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Wagner S, Auerbach H, Tait CE, Martinaiou I, Kumar SCN, Kübel C, Sergeev I, Wille H, Behrends J, Wolny JA, Schünemann V, Kramm UI. Elucidating the Structural Composition of an Fe–N–C Catalyst by Nuclear‐ and Electron‐Resonance Techniques. Angew Chem Int Ed Engl 2019; 58:10486-10492. [DOI: 10.1002/anie.201903753] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/15/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Stephan Wagner
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Hendrik Auerbach
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Claudia E. Tait
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Ioanna Martinaiou
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Shyam C. N. Kumar
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christian Kübel
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- Karlsruhe Institute of Technology (KIT)Nano Micro FacilityCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Ilya Sergeev
- Deutsches Elektronen-Synchrotron Notkestraße 85 22607 Hamburg Germany
| | | | - Jan Behrends
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Juliusz A. Wolny
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Volker Schünemann
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Ulrike I. Kramm
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
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2
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Wagner S, Auerbach H, Tait CE, Martinaiou I, Kumar SCN, Kübel C, Sergeev I, Wille H, Behrends J, Wolny JA, Schünemann V, Kramm UI. Elucidating the Structural Composition of an Fe–N–C Catalyst by Nuclear‐ and Electron‐Resonance Techniques. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903753] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stephan Wagner
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Hendrik Auerbach
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Claudia E. Tait
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Ioanna Martinaiou
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Shyam C. N. Kumar
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christian Kübel
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- Karlsruhe Institute of Technology (KIT)Nano Micro FacilityCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Ilya Sergeev
- Deutsches Elektronen-Synchrotron Notkestraße 85 22607 Hamburg Germany
| | | | - Jan Behrends
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Juliusz A. Wolny
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Volker Schünemann
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Ulrike I. Kramm
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
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3
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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: 145] [Impact Index Per Article: 24.2] [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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4
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Ohta T, Shibata T, Kobayashi Y, Yoda Y, Ogura T, Neya S, Suzuki A, Seto M, Yamamoto Y. A Nuclear Resonance Vibrational Spectroscopic Study of Oxy Myoglobins Reconstituted with Chemically Modified Heme Cofactors: Insights into the Fe-O 2 Bonding and Internal Dynamics of the Protein. Biochemistry 2018; 57:6649-6652. [PMID: 30422640 DOI: 10.1021/acs.biochem.8b00829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular mechanism of O2 binding to hemoglobin (Hb) and myoglobin (Mb) is a long-standing issue in the field of bioinorganic and biophysical chemistry. The nature of Fe-O2 bond in oxy Hb and Mb had been extensively investigated by resonance Raman spectroscopy, which assigned the Fe-O2 stretching bands at ∼570 cm-1. However, resonance Raman assignment of the vibrational mode had been elusive due to the spectroscopic selection rule and to the limited information available about the ground-state molecular structure. Thus, nuclear resonance vibrational spectroscopy was applied to oxy Mbs reconstituted with 57Fe-labeled native heme cofactor and two chemically modified ones. This advanced spectroscopy in conjunction with DFT analyses gave new insights into the nature of the Fe-O2 bond of oxy heme by revealing the effect of heme peripheral substitutions on the vibrational dynamics of heme Fe atom, where the main Fe-O2 stretching band of the native protein was characterized at ∼420 cm-1.
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Affiliation(s)
- Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science , University of Hyogo, RSC-UH LP Center , Hyogo 679-5148 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science , Kyoto University , Osaka 590-0494 , Japan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute , Hyogo 679-5198 , Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science , University of Hyogo, RSC-UH LP Center , Hyogo 679-5148 , Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences , Chiba University , Chiba 260-8657 , Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology , Nagaoka College , Nagaoka 940-8532 , Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science , Kyoto University , Osaka 590-0494 , Japan.,Japan Atomic Energy Agency , Hyogo 679-5148 , Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
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5
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Abstract
The synthesis and structural analysis of two new bis imidazole-ligated iron(II) porphyrinates are reported. The reacting porphyrin used in the studies was the four-coordinate [Formula: see text] atropisomer of [Fe(TpivPP)] (picket fence porphyrin); the axial ligands are 2-methylimidazole and 1,2-dimethylimidazole. Crystal structure analysis revealed that the [Fe(TpivPP)(2-MeHIm)[Formula: see text]] complex had a strongly ruffled porphyrin core that accommodated the hindered ligands on both the picket side and the open face of the porphyrin. Reaction with 1,2-dimethylimidazole with the four-coordinate [Fe(TpivPP)] starting material led to an isomerized form of the picket fence porphyrin. The structure analysis showed that the product obtained was the [Formula: see text] atropisomer. Strong ruffling caused by the bulky 1,2-dimethylimidazole ligand must allow the requisite rotation about the methine carbon to phenyl carbon single bond and yields what is probably the most stable form of the complex. The relative orientation of the two axial ligands in both complexes are approximately perpendicular to each other. Other structural parameters are in general accord with six-coordinate iron(II) porphyrinates.
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Affiliation(s)
- Haimang Wang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing 101408, China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing 101408, China
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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6
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Scheidt WR, Li J, Sage JT. What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes. Chem Rev 2017; 117:12532-12563. [PMID: 28921972 PMCID: PMC5639469 DOI: 10.1021/acs.chemrev.7b00295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Nuclear resonance
vibrational spectroscopy (NRVS; also known as
nuclear inelastic scattering, NIS) is a synchrotron-based method that
reveals the full spectrum of vibrational dynamics for Mössbauer
nuclei. Another major advantage, in addition to its completeness (no
arbitrary optical selection rules), is the unique selectivity of NRVS.
The basics of this recently developed technique are first introduced
with descriptions of the experimental requirements and data analysis
including the details of mode assignments. We discuss the use of NRVS
to probe 57Fe at the center of heme and heme protein derivatives
yielding the vibrational density of states for the iron. The application
to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode
character. The availability of the complete vibrational spectrum of
iron allows the identification of modes not available by other techniques.
This permits the correlation of frequency with other physical properties.
A significant example is the correlation we find between the Fe–Im
stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im)
bond distance, not possible previously. NRVS also provides uniquely
quantitative insight into the dynamics of the iron. For example, it
provides a model-independent means of characterizing the strength
of iron coordination. Prediction of the temperature-dependent mean-squared
displacement from NRVS measurements yields a vibrational “baseline”
for Fe dynamics that can be compared with results from techniques
that probe longer time scales to yield quantitative insights into
additional dynamical processes.
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Affiliation(s)
- W Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556 United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , YanQi Lake, HuaiRou District, Beijing 101408, China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , 120 Forsyth Street, Boston, Massachusetts 02115, United States
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7
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Sun Y, Benabbas A, Zeng W, Muralidharan S, Boon EM, Champion PM. Kinetic Control of O2 Reactivity in H-NOX Domains. J Phys Chem B 2016; 120:5351-8. [PMID: 27229134 DOI: 10.1021/acs.jpcb.6b03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O2 binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron-histidine mode near 217 cm(-1) following photoexcitation, which indicates that O2 can be dissociated in these proteins. However, the quantum yield of O2 photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O2 and NO in both of these proteins is very fast (∼1.4 × 10(11) s(-1)) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O2 off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O2 ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe-O2 bond that is correlated with the significant heme ruffing and saddling distortions, explains the unusually high O2 affinity of WT Tt H-NOX and the even higher affinity found in the P115A mutant.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Sandhya Muralidharan
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Elizabeth M Boon
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
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8
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Peng Q, Pavlik JW, Silvernail NJ, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy. Chemistry 2016; 22:6323-6332. [PMID: 26999733 PMCID: PMC4999340 DOI: 10.1002/chem.201505155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Indexed: 11/08/2022]
Abstract
The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1-MeIm)(NO)] (TpFPP=tetra-para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X=N, C, and O) complexes is correlated with the Fe-XO bond lengths. The nature of highest frequency band at ≈560 cm(-1) has also been examined in two additional new derivatives. Previously assigned as the Fe-NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.
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Affiliation(s)
- Qian Peng
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Jeffrey W. Pavlik
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - Nathan J. Silvernail
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Michael Y. Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, MA 02115, USA
| | - W. Robert Scheidt
- Contribution from Department of Chemistry and Biochemistry, University of Notre Dame, University of Notre Dame, Notre Dame, Indiana 46556 USA
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9
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He B, Schulz CE, Li J. Synthesis and characterization of a modified "picket fence" porphyrin complex - stronger π bonding interactions between Fe(ii) and axial ligands. Dalton Trans 2015; 44:13651-61. [PMID: 26145452 DOI: 10.1039/c5dt00941c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new, modified "picket fence" porphyrin is synthesized and its bis(imidazole)-ligated iron(ii) derivative [Fe(MbenTpivPP)(1-MeIm)(2)] is investigated. X-ray structure determinations demonstrate that [Fe(MbenTpivPP)(1-MeIm)(2)] has structural features of a near planar porphyrin plane, a relative perpendicular ligand orientation, and one unusually large absolute ligand orientation (φ). The combination of these features leads to a new type of species that is different from previously reported analogues. Further structural examination reveals a strong correlation between the mutual ligand orientations (θ) and the axial Fe-N(Im) bond distances, which is detailed for the first time. Mössbauer spectroscopic characterization shows that the low spin derivative has a quadrupole splitting of 0.99 mm s(-1) at 100 K.
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Affiliation(s)
- Baiyin He
- College of Materials Science and Opto-electronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing, 101408, China.
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10
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Abstract
In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.
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11
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Li J, Peng Q, Oliver A, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes. J Am Chem Soc 2014; 136:18100-10. [PMID: 25490350 PMCID: PMC4295236 DOI: 10.1021/ja5105766] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 01/06/2023]
Abstract
Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO}(6) porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quite distinct from those found for CO or {FeNO}(7) heme species. This is the result of unchanging Fe-N(NO) bonding interactions in the {FeNO}(6) species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe-Im stretch in six-coordinate heme derivatives. NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O2 reveal a strong correlation between the Fe-Im stretch and Fe-N(Im) bond distance that is detailed for the first time.
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Affiliation(s)
- Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, YanQi Lake, HuaiRou District, Beijing 101408, China
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qian Peng
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Allen
G. Oliver
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael Y. Hu
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
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12
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Pavlik J, Peng Q, Silvernail N, Alp EE, Hu MY, Zhao J, Sage JT, Scheidt WR. Anisotropic iron motion in nitrosyl iron porphyrinates: natural and synthetic hemes. Inorg Chem 2014; 53:2582-90. [PMID: 24528178 PMCID: PMC3993889 DOI: 10.1021/ic4028964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 02/05/2023]
Abstract
The vibrational spectra of two five-coordinate nitrosyl iron porphyrinates, [Fe(OEP)(NO)] (OEP = dianion of 2,3,7,8,12,13,17,18-octaethylporphyrin) and [Fe(DPIX)(NO)] (DPIX = deuteroporphyrin IX), have been studied by oriented single-crystal nuclear resonance vibrational spectroscopy. Single crystals (both are in the triclinic crystal system) were oriented to give vibrational spectra perpendicular to the porphyrin plane. Additionally, two orthogonal in-plane measurements that were also either perpendicular or parallel to the projection of the FeNO plane onto the porphyrin plane yield the complete set of vibrations with iron motion. In addition to cleanly enabling the assignment of the FeNO bending and stretching modes, the measurements reveal that the two in-plane spectra from the parallel and perpendicular in-plane directions for both compounds have substantial differences. The assignment of these in-plane vibrations were aided by density functional theory predictions. The differences in the two in-plane directions result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is thus found to be largely parallel and perpendicular to the projection of the FeNO plane on the porphyrin plane. These axial ligand effects on the in-plane iron motion are related to the strength of the axial ligand-to-iron bond.
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Affiliation(s)
- Jeffrey
W. Pavlik
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qian Peng
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nathan
J. Silvernail
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael Y. Hu
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - J. Timothy Sage
- Department
of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 120 Forsyth Street, Boston, Massachusetts 02115, United States
| | - W. Robert Scheidt
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre Dame, Indiana 46556, United States
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Li J, Noll BC, Oliver AG, Schulz CE, Scheidt WR. Correlated ligand dynamics in oxyiron picket fence porphyrins: structural and Mössbauer investigations. J Am Chem Soc 2013; 135:15627-41. [PMID: 24025123 PMCID: PMC3827975 DOI: 10.1021/ja408431z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disorder in the position of the dioxygen ligand is a well-known problem in dioxygen complexes and, in particular, those of picket fence porphyrin species. The dynamics of Fe-O2 rotation and tert-butyl motion in three different picket fence porphyrin derivatives has been studied by a combination of multitemperature X-ray structural studies and Mössbauer spectroscopy. Structural studies show that the motions of the dioxygen ligand also require motions of the protecting pickets of the ligand binding pocket. The two motions appear to be correlated, and the temperature-dependent change in the O2 occupancies cannot be governed by a simple Boltzmann distribution. The three [Fe(TpivPP)(RIm)(O2)] derivatives studied have RIm = 1-methyl-, 1-ethyl-, or 2-methylimidazole. In all three species there is a preferred orientation of the Fe-O2 moiety with respect to the trans imidazole ligand and the population of this orientation increases with decreasing temperature. In the 1-MeIm and 1-EtIm species the Fe-O2 unit is approximately perpendicular to the imidazole plane, whereas in the 2-MeHIm species the Fe-O2 unit is approximately parallel. This reflects the low energy required for rotation of the Fe-O2 unit and the small energy differences in populating the possible pocket quadrants. All dioxygen complexes have a crystallographically required 2-fold axis of symmetry that limits the accuracy of the determined Fe-O2 geometry. However, the 80 K structure of the 2-MeHIm derivative allowed for resolution of the two bonded oxygen atom positions and provided the best geometric description for the Fe-O2 unit. The values determined are Fe-O = 1.811(5) Å, Fe-O-O = 118.2(9)°, O-O = 1.281(12) Å, and an off-axis tilt of 6.2°. Demonstration of the off-axis tilt is a first. We present detailed temperature-dependent simulations of the Mössbauer spectra that model the changing value of the quadrupole splitting and line widths. Residuals to fits are poorer at higher temperature. We believe that this is consistent with the idea that population of the two conformers is related to the concomitant motions of both Fe-O2 rotations and motions of the protecting tert-butyl pickets.
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Affiliation(s)
- Jianfeng Li
- To whom correspondence should be addressed. JL: , CES: , WRS:
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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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A convenient, high-yielding, chromatography-free method for the insertion of transition metal acetates into porphyrins. Polyhedron 2013. [DOI: 10.1016/j.poly.2012.05.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Kepp KP, Dasmeh P. Effect of Distal Interactions on O2 Binding to Heme. J Phys Chem B 2013; 117:3755-70. [DOI: 10.1021/jp400260u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Pouria Dasmeh
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface. Proc Natl Acad Sci U S A 2012; 109:8896-900. [PMID: 22619327 DOI: 10.1073/pnas.1200345109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The active site of cytochrome c (Cyt c) consists of a heme covalently linked to a pentapeptide segment (Cys-X-X-Cys-His), which provides a link between the heme and the protein surface, where the redox partners of Cyt c bind. To elucidate the vibrational properties of heme c, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on (57)Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c(552), including (13)C(8)-heme-, (13)C(5)(15)N-Met-, and (13)C(15)N-polypeptide (pp)-labeled samples, revealing heme-based vibrational modes in the 200- to 450-cm(-1) spectral region. Simulations of the NRVS spectra of H. thermophilus cytochrome c(552) allowed for a complete assignment of the Fe vibrational spectrum of the protein-bound heme, as well as the quantitative determination of the amount of mixing between local heme vibrations and pp modes from the Cys-X-X-Cys-His motif. These results provide the basis to propose that heme-pp vibrational dynamic couplings play a role in electron transfer (ET) by coupling vibrations of the heme directly to vibrations of the pp at the protein-protein interface. This could allow for the direct transduction of the thermal (vibrational) energy from the protein surface to the heme that is released on protein/protein complex formation, or it could modulate the heme vibrations in the protein/protein complex to minimize reorganization energy. Both mechanisms lower energy barriers for ET. Notably, the conformation of the distal Met side chain is fine-tuned in the protein to localize heme-pp mixed vibrations within the 250- to 400-cm(-1) spectral region. These findings point to a particular orientation of the distal Met that maximizes ET.
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Zeng W, Barabanschikov A, Wang N, Lu Y, Zhao J, Sturhahn W, Alp EE, Sage JT. Vibrational dynamics of oxygenated heme proteins. Chem Commun (Camb) 2012; 48:6340. [PMID: 22498848 DOI: 10.1039/c2cc31239e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Advanced spectroscopic techniques coupled with DFT calculations reveal the vibrational dynamics of the iron in stable dioxygen complexes with myoglobin and with a mutant engineered to model the catalytic site of heme-copper oxidases. The unprecedented level of detail will constrain computational modelling of reactions with oxygen.
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Affiliation(s)
- Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, BostonMA 02115, USA.
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Peng Q, Pavlik JW, Scheidt WR, Wiest O. Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]. J Chem Theory Comput 2012; 8:214-223. [PMID: 23204948 PMCID: PMC3507453 DOI: 10.1021/ct2006456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.
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Affiliation(s)
- Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Jeffrey W. Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA)
- School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
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