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Bonitatibus PJ, Alvarez S, Armstrong WH, Baldansuren A, Gaspard ME, Lakshmi KV, Ziegler MS, Charles P. Synthesis, Crystal Structure, EPR, and DFT Studies of an Unusually Distorted Vanadium(II) Complex. Dalton Trans 2022; 51:12031-12036. [DOI: 10.1039/d2dt02392j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a synthesis and structure of the most highly distorted four-coordinate d3 ion known to date that also serves as the second known example of a bis(biphenolato) transition metal...
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2
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Gu NX, Oyala PH, Peters JC. H 2 Evolution from a Thiolate-Bound Ni(III) Hydride. J Am Chem Soc 2020; 142:7827-7835. [PMID: 32249575 DOI: 10.1021/jacs.0c00712] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Terminal NiIII hydrides are proposed intermediates in proton reduction catalyzed by both molecular electrocatalysts and metalloenzymes, but well-defined examples of paramagnetic nickel hydride complexes are largely limited to bridging hydrides. Herein, we report the synthesis of an S = 1/2, terminally bound thiolate-NiIII-H complex. This species and its terminal hydride ligand in particular have been thoroughly characterized by vibrational and EPR techniques, including pulse EPR studies. Corresponding DFT calculations suggest appreciable spin leakage onto the thiolate ligand. The hyperfine coupling to the terminal hydride ligand of the thiolate-NiIII-H species is comparable to that of the hydride ligand proposed for the Ni-C hydrogenase intermediate (NiIII-H-FeII). Upon warming, the featured thiolate-NiIII-H species undergoes bimolecular reductive elimination of H2. Associated kinetic studies are discussed and compared with a structurally related FeIII-H species that has also recently been reported to undergo bimolecular H-H coupling.
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Affiliation(s)
- Nina X Gu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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4
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DFT Protocol for EPR Prediction of Paramagnetic Cu(II) Complexes and Application to Protein Binding Sites. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4040055] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
With the aim to provide a general protocol to interpret electron paramagnetic resonance (EPR) spectra of paramagnetic copper(II) coordination compounds, density functional theory (DFT) calculations of spin Hamiltonian parameters g and A for fourteen Cu(II) complexes with different charges, donor sets, and geometry were carried out using ORCA software. The performance of eleven functionals was tested, and on the basis of the mean absolute percent deviation (MAPD) and standard deviation (SD), the ranking of the functionals for Az is: B3LYP > B3PW91 ~ B3P86 > PBE0 > CAM-B3LYP > TPSSh > BH and HLYP > B2PLYP > MPW1PW91 > ω-B97x-D >> M06; and for gz is: PBE0 > BH and HLYP > B2PLYP > ω-B97x-D > B3PW91~B3LYP~B3P86 > CAM-B3LYP > TPSSh~MPW1PW91 >> M06. With B3LYP the MAPD with respect to A z exp t l is 8.6% with a SD of 4.2%, while with PBE0 the MAPD with respect to g z exp t l is 2.9% with a SD of 1.1%. The results of the validation confirm the fundamental role of the second order spin-orbit contribution to Az. The computational procedure was applied to predict the values of gz and Az of the adducts formed by Cu(II) with albumin and two fragments of prion protein, 106–126 and 180–193.
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5
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Bader K, Schlindwein SH, Gudat D, van Slageren J. Molecular qubits based on potentially nuclear-spin-free nickel ions. Phys Chem Chem Phys 2017; 19:2525-2529. [PMID: 28058424 DOI: 10.1039/c6cp08161d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular qubits with the longest coherence times thus far are based on nuclear-spin-carrying central ions. These nuclear spins can cause quantum state leakage, which is detrimental to quantum algorithm performance. We present two novel molecular qubits based on potentially nuclear spin-free Ni in the formal oxidation state 3+. (d20-PPh4)[Ni(mnt)2] (Ni-mnt, mnt2- = maleonitrile-1,2-dithiolate) possesses a coherence time of up to 38.7 μs at 7 K. Functionalization of the dithiolate ligand decreases the coherence time by a factor of only four in (HNEt3)[Ni(dip)2] (Ni-dip, dip2- = 3-(diphenylphosphoryl)-methylbenzene-1,2-dithiolate), indicating that monoanionic Ni-dithiolene complexes are promising and robust building blocks for polynuclear molecular qubit gates.
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Affiliation(s)
- K Bader
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
| | - S H Schlindwein
- Institut für Anorganische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - D Gudat
- Institut für Anorganische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - J van Slageren
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany. and Center for Integrated Quantum Science and Technology (IQST), Stuttgart/Ulm, Germany
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6
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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7
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Pietrzyk P, Mazur T, Podolska-Serafin K, Chiesa M, Sojka Z. Intimate Binding Mechanism and Structure of Trigonal Nickel(I) Monocarbonyl Adducts in ZSM-5 Zeolite—Spectroscopic Continuous Wave EPR, HYSCORE, and IR Studies Refined with DFT Quantification of Disentangled Electron and Spin Density Redistributions along σ and π Channels. J Am Chem Soc 2013; 135:15467-78. [DOI: 10.1021/ja405874t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piotr Pietrzyk
- Faculty
of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | - Tomasz Mazur
- Faculty
of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
| | | | - Mario Chiesa
- Dipartimento
di Chimica, Università di Torino and NIS Centre of Excellence, via
P. Giuria 7, 10125, Torino, Italy
| | - Zbigniew Sojka
- Faculty
of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland
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8
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Roemelt M, Maganas D, DeBeer S, Neese F. A combined DFT and restricted open-shell configuration interaction method including spin-orbit coupling: Application to transition metal L-edge X-ray absorption spectroscopy. J Chem Phys 2013; 138:204101. [DOI: 10.1063/1.4804607] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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9
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Verma P, Autschbach J. Relativistic Density Functional Calculations of Hyperfine Coupling with Variational versus Perturbational Treatment of Spin–Orbit Coupling. J Chem Theory Comput 2013; 9:1932-48. [DOI: 10.1021/ct301114z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Prakash Verma
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000
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10
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Computational study of the electronic structure and magnetic properties of the Ni–C state in [NiFe] hydrogenases including the second coordination sphere. J Biol Inorg Chem 2012; 17:1269-81. [DOI: 10.1007/s00775-012-0941-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/11/2012] [Indexed: 10/27/2022]
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11
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Schott E, Zarate X, Arratia-Pérez R. Electronic structure and molecular properties of paramagnetic hexanuclear Tantalum [Ta6X12Y6]3− (X and Y=F, Cl, Br, I) cluster compounds. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Stephen E, Blake AJ, Carter E, Collison D, Davies ES, Edge R, Lewis W, Murphy DM, Wilson C, Gould RO, Holder AJ, McMaster J, Schröder M. Redox Non-innocence of Thioether Crowns: Elucidation of the Electronic Structure of the Mononuclear Pd(III) Complexes [Pd([9]aneS3)2]3+ and [Pd([18]aneS6)]3+. Inorg Chem 2012; 51:1450-61. [DOI: 10.1021/ic2017006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emma Stephen
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, U.K
| | | | - Emma Carter
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, U.K
| | - David Collison
- EPSRC Multi-Frequency EPR Centre,
School of Chemistry, University of Manchester, Manchester, M13 9PL, U.K
| | | | - Ruth Edge
- EPSRC Multi-Frequency EPR Centre,
School of Chemistry, University of Manchester, Manchester, M13 9PL, U.K
| | - William Lewis
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, U.K
| | | | - Claire Wilson
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, U.K
| | - Robert O. Gould
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ, U.K
| | - Alan J. Holder
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ, U.K
| | - Jonathan McMaster
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, U.K
| | - Martin Schröder
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, U.K
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13
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Stein M. Comment on "A nickel(II)-based radical-ligand complex as a functional model of hydrogenase". Chemistry 2011; 17:15046-8; author reply 15049-50. [PMID: 22170220 DOI: 10.1002/chem.201002985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Hedegård ED, Kongsted J, Sauer SPA. Optimized Basis Sets for Calculation of Electron Paramagnetic Resonance Hyperfine Coupling Constants: aug-cc-pVTZ-J for the 3d Atoms Sc-Zn. J Chem Theory Comput 2011; 7:4077-87. [PMID: 26598353 DOI: 10.1021/ct200587k] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The hyperfine coupling tensor of electron paramagnetic resonance (EPR), describing the interaction between an electron and a given nuclei, depends strongly on the electron density at the nucleus. With standard Gaussian-type orbital basis sets (GTOs), employed in most calculations, it is difficult to obtain converged results of the hyperfine coupling tensor, and basis sets with more flexible core regions have therefore been devised. To this class of core property basis sets belong the aug-cc-pVTZ-J basis sets developed for the s- and p-block atoms. Here, we extend the aug-cc-pVTZ-J basis sets to include the 3d elements Sc-Zn. The converged optimal basis sets are throughout the series described by a (25s17p10d3f2g)/[17s10p7d3f2g] contraction scheme, where four tight s-, one tight p-, and one tight d-type function have been added to the original aug-cc-pVTZ basis sets. The basis sets are generally contracted, and molecular orbital coefficients are used as contraction coefficients. By validation studies with different functionals and compounds, it is shown that the values of the contraction coefficient are effectively independent of the compound used in their generation and the exchange-correlation functional employed in the calculation.
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Affiliation(s)
- Erik Donovan Hedegård
- Department of Chemistry and Physics, University of Southern Denmark , Odense, Denmark
| | - Jacob Kongsted
- Department of Chemistry and Physics, University of Southern Denmark , Odense, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen , Copenhagen, Denmark
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15
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Kállay C, Dávid A, Timári S, Nagy EM, Sanna D, Garribba E, Micera G, De Bona P, Pappalardo G, Rizzarelli E, Sóvágó I. Copper(II) complexes of rat amylin fragments. Dalton Trans 2011; 40:9711-21. [PMID: 21858342 DOI: 10.1039/c1dt10835b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The fragments of rat amylin rIAPP(17-29) (Ac-VRSSNNLGPVLPP-NH(2)), rIAPP(17-22) (Ac-VRSSNN-NH(2)), rIAPP(19-22) (Ac-SSNN-NH(2)) and rIAPP(17-20) (Ac-VRSS-NH(2)) together with the related mutant peptides (Ac-VASS-NH(2) and Ac-VRAA-NH(2)) have been synthesized and their copper(II) complexes studied by potentiometric, UV-Vis, CD and EPR spectroscopic methods. Despite the lack of any common strongly coordinating donor functions some of these fragments are able to bind copper(II) ions in the physiological pH range. The longest fragment rat amylin(17-29) keeps one equivalent copper(II) ion in solution in the whole pH range, while two other peptides Ac-VRSSNN-NH(2) and Ac-SSNN-NH(2) are also able to interact with copper(II) ions in the slightly alkaline pH range. According to the spectral parameters of the complexes, the peptides can be classified into two different categories: (i) the tetrapeptides Ac-VRSS-NH(2), Ac-VASS-NH(2) and Ac-VRAA-NH(2) can interact with copper(II) only under strongly alkaline conditions (pH > 10.0) and the formation of only one species with four amide nitrogen coordination can be detected; (ii) the peptides Ac-VRSSNNLGPVLPP-NH(2), Ac-VRSSNN-NH(2) and Ac-SSNN-NH(2) can form complexes above pH 6.0 with the major stoichiometries [CuH(-2)L], [CuH(-3)L](-) and [CuH(-4)L](2-). These data support that rIAPP(17-29) can interact with copper(II) ions under physiological conditions and the SSNN tetrapeptide fragment can be considered as the shortest sequence responsible for metal binding. Density functional theory (DFT) calculations provide some information on the possible coordination modes of Ac-SSNN-NH(2) towards the copper(II) ion and suggest that for [CuH(-2)L], [CuH(-3)L](-) and [CuH(-4)L](2-), the binding of two, three and four deprotonated amide nitrogens, with NH(-) of the side chain of asparagine as anchoring group, is probable. Moreover, these data reveal that peptides can be effective metal binding ligands even in the absence of anchoring groups, if more polar side chains are present in a specific sequence.
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Affiliation(s)
- Csilla Kállay
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Hungary.
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16
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Stephen E, Huang D, Shaw JL, Blake AJ, Collison D, Davies ES, Edge R, Howard JAK, McInnes EJL, Wilson C, Wolowska J, McMaster J, Schröder M. Redox Non-Innocence of Thioether Crowns: Spectroelectrochemistry and Electronic Structure of Formal Nickel(III) Complexes of Aza-Thioether Macrocycles. Chemistry 2011; 17:10246-58. [DOI: 10.1002/chem.201100812] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Indexed: 11/06/2022]
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17
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Micera G, Garribba E. Is the spin-orbit coupling important in the prediction of the 51V hyperfine coupling constants of V(IV) O2+ species? ORCA versus Gaussian performance and biological applications. J Comput Chem 2011; 32:2822-35. [PMID: 21735449 DOI: 10.1002/jcc.21862] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/01/2011] [Accepted: 05/15/2011] [Indexed: 01/26/2023]
Abstract
Density functional theory calculations of the (51)V hyperfine coupling (HFC) tensor A, have been completed for eighteen V(IV)O(2+) complexes with different donor set, electric charge and coordination geometry. A tensor was calculated with ORCA software with several functionals and basis sets taking into account the spin-orbit coupling contribution. The results were compared with those obtained with Gaussian 03 software using the half-and-half functional BHandHLYP and 6-311g(d,p) basis set. The order of accuracy of the functionals in the prediction of A(iso), A(z) and dipolar term A(z,anis) is BHandHLYP > PBE0 >> B3PW > TPSSh >> B3LYP >> BP86 > VWN5 (for A(iso)), BHandHLYP > PBE0 >> B3PW > TPSSh > B3LYP >> BP86 > VWN5 (for A(z)), B3LYP > PBE0 ∼ B3PW ∼ BHandHLYP >> TPSSh > BP86 ∼ VWN5 (for A(z,anis)). The good agreement in the prediction of A(z) with BHandHLYP is due to a compensation between the overestimation of A(iso) and underestimation of A(z,anis) (A(z) = A(iso) + A(z,anis)), whereas among the hybrid functionals PBE0 performs better than the other ones. BHandHLYP functional and Gaussian software are recommended when the V(IV)O(2+) species contains only V-O and/or V-N bonds, whereas PBE0 functional and ORCA software for V(IV)O(2+) complexes with one or more V-S bonds. Finally, the application of these methods to the coordination environment of V(IV)O(2+) ion in V-proteins, like vanadyl-substituted insulin, carbonic anhydrase, collagen and S-adenosylmethionine synthetase, was discussed.
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Affiliation(s)
- Giovanni Micera
- Dipartimento di Chimica e Centro Interdisciplinare per lo Sviluppo della Ricerca Biotecnologica e per lo Studio della Biodiversità della Sardegna, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy
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18
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Pietrzyk P, Podolska K, Sojka Z. Resolving Conformation Dichotomy for Y- and T-Shaped Three-Coordinate NiICarbonyl Complexes with Relativistic DFT Analysis of EPR Fingerprints. Chemistry 2009; 15:11802-7. [DOI: 10.1002/chem.200901805] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Pietrzyk P, Podolska K, Sojka Z. DFT Analysis of g and 13C Hyperfine Coupling Tensors for Model NiI(CO)nLm (n = 1−4, L = H2O, OH−) Complexes Epitomizing Surface Nickel(I) Carbonyls. J Phys Chem A 2008; 112:12208-19. [DOI: 10.1021/jp8067848] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Piotr Pietrzyk
- Faculty of Chemistry and Regional Laboratory for Physicochemical Analyses and Structural Research, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Podolska
- Faculty of Chemistry and Regional Laboratory for Physicochemical Analyses and Structural Research, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Zbigniew Sojka
- Faculty of Chemistry and Regional Laboratory for Physicochemical Analyses and Structural Research, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
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21
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Rinkevicius Z, de Almeida KJ, Oprea CI, Vahtras O, Ågren H, Ruud K. Degenerate Perturbation Theory for Electronic g Tensors: Leading-Order Relativistic Effects. J Chem Theory Comput 2008; 4:1810-28. [DOI: 10.1021/ct800053f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Katia Julia de Almeida
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Cornel I. Oprea
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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22
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Huang D, Zhang X, McInnes EJL, McMaster J, Blake AJ, Davies ES, Wolowska J, Wilson C, Schröder M. Crystallographic, Electrochemical, and Electronic Structure Studies of the Mononuclear Complexes of Au(I)/(II)/(III) with [9]aneS2O ([9]aneS2O = 1-oxa-4,7-dithiacyclononane). Inorg Chem 2008; 47:9919-29. [DOI: 10.1021/ic8010037] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deguang Huang
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Xiaofeng Zhang
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Eric J. L. McInnes
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Jonathan McMaster
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Alexander J. Blake
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - E. Stephen Davies
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Joanna Wolowska
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Claire Wilson
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
| | - Martin Schröder
- School of Chemistry, University of Nottingham, Nottingham NG9 2RD, U.K., and EPSRC Multi-Frequency EPR Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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23
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Ren X, Sui Y, Liu G, Xie J. Observation of intermolecular charge transfer in a quasi-one-dimensional molecular alloy system. J Phys Chem A 2008; 112:8009-14. [PMID: 18693711 DOI: 10.1021/jp8009194] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-band single-crystal electron paramagnetic resonance (EPR) studies of the molecular alloy [NO 2BzPy][Au 0.57Ni 0.43(mnt) 2] are presented in this paper. At room temperature, EPR spectra show both intense resonance signals (main signals) and weak satellite quartet lines. The characteristics of both intense and weak EPR signals depend on the magnetic field orientation. The main signals arise from two magnetically nonequivalent [Ni(mnt) 2] (-) anions, and their corresponding principal values of the g tensor are ( g x ') 1 = 2.04653, ( g y ') 1 = 2.00096, and ( g z ') 1 = 2.15319 and ( g x ') 2 = 2.04520, ( g y ') 2 = 1.99734, and ( g z ') 2 = 2.15361, respectively. The weak satellite lines, whose patterns strongly depend on the magnetic field direction, can be attributed to the hyperfine coupling of the electron spin with the (197)Au nucleus of the [Au(mnt) 2] (-) species. Density functional theory calculations for the spin and charge distributions of the dimer {[Ni(mnt) 2][Au(mnt) 2]} (2-) indicate that the hyperfine interaction of the electron spin with the (197)Au nuclear spins is caused, in part, by the charge transfer between the [Ni(mnt) 2] (-) and the [Au(mnt) 2] (-) species.
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Affiliation(s)
- Xiaoming Ren
- College of Science, Nanjing University of Technology, People's Republic of China.
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24
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Colombo MC, Vandevondele J, Van Doorslaer S, Laio A, Guidoni L, Rothlisberger U. Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study. Proteins 2008; 70:1084-98. [PMID: 17876822 DOI: 10.1002/prot.21604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a hybrid QM/MM Car-Parrinello molecular dynamics study of the copper-loaded C-terminal domain of the mouse prion protein. By means of a statistical analysis of copper coordination in known protein structures, we localized the protein regions with the highest propensity for copper ion binding. The identified candidate structures were subsequently refined via QM/MM simulations. Their EPR characteristics were computed to make contact with the experimental data and to probe the sensitivity to structural and chemical changes. Overall best agreement with the experimental EPR data (Van Doorslaer et al., J Phys Chem B 2001; 105: 1631-1639) and the information currently available in the literature is observed for a binding site involving H187. Moreover, a reinterpretation of the experimental proton hyperfine couplings was possible in the light of the present computational findings.
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Affiliation(s)
- Maria Carola Colombo
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, EPFL, CH-1015 Lausanne, Switzerland
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25
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Shaw JL, Wolowska J, Collison D, Howard JAK, McInnes EJL, McMaster J, Blake AJ, Wilson C, Schröder M. Redox Non-innocence of Thioether Macrocycles: Elucidation of the Electronic Structures of Mononuclear Complexes of Gold(II) and Silver(II). J Am Chem Soc 2006; 128:13827-39. [PMID: 17044711 DOI: 10.1021/ja0636439] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mononuclear +2 oxidation state metal complexes [Au([9]aneS(3))(2)](2+) and [Ag([18]aneS(6))](2+) have been synthesized and characterized crystallographically. The crystal structure of the Au(II) species [Au([9]aneS(3))(2)](BF(4))(2) shows a Jahn-Teller tetragonally distorted geometry with Au-S(1) = 2.839(5), Au-S(2) = 2.462(5), and Au-S(3) = 2.452(5) A. The related Ag(II) complex [Ag([18]aneS(6))](ClO(4))(2) has been structurally characterized at both 150 and 30 K and is the first structurally characterized complex of Ag(II) with homoleptic thioether S-coordination. The single-crystal X-ray structure of [Ag([18]aneS(6))](ClO(4))(2) confirms octahedral homoleptic S(6)-thioether coordination. At 150 K, the structure contains two independent Ag(II)-S distances of 2.569(7) and 2.720(6) A. At 30 K, the structure retains two independent Ag(II)-S distances of 2.615(6) and 2.620(6) A, with the complex cation retaining 3-fold symmetry. The electronic structures of [Au([9]aneS(3))(2)](2+) and [Ag([18]aneS(6))](2+) have been probed in depth using multifrequency EPR spectroscopy coupled with DFT calculations. For [Au([9]aneS(3))(2)](2+), the spectra are complex due to large quadrupole coupling to (197)Au. Simulation of the multifrequency spectra gives the principal g values, hyperfine (A) and quadrupole (P) couplings, and furthermore reveals non-co-incidence of the principal axes of the P tensor with respect to the A and g matrices. These results are rationalized in terms of the electronic and geometric structure and reveal that the SOMO has ca. 30% Au 5d(xy)() character, consistent with DFT calculations (27% Au character). For [Ag([18]aneS(6))](2+), detailed EPR spectroscopic analysis confirms that the SOMO has ca. 26% Ag 4d(xy)() character and DFT calculations are consistent with this result (22% Ag character).
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Affiliation(s)
- Jennifer L Shaw
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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26
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Fiedler AT, Brunold TC. Computational Studies of the H-Cluster of Fe-Only Hydrogenases: Geometric, Electronic, and Magnetic Properties and Their Dependence on the [Fe4S4] Cubane. Inorg Chem 2005; 44:9322-34. [PMID: 16323916 DOI: 10.1021/ic050946f] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active sites of Fe-only hydrogenases (FeHases) feature an unusual polynuclear iron-sulfur cluster, known as the H-cluster, that consists of a [Fe4S4] cubane linked to a di-iron subunit (the [2Fe]H component) via a bridging cysteine ligand (SCys). While previous computational studies of FeHases employed H-cluster models that only included the [2Fe]H component, we have utilized density functional theory (DFT), in conjunction with the broken-symmetry (BS) approach, to explore the geometric, electronic, and magnetic properties of the entire H-cluster. These calculations have allowed us to evaluate, for the first time, the influence of the [Fe4S4] cubane on the [2Fe]H component of the H-cluster in its active (Hox) and CO-inhibited (Hox-CO) states, both of which are paramagnetic (S=1/2). Our results reveal that the presence of the cubane tunes both the position and the donor strength of the SCys ligand, which, in turn, modulates the internal geometric and electronic structures of the [2Fe]H subcluster. Importantly, the BS methodology provides an accurate description of the exchange interactions within the H-cluster, permitting insight into the electronic origin of the changes in magnetic properties observed experimentally upon conversion of Hox to Hox-CO. Specifically, while the unpaired spin density in the Hox state is localized on the distal Fe center, in the Hox-CO state, it is delocalized over the [2Fe]H component, such that the proximal Fe center acquires significant spin density (where distal and proximal refer to the positions of the Fe centers relative to the cubane). To validate our H-cluster models on the basis of experimental data, two DFT-based approaches and the semiempirical INDO/S method have been employed to compute electron paramagnetic resonance parameters for the H-cluster states. While most computations yield reasonably accurate g values and ligand hyperfine coupling constants (i.e., A values) for the Hox and Hox-CO states, they fail to reproduce the isotropic 57Fe A tensors found experimentally. Finally, extension of the computational methodology employed successfully for the Hox and Hox-CO states to the metastable Hoxphoto state, generated by irradiation of the Hox-CO state at cryogenic temperatures, has allowed us to discriminate between proposed structural models for this species.
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Affiliation(s)
- Adam T Fiedler
- Department of Chemistry, University of Wisconsin-Madison, 1101 West University Avenue, Madison, Wisconsin 53706, USA
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27
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Ni Z, Ren X, Ma J, Xie J, Ni C, Chen Z, Meng Q. Theoretical Studies on the Magnetic Switching Controlled by Stacking Patterns of Bis(maleonitriledithiolato) Nickelate(III) Dimers. J Am Chem Soc 2005; 127:14330-8. [PMID: 16218627 DOI: 10.1021/ja050631z] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magnetic switchable maleonitriledithiolate (mnt) complexes were studied by density functional theory. The calculations were performed for anion dimers of [RBzPyR'][Ni(mnt)(2)] (RBzPyR' = derivatives of benzylpyridinium) to elucidate magnetostructural correlations and the nature of the weak intermolecular chemical bonding. The calculated results showed that the spin delocalization, favored by the eclipsed stacking and the shorter interlayer distance, was responsible for the diamagnetic character of [1-benzyl-4-aminopyridinium][Ni(mnt)(2)] at low temperature. The weak antiferromagnetic and ferromagnetic interactions were also reproduced for [1-benzyl-4-aminopyridinium][Ni(mnt)(2)] and [1-(4'-fluorobenzyl)pyridinium][Ni(mnt)(2)] at high temperature, respectively. The natural bond orbital analysis suggested that the cooperative effect of the weak intermolecular bondings may be the intrinsic driving force resulting in the switchable property, which is essentially similar to those in organic radicals exhibiting magnetic bistability. Further investigations with varying interlayer distance d, the extent of slippage (slipping distance r and deviation angle alpha), and rotational angle theta suggested that the extent of slippage played an important role in magnetic interactions. Therefore, the abrupt modulation of the extent of slippage in the [Ni(mnt)(2)](-) complexes by external perturbations provided new possibilities for the design of molecular magnetic switching devices.
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Affiliation(s)
- Zhaoping Ni
- Coordination Chemistry Institute, State Key Laboratory of Coordination Chemistry, and Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210093, P. R. China
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28
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Ziegler T, Autschbach J. Theoretical methods of potential use for studies of inorganic reaction mechanisms. Chem Rev 2005; 105:2695-722. [PMID: 15941226 DOI: 10.1021/cr0307188] [Citation(s) in RCA: 367] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tom Ziegler
- Department of Chemistry, University of Calgary, Canada.
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30
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Stein M, Lubitz W. Relativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase: a contribution to understanding the enzymatic mechanism. J Inorg Biochem 2005; 98:862-77. [PMID: 15134933 DOI: 10.1016/j.jinorgbio.2004.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Revised: 03/18/2004] [Accepted: 03/22/2004] [Indexed: 10/26/2022]
Abstract
Structures and spectroscopic observables of the paramagnetic intermediates of the enzymatic reaction cycle of the metalloenzyme [NiFe] hydrogenase were calculated using relativistic density functional theory (DFT) within the zero-order regular approximation (ZORA). By comparing experimental and calculated magnetic resonance parameters (g- and hyperfine tensors) for the states Ni-A, Ni-B, Ni-C, Ni-L, and Ni-CO the details of the atomic composition of these paramagnetic intermediates could be elucidated that are mostly not available from X-ray structure analysis. In general, good agreement between calculated and experimental observables could be obtained. A detailed picture of the changes of the active center during the catalytic cycle was deduced from the obtained structures. Based on these results, a consistent model for the sequence of redox states including protonation steps is proposed which is important for understanding the mechanism of the [NiFe] hydrogenase.
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Affiliation(s)
- Matthias Stein
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
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31
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Stevens F, Van Speybroeck V, Pauwels E, Vrielinck H, Callens F, Waroquier M. Level of theory study of magnetic resonance parameters of chalcogen XY−(X, Y = O, S and Se) defects in alkali halides. Phys Chem Chem Phys 2005; 7:240-9. [DOI: 10.1039/b412408a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Cui X, Calhorda M, Costa P, Delgado R, Drew M, Félix V. Structure, Characterization, and Metal-Complexation Properties of a New Tetraazamacrocycle Containing Two Phenolic Pendant Arms. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Bruschi M, De Gioia L, Zampella G, Reiher M, Fantucci P, Stein M. A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site. J Biol Inorg Chem 2004; 9:873-84. [PMID: 15365900 DOI: 10.1007/s00775-004-0588-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 07/29/2004] [Indexed: 11/26/2022]
Abstract
We have applied density functional theory, using both pure (BP86) and hybrid (B3LYP and B3LYP*) functionals, to investigate structural parameters and reaction energies for nickel(II)-sulfur coordination compounds, as well as for small cluster models of the Ni-SI and Ni-R redox state of [NiFe] hydrogenases. Results obtained investigating experimentally well-characterized complexes show that BP86 is well suited to describe the structural features of this class of compounds. However, the singlet-triplet energy splitting and even the computed ground state are strongly dependent on the applied functional. Results for the cluster models of [NiFe] hydrogenases lead to the conclusion that in the reduced protein structures characterized by X-ray diffraction a hydride bridges the two metal centres. The energy splitting of the singlet and triplet states in Ni-R and Ni-SI models is calculated to be very small and may be overcome at room temperature to allow a spin crossover. Moreover, the relative stability of the Ni-SI and Ni-R structures adopted in the present investigation is fully compatible with their involvement in the reversible heterolytic cleavage of H(2).
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Affiliation(s)
- Maurizio Bruschi
- Department of Environmental Science, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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34
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Ienco A, Calhorda MJ, Reinhold J, Reineri F, Bianchini C, Peruzzini M, Vizza F, Mealli C. Activation of Molecular Hydrogen over a Binuclear Complex with Rh2S2 Core: DFT Calculations and NMR Mechanistic Studies. J Am Chem Soc 2004; 126:11954-65. [PMID: 15382931 DOI: 10.1021/ja047992j] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dicationic complex [(triphos)Rh(mu-S)(2)Rh(triphos)](2+), 1 (modeled as 1c) [triphos = CH(3)C(CH(2)PPh(2))(3)], is known to activate two dihydrogen molecules and produce the bis(mu-hydrosulfido) product [(triphos)(H)Rh(mu-SH)(2)Rh(H)(triphos)](2+), 2 (modeled as 2b), from which 1 is reversibly obtained. The possible steps of the process have been investigated with DFT calculations. It has been found that each d(6) metal ion in 1c, with local square pyramidal geometry, is able to anchor one H(2) molecule in the side-on coordination. The step is followed by heterolytic splitting of the H-H bond over one adjacent and polarized Rh-S linkage. The process may be completed before the second H(2) molecule is added. Alternatively, both H(2) molecules are trapped by the Rh(2)S(2) core before being split in two distinct steps. Since the ambiguity could not be solved by calculations, (31)P and (1)H NMR experiments, including para-hydrogen techniques, have been performed to identify the actual pathway. In no case is there experimental evidence for any Rh-(eta(2)-H(2)) adduct, probably due to its very short lifetime. Conversely, (1)H NMR analysis of the hydride region indicates only one reaction intermediate which corresponds to the monohydride-mu-hydrosulfide complex [(triphos)Rh(H)(mu-SH)(mu-S)Rh(triphos)](2+) (3) (model 5a). This excludes the second hypothesized pathway. From an energetic viewpoint the computational results support the feasibility of the whole process. In fact, the highest energy for H(2) activation is 8.6 kcal mol(-1), while a larger but still surmountable barrier of 34.6 kcal mol(-1) is in line with the reversibility of the process.
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Affiliation(s)
- Andrea Ienco
- Istituto di Chimica dei Composti OrganoMetallici, CNR, Via Madonna del Piano, I-50019 Sesto Fiorentino, Firenze, Italy
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35
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Marcos Ramos A, Meskers SCJ, Beckers EHA, Prince RB, Brunsveld L, Janssen RAJ. Supramolecular Control over Donor−Acceptor Photoinduced Charge Separation. J Am Chem Soc 2004; 126:9630-44. [PMID: 15291567 DOI: 10.1021/ja0390909] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel donor-bridge-acceptor system has been synthesized by covalently linking a p-phenylene vinylene oligomer (OPV) and a perylene diimid (PERY) at opposite ends of a m-phenylene ethynylene oligomer (FOLD) of twelve phenyl rings, containing nonpolar (S)-3,7-dimethyl-1-octanoxy side chains. For comparison, model compounds have been prepared in which either the donor or acceptor is absent. In chloroform, the oligomeric bridge is in a random coil conformation. Upon addition of an apolar solvent (heptane) the oligomeric bridge first folds into a helical stack and subsequently intermolecular self-assembly of the stacks into columnar architectures occurs. Photoexcitation in the random coil conformation, where the interaction between the donor and acceptor chromophores is small, results only in long-range intramolecular energy transfer in which the OPV singlet-excited state is transformed into the PERY singlet-excited state. In the folded conformation of the bridge, donor and acceptor are closer and their enhanced interaction favors the formation the OPV(*)(+)-FOLD-PERY(*)(-) charge-separated state upon photoexcitation. As a result, the extent of photoinduced charge separation depends on the degree of folding of the bridge between donor and acceptor and therefore on the apolar nature of the medium. As a consequence, and contrary to conventional photoinduced charge separation processes, the formation of the OPV(*)(+)-FOLD-PERY(*)(-) charge-separated state is more favored in apolar media.
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Affiliation(s)
- Alicia Marcos Ramos
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Abstract
▪ Abstract Two current frontiers in EPR research are high-field ([Formula: see text]) electron paramagnetic resonance (EPR) and high-field electron-nuclear double resonance (ENDOR). This review focuses on recent advances in high-field ENDOR and its applications to the study of proteins containing native paramagnetic sites. It concentrates on two aspects; the first concerns the determination of the location of protons and is related to the site geometry, and the second focuses on the spin density distribution within the site, which is inherent to the electronic structure. Both spin density and proton locations can be derived from ligand hyperfine couplings determined by ENDOR measurements. A brief description of the experimental methods is presented along with a discussion of the advantages and disadvantages of high-field ENDOR compared with conventional X-band (∼ 9.5 GHz) experiments. Specific examples of both protein single crystals and frozen solutions are then presented. These include the determination of the coordinates of water ligand protons in the Mn(II) site of concanavalin A, the detection of hydrogen bonds in a quinone radical in the bacterial photosynthetic reaction center as well as in the tyrosyl radical in ribonuclease reductase, and the study of the spin distribution in copper proteins. The copper proteins discussed are the type I copper of azurin and the binuclear CuA center in a number of proteins. The last part of the review presents a brief discussion of the interpretation of hyperfine couplings using quantum chemical calculations, primarily density functional theory (DFT) methods. Such methods are becoming an integral part of the data analysis tools, as they can facilitate signal assignment and provide the ultimate relation between the experimental hyperfine couplings and the electronic wave function.
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Affiliation(s)
- D Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100.
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37
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Remenyi C, Reviakine R, Arbuznikov AV, Vaara J, Kaupp M. Spin−Orbit Effects on Hyperfine Coupling Tensors in Transition Metal Complexes Using Hybrid Density Functionals and Accurate Spin−Orbit Operators. J Phys Chem A 2004. [DOI: 10.1021/jp049395p] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian Remenyi
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, and Laboratory of Physical Chemistry, Department of Chemistry, P.O. Box 55 (A. I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Roman Reviakine
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, and Laboratory of Physical Chemistry, Department of Chemistry, P.O. Box 55 (A. I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Alexei V. Arbuznikov
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, and Laboratory of Physical Chemistry, Department of Chemistry, P.O. Box 55 (A. I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Juha Vaara
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, and Laboratory of Physical Chemistry, Department of Chemistry, P.O. Box 55 (A. I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Martin Kaupp
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, and Laboratory of Physical Chemistry, Department of Chemistry, P.O. Box 55 (A. I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
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Arbuznikov AV, Vaara J, Kaupp M. Relativistic spin-orbit effects on hyperfine coupling tensors by density-functional theory. J Chem Phys 2004; 120:2127-39. [PMID: 15268351 DOI: 10.1063/1.1636720] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A second-order perturbation theory treatment of spin-orbit corrections to hyperfine coupling tensors has been implemented within a density-functional framework. The method uses the all-electron atomic mean-field approximation and/or spin-orbit pseudopotentials in incorporating one- and two-electron spin-orbit interaction within a first-principles framework. Validation of the approach on a set of main-group radicals and transition metal complexes indicates good agreement between all-electron and pseudopotential results for hyperfine coupling constants of the lighter nuclei in the system, except for cases in which scalar relativistic effects become important. The nonrelativistic Fermi contact part of the isotropic hyperfine coupling constants is not always accurately reproduced by the exchange-correlation functionals employed, particularly for the triplet and pi-type doublet radicals in the present work. For this reason, ab initio coupled-cluster singles and doubles with perturbative triples results for the first-order contributions have been combined in the validation calculations with the density-functional results for the second-order spin-orbit contributions. In the cases where spin-orbit corrections are of significant magnitude relative to the nonrelativistic first-order terms, they improve the agreement with experiment. Antisymmetric contributions to the hyperfine tensor arise from the spin-orbit contributions and are discussed for the IO2 radical, whereas rovibrational effects have been evaluated for RhC, NBr, and NI.
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Affiliation(s)
- Alexei V Arbuznikov
- Institut fur Anorganische Chemie, Universitat Wurzburg, Am Hubland, D-97074 Wurzburg, Germany.
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39
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Brecht M, van Gastel M, Buhrke T, Friedrich B, Lubitz W. Direct Detection of a Hydrogen Ligand in the [NiFe] Center of the Regulatory H2-Sensing Hydrogenase from Ralstonia eutropha in Its Reduced State by HYSCORE and ENDOR Spectroscopy. J Am Chem Soc 2003; 125:13075-83. [PMID: 14570480 DOI: 10.1021/ja036624x] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulatory H2-sensing [NiFe] hydrogenase of the beta-proteobacterium Ralstonia eutropha displays an Ni-C "active" state after reduction with H2 that is very similar to the reduced Ni-C state of standard [NiFe] hydrogenases. Pulse electron nuclear double resonance (ENDOR) and four-pulse ESEEM (hyperfine sublevel correlation, HYSCORE) spectroscopy are applied to obtain structural information on this state via detection of the electron-nuclear hyperfine coupling constants. Two proton hyperfine couplings are determined by analysis of ENDOR spectra recorded over the full magnetic field range of the EPR spectrum. These are associated with nonexchangeable protons and belong to the beta-CH(2) protons of a bridging cysteine of the NiFe center. The signals of a third proton exhibit a large anisotropic coupling (Ax = 18.4 MHz, Ay = -10.8 MHz, Az = -18 MHz). They disappear from the 1H region of the ENDOR spectra after exchange of H2O with 2H2O and activation with 2H2 instead of H2 gas. They reappear in the 2H region of the ENDOR and HYSCORE spectra. Based on a comparison with the spectroscopically similar [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F, for which the g-tensor orientation of the Ni-C state with respect to the crystal structure is known (Foerster et al. J. Am. Chem. Soc. 2003, 125, 83-93), an assignment of the 1H hyperfine couplings is proposed. The exchangeable proton resides in a bridging position between the Ni and Fe and is assigned to a formal hydride ion. After illumination at low temperature (T = 10 K), the Ni-L state is formed. For the Ni-L state, the strong hyperfine coupling observed for the exchangeable hydrogen in Ni-C is lost, indicating a cleavage of the metal-hydride bond(s). These experiments give first direct information on the position of hydrogen binding in the active NiFe center of the regulatory hydrogenase. It is proposed that such a binding situation is also present in the active Ni-C state of standard hydrogenases.
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Affiliation(s)
- Marc Brecht
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Fakultät für Mathematik und Naturwissenschaften, Technische Universität Berlin, D-10623 Berlin, Germany
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40
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Saladino AC, Larsen SC. Relativistic DFT Calculations of Copper Hyperfine Coupling Constants: Effect of Spin−Orbit Coupling. J Phys Chem A 2003. [DOI: 10.1021/jp022671k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Sarah C. Larsen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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41
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Hsieh CH, Hsu IJ, Lee CM, Ke SC, Wang TY, Lee GH, Wang Y, Chen JM, Lee JF, Liaw WF. Nickel complexes of o-amidochalcogenophenolate(2-)/o-iminochalcogenobenzosemiquinonate(1-) pi-radical: synthesis, structures, electron spin resonance, and x-ray absorption spectroscopic evidence. Inorg Chem 2003; 42:3925-33. [PMID: 12793831 DOI: 10.1021/ic034211r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preparation of complexes trans-[Ni(-SeC(6)H(4)-o-NH-)(2)](-) (1), cis-[Ni(-TeC(6)H(4)-o-NH-)(2)](-) (2), trans-[Ni(-SC(6)H(4)-o-NH-)(2)](-) (3), and [Ni(-SC(6)H(4)-o-S-)(2)](-) (4) by oxidative addition of 2-aminophenyl dichalcogenides to anionic [Ni(CO)(SePh)(3)](-) proves to be a successful approach in this direction. The cis arrangement of the two tellurium atoms in complex 2 is attributed to the intramolecular Te.Te contact interaction (Te.Te contact distance of 3.455 A). The UV-vis electronic spectra of complexes 1 and 2 exhibit an intense absorption at 936 and 942 nm, respectively, with extinction coefficient epsilon > 10000 L mol(-)(1) cm(-)(1). The observed small g anisotropy, the principal g values at g(1) = 2.036, g(2) = 2.062, and g(3) = 2.120 for 1 and g(1) = 2.021, g(2) = 2.119, and g(3) = 2.250 for 2, respectively, indicates the ligand radical character accompanied by the contribution of the singly occupied d orbital of Ni(III). The X-ray absorption spectra of all four complexes show L(III) peaks at approximately 854.5 and approximately 853.5 eV. This may indicate a variation of contribution of the Ni(II)-Ni(III) valence state. According to the DFT calculation, the unpaired electron of complex 1 and 2 is mainly distributed on the 3d(xz)() orbital of the nickel ion and on the 4p(z)() orbital of selenium (tellurium, 5p(z)()) as well as the 2p(z)() orbital of nitrogen of the ligand. On the basis of X-ray structural data, UV-vis absorption, electron spin resonance, magnetic properties, DFT computation, and X-ray absorption (K- and L-edge) spectroscopy, the monoanionic trans-[Ni(-SeC(6)H(4)-o-NH-)(2)](-) and cis-[Ni(-TeC(6)H(4)-o-NH-)(2)](-) complexes are appositely described as a resonance hybrid form of Ni(III)-bis(o-amidochalcogenophenolato(2-)) and Ni(II)-(o-amidochalcogenophenolato(2-))-(o-iminochalcogenobenzosemiquinonato(1-) pi-radical; i.e., complexes 1 and 2 contain delocalized oxidation levels of the nickel ion and ligands.
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Affiliation(s)
- Chung-Hung Hsieh
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan
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42
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Saladino AC, Larsen SC. Density Functional Theory Calculations of Nitrogen Hyperfine and Quadrupole Coupling Constants in Oxovanadium(IV) Complexes. J Phys Chem A 2003. [DOI: 10.1021/jp030051t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sarah C. Larsen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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43
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Neese F. Metal and ligand hyperfine couplings in transition metal complexes: The effect of spin–orbit coupling as studied by coupled perturbed Kohn–Sham theory. J Chem Phys 2003. [DOI: 10.1063/1.1540619] [Citation(s) in RCA: 335] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Saladino AC, Larsen SC. Density Functional Theory Calculations of the Electron Paramagnetic Resonance Parameters for VO2+ Complexes. J Phys Chem A 2003. [DOI: 10.1021/jp022297o] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Sarah C. Larsen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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45
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Neese F. Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds: EPR and Mössbauer properties. Curr Opin Chem Biol 2003; 7:125-35. [PMID: 12547437 DOI: 10.1016/s1367-5931(02)00006-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently developed theoretical methods to predict EPR and Mössbauer parameters open the way for close interactions between theorists and experimentalists to elucidate the geometric and electronic structures of metalloenzymes and model complexes and to obtain insight into their reactive properties. Spectral calculations (g-values, hyperfine couplings, zero-field splittings, isomer shifts and quadrupole splittings) are also a means to validate theoretical approaches and therefore complement the prediction of geometries, reaction energies and transition states.
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Affiliation(s)
- Frank Neese
- Max-Planck Institut für Strahlenchemie, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.
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46
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Foerster S, Stein M, Brecht M, Ogata H, Higuchi Y, Lubitz W. Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Am Chem Soc 2003; 125:83-93. [PMID: 12515509 DOI: 10.1021/ja027522u] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the catalytic cycle of [NiFe] hydrogenase the paramagnetic Ni-C intermediate is of key importance, since it is believed to carry the substrate hydrogen, albeit in a yet unknown geometry. Upon illumination at low temperatures, Ni-C is converted to the so-called Ni-L state with markedly different spectroscopic parameters. It is suspected that Ni-L has lost the "substrate hydrogen". In this work, both paramagnetic states have been generated in single crystals obtained from the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. Evaluation of the orientation dependent spectra yielded the magnitudes of the g tensors and their orientations in the crystal axes system for both Ni-C and Ni-L. The g tensors could further be related to the atomic structure by comparison with the X-ray crystallographic structure of the reduced enzyme. Although the g tensor magnitudes of Ni-C and Ni-L are quite different, the orientations of the resulting g tensors are very similar but differ from those obtained earlier for Ni-A and Ni-B (Trofanchuk et al. J. Biol. Inorg. Chem. 2000, 5, 36-44). The g tensors were also calculated by density functional theory (DFT) methods using various structural models of the active site. The calculated g tensor of Ni-C is, concerning magnitudes and orientation, in good agreement with the experimental one for a formal Ni(III) oxidation state with a hydride (H(-)) bridge between the Ni and the Fe atom. Satisfying agreement is obtained for the Ni-L state when a formal Ni(I) oxidation state is assumed for this species with a proton (H(+)) removed from the bridge between the nickel and the iron atom.
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Affiliation(s)
- Stefanie Foerster
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Fakultät für Mathematik und Naturwissenschaften, Technische Universität Berlin, D-10623 Berlin, Germany
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47
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Saladino AC, Larsen SC. Computational Study of the Effect of the Imidazole Ring Orientation on the EPR Parameters for Vanadyl−Imidazole Complexes. J Phys Chem A 2002. [DOI: 10.1021/jp0215163] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Sarah C. Larsen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
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48
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Stadler C, de Lacey AL, Hernández B, Fernández VM, Conesa JC. Density functional calculations for modeling the oxidized states of the active site of nickel-iron hydrogenases. 1. Verification of the method with paramagnetic Ni and Co complexes. Inorg Chem 2002; 41:4417-23. [PMID: 12184758 DOI: 10.1021/ic020015t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ZORA relativistic DFT calculations are presented which aim to reproduce geometric structures and EPR properties of [Ni(mnt)(2)](-) (H(2)mnt = maleonitrildithiol), two other paramagnetic low-spin Ni(III) complexes, and an asymmetric paramagnetic Co(II) complex. The study tests the accuracy of the computational method as a prior step to the modeling of the geometric and electronic structure of the active site of NiFe hydrogenases in its EPR-active oxidized states Ni-A and Ni-B. Systematic deviations from experiment are found for the calculated g-values; relative differences among them are, however, well reproduced. Because no significant improvements have been achieved by using larger basis sets or more sophisticated functionals, g-values may be calculated rather rapidly at the VWN level. This is most important for the modeling of the active site of NiFe hydrogenases because its complexity does not permit calculations at high levels of theory. For [Ni(mnt)(2)](-), excellent agreement between calculated and experimental results is obtained for the (14)N quadrupole coupling, whereas the calculated hyperfine couplings are not always in good agreement with experimental data.
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Affiliation(s)
- Christian Stadler
- Instituto de Catálisis y Petroleoquímica, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain
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49
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Kaupp M, Reviakine R, Malkina OL, Arbuznikov A, Schimmelpfennig B, Malkin VG. Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators. J Comput Chem 2002; 23:794-803. [PMID: 12012356 DOI: 10.1002/jcc.10049] [Citation(s) in RCA: 168] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report the first implementation of the calculation of electronic g-tensors by density functional methods with hybrid functionals. Spin-orbit coupling is treated by the atomic meanfield approximation. g-Tensors for a set of small main group radicals and for a series of ten 3d and two 4d transition metal complexes have been compared using the local density approximation (VWN functional), the generalized gradient approximation (BP86 functional), as well as B3-type (B3PW91) and BH-type (BHPW91) hybrid functionals. For main group radicals, the effect of exact-exchange mixing is small. In contrast, significant differences between the various functionals arise for transition metal complexes. As has been shown previously, local and in particular gradient-corrected functionals tend to underestimate the "paramagnetic" contributions to the g-tensors in these cases and thereby recover only about 40-50% of the range of experimental g-tensor components. This is improved to ca. 60% by the B3PW91 functional, which also gives slightly reduced standard deviations. The range increases to almost 100% using the half-and-half functional BHPW91. However, the quality of the correlation with experimental data worsens due to a significant overestimate of some intermediate g-tensor values. The worse performance of the BHPW91 functional in these cases is accompanied by spin contamination. Although none of the functionals tested thus appears to be ideal for the treatment of electronic g-tensors in transition metal complexes, the B3PW91 hybrid functional exhibited the overall most satisfactory performance. Apart from the validation of hybrid functionals, some aspects in the treatment of spin-orbit contributions to the g-tensor are discussed.
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Affiliation(s)
- Martin Kaupp
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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50
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Neyman KM, Ganyushin DI, Matveev AV, Nasluzov VA. Calculation of Electronic g-Tensors Using a Relativistic Density Functional Douglas−Kroll Method. J Phys Chem A 2002. [DOI: 10.1021/jp0204253] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Konstantin M. Neyman
- Institut für Physikalische und Theoretische Chemie, Technische Universität Munchen, 85747 Garching, Germany
| | - Dmitri I. Ganyushin
- Institut für Physikalische und Theoretische Chemie, Technische Universität Munchen, 85747 Garching, Germany
| | - Alexei V. Matveev
- Institut für Physikalische und Theoretische Chemie, Technische Universität Munchen, 85747 Garching, Germany
| | - Vladimir A. Nasluzov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russia
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