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Rovaletti A, Ryde U, Moro G, Cosentino U, Greco C. How general is the effect of the bulkiness of organic ligands on the basicity of metal-organic catalysts? H 2-evolving Mo oxides/sulphides as case studies. Phys Chem Chem Phys 2022; 24:29471-29479. [PMID: 36437742 DOI: 10.1039/d2cp03996f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Tailoring the activity of an organometallic catalyst usually requires a targeted ligand design. Tuning the ligand bulkiness and tuning the electronic properties are popular approaches, which are somehow interdependent because substituents of different sizes within ligands can determine inter alia the occurrence of different degrees of inductive effects. Ligand basicity, in particular, turned out to be a key property for the modulation of protonation reactions occurring in vacuo at the metals in complexes bearing organophosphorus ligands; however, when the same reactions take place in a polar organic solvent, their energetics becomes dependent on the trade-off between ligand basicity and bulkiness, with the polarity of the solvent playing a key role in this regard [Bancroft et al., Inorg. Chem., 1986, 25, 3675; Rovaletti et al., J. Phys. Org. Chem., 2018, 31, e3748]. In the present contribution, we carried out molecular dynamics and density functional theory calculations on water-soluble Mo-based catalysts for proton reduction, in order to study the energetics of protonation reactions in complexes where the incipient proton binds a catalytically active ligand (i.e., an oxide or a disulphide). We considered complexes either soaked in water or in a vacuum, and featuring N-based ancillary ligands of different bulkiness (i.e. cages constituted either by pyridine or isoquinoline moieties). Our results show that the energetics of protonation events can be affected by ancillary ligand bulkiness even when the metal center does not play the role of the H+ acceptor. In vacuo, protonation at the O or S atom in the α position relative to the metal in complexes featuring the bulky isoquinoline-based ligand is more favored by around 10 kcal mol-1 when compared to the case of the pyridine-based counterparts, a difference that is almost zero when the same reactions occur in water. Such an outcome is rationalized in light of the different electrostatic properties of complexes bearing ancillary ligands of different sizes. The overall picture from theory indicates that such effects of ligand bulkiness can be relevant for the design of green chemistry catalysts that undergo protonation steps in water solutions.
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Affiliation(s)
- Anna Rovaletti
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, Milano, Italy.
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Giorgio Moro
- Department of Biotechnology and Biosciences, Milano-Bicocca University, Piazza della Scienza 2, Milano, Italy
| | - Ugo Cosentino
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, Milano, Italy.
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, Milano, Italy.
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2
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Felbek C, Arrigoni F, de Sancho D, Jacq-Bailly A, Best RB, Fourmond V, Bertini L, Léger C. Mechanism of Hydrogen Sulfide-Dependent Inhibition of FeFe Hydrogenase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christina Felbek
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20080 Donostia-San Sebastián, Spain
| | - Aurore Jacq-Bailly
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, Maryland 20892-0520, United States
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille Cedex 20 13402, France
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3
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The Photochemistry of Fe2(S2C3H6)(CO)6(µ-CO) and Its Oxidized Form, Two Simple [FeFe]-Hydrogenase CO-Inhibited Models. A DFT and TDDFT Investigation. INORGANICS 2021. [DOI: 10.3390/inorganics9020016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
FeIFeI Fe2(S2C3H6)(CO)6(µ-CO) (1a–CO) and its FeIFeII cationic species (2a+–CO) are the simplest model of the CO-inhibited [FeFe] hydrogenase active site, which is known to undergo CO photolysis within a temperature-dependent process whose products and mechanism are still a matter of debate. Using density functional theory (DFT) and time-dependent density functional theory (TDDFT) computations, the ground state and low-lying excited-state potential energy surfaces (PESs) of 1a–CO and 2a+–CO have been explored aimed at elucidating the dynamics of the CO photolysis yielding Fe2(S2C3H6)(CO)6 (1a) and [Fe2(S2C3H6)(CO)6]+ (2a+), two simple models of the catalytic site of the enzyme. Two main results came out from these investigations. First, a–CO and 2a+–CO are both bound with respect to any CO dissociation with the lowest free energy barriers around 10 kcal mol−1, suggesting that at least 2a+–CO may be synthesized. Second, focusing on the cationic form, we found at least two clear excited-state channels along the PESs of 2a+–CO that are unbound with respect to equatorial CO dissociation.
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Kretz B, Egger DA. Accurate Molecular Geometries in Complex Excited-State Potential Energy Surfaces from Time-Dependent Density Functional Theory. J Chem Theory Comput 2021; 17:357-366. [PMID: 33284603 DOI: 10.1021/acs.jctc.0c00858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interplay of electronic excitations and structural changes in molecules impacts nonradiative decay and charge transfer in the excited state, thus influencing excited-state lifetimes and photocatalytic reaction rates in optoelectronic and energy devices. To capture such effects requires computational methods providing an accurate description of excited-state potential energy surfaces and geometries. We suggest time-dependent density functional theory using optimally tuned range-separated hybrid (OT-RSH) functionals as an accurate approach to obtain excited-state molecular geometries. We show that OT-RSH provides accurate molecular geometries in excited-state potential energy surfaces that are complex and involve an interplay of local and charge-transfer excitations, for which conventional semilocal and hybrid functionals fail. At the same time, the nonempirical OT-RSH approach maintains the high accuracy of parametrized functionals (e.g., B3LYP) for predicting excited-state geometries of small organic molecules showing valence excited states.
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Affiliation(s)
- Bernhard Kretz
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - David A Egger
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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5
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Abul-Futouh H, Almazahreh LR, Abaalkhail SJ, Görls H, Stripp ST, Weigand W. Ligand effects on structural, protophilic and reductive features of stannylated dinuclear iron dithiolato complexes. NEW J CHEM 2021. [DOI: 10.1039/d0nj04790b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and characterization of Fe2(CO)5(L){μ-(SCH2)2SnMe2} (L = PPh3 (2) and P(OMe)3 (3)) derived from the parent hexacarbonyl complex Fe2(CO)6{μ-(SCH2)2}SnMe2 (1) are reported.
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Affiliation(s)
- Hassan Abul-Futouh
- Department of Pharmacy
- Al-Zaytoonah University of Jordan
- Amman 11733
- Jordan
| | - Laith R. Almazahreh
- ERCOSPLAN Ingenieurbüro Anlagentechnik GmbH
- 99096 Erfurt
- Germany
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
| | - Sara J. Abaalkhail
- Department of Pharmacy
- Al-Zaytoonah University of Jordan
- Amman 11733
- Jordan
| | - Helmar Görls
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
- 07743 Jena
- Germany
| | - Sven T. Stripp
- Bioinorganic Spectroscopy
- Department of Physics
- Freie Universität Berlin
- 1495 Berlin
- Germany
| | - Wolfgang Weigand
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
- 07743 Jena
- Germany
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6
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Abstract
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The
energetics for proton reduction in FeFe-hydrogenase has been
reinvestigated by theoretical modeling, in light of recent experiments.
Two different mechanisms have been considered. In the first one, the
bridging hydride position was blocked by the enzyme, which is the
mechanism that has been supported by a recent spectroscopic study
by Cramer et al. A major difficulty in
the present study to agree with experimental energetics was to find
the right position for the added proton in the first reduction step.
It was eventually found that the best position was as a terminal hydride
on the distal iron, which has not been suggested in any of the recent,
experimentally based mechanisms. The lowest transition state was surprisingly
found to be a bond formation between a proton on a cysteine and the
terminal hydride. This type of TS is similar to the one for heterolytic
H2 cleavage in NiFe hydrogenase. The second mechanism investigated
here is not supported by the present calculations or the recent experiments
by Cramer et al., but was still studied as an interesting comparison.
In that mechanism, the formation of the bridging hydride was allowed.
The H–H formation barrier is only 3.6 kcal/mol higher than
for the first mechanism, but there are severe problems concerning
the motion of the protons.
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Affiliation(s)
- Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory for Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Media, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
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Mai S, González L. Molecular Photochemistry: Recent Developments in Theory. Angew Chem Int Ed Engl 2020; 59:16832-16846. [PMID: 32052547 PMCID: PMC7540682 DOI: 10.1002/anie.201916381] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/12/2020] [Indexed: 12/16/2022]
Abstract
Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.
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Affiliation(s)
- Sebastian Mai
- Photonics InstituteVienna University of TechnologyGusshausstrasse 27–291040ViennaAustria
| | - Leticia González
- Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Strasse 171090ViennaAustria
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8
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Cappelluti F, Bencivenni L, Guidoni L. Spin-symmetrised structures and vibrational frequencies of iron-sulfur clusters. Phys Chem Chem Phys 2020; 22:16655-16664. [PMID: 32667376 DOI: 10.1039/d0cp01591a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calculations of relaxed geometries of multi-centre transition metal compounds are routinely carried out using Broken Symmetry Density Functional Theory. The resulting low-spin open shell electronic state is described by one single Slater determinant and is affected by spin contamination. To alleviate this symmetry breaking, the Extended Broken Symmetry (EBS) approach can be applied to complexes with an arbitrary number of local high-spin metal ions. The actual symmetry is therefore reconstructed through minimization of an effective Hamiltonian leading to a relaxed geometry consistent with the magnetic couplings. In the present work we extend the approach already introduced by [Chu et al., J. Chem. Theory Comput., 2017, 13, 4675] to the calculation of vibrational frequencies. As prototypes we have considered the iron-sulfur clusters Fe2S2Cl42- and Fe4S4Cl4. We have compared the results obtained for different spin states (high spin, broken symmetry and extended broken symmetry) and by using different DFT functionals (B3LYP, OPBE, BP, M06 and B2PLYP) and a post-HF method (SCS-MP2). The data have shown that for specific vibrational modes the EBS technique produces shifts up to 40 cm-1 with respect to the routinely used Broken Symmetry approach, indicating that the use of a consistent spin-symmetrised state is a crucial ingredient for an accurate description of vibrational properties, as certified by the comparison with the experimental data for the Fe2S2Cl42- cluster.
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Affiliation(s)
- Francesco Cappelluti
- University of L'Aquila - Department of Engineering, Information Science and Mathematics, via Vetoio (Coppito), L'Aquila, Italy
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9
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Mai S, González L. Molekulare Photochemie: Moderne Entwicklungen in der theoretischen Chemie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sebastian Mai
- Institut für Photonik Technische Universität Wien Gußhausstraße 27–29 1040 Wien Österreich
| | - Leticia González
- Institut für theoretische Chemie Fakultät für Chemie Universität Wien Währinger Straße 17 1090 Wien Österreich
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10
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Land H, Senger M, Berggren G, Stripp ST. Current State of [FeFe]-Hydrogenase Research: Biodiversity and Spectroscopic Investigations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01614] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Henrik Land
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Moritz Senger
- Physical Chemistry, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Sven T. Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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11
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Villa AM, Doglia SM, De Gioia L, Bertini L, Natalello A. Anomalous Intrinsic Fluorescence of HCl and NaOH Aqueous Solutions. J Phys Chem Lett 2019; 10:7230-7236. [PMID: 31689111 DOI: 10.1021/acs.jpclett.9b02163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The unique properties of liquid water mainly arise from its hydrogen bond network. The geometry and dynamics of this network play a key role in shaping the characteristics of soft matter, from simple solutions to biosystems. Here we report an anomalous intrinsic fluorescence of HCl and NaOH aqueous solutions at room temperature that shows important differences in the excitation and emission bands between the two solutes. From ab initio time-dependent density functional theory modeling we propose that fluorescence emission could originate from hydrated ion species contained in transient cavities of the bulk solvent. These cavities, which are characterized by a stiff surface, could provide an environment that, upon trapping the excited state, suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway.
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Affiliation(s)
- Anna Maria Villa
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
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12
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Caserta G, Papini C, Adamska-Venkatesh A, Pecqueur L, Sommer C, Reijerse E, Lubitz W, Gauquelin C, Meynial-Salles I, Pramanik D, Artero V, Atta M, Del Barrio M, Faivre B, Fourmond V, Léger C, Fontecave M. Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O 2 Resistance and Catalytic Bias? J Am Chem Soc 2018; 140:5516-5526. [PMID: 29595965 DOI: 10.1021/jacs.8b01689] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe]-hydrogenases, HydAs, are unique biocatalysts for proton reduction to H2. However, they suffer from a number of drawbacks for biotechnological applications: size, number and diversity of metal cofactors, oxygen sensitivity. Here we show that HydA from Megasphaera elsdenii (MeHydA) displays significant resistance to O2. Furthermore, we produced a shorter version of this enzyme (MeH-HydA), lacking the N-terminal domain harboring the accessory FeS clusters. As shown by detailed spectroscopic and biochemical characterization, MeH-HydA displays the following interesting properties. First, a functional active site can be assembled in MeH-HydA in vitro, providing the enzyme with excellent hydrogenase activity. Second, the resistance of MeHydA to O2 is conserved in MeH-HydA. Third, MeH-HydA is more biased toward proton reduction than MeHydA, as the result of the truncation changing the rate limiting steps in catalysis. This work shows that it is possible to engineer HydA to generate an active hydrogenase that combines the resistance of the most resistant HydAs and the simplicity of algal HydAs, containing only the H-cluster.
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Affiliation(s)
- Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Charles Gauquelin
- LISBP , Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Melisa Del Barrio
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
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13
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del Barrio M, Sensi M, Orain C, Baffert C, Dementin S, Fourmond V, Léger C. Electrochemical Investigations of Hydrogenases and Other Enzymes That Produce and Use Solar Fuels. Acc Chem Res 2018. [PMID: 29517230 DOI: 10.1021/acs.accounts.7b00622] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many enzymes that produce or transform small molecules such as O2, H2, and CO2 embed inorganic cofactors based on transition metals. Their active site, where the chemical reaction occurs, is buried in and protected by the protein matrix, and connected to the solvent in several ways: chains of redox cofactors mediate long-range electron transfer; static or dynamic tunnels guide the substrate, product and inhibitors; amino acids and water molecules transfer protons. The catalytic mechanism of these enzymes is therefore delocalized over the protein and involves many different steps, some of which determine the response of the enzyme under conditions of stress (extreme redox conditions, presence of inhibitors, light), the catalytic rates in the two directions of the reaction and their ratio (the "catalytic bias"). Understanding all the steps in the catalytic cycle, including those that occur on sites of the protein that are remote from the active site, requires a combination of biochemical, structural, spectroscopic, theoretical, and kinetic methods. Here we argue that kinetics should be used to the fullest extent, by extracting quantitative information from the comparison of data and kinetic models and by exploring the combination of experimental kinetics and theoretical chemistry. In studies of these catalytic mechanisms, direct electrochemistry, the technique which we use and contribute to develop, has become unescapable. It simply consists in monitoring the changes in activity of an enzyme that is wired to an electrode by recording an electric current. We have described kinetic models that can be used to make sense of these data and to learn about various aspects of the mechanism that are difficult to probe using more conventional methods: long-range electron transfer, diffusion along gas channels, redox-driven (in)activations, active site chemistry and photoreactivity under conditions of turnover. In this Account, we highlight a few results that illustrate our approach. We describe how electrochemistry can be used to monitor substrate and inhibitor diffusion along the gas channels of hydrogenases and we discuss how the kinetics of intramolecular diffusion relates to global properties such as resistance to oxygen and catalytic bias. The kinetics and/or thermodynamics of intramolecular electron transfer may also affect the catalytic bias, the catalytic potentials on either side of the equilibrium potential, and the overpotentials for catalysis (defined as the difference between the catalytic potentials and the open circuit potential). This is understood by modeling the shape of the steady-state catalytic response of the enzyme. Other determinants of the catalytic rate, such as domain motions, have been probed by examining the transient catalytic response recorded at fast scan rates. Last, we show that combining electrochemical investigations and MD, DFT, and TD-DFT calculations is an original way of probing the reactivity of the H-cluster of hydrogenase, in particular its reactions with CO, O2, and light. This approach contrasts with the usual strategy which aims at stabilizing species that are presumed to be catalytic intermediates, and determining their structure using spectroscopic or structural methods.
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Affiliation(s)
- Melisa del Barrio
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Matteo Sensi
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Christophe Orain
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Carole Baffert
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Sébastien Dementin
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Vincent Fourmond
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
| | - Christophe Léger
- Aix Marseille Univ., CNRS, BIP, Laboratoire
de Bioénergétique et Ingénierie des Protéines,
UMR7281, Marseille France
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14
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Jia AQ, Tang LH, Dong XP, Xin Z, Zhang QF. Syntheses, structures and reactivity of dinuclear organoruthenium-nickel complexes with N , N ′-bis(2-thiobenzylidene)-1,2-phenylenediaminato (tsalphen) ligand. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Bertini L, Breglia R, Lambrughi M, Fantucci P, De Gioia L, Borsari M, Sola M, Bortolotti CA, Bruschi M. Catalytic Mechanism of Fungal Lytic Polysaccharide Monooxygenases Investigated by First-Principles Calculations. Inorg Chem 2017; 57:86-97. [PMID: 29232119 DOI: 10.1021/acs.inorgchem.7b02005] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes that facilitate the degradation of recalcitrant polysaccharides by the oxidative cleavage of glycosidic bonds. They are gaining rapidly increasing attention as key players in biomass conversion, especially for the production of second-generation biofuels. Elucidation of the detailed mechanism of the LPMO reaction is a major step toward the assessment and optimization of LPMO efficacy in industrial biotechnology, paving the way to utilization of sustainable fuel sources. Here, we used density functional theory calculations to study the reaction pathways suggested to date, exploiting a very large active-site model for a fungal AA9 LPMO and using a celloheptaose unit as a substrate mimic. We identify a copper oxyl intermediate as being responsible for H-atom abstraction from the substrate, followed by a rapid, water-assisted hydroxyl rebound, leading to substrate hydroxylation.
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Affiliation(s)
- Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, University of Milan-Bicocca , Piazza della Scienza 1, 20126 Milan, Italy
| | | | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | | | | | | | - Maurizio Bruschi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca , Piazza della Scienza 1, 20126 Milan, Italy
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16
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Chu S, Bovi D, Cappelluti F, Orellana AG, Martin H, Guidoni L. Effects of Static Correlation between Spin Centers in Multicenter Transition Metal Complexes. J Chem Theory Comput 2017; 13:4675-4683. [PMID: 28763210 DOI: 10.1021/acs.jctc.7b00316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multicenter transition metal complexes are the key moieties of many processes in chemistry, biochemistry, and materials science such as in the active sites of enzymes, molecular catalysts, and biological electron carriers. Their electronic structure, often characterized by high-spin-polarized metal sites, is a challenge for theoretical chemists because of their high degree of dynamical and static correlation. Static correlation is necessary both for the appropriate description of the metal-ligand bonding and for a correct description of the multideterminant character arising from the magnetic interactions between spin centers. Density functional theory (DFT) is usually applied using a single-determinant broken-symmetry state that is lacking the correct spin symmetry when the ground state has total low-spin character. To alleviate this drawback, we use the extended broken-symmetry (EBS) approach to derive approximate ground-state energies and, for the first time, forces for the correctly symmetric ground state of an arbitrary number of spin centers within the framework of the Heisenberg-Dirac-van Vleck Hamiltonian. Remarkably, the proposed procedure supplies relaxed geometries that are fully consistent with the calculated J-coupling constants. We apply the method to investigate the relaxed geometrical structure of the low-spin ground state of iron-sulfur clusters with two, three, and four iron centers. We observed significant differences in both geometrical parameters and coupling constant J between the symmetrized ground state, the high-spin, and the broken-symmetry optimized structures. These changes are often comparable with the differences observed by using different functionals, and the use of EBS always improves the description of the studied systems. It will be therefore important to include it in any DFT attempt to quantitatively describe multicenter transition metal complexes in the future.
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Affiliation(s)
- Shibing Chu
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , Via Vetoio (Coppito), 67100 L'Aquila, Italy
| | - Daniele Bovi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , Via Vetoio (Coppito), 67100 L'Aquila, Italy
| | | | | | - Henry Martin
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , Via Vetoio (Coppito), 67100 L'Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , Via Vetoio (Coppito), 67100 L'Aquila, Italy
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17
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Sensi M, Baffert C, Fradale L, Gauquelin C, Soucaille P, Meynial-Salles I, Bottin H, de Gioia L, Bruschi M, Fourmond V, Léger C, Bertini L. Photoinhibition of FeFe Hydrogenase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02252] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matteo Sensi
- Aix Marseille University, CNRS, BIP UMR 7281, 13402 CEDEX 20 Marseille, France
- Department
of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Carole Baffert
- Aix Marseille University, CNRS, BIP UMR 7281, 13402 CEDEX 20 Marseille, France
| | - Laura Fradale
- Aix Marseille University, CNRS, BIP UMR 7281, 13402 CEDEX 20 Marseille, France
| | - Charles Gauquelin
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135
CNRS:UMR 5504, Avenue
de Rangueil, 31077 Toulouse, France
| | - Philippe Soucaille
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135
CNRS:UMR 5504, Avenue
de Rangueil, 31077 Toulouse, France
| | - Isabelle Meynial-Salles
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792,135
CNRS:UMR 5504, Avenue
de Rangueil, 31077 Toulouse, France
| | - Hervé Bottin
- Institut
de Biologie Intégrative de la Cellule (I2BC), Institut Frédéric
Joliot, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198 CEDEX Gif-Sur-Yvette, France
| | - Luca de Gioia
- Department
of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Maurizio Bruschi
- Department
of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della
Scienza 1, 20126 Milan, Italy
- Department
of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Vincent Fourmond
- Aix Marseille University, CNRS, BIP UMR 7281, 13402 CEDEX 20 Marseille, France
| | - Christophe Léger
- Aix Marseille University, CNRS, BIP UMR 7281, 13402 CEDEX 20 Marseille, France
| | - Luca Bertini
- Department
of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
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