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Zhang H, Wang C, Guo F, Jin L, Song R, Yang F, Ji L, Yu H. In Silico simulation of Cytochrome P450-Mediated metabolism of aromatic amines: A case study of N-Hydroxylation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113544. [PMID: 35483145 DOI: 10.1016/j.ecoenv.2022.113544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Aromatic amines, the widely used raw materials in industry, cause long-term exposure to human bodies. They can be metabolized by cytochrome P450 enzymes to form active electrophilic compounds, which will potentially react with nucleophilic DNA to exert carcinogenesis. The short lifetime and versatility of the oxidant (a high-valent iron (IV)-oxo species, compound I) of P450 enzymes prompts us to use theoretical methods to investigate the metabolism of aromatic amines. In this work, the density functional theory (DFT) has been employed to simulate the hydroxylation metabolism through H-abstraction and to calculate the activation energy of this reaction for 28 aromatic amines. The results indicate that the steric effects, inductive effects and conjugative effects greatly contribute to the metabolism activity of the chemicals. The further correlation reveals that the dissociation energy of -NH2 (BDEN-H) can successfully predict the time-consuming calculated activation energy (R2 for aromatic and heteroaromatic amines are 0.93 and 0.86, respectively), so BDEN-H can be taken as a key parameter to characterize the relative stability of aromatic amines in P450 enzymes and further to quickly assess their potential toxicity. The validation results prove such relationship has good statistical performance (qcv2 for aromatic and heteroaromatic amines are 0.95 and 0.90, respectively) and can be used to other aromatic amines in the application domain, greatly reducing computational cost and providing useful support for experimental research.
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Affiliation(s)
- Huanni Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangjie Guo
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Quality and Safety Engineering Institute of Food and Drug, School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, China
| | - Lingmin Jin
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangxing Yang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China.
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Yu M, Yang Q, Yuan X, Li Y, Chen X, Feng Y, Liu J. Boosting oxygen reduction and permeability properties of doped iron-porphyrin membrane cathode in microbial fuel cells. BIORESOURCE TECHNOLOGY 2021; 320:124343. [PMID: 33166886 DOI: 10.1016/j.biortech.2020.124343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
To achieve a membrane cathode with excellent performance, iron-porphyrin (Fe(por)) was doped to boost the catalytic and permeability properties in microbial fuel cell (MFC). The membrane cathode with the optimal 0.05 g of Fe(por) (denoted as Fe(por)-0.05) had the highest current density of 10.3 A m-2 and the lowest charge transfer resistance of 12.6 ± 0.3 Ω. The ring-disk electrode (RDE) results further proved that the oxygen reduction reaction (ORR) occurred on the Fe(por)-0.05 through a direct four-electron transfer pathway. Moreover, the membrane cathode performed better permeability properties under electric filed and the Fe(por)-0.05 + E (E was electric field) obtained the lowest flux attenuation ratio of 14.1 ± 0.2%, which was related to its superior hydrophilicity and strong electrostatic repulsion force. Iron-porphyrin can simultaneously enhance the ORR activity and permeability of membrane cathode, providing a new direction for the practical application in MFCs.
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Affiliation(s)
- Meiying Yu
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Qiao Yang
- School of Ocean Science and Technology, Dalian University of Technology, No. 2 Dagong Road, Panjin 124221, China
| | - Xiaole Yuan
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yunfei Li
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xuepeng Chen
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yujie Feng
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Jia Liu
- School of Environmental Science and Engineering, Academy of Environment and Ecology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
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Geng C, Ye S, Neese F. Does a higher metal oxidation state necessarily imply higher reactivity toward H-atom transfer? A computational study of C-H bond oxidation by high-valent iron-oxo and -nitrido complexes. Dalton Trans 2014; 43:6079-86. [PMID: 24492533 DOI: 10.1039/c3dt53051e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this work, the reactions of C-H bond activation by two series of iron-oxo ( (Fe(IV)), (Fe(V)), (Fe(VI))) and -nitrido model complexes ( (Fe(IV)), (Fe(V)), (Fe(VI))) with a nearly identical coordination geometry but varying iron oxidation states ranging from iv to vi were comprehensively investigated using density functional theory. We found that in a distorted octahedral coordination environment, the iron-oxo species and their isoelectronic nitrido analogues feature totally different intrinsic reactivities toward C-H bond cleavage. In the case of the iron-oxo complexes, the reaction barrier monotonically decreases as the iron oxidation state increases, consistent with the gradually enhanced electrophilicity across the series. The iron-nitrido complex is less reactive than its isoelectronic iron-oxo species, and more interestingly, a counterintuitive reactivity pattern was observed, i.e. the activation barriers essentially remain constant independent of the iron oxidation states. The detailed analysis using the Polanyi principle demonstrates that the different reactivities between these two series originate from the distinct thermodynamic driving forces, more specifically, the bond dissociation energies (BDEE-Hs, E = O, N) of the nascent E-H bonds in the FeE-H products. Further decomposition of the BDEE-Hs into the electron and proton affinity components shed light on how the oxidation states modulate the BDEE-Hs of the two series.
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Affiliation(s)
- Caiyun Geng
- Max-Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.
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Quantum chemical studies on the role of water microsolvation in interactions between group 12 metal species (Hg2+, Cd2+, and Zn2+) and neutral and deprotonated cysteines. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hessenauer-Ilicheva N, Franke A, Wolak M, Higuchi T, van Eldik R. Spectroscopic and Mechanistic Studies on Oxidation Reactions Catalyzed by the Functional Model SR Complex for Cytochrome P450: Influence of Oxidant, Substrate, and Solvent. Chemistry 2009; 15:12447-59. [DOI: 10.1002/chem.200901712] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yanai T, Mori S. Density Functional Studies on Isomerization of Prostaglandin H2to Prostacyclin Catalyzed by Cytochrome P450. Chemistry 2009; 15:4464-73. [DOI: 10.1002/chem.200802550] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Yanai TK, Mori S. Density functional studies on thromboxane biosynthesis: mechanism and role of the heme-thiolate system. Chem Asian J 2009; 3:1900-11. [PMID: 18844316 DOI: 10.1002/asia.200800253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Reaction mechanisms for the isomerization of prostaglandin H(2) to thromboxane A(2), and degradation to 12-L-hydroxy-5,8,10-heptadecatrienoic acid (HHT) and malondialdehyde (MDA), catalyzed by thromboxane synthase, were investigated using the unrestricted Becke-three-parameter plus Lee-Yang-Parr (UB3LYP) density functional level theory. In addition to the reaction pathway through Fe(IV)-porphyrin intermediates, a new reaction pathway through Fe(III)-porphyrin pi-cation radical intermediates was found. Both reactions proceed with the homolytic cleavage of endoperoxide O-O to give an alkoxy radical. This intermediate converts into an allyl radical intermediate by a C-C homolytic cleavage, followed by the formation of thromboxane A(2) having a 6-membered ring through a one electron transfer, or the degradation into HHT and MDA. The proposed mechanism shows that an iron(III)-containing system having electron acceptor ability is essential for the 6-membered ring formation leading to thromboxane A(2). Our results suggest that the step of the endoperoxide O-O homolytic bond cleavage has the highest activation energy following the binding of prostaglandin H(2) to thromboxane synthase.
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Affiliation(s)
- Tetsuya K Yanai
- Faculty of Science, Ibaraki University, Bunkyo, Mito 310-8512, Japan
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Kamachi T, Kouno T, Nam W, Yoshizawa K. How axial ligands control the reactivity of high-valent iron(IV)–oxo porphyrin π-cation radicals in alkane hydroxylation: A computational study. J Inorg Biochem 2006; 100:751-4. [PMID: 16516298 DOI: 10.1016/j.jinorgbio.2006.01.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/04/2006] [Indexed: 11/25/2022]
Abstract
The push effect of anionic axial ligands of high-valent iron(IV)-oxo porphyrin pi-cation radicals, (Porp)(+.)Fe(IV)(O)(X) (X=OH(-), AcO(-), Cl(-), and CF(3)SO(3)(-)), in alkane hydroxylation is investigated by B3LYP DFT calculations. The electron-donating ability of anionic axial ligands influences the activation energy for the alkane hydroxylation by the iron(IV)-oxo intermediates and the Fe-O bond distance of the iron-oxo species in transition state.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 812-8581, Japan
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Sturm A, Schierhorn A, Lindenstrauss U, Lilie H, Brüser T. YcdB from Escherichia coli reveals a novel class of Tat-dependently translocated hemoproteins. J Biol Chem 2006; 281:13972-8. [PMID: 16551627 DOI: 10.1074/jbc.m511891200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Tat (twin-arginine translocation) system of Escherichia coli serves to translocate folded proteins across the cytoplasmic membrane. The reasons established so far for the Tat dependence are cytoplasmic cofactor assembly and/or heterodimerization of the respective proteins. We were interested in the reasons for the Tat dependence of novel Tat substrates and focused on two uncharacterized proteins, YcdO and YcdB. Both proteins contain predicted Tat signal sequences. However, we found that only YcdB was indeed Tat-dependently translocated, whereas YcdO was equally well translocated in a Tat-deficient strain. YcdB is a dimeric protein and contains a heme cofactor that was identified to be a high-spin Fe(III)-protoporphyrin IX complex. In contrast to all other periplasmic hemoproteins analyzed so far, heme was assembled into YcdB in the cytoplasm, suggesting that heme assembly could take place prior to translocation. The function of YcdB in the periplasm may be related to a detoxification reaction under specific conditions because YcdB had peroxidase activity at acidic pH, which coincides well with the known acid-induced expression of the gene. The data demonstrate the existence of a class of heme-containing Tat substrates, the first member of which is YcdB.
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Affiliation(s)
- Alexander Sturm
- Institute for Microbiology, Martin Luther University of Halle-Wittenberg, Kurt-Mothes-Strasse 3, Halle, Germany
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