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Matrix isolation infrared study of the interaction of dioxygen with chromium(II)tetraphenylporphyrin. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Noodleman L, Han Du WG, McRee D, Chen Y, Goh T, Götz AW. Coupled transport of electrons and protons in a bacterial cytochrome c oxidase-DFT calculated properties compared to structures and spectroscopies. Phys Chem Chem Phys 2021; 22:26652-26668. [PMID: 33231596 DOI: 10.1039/d0cp04848h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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3
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Sacramento JJD, Goldberg DP. Oxidation of an indole substrate by porphyrin iron(iii) superoxide: relevance to indoleamine and tryptophan 2,3-dioxygenases. Chem Commun (Camb) 2020; 56:3089-3092. [PMID: 32052805 PMCID: PMC7065957 DOI: 10.1039/c9cc10019a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reaction of FeIII(O2˙-)(TPP) with 2,3-dimethylindole at -40 °C gives the ring-opened, dioxygenated N-(2-acetyl-phenyl)-acetamide product. The reaction was monitored in situ by low-temperature UV-vis and 1H NMR spectroscopies. This work demonstrates that a discrete iron(iii)(superoxo) porphyrin is competent to carry out indole oxidation, as proposed for the tryptophan and indoleamine 2,3-dioxygenases.
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Affiliation(s)
- Jireh Joy D Sacramento
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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4
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Weak coordination of H2S to the solid-state ferrous porphyrin complexes with diatomic molecules. Characterization of 6-coordinate adducts at low temperature. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.07.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Nguyen D, Kang G, Chiang N, Chen X, Seideman T, Hersam MC, Schatz GC, Van Duyne RP. Probing Molecular-Scale Catalytic Interactions between Oxygen and Cobalt Phthalocyanine Using Tip-Enhanced Raman Spectroscopy. J Am Chem Soc 2018; 140:5948-5954. [DOI: 10.1021/jacs.8b01154] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Abstract
Superoxide ion (O2(•-)) is of great significance as a radical species implicated in diverse chemical and biological systems. However, the chemistry knowledge of O2(•-) is rather scarce. In addition, numerous studies on O2(•-) were conducted within the latter half of the 20th century. Therefore, the current advancement in technology and instrumentation will certainly provide better insights into mechanisms and products of O2(•-) reactions and thus will result in new findings. This review emphasizes the state-of-the-art research on O2(•-) so as to enable researchers to venture into future research. It comprises the main characteristics of O2(•-) followed by generation methods. The reaction types of O2(•-) are reviewed, and its potential applications including the destruction of hazardous chemicals, synthesis of organic compounds, and many other applications are highlighted. The O2(•-) environmental chemistry is also discussed. The detection methods of O2(•-) are categorized and elaborated. Special attention is given to the feasibility of using ionic liquids as media for O2(•-), addressing the latest progress of generation and applications. The effect of electrodes on the O2(•-) electrochemical generation is reviewed. Finally, some remarks and future perspectives are concluded.
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Affiliation(s)
| | | | - Inas M AlNashef
- Department of Chemical and Environmental Engineering, Masdar Institute of Science and Technology , Abu Dhabi, United Arab Emirates
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8
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Fu H, Cao M, She Y, Sun Z, Yu Y. Electronic effects of the substituent on the dioxygen-activating abilities of substituted iron tetraphenylporphyrins: a theoretical study. J Mol Model 2015; 21:92. [DOI: 10.1007/s00894-015-2619-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
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9
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Quantum chemical DFT study of the interaction between molecular oxygen and FeN4 complexes, and effect of the macrocyclic ligand. J Mol Model 2014; 20:2131. [DOI: 10.1007/s00894-014-2131-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
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Soldatova AV, Ibrahim M, Spiro TG. Electronic structure and ligand vibrations in FeNO, CoNO, and FeOO porphyrin adducts. Inorg Chem 2013; 52:7478-86. [PMID: 23763617 PMCID: PMC3766410 DOI: 10.1021/ic400364x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gaseous ligands, CO, NO, and O2 interact with the Fe ion in heme proteins largely via backbonding of Fe electrons to the π* orbitals of the XO (X = C, N, O) ligands. In these FeXO adducts, the Fe-X stretching frequency varies inversely with the X-O stretching frequency, since increased backbonding strengthens the Fe-X bond while weakening the X-O bond. Inverse frequency correlations have been observed for all three ligands, despite differing electronic and geometric structures, and despite variable composition of the "FeX" vibrational mode, in which Fe-X stretching and Fe-X-O coordinates are mixed for bent FeXO adducts. We report experimental data for 5-coordinate Co(II)(NO) porphyrin adducts (isoelectronic with Fe(II)(OO) adducts), and the results of density functional theory (DFT) modeling for 5-coordinate Fe(II)(NO), Co(II)(NO), and Fe(II)(OO) adducts. Inverse ν(MX)/ν(XO) correlations are obtained computationally, using model porphyrins with graded electron-donating and -withdrawing substituents to modulate the backbonding. Computed slopes agree satisfactorily with experiment, provided nonhybrid functionals are used, which avoid overemphasizing high-spin states. The BP86 functional gives correct ground states, a closed-shell singlet for Co(II)(NO) and an open-shell singlet for the isoelectronic Fe(II)(OO), as corroborated by structural data for Co(II)(NO), and the ν(MX)/ν(XO) slope agreement with experiment for both adducts. However, for Fe(II)(OO) adducts, the computed inverse ν(MX)/ν(XO) correlation applies only to porphyrins with electron-donating and withdrawing substituents of moderate strength. For substituents more donating than -CH3, a direct correlation is obtained, the Fe-O and O-O bonds weakening in concert. This effect is ascribed to the dominance of σ bonding via the in-plane dxz(+dz(2))-π* orbital, when electron-donating substituents raise the d orbital energies sufficiently to render backbonding (dyz-π*) unimportant.
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Affiliation(s)
- Alexandra V. Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | | | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
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POPOVICI S, LEYFFER W, HOLZE R. On the Mechanism of Dioxygen Electroreduction at Transition Metal meso-Tetrakis Pyridyl Porphyrins—a Comparative Spectroelectrochemical Study. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1002/(sici)1099-1409(199904)3:4<265::aid-jpp131>3.0.co;2-e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The mode of interaction with and the mechanism of the dioxygen reduction reaction at six transition metal α,β,γ,δ-tetra(4-pyridyl)porphyrins (MeTPyPs) deposited on carbon and silver supporting electrodes were investigated with cyclic voltammetry, FTIR and UV-vis spectroscopy and resonance Raman spectroscopy. Results indicate a strong influence of both the ligand and the central metal ion upon the reduction electrocatalysis in terms of electrode overpotentials. Spectroelectrochemical results support a two-electron pathway resulting in hydrogen peroxide as the primary reduction product. A significant influence of the central ion on the vibrational behaviour and the dioxygen reduction mechanism was not found.
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Affiliation(s)
- S. POPOVICI
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
| | - W. LEYFFER
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
| | - R. HOLZE
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
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12
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POPOVICI S, LEYFFER W, HOLZE R. The Mechanism of Dioxygen Reduction at Iron meso-Tetrakis (Pyridyl) Porphyrin: a Spectroelectrochemical Study. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1002/(sici)1099-1409(199805/06)2:3<249::aid-jpp77>3.0.co;2-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of the dioxygen interaction with and reduction reaction at iron α,β,γ,δ-tetra(4-pyridyl) porphyrin ( FeTPyP ) deposited on carbon and silver supporting electrodes was investigated with cyclic voltammetry and FTIR, UV-vis and resonance Raman spectroscopies. Results indicate a strong influence of the ligand upon the reduction electrocatalysis. Spectroelectrochemical results support a two-electron pathway resulting most probably in hydrogen peroxide as the primary reduction product.
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Affiliation(s)
- S. POPOVICI
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
| | - W. LEYFFER
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
| | - R. HOLZE
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
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13
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Kurtikyan TS, Ogden JS, Kazaryan RK, Madakyan VN. Interaction of diatomic ligands with Fe(II) meso-mono-4-pyridyl-tri-phenyl-porphyrinate. Spectral evidence of self-assembly in sublimed layers. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424603000781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The interaction of CO , NO and O2 gases with thin layers of meso-mono-4-pyridyl-tri-phenylporphyrinatoiron(II) ( FeMPyTPP ) obtained by sublimation onto low-temperature (T = 77 K ) substrates has been investigated by means of IR and UV-visible spectroscopy. In contrast to the closely-related meso-tetraphenylporphyrinatoiron(II) ( FeTPP ), the formation of two types of axial complexes has been observed. In one of these the 5th coordination site is occupied by the pyridyl group of an adjacent molecule indicating the self-assembly of Fe ( MPyTPP ) in layers with formation of coordinatively linked oligomers. The degree of oligomerisation depends on the nature of the interacting gas. Due to the specificity of the supramolecular structure, the layers are fairly stable in ambient conditions and conserve their microporosity to bind reversibly with the aforementioned ligands.
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Affiliation(s)
- Tigran S. Kurtikyan
- Molecular Structure Research Center, Azatutyan Ave. 26, 375014 Yerevan, Armenia
- Institute of Applied Chemistry, (ARIAC), Artashat Highway 5/2, 375053 Yerevan, Armenia
| | - J. Steven Ogden
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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14
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Kurtikyan TS, Mardyukov AN, Kazaryan RK, Goodwin JA. Microporous porphyrin assemblies: Interaction of NO2 gas with sublimed layers of meso-mono-4-pyridyl-tri-phenylporphyrinatocobalt(II). J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424603000951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The interaction of NO 2 (15 NO 2) gas with sublimed layers of meso-mono-4-pyridyl-triphenylporphyrinatocobalt(II) (CoMPyTPP) has been investigated by means of IR and UV-visible spectroscopies. These studies have led to the characterisation of two nitro-complexes: (1) the five-coordinated nitro complex similar to that observed earlier for the closely-related meso-tetraphenylporphyrinatocobalt(II) (CoTPP), and (2) the six-coordinated complex, in which the fifth coordination site is occupied by the pyridyl group of an adjacent molecule. Upon storage of the films, the concentration of six-coordinate complexes increases at the expense of the five-coordinate. These experimental observations indicate the self-assembly of CoMPyTPP in layers with formation of coordinatively linked oligomers. Due to the specificity of the supramolecular structure, the layers conserve their microporosity upon storage and reveal the oxo-transfer activity relative to appropriate oxygen acceptors.
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Affiliation(s)
- Tigran S. Kurtikyan
- Molecular Structure Research Center, Azatutyan ave. 26, 375014, Yerevan, Armenia
- Institute of Applied Chemistry, (ARIAC), Bagratunyats st. 70, 375029, Yerevan, Armenia
| | - Arthur N. Mardyukov
- Molecular Structure Research Center, Azatutyan ave. 26, 375014, Yerevan, Armenia
| | | | - John A. Goodwin
- Department of Chemistry and Physics, Coastal Carolina University, P. O. Box 261954, Conway, South Carolina 29526-6054, USA
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Bloch ED, Murray LJ, Queen WL, Chavan S, Maximoff SN, Bigi JP, Krishna R, Peterson VK, Grandjean F, Long GJ, Smit B, Bordiga S, Brown CM, Long JR. Selective Binding of O2 over N2 in a Redox–Active Metal–Organic Framework with Open Iron(II) Coordination Sites. J Am Chem Soc 2011; 133:14814-22. [DOI: 10.1021/ja205976v] [Citation(s) in RCA: 403] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Leslie J. Murray
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Wendy L. Queen
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sachin Chavan
- Department of Inorganic, Physical, and Materials Chemistry, NIS Centre of Excellence and INSTM Centre of Reference, University of Turin, Via Quarello 11, I-10135 Torino, Italy
| | | | | | - Rajamani Krishna
- Van’t Hoff Institute for Molecular Sciences, Univeristy of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Vanessa K. Peterson
- The Bragg Institute, Australian Nuclear Science and Technology Organisation, PMB1, Menai, NSW, Australia
| | | | - Gary J. Long
- Department of Chemistry, Missouri University of Science and Technology, University of Missouri, Rolla, Missouri 65409-0010, United States
| | | | - Silvia Bordiga
- Department of Inorganic, Physical, and Materials Chemistry, NIS Centre of Excellence and INSTM Centre of Reference, University of Turin, Via Quarello 11, I-10135 Torino, Italy
| | - Craig M. Brown
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- The Bragg Institute, Australian Nuclear Science and Technology Organisation, PMB1, Menai, NSW, Australia
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16
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Shubina TE. Computational Studies on Properties, Formation, and Complexation of M(II)-Porphyrins. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62007-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Kitagawa T, Ozaki Y. Infrared and Raman spectra of metalloporphyrins. STRUCTURE AND BONDING 2006. [DOI: 10.1007/bfb0036790] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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De Angelis F, Jarzecki AA, Car R, Spiro TG. Quantum Chemical Evaluation of Protein Control over Heme Ligation: CO/O2 Discrimination in Myoglobin. J Phys Chem B 2005; 109:3065-70. [PMID: 16851321 DOI: 10.1021/jp0451851] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Control of O2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8 degrees ) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O2 decreased by 0.8 and 4.1 kcal/mol for MbCO and MbO2, in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO2 that may play a key role in MbO2 photodynamics.
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Affiliation(s)
- Filippo De Angelis
- Chemistry Department, Princeton University, Princeton, New Jersey 08544, USA
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21
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Fry HC, Hoertz PG, Wasser IM, Karlin KD, Meyer GJ. Efficient Photodissociation of O2 from Synthetic Heme and Heme/M (M = Fe, Cu) Complexes. J Am Chem Soc 2004; 126:16712-3. [PMID: 15612695 DOI: 10.1021/ja045195f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single wavelength excitation (lambdaex = 355 or 532 nm) of low-temperature stabilized (198 K) synthetic heme-dioxygen and heme-dioxygen/M complexes, where M = copper or iron in a non-heme environment, results in the dissociation of dioxygen as indicated by the generation of the ferrous heme (Soret band, 427 nm) and the bleaching of the ferric-superoxide (FeIII(O2-)) 410-nm Soret band in the transient absorption difference spectrum. Dioxygen rebinds to the four heme complexes studied with comparable rate constants ( approximately 6-9 x 105 M-1 s-1). However, the quantum yield for complete dissociation of O2 from our simplest heme-O2 complex (F8)FeIII(O2-) (phi = 0.60) is higher than the other complexes measured (phi = approximately 0.2-0.3) as well as that for oxy-myoglobin (phi = 0.3).
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Affiliation(s)
- H Christopher Fry
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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22
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Leu BM, Zgierski MZ, Wyllie GRA, Scheidt WRE, Sturhahn W, Alp EE, Durbin SM, Sage JT. Quantitative vibrational dynamics of iron in nitrosyl porphyrins. J Am Chem Soc 2004; 126:4211-27. [PMID: 15053610 PMCID: PMC1570756 DOI: 10.1021/ja038526h] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.
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Affiliation(s)
- Bogdan M. Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
| | - Marek Z. Zgierski
- Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Graeme R. A. Wyllie
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - W. Rob ert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | | | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115
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De Angelis F, Car R, Spiro TG. Role of Ligand Bending in the Photodissociation of O2 vs CO-heme: A Time-Dependent Density Functional Study. J Am Chem Soc 2003; 125:15710-1. [PMID: 14677938 DOI: 10.1021/ja037373v] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-dependent DFT calculations reveal a strong dependence of low-lying excited states on the <Fe-O-O angle of a model O2-heme adduct and ready access to a metastable side-on isomer. The predicted state crossings provide a pathway for internal conversion to the ground state and account for the low quantum yield for O2 dissociation, while the side-on isomer can account for the observation of an unphotolyzable fraction at low temperature. For CO-heme, the angle-sensitive states lie above the photoaccessed Q state and do not participate in photodissociation.
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Affiliation(s)
- Filippo De Angelis
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
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Ye X, Demidov A, Champion PM. Measurements of the photodissociation quantum yields of MbNO and MbO(2) and the vibrational relaxation of the six-coordinate heme species. J Am Chem Soc 2002; 124:5914-24. [PMID: 12010067 DOI: 10.1021/ja017359n] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (t approximately 0) photodissociation quantum yields (Y(0)) of MbNO and MbO(2) are measured to be 50 +/- 5 and 28 +/- 6%, respectively, using MbCO (Y(0) = 100%) as a reference. When photolysis does not take place, we find that a significant portion of the photon energy contributes to heating of the residual six-coordinate heme (MbNO and MbO(2)). The time constant for vibrational relaxation of the six-coordinate ligand-bound heme is found to be close to 1 ps for both samples. The MbO(2) sample also shows a approximately 4-ps optical response that is assigned to a rapid phase (25-30% amplitude) of O(2) geminate rebinding. We observe no additional geminate recombination in the MbO(2) sample out to 120 ps. In contrast, the MbNO sample displays significant geminate recombination over the first 120 ps, which can be adequately fit with two exponentials whose amplitudes and time constants appear to depend weakly on the pump wavelength. This more complex kinetic behavior conceivably arises due to heating of the photodissociated heme and its effect on the geminate recombination as the system cools. Overall, the data are consistent with a hypothesis that distortions along the iron-ligand bending coordinate play a key role in the photodissociation process. The transient formation of an unphotolyzable FeO(2) side-on binding geometry is suggested to be responsible for the lowered quantum yield of MbO(2) relative to MbNO.
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Affiliation(s)
- Xiong Ye
- Physics Department and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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Nakamoto K. Resonance Raman spectra and biological significance of high-valent iron(IV,V) porphyrins. Coord Chem Rev 2002. [DOI: 10.1016/s0010-8545(01)00425-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aramata K, Kajiwara A, Kamachi M, Umemura Y, Yamagishi A. Polymer Effects on Reversible Formation of Dioxygen Adduct with Silver(II) Tetraphenylporphyrin Moieties. Macromolecules 1998. [DOI: 10.1021/ma971252w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kaoru Aramata
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560, Japan, Department of Chemistry, National Defense Academy, Yokosuka, Kanagawa 239, Japan, and Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060, Japan
| | - Atsushi Kajiwara
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560, Japan, Department of Chemistry, National Defense Academy, Yokosuka, Kanagawa 239, Japan, and Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060, Japan
| | - Mikiharu Kamachi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560, Japan, Department of Chemistry, National Defense Academy, Yokosuka, Kanagawa 239, Japan, and Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060, Japan
| | - Yasushi Umemura
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560, Japan, Department of Chemistry, National Defense Academy, Yokosuka, Kanagawa 239, Japan, and Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060, Japan
| | - Akihiko Yamagishi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560, Japan, Department of Chemistry, National Defense Academy, Yokosuka, Kanagawa 239, Japan, and Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060, Japan
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Tachibana J, Imamura T, Sasaki Y. A Reversible Metalloporphyrin Oxygen Carrier Both in the Solid State and in Solution: Preparation, Characterization, and Kinetics of Formation of a Molybdenum(VI) 5,10,15,20-Tetramesitylporphyrin Dioxygen Complex. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1998. [DOI: 10.1246/bcsj.71.363] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Metal phthalocyanine catalyzed oxidation of organic substrates with dioxygen - Aldehyde system. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0167-2991(98)80379-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Chertihin GV, Citra A, Andrews L, Bauschlicher CW. Reactions of Laser-Ablated Cobalt Atoms with O2. Infrared Spectra of Cobalt Oxides in Solid Argon. J Phys Chem A 1997. [DOI: 10.1021/jp972022m] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George V. Chertihin
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901
| | - Angelo Citra
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901
| | - Lester Andrews
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901
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Rovira C, Kunc K, Hutter J, Ballone P, Parrinello M. Equilibrium Geometries and Electronic Structure of Iron−Porphyrin Complexes: A Density Functional Study. J Phys Chem A 1997. [DOI: 10.1021/jp9722115] [Citation(s) in RCA: 337] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carme Rovira
- Max-Planck Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart, Germany, and Laboratoire d’Optique des Solides, University Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris-Cedex 05, France 10000
| | - Karel Kunc
- Max-Planck Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart, Germany, and Laboratoire d’Optique des Solides, University Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris-Cedex 05, France 10000
| | - Jürg Hutter
- Max-Planck Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart, Germany, and Laboratoire d’Optique des Solides, University Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris-Cedex 05, France 10000
| | - Pietro Ballone
- Max-Planck Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart, Germany, and Laboratoire d’Optique des Solides, University Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris-Cedex 05, France 10000
| | - Michele Parrinello
- Max-Planck Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart, Germany, and Laboratoire d’Optique des Solides, University Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris-Cedex 05, France 10000
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Nakamoto K. Structure, spectra and biological significance of high-valent iron(IV,V) porphyrins. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09670-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Proniewicz LM, Kincaid JR. Vibrational coupling effects in the resonance Raman spectra of O2 adducts of heme proteins and model compounds. Coord Chem Rev 1997. [DOI: 10.1016/s0010-8545(97)90133-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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An in-situ Raman study of the effect of the support for adsorbed iridium-chelates in catalysing oxygen reduction. J Electroanal Chem (Lausanne) 1996. [DOI: 10.1016/0022-0728(95)04420-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Chertihin GV, Saffel W, Yustein JT, Andrews L, Neurock M, Ricca A, Bauschlicher CW. Reactions of Laser-Ablated Iron Atoms with Oxygen Molecules in Condensing Argon. Infrared Spectra and Density Functional Calculations of Iron Oxide Product Molecules. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953198w] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Matthew Neurock
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22901
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Andrews L, Chertihin GV, Ricca A, Bauschlicher CW. Reactions of Laser-Ablated Iron Atoms with Oxygen Molecules: Matrix Infrared Spectra and Density Functional Calculations of OFeO, FeOO, and Fe(O2). J Am Chem Soc 1996. [DOI: 10.1021/ja953338f] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lester Andrews
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and STC-230-3, NASA Ames Research Center, Moffett Field, California 94035
| | - George V. Chertihin
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and STC-230-3, NASA Ames Research Center, Moffett Field, California 94035
| | - Alessandra Ricca
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and STC-230-3, NASA Ames Research Center, Moffett Field, California 94035
| | - Charles W. Bauschlicher
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, and STC-230-3, NASA Ames Research Center, Moffett Field, California 94035
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Lewandowski W, Proniewicz LM, Nakamoto K. The infrared spectra of ‘base-free’ dioxygen adducts of ruthenium(II) and osmium(II) porphyrins. Inorganica Chim Acta 1991. [DOI: 10.1016/s0020-1693(00)80243-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Proniewicz LM, Kuroi T, Nakamoto K. Infrared spectra of carbonyl complexes of Fe(II) phthalocyanine and Fe(II) salen in low temperature matrices. J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)85001-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Proniewicz L, Paeng I, Lewandowski W, Nakamoto K. Vibrational spectra of dioxygen adducts and oxo complexes of ruthenium tetraphenylporphine (RuTPP). J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)80078-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Infrared spectra of dioxygen adducts of iron(II)(salen): observation of two OO stretching bands. Inorganica Chim Acta 1989. [DOI: 10.1016/s0020-1693(00)89287-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Unstable complexes of sandwich compounds with small molecules. Communication 3. Complexation of metallocenes of the 3d series with molecular oxygen at low temperatures. Russ Chem Bull 1988. [DOI: 10.1007/bf00962655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Simic-Glavaski B, Tanaka A, Kenney M, Yeager E. Spectroscopic and electrochemical studies of transition-metal tetrasulfonated phthalocyanines. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0022-0728(87)85146-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zecchina A, Scarano D, Spoto G. Dioxygen adducts of iron(II) at the surface of MgO-FeO solid solutions. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0304-5102(86)85035-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Matrix-isolation infrared spectra of oxy(tetraphenylporphyrinato)iron(II) containing CS2 and SO2 as axial ligands. J Mol Struct 1986. [DOI: 10.1016/0022-2860(86)80287-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vibrational spectroscope of complexes of platinum(0)—I. Tetrakis(triphenylphosphine)platinum(0) and Dioxygenbis(triphenylphosphine)platinum(0). ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0584-8539(86)80232-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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