1
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York NJ, Lockart MM, Schmittou AN, Pierce BS. Cyanide replaces substrate in obligate-ordered addition of nitric oxide to the non-heme mononuclear iron AvMDO active site. J Biol Inorg Chem 2023; 28:285-299. [PMID: 36809458 PMCID: PMC10075186 DOI: 10.1007/s00775-023-01990-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2023] [Indexed: 02/23/2023]
Abstract
Thiol dioxygenases are a subset of non-heme mononuclear iron oxygenases that catalyze the O2-dependent oxidation of thiol-bearing substrates to yield sulfinic acid products. Cysteine dioxygenase (CDO) and 3-mercaptopropionic acid (3MPA) dioxygenase (MDO) are the most extensively characterized members of this enzyme family. As with many non-heme mononuclear iron oxidase/oxygenases, CDO and MDO exhibit an obligate-ordered addition of organic substrate before dioxygen. As this substrate-gated O2-reactivity extends to the oxygen-surrogate, nitric oxide (NO), EPR spectroscopy has long been used to interrogate the [substrate:NO:enzyme] ternary complex. In principle, these studies can be extrapolated to provide information about transient iron-oxo intermediates produced during catalytic turnover with dioxygen. In this work, we demonstrate that cyanide mimics the native thiol-substrate in ordered-addition experiments with MDO cloned from Azotobacter vinelandii (AvMDO). Following treatment of the catalytically active Fe(II)-AvMDO with excess cyanide, addition of NO yields a low-spin (S = 1/2) (CN/NO)-Fe-complex. Continuous wave and pulsed X-band EPR characterization of this complex produced in wild-type and H157N variant AvMDO reveal multiple nuclear hyperfine features diagnostic of interactions within the first- and outer-coordination sphere of the enzymatic Fe-site. Spectroscopically validated computational models indicate simultaneous coordination of two cyanide ligands replaces the bidentate (thiol and carboxylate) coordination of 3MPA allowing for NO-binding at the catalytically relevant O2-binding site. This promiscuous substrate-gated reactivity of AvMDO with NO provides an instructive counterpoint to the high substrate-specificity exhibited by mammalian CDO for L-cysteine.
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Affiliation(s)
- Nicholas J York
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Molly M Lockart
- Department of Chemistry and Biochemistry, Samford University, 800 Lakeshore Drive, Homewood, AL, 35229, USA
| | - Allison N Schmittou
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Brad S Pierce
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
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2
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Miller JR, Brunold TC. Spectroscopic analysis of the mammalian enzyme cysteine dioxygenase. Methods Enzymol 2023; 682:101-135. [PMID: 36948699 PMCID: PMC11230041 DOI: 10.1016/bs.mie.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
l-Cysteine (Cys) is an essential building block for the synthesis of new proteins and serves as a precursor for several biologically important sulfur-containing molecules, such as coenzyme A, taurine, glutathione, and inorganic sulfate. However, organisms must tightly regulate the concentration of free Cys, as elevated levels of this semi-essential amino acid can be extremely harmful. The non-heme iron enzyme cysteine dioxygenase (CDO) serves to maintain the proper levels of Cys by catalyzing its oxidation to cysteine sulfinic acid. Crystal structures of resting and substrate-bound mammalian CDO revealed two surprising structural motifs in the first and second coordination spheres of the Fe center. The first is the existence of a neutral three histidine (3-His) facial triad that coordinates the Fe ion, as opposed to an anionic 2-His-1-carboxylate facial triad that is typically observed in mononuclear non-heme Fe(II) dioxygenases. The second unusual structural feature exhibited by mammalian CDO is the presence of a covalent crosslink between the sulfur of a Cys residue and an ortho-carbon of a tyrosine residue. Spectroscopic studies of CDO have provided invaluable insights into the roles that these unusual features play with regards to substrate Cys and co-substrate O2 binding and activation. In this chapter, we summarize results obtained from electronic absorption, electron paramagnetic resonance, magnetic circular dichroism, resonance Raman, and Mössbauer spectroscopic studies of mammalian CDO carried out in the last two decades. Pertinent results obtained from complementary computational studies are also briefly summarized.
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Affiliation(s)
- Joshua R Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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3
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Freitag L, Lindenbauer L, Oppel M, González L. A Density Matrix Renormalization Group Study of the Low-Lying Excited States of a Molybdenum Carbonyl-Nitrosyl Complex. Chemphyschem 2021; 22:2371-2377. [PMID: 34495578 PMCID: PMC9292996 DOI: 10.1002/cphc.202100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/06/2021] [Indexed: 11/07/2022]
Abstract
A density matrix renormalization group-self consistent field (DMRG-SCF) study has been carried out to calculate the low-lying excited states of CpMo(CO)2 NO, a molybdenum complex containing NO and CO ligands. In order to automatically select an appropriate active space, a novel procedure employing the maximum single-orbital entropy for several states has been introduced and shown to be efficient and easy-to-implement when several electronic states are simultaneously considered. The analysis of the resulting natural transition orbitals and charge-transfer numbers shows that the lowest five excited electronic states are excitation into metal-NO antibonding orbitals, which offer the possibility for nitric oxide (NO) photorelease after excitation with visible light. Higher excited states are metal-centered excitations with contributions of metal-CO antibonding orbitals, which may serve as a gateway for carbon monoxide (CO) delivery. Time-dependent density functional theory calculations done for comparison, show that the state characters agree remarkably well with those from DMRG-SCF, while excitation energies are 0.4-1.0 eV red-shifted with respect to the DMRG-SCF ones.
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Affiliation(s)
- Leon Freitag
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
| | - Leopold Lindenbauer
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
| | - Markus Oppel
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria.,Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
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4
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Beckmann F, Kass D, Keck M, Yelin S, Hoof S, Cula B, Herwig C, Krause KB, Ar D, Limberg C. High‐spin square planar iron(II) alkali metal siloxide complexes – influence of the alkali metal and reactivity towards O
2
and NO. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fabian Beckmann
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Dustin Kass
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Matthias Keck
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Stefan Yelin
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Santina Hoof
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Beatrice Cula
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Christian Herwig
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Konstantin B. Krause
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Deniz Ar
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Christian Limberg
- Institut für Chemie Humboldt-Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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5
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Vlasenko VG, Guda AA, Starikov AG, Chegerev MG, Piskunov AV, Ershova IV, Trigub AL, Tereshchenko AA, Rusalev YV, Kubrin SP, Soldatov AV. Structural Changes in Five‐Coordinate Bromido‐bis(o‐iminobenzo‐semiquinonato)iron(III) Complex: Spin‐Crossover or Ligand‐Metal Antiferromagnetic Interactions? Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202001033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Valery G. Vlasenko
- Research Institute of Physics Southern Federal University 194 Stachki Ave. 344090 Rostov-on-Don Russia
| | - Alexander A. Guda
- The Smart Materials Research Institute Southern Federal University 178/24 A. Sladkova street 344090 Rostov-on-Don Russia
| | - Andrey G. Starikov
- Institute of Physical and Organic Chemistry Southern Federal University 194/2 Stachki Ave. 344090 Rostov-on-Don Russia
| | - Maxim G. Chegerev
- Institute of Physical and Organic Chemistry Southern Federal University 194/2 Stachki Ave. 344090 Rostov-on-Don Russia
| | - Alexander V. Piskunov
- G. A. Razuvaev Institute of Organometallic Chemistry Russian Academy of Sciences 49 Tropinina Str. 603950 Nizhny Novgorod Russia
| | - Irina V. Ershova
- G. A. Razuvaev Institute of Organometallic Chemistry Russian Academy of Sciences 49 Tropinina Str. 603950 Nizhny Novgorod Russia
| | - Alexander L. Trigub
- National Research Center “Kurchatov Institute” 1 pl. Academician Kurchatov 123182 Moscow Russia
| | - Andrei A. Tereshchenko
- The Smart Materials Research Institute Southern Federal University 178/24 A. Sladkova street 344090 Rostov-on-Don Russia
| | - Yurii V. Rusalev
- The Smart Materials Research Institute Southern Federal University 178/24 A. Sladkova street 344090 Rostov-on-Don Russia
| | - Stanislav P. Kubrin
- Research Institute of Physics Southern Federal University 194 Stachki Ave. 344090 Rostov-on-Don Russia
| | - Alexander V. Soldatov
- The Smart Materials Research Institute Southern Federal University 178/24 A. Sladkova street 344090 Rostov-on-Don Russia
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6
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Yadav V, Siegler MA, Goldberg DP. Temperature-Dependent Reactivity of a Non-heme Fe III(OH)(SR) Complex: Relevance to Isopenicillin N Synthase. J Am Chem Soc 2021; 143:46-52. [PMID: 33356198 DOI: 10.1021/jacs.0c09688] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-heme iron complexes with cis-FeIII(OH)(SAr/OAr) coordination were isolated and examined for their reactivity with a tertiary carbon radical. The sulfur-ligated complex shows a temperature dependence on •OH versus ArS• transfer, whereas the oxygen-ligated complex does not. These results provide the first working model for C-S bond formation in isopenicillin N synthase and indicate that kinetic control may be a key factor in the selectivity of non-heme iron "rebound" processes.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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7
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Datta D, Saitow M, Sandhöfer B, Neese F. 57Fe Mössbauer parameters from domain based local pair-natural orbital coupled-cluster theory. J Chem Phys 2020; 153:204101. [PMID: 33261496 DOI: 10.1063/5.0022215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on applications of the domain based local pair-natural orbital (PNO) coupled-cluster method within the singles and doubles approximation (DLPNO-CCSD) to the calculation of 57Fe isomer shifts and quadrupole splittings in a small training set of iron complexes consisting of large molecular ligands and iron atoms in varying charge, spin, and oxidation states. The electron densities and electric field gradients needed for these calculations were obtained within the recently implemented analytic derivative scheme. A method for the direct treatment of scalar relativistic effects in the calculation of effective electron densities is described by using the first-order Douglas-Kroll-Hess Hamiltonian and a Gaussian charge distribution model for the nucleus. The performance of DLPNO-CCSD is compared with four modern-day density functionals, namely, RPBE, TPSS, B3LYP, and B2PLYP, as well as with the second-order Møller-Plesset perturbation theory. An excellent correlation between the calculated electron densities and the experimental isomer shifts is attained with the DLPNO-CCSD method. The correlation constant a obtained from the slope of the linear correlation plot is found to be ≈-0.31 a.u.3 mm s-1, which agrees very well with the experimental calibration constant α = -0.31 ± 0.04 a.u.3 mm s-1. This value of a is obtained consistently using both nonrelativistic and scalar relativistic DLPNO-CCSD electron densities. While the B3LYP and B2PLYP functionals achieve equally good correlation between theory and experiment, the correlation constant a is found to deviate from the experimental value. Similar trends are observed also for quadrupole splittings. The value of the nuclear quadrupole moment for 57Fe is estimated to be 0.15 b at the DLPNO-CCSD level. This is consistent with previous results and is here supported by a higher level of theory. The DLPNO-CCSD results are found to be insensitive to the intrinsic approximations in the method, in particular the PNO occupation number truncation error, while the results obtained with density functional theory (DFT) are found to depend on the choice of the functional. In a statistical sense, i.e., on the basis of the linear regression analysis, however, the accuracies of the DFT and DLPNO-CCSD results can be considered comparable.
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Affiliation(s)
- Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, 201 Spedding Hall, 2416 Pammel Drive, Ames, Iowa 50011-2416, USA
| | - Masaaki Saitow
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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8
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Credendino L, Sproules S. Modulating Iron Spin States with Radical Ligands: A Density Functional Theoretical Study. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.201900626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Stephen Sproules
- WestCHEM School of ChemistryUniversity of Glasgow Glasgow G12 8QQ UK
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9
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Beagan DM, Carta V, Caulton KG. A reagent for heteroatom borylation, including iron mediated reductive deoxygenation of nitrate yielding a dinitrosyl complex. Dalton Trans 2020; 49:1681-1687. [PMID: 31956885 DOI: 10.1039/d0dt00077a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4,4'-Bipyridyl is shown to be a catalyst for transfer of pinacolboryl groups from (Bpin)2 to nitrogen heterocycles and to Me3SiN3. Using stoichiometric (Bpin)2(pyrazine) or (Bpin)2(bipyridine) in an analogous manner, an aromatic nitro group is deoxygenated and subsequently borylated, and four-fold deoxygenation of (DIM)Fe(NO3)2(MeCN) to yield the dinitrosyl complex (DIM)Fe(NO)2 is facile. The co-product O(Bpin)2 is the quantitative fate of the removed oxo groups. With borylation of both nitrogen heterocycles and doubly deoxygenating two nitrates coordinated to a single metal center, broad spectrum methodology is demonstrated.
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Affiliation(s)
- Daniel M Beagan
- Indiana University, Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN 47401, USA.
| | - Veronica Carta
- Indiana University, Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN 47401, USA.
| | - Kenneth G Caulton
- Indiana University, Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN 47401, USA.
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10
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Sardar S, Weitz A, Hendrich MP, Pierce BS. Outer-Sphere Tyrosine 159 within the 3-Mercaptopropionic Acid Dioxygenase S-H-Y Motif Gates Substrate-Coordination Denticity at the Non-Heme Iron Active Site. Biochemistry 2019; 58:5135-5150. [PMID: 31750652 PMCID: PMC10071547 DOI: 10.1021/acs.biochem.9b00674] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiol dioxygenases are non-heme mononuclear iron enzymes that catalyze the O2-dependent oxidation of free thiols (-SH) to produce the corresponding sulfinic acid (-SO2-). Regardless of the phylogenic domain, the active site for this enzyme class is typically comprised of two major features: (1) a mononuclear ferrous iron coordinated by three protein-derived histidines and (2) a conserved sequence of outer Fe-coordination-sphere amino acids (Ser-His-Tyr) spatially adjacent to the iron site (∼3 Å). Here, we utilize a promiscuous 3-mercaptopropionic acid dioxygenase cloned from Azotobacter vinelandii (Av MDO) to explore the function of the conserved S-H-Y motif. This enzyme exhibits activity with 3-mercaptopropionic acid (3mpa), l-cysteine (cys), as well as several other thiol-bearing substrates, thus making it an ideal system to study the influence of residues within the highly conserved S-H-Y motif (H157 and Y159) on substrate specificity and reactivity. The pKa values for these residues were determined by pH-dependent steady-state kinetics, and their assignments verified by comparison to H157N and Y159F variants. Complementary electron paramagnetic resonance and Mössbauer studies demonstrate a network of hydrogen bonds connecting H157-Y159 and Fe-bound ligands within the enzymatic Fe site. Crucially, these experiments suggest that the hydroxyl group of Y159 hydrogen bonds to Fe-bound NO and, by extension, Fe-bound oxygen during native catalysis. This interaction alters both the NO binding affinity and rhombicity of the 3mpa-bound iron-nitrosyl site. In addition, Fe coordination of cys is switched from thiolate only to bidentate (thiolate/amine) for the Y159F variant, indicating that perturbations within the S-H-Y proton relay network also influence cys Fe binding denticity.
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Affiliation(s)
- Sinjinee Sardar
- Department of Chemistry and Biochemistry , The University of Texas at Arlington , 700 Planetarium Place , Arlington , Texas 76019 , United States
| | - Andrew Weitz
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Michael P Hendrich
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Brad S Pierce
- Department of Chemistry and Biochemistry , University of Alabama , 250 Hackberry Lane , Tuscaloosa , Alabama 35487 , United States
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11
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Rittle J, Field MJ, Green MT, Tezcan FA. An efficient, step-economical strategy for the design of functional metalloproteins. Nat Chem 2019; 11:434-441. [PMID: 30778140 PMCID: PMC6483823 DOI: 10.1038/s41557-019-0218-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/11/2019] [Indexed: 01/31/2023]
Abstract
The bottom-up design and construction of functional metalloproteins remains a formidable task in biomolecular design. Although numerous strategies have been used to create new metalloproteins, pre-existing knowledge of the tertiary and quaternary protein structure is often required to generate suitable platforms for robust metal coordination and activity. Here we report an alternative and easily implemented approach (metal active sites by covalent tethering or MASCoT) in which folded protein building blocks are linked by a single disulfide bond to create diverse metal coordination environments within evolutionarily naive protein-protein interfaces. Metalloproteins generated using this strategy uniformly bind a wide array of first-row transition metal ions (MnII, FeII, CoII, NiII, CuII, ZnII and vanadyl) with physiologically relevant thermodynamic affinities (dissociation constants ranging from 700 nM for MnII to 50 fM for CuII). MASCoT readily affords coordinatively unsaturated metal centres-including a penta-His-coordinated non-haem Fe site-and well-defined binding pockets that can accommodate modifications and enable coordination of exogenous ligands such as nitric oxide to the interfacial metal centre.
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Affiliation(s)
- Jonathan Rittle
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mackenzie J Field
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Michael T Green
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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12
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Speelman AL, White CJ, Zhang B, Alp EE, Zhao J, Hu M, Krebs C, Penner-Hahn J, Lehnert N. Non-heme High-Spin {FeNO} 6-8 Complexes: One Ligand Platform Can Do It All. J Am Chem Soc 2018; 140:11341-11359. [PMID: 30107126 DOI: 10.1021/jacs.8b06095] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heme and non-heme iron-nitrosyl complexes are important intermediates in biology. While there are numerous examples of low-spin heme iron-nitrosyl complexes in different oxidation states, much less is known about high-spin (hs) non-heme iron-nitrosyls in oxidation states other than the formally ferrous NO adducts ({FeNO}7 in the Enemark-Feltham notation). In this study, we present a complete series of hs-{FeNO}6-8 complexes using the TMG3tren coligand. Redox transformations from the hs-{FeNO}7 complex [Fe(TMG3tren)(NO)]2+ to its {FeNO}6 and {FeNO}8 analogs do not alter the coordination environment of the iron center, allowing for detailed comparisons between these species. Here, we present new MCD, NRVS, XANES/EXAFS, and Mössbauer data, demonstrating that these redox transformations are metal based, which allows us to access hs-Fe(II)-NO-, Fe(III)-NO-, and Fe(IV)-NO- complexes. Vibrational data, analyzed by NCA, directly quantify changes in Fe-NO bonding along this series. Optical data allow for the identification of a "spectator" charge-transfer transition that, together with Mössbauer and XAS data, directly monitors the electronic changes of the Fe center. Using EXAFS, we are also able to provide structural data for all complexes. The magnetic properties of the complexes are further analyzed (from magnetic Mössbauer). The properties of our hs-{FeNO}6-8 complexes are then contrasted to corresponding, low-spin iron-nitrosyl complexes where redox transformations are generally NO centered. The hs-{FeNO}8 complex can further be protonated by weak acids, and the product of this reaction is characterized. Taken together, these results provide unprecedented insight into the properties of biologically relevant non-heme iron-nitrosyl complexes in three relevant oxidation states.
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Affiliation(s)
- Amy L Speelman
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Corey J White
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Bo Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Michael Hu
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - James Penner-Hahn
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
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13
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Van Stappen C, Lehnert N. Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases. Inorg Chem 2018; 57:4252-4269. [DOI: 10.1021/acs.inorgchem.7b02333] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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14
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McWilliams SF, Brennan-Wydra E, MacLeod KC, Holland PL. Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes. ACS OMEGA 2017; 2:2594-2606. [PMID: 28691111 PMCID: PMC5494642 DOI: 10.1021/acsomega.7b00595] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 05/24/2017] [Indexed: 05/09/2023]
Abstract
The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together.
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Affiliation(s)
- Sean F McWilliams
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Emma Brennan-Wydra
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - K Cory MacLeod
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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15
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Proppe J, Reiher M. Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models. J Chem Theory Comput 2017; 13:3297-3317. [PMID: 28581746 DOI: 10.1021/acs.jctc.7b00235] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the major challenges in computational science is to determine the uncertainty of a virtual measurement, that is the prediction of an observable based on calculations. As highly accurate first-principles calculations are in general unfeasible for most physical systems, one usually resorts to parameteric property models of observables, which require calibration by incorporating reference data. The resulting predictions and their uncertainties are sensitive to systematic errors such as inconsistent reference data, parametric model assumptions, or inadequate computational methods. Here, we discuss the calibration of property models in the light of bootstrapping, a sampling method that can be employed for identifying systematic errors and for reliable estimation of the prediction uncertainty. We apply bootstrapping to assess a linear property model linking the 57Fe Mössbauer isomer shift to the contact electron density at the iron nucleus for a diverse set of 44 molecular iron compounds. The contact electron density is calculated with 12 density functionals across Jacob's ladder (PWLDA, BP86, BLYP, PW91, PBE, M06-L, TPSS, B3LYP, B3PW91, PBE0, M06, TPSSh). We provide systematic-error diagnostics and reliable, locally resolved uncertainties for isomer-shift predictions. Pure and hybrid density functionals yield average prediction uncertainties of 0.06-0.08 mm s-1 and 0.04-0.05 mm s-1, respectively, the latter being close to the average experimental uncertainty of 0.02 mm s-1. Furthermore, we show that both model parameters and prediction uncertainty depend significantly on the composition and number of reference data points. Accordingly, we suggest that rankings of density functionals based on performance measures (e.g., the squared coefficient of correlation, r2, or the root-mean-square error, RMSE) should not be inferred from a single data set. This study presents the first statistically rigorous calibration analysis for theoretical Mössbauer spectroscopy, which is of general applicability for physicochemical property models and not restricted to isomer-shift predictions. We provide the statistically meaningful reference data set MIS39 and a new calibration of the isomer shift based on the PBE0 functional.
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Affiliation(s)
- Jonny Proppe
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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16
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Wolf M, Klüfers P. Structure and Bonding of High‐Spin Nitrosyl–Iron(II) Compounds with Mixed N,O‐Chelators and Aqua Ligands. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601329] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Wolf
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
| | - Peter Klüfers
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
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17
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Aas BM, Klüfers P. The Structural Chemistry of Stable High‐Spin Nitrosyl–Iron(II) Compounds with Aminecarboxylato Co‐Ligands in Aqueous Solution. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Bianca M. Aas
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
| | - Peter Klüfers
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
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18
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Piñeiro-López L, Ortega-Villar N, Muñoz MC, Molnár G, Cirera J, Moreno-Esparza R, Ugalde-Saldívar VM, Bousseksou A, Ruiz E, Real JA. Electronic Structure Modulation in an Exceptionally Stable Non-Heme Nitrosyl Iron(II) Spin-Crossover Complex. Chemistry 2016; 22:12741-51. [DOI: 10.1002/chem.201601172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Lucía Piñeiro-López
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; 46980 Paterna Valencia Spain
| | - Norma Ortega-Villar
- Facultad de Química (UNAM); Edificio B.; Av. Universidad 3000, Coyoacán México D.F. 04510 México
| | - M. Carmen Muñoz
- Departamento de Física Aplicada; Universitat Politècnica de València; 46022 Valencia Spain
| | - Gábor Molnár
- LCC; CNRS & Université de Toulouse (UPS, INP); 205 route de Narbonne 31077 Toulouse France
| | - Jordi Cirera
- Departament de Química Inorgànica i Orgànica; Secció de Química Inorgànica; Institut de Recerca de Química Teòrica i Computacional; Universitat de Barcelona; Diagonal 645 Barcelona 08028 Spain
| | - Rafael Moreno-Esparza
- Facultad de Química (UNAM); Edificio B.; Av. Universidad 3000, Coyoacán México D.F. 04510 México
| | | | - Azzedine Bousseksou
- LCC; CNRS & Université de Toulouse (UPS, INP); 205 route de Narbonne 31077 Toulouse France
| | - Eliseo Ruiz
- Departament de Química Inorgànica i Orgànica; Secció de Química Inorgànica; Institut de Recerca de Química Teòrica i Computacional; Universitat de Barcelona; Diagonal 645 Barcelona 08028 Spain
| | - José A. Real
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; 46980 Paterna Valencia Spain
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19
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Speelman AL, Zhang B, Silakov A, Skodje KM, Alp EE, Zhao J, Hu MY, Kim E, Krebs C, Lehnert N. Unusual Synthetic Pathway for an {Fe(NO)2}9 Dinitrosyl Iron Complex (DNIC) and Insight into DNIC Electronic Structure via Nuclear Resonance Vibrational Spectroscopy. Inorg Chem 2016; 55:5485-501. [DOI: 10.1021/acs.inorgchem.6b00510] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amy L. Speelman
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Zhang
- Department of Chemistry and Department of Biochemistry and Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry and Department of Biochemistry and Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kelsey M. Skodje
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- 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
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Speelman AL, Zhang B, Krebs C, Lehnert N. Structural and Spectroscopic Characterization of a High-Spin {FeNO}(6) Complex with an Iron(IV)-NO(-) Electronic Structure. Angew Chem Int Ed Engl 2016; 55:6685-8. [PMID: 27101151 DOI: 10.1002/anie.201601742] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 11/10/2022]
Abstract
Although the interaction of low-spin ferric complexes with nitric oxide has been well studied, examples of stable high-spin ferric nitrosyls (such as those that could be expected to form at typical non-heme iron sites in biology) are extremely rare. Using the TMG3 tren co-ligand, we have prepared a high-spin ferric NO adduct ({FeNO}(6) complex) via electrochemical or chemical oxidation of the corresponding high-spin ferrous NO {FeNO}(7) complex. The {FeNO}(6) compound is characterized by UV/Visible and IR spectroelectrochemistry, Mössbauer and NMR spectroscopy, X-ray crystallography, and DFT calculations. The data show that its electronic structure is best described as a high-spin iron(IV) center bound to a triplet NO(-) ligand with a very covalent iron-NO bond. This finding demonstrates that this high-spin iron nitrosyl compound undergoes iron-centered redox chemistry, leading to fundamentally different properties than corresponding low-spin compounds, which undergo NO-centered redox transformations.
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Affiliation(s)
- Amy L Speelman
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI, 48109, USA
| | - Bo Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Carsten Krebs
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI, 48109, USA.
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21
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Speelman AL, Zhang B, Krebs C, Lehnert N. Structural and Spectroscopic Characterization of a High‐Spin {FeNO}
6
Complex with an Iron(IV)−NO
−
Electronic Structure. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Amy L. Speelman
- Department of Chemistry University of Michigan 930 N University Avenue Ann Arbor MI 48109 USA
| | - Bo Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA 16802 USA
| | - Carsten Krebs
- Department of Chemistry, Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA 16802 USA
| | - Nicolai Lehnert
- Department of Chemistry University of Michigan 930 N University Avenue Ann Arbor MI 48109 USA
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22
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McQuilken AC, Matsumura H, Dürr M, Confer AM, Sheckelton JP, Siegler MA, McQueen TM, Ivanović-Burmazović I, Moënne-Loccoz P, Goldberg DP. Photoinitiated Reactivity of a Thiolate-Ligated, Spin-Crossover Nonheme {FeNO}(7) Complex with Dioxygen. J Am Chem Soc 2016; 138:3107-17. [PMID: 26919583 DOI: 10.1021/jacs.5b12741] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nonheme iron complex, [Fe(NO)(N3PyS)]BF4, is a rare example of an {FeNO}(7) species that exhibits spin-crossover behavior. The comparison of X-ray crystallographic studies at low and high temperatures and variable-temperature magnetic susceptibility measurements show that a low-spin S = 1/2 ground state is populated at 0-150 K, while both low-spin S = 1/2 and high-spin S = 3/2 states are populated at T > 150 K. These results explain the observation of two N-O vibrational modes at 1737 and 1649 cm(-1) in CD3CN for [Fe(NO)(N3PyS)]BF4 at room temperature. This {FeNO}(7) complex reacts with dioxygen upon photoirradiation with visible light in acetonitrile to generate a thiolate-ligated, nonheme iron(III)-nitro complex, [Fe(III)(NO2)(N3PyS)](+), which was characterized by EPR, FTIR, UV-vis, and CSI-MS. Isotope labeling studies, coupled with FTIR and CSI-MS, show that one O atom from O2 is incorporated in the Fe(III)-NO2 product. The O2 reactivity of [Fe(NO)(N3PyS)]BF4 in methanol is dramatically different from CH3CN, leading exclusively to sulfur-based oxidation, as opposed to NO· oxidation. A mechanism is proposed for the NO· oxidation reaction that involves formation of both Fe(III)-superoxo and Fe(III)-peroxynitrite intermediates and takes into account the experimental observations. The stability of the Fe(III)-nitrite complex is limited, and decay of [Fe(III)(NO2)(N3PyS)](+) leads to {FeNO}(7) species and sulfur oxygenated products. This work demonstrates that a single mononuclear, thiolate-ligated nonheme {FeNO}(7) complex can exhibit reactivity related to both nitric oxide dioxygenase (NOD) and nitrite reductase (NiR) activity. The presence of the thiolate donor is critical to both pathways, and mechanistic insights into these biologically relevant processes are presented.
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Affiliation(s)
- Alison C McQuilken
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Hirotoshi Matsumura
- Oregon Health & Science University, Institute of Environmental Health, Portland, Oregon 97239, United States
| | - Maximilian Dürr
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg , 91058, Erlangen, Germany
| | - Alex M Confer
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - John P Sheckelton
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States.,Institute for Quantum Matter and Department of Physics and Astronomy, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Tyrel M McQueen
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States.,Institute for Quantum Matter and Department of Physics and Astronomy, The Johns Hopkins University , Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | - Pierre Moënne-Loccoz
- Oregon Health & Science University, Institute of Environmental Health, Portland, Oregon 97239, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
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23
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Chang KC, Huang CJ, Chang YH, Wu ZH, Kuo TS, Hsu HF. Reactivity of a Fe(III)-Bound Methoxide Supported with a Tris(thiolato)phosphine Ligand: Activation of C-Cl Bond in CH2Cl2 by Nucleophilic Attack of a Fe(III)-OCH3 Moiety. Inorg Chem 2015; 55:566-72. [PMID: 26699874 DOI: 10.1021/acs.inorgchem.5b02135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two mononuclear nonheme Fe(III) complexes, [PPh4][Fe(III)(PS3″)(OCH3)] (1) and [PPh4][Fe(III)(PS3″)(Cl)] (2), supported by a tris(benzenethiolato)phosphine derivative PS3″ (PS3″ = P(C6H3-3-Me3Si-2-S)3(3-)) have been synthesized and characterized. The structures resolved from X-ray crystallography show that Fe(III) centers in both complexes adopt distorted trigonal-bipyramidal geometry with a methoxide or a chloride binding in the axial position. The magnetic data for both are consistent with intermediate-spin Fe(III) centers with a C3 symmetry (S = 3/2 ground state). The bound methoxide in 1 is labile and can be replaced by a CH3CN molecule. The forming Fe(III)-CH3CN species can be further reduced by cobaltcene quantitatively to a stable Fe(II)-CH3CN complex, [Fe(PS3″)(CH3CN)](-). One-electron oxidation of 2 by ferrocenium gave a Fe(IV) analogue, [Fe(IV)(PS3″)(Cl)]. Importantly, the Fe(III)-OCH3 moiety in complex 1 acts as a strong nucleophile that activates the C-Cl bond in CH2Cl2, leading to the formation of complex 2 quantitatively. Complex 1 also reacts with other electrophiles, benzyl chloride and benzyl bromide, to generate Fe(III)-X species (X = Cl or Br). The reactions were investigated and monitored by UV-vis-NIR, NMR, and ESI-MS spectroscopies.
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Affiliation(s)
- Kai-Chun Chang
- Department of Chemistry, National Cheng Kung University , Tainan 701, Taiwan
| | - Ching-Ju Huang
- Department of Chemistry, National Cheng Kung University , Tainan 701, Taiwan
| | - Ya-Ho Chang
- Department of Chemistry, National Cheng Kung University , Tainan 701, Taiwan
| | - Zong-Han Wu
- Department of Chemistry, National Cheng Kung University , Tainan 701, Taiwan
| | - Ting-Shen Kuo
- Department of Chemistry, National Taiwan Normal University , Taipei 116, Taiwan
| | - Hua-Fen Hsu
- Department of Chemistry, National Cheng Kung University , Tainan 701, Taiwan
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24
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Pierce BS, Subedi BP, Sardar S, Crowell JK. The "Gln-Type" Thiol Dioxygenase from Azotobacter vinelandii is a 3-Mercaptopropionic Acid Dioxygenase. Biochemistry 2015; 54:7477-90. [PMID: 26624219 DOI: 10.1021/acs.biochem.5b00636] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cysteine dioxygenase (CDO) is a non-heme iron enzyme that catalyzes the O2-dependent oxidation of l-cysteine to produce cysteinesulfinic acid. Bacterial CDOs have been subdivided as either "Arg-type" or "Gln-type" on the basis of the identity of conserved active site residues. To date, "Gln-type" enzymes remain largely uncharacterized. It was recently noted that the "Gln-type" enzymes are more homologous with another thiol dioxygenase [3-mercaptopropionate dioxygenase (MDO)] identified in Variovorax paradoxus, suggesting that enzymes of the "Gln-type" subclass are in fact MDOs. In this work, a putative "Gln-type" thiol dioxygenase from Azotobacter vinelandii (Av) was purified to homogeneity and characterized. Steady-state assays were performed using three substrates [3-mercaptopropionic acid (3mpa), l-cysteine (cys), and cysteamine (ca)]. Despite comparable maximal velocities, the "Gln-type" Av enzyme exhibited a specificity for 3mpa (kcat/KM = 72000 M(-1) s(-1)) nearly 2 orders of magnitude greater than those for cys (110 M(-1) s(-1)) and ca (11 M(-1) s(-1)). Supporting X-band electron paramagnetic resonance (EPR) studies were performed using nitric oxide (NO) as a surrogate for O2 binding to confirm obligate-ordered addition of substrate prior to NO. Stoichimetric addition of NO to solutions of 3mpa-bound enzyme quantitatively yields an iron-nitrosyl species (Av ES-NO) with EPR features consistent with a mononuclear (S = (3)/2) {FeNO}(7) site. Conversely, two distinct substrate-bound conformations were observed in Av ES-NO samples prepared with cys and ca, suggesting heterogeneous binding within the enzymatic active site. Analytical EPR simulations are provided to establish the relative binding affinity for each substrate (3map > cys > ca). Both kinetic and spectroscopic results presented here are consistent with 3mpa being the preferred substrate for this enzyme.
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Affiliation(s)
- Brad S Pierce
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Bishnu P Subedi
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Sinjinee Sardar
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Joshua K Crowell
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
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25
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Freitag L, Knecht S, Keller SF, Delcey MG, Aquilante F, Pedersen TB, Lindh R, Reiher M, González L. Orbital entanglement and CASSCF analysis of the Ru-NO bond in a Ruthenium nitrosyl complex. Phys Chem Chem Phys 2015; 17:14383-92. [PMID: 25767830 PMCID: PMC4447059 DOI: 10.1039/c4cp05278a] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiconfigurational wavefunction analysis and entanglement measures based on von Neumann entropy shed light on the electronic structure of a Ru nitrosyl complex, in particular on the Ru–NO bond.
Complete active space self-consistent field (CASSCF) wavefunctions and an orbital entanglement analysis obtained from a density-matrix renormalisation group (DMRG) calculation are used to understand the electronic structure, and, in particular, the Ru–NO bond of a Ru nitrosyl complex. Based on the configurations and orbital occupation numbers obtained for the CASSCF wavefunction and on the orbital entropy measurements evaluated for the DMRG wavefunction, we unravel electron correlation effects in the Ru coordination sphere of the complex. It is shown that Ru–NO π bonds show static and dynamic correlation, while other Ru–ligand bonds feature predominantly dynamic correlation. The presence of static correlation requires the use of multiconfigurational methods to describe the Ru–NO bond. Subsequently, the CASSCF wavefunction is analysed in terms of configuration state functions based on localised orbitals. The analysis of the wavefunctions in the electronic singlet ground state and the first triplet state provides a picture of the Ru–NO moiety beyond the standard representation based on formal oxidation states. A distinct description of the Ru and NO fragments is advocated. The electron configuration of Ru is an equally weighted superposition of RuII and RuIII configurations, with the RuIII configuration originating from charge donation mostly from Cl ligands. However, and contrary to what is typically assumed, the electronic configuration of the NO ligand is best described as electroneutral.
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Affiliation(s)
- Leon Freitag
- Institut für theoretische Chemie, Universität Wien, Währinger Str. 17, 1090 Vienna, Austria.
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26
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Foi A, Di Salvo F, Doctorovich F, Roy TG, Stirnat K, Biewer C, Klein A. Tracing the Iron Nitrosyl Complex [Fe(2,2′‐bipyridine)(CN)
3
(NO)]
–. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201403145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ana Foi
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE‐CONICET, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Florencia Di Salvo
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE‐CONICET, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE‐CONICET, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | | | - Kathrin Stirnat
- Universität zu Köln, Institut für Anorganische Chemie, Greinstraße 6, 50939 Köln, http://www.klein.uni‐koeln.de/
| | - Christian Biewer
- Universität zu Köln, Institut für Anorganische Chemie, Greinstraße 6, 50939 Köln, http://www.klein.uni‐koeln.de/
| | - Axel Klein
- Universität zu Köln, Institut für Anorganische Chemie, Greinstraße 6, 50939 Köln, http://www.klein.uni‐koeln.de/
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27
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Tsou CC, Chiu WC, Ke CH, Tsai JC, Wang YM, Chiang MH, Liaw WF. Iron(III) Bound by Hydrosulfide Anion Ligands: NO-Promoted Stabilization of the [FeIII–SH] Motif. J Am Chem Soc 2014; 136:9424-33. [DOI: 10.1021/ja503683y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chih-Chin Tsou
- Department
of Chemistry and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wei-Chun Chiu
- Department
of Chemistry and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Hung Ke
- Department
of Chemistry and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jia-Chun Tsai
- Department
of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yun-Ming Wang
- Department
of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Ming-Hsi Chiang
- Institute
of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Wen-Feng Liaw
- Department
of Chemistry and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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28
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Li J, Banerjee A, Pawlak PL, Brennessel WW, Chavez FA. Highest Recorded N–O Stretching Frequency for 6-Coordinate {Fe-NO}7 Complexes: An Iron Nitrosyl Model for His3 Active Sites. Inorg Chem 2014; 53:5414-6. [DOI: 10.1021/ic500558j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jia Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Piotr L. Pawlak
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Ferman A. Chavez
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
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29
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and Computational Study of a Nonheme Iron Nitrosyl Center in a Biosynthetic Model of Nitric Oxide Reductase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308431] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase. Angew Chem Int Ed Engl 2014; 53:2417-21. [PMID: 24481708 DOI: 10.1002/anie.201308431] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/27/2013] [Indexed: 11/07/2022]
Abstract
A major barrier to understanding the mechanism of nitric oxide reductases (NORs) is the lack of a selective probe of NO binding to the nonheme FeB center. By replacing the heme in a biosynthetic model of NORs, which structurally and functionally mimics NORs, with isostructural ZnPP, the electronic structure and functional properties of the FeB nitrosyl complex was probed. This approach allowed observation of the first S=3/2 nonheme {FeNO}(7) complex in a protein-based model system of NOR. Detailed spectroscopic and computational studies show that the electronic state of the {FeNO}(7) complex is best described as a high spin ferrous iron (S=2) antiferromagnetically coupled to an NO radical (S=1/2) [Fe(2+)-NO(.)]. The radical nature of the FeB -bound NO would facilitate N-N bond formation by radical coupling with the heme-bound NO. This finding, therefore, supports the proposed trans mechanism of NO reduction by NORs.
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Affiliation(s)
- Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL (USA)
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31
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Hedegård ED, Knecht S, Ryde U, Kongsted J, Saue T. Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates. Phys Chem Chem Phys 2014; 16:4853-63. [DOI: 10.1039/c3cp54393e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational protocol for 57Fe isomer shifts, based on the relativistic eXact 2-Component Hamiltonian (X2C), is applied to discriminate between proposed intermediates of [Fe]-hydrogenase. Detailed analysis reveals that the difference in isomer shifts between two intermediates is due to an overlap effect.
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Affiliation(s)
- Erik Donovan Hedegård
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- Odense 5420 M, Denmark
| | - Stefan Knecht
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- Odense 5420 M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- S-221 00 Lund, Sweden
| | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- Odense 5420 M, Denmark
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques (UMR 5626)
- CNRS/Université Toulouse III – Paul Sabatier
- F-31062 Toulouse cedex, France
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32
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Historical Introduction to Nitrosyl Complexes. NITROSYL COMPLEXES IN INORGANIC CHEMISTRY, BIOCHEMISTRY AND MEDICINE I 2014. [DOI: 10.1007/430_2013_116] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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33
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Tsou CC, Yang WL, Liaw WF. Nitrite activation to nitric oxide via one-fold protonation of iron(II)-O,O-nitrito complex: relevance to the nitrite reductase activity of deoxyhemoglobin and deoxyhemerythrin. J Am Chem Soc 2013; 135:18758-61. [PMID: 24289743 DOI: 10.1021/ja4105864] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reversible transformations [(Bim)3Fe(κ(2)-O2N)][BF4] (3) <-> [(Bim)3Fe(NO)(κ(1)-ONO)][BF4]2 (4) were demonstrated and characterized. Transformation of O,O-nitrito-containing complex 3 into [(Bim)3Fe(μ-O)(μ-OAc)Fe(Bim)3](3+) (5) along with the release of NO and H2O triggered by 1 equiv of AcOH implicates that nitrite-to-nitric oxide conversion occurs, in contrast to two protons needed to trigger nitrite reduction producing NO observed in the protonation of [Fe(II)-nitro] complexes.
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Affiliation(s)
- Chih-Chin Tsou
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, 30013, Taiwan
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34
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Gubler J, Finkelmann AR, Reiher M. Theoretical 57Fe Mössbauer Spectroscopy for Structure Elucidation of [Fe] Hydrogenase Active Site Intermediates. Inorg Chem 2013; 52:14205-15. [DOI: 10.1021/ic4021349] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Joël Gubler
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Arndt R. Finkelmann
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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35
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McQuilken AC, Ha Y, Sutherlin KD, Siegler MA, Hodgson KO, Hedman B, Solomon EI, Jameson GNL, Goldberg DP. Preparation of non-heme {FeNO}7 models of cysteine dioxygenase: sulfur versus nitrogen ligation and photorelease of nitric oxide. J Am Chem Soc 2013; 135:14024-7. [PMID: 24040838 DOI: 10.1021/ja4064487] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present the synthesis and spectroscopic characterization of [Fe(NO)(N3PyS)]BF4 (3), the first structural and electronic model of NO-bound cysteine dioxygenase. The nearly isostructural all-N-donor analogue [Fe(NO)(N4Py)](BF4)2 (4) was also prepared, and comparisons of 3 and 4 provide insight regarding the influence of S vs N ligation in {FeNO}(7) species. One key difference occurs upon photoirradiation, which causes the fully reversible release of NO from 3, but not from 4.
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Affiliation(s)
- Alison C McQuilken
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
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36
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Blaesi EJ, Gardner JD, Fox BG, Brunold TC. Spectroscopic and computational characterization of the NO adduct of substrate-bound Fe(II) cysteine dioxygenase: insights into the mechanism of O2 activation. Biochemistry 2013; 52:6040-51. [PMID: 23906193 DOI: 10.1021/bi400825c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine dioxygenase (CDO) is a mononuclear nonheme iron(II)-dependent enzyme critical for maintaining appropriate cysteine (Cys) and taurine levels in eukaryotic systems. Because CDO possesses both an unusual 3-His facial ligation sphere to the iron center and a rare Cys-Tyr cross-link near the active site, the mechanism by which it converts Cys and molecular oxygen to cysteine sulfinic acid is of broad interest. However, as of yet, direct experimental support for any of the proposed mechanisms is still lacking. In this study, we have used NO as a substrate analogue for O2 to prepare a species that mimics the geometric and electronic structures of an early reaction intermediate. The resultant unusual S = (1)/2 {FeNO}(7) species was characterized by magnetic circular dichroism, electron paramagnetic resonance, and electronic absorption spectroscopies as well as computational methods including density functional theory and semiempirical calculations. The NO adducts of Cys- and selenocysteine (Sec)-bound Fe(II)CDO exhibit virtually identical electronic properties; yet, CDO is unable to oxidize Sec. To explore the differences in reactivity between Cys- and Sec-bound CDO, the geometries and energies of viable O2-bound intermediates were evaluated computationally, and it was found that a low-energy quintet-spin intermediate on the Cys reaction pathway adopts a different geometry for the Sec-bound adduct. The absence of a low-energy O2 adduct for Sec-bound CDO is consistent with our experimental data and may explain why Sec is not oxidized by CDO.
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Affiliation(s)
- Elizabeth J Blaesi
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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37
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Bučinský L, Büchel GE, Ponec R, Rapta P, Breza M, Kožíšek J, Gall M, Biskupič S, Fronc M, Schiessl K, Cuzan O, Prodius D, Turta C, Shova S, Zając DA, Arion VB. On the Electronic Structure ofmer,trans-[RuCl3(1H-indazole)2(NO)], a Hypothetical Metabolite of the Antitumor Drug Candidate KP1019: An Experimental and DFT Study. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201201526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Berto TC, Speelman AL, Zheng S, Lehnert N. Mono- and dinuclear non-heme iron–nitrosyl complexes: Models for key intermediates in bacterial nitric oxide reductases. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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The structures of the dicationic tetranitrosyl iron complex with cysteamine [Fe2S2(CH2CH2NH3)2(NO)4]2+ and its decomposition products in protic media: an experimental and theoretical study. Russ Chem Bull 2012. [DOI: 10.1007/s11172-012-0001-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Kure B, Taniguchi A, Nakajima T, Tanase T. Hydride-Bridged NiRh Complexes with Tunable N3S2 Dithiolato Ligands and Their Utilization as Catalysts for Hydrogenation of Aldehydes and CO2 in Aqueous Media. Organometallics 2012. [DOI: 10.1021/om300350u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bunsho Kure
- Department of Chemistry,
Faculty of Science, Nara Women’s University, Kitauoya-nishi-machi,
Nara, 630-8506, Japan
| | - Ayami Taniguchi
- Department of Chemistry,
Faculty of Science, Nara Women’s University, Kitauoya-nishi-machi,
Nara, 630-8506, Japan
| | - Takayuki Nakajima
- Department of Chemistry,
Faculty of Science, Nara Women’s University, Kitauoya-nishi-machi,
Nara, 630-8506, Japan
| | - Tomoaki Tanase
- Department of Chemistry,
Faculty of Science, Nara Women’s University, Kitauoya-nishi-machi,
Nara, 630-8506, Japan
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41
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Jayarathne U, Williams K, Kasyanenko VM, Mague JT, Rubtsov IV, Donahue JP. Structural characterization of [Fe(NO)(mnt)2]1−/2− salts. Polyhedron 2012. [DOI: 10.1016/j.poly.2011.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Surawatanawong P, Sproules S, Neese F, Wieghardt K. Electronic Structures and Spectroscopy of the Electron Transfer Series [Fe(NO)L2]z (z = 1+, 0, 1–, 2–,3–; L = Dithiolene). Inorg Chem 2011; 50:12064-74. [DOI: 10.1021/ic201565d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Panida Surawatanawong
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Stephen Sproules
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- EPSRC National UK EPR Facility and Service, Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Frank Neese
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
| | - Karl Wieghardt
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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43
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Tomson NC, Crimmin MR, Petrenko T, Rosebrugh LE, Sproules S, Boyd WC, Bergman RG, DeBeer S, Toste FD, Wieghardt K. A step beyond the Feltham-Enemark notation: spectroscopic and correlated ab initio computational support for an antiferromagnetically coupled M(II)-(NO)- description of Tp*M(NO) (M = Co, Ni). J Am Chem Soc 2011; 133:18785-801. [PMID: 22047035 DOI: 10.1021/ja206042k] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Multiple spectroscopic and computational methods were used to characterize the ground-state electronic structure of the novel {CoNO}(9) species Tp*Co(NO) (Tp* = hydro-tris(3,5-Me(2)-pyrazolyl)borate). The metric parameters about the metal center and the pre-edge region of the Co K-edge X-ray absorption spectrum were reproduced by density functional theory (DFT), providing a qualitative description of the Co-NO bonding interaction as a Co(II) (S(Co) = 3/2) metal center, antiferromagnetically coupled to a triplet NO(-) anion (S(NO) = 1), an interpretation of the electronic structure that was validated by ab initio multireference methods (CASSCF/MRCI). Electron paramagnetic resonance (EPR) spectroscopy revealed significant g-anisotropy in the S = ½ ground state, but the linear-response DFT performed poorly at calculating the g-values. Instead, CASSCF/MRCI computational studies in conjunction with quasi-degenerate perturbation theory with respect to spin-orbit coupling were required for obtaining accurate modeling of the molecular g-tensor. The computational portion of this work was extended to the diamagnetic Ni analogue of the Co complex, Tp*Ni(NO), which was found to consist of a Ni(II) (S(Ni) = 1) metal center antiferromagnetically coupled to an S(NO) = 1 NO(-). The similarity between the Co and Ni complexes contrasts with the previously studied Cu analogues, for which a Cu(I) bound to NO(0) formulation has been described. This discrepancy will be discussed along with a comparison of the DFT and ab initio computational methods for their ability to predict various spectroscopic and molecular features.
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Affiliation(s)
- Neil C Tomson
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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44
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Villar-Acevedo G, Nam E, Fitch S, Benedict J, Freudenthal J, Kaminsky W, Kovacs JA. Influence of thiolate ligands on reductive N-O bond activation. Probing the O2(-) binding site of a biomimetic superoxide reductase analogue and examining the proton-dependent reduction of nitrite. J Am Chem Soc 2011; 133:1419-27. [PMID: 21207999 PMCID: PMC3178331 DOI: 10.1021/ja107551u] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) is frequently used to probe the substrate-binding site of "spectroscopically silent" non-heme Fe(2+) sites of metalloenzymes, such as superoxide reductase (SOR). Herein we use NO to probe the superoxide binding site of our thiolate-ligated biomimetic SOR model [Fe(II)(S(Me(2))N(4)(tren))](+) (1). Like NO-bound trans-cysteinate-ligated SOR (SOR-NO), the rhombic S = 3/2 EPR signal of NO-bound cis-thiolate-ligated [Fe(S(Me(2))N(4)(tren)(NO)](+) (2; g = 4.44, 3.54, 1.97), the isotopically sensitive ν(NO)(ν((15)NO)) stretching frequency (1685(1640) cm(-1)), and the 0.05 Å decrease in Fe-S bond length are shown to be consistent with the oxidative addition of NO to Fe(II) to afford an Fe(III)-NO(-) {FeNO}(7) species containing high-spin (S = 5/2) Fe(III) antiferromagnetically coupled to NO(-) (S = 1). The cis versus trans positioning of the thiolate does not appear to influence these properties. Although it has yet to be crystallographically characterized, SOR-NO is presumed to possess a bent Fe-NO similar to that of 2 (Fe-N-O = 151.7(4)°). The N-O bond is shown to be more activated in 2 relative to N- and O-ligated {FeNO}(7) complexes, and this is attributed to the electron-donating properties of the thiolate ligand. Hydrogen-bonding to the cysteinate sulfur attenuates N-O bond activation in SOR, as shown by its higher ν(NO) frequency (1721 cm(-1)). In contrast, the ν(O-O) frequency of the SOR peroxo intermediate and its analogues is not affected by H-bonds to the cysteinate sulfur or other factors influencing the Fe-SR bond strength; these only influence the ν(Fe-O) frequency. Reactions between 1 and NO(2)(-) are shown to result in the proton-dependent heterolytic cleavage of an N-O bond. The mechanism of this reaction is proposed to involve both Fe(II)-NO(2)(-) and {FeNO}(6) intermediates similar to those implicated in the mechanism of NiR-promoted NO(2)(-) reduction.
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Affiliation(s)
| | - Elaine Nam
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Sarah Fitch
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | | | | | | | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Seattle, WA 98195
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45
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Sun N, Liu LV, Dey A, Villar-Acevedo G, Kovacs JA, Darensbourg MY, Hodgson KO, Hedman B, Solomon EI. S K-edge X-ray absorption spectroscopy and density functional theory studies of high and low spin {FeNO}7 thiolate complexes: exchange stabilization of electron delocalization in {FeNO}7 and {FeO2}8. Inorg Chem 2011; 50:427-36. [PMID: 21158471 PMCID: PMC3130116 DOI: 10.1021/ic1006378] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S K-edge X-ray absorption spectroscopy (XAS) is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and density functional theory (DFT) calculations indicates that the electronic structures of {FeNO}(7) (S = 3/2) (S(Me2)N4(tren)Fe(NO), complex I) and {FeNO}(7) (S = 1/2) ((bme-daco)Fe(NO), complex II) are Fe(III)(S = 5/2)-NO(-)(S = 1) and Fe(III)(S = 3/2)-NO(-)(S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes Fe(II)(S = 0)-NO•(S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}(7) and {FeO2}(8) sites.
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Affiliation(s)
- Ning Sun
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Lei V. Liu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, California 94305
| | | | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | | | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025
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46
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De P, Maji S, Dutta Chowdhury A, Mobin SM, Kumar Mondal T, Paretzki A, Lahiri GK. Ruthenium nitrosyl complexes with 1,4,7-trithiacyclononane and 2,2′-bipyridine (bpy) or 2-phenylazopyridine (pap) coligands. Electronic structure and reactivity aspects. Dalton Trans 2011; 40:12527-39. [DOI: 10.1039/c1dt10761e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Zueva EM, Sameera WMC, Piñero DM, Chakraborty I, Devlin E, Baran P, Lebruskova K, Sanakis Y, McGrady JE, Raptis RG. Experimental and theoretical Mössbauer study of an extended family of [Fe8(μ4-O)4(μ-4-R-px)12X4] clusters. Inorg Chem 2010; 50:1021-9. [PMID: 21188980 DOI: 10.1021/ic101691q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Six [Fe(8)(μ(4)-O)(4)(μ-4-R-pyrazolato)(12)X(4)] complexes containing an identical Fe(8)(μ(4)-O)(4) core have been structurally characterized and studied by Mössbauer spectroscopy. In each case, an inner μ(4)-O bridged Fe(III) cubane core is surrounded by four trigonal bipyramidal iron centers, the two distinct sites occurring in a 1:1 ratio. The Mössbauer spectrum of each of the clusters consists of two quadrupole doublets, which, with one exception (X = NCS, R = H), overlap to give three absorption lines. The systematic variation of X and R causes significant changes in the Mössbauer spectra. A comparison with values for the same clusters computed using density functional theory allows us to establish an unequivocal assignment of these peaks in terms of a nested model for the overlapping doublets. The changes in Mössbauer parameters (both experimental and computed) for the 1-electron reduced species [Fe(8)(μ(4)-O)(4)(μ-4-Cl-pyrazolato)(12)Cl(4)](-) are consistent with a redox event that is localized within the cubane core.
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Affiliation(s)
- Ekaterina M Zueva
- Department of Inorganic Chemistry, Kazan State Technological University, Kazan, Russia
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48
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Abstract
Although DFT calculations have provided a first-order electronic-structural description for Roussin's red and black salts, a detailed study of spin coupling in these species has yet to be reported. Such an analysis is presented here for the first time, based on broken-symmetry density functional theory (DFT, chiefly OLYP/STO-TZP) calculations. Both the Noodleman and Yamaguchi formulas were used to evaluate the Heisenberg coupling constants (J). Three nitrosylated binuclear clusters were studied: [Fe(2)(NO)(2)(Et-HPTB)(O(2)CPh)](2+) (1; Et-HPTB=N,N,N',N'-tetrakis-(N-ethyl-2-benzimidazolylmethyl)-2-hydroxy-1,3-diaminopropane), [Fe(NO)(2){Fe(NO)(NS(3))}-S,S'] (2), and Roussin's red salt anion [Fe(2)(NO)(4)(μ-S)(2)](2-) (3). Although the Heisenberg J for 1 is small (≈10(2) cm(-1)), 2 and 3 exhibit J values that are at least an order of magnitude higher (≈10(3) cm(-1)), where the J values refer to the following Heisenberg spin Hamiltonian: ℋ=JS(A)⋅S(B). For Roussin's black salt anion, [Fe(4)(NO)(7)(μ(3)-S)(3)](-) (4), the Heisenberg spin Hamiltonian describing spin coupling between the {FeNO}(7) unit (S(A)=3/2) and the three {Fe(NO)(2)}(9) units (S(B)=S(C)=S(D)=1/2) in [Fe(4)(NO)(7)(μ(3)-S)(3)](-) was assumed to have the form: ℋ=J(12)(S(A)⋅S(B)+S(A)⋅S(C)+S(A)⋅S(D))+J(22)(S(B)⋅S(C)+S(B)⋅S(D)+S(C)⋅S(D)), in which J(12) corresponds to the interaction between the apical iron and a basal iron, and J(22) refers to that between any two basal iron centers. Although the basal-basal coupling constant J(22) was found to be small (≈10(2) cm(-1)), the apical-basal coupling constant J(12) is some forty times higher (≈4000 cm(-1)). Thus, the nitrosylated iron-sulfur clusters feature some exceptionally high J values relative to the non-nitrosylated {2Fe2S} and {4Fe4S} clusters. An analysis of spin-dependent bonding energies shed light on this curious feature. In essence, the energy difference between the high-spin (i.e., ferromagnetically coupled iron sites) and low-spin (i.e., maximum spin coupling) states of Roussin's salts are indeed rather similar to those of analogous non-nitrosylated iron-sulfur clusters. However, the individual Fe(NO)(x) (x=1, 2) site spins are lower in the nitrosylated systems, resulting in a smaller denominator in both the Noodleman and Yamaguchi formulas for J, which in turn translates into the very high J values.
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Affiliation(s)
- Kathrin H Hopmann
- Center for Theoretical and Computational Chemistry and Department of Chemistry, University of Tromsø, 9037 Tromsø, Norway
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49
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Bochevarov AD, Friesner RA, Lippard SJ. The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study. J Chem Theory Comput 2010; 6:3735-3749. [PMID: 21258606 PMCID: PMC3023914 DOI: 10.1021/ct100398m] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the performance of eight density functionals (B3LYP, BPW91, OLYP, O3LYP, M06, M06-2X, PBE, and SVWN5) in two Gaussian basis sets (Wachters and Partridge-1 on iron atoms; cc-pVDZ on the rest of atoms) for the prediction of the isomer shift (IS) and the quadrupole splitting (QS) parameters of Mössbauer spectroscopy. Two sources of geometry (density functional theory-optimized and X-ray) are used. Our data set consists of 31 iron-containing compounds (35 signals), the Mössbauer spectra of which were determined at liquid helium temperature and where the X-ray geometries are known. Our results indicate that the larger and uncontracted Partridge-1 basis set produces slightly more accurate linear correlations of electronic density used for the prediction of IS and noticeably more accurate results for the QS parameter. We confirm and discuss the earlier observation of Noodleman and co-workers that different oxidation states of iron produce different IS calibration lines. The B3LYP and O3LYP functionals have the lowest errors for either IS or QS. BPW91, OLYP, PBE, and M06 have a mixed success whereas SVWN5 and M06-2X demonstrate the worst performance. Finally, our calibrations and conclusions regarding the best functional to compute the Mössbauer characteristics are applied to candidate structures for the peroxo and Q intermediates of the enzyme methane monooxygenase hydroxylase (MMOH), and compared to experimental data in the literature.
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Jaworska M, Stopa G, Stasicka Z. Photochemical NO-removal and NOx-release in the presence of Fe–EDTA complexes. DFT calculations of electronic structure and spectroscopy of the [Fe(edta)(NO)]2− complex. Nitric Oxide 2010; 23:227-33. [DOI: 10.1016/j.niox.2010.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 07/01/2010] [Accepted: 07/09/2010] [Indexed: 11/25/2022]
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