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Transue WJ, Snyder RA, Caranto JD, Kurtz DM, Solomon EI. Particle Swarm Fitting of Spin Hamiltonians: Magnetic Circular Dichroism of Reduced and NO-Bound Flavodiiron Protein. Inorg Chem 2022; 61:16520-16527. [PMID: 36223761 PMCID: PMC9942269 DOI: 10.1021/acs.inorgchem.2c02234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A particle swarm optimization (PSO) algorithm is described for the fitting of ground-state spin Hamiltonian parameters from variable-temperature/variable-field (VTVH) magnetic circular dichroism (MCD) data. This PSO algorithm is employed to define the ground state of two catalytic intermediates from a flavodiiron protein (FDP), a class of enzymes with nitric oxide reductase activity. The bimetallic iron active site of this enzyme proceeds through a biferrous intermediate and a mixed ferrous-{FeNO}7 intermediate during the catalytic cycle, and the MCD spectra of these intermediates are presented and analyzed. The fits of the spin Hamiltonians are shown to provide important geometric and electronic insight into these species that is compared and contrasted with previous reports.
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Affiliation(s)
| | - Rae Ana Snyder
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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Suturina EA, Nehrkorn J, Zadrozny JM, Liu J, Atanasov M, Weyhermüller T, Maganas D, Hill S, Schnegg A, Bill E, Long JR, Neese F. Magneto-Structural Correlations in Pseudotetrahedral Forms of the [Co(SPh)4]2– Complex Probed by Magnetometry, MCD Spectroscopy, Advanced EPR Techniques, and ab Initio Electronic Structure Calculations. Inorg Chem 2017; 56:3102-3118. [DOI: 10.1021/acs.inorgchem.7b00097] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizaveta A. Suturina
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
- Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Joscha Nehrkorn
- Berlin Joint EPR Lab, Institute for Nanospectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Kekuléstraße
5, 12489 Berlin, Germany
| | - Joseph M. Zadrozny
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Junjie Liu
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Mihail Atanasov
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
- Bulgarian Academy of Sciences, Institute of General and Inorganic
Chemistry, Akad. Georgi
Bontchev Street 11, 1113 Sofia, Bulgaria
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios Maganas
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - Stephen Hill
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Alexander Schnegg
- Berlin Joint EPR Lab, Institute for Nanospectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Kekuléstraße
5, 12489 Berlin, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - Jeffrey R. Long
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
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Gendron F, Fleischauer VE, Duignan TJ, Scott BL, Löble MW, Cary SK, Kozimor SA, Bolvin H, Neidig ML, Autschbach J. Magnetic circular dichroism of UCl6− in the ligand-to-metal charge-transfer spectral region. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02572f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl6− complex ion in the UV-Vis spectral region.
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Affiliation(s)
- Frédéric Gendron
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
| | | | - Thomas J. Duignan
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
| | - Brian L. Scott
- Los Alamos National Laboratory
- Los Alamos
- New Mexico 87544
- USA
| | | | | | | | - Hélène Bolvin
- Laboratoire de Chimie et de Physique Quantiques
- 31062 Toulouse
- France
| | | | - Jochen Autschbach
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
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Ye S, Kupper C, Meyer S, Andris E, Navrátil R, Krahe O, Mondal B, Atanasov M, Bill E, Roithová J, Meyer F, Neese F. Magnetic Circular Dichroism Evidence for an Unusual Electronic Structure of a Tetracarbene-Oxoiron(IV) Complex. J Am Chem Soc 2016; 138:14312-14325. [PMID: 27682505 DOI: 10.1021/jacs.6b07708] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In biology, high valent oxo-iron(IV) species have been shown to be pivotal intermediates for functionalization of C-H bonds in the catalytic cycles of a range of O2-activating iron enzymes. This work details an electronic-structure investigation of [FeIV(O)(LNHC)(NCMe)]2+ (LNHC = 3,9,14,20-tetraaza-1,6,12,17-tetraazoniapenta-cyclohexacosane-1(23),4,6(26),10,12(25),15,17(24),21-octaene, complex 1) using helium tagging infrared photodissociation (IRPD), absorption, and magnetic circular dichroism (MCD) spectroscopy, coupled with DFT and highly correlated wave function based multireference calculations. The IRPD spectrum of complex 1 reveals the Fe-O stretching vibration at 832 ± 3 cm-1. By analyzing the Franck-Condon progression, we can determine the same vibration occurring at 616 ± 10 cm-1 in the E(dxy → dxz,yz) excited state. Both values are similar to those measured for [FeIV(O)(TMC)(NCMe)]2+ (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane). The low-temperature MCD spectra of complex 1 exhibit three pseudo A-term signals around 12 500, 17 000, and 24 300 cm-1. We can unequivocally assign them to the ligand field transitions of dxy → dxz,yz, dxz,yz → dz2, and dxz,yz → dx2-y2, respectively, through direct calculations of MCD spectra and independent determination of the MCD C-term signs from the corresponding electron donating and accepting orbitals. In comparison with the corresponding transitions observed for [FeIV(O) (SR-TPA)(NCMe)]2+ (SR-TPA = tris(3,5-dimethyl-4-methoxypyridyl-2-methy)amine), the excitations within the (FeO)2+ core of complex 1 have similar transition energies, whereas the excitation energy for dxz,yz → dx2-y2 is significantly higher (∼12 000 cm-1 for [FeIV(O)(SR-TPA)(NCMe)]2+). Our results thus substantiate that the tetracarbene ligand (LNHC) of complex 1 does not significantly affect the bonding in the (FeO)2+ unit but strongly destabilizes the dx2-y2 orbital to eventually lift it above dz2. As a consequence, this unusual electron configuration leads to an unprecedentedly larger quintet-triplet energy separation for complex 1, which largely rules out the possibility that the H atom transfer reaction may take place on the quintet surface and hence quenches two-state reactivity. The resulting mechanistic implications are discussed.
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Affiliation(s)
- Shengfa Ye
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Claudia Kupper
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen , Tammannstr. 4, D-37077 Göttingen, Germany
| | - Steffen Meyer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen , Tammannstr. 4, D-37077 Göttingen, Germany
| | - Erik Andris
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Rafael Navrátil
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Oliver Krahe
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Bhaskar Mondal
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Mihail Atanasov
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.,Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences , 1113 Sofia, Bulgaria
| | - Eckhard Bill
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Franc Meyer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen , Tammannstr. 4, D-37077 Göttingen, Germany
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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Ye S, Xue G, Krivokapic I, Petrenko T, Bill E, Que Jr L, Neese F. Magnetic circular dichroism and computational study of mononuclear and dinuclear iron(IV) complexes. Chem Sci 2015; 6:2909-2921. [PMID: 26417426 PMCID: PMC4583211 DOI: 10.1039/c4sc03268c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
High-valent iron(IV)-oxo species are key intermediates in the catalytic cycles of a range of O2-activating iron enzymes. This work presents a detailed study of the electronic structures of mononuclear ([FeIV(O)(L)(NCMe)]2+, 1, L = tris(3,5-dimethyl-4-methoxylpyridyl-2-methyl)amine) and dinuclear ([(L)FeIV(O)(μ-O)FeIV(OH)(L)]3+, 2) iron(IV) complexes using absorption (ABS), magnetic circular dichroism (MCD) spectroscopy and wave-function-based quantum chemical calculations. For complex 1, the experimental MCD spectra at 2-10 K are dominated by a broad positive C-term band between 12000 and 18000 cm-1. As the temperature increases up to ~20 K, this feature is gradually replaced by a derivative-shaped signal. The computed MCD spectra are in excellent agreement with experiment, which reproduce not only the excitation energies and the MCD signs of key transitions but also their temperature-dependent intensity variations. To further corroborate the assignments suggested by the calculations, the individual MCD sign for each transition is independently determined from the corresponding electron donating and accepting orbitals. Thus, unambiguous assignments can be made for the observed transitions in 1. The ABS/MCD data of complex 2 exhibit ten features that are assigned as ligand-field transitions or oxo- or hydroxo-to-metal charge transfer bands, based on MCD/ABS intensity ratios, calculated excitation energies, polarizations, and MCD signs. In comparison with complex 1, the electronic structure of the FeIV=O site is not significantly perturbed by the binding to another iron(IV) center. This may explain the experimental finding that complexes 1 and 2 have similar reactivities toward C-H bond activation and O-atom transfer.
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Affiliation(s)
- Shengfa Ye
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Genqiang Xue
- Department of Chemistry , Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant St. SE , Minneapolis , Minnesota 55455 , USA .
| | - Itana Krivokapic
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Taras Petrenko
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Eckhard Bill
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
| | - Lawrence Que Jr
- Department of Chemistry , Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant St. SE , Minneapolis , Minnesota 55455 , USA .
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion , Stiftstraße 34-36 , D-45470 Mülheim an der Ruhr , Germany . ; ;
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Yong SC, Roversi P, Lillington J, Rodriguez F, Krehenbrink M, Zeldin OB, Garman EF, Lea SM, Berks BC. A complex iron-calcium cofactor catalyzing phosphotransfer chemistry. Science 2014; 345:1170-1173. [PMID: 25190793 DOI: 10.1126/science.1254237] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alkaline phosphatases play a crucial role in phosphate acquisition by microorganisms. To expand our understanding of catalysis by this class of enzymes, we have determined the structure of the widely occurring microbial alkaline phosphatase PhoX. The enzyme contains a complex active-site cofactor comprising two antiferromagnetically coupled ferric iron ions (Fe(3+)), three calcium ions (Ca(2+)), and an oxo group bridging three of the metal ions. Notably, the main part of the cofactor resembles synthetic oxide-centered triangular metal complexes. Structures of PhoX-ligand complexes reveal how the active-site metal ions bind substrate and implicate the cofactor oxo group in the catalytic mechanism. The presence of iron in PhoX raises the possibility that iron bioavailability limits microbial phosphate acquisition.
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Affiliation(s)
- Shee Chien Yong
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Pietro Roversi
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - James Lillington
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Fernanda Rodriguez
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Martin Krehenbrink
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Oliver B Zeldin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Rodriguez F, Lillington J, Johnson S, Timmel CR, Lea SM, Berks BC. Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site. J Biol Chem 2014; 289:30889-99. [PMID: 25217636 PMCID: PMC4223295 DOI: 10.1074/jbc.m114.604892] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe3+ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca2+ ions instead of the single extra Fe2+, Mn2+, or Zn2+ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe3+ and Ca2+ ions.
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Affiliation(s)
- Fernanda Rodriguez
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU
| | - James Lillington
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Steven Johnson
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Christiane R Timmel
- the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Susan M Lea
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Ben C Berks
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
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Application of magnetically-perturbed time-dependent density functional theory to magnetic circular dichroism. IV. The influence of zero-field splitting on the spectra of S>1/2 molecules. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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McMaster J, Oganesyan VS. Magnetic circular dichroism spectroscopy as a probe of the structures of the metal sites in metalloproteins. Curr Opin Struct Biol 2010; 20:615-22. [PMID: 20619632 DOI: 10.1016/j.sbi.2010.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/07/2010] [Accepted: 06/09/2010] [Indexed: 11/30/2022]
Abstract
Magnetic circular dichroism (MCD) is a powerful probe of the electronic and geometric structures of metal centres in metalloproteins. MCD has provided significant insight into the nature of the axial donors at haem centres and, more recently, sophisticated methods for the analysis of MCD spectra have had a major impact on the study of the electronic structures of the ground states of a range of Cu, non-haem iron and Mo-containing active sites. This detail, together with data from other complimentary spectroscopies, has played a major role in defining the chemistry underpinning the catalysis achieved by these metal centres.
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Affiliation(s)
- Jonathan McMaster
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, UK.
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Calculation of Magnetic Circular Dichroism Spectra With Time-Dependent Density Functional Theory. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62002-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sundararajan M, Ganyushin D, Ye S, Neese F. Multireference ab initio studies of zero-field splitting and magnetic circular dichroism spectra of tetrahedral Co(II) complexes. Dalton Trans 2009:6021-36. [PMID: 19623403 DOI: 10.1039/b902743b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly developed multireference (MR) ab initio method for the calculation of magnetic circular dichroism (MCD) spectra was calibrated through the calculation of the ground- and excited state properties of seven high-spin (S = 3/2) Co(II) complexes. The MCD spectra were computed by the explicit treatment of spin-orbit coupled (SOC) and spin-spin coupled (SSC) N-electron states. For the complexes studied in this work, we found that the SOC is more important than the SSC for determining the ground state zero field splitting (ZFS). Our computed ZFS parameter D for the [Co(PPh(3))(2)Cl(2)] model complex is -17.6 cm(-1), which is reasonably close to the experimental value of -14.8 cm(-1). Generally, the computed absorption and MCD spectra are in fair agreement with experiment for all investigated complexes. Thus, reliable electronic structure and spectroscopic predictions for medium sized transition metal complexes are feasible on the basis of this methodology. This characterizes the presented method as a promising tool for MCD spectra interpretations of transition metal complexes in a variety of areas of chemistry and biology.
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Affiliation(s)
- Mahesh Sundararajan
- Institut für Physikalische und Theoretische Chemie, Wegelerstr. 12, University of Bonn, D-53115 Bonn, Germany
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Novak R, Pineider F, de Julián Fernández C, Gorini L, Bogani L, Danieli C, Cavigli L, Cornia A, Sessoli R. Magneto-optical studies on the molecular cluster Fe4 in different polymeric environments. Inorganica Chim Acta 2008. [DOI: 10.1016/j.ica.2008.03.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Seth M, Ziegler T, Autschbach J. Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism. III. Temperature-dependent magnetic circular dichroism induced by spin-orbit coupling. J Chem Phys 2008; 129:104105. [DOI: 10.1063/1.2976568] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Grove LE, Xie J, Yikilmaz E, Miller AF, Brunold TC. Spectroscopic and computational investigation of second-sphere contributions to redox tuning in Escherichia coli iron superoxide dismutase. Inorg Chem 2008; 47:3978-92. [PMID: 18433120 DOI: 10.1021/ic702412y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Fe- and Mn-dependent superoxide dismutases (SODs), second-sphere residues have been implicated in precisely tuning the metal ion reduction potential to maximize catalytic activity (Vance, C. K.; Miller, A.-F. J. Am. Chem. Soc. 1998, 120, 461-467). In the present study, spectroscopic and computational methods were used to characterize three distinct Fe-bound SOD species that possess different second-coordination spheres and, consequently, Fe(3+/2+)reduction potentials that vary by approximately 1 V, namely, FeSOD, Fe-substituted MnSOD (Fe(Mn)SOD), and the Q69E FeSOD mutant. Despite having markedly different metal ion reduction potentials, FeSOD, Fe(Mn)SOD, and Q69E FeSOD exhibit virtually identical electronic absorption, circular dichroism, and magnetic circular dichroism (MCD) spectra in both their oxidized and reduced states. Likewise, variable-temperature, variable-field MCD data obtained for the oxidized and reduced species do not reveal any significant electronic, and thus geometric, variations within the Fe ligand environment. To gain insight into the mechanism of metal ion redox tuning, complete enzyme models for the oxidized and reduced states of all three Fe-bound SOD species were generated using combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations. Consistent with our spectroscopic data, density functional theory computations performed on the corresponding active-site models predict that the three SOD species share similar active-site electronic structures in both their oxidized and reduced states. By using the QM/MM-optimized active-site models in conjunction with the conductor-like screening model to calculate the proton-coupled Fe(3+/2+) reduction potentials, we found that different hydrogen-bonding interactions with the conserved second-sphere Gln (changed to Glu in Q69E FeSOD) greatly perturb the p K of the Fe-bound solvent ligand and, thus, drastically affect the proton-coupled metal ion reduction potential.
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Affiliation(s)
- Laurie E Grove
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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15
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Ganyushin D, Neese F. First-principles calculations of magnetic circular dichroism spectra. J Chem Phys 2008; 128:114117. [DOI: 10.1063/1.2894297] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Oganesyan VS, Cheesman MR, Thomson AJ. Magnetic Circular Dichroism Evidence for a Weakly Coupled Heme-Radical Pair at the Active Site of Cytochrome cd1, a Nitrite Reductase. Inorg Chem 2007; 46:10950-2. [DOI: 10.1021/ic701556y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vasily S. Oganesyan
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Myles R. Cheesman
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andrew J. Thomson
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
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Wasinger EC, Davis MI, Pau MYM, Orville AM, Zaleski JM, Hedman B, Lipscomb JD, Hodgson KO, Solomon EI. Spectroscopic studies of the effect of ligand donor strength on the Fe-NO bond intradiol dioxygenases. Inorg Chem 2003; 42:365-76. [PMID: 12693216 DOI: 10.1021/ic025906f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The geometric and electronic structure of NO bound to reduced protocatechuate 3,4-dioxygenase and its substrate (3,4-dihydroxybenzoate, PCA) complex have been examined by X-ray absorption (XAS), UV-vis absorption (Abs), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The results are compared to those previously published on model complexes described as [FeNO]7 systems in which an S = 5/2 ferric center is antiferromagnetically coupled to an S = 1 NO-. XAS pre-edge analysis indicates that the Fe-NO units in FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] lack the greatly increased pre-edge intensity representative of most [FeNO]7 model sites. Furthermore, from extended X-ray absorption fine structure (EXAFS) analysis, the FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] active sites are shown to have an Fe-NO distance of at least 1.91 A, approximately 0.2 A greater than those found in the model complexes. The weakened Fe-NO bond is consistent with the overall lengthening of the bond lengths and the fact that VTVH MCD data show that NO(-)-->FeIII CT transitions are no longer polarized along the z-axis of the zero-field splitting tensor. The weaker Fe-NO bond derives from the strong donor interaction of the endogenous phenolate and substrate catecholate ligands, which is observed from the increased intensity in the CT region relative to that of [FeNO]7 model complexes, and from the shift in XAS edge position to lower energy. As NO is an analogue of O2, the effect of endogenous ligand donor strength on the Fe-NO bond has important implications with respect to O2 activation by non-heme iron enzymes.
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Affiliation(s)
- Erik C Wasinger
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Jackson TA, Xie J, Yikilmaz E, Miller AF, Brunold TC. Spectroscopic and computational studies on iron and manganese superoxide dismutases: nature of the chemical events associated with active-site pKs. J Am Chem Soc 2002; 124:10833-45. [PMID: 12207539 DOI: 10.1021/ja0266058] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined spectroscopic/computational approach has been utilized to explore the chemical origins of the active-site pKs of the structurally homologous Fe- and Mn-dependent superoxide dismutases (SODs). Absorption, circular dichroism, magnetic circular dichroism, and variable-temperature, variable-field magnetic circular dichroism spectroscopic experiments have permitted us to determine electronic transition energies and polarizations, as well as ground-state spin Hamiltonian parameters. These experimental data have been used in conjunction with semiempirical intermediate neglect of differential overlap/spectroscopic parametrization configuration interaction (INDO/S-CI) computations for evaluating hypothetical active-site models for the high-pH species generated by density functional theory (DFT) geometry optimizations. Our experimental and computational data indicate that both reduced FeSOD and oxidized MnSOD do not bind hydroxide at high pH; rather, the active-site pK for these two species is attributed to deprotonation of a second-sphere tyrosine. Conversely, our data obtained on oxidized FeSOD indicate that hydroxide binding is responsible for the observed active-site pK for this species. Intriguingly, in the Fe-substituted form of MnSOD this identical chemical event occurs at a significantly lower pH. Overall, our results suggest an important role for second-sphere amino acids in tuning the active sites' interaction with small anions and bring into question the assumption that these homologous enzymes operate by the same molecular mechanism.
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Affiliation(s)
- Timothy A Jackson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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McInnes EJL, Pidcock E, Oganesyan VS, Cheesman MR, Powell AK, Thomson AJ. Optical detection of spin polarization in single-molecule magnets [Mn(12)O(12)(O(2)CR)(16)(H(2)O)(4)]. J Am Chem Soc 2002; 124:9219-28. [PMID: 12149028 DOI: 10.1021/ja020456b] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A magneto-optical study has been undertaken of the mixed-valence single-molecule magnet [Mn(IV)(4)Mn(III)(8)O(12)L(16)] in which the ligands, L, are acetate (Mn(12)Ac) or the long-chain carboxylic acid, C(14)H(29)COOH (Mn(12)C(15)), that confers better solubility in organic solvents. Thin polymer films of these compounds in poly(methyl methacrylate) (PMM) have been cast by solvent evaporation to provide samples suitable for variable-temperature and field magnetic circular dichroism (MCD) studies. The absorption spectra in isotropic light are featureless, whereas the low-temperature MCD spectra contain resolved peaks, both positive and negative. MCD magnetization curves measured at temperatures above 4.2 K have established a ground-state spin of S = 10 and an axial zero-field parameter, D, of -0.61 K, similar to that determined for single crystals of Mn(12)Ac. By studying at a variety of optical wavelengths, the polarization ratios of the optical transitions relative to the unique axis of the zero-field distortion have been determined. The MCD magnetization curves measured at 4.2 K between 0 and 5 T for the case of Mn(12)C(15) in the PMM film can be fitted only on the assumption of nonrandom distribution of molecular z-axes arising from stresses in the polymer film during the process of casting. MCD-detected hysteresis curves measured in both frozen solution and PMM films, below the blocking temperature of approximately 3 K, show a high retention of spin polarization after reduction to zero of a polarizing magnetic field. This generates intense zero-field circular dichroism (CD) with maximum intensity for xy-polarized optical transitions whose sign depends on the direction of the original polarizing field. The optical polarization and the selection rules for MCD select a subset of molecular orientations with respect to the direction of field. Thus, the magnetically induced CD provides a highly sensitive and rapid optical method of reading the spin polarization of molecular magnets.
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Affiliation(s)
- Eric J L McInnes
- School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Davis MI, Orville AM, Neese F, Zaleski JM, Lipscomb JD, Solomon EI. Spectroscopic and electronic structure studies of protocatechuate 3,4-dioxygenase: nature of tyrosinate-Fe(III) bonds and their contribution to reactivity. J Am Chem Soc 2002; 124:602-14. [PMID: 11804491 DOI: 10.1021/ja011945z] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometric and electronic structure of the high-spin ferric active site of protocatechuate 3,4-dioxygenase (3,4-PCD) has been examined by absorption (Abs), circular dichroism (CD), magnetic CD (MCD), and variable-temperature-variable-field (VTVH) MCD spectroscopies. Density functional (DFT) and INDO/S-CI molecular orbital calculations provide complementary insight into the electronic structure of 3,4-PCD and allow an experimentally calibrated bonding scheme to be developed. Abs, CD, and MCD indicate that there are at least seven transitions below 35 000 cm(-1) which arise from tyrosinate ligand-to-metal-charge transfer (LMCT) transitions. VTVH MCD spectroscopy gives the polarizations of these LMCT bands in the principal axis system of the D-tensor, which is oriented relative to the molecular structure from the INDO/S-CI calculations. Three transitions are associated with the equatorial tyrosinate and four with the axial tyrosinate. This large number of transitions per tyrosinate is due to the pi and importantly the sigma overlap of the two tyrosinate valence orbitals with the metal d orbitals and is governed by the Fe-O-C angle and the Fe-O-C-C dihedral angles. The previously reported crystal structure indicates that the Fe-O-C angles are 133 degrees and 148 degrees for the equatorial and axial tyrosinate, respectively. Each tyrosinate has transitions at different energies with different intensities, which correlate with differences in geometry that reflect pseudo-sigma bonding to the Fe(III) and relate to reactivity. These factors reflect the metal-ligand bond strength and indicate that the axial tyrosinate-Fe(III) bond is weaker than the equatorial tyrosinate-Fe(III) bond. Furthermore, it is found that the differences in geometry, and hence electronic structure, are imposed by the protein. The consequences to catalysis are significant because the axial tyrosinate has been shown to dissociate upon substrate binding and the equatorial tyrosinate in the enzyme-substrate complex is thought to influence asymmetric binding of the chelated substrate moiety via a strong trans influence which activates the substrate for reaction with O2.
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Affiliation(s)
- Mindy I Davis
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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Börger B, Suter D. Magnetic and optical anisotropy ofClostridium pasteurianumrubredoxin from optically detected electron paramagnetic resonance. J Chem Phys 2001. [DOI: 10.1063/1.1415461] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Spectroscopic methods covering many energy regions together provide complementary insight into metalloenzyme active sites. These methods probe geometric and electronic structure and define these contributions to reactivity. Two recent advances--determination of the polarizations of electronic transitions in solution using magnetic circular dichroism, electron paramagnetic resonance and quantum chemistry, and experimental estimation of covalency using metal L-edges and ligand K-edges--are particularly important.
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Affiliation(s)
- N Lehnert
- Department of Chemistry, Stanford University, CA 94305, USA
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