidants are common reactive species in synthetic catalysts as well as heme and nonheme iron enzymes. In general, they efficiently react with substrates through oxygen atom transfer, and for a number of cases, experimental rate constants have been determined. However, because these rate constants are generally measured in a polar solution, it has been found difficult to find computational methodologies to reproduce experimental trends and reactivities. In this work, we present a detailed computational study into para-substituted thioanisole sulfoxidation by a nonheme iron(IV)-oxo complex. A range of density functional theory methods and basis sets has been tested for their suitability to describe the reaction mechanism and compared with experimentally obtained free energies of activation. It is found that the enthalpy of activation is reproduced well, but all methods overestimate the entropy of activation by about 50%, for which we recommend a correction factor. The effect of solvent and dispersion on the barrier heights is explored both at the single-point level and also through inclusion in geometry optimizations, and particularly, solvent is seen as highly beneficial to reproduce experimental free energies of activation. Interestingly, in general, experimental trends and Hammett plots are reproduced well with almost all methods and procedures, and only a systematic error seems to apply for these chemical systems. Very good agreement between experiment and theory is found for a number of different methods, including B3LYP and PBE0, and procedures that are highlighted in the paper.
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Affiliation(s)
- Fabián G Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - 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
| | - 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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17
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Cantú Reinhard FG, Sainna MA, Upadhyay P, Balan GA, Kumar D, Fornarini S, Crestoni ME, de Visser SP. A Systematic Account on Aromatic Hydroxylation by a Cytochrome P450 Model Compound I: A Low-Pressure Mass Spectrometry and Computational Study. Chemistry 2016; 22:18608-18619. [PMID: 27727524 DOI: 10.1002/chem.201604361] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Indexed: 01/20/2023]
Abstract
Cytochrome P450 enzymes are heme-containing mono-oxygenases that mainly react through oxygen-atom transfer. Specific features of substrate and oxidant that determine the reaction rate constant for oxygen atom transfer are still poorly understood and therefore, we did a systematic gas-phase study on reactions by iron(IV)-oxo porphyrin cation radical structures with arenes. We present herein the first results obtained by using Fourier transform-ion cyclotron resonance mass spectrometry and provide rate constants and product distributions for the assayed reactions. Product distributions and kinetic isotope effect studies implicate a rate-determining aromatic hydroxylation reaction that correlates with the ionization energy of the substrate and no evidence of aliphatic hydroxylation products is observed. To further understand the details of the reaction mechanism, a computational study on a model complex was performed. These studies confirm the experimental hypothesis of dominant aromatic over aliphatic hydroxylation and show that the lack of an axial ligand affects the aliphatic pathways. Moreover, a two-parabola valence bond model is used to rationalize the rate constant and identify key properties of the oxidant and substrate that drive the reaction. In particular, the work shows that aromatic hydroxylation rates correlate with the ionization energy of the substrate as well as with the electron affinity of the oxidant.
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Affiliation(s)
- Fabián G Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Mala A Sainna
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Pranav Upadhyay
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (UP, 226025, India
| | - G Alex Balan
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (UP, 226025, India
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - 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, UK
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18
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Yang T, Quesne MG, Neu HM, Cantú Reinhard FG, Goldberg DP, de Visser SP. Singlet versus Triplet Reactivity in an Mn(V)-Oxo Species: Testing Theoretical Predictions Against Experimental Evidence. J Am Chem Soc 2016; 138:12375-86. [PMID: 27545752 PMCID: PMC5228574 DOI: 10.1021/jacs.6b05027] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Discerning the factors that control the reactivity of high-valent metal-oxo species is critical to both an understanding of metalloenzyme reactivity and related transition metal catalysts. Computational studies have suggested that an excited higher spin state in a number of metal-oxo species can provide a lower energy barrier for oxidation reactions, leading to the conclusion that this unobserved higher spin state complex should be considered as the active oxidant. However, testing these computational predictions by experiment is difficult and has rarely been accomplished. Herein, we describe a detailed computational study on the role of spin state in the reactivity of a high-valent manganese(V)-oxo complex with para-Z-substituted thioanisoles and utilize experimental evidence to distinguish between the theoretical results. The calculations show an unusual change in mechanism occurs for the dominant singlet spin state that correlates with the electron-donating property of the para-Z substituent, while this change is not observed on the triplet spin state. Minimum energy crossing point calculations predict small spin-orbit coupling constants making the spin state change from low spin to high spin unlikely. The trends in reactivity for the para-Z-substituted thioanisole derivatives provide an experimental measure for the spin state reactivity in manganese-oxo corrolazine complexes. Hence, the calculations show that the V-shaped Hammett plot is reproduced by the singlet surface but not by the triplet state trend. The substituent effect is explained with valence bond models, which confirm a change from an electrophilic to a nucleophilic mechanism through a change of substituent.
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Affiliation(s)
- Tzuhsiung Yang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Matthew G. Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Heather M. Neu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - 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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19
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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20
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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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Faponle AS, Quesne MG, Sastri CV, Banse F, de Visser SP. Differences and comparisons of the properties and reactivities of iron(III)-hydroperoxo complexes with saturated coordination sphere. Chemistry 2015; 21:1221-36. [PMID: 25399782 PMCID: PMC4316188 DOI: 10.1002/chem.201404918] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 11/06/2022]
Abstract
Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)-oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)-hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)-hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)-hydroperoxo reacted directly with substrates or that an initial O-O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)-hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)-hydroperoxo complex with pentadentate ligand system (L5(2)). Direct C-O bond formation by an iron(III)-hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L5(2))Fe(III)(OOH)](2+) should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)-hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O-O bond, whereas a heterolytic O-O bond breaking in heme iron(III)-hydroperoxo is found.
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Affiliation(s)
- Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati781039, Assam (India)
| | - Frédéric Banse
- Institut de Chimie Moleculaire et des Materiaux d'Orsay, Laboratoire de Chimie Inorganique, Université Paris-Sud11 91405 Orsay Cedex (France) E-mail:
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
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22
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Das PK, Dey A. Resonance Raman, Electron Paramagnetic Resonance, and Density Functional Theory Calculations of a Phenolate-Bound Iron Porphyrin Complex: Electrostatic versus Covalent Contribution to Bonding. Inorg Chem 2014; 53:7361-70. [DOI: 10.1021/ic500716d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pradip Kumar Das
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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24
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Sun X, Geng C, Huo R, Ryde U, Bu Y, Li J. Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes. J Phys Chem B 2014; 118:1493-500. [PMID: 24471414 DOI: 10.1021/jp410727r] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this article, we present density functional theory (DFT) calculations on the iron(IV)-oxo catalyzed methane C-H activation reactions for complexes in which the Fe(IV)═O core is surrounded by five negatively charged ligands. We found that it follows a hybrid pathway that mixes features of the classical σ- and π-pathways in quintet surfaces. These calculations show that the Fe-O-H arrangement in this hybrid pathway is bent in sharp contrast to the collinear character as observed for the classical quintet σ-pathways before. The calculations have also shown that it is the equatorial ligands that play key roles in tuning the reactivity of Fe(IV)═O complexes. The strong π-donating equatorial ligands employed in the current study cause a weak π(FeO) bond and thereby shift the electronic accepting orbitals (EAO) from the vertically orientated O pz orbital to the horizontally orientated O px. In addition, all the equatorial ligands are small in size and would therefore be expected have small steric effects upon substrate horizontal approaching. Therefore, for the small and strong π-donating equatorial ligands, the collinear Fe-O-H arrangement is not the best choice for the quintet reactivity. This study adds new element to iron(IV)-oxo catalyzed C-H bond activation reactions.
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Affiliation(s)
- Xiaoli Sun
- State Key Lab of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Liutiao Road 2, Changchun 130023, People's Republic of China
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25
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de Visser SP, Quesne MG, Martin B, Comba P, Ryde U. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. Chem Commun (Camb) 2014; 50:262-82. [DOI: 10.1039/c3cc47148a] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Samanta S, Das PK, Chatterjee S, Sengupta K, Mondal B, Dey A. O2 Reduction Reaction by Biologically Relevant Anionic Ligand Bound Iron Porphyrin Complexes. Inorg Chem 2013; 52:12963-71. [DOI: 10.1021/ic4020652] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subhra Samanta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Pradip Kumar Das
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Biswajit Mondal
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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27
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Liu LV, Hong S, Cho J, Nam W, Solomon EI. Comparison of high-spin and low-spin nonheme Fe(III)-OOH complexes in O-O bond homolysis and H-atom abstraction reactivities. J Am Chem Soc 2013; 135:3286-99. [PMID: 23368958 PMCID: PMC3614352 DOI: 10.1021/ja400183g] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The geometric and electronic structures and reactivity of an S = 5/2 (HS) mononuclear nonheme (TMC)Fe(III)-OOH complex are studied by spectroscopies, calculations, and kinetics and compared with the results of previous studies of S = 1/2 (LS) Fe(III)-OOH complexes to understand parallels and differences in mechanisms of O-O bond homolysis and electrophilic H-atom abstraction reactions. The homolysis reaction of the HS [(TMC)Fe(III)-OOH](2+) complex is found to involve axial ligand coordination and a crossing to the LS surface for O-O bond homolysis. Both HS and LS Fe(III)-OOH complexes are found to perform direct H-atom abstraction reactions but with very different reaction coordinates. For the LS Fe(III)-OOH, the transition state is late in O-O and early in C-H coordinates. However, for the HS Fe(III)-OOH, the transition state is early in O-O and further along in the C-H coordinate. In addition, there is a significant amount of electron transfer from the substrate to the HS Fe(III)-OOH at transition state, but that does not occur in the LS transition state. Thus, in contrast to the behavior of LS Fe(III)-OOH, the H-atom abstraction reactivity of HS Fe(III)-OOH is found to be highly dependent on both the ionization potential and the C-H bond strength of the substrate. LS Fe(III)-OOH is found to be more effective in H-atom abstraction for strong C-H bonds, while the higher reduction potential of HS Fe(III)-OOH allows it to be active in electrophilic reactions without the requirement of O-O bond cleavage. This is relevant to the Rieske dioxygenases, which are proposed to use a HS Fe(III)-OOH to catalyze cis-dihydroxylation of a wide range of aromatic compounds.
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Affiliation(s)
- Lei V. Liu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Seungwoo Hong
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeheung Cho
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
- Department of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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Tang H, Guan J, Liu H, Huang X. Comparative Insight into Electronic Properties and Reactivities toward C–H Bond Activation by Iron(IV)–Nitrido, Iron(IV)–Oxo, and Iron(IV)–Sulfido Complexes: A Theoretical Investigation. Inorg Chem 2013; 52:2684-96. [DOI: 10.1021/ic302766f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hao Tang
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Jia Guan
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Huiling Liu
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Xuri Huang
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
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29
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Latifi R, Sainna MA, Rybak-Akimova EV, de Visser SP. Does Hydrogen-Bonding Donation to Manganese(IV)-Oxo and Iron(IV)-Oxo Oxidants Affect the Oxygen-Atom Transfer Ability? A Computational Study. Chemistry 2013; 19:4058-68. [DOI: 10.1002/chem.201202811] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 11/16/2012] [Indexed: 12/21/2022]
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30
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Intrinsic properties and reactivities of mononuclear nonheme iron–oxygen complexes bearing the tetramethylcyclam ligand. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Das PK, Chatterjee S, Samanta S, Dey A. EPR, resonance Raman, and DFT calculations on thiolate- and imidazole-bound iron(III) porphyrin complexes: role of the axial ligand in tuning the electronic structure. Inorg Chem 2012; 51:10704-14. [PMID: 23013308 DOI: 10.1021/ic3016035] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Iron(III) porphyrin complexes bearing covalently attached imidazole and thiolate axial ligands are investigated using resonance Raman, electron paramagnetic resonance, and cyclic voltammetry. The thiolate ligand stabilizes a low-spin ground state in solvent-bound six-coordinate species, weakens the Fe-N(pyr) bonds, and shifts the Fe(III/II) potential more negative by ~500 mV relative to an imidazole-bound species. Density functional theory calculations reproduce the experimental observation and indicate that the covalent charge donation from thiolate to iron reduces the Z(eff) on the iron. This increases the Fe(3d) orbital energies, which changes the bonding interaction present in these complexes significantly. In particular, the increase of the Fe(3d) energies activates an iron-to-porphyrin π*-back-bonding interaction not present in the imidazole-bound complex.
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Affiliation(s)
- Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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32
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Regioselectivity of substrate hydroxylation versus halogenation by a nonheme iron(IV)–oxo complex: possibility of rearrangement pathways. J Biol Inorg Chem 2012; 17:841-52. [DOI: 10.1007/s00775-012-0901-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
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33
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Jaccob M, Rajaraman G. A computational examination on the structure, spin-state energetics and spectroscopic parameters of high-valent FeIVNTs species. Dalton Trans 2012; 41:10430-9. [DOI: 10.1039/c2dt31071f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Tang H, Guan J, Zhang L, Liu H, Huang X. The effect of the axial ligand on distinct reaction tunneling for methane hydroxylation by nonheme iron(iv)–oxo complexes. Phys Chem Chem Phys 2012; 14:12863-74. [DOI: 10.1039/c2cp42423a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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de Visser SP. Predictive studies of oxygen atom transfer reactions by Compound I of cytochrome P450. ADVANCES IN INORGANIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396462-5.00001-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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36
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Kumar D, Sastry GN, de Visser SP. Axial Ligand Effect On The Rate Constant of Aromatic Hydroxylation By Iron(IV)–Oxo Complexes Mimicking Cytochrome P450 Enzymes. J Phys Chem B 2011; 116:718-30. [DOI: 10.1021/jp2113522] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow 226 025, India
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
| | - G. Narahari Sastry
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
| | - Sam P. de Visser
- Manchester Interdisciplinary Biocenter and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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37
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Kumar D, Sastry GN, Goldberg DP, de Visser SP. Mechanism of S-oxygenation by a cysteine dioxygenase model complex. J Phys Chem A 2011; 116:582-91. [PMID: 22091701 DOI: 10.1021/jp208230g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we present the first computational study on a biomimetic cysteine dioxygenase model complex, [Fe(II)(LN(3)S)](+), in which LN(3)S is a tetradentate ligand with a bis(imino)pyridyl scaffold and a pendant arylthiolate group. The reaction mechanism of sulfur dioxygenation with O(2) was examined by density functional theory (DFT) methods and compared with results obtained for cysteine dioxygenase. The reaction proceeds via multistate reactivity patterns on competing singlet, triplet, and quintet spin state surfaces. The reaction mechanism is analogous to that found for cysteine dioxygenase enzymes (Kumar, D.; Thiel, W.; de Visser, S. P. J. Am. Chem. Soc. 2011, 133, 3869-3882); hence, the computations indicate that this complex can closely mimic the enzymatic process. The catalytic mechanism starts from an iron(III)-superoxo complex and the attack of the terminal oxygen atom of the superoxo group on the sulfur atom of the ligand. Subsequently, the dioxygen bond breaks to form an iron(IV)-oxo complex with a bound sulfenato group. After reorganization, the second oxygen atom is transferred to the substrate to give a sulfinic acid product. An alternative mechanism involving the direct attack of dioxygen on the sulfur, without involving any iron-oxygen intermediates, was also examined. Importantly, a significant energetic preference for dioxygen coordinating to the iron center prior to attack at sulfur was discovered and serves to elucidate the function of the metal ion in the reaction process. The computational results are in good agreement with experimental observations, and the differences and similarities of the biomimetic complex and the enzymatic cysteine dioxygenase center are highlighted.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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Kumar D, Sastry GN, de Visser SP. Effect of the axial ligand on substrate sulfoxidation mediated by iron(IV)-oxo porphyrin cation radical oxidants. Chemistry 2011; 17:6196-205. [PMID: 21469227 DOI: 10.1002/chem.201003187] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Indexed: 11/09/2022]
Abstract
Cytochromes P450 catalyze a range of different oxygen-transfer processes including aliphatic and aromatic hydroxylation, epoxidation, and sulfoxidation reactions. Herein, we have investigated substrate sulfoxidation mediated by models of P450 enzymes as well as by biomimetic oxidants using density functional-theory methods and we have rationalized the sulfoxidation reaction barriers and rate constants. We carried out two sets of calculations: first, we calculated the sulfoxidation by an iron(IV)-oxo porphyrin cation radical oxidant [Fe(IV)=O(Por(+.))SH] that mimics the active site of cytochrome P450 enzymes with a range of different substrates, and second, we studied one substrate (dimethyl sulfide) with a selection of different iron(IV)-oxo porphyrin cation radical oxidants [Fe(IV)=O(Por(+.))L] with varying axial ligands L. The study presented herein shows that the barrier height for substrate sulfoxidation correlates linearly with the ionization potential of the substrate, thus reflecting the electron-transfer processes in the rate-determining step of the reaction. Furthermore, the axial ligand of the oxidant influences the pK(a) value of the iron(IV)-oxo group, and, as a consequence, the bond dissociation energy (BDE(OH) value correlates with the barrier height for the reverse sulfoxidation reaction. These studies have generalized substrate-sulfoxidation reactions and have shown how they fundamentally compare with substrate hydroxylation and epoxidation reactions.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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39
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Bernasconi L, Belanzoni P, Baerends EJ. An abiotic analogue of the diiron(iv)oxo “diamond core” of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(ii)/EDTA solutions: thermodynamics and electronic structure. Phys Chem Chem Phys 2011; 13:15272-82. [DOI: 10.1039/c1cp21244c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Seo MS, Kim NH, Cho KB, So JE, Park SK, Clémancey M, Garcia-Serres R, Latour JM, Shaik S, Nam W. A mononuclear nonheme iron(iv)-oxo complex which is more reactive than cytochrome P450 model compound I. Chem Sci 2011. [DOI: 10.1039/c1sc00062d] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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41
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Cho J, Woo J, Eun Han J, Kubo M, Ogura T, Nam W. Chromium(v)-oxo and chromium(iii)-superoxo complexes bearing a macrocyclic TMC ligand in hydrogen atom abstraction reactions. Chem Sci 2011. [DOI: 10.1039/c1sc00386k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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