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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Lee JHZ, Bruning JB, Bell SG. An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Chemistry 2024; 30:e202303335. [PMID: 37971151 DOI: 10.1002/chem.202303335] [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: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.
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Affiliation(s)
- Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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3
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Xu W, Wu Y, Gu W, Du D, Lin Y, Zhu C. Atomic-level design of metalloenzyme-like active pockets in metal-organic frameworks for bioinspired catalysis. Chem Soc Rev 2024; 53:137-162. [PMID: 38018371 DOI: 10.1039/d3cs00767g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Natural metalloenzymes with astonishing reaction activity and specificity underpin essential life transformations. Nevertheless, enzymes only operate under mild conditions to keep sophisticated structures active, limiting their potential applications. Artificial metalloenzymes that recapitulate the catalytic activity of enzymes can not only circumvent the enzymatic fragility but also bring versatile functions into practice. Among them, metal-organic frameworks (MOFs) featuring diverse and site-isolated metal sites and supramolecular structures have emerged as promising candidates for metalloenzymes to move toward unparalleled properties and behaviour of enzymes. In this review, we systematically summarize the significant advances in MOF-based metalloenzyme mimics with a special emphasis on active pocket engineering at the atomic level, including primary catalytic sites and secondary coordination spheres. Then, the deep understanding of catalytic mechanisms and their advanced applications are discussed. Finally, a perspective on this emerging frontier research is provided to advance bioinspired catalysis.
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Affiliation(s)
- Weiqing Xu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Yu Wu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Wenling Gu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, 99164, Pullman, USA.
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, 99164, Pullman, USA.
| | - Chengzhou Zhu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
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4
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Zhang Y, Mokkawes T, de Visser SP. Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202310785. [PMID: 37641517 DOI: 10.1002/anie.202310785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.
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Affiliation(s)
- Yi Zhang
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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5
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [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: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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6
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Podgorski MN, Keto AB, Coleman T, Bruning JB, De Voss JJ, Krenske EH, Bell SG. The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes. Chemistry 2023; 29:e202301371. [PMID: 37338048 DOI: 10.1002/chem.202301371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The cytochrome P450 (CYP) superfamily of monooxygenase enzymes play important roles in the metabolism of molecules which contain heterocyclic, aromatic functional groups. Here we study how oxygen- and sulfur-containing heterocyclic groups interact with and are oxidized using the bacterial enzyme CYP199A4. This enzyme oxidized both 4-(thiophen-2-yl)benzoic acid and 4-(thiophen-3-yl)benzoic acid almost exclusively via sulfoxidation. The thiophene oxides produced were activated towards Diels-Alder dimerization after sulfoxidation, forming dimeric metabolites. Despite X-ray crystal structures demonstrating that the aromatic carbon atoms of the thiophene ring were located closer to the heme than the sulfur, sulfoxidation was still favoured with 4-(thiophen-3-yl)benzoic acid. These results highlight a preference of this cytochrome P450 enzyme for sulfoxidation over aromatic hydroxylation. Calculations predict a strong preference for homodimerization of the enantiomers of the thiophene oxides and the formation of a single major product, in broad agreement with the experimental data. 4-(Furan-2-yl)benzoic acid was oxidized to 4-(4'-hydroxybutanoyl)benzoic acid using a whole-cell system. This reaction proceeded via a γ-keto-α,β-unsaturated aldehyde species which could be trapped in vitro using semicarbazide to generate a pyridazine species. The combination of the enzyme structures, the biochemical data and theoretical calculations provides detailed insight into the formation of the metabolites formed from these heterocyclic compounds.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Angus B Keto
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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7
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Lin Y, Wang H, King RB. Unraveling the Major Differences between the Trinuclear Cyclopentadienylmetal Carbonyl Chemistry of Cobalt and That of Nickel-A Theoretical Study. ACS OMEGA 2023; 8:25392-25400. [PMID: 37483223 PMCID: PMC10357559 DOI: 10.1021/acsomega.3c02849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023]
Abstract
The geometries and energetics of the trinuclear cyclopentadienylmetal carbonyls Cp3M3(CO)n (Cp = η5-C5H5); M = Co, Ni; n = 3, 2, 1, 0) have been investigated by density functional theory. The cobalt and nickel systems are found to be rather different owing to the different electronic configurations of the metal atoms. For cobalt, the small calculated energy separation of 5.0 kcal/mol between the two lowest-energy singlet Cp3Co3(μ3-CO)(μ-CO)2 and Cp3Co3(μ-CO)3 tricarbonyl structures accounts for the experimental results of both isomers as stable species that can be isolated and structurally characterized by X-ray crystallography. The corresponding Cp3Ni3(CO)3 species in the nickel system are predicted not to be viable owing to exothermic CO dissociation to give the experimentally observed very stable Cp3Ni3(μ-CO)2, which is found to be the lowest-energy isomer by a substantial margin of ∼25 kcal/mol. In all of the low-energy Cp3M3(CO)n (n = 2, 1) structures, including that of the experimentally known triplet spin state Cp3Co3(μ3-CO)2, all of the carbonyl groups are face-bridging or face-semi-bridging μ3-CO groups bonded to all three metal atoms of the M3 triangle. In the lowest-energy carbonyl-free Cp3M3 (M = Co, Ni) structures, agostic C-H-M interactions are found using hydrogens of the Cp rings. In addition, the lowest-energy Cp3Ni3 is the only structure among all of the low-energy Cp3M3(CO)n (M = Co, Ni; n = 3, 2, 1, 0) structures in which each Cp ring is a bridging rather than terminal ligand.
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Affiliation(s)
- Yuexia Lin
- School
of Physical Science and Technology, Key Laboratory of Advanced Technologies
of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
| | - Hongyan Wang
- School
of Physical Science and Technology, Key Laboratory of Advanced Technologies
of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
| | - R. Bruce King
- Department
of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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8
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Mokkawes T, de Visser SP. Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1? Int J Mol Sci 2023; 24:ijms24043651. [PMID: 36835057 PMCID: PMC9959256 DOI: 10.3390/ijms24043651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Correspondence:
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9
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Sun MZ, Lyu LS, Zheng QC. How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study. Phys Chem Chem Phys 2023; 25:5164-5173. [PMID: 36723118 DOI: 10.1039/d2cp05634h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.
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Affiliation(s)
- Min-Zhang Sun
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Ling-Shan Lyu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130023, China. .,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
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10
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Podgorski MN, Coleman T, Churchman LR, Bruning JB, De Voss JJ, Bell SG. Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Chemistry 2022; 28:e202202428. [PMID: 36169207 PMCID: PMC10100219 DOI: 10.1002/chem.202202428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H2 O2 complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H2 O2 complex which would be more abundant in the peroxide-driven reactions.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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11
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Nath AK, Roy M, Dey C, Dey A, Dey SG. Spin state dependent peroxidase activity of heme bound amyloid β peptides relevant to Alzheimer's disease. Chem Sci 2022; 13:14305-14319. [PMID: 36545147 PMCID: PMC9749105 DOI: 10.1039/d2sc05008k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
The colocalization of heme rich deposits in the senile plaque of Aβ in the cerebral cortex of the Alzheimer's disease (AD) brain along with altered heme homeostasis and heme deficiency symptoms in AD patients has invoked the association of heme in AD pathology. Heme bound Aβ complexes, depending on the concentration of the complex or peptide to heme ratio, exhibit an equilibrium between a high-spin mono-His bound peroxidase-type active site and a low-spin bis-His bound cytochrome b type active site. The high-spin heme-Aβ complex shows higher peroxidase activity than free heme, where compound I is the reactive oxidant. It is also capable of oxidizing neurotransmitters like serotonin in the presence of peroxide, owing to the formation of compound I. The low-spin bis-His heme-Aβ complex on the other hand shows enhanced peroxidase activity relative to high-spin heme-Aβ. It reacts with H2O2 to produce two stable intermediates, compound 0 and compound I, which are characterized by absorption, EPR and resonance Raman spectroscopy. The stability of compound I of low-spin heme-Aβ is accountable for its enhanced peroxidase activity and oxidation of the neurotransmitter serotonin. The effect of the second sphere Tyr10 residue of Aβ on the formation and stability of the intermediates of low-spin heme-Aβ has also been investigated. The higher stability of compound I for low-spin heme-Aβ is likely due to H-bonding interactions involving Tyr10 in the distal pocket.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Chinmay Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
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12
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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13
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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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14
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Reliably assessing the electronic structure of cytochrome P450 on today's classical computers and tomorrow's quantum computers. Proc Natl Acad Sci U S A 2022; 119:e2203533119. [PMID: 36095200 PMCID: PMC9499570 DOI: 10.1073/pnas.2203533119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chemical simulation is one of the most promising applications for future quantum computers. It is thought that quantum computers may enable accurate simulation for complex molecules that are otherwise impossible to simulate classically; that is, it displays quantum advantage. To better understand quantum advantage in chemical simulation, we explore what quantum and classical resources are required to simulate a series of pharmaceutically relevant molecules. Using classical methods, we show that reliable classical simulation of these molecules requires significant resources and therefore is a promising candidate for quantum simulation. We estimate the quantum resources, both in overall simulation time and the size. The insights from this study pave the way for future quantum simulation of complex molecules. An accurate assessment of how quantum computers can be used for chemical simulation, especially their potential computational advantages, provides important context on how to deploy these future devices. To perform this assessment reliably, quantum resource estimates must be coupled with classical computations attempting to answer relevant chemical questions and to define the classical algorithms simulation frontier. Herein, we explore the quantum computation and classical computation resources required to assess the electronic structure of cytochrome P450 enzymes (CYPs) and thus define a classical–quantum advantage boundary. This is accomplished by analyzing the convergence of density matrix renormalization group plus n-electron valence state perturbation theory (DMRG+NEVPT2) and coupled-cluster singles doubles with noniterative triples [CCSD(T)] calculations for spin gaps in models of the CYP catalytic cycle that indicate multireference character. The quantum resources required to perform phase estimation using qubitized quantum walks are calculated for the same systems. Compilation into the surface code provides runtime estimates to compare directly to DMRG runtimes and to evaluate potential quantum advantage. Both classical and quantum resource estimates suggest that simulation of CYP models at scales large enough to balance dynamic and multiconfigurational electron correlation has the potential to be a quantum advantage problem and emphasizes the important interplay between classical computations and quantum algorithms development for chemical simulation.
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15
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Lin Y, Wang H, Wang X, Wang H, King RB. Alternatives to Triple-Decker Sandwich Structures for Binuclear Cyclooctatetraene First-Row Transition Metal Complexes of the Type (C 8H 8) 3M 2. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuexia Lin
- School of Physical Science and Technology, Southwest Jiaotong University, Key Laboratory of Advanced Technologies of Materials, Ministry of Education of China, Chengdu 610031, China
| | - Hongyan Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Key Laboratory of Advanced Technologies of Materials, Ministry of Education of China, Chengdu 610031, China
| | - Xiaoting Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Key Laboratory of Advanced Technologies of Materials, Ministry of Education of China, Chengdu 610031, China
| | - Hui Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Key Laboratory of Advanced Technologies of Materials, Ministry of Education of China, Chengdu 610031, China
| | - R. Bruce King
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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16
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Sabri Bens M, Dassamiour S, Hambaba L, Akram Mela M, Sami R, M. Al-Mush AA, Benajiba N, Al Masoudi LM. In silico Investigation and BSA Denaturation Inhibitory Activity of Ethyl Acetate and N-butanol Extracts of Centaurea tougourensis Boiss. and Reut. INT J PHARMACOL 2022. [DOI: 10.3923/ijp.2022.1296.1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Fan Q, Li H, Fan Z, Fu J, Xie Y, King RB. Effect of methyl substituents on the preferred conformations of Bis(pentadienyl) open metallocenes. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Paularokiadoss F, Christopher Jeyakumar T, Thomas R, Sekar A, Bhakiaraj D. Group 13 monohalides [AX (A = B, Al, Ga and In; X = Halogens)] as alternative ligands for carbonyl in organometallics: Electronic structure and bonding analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Carbon-hydrogen bond activation in bridging cyclobutadiene ligands in unsaturated binuclear vanadium carbonyl derivatives. J Mol Model 2022; 28:39. [DOI: 10.1007/s00894-021-05009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022]
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20
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Prolate octahedral Ti2C4 clusters in binuclear cyclobutadiene titanium carbonyls. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Chen H, Zhou A, Sun D, Zhao Y, Wang Y. Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference. J Phys Chem B 2021; 125:8419-8430. [PMID: 34313131 DOI: 10.1021/acs.jpcb.1c04088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9δ+-Oδ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.
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Affiliation(s)
- Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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22
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Binuclear 1,3-diphosphacyclobutadiene vanadium carbonyls: Bending of the P2C2 ring in an unsaturated system with a vanadium-vanadium multiple bond. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Zhao Y, Chen Q, He M, Zhang Z, Feng X, Xie Y, King RB, Schaefer HF. Tris(Butadiene) Compounds versus Butadiene Oligomerization in Second-Row Transition Metal Chemistry: Effects of Increased Ligand Fields. Molecules 2021; 26:molecules26082220. [PMID: 33921443 PMCID: PMC8068848 DOI: 10.3390/molecules26082220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/20/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
The geometries, energetics, and preferred spin states of the second-row transition metal tris(butadiene) complexes (C4H6)3M (M = Zr–Pd) and their isomers, including the experimentally known very stable molybdenum derivative (C4H6)3Mo, have been examined by density functional theory. Such low-energy structures are found to have low-spin singlet and doublet spin states in contrast to the corresponding derivatives of the first-row transition metals. The three butadiene ligands in the lowest-energy (C4H6)3M structures of the late second-row transition metals couple to form a C12H18 ligand that binds to the central metal atom as a hexahapto ligand for M = Pd but as an octahapto ligand for M = Rh and Ru. However, the lowest-energy (C4H6)3M structures of the early transition metals have three separate tetrahapto butadiene ligands for M = Zr, Nb, and Mo or two tetrahapto butadiene ligands and one dihapto butadiene ligand for M = Tc. The low energy of the experimentally known singlet (C4H6)3Mo structure contrasts with the very high energy of its experimentally unknown singlet chromium (C4H6)3Cr analog relative to quintet (C12H18)Cr isomers with an open-chain C12H18 ligand.
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Affiliation(s)
- Yi Zhao
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China; (Y.Z.); (Q.C.); (M.H.); (Z.Z.)
- Research Institute of Petroleum Processing (RIPP), SINOPEC, Beijing 100083, China
| | - Qun Chen
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China; (Y.Z.); (Q.C.); (M.H.); (Z.Z.)
| | - Mingyang He
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China; (Y.Z.); (Q.C.); (M.H.); (Z.Z.)
| | - Zhihui Zhang
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China; (Y.Z.); (Q.C.); (M.H.); (Z.Z.)
| | - Xuejun Feng
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China; (Y.Z.); (Q.C.); (M.H.); (Z.Z.)
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA; (Y.X.); (H.F.S.)
- Correspondence: (X.F.); (R.B.K.)
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA; (Y.X.); (H.F.S.)
| | - Robert Bruce King
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA; (Y.X.); (H.F.S.)
- Correspondence: (X.F.); (R.B.K.)
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA; (Y.X.); (H.F.S.)
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24
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The role of the phosphorus lone pair in the low-energy binuclear phospholyl vanadium carbonyl structures: comparison with cyclopentadienyl analogues. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02692-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Don CG, Smieško M. Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations. J Chem Inf Model 2020; 60:6642-6653. [PMID: 33269921 DOI: 10.1021/acs.jcim.0c01091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xenobiotic metabolizing enzyme CYP2D6 is the P450 cytochrome family member with the highest rate of polymorphism. This causes changes in the enzyme activity and specificity, which can ultimately lead to adverse reactions during drug treatment. To avoid or lower CYP-related toxicity risks, prediction of the most likely positions within a molecule where a metabolic reaction might occur is paramount. In order to obtain accurate predictions, it is crucial to understand all phenomena within the active site of the enzyme that contribute to an efficient substrate recognition and the subsequent catalytic reaction together with their relative weight within the overall thermodynamic context. This study aims to define the weight of the driving forces upon the C-H bond activation within CYP2D6 wild-type and a clinically relevant allelic variant with increased activity (CYP2D6*53) featuring two amino acid mutations in close vicinity of the heme. First, we investigated the steric and electrostatic complementarity of the substrate bufuralol using well-tempered metadynamics simulations with the aim to obtain the free energy profiles for each site of metabolism (SoM) within the different active sites. Second, the stereoelectronic complementarity was determined for each SoM within the two different active-site environments. Relying on the well-tempered metadynamics simulation energy profiles of each SoM, we identified the binding mode that was closest to the preferred transition-state geometry for efficient C-H bond activation. The binding modes were then used as starting structures for the quantum mechanics/molecular mechanics calculations performed to quantify the corresponding activation barriers. Our results show the relevance of the steric component in orienting the SoM in an energetically accessible position toward the heme. However, the corresponding intrinsic reactivity and electronic complementarity within the active site must be accurately evaluated in order to obtain a meaningful reaction prediction, from which the predominant SoM can be determined. The F120I mutation lowered the activation barrier for the major site and one of the minor SoMs. However, it had an impact neither on the CYP2D6 enantioselectivity preference of the oxidation reaction nor on the stereoselectivity from the substrate point of view.
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Affiliation(s)
- Charleen G Don
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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26
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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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27
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Ali HS, Henchman RH, de Visser SP. Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA. Chemistry 2020; 26:13093-13102. [PMID: 32613677 PMCID: PMC7590115 DOI: 10.1002/chem.202002203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/12/2022]
Abstract
A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Richard H. Henchman
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Sam P. de Visser
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of Chemical Engineering and Analytical ScienceThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
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28
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Chen W, Wan X, Xie S, Chen X, Jin R, Du Q, Xie Y, King RB. Bridging cyclobutadiene ligands with agostic hydrogen atoms in binuclear chromium carbonyl derivatives. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Paularokiadoss F, Sekar A, Christopher Jeyakumar T. A DFT study on structural and bonding analysis of transition-metal carbonyls with terminal haloborylene ligands [M(CO)3(BX)] (M = Ni, Pd, and Pt; X = F, Cl, Br, and I). COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Wen L, Li G, Xie Y, King RB, Schaefer HF. Perfluoroolefin complexes versus perfluorometallacycles and perfluorocarbene complexes in cyclopentadienylcobalt chemistry. Phys Chem Chem Phys 2020; 22:7616-7624. [PMID: 32226987 DOI: 10.1039/c9cp06685c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorocarbons have been shown experimentally by Baker and coworkers to combine with the cyclopentadienylcobalt (CpCo) moiety to form fluoroolefin and fluorocarbene complexes as well as fluorinated cobaltacyclic rings. In this connection density functional theory (DFT) studies on the cyclopentadienylcobalt fluorocarbon complexes CpCo(L)(CnF2n) (L = CO, PMe3; n = 3 and 4) indicate structures with perfluoroolefin ligands to be the lowest energy structures followed by perfluorometallacycle structures and finally by structures with perfluorocarbene ligands. Thus, for the CpCo(L)(C3F6) (L = CO, PMe3) complexes, the perfluoropropene structure has the lowest energy, followed by the perfluorocobaltacyclobutane structure and the perfluoroisopropylidene structure less stable by 8 to 11 kcal mol-1, and the highest energy perfluoropropylidene structure less stable by more than 12 kcal mol-1. For the two metal carbene structures Cp(L)Co[double bond, length as m-dash]C(CF3)2 and Cp(L)Co[double bond, length as m-dash]CF(C2F5), the former is more stable than the latter, even though the latter has Fischer carbene character. For the CpCo(L)(C4F8) (L = CO, PMe3) complexes, the perfluoroolefin complex structures have the lowest energies, followed by the perfluorometallacycle structures at 10 to 20 kcal mol-1, and the structures with perfluorocarbene ligands at yet higher energies more than 20 kcal mol-1 above the lowest energy structure. This is consistent with the experimentally observed isomerization of the perfluorinated cobaltacyclobutane complexes CpCo(PPh2Me)(-CFR-CF2-CF2-) (R = F, CF3) to the perfluoroolefin complexes CpCo(PPh2Me)(RCF[double bond, length as m-dash]CF2) in the presence of catalytic quantities of HN(SO2CF3)2. Further refinement of the relative energies by the state-of-the-art DLPNO-CCSD(T) method gives results essentially consistent with the DFT results summarized above.
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Affiliation(s)
- Limei Wen
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Center for Computational Quantum Chemistry, School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
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31
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Li CL, Hsieh CH, Tsai TH. Preclinical Pharmacokinetics of Lamivudine and Its Interaction with Schisandra chinensis Extract in Rats. ACS OMEGA 2020; 5:1997-2004. [PMID: 32039337 PMCID: PMC7003501 DOI: 10.1021/acsomega.9b03922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Schisandra chinensis (Turcz.) Baill. (S. chinensis) extract and its active ingredient, schizandrin, have been used as a botanical medicine and dietary supplement for the treatment of hepatitis. Lamivudine is an antiretroviral drug and is used to treat hepatitis B viral infection. The aim of this study was to develop an ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for the measurement of lamivudine and to determine the pharmacokinetic behaviors of an aqueous-ethanol extract of S. chinensis in rats. The separation was performed on a phenyl column maintained at 40 °C. The experimental animals were distributed into three groups: (1) lamivudine alone (10 mg/kg, i.v.); (2) lamivudine (10 mg/kg, i.v.) + pretreatment with S. chinensis (3 g/kg, p.o.); and (3) lamivudine (10 mg/kg, i.v.) + pretreatment with S. chinensis (10 g/kg, p.o.). The experimental results indicated that neither treatment with lamivudine alone nor pretreatment with S. chinensis (3 or 10 g/kg) significantly changed the pharmacokinetic parameters. In conclusion, based on the above preclinical experimental model, the combination of lamivudine with the herbal extract of S. chinensis did not exhibit significant pharmacokinetic interactions. These data offer useful information for assessing the preclinical safety of nutritional supplementation with lamivudine.
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Affiliation(s)
- Chi-Lin Li
- Institute
of Traditional Medicine, School
of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Chen-Hsi Hsieh
- Institute
of Traditional Medicine, School
of Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Division
of Radiation Oncology, Department of Radiology, Far Eastern Memorial Hospital, Taipei 220, Taiwan
- Faculty
of Medicine, School of Medicine, National
Yang-Ming University, Taipei 112, Taiwan
| | - Tung-Hu Tsai
- Institute
of Traditional Medicine, School
of Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Graduate
Institute of Acupuncture Science, China
Medical University, Taichung 40402, Taiwan
- School
of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department
of Chemical Engineering, National United
University, Miaoli 36063, Taiwan
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32
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Wan X, Wang X, Chen X, Jin R, Du Q, Xie Y, Bruce King R. 1,3-Diphosphacyclobutadiene sandwich compounds as bidentate ligands in metal carbonyl chemistry: Binuclear chromium derivatives. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Podgorski MN, Coleman T, Chao RR, De Voss JJ, Bruning JB, Bell SG. Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions. J Inorg Biochem 2019; 203:110913. [PMID: 31759265 DOI: 10.1016/j.jinorgbio.2019.110913] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/03/2023]
Abstract
The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover parameters, with different meta-substituted benzoic acids in order to establish which criteria are important for efficient catalysis. When compared to the para isomers, the meta-substituted benzoic acids were less efficiently oxidized. For example, 3-formylbenzoic acid was oxidized with lower activity than the equivalent para isomer and 3-methoxybenzoic acid did not undergo O-demethylation by CYP199A4. The structural data highlighted that the meta-substituted benzoic acids bound in the enzyme active site in a modified position with incomplete loss of the distal water ligand of the heme moiety. However, for both sets of isomers the meta- or para-substituent pointed towards, and was in close proximity, to the heme iron. The absence of oxidation activity with 3-methoxybenzoic acid was assigned to the observation that the CH bonds of this molecule point away from the heme iron. In contrast, in the para isomer they are in an ideal location for abstraction. These findings were confirmed by using the bulkier 3-ethoxybenzoic acid as a substrate which removed the water ligand and reoriented the meta-substituent so that the methylene hydrogens pointed towards the heme, enabling more efficient oxidation. Overall we show relatively small changes in substrate structure and position in the active site can have a dramatic effect on the activity.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Rebecca R Chao
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, Qld 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.
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Schneider M, Pons JL, Labesse G, Bourguet W. In Silico Predictions of Endocrine Disruptors Properties. Endocrinology 2019; 160:2709-2716. [PMID: 31265055 PMCID: PMC6804484 DOI: 10.1210/en.2019-00382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/26/2019] [Indexed: 01/12/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) are a broad class of molecules present in our environment that are suspected to cause adverse effects in the endocrine system by interfering with the synthesis, transport, degradation, or action of endogenous ligands. The characterization of the harmful interaction between environmental compounds and their potential cellular targets and the development of robust in vivo, in vitro, and in silico screening methods are important for assessment of the toxic potential of large numbers of chemicals. In this context, computer-aided technologies that will allow for activity prediction of endocrine disruptors and environmental risk assessments are being developed. These technologies must be able to cope with diverse data and connect chemistry at the atomic level with the biological activity at the cellular, organ, and organism levels. Quantitative structure-activity relationship methods became popular for toxicity issues. They correlate the chemical structure of compounds with biological activity through a number of molecular descriptors (e.g., molecular weight and parameters to account for hydrophobicity, topology, or electronic properties). Chemical structure analysis is a first step; however, modeling intermolecular interactions and cellular behavior will also be essential. The increasing number of three-dimensional crystal structures of EDCs' targets has provided a wealth of structural information that can be used to predict their interactions with EDCs using docking and scoring procedures. In the present review, we have described the various computer-assisted approaches that use ligands and targets properties to predict endocrine disruptor activities.
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Affiliation(s)
- Melanie Schneider
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Jean-Luc Pons
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
| | - William Bourguet
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
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Ugur I, Chandrasekhar P. Proton relay network in P450cam formed upon docking of putidaredoxin. Proteins 2019; 88:558-572. [PMID: 31597203 DOI: 10.1002/prot.25835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/13/2019] [Accepted: 09/28/2019] [Indexed: 11/08/2022]
Abstract
Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor-bound): (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)-docked-WT, FeOO state. (d) Pdx-docked WT, Cpd(0). (e) Pdx-docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH 2 O⋯D251 in WT; FeOO(H)⋯nH 2 O⋯D251 in T252A mutant; both occur with Pdx docking. (c) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H-bonding network, second protonation appears to be facilitated.
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Affiliation(s)
- Ilke Ugur
- Research Division, Ashwin-Ushas Corporation, Marlboro, New Jersey
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36
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Comparison of binuclear phospholyl chromium carbonyl derivatives with their cyclopentadienyl analogues: Role of the phosphorus atom in ligand-metal bonding. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Fan Q, Li H, Fu J, Fan Z, Xu Y, Feng H, Xie Y, King RB, Schaefer HF. Tris(butadiene) Metal Complexes of the First-Row Transition Metals versus Coupling of Butadiene to Eight- and Twelve-Carbon Hydrocarbon Chains. J Phys Chem A 2019; 123:5542-5554. [PMID: 31181165 DOI: 10.1021/acs.jpca.9b03063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role that zerovalent nickel plays in catalyzing the trimerization of butadiene to 1,5,9-cyclododecatriene conveys interest in the properties of the tris(butadiene)metal complexes (C4H6)3M. In this connection the complexes (C4H6)3M (M = Ti-Ni) of the first-row transition metals have been investigated by density functional theory. The intermediate C12H18Ni which has been isolated in the nickel-catalyzed trimerization of butadiene but is too unstable for X-ray crystallography is suggested here to have an open-chain hexahapto η3,3-C12H18 ligand rather than the octahapto such ligand suggested by some investigators. The lowest energy (C4H6)3M structures of the other first-row transition metals from vanadium to cobalt are found to have related structures with open-chain C12H18 ligands having hapticities ranging from four to eight with hexahapto structures being most common. The nickel and cobalt (C12H18)M derivatives favor low-spin singlet and doublet spin states, respectively, whereas the manganese derivative (C12H18)Mn favors the high-spin sextet state corresponding to the half-filled d5 shell of Mn(II). A (C4H6)3Cr structure with three separate tetrahapto butadiene ligands analogous to the very stable (η4-C4H6)3M (M = Mo, W) with the favored 18-electron metal configuration is found to be a very high energy structure relative to isomers containing an open-chain C12H18 ligand.
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Affiliation(s)
- Qunchao Fan
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Huidong Li
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Jia Fu
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Zhixiang Fan
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Yonggen Xu
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Hao Feng
- School of Science, Key Laboratory of High Performance Scientific Computation , Xihua University , Chengdu , China 610039
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - R Bruce King
- Department of Chemistry and Center for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Henry F Schaefer
- Department of Chemistry and Center for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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38
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Chen J, Feng H, Xie Y, King RB. Agostic hydrogen atoms versus cobalt-cobalt multiple bonding in binuclear borole cobalt carbonyls. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Xu L, Li QS, King RB. Coupling of fluoroborylene ligands in manganese carbonyl chemistry to give a difluorodiborene ligand. NEW J CHEM 2019. [DOI: 10.1039/c9nj01209e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bridging difluorodiborene μ-B2F2 ligand has been observed in two of the three lowest energy Mn2(BF)2(CO)7 structures as well as in the lowest energy Mn2(BF)2(CO)6 structure.
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Affiliation(s)
- Liancai Xu
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P. R. China
| | - Qian-shu Li
- Center for Computational Quantum Chemistry
- South China Normal University
- Guangzhou 510631
- P. R. China
- Institute of Chemical Physics
| | - R. Bruce King
- Center for Computational Quantum Chemistry
- South China Normal University
- Guangzhou 510631
- P. R. China
- Department of Chemistry and Center for Computational Chemistry
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40
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Huang L, Li J, Li G, Xie Y, King RB, Schaefer HF. Alternative modes of bonding of C 4F 8 units in mononuclear and binuclear iron carbonyl complexes. NEW J CHEM 2019. [DOI: 10.1039/c9nj00882a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The lowest energy C4F8Fe(CO)4 structure is not the experimentally known ferracyclopentane complex but instead isomeric (perfluorobutene)iron tetracarbonyls. However, activation energies for the fluorine shifts required to form the latter isomers are very high. The lowest energy (C4F8)2Fe2(CO)n (n = 7, 6) structures have bridging perfluorocarbene and terminal perfluoroolefin ligands.
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Affiliation(s)
- Liping Huang
- Key Laboratory of Theoretical Chemistry of the Environment
- Ministry of Education
- Center for Computational Quantum Chemistry
- School of Chemistry and Environment
- South China Normal University
| | - Jing Li
- Key Laboratory of Theoretical Chemistry of the Environment
- Ministry of Education
- Center for Computational Quantum Chemistry
- School of Chemistry and Environment
- South China Normal University
| | - Guoliang Li
- Key Laboratory of Theoretical Chemistry of the Environment
- Ministry of Education
- Center for Computational Quantum Chemistry
- School of Chemistry and Environment
- South China Normal University
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - R. Bruce King
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
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41
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Chen J, Feng H, Xie Y, King RB, Schaefer HF. Higher spin states in some low-energy bis(tetramethyl-1,2-diaza-3,5-diborolyl) sandwich compounds of the first row transition metals: boraza analogues of the metallocenes. NEW J CHEM 2019. [DOI: 10.1039/c8nj05517c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Density functional studies on (Me4B2N2CH)2M (M = Ti, V, Cr, Mn, Fe, Co, Ni) show low-energy sandwich structures for all seven metals. The lowest-energy such Cr and Mn derivatives have higher spin states than the corresponding metallocenes.
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Affiliation(s)
- Jianlin Chen
- School of Science
- Research Center for Advanced Computation Xihua University
- Chengdu 610039
- China
| | - Hao Feng
- School of Science
- Research Center for Advanced Computation Xihua University
- Chengdu 610039
- China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry University of Georgia
- Athens
- USA
| | - R. Bruce King
- School of Science
- Research Center for Advanced Computation Xihua University
- Chengdu 610039
- China
- Department of Chemistry and Center for Computational Chemistry University of Georgia
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry University of Georgia
- Athens
- USA
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42
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Fu Z, Chen J, Wang Y, Hong H, Xie H. Quantum chemical simulations revealed the toxicokinetic mechanisms of organic phosphorus flame retardants catalyzed by P450 enzymes. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2018; 36:272-291. [PMID: 30457030 DOI: 10.1080/10590501.2018.1537564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The metabolic fate and toxicokinetics of organic phosphorus flame retardants catalyzed by cytochrome P450 enzymes (CYPs) are here investigated by in silico simulations, leveraging an active center model to mimic the CYPs, triphenyl phosphate (TPHP), tris(2-butoxyethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate as substrates. Our calculations elucidated key main pathways and predicted products, which were corroborated by current in vitro data. Results showed that alkyl OPFRs are eliminated faster than aryl and halogenated alkyl-substituted OPFRs. In addition, we discovered a proton shuttle pathway for aryl hydroxylation of TPHP and P = O bond-assisted H-transfer mechanisms (rather than nonenzymatic hydrolysis) that lead to O-dealkylation/dearylation of phosphotriesters.
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Affiliation(s)
- Zhiqiang Fu
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology , Dalian University of Technology , Dalian , China
| | - Jingwen Chen
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology , Dalian University of Technology , Dalian , China
| | - Yong Wang
- b State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou , China
| | - Huixiao Hong
- c National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Hongbin Xie
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology , Dalian University of Technology , Dalian , China
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43
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Zhang Z, Feng X, Chen Q, He M, Xie Y, King RB. Energetics of Variable Hapticity of Carbocyclic Rings in Cyclopentadienylmetal Carbonyl Systems of the Second Row Transition Metals C 5H 5M(CO) nC mH m (M = Ru, Tc, Mo, Nb) Including Mechanistic Studies of Carbonyl Dissociation. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhihui Zhang
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, PR China
| | - Xuejun Feng
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, PR China
| | - Qun Chen
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, PR China
| | - Mingyang He
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, PR China
| | - Yaoming Xie
- Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- Center for Computational Chemistry and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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44
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Coleman T, Wong SH, Podgorski MN, Bruning JB, De Voss JJ, Bell SG. Cytochrome P450 CYP199A4 from Rhodopseudomonas palustris Catalyzes Heteroatom Dealkylations, Sulfoxidation, and Amide and Cyclic Hemiacetal Formation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00909] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Siew Hoon Wong
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | | | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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45
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Binuclear vanadium dimethylphosphino carbonyls: vanadium-vanadium multiple bonds and four-electron donor carbonyl groups as structural features in unsaturated systems. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Gong S, Chen G, Li QS, Luo Q, Xie Y, King RB. Cyclopentadienyliron boronyl carbonyls as isoelectronic analogues of cyclopentadienylmanganese carbonyls except for boronyl ligand coupling reactions. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.07.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Chang Y, Li QS, Xie Y, Bruce King R. Preference of three-electron donor boronyl groups over metal-metal multiple bonding in unsaturated binuclear manganese carbonyl boronyls: Comparison with isoelectronic binuclear chromium carbonyls. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Fan Q, Fu J, Li H, Feng H, Sun W, Xie Y, King RB, Schaefer HF. Butadiene as a ligand in open sandwich compounds. Phys Chem Chem Phys 2018; 20:5683-5691. [DOI: 10.1039/c7cp07379h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory shows the lowest energy bis(butadiene)metal structures (C4H6)2M (M = Ti to Ni) to have a staggered orientation of the two butadiene ligands corresponding to a tetrahedral coordination of the central metal atom.
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Affiliation(s)
- Qunchao Fan
- School of Science
- Key Laboratory of High Performance Scientific Computation
- Xihua University
- Chengdu 610039
- China
| | - Jia Fu
- School of Science
- Key Laboratory of High Performance Scientific Computation
- Xihua University
- Chengdu 610039
- China
| | - Huidong Li
- School of Science
- Key Laboratory of High Performance Scientific Computation
- Xihua University
- Chengdu 610039
- China
| | - Hao Feng
- School of Science
- Key Laboratory of High Performance Scientific Computation
- Xihua University
- Chengdu 610039
- China
| | - Weiguo Sun
- School of Science
- Key Laboratory of High Performance Scientific Computation
- Xihua University
- Chengdu 610039
- China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - R. Bruce King
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
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49
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Rong D, Gong S, Wang C, Luo Q, Li QS, Xie Y, King RB, Schaefer HF. Binuclear Cyclopentadienylmetal Methylene Sulfur Dioxide Complexes of Rhodium and Iridium Related to a Photochromic Metal Dithionite Complex. Inorg Chem 2017; 56:14486-14493. [PMID: 29140087 DOI: 10.1021/acs.inorgchem.7b02064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photochromic dithionite complex Cp*2Rh2(μ-CH2)2(μ-O2SSO2) (Cp* = η5-Me5C5) is of interest because it undergoes an unusual fully reversible unimolecular photochemical rearrangement to the isodithionite complex Cp*2Rh2(μ-CH2)2(μ-O2SOSO). In order to obtain more insight into these systems, a comprehensive density functional theory study has been carried out on isomeric Cp2M2(CH2)2(SO2)2 (M = Rh, Ir) derivatives. The experimentally observed rhodium complexes with coupled sulfur dioxide (SO2) units to give dithionite or isodithionite ligands are surprisingly high-energy kinetic isomers in our analysis, reflecting the need for dithionite rather than SO2 for their synthesis. Many isomeric structures containing two separate SO2 ligands are found to lie at lower energies than these dithionite and isodithionite complexes. In the lowest-energy Cp2M2(CH2)2(SO2)2 isomers, the two methylene groups couple to form an ethylene ligand that can be either terminal or bridging. In slightly higher energy structures, a formal hydrogen shift is predicted to occur within the ethylene ligand to give a methylcarbene CH3CH ligand. Isomers with a bridging methylcarbene ligand are energetically preferred over isomers with a terminal methylcarbene ligand. Generation of the lower-energy Cp2Rh2(CH2)2(SO2)2 isomers containing separate SO2 ligands should be achievable through reactions of SO2 with more highly reduced cyclopentadienylrhodium methylene complexes such as Cp*2Rh2(μ-CH2)2.
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Affiliation(s)
- Dongsheng Rong
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China
| | - Shida Gong
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China.,School of Chemistry and Chemical Engineering, Qingdao University , Qingdao 266071, P. R. China
| | - Chaoyang Wang
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China
| | - Qiong Luo
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China
| | - Qian-Shu Li
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China
| | - Yaoming Xie
- Department of Chemistry and Center for Computational Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - R Bruce King
- MOE Key Laboratory of Theoretical Environmental Chemistry, Center for Computational Quantum Chemistry, South China Normal University , Guangzhou 510631, P. R. China.,Department of Chemistry and Center for Computational Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Henry F Schaefer
- Department of Chemistry and Center for Computational Chemistry, University of Georgia , Athens, Georgia 30602, United States
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50
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Binuclear chromium carbonyl complexes of the highly basic small bite bidentate diphosphine bis(dimethylphosphino)methane. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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