4.6 Article

DFT mechanistic study of biomimetic diiron complex catalyzed dehydrogenation: Unexpected Fe(III)Fe(III)-1,1-μ-hydroperoxy active species for hydride abstraction

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

Mechanism for the synthesis of medium-chain 1-alkenes from fatty acids catalyzed by binuclear iron UndA decarboxylase

Ying Wang et al.

Summary: Terminal olefins synthesized by decarboxylation of fatty acids are important chemicals. PfUndA is a di-iron oxidase that can convert medium-chain fatty acids into 1-alkenes. The mechanism involves H+/e(-) introduction, O - O bond dissociation, formation of intermediates and substrate Cb radical, stepwise decarboxylation, and protonation of Fe-bound hydroxides. The low catalytic efficiency of UndA may be due to the energy penalty caused by the drop of active high-spin Fe(III)-O· to inert medium-spin Fe(IV)=O. (c) 2023 Elsevier Inc. All rights reserved.

JOURNAL OF CATALYSIS (2023)

Article Chemistry, Physical

Peroxo-Diiron(III/III) as the Reactive Intermediate for N-Hydroxylation Reactions in the Multidomain Metalloenzyme SznF: Evidence from Molecular Dynamics and Quantum Mechanical/ Molecular Mechanical Calculations

Jia Liu et al.

Summary: The catalytic mechanism of the diiron active site in SznF has been comprehensively studied using molecular docking, classical MD, QM/MM MD simulations, and hybrid QM/MM calculations. The study reveals that the peroxo-diiron(III/III) intermediate in SznF maintains a butterfly-like conformation and further protonation of the diiron(III/III) intermediate is thermodynamically unfavorable. The nucleophilic attack of the guanidium group onto the peroxo group of P1 is the most favorable mechanism for N-hydroxylation. The study expands our understanding of O2 activation and N-hydroxylation by non-heme diiron enzymes.

ACS CATALYSIS (2023)

Review Chemistry, Physical

Mixed Valence (μ-Phenoxido) FeIIFeIII et FeIIIFeIV Compounds: Electron and Proton Transfers

Patrick Dubourdeaux et al.

Summary: Mixed-valence non-heme diiron centers are present in the active sites of certain enzymes, exhibiting interesting reactivities with two ions acting in concert. Studies have shown that (mu-phenoxido)diiron complexes can mimic enzyme catalytic mechanisms and produce various electron transfers, proton transfers, and coupled electron and proton transfers.

CHEMPHYSCHEM (2022)

Article Chemistry, Physical

Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ

Xitong Song et al.

Summary: Organophosphonate (Pn) catabolism is the major source of inorganic phosphate (Pi), and the enzyme PhnZ catalyzes the oxidative transformation of Pn. Through calculations, the oxygen activation and organophosphonate catabolism mechanisms of PhnZ are uncovered, along with the proposed catalytic cycle. These studies expand our understanding of the catalysis and function of this enzyme.

ACS CATALYSIS (2022)

Article Biochemistry & Molecular Biology

Substrate-Triggered μ-Peroxodiiron(III) Intermediate in the 4-Chloro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate

Molly J. McBride et al.

Summary: A newly discovered enzyme BesC from Streptomyces cattleya has been found to catalyze the biosynthesis of beta-ethynyl-L-serine. The enzyme can fragment 4-chloro-L-lysine and L-lysine itself, and the degradation of the intermediate formed during the reaction is influenced by the presence of different analogues. The study also suggests that hydrogen atom extraction plays a role in olefin formation.

BIOCHEMISTRY (2022)

Article Biochemistry & Molecular Biology

Second Coordination Sphere Effects on the Mechanistic Pathways for Dioxygen Activation by a Ferritin: Involvement of a Tyr Radical and the Identification of a Cation Binding Site

Chieh-Chih George Yeh et al.

Summary: Ferritins are widespread diiron enzymes that play a role in iron detoxification and oxidative stress responses, as well as serving as metabolic iron storage. Computational studies have provided insights into the structure and reactivity of ferritins, revealing the importance of the active site tyrosine residue and a potential cation binding site. The findings offer new details on the early mechanistic steps of ferritin enzymes.

CHEMBIOCHEM (2022)

Article Chemistry, Multidisciplinary

Methane Monooxygenase Mimic Asymmetric Oxidation: Self-Assemblingμ-Hydroxo, Carboxylate-Bridged Diiron(III)-CatalyzedEnantioselective Dehydrogenation

Honghao Guan et al.

Summary: Mimicking naturally occurring metalloenzymes for catalytic asymmetric oxidation reactions has been a long-standing goal in modern chemistry. In this study, a series of chiral diiron complexes mimicking methane monooxygenase (MMO) were designed and synthesized, exhibiting efficient catalytic reactivity in dehydrogenative kinetic resolution. The C9 complex was identified as the optimal catalyst with high chiral recognition.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

Article Chemistry, Multidisciplinary

C(sp3)-H Hydroxylation in Diiron β-Hydroxylase CmlA Transpires by Amine-Assisted O2 Activation Avoiding Fe2IVO2 Species

Jiarui Lu et al.

Summary: Through QM/MM modeling, it was discovered that C(sp(3))-H beta-hydroxylation in the diiron hydroxylase CmlA occurs through traceless amine-assisted O-2 activation. This unique mode of O-2 activation generates a diferric (Fe2O2)-O-III species instead of the conventional diferryl (Fe22O2)-O-IV species, resulting in a different C(sp(3))-H hydroxylation mechanism compared to other diiron hydroxylases. This substrate-modulated O-2 activation in CmlA has significant implications for understanding the mechanism of other diiron hydroxylases with similar amine groups adjacent to C-H bonds. Furthermore, the adapted coordination environment of the diiron cofactor upon O-2 binding in CmlA opens up possibilities for O-2 activation in non-heme diiron enzymes.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Article Chemistry, Inorganic & Nuclear

Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis

Shiqing Zhang et al.

Summary: PtmU3 is a newly identified nonheme diiron monooxygenase with a special active site structure that can incorporate both atoms of a dioxygen molecule into substrates through successive reactions.

INORGANIC CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

BesC Initiates C-C Cleavage through a Substrate-Triggered and Reactive Diferric-Peroxo Intermediate

Olivia M. Manley et al.

Summary: BesC is a member of an emerging family of diiron enzymes that catalyze an unusual type of carbon-carbon cleavage reaction. It activates O-2 in a substrate-gated manner to generate a diferric-peroxo intermediate, initiating a unique reaction trajectory by cleaving the C4-H bond as the rate-limiting step in a single turnover reaction.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations

Christine E. Schulz et al.

Summary: This study extensively simulated possible conformations of intermediates in the sMMOH catalytic cycle using a quantum mechanics/molecular mechanics approach, providing strong support for an open-core configuration in MMOHQ. The implications of this open-core intermediate Q on the reaction mechanism of sMMO are discussed.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Physical

Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O-O Bond Activation in Nonheme Diiron Monooxygenase MIOX

Jia Liu et al.

Summary: The study demonstrates a spin-regulated inner-sphere electron transfer mechanism involved in catalytic reactions of MIOX, leading to the formation of an unprecedented Fe2(III)Fe1(II)-peroxyhemiketal intermediate responsible for reductive O-O cleavage. The cooperation of both Fe sites in O-2 activation in MIOX is well regulated by the spin-dependent inner-sphere electron transfer, which may have significant implications on other related nonheme diiron monooxygenases.

ACS CATALYSIS (2021)

Review Chemistry, Inorganic & Nuclear

O2 and H2O2 activations at dinuclear Mn and Fe active sites

Beatrice Battistella et al.

COORDINATION CHEMISTRY REVIEWS (2020)

Article Chemistry, Multidisciplinary

Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

Daniel Bim et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Multidisciplinary Sciences

An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin

Tai L. Ng et al.

NATURE (2019)

Article Chemistry, Multidisciplinary

Oxidative Decarboxylase UndA Utilizes a Dinuclear Iron Cofactor

Olivia M. Manley et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Chemistry, Multidisciplinary

Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA

Bo Zhang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Review Biochemistry & Molecular Biology

Diiron monooxygenases in natural product biosynthesis

Anna J. Komor et al.

NATURAL PRODUCT REPORTS (2018)

Article Chemistry, Multidisciplinary

Convergent Theoretical Prediction of Reactive Oxidant Structures in Diiron Arylamine Oxygenases AurF and Cmll: Peroxo or Hydroperoxo?

Chao Wang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Chemistry, Multidisciplinary

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

Kiyoung Park et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Chemistry, Multidisciplinary

Unprecedented (μ-1,1-Peroxo)diferric Structure for the Ambiphilic Orange Peroxo Intermediate of the Nonheme N-Oxygenase Cmll

Andrew J. Jasniewski et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Review Chemistry, Multidisciplinary

Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics

Vincent C. -C. Wang et al.

CHEMICAL REVIEWS (2017)

Article Biochemistry & Molecular Biology

Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway

Cory J. Knoot et al.

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2016)

Article Chemistry, Multidisciplinary

Mechanism for Six-Electron Aryl-N-Oxygenation by the Non-Heme Diiron Enzyme CmII

Anna J. Komor et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

Article Chemistry, Multidisciplinary

Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

Tibor Andras Rokob

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

Article Biochemistry & Molecular Biology

Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor

Julia J. Griese et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2015)

Article Chemistry, Multidisciplinary

An Unusual Peroxo Intermediate of the Arylamine Oxygenase of the Chloramphenicol Biosynthetic Pathway

Thomas M. Makris et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Multidisciplinary Sciences

Structure of the key species in the enzymatic oxidation of methane to methanol

Rahul Banerjee et al.

NATURE (2015)

Article Chemistry, Multidisciplinary

Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB

Rong-Zhen Liao et al.

CHEMICAL SCIENCE (2015)

Article Chemistry, Multidisciplinary

Reactivity of the Binuclear Non-Heme Iron Active Site of Δ9 Desaturase Studied by Large-Scale Multireference Ab Initio Calculations

Jakub Chalupsky et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Chemistry, Multidisciplinary

Effect of the Damping Function in Dispersion Corrected Density Functional Theory

Stefan Grimme et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Review Chemistry, Multidisciplinary

Current challenges of modeling diiron enzyme active sites for dioxygen activation by biomimetic synthetic complexes

Simone Friedle et al.

CHEMICAL SOCIETY REVIEWS (2010)

Article Chemistry, Multidisciplinary

A Long-Lived, Substrate-Hydroxylating Peroxodiiron(III/III) Intermediate in the Amine Oxygenase, AurF, from Streptomyces thioluteus

Victoria Korneeva Korboukh et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Chemistry, Inorganic & Nuclear

Bioinorganic Chemistry Modeled with the TPSSh Density Functional

Kasper P. Jensen

INORGANIC CHEMISTRY (2008)

Review Multidisciplinary Sciences

Biologically inspired oxidation catalysis

Lawrence Que et al.

NATURE (2008)

Article Multidisciplinary Sciences

In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis

Yoo Seong Choi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

A synthetic precedent for the [FeIV2(μ-O)2] diamond core proposed for methane monooxygenase intermediate Q

Genqiang Xue et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Multidisciplinary

Semiempirical GGA-type density functional constructed with a long-range dispersion correction

Stefan Grimme

JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)

Article Chemistry, Multidisciplinary

Reactions of the peroxo intermediate of soluble methane monooxygenase hydroxylase with ethers

LG Beauvais et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Multidisciplinary

Substrate hydroxylation in methane monooxygenase: Quantitative modeling via mixed quantum mechanics/molecular mechanics techniques

BF Gherman et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Physical

A new hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP)

T Yanai et al.

CHEMICAL PHYSICS LETTERS (2004)

Review Chemistry, Multidisciplinary

Reactions of the diiron enzyme stearoyl-acyl carrier protein desaturase

BG Fox et al.

ACCOUNTS OF CHEMICAL RESEARCH (2004)

Review Chemistry, Multidisciplinary

Mechanistic studies on the hydroxylation of methane by methane monooxygenase

MH Baik et al.

CHEMICAL REVIEWS (2003)

Review Chemistry, Multidisciplinary

A non-radical mechanism for methane hydroxylation at the diiron active site of soluble methane monooxygenase

K Yoshizawa et al.

CHEMISTRY-A EUROPEAN JOURNAL (2003)

Article Chemistry, Multidisciplinary

Hydroxylation of methane by non-heme diiron enzymes: Molecular orbital analysis of C-H bond activation by reactive intermediate Q

MH Baik et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Chemistry, Multidisciplinary

Reactions of methane monooxygenase intermediate Q with derivatized methanes

EA Ambundo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Chemistry, Multidisciplinary

Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase

V Guallar et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Chemistry, Multidisciplinary

A synthetically useful, self-assembling MMO mimic system for catalytic alkene epoxidation with aqueous H2O2

MC White et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Biochemistry & Molecular Biology

Two-step concerted mechanism for methane hydroxylation on the diiron active site of soluble methane monooxygenase

K Yoshizawa

JOURNAL OF INORGANIC BIOCHEMISTRY (2000)