1
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Sirohiwal A, Gamiz-Hernandez AP, Kaila VRI. Mechanistic Principles of Hydrogen Evolution in the Membrane-Bound Hydrogenase. J Am Chem Soc 2024; 146:18019-18031. [PMID: 38888987 PMCID: PMC11228991 DOI: 10.1021/jacs.4c04476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
The membrane-bound hydrogenase (Mbh) from Pyrococcus furiosus is an archaeal member of the Complex I superfamily. It catalyzes the reduction of protons to H2 gas powered by a [NiFe] active site and transduces the free energy into proton pumping and Na+/H+ exchange across the membrane. Despite recent structural advances, the mechanistic principles of H2 catalysis and ion transport in Mbh remain elusive. Here, we probe how the redox chemistry drives the reduction of the proton to H2 and how the catalysis couples to conformational dynamics in the membrane domain of Mbh. By combining large-scale quantum chemical density functional theory (DFT) and correlated ab initio wave function methods with atomistic molecular dynamics simulations, we show that the proton transfer reactions required for the catalysis are gated by electric field effects that direct the protons by water-mediated reactions from Glu21L toward the [NiFe] site, or alternatively along the nearby His75L pathway that also becomes energetically feasible in certain reaction steps. These local proton-coupled electron transfer (PCET) reactions induce conformational changes around the active site that provide a key coupling element via conserved loop structures to the ion transport activity. We find that H2 forms in a heterolytic proton reduction step, with spin crossovers tuning the energetics along key reaction steps. On a general level, our work showcases the role of electric fields in enzyme catalysis and how these effects are employed by the [NiFe] active site of Mbh to drive PCET reactions and ion transport.
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Affiliation(s)
- Abhishek Sirohiwal
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ana P. Gamiz-Hernandez
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry
and Biophysics, Stockholm University, Stockholm 10691, Sweden
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2
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Jørgensen FK, Delcey MG, Hedegård ED. Perspective: multi-configurational methods in bio-inorganic chemistry. Phys Chem Chem Phys 2024; 26:17443-17455. [PMID: 38868993 DOI: 10.1039/d4cp01297f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the electronic structure and properties of metalloproteins poses significant challenges due to the complex nature of their electronic configurations and strong correlation effects. Multiconfigurational quantum chemistry methods are, in principle, the most appropriate tools for addressing these challenges, offering the capability to capture the inherent multi-reference character and strong electron correlation present in bio-inorganic systems. Yet their computational cost has long hindered wider adoption, making methods such as density functional theory (DFT) the method of choice. However, advancements over the past decade have substantially alleviated this limitation, rendering multiconfigurational quantum chemistry methods more accessible and applicable to a wider range of bio-inorganic systems. In this perspective, we discuss some of these developments and how they have already been used to answer some of the most important questions in bio-inorganic chemistry. We also comment on ongoing developments in the field and how the future of the field may evolve.
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Affiliation(s)
- Frederik K Jørgensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Mickaël G Delcey
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Erik D Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
- Department of Chemistry, Lund University, Naturvetarvägen 14, 221 00 Lund, Sweden
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3
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Suremann NF, McCarthy BD, Gschwind W, Kumar A, Johnson BA, Hammarström L, Ott S. Molecular Catalysis of Energy Relevance in Metal-Organic Frameworks: From Higher Coordination Sphere to System Effects. Chem Rev 2023; 123:6545-6611. [PMID: 37184577 DOI: 10.1021/acs.chemrev.2c00587] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The modularity and synthetic flexibility of metal-organic frameworks (MOFs) have provoked analogies with enzymes, and even the term MOFzymes has been coined. In this review, we focus on molecular catalysis of energy relevance in MOFs, more specifically water oxidation, oxygen and carbon dioxide reduction, as well as hydrogen evolution in context of the MOF-enzyme analogy. Similar to enzymes, catalyst encapsulation in MOFs leads to structural stabilization under turnover conditions, while catalyst motifs that are synthetically out of reach in a homogeneous solution phase may be attainable as secondary building units in MOFs. Exploring the unique synthetic possibilities in MOFs, specific groups in the second and third coordination sphere around the catalytic active site have been incorporated to facilitate catalysis. A key difference between enzymes and MOFs is the fact that active site concentrations in the latter are often considerably higher, leading to charge and mass transport limitations in MOFs that are more severe than those in enzymes. High catalyst concentrations also put a limit on the distance between catalysts, and thus the available space for higher coordination sphere engineering. As transport is important for MOF-borne catalysis, a system perspective is chosen to highlight concepts that address the issue. A detailed section on transport and light-driven reactivity sets the stage for a concise review of the currently available literature on utilizing principles from Nature and system design for the preparation of catalytic MOF-based materials.
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Affiliation(s)
- Nina F Suremann
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Brian D McCarthy
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Wanja Gschwind
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Amol Kumar
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Ben A Johnson
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
- Technical University Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315 Straubing, Germany
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Sascha Ott
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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4
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Ruiz-Rodríguez MA, Cooper CD, Rocchia W, Casalegno M, López de los Santos Y, Raos G. Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode. J Phys Chem B 2022; 126:8777-8790. [PMID: 36269122 PMCID: PMC9639099 DOI: 10.1021/acs.jpcb.2c05371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.
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Affiliation(s)
| | - Christopher D. Cooper
- Department
of Mechanical Engineering and Centro Científico Tecnológico
de Valparaíso, Universidad Técnica
Federico Santa María, Valparaíso, 2340000, Chile
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, 16163Genova, Italy
| | - Mosè Casalegno
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy
| | - Yossef López de los Santos
- Centre
Armand-Frappier Santé, Biotechnologie, Institut national de
la recherche scientifique (INRS), Université
du Québec, Laval, QuébecHV7 1B7, Canada
| | - Guido Raos
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy,
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5
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Gorantla KR, Mallik BS. Catalytic Mechanism of Competing Proton Transfer Events from Water and Acetic Acid by [Co II(bpbH 2)Cl 2] for Water Splitting Processes. J Phys Chem A 2022; 126:1321-1328. [PMID: 35172100 DOI: 10.1021/acs.jpca.1c07353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We performed first principles simulations to explore the water reduction process of the cobalt complex [CoII(bpbH2)Cl2], where bpbH2 = N,N'-bis(2'-pyridine carboxamide)-1,2-benzene. We considered the sequence steps of electron reduction followed by the proton addition process to observe the hydrogen evolution process. An experimental study of the catalyst showed that the increase in the acetic acid concentration triggers catalytic current and reduction of Co(II) to Co(I), and protonation occurred, yielding a Co(III)-H intermediate. Therefore, we used water and acetic acid as the proton sources. We compare the proton transfer kinetics from both the water and acetic acid. The reduction potentials and proton transfer kinetics from water or acetic acid to the reaction center were studied in a DMF solvent through the implicit solvent model. The first proton transfer from the acetic acid is more favorable, forming a CoIII-H complex and further reducing to CoII-H. The second proton transfer from water to the CoII-H moiety requires less free energy than acetic acid and is the rate-limiting step. The nature of the reduction process is also examined through the charge analysis, which reveals that the ligand becomes softer due to the C═O groups.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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6
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Activation of Small Molecules and Hydrogenation of CO2 Catalyzed by Frustrated Lewis Pairs. Catalysts 2022. [DOI: 10.3390/catal12020201] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The chemistry of frustrated Lewis pair (FLP) is widely explored in the activation of small molecules, the hydrogenation of CO2, and unsaturated organic species. A survey of several experimental works on the activation of small molecules by FLPs and the related mechanistic insights into their reactivity from electronic structure theory calculation are provided in the present review, along with the catalytic hydrogenation of CO2. The mechanistic insight into H2 activation is thoroughly discussed, which may provide a guideline to design more efficient FLP for H2 activation. FLPs can activate other small molecules like, CO, NO, CO2, SO2, N2O, alkenes, alkynes, etc. by cooperative action of the Lewis centers of FLPs, as revealed by several computational analyses. The activation barrier of H2 and other small molecules by the FLP can be decreased by utilizing the aromaticity criterion in the FLP as demonstrated by the nucleus independent chemical shift (NICS) analysis. The term boron-ligand cooperation (BLC), which is analogous to the metal-ligand cooperation (MLC), is invoked to describe a distinct class of reactivity of some specific FLPs towards H2 activation.
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7
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Henriques Pereira DP, Leethaus J, Beyazay T, do Nascimento Vieira A, Kleinermanns K, Tüysüz H, Martin WF, Preiner M. Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD . FEBS J 2021; 289:3148-3162. [PMID: 34923745 PMCID: PMC9306933 DOI: 10.1111/febs.16329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
Hydrogen gas, H2, is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H2 is converted by hydrogenases into organically bound hydrides (H–), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H2. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors—possibly as a geochemical protoenzyme, a ‘geozyme’— at the origin of metabolism. To test this idea, we investigated the ability of H2 to reduce NAD+ in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H2, all three metals specifically reduce NAD+ to the biologically relevant form, 1,4‐NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40 °C. Using Henry's law, the partial pressure of H2 in our reactions corresponds to 3.6 mm, a concentration observed in many modern serpentinizing systems. While the reduction of NAD+ by Ni is strictly H2‐dependent, experiments in heavy water (2H2O) indicate that native Fe can reduce NAD+ both with and without H2. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H2‐dependent NAD+ reduction could have preceded the hydrogenase‐dependent reaction in evolution.
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Affiliation(s)
| | - Jana Leethaus
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Tugce Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Martina Preiner
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Utrecht University, The Netherlands
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8
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Zhu R, He L, Li Q, Huang T, Gao M, Jiang Q, Liu J, Cai A, Shi D, Gu L, He Q. Mechanism study of improving anaerobic co-digestion performance of waste activated sludge and food waste by Fe 3O 4. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113745. [PMID: 34547575 DOI: 10.1016/j.jenvman.2021.113745] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
A large amount of waste activated sludge (WAS) and food waste (FW) are produced every year in China. Anaerobic co-digestion is considered to be an effective way to solve this problem. This study applied FW/WAS mixture as co-substrate to create different digestive environment, aiming to understand the mechanism of Fe3O4 particles in promoting AD performance. The results showed that the addition of Fe3O4 presented various performances when facing different digestive acidification stress brought by different mixing ratios of WAS and FW. Methanogenic pathways and microbial communities varied with substrates' properties. For group A (WAS mono-digestion), the acetoclastic methanogens dominated, 20 mg/g VS (according to the iron element) Fe3O4 could promote methane production, while 200 mg/g VS Fe3O4 would inhibit microbial activity. The promoted methane production by Fe3O4 was attributable to the promotion of sludge hydrolysis. For group B (WAS: FW = 1:0.5, based on VS addition, similarly hereinafter), Fe3O4 triggered direct interspecific electron transfer (DIET) between bacteria and methanogens. For group C (WAS: FW = 1:1), the hydrogenotrophic methanogens dominated, bacteria excreted more non-conductive polysaccharides in EPS to resist unfavorable environment, thereby it prevented their contact with Fe3O4 particles. So, it was difficult for Fe3O4 to trigger DIET and promote the digestive performance of batch experiments in such condition.
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Affiliation(s)
- Ruilin Zhu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Linyan He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Qianyi Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - TingXuan Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Meng Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Qin Jiang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Junyan Liu
- Chongqing Three Gorges Water Drainage (Wulong) Co., Ltd, 130 Jianshe West Road, Wulong County, Chongqing, 408500, PR China
| | - Anrong Cai
- Chongqing Yuxi Water Co., Ltd, No. 36, Fenghuang Avenue, Yongchuan District, Chongqing, 402160, PR China
| | - Dezhi Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Li Gu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China.
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
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9
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Mühlbauer ME, Gamiz-Hernandez AP, Kaila VRI. Functional Dynamics of an Ancient Membrane-Bound Hydrogenase. J Am Chem Soc 2021; 143:20873-20883. [PMID: 34846879 PMCID: PMC8679088 DOI: 10.1021/jacs.1c09356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The membrane-bound
hydrogenase (Mbh) is a redox-driven Na+/H+ transporter
that employs the energy from hydrogen
gas (H2) production to catalyze proton pumping and Na+/H+ exchange across cytoplasmic membranes of archaea.
Despite a recently resolved structure of this ancient energy-transducing
enzyme [Yu et al. Cell2018, 173, 1636–1649], the molecular principles of its
redox-driven ion-transport mechanism remain puzzling and of major
interest for understanding bioenergetic principles of early cells.
Here we use atomistic molecular dynamics (MD) simulations in combination
with data clustering methods and quantum chemical calculations to
probe principles underlying proton reduction as well as proton and
sodium transport in Mbh from the hyperthermophilic archaeon Pyrococcus furiosus. We identify putative Na+ binding sites and proton pathways leading across the membrane
and to the NiFe-active center as well as conformational changes that
regulate ion uptake. We suggest that Na+ binding and protonation
changes at a putative ion-binding site couple to proton transfer across
the antiporter-like MbhH subunit by modulating the conformational
state of a conserved ion pair at the subunit interface. Our findings
illustrate conserved coupling principles within the complex I superfamily
and provide functional insight into archaeal energy transduction mechanisms.
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Affiliation(s)
- Max E Mühlbauer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.,Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.,Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
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10
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11
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Almazahreh LR, Arrigoni F, Abul-Futouh H, El-khateeb M, Görls H, Elleouet C, Schollhammer P, Bertini L, De Gioia L, Rudolph M, Zampella G, Weigand W. Proton Shuttle Mediated by (SCH 2) 2P═O Moiety in [FeFe]-Hydrogenase Mimics: Electrochemical and DFT Studies. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05563] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laith R. Almazahreh
- ERCOSPLAN Ingenieurbüro Anlagentechnik GmbH Arnstädter Straße 28, 99096 Erfurt, Germany
- Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität Jena, Humboldt Str. 8, 07743 Jena, Germany
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Hassan Abul-Futouh
- Department of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733 Jordan
| | - Mohammad El-khateeb
- Chemistry Department, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Helmar Görls
- Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität Jena, Humboldt Str. 8, 07743 Jena, Germany
| | - Catherine Elleouet
- UMR CNRS 6521, Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques, Cs 93837, 29238 CEDEX 3 Brest, France
| | - Philippe Schollhammer
- UMR CNRS 6521, Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques, Cs 93837, 29238 CEDEX 3 Brest, France
| | - Luca Bertini
- 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
| | - Manfred Rudolph
- Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität Jena, Humboldt Str. 8, 07743 Jena, Germany
| | - Giuseppe Zampella
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Wolfgang Weigand
- Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität Jena, Humboldt Str. 8, 07743 Jena, Germany
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12
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Meyers A, Heilweil EJ, Stromberg CJ. Photodynamics of Asymmetric Di-Iron-Cyano Hydrogenases Examined by Time-Resolved Mid-Infrared Spectroscopy. J Phys Chem A 2021; 125:1413-1423. [PMID: 33567824 DOI: 10.1021/acs.jpca.0c08921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two anionic asymmetric Fe-Fe hydrogenase model compounds containing a single cyano (CN) and five carboxyl (CO) ligands, [Et4N][Fe2(μ-S2C3H6)(CO)5(CN)1] and [Et4N][Fe2(μ-S2C2H4)(CO)5(CN)1], dissolved in room-temperature acetonitrile, are examined. The molecular asymmetry affects the redox potentials of the central iron atoms, thus changing the photophysics and possible catalytic properties of the compounds. Femtosecond ultraviolet excitation with mid-infrared probe spectroscopy of the model compounds was employed to better understand the ultrafast dynamics of the enzyme-active site. Continuous ultraviolet lamp excitation with Fourier transform infrared (FTIR) spectroscopy was also used to explore stable product formation on the second timescale. For both model compounds, two timescales are observed; a 20-30 ps decay and the formation of a long-lived photoproduct. The picosecond decay is assigned to vibrational cooling and rotational dynamics, while the residual spectra remain for up to 300 ps, suggesting the formation of new photoproducts. Static FTIR spectroscopy yielded a different stable photoproduct than that observed on the ultrafast timescale. Density functional theory calculations simulated photoproducts for CO-loss and CN-loss isomers, and the resulting photoproduct spectra suggest that the picosecond transients arise from a complex mixture of isomerization after CO-loss, while dimerization and formation of a CN-containing Fe-CO-Fe bridged species are also considered.
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Affiliation(s)
- Amber Meyers
- Department of Chemistry and Physics, Hood College, Frederick, Maryland 21701-8524, United States
| | - Edwin J Heilweil
- Nanoscale Device Characterization Division, Physical Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Stromberg
- Department of Chemistry and Physics, Hood College, Frederick, Maryland 21701-8524, United States
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13
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Pandey I, Agarwal T, Mobin SM, Stein M, Kaur-Ghumaan S. Switching Site Reactivity in Hydrogenase Model Systems by Introducing a Pendant Amine Ligand. ACS OMEGA 2021; 6:4192-4203. [PMID: 33644543 PMCID: PMC7906588 DOI: 10.1021/acsomega.0c04901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Hydrogenases are versatile enzymatic catalysts with an unmet hydrogen evolution reactivity (HER) from synthetic bio-inspired systems. The binuclear active site only has one-site reactivity of the distal Fed atom. Here, binuclear complexes [Fe2(CO)5(μ-Mebdt)(P(4-C6H4OCH3)3)] 1 and [Fe2(CO)5(μ-Mebdt)(PPh2Py)] 2 are presented, which show electrocatalytic activity in the presence of weak acids as a proton source for the HER. Despite almost identical structural and spectroscopic properties (bond distances and angles from single-crystal X-ray; IR, UV/vis, and NMR), introduction of a nitrogen base atom in the phosphine ligand in 2 markedly changes site reactivity. The bridging benzenedithiolate ligand Mebdt interacts with the terminal ligand's phenyl aromatic rings and stabilizes the reduced states of the catalysts. Although 1 with monodentate phosphine terminal ligands only shows a distal iron atom HER activity by a sequence of electrochemical and protonation steps, the lone pair of pyridine nitrogen in 2 acts as the primary site of protonation. This swaps the iron atom catalytic activity toward the proximal iron for complex 2. Density-functional theory (DFT) calculations reveal the role of terminal phosphines ligands without/with pendant amines by directing the proton transfer steps. The reactivity of 1 is a thiol-based protonation of a dangling bond in 1- and distal iron hydride mechanism, which may follow either an ECEC or EECC sequence, depending on the choice of acid. The pendant amine in 2 enables a terminal ligand protonation and an ECEC reactivity. The introduction of a terminal nitrogen atom enables the control of site reactivity in a binuclear system.
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Affiliation(s)
| | - Tashika Agarwal
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Shaikh M. Mobin
- Discipline
of Chemistry, Indian Institute of Technology
Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Matthias Stein
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Sandeep Kaur-Ghumaan
- Department
of Chemistry, University of Delhi, Delhi 110007, India
- Max
Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
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14
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Rovaletti A, Greco C, Ryde U. QM/MM study of the binding of H 2 to MoCu CO dehydrogenase: development and applications of improved H 2 van der Waals parameters. J Mol Model 2021; 27:68. [PMID: 33538901 PMCID: PMC7862525 DOI: 10.1007/s00894-020-04655-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/20/2020] [Indexed: 11/28/2022]
Abstract
The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.
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Affiliation(s)
- Anna Rovaletti
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, 20126, Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, Milano-Bicocca University, Piazza della Scienza 1, 20126, Milan, Italy.
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00, Lund, Sweden.
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15
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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16
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Siegbahn PEM. A quantum chemical approach for the mechanisms of redox-active metalloenzymes. RSC Adv 2021; 11:3495-3508. [PMID: 35424322 PMCID: PMC8694229 DOI: 10.1039/d0ra10412d] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading electronic structure tool. An understanding of how the method works in practice has significantly improved the accuracy and applicability. During the past ten years, it has been found that the results for redox enzymes mainly depend on the chosen fraction of exact exchange in the functional, and that a choice of 15% has worked best. The idea has therefore been to vary that fraction over a reasonable range and study the relative energy dependence. For modeling the enzymes, a cluster approach has been developed. In the present review the development of the method we used is described from its start in work on photosystem II, fifteen years ago. Examples from a few recent applications are described, where the metals have been iron, nickel, copper, cobalt or manganese. The results are in excellent agreement with available experiments, and a large number of new predictions have been made. During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.![]()
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry
- Arrhenius Laboratory
- Stockholm University
- Stockholm
- Sweden
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17
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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18
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Abstract
![]()
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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19
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Caserta G, Pelmenschikov V, Lorent C, Tadjoung Waffo AF, Katz S, Lauterbach L, Schoknecht J, Wang H, Yoda Y, Tamasaku K, Kaupp M, Hildebrandt P, Lenz O, Cramer SP, Zebger I. Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations. Chem Sci 2020; 12:2189-2197. [PMID: 34163984 PMCID: PMC8179317 DOI: 10.1039/d0sc05022a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site. Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two NiIIFeII and NiIIIFeII resting states, contributing in combination with DFT modeling to rationalized structural candidates.![]()
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Affiliation(s)
- Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Armel F Tadjoung Waffo
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Lars Lauterbach
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View CA 94043 USA
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI) SPring-8, 1-1-1 Kouto, Sayo-gun Hyogo 679-5198 Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5148 Japan
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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20
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Arrigoni F, Rizza F, Vertemara J, Breglia R, Greco C, Bertini L, Zampella G, De Gioia L. Rational Design of Fe 2 (μ-PR 2 ) 2 (L) 6 Coordination Compounds Featuring Tailored Potential Inversion. Chemphyschem 2020; 21:2279-2292. [PMID: 32815583 DOI: 10.1002/cphc.202000623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/19/2020] [Indexed: 01/04/2023]
Abstract
It was recently discovered that some redox proteins can thermodynamically and spatially split two incoming electrons towards different pathways, resulting in the one-electron reduction of two different substrates, featuring reduction potential respectively higher and lower than the parent reductant. This energy conversion process, referred to as electron bifurcation, is relevant not only from a biochemical perspective, but also for the ground-breaking applications that electron-bifurcating molecular devices could have in the field of energy conversion. Natural electron-bifurcating systems contain a two-electron redox centre featuring potential inversion (PI), i. e. with second reduction easier than the first. With the aim of revealing key factors to tailor the span between first and second redox potentials, we performed a systematic density functional study of a 26-molecule set of models with the general formula Fe2 (μ-PR2 )2 (L)6 . It turned out that specific features such as i) a Fe-Fe antibonding character of the LUMO, ii) presence of electron-donor groups and iii) low steric congestion in the Fe's coordination sphere, are key ingredients for PI. In particular, the synergic effects of i)-iii) can lead to a span between first and second redox potentials larger than 700 mV. More generally, the "molecular recipes" herein described are expected to inspire the synthesis of Fe2 P2 systems with tailored PI, of primary relevance to the design of electron-bifurcating molecular devices.
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Affiliation(s)
- Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Fabio Rizza
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, University of Milano - Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano - Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Giuseppe Zampella
- 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
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21
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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, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, People’s Republic of China
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22
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Bose M, Li Z, Matsumoto T, Tatsumi K. A Dithiolato and Hydrido Bridged (CO/CN)Fe-Ni Complex with Unprotected CN: A Model for the [Ni-R] State of the [Ni-Fe] Hydrogenase Active Site. Inorg Chem 2020; 59:968-971. [PMID: 31891256 DOI: 10.1021/acs.inorgchem.9b03082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dithiolate/hydride bridged Fe-Ni complex, [(CN)(CO)2FeII(μ-pdt)(μ-H)NiII(CN)(PCy3)]- (2, pdt = propane-1,3-dithiolate) has been synthesized by the reaction of [(CN)2(CO)2FeII(pdt)]2- with [NiII(Cl)(H)(PCy3)2] as a synthetic analogue of the Ni-R state of the active site of the [Ni-Fe] hydrogenase. X-ray crystallography of this model complex suggests that the hydride unsymmetrically binds to Ni and Fe similar to natural [Ni-Fe] hydrogenases.
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Affiliation(s)
- Moumita Bose
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science , Nagoya University , Furo-Cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Zilong Li
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science , Nagoya University , Furo-Cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Furo-Cho, Chikusa-ku, Nagoya 464-8601 , Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science , Nagoya University , Furo-Cho, Chikusa-ku, Nagoya 464-8602 , Japan
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23
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Isegawa M, Matsumoto T, Ogo S. Selective Oxidation of H 2 and CO by NiIr Catalyst in Aqueous Solution: A DFT Mechanistic Study. Inorg Chem 2020; 59:1014-1028. [PMID: 31898897 DOI: 10.1021/acs.inorgchem.9b02400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the challenges in utilizing hydrogen gas (H2) as a sustainable fossil fuel alternative is the inhibition of H2 oxidation by carbon monoxide (CO), which is involved in the industrial production of H2 sources. To solve this problem, a catalyst that selectively oxidizes either CO or H2 or one that co-oxidizes H2 and CO is needed. Recently, a NiIr catalyst [NiIICl(X)IrIIICl(η5-C5Me5)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H2 or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H2 and CO oxidation catalyzed by this NiIr catalyst. During H2 oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH3COO-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO2 leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H2, OH-, H2O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H2O and H2. These calculations indicate that H2 oxidation is inhibited by CO and OH- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH- attack to a carbonyl-C and the binding of OH- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H2 and CO.
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Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) , Kyushu University , 744 Moto-oka , Nishi-ku, Fukuoka 819-0395 , Japan
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24
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Pieri C, Bhattacharjee A, Barrozo A, Faure B, Giorgi M, Fize J, Réglier M, Field M, Orio M, Artero V, Hardré R. Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex. Chem Commun (Camb) 2020; 56:11106-11109. [DOI: 10.1039/d0cc04174b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A trinuclear nickel complex with S-based ligands is reported as a bio-inspired model of the [NiFe] hydrogenases' active site. DFT calculations indicate that thiolate and thioether functions are involved as proton relays in the H2 evolution mechanism.
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Affiliation(s)
- Cyril Pieri
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | | | | | - Bruno Faure
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | - Michel Giorgi
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- Marseille
- France
| | - Jennifer Fize
- Univ. Grenoble Alpes
- CNRS
- CEA
- IRIG
- Laboratoire de Chimie et Biologie des Métaux
| | | | - Martin Field
- Univ. Grenoble Alpes
- CNRS
- CEA
- IRIG
- Laboratoire de Chimie et Biologie des Métaux
| | - Maylis Orio
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | - Vincent Artero
- Univ. Grenoble Alpes
- CNRS
- CEA
- IRIG
- Laboratoire de Chimie et Biologie des Métaux
| | - Renaud Hardré
- Aix Marseille Univ
- CNRS
- Centrale Marseille
- iSm2
- Marseille
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25
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Barrozo A, Orio M. Molecular Electrocatalysts for the Hydrogen Evolution Reaction: Input from Quantum Chemistry. CHEMSUSCHEM 2019; 12:4905-4915. [PMID: 31557393 DOI: 10.1002/cssc.201901828] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Indexed: 06/10/2023]
Abstract
In the pursuit of carbon-free fuels, hydrogen can be considered as an apt energy carrier. The design of molecular electrocatalysts for hydrogen production is important for the development of renewable energy sources that are abundant, inexpensive, and environmentally benign. Over the last 20 years, a large number of electrocatalysts have been developed, and considerable efforts have been directed toward the design of earth-abundant, first-row transition-metal complexes capable of promoting electrocatalytic hydrogen evolution reaction (HER). In this context, numerical approaches have emerged as powerful tools to study the catalytic performances of these complexes. This review covers some of the most significant theoretical mechanistic studies of biomimetic and bioinspired homogeneous HER catalysts. The approaches employed to study the free energy landscapes are discussed and methods used to obtain accurate estimates of relevant observables required to study the HER are presented. Furthermore, the structural and electronic parameters that govern the reactivity, and are necessary to achieve efficient hydrogen production, are discussed in view of future research directions.
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Affiliation(s)
- Alexandre Barrozo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
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26
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TAKENO Y, KAWAMURA J. Chemical and Electrochemical Reduction of H 3PMo 12O 40 and Its Utilization as an Inexpensive Anode Catalyst for H 2-O 2 Fuel Cells at Room Temperature. ELECTROCHEMISTRY 2019. [DOI: 10.5796/electrochemistry.19-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yukio TAKENO
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
| | - Junichi KAWAMURA
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
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27
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Mondragón-Díaz A, Robles-Marín E, Murueta-Cruz BA, Aquite JC, Martínez-Alanis PR, Flores-Alamo M, Aullón G, Benítez LN, Castillo I. Conformational Effects of [Ni 2 (μ-ArS) 2 ] Cores on Their Electrocatalytic Activity. Chem Asian J 2019; 14:3301-3312. [PMID: 31400087 DOI: 10.1002/asia.201901037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Indexed: 11/11/2022]
Abstract
Two nickel complexes supported by tridentate NS2 ligands, [Ni2 (κ-N,S,S,S'-NPh {CH2 (MeC6 H2 R')S}2 )2 ] (1; R'=3,5-(CF3 )2 C6 H3 ) and [Ni2 (κ-N,S,S,S'-NiBu {CH2 C6 H4 S}2 )2 ] (2), were prepared as bioinspired models of the active site of [NiFe] hydrogenases. The solid-state structure of 1 reveals that the [Ni2 (μ-ArS)2 ] core is bent, with the planes of the nickel centers at a hinge angle of 81.3(5)°, whereas 2 shows a coplanar arrangement between both nickel(II) ions in the dimeric structure. Complex 1 electrocatalyzes proton reduction from CF3 COOH at -1.93 (overpotential of 1.04 V, with icat /ip ≈21.8) and -1.47 V (overpotential of 580 mV, with icat /ip ≈5.9) versus the ferrocene/ferrocenium redox couple. The electrochemical behavior of 1 relative to that of 2 may be related to the bent [Ni2 (μ-ArS)2 ] core, which allows proximity of the two Ni⋅⋅⋅Ni centers at 2.730(8) Å; thus possibly favoring H+ reduction. In contrast, the planar [Ni2 (μ-ArS)2 ] core of 2 results in a Ni⋅⋅⋅Ni distance of 3.364(4) Å and is unstable in the presence of acid.
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Affiliation(s)
- Alexander Mondragón-Díaz
- Departamento de Química, Facultad de Ciencias, Universidad del Valle, Ciudad Universitaria Meléndez, Calle 13, Cali, #100-00, Colombia
| | - Elvis Robles-Marín
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico, 04510, Mexico
| | - Brenda A Murueta-Cruz
- Departamento de Química, Facultad de Ciencias, Universidad del Valle, Ciudad Universitaria Meléndez, Calle 13, Cali, #100-00, Colombia
| | - Juan C Aquite
- Departamento de Química, Facultad de Ciencias, Universidad del Valle, Ciudad Universitaria Meléndez, Calle 13, Cali, #100-00, Colombia
| | - Paulina R Martínez-Alanis
- Departament de Química Inorgánica i Orgànica, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Marcos Flores-Alamo
- Facultad de Química, División de Estudios de Posgrado, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico, 04510, Mexico
| | - Gabriel Aullón
- Departament de Química Inorgánica i Orgànica, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Luis Norberto Benítez
- Departamento de Química, Facultad de Ciencias, Universidad del Valle, Ciudad Universitaria Meléndez, Calle 13, Cali, #100-00, Colombia
| | - Ivan Castillo
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico, 04510, Mexico
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Niu S, Nelson AE, De La Torre P, Li H, Works CF, Hall MB. Photoinduced Terminal Hydride of [FeFe]-Hydrogenase Biomimetic Complexes. Inorg Chem 2019; 58:13737-13741. [DOI: 10.1021/acs.inorgchem.9b01738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Anne E. Nelson
- Department of Chemistry, Sonoma State University, Rohnert Park, California 94928, United States
| | - Patricia De La Torre
- Department of Chemistry, Sonoma State University, Rohnert Park, California 94928, United States
| | - Haixia Li
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Carmen F. Works
- Department of Chemistry, Sonoma State University, Rohnert Park, California 94928, United States
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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29
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Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
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30
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Thornley W, Wirick SA, Riedel-Topper M, DeYonker NJ, Bitterwolf TE, Stromberg CJ, Heilweil EJ. Photodynamics of [FeFe]-Hydrogenase Model Compounds with Bidentate Heterocyclic Ligands. J Phys Chem B 2019; 123:7137-7148. [PMID: 31334657 PMCID: PMC6857538 DOI: 10.1021/acs.jpcb.9b04675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two asymmetrically structured model compounds for the hydrogen-generating [Fe-Fe]-hydrogenase active site were investigated to determine the ultrafast photodynamics, structural intermediates, and photoproducts compared to more common symmetric di-iron species. The bidentate-ligand-containing compounds studied were Fe2(μ-S2C3H6)(CO)4(bipy), 1, and Fe2(μ-S2C3H6)(CO)4(phen), 2, in dilute room temperature acetonitrile solution and low-temperature 2Me-THF matrix isolation using static FTIR difference and time-resolved infrared spectroscopic methods (TRIR). Ultraviolet-visible spectra were also compared to time-dependent density functional theory (TD-DFT) to ascertain the orbital origins of long wavelength electronic absorption features. The spectroscopic evidence supports the conclusions that only a propyl-bridge flip occurs in low-temperature matrix, while early time CO ejection leads to the formation of solvated isomeric species on the 25 ps time scale in room temperature solution.
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Affiliation(s)
- Wyatt Thornley
- Department of Chemistry, University of Idaho, 875 Perimeter Dr., MS 2343, Moscow, ID 83844-2343, United States
| | - Sarah A. Wirick
- Department of Chemistry and Physics, Hood College, 401 Rosemont Ave., Frederick, MD 21701-8524, United States
| | - Maximilian Riedel-Topper
- Department of Chemistry and Physics, Hood College, 401 Rosemont Ave., Frederick, MD 21701-8524, United States
| | - Nathan J. DeYonker
- Department of Chemistry, The University of Memphis, 411 Smith Hall, 3744 Walker Avenue, Memphis, TN 38152
| | - Thomas E. Bitterwolf
- Department of Chemistry, University of Idaho, 875 Perimeter Dr., MS 2343, Moscow, ID 83844-2343, United States
| | - Christopher J. Stromberg
- Department of Chemistry and Physics, Hood College, 401 Rosemont Ave., Frederick, MD 21701-8524, United States
| | - Edwin J. Heilweil
- Nanoscale Device Characterization Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8443 United States
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31
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Borthakur B, Phukan AK. Can carbene decorated [FeFe]-hydrogenase model complexes catalytically produce dihydrogen? An insight from theory. Dalton Trans 2019; 48:11298-11307. [PMID: 31270518 DOI: 10.1039/c9dt01855g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic alkyl amino carbene (CAAC) anchored [FeFe]-hydrogenase model complex featuring rotated conformation at one of the iron centers are found to be promising candidate for effective production of dihydrogen. A stepwise comparison of the complete mechanism using the CAAC stabilized model complex [1]0 has been performed with that of an experimentally isolated one ([2]0). Interestingly, the reduction events involved in the catalytic cycles are found to be more favorable than those previously reported for a similar experimentally known system. Furthermore, the computed ΔpKa values indicate that the distal iron center with a vacant coordination site is more basic compared to the amino nitrogen atom of the azadithiolate bridge. We also made an attempt to determine the oxidation states of the iron centers for the intermediates involved in the catalytic cycles on the basis of the computed Mössbauer isomer shift and Mulliken spin density values.
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Affiliation(s)
- Bitupon Borthakur
- Department of Chemical Sciences, Tezpur University, Napaam 784028, Assam, India.
| | - Ashwini K Phukan
- Department of Chemical Sciences, Tezpur University, Napaam 784028, Assam, India.
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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33
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Qiu S, Li Q, Xu Y, Shen S, Sun C. Learning from nature: Understanding hydrogenase enzyme using computational approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Qinye Li
- School of Chemical Engineering Monash University Clayton Victoria Australia
| | - Yongjun Xu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Shaohua Shen
- International Research Center for Renewable Energy, State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Shaanxi China
| | - Chenghua Sun
- Department of Chemistry and Biotechnology, and Center for Translational Atomaterials Swinburne University of Technology Hawthorn Victoria Australia
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34
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New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2463-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Wodrich MD, Sawatlon B, Solel E, Kozuch S, Corminboeuf C. Activity-Based Screening of Homogeneous Catalysts through the Rapid Assessment of Theoretically Derived Turnover Frequencies. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00717] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Matthew D. Wodrich
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Boodsarin Sawatlon
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ephrath Solel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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36
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Borthakur B, Vargas A, Phukan AK. A Computational Study of Carbene Ligand Stabilization of Biomimetic Models of the Rotated H
red
State of [FeFe]‐Hydrogenase. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Bitupon Borthakur
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
| | - Alfredo Vargas
- Department of Chemistry, School of Life Sciences University of Sussex Brighton BN1 9QJ Sussex United Kingdom
| | - Ashwini K. Phukan
- Department of Chemical Sciences Tezpur University Napaam 784028 Assam India
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37
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Vogiatzis KD, Polynski MV, Kirkland JK, Townsend J, Hashemi A, Liu C, Pidko EA. Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem Rev 2019; 119:2453-2523. [PMID: 30376310 PMCID: PMC6396130 DOI: 10.1021/acs.chemrev.8b00361] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.
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Affiliation(s)
| | | | - Justin K. Kirkland
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jacob Townsend
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ali Hashemi
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chong Liu
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Evgeny A. Pidko
- TheoMAT
group, ITMO University, Lomonosova 9, St. Petersburg 191002, Russia
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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38
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Basu D, Bailey TS, Lalaoui N, Richers CP, Woods TJ, Rauchfuss TB, Arrigoni F, Zampella G. Synthetic Designs and Structural Investigations of Biomimetic Ni-Fe Thiolates. Inorg Chem 2019; 58:2430-2443. [PMID: 30707014 DOI: 10.1021/acs.inorgchem.8b02991] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Described are the syntheses of several Ni(μ-SR)2Fe complexes, including hydride derivatives, in a search for improved models for the active site of [NiFe]-hydrogenases. The nickel(II) precursors include (i) nickel with tripodal ligands: Ni(PS3)- and Ni(NS3)- (PS33- = tris(phenyl-2-thiolato)phosphine, NS33- = tris(benzyl-2-thiolato)amine), (ii) traditional diphosphine-dithiolates, including chiral diphosphine R,R-DIPAMP, (iii) cationic Ni(phosphine-imine/amine) complexes, and (iv) organonickel precursors Ni( o-tolyl)Cl(tmeda) and Ni(C6F5)2. The following new nickel precursor complexes were characterized: PPh4[Ni(NS3)] and the dimeric imino/amino-phosphine complexes [NiCl2(PCH═NAn)]2 and [NiCl2(PCH2NHAn)]2 (P = Ph2PC6H4-2-). The iron(II) reagents include [CpFe(CO)2(thf)]BF4, [Cp*Fe(CO)(MeCN)2]BF4, FeI2(CO)4, FeCl2(diphos)(CO)2, and Fe(pdt)(CO)2(diphos) (diphos = chelating diphosphines). Reactions of the nickel and iron complexes gave the following new Ni-Fe compounds: Cp*Fe(CO)Ni(NS3), [Cp(CO)Fe(μ-pdt)Ni(dppbz)]BF4, [( R,R-DIPAMP)Ni(μ-pdt)(H)Fe(CO)3]BArF4, [(PCH═NAn)Ni(μ-pdt)(Cl)Fe(dppbz)(CO)]BF4, [(PCH2NHAn)Ni(μ-pdt)(Cl)Fe(dppbz)(CO)]BF4, [(PCH═NAn)Ni(μ-pdt)(H)Fe(dppbz)(CO)]BF4, [(dppv)(CO)Fe(μ-pdt)]2Ni, {H[(dppv)(CO)Fe(μ-pdt)]2Ni]}BF4, and (C6F5)2Ni(μ-pdt)Fe(CO)2(dppv) (DIPAMP = (CH2P(C6H4-2-OMe)2)2; BArF4- = [B(C6H3-3,5-(CF3)2]4-)) Within the context of Ni-(SR)2-Fe complexes, these new complexes feature new microenvironments for the nickel center: tetrahedral Ni, chirality, imine, and amine coligands, and Ni-C bonds. In the case of {H[(dppv)(CO)Fe(μ-pdt)]2Ni}+, four low-energy isomers are separated by ≤3 kcal/mol, one of which features a biomimetic HNi(SR)4 site, as supported by density functional theory calculations.
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Affiliation(s)
- Debashis Basu
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - T Spencer Bailey
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Noémie Lalaoui
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Casseday P Richers
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Toby J Woods
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 20126 Milan , Italy
| | - Giuseppe Zampella
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 20126 Milan , Italy
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39
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Qiu S, Azofra LM, Macfarlane DR, Sun C. Hydrogen Evolution in [NiFe] Hydrogenases: A Case of Heterolytic Approach between Proton and Hydride. Inorg Chem 2019; 58:2979-2986. [DOI: 10.1021/acs.inorgchem.8b02812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Luis Miguel Azofra
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Douglas R. Macfarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Chenghua Sun
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
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40
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Yang X, Gianetti TL, Wörle MD, van Leest NP, de Bruin B, Grützmacher H. A low-valent dinuclear ruthenium diazadiene complex catalyzes the oxidation of dihydrogen and reversible hydrogenation of quinones. Chem Sci 2019; 10:1117-1125. [PMID: 30774909 PMCID: PMC6346631 DOI: 10.1039/c8sc02864h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
The dinuclear ruthenium complex [Ru2H(μ-H)(Me2dad)(dbcot)2] contains a 1,4-dimethyl-diazabuta-1,3-diene (Me2dad) as a non-innocent bridging ligand between the metal centers to give a [Ru2(Me2dad)] core. In addition, each ruthenium is bound to one dibenzo[a,e]cyclooctatetraene (dbcot) ligand. This Ru dimer converts H2 to protons and electrons. It also catalyzes reversibly under mild conditions the selective hydrogenation of vitamins K2 and K3 to their corresponding hydroquinone equivalents without affecting the C[double bond, length as m-dash]C double bonds. Mechanistic studies suggest that the [Ru2(Me2dad)] moiety, like hydrogenases, reacts with H2 and releases electrons and protons stepwise.
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Affiliation(s)
- Xiuxiu Yang
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
| | - Thomas L Gianetti
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland . .,Department of Chemistry and Biochemistry , The University of Arizona , Tucson , Arizona 85721 , USA .
| | - Michael D Wörle
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
| | - Nicolaas P van Leest
- Van't Hoff Institute for Molecular Sciences (HIMS) , University of Amsterdam (UvA) , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Bas de Bruin
- Van't Hoff Institute for Molecular Sciences (HIMS) , University of Amsterdam (UvA) , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Hansjörg Grützmacher
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 1 , 8093 Zürich , Switzerland .
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41
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Chen K, Wu CD. Designed fabrication of biomimetic metal–organic frameworks for catalytic applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.01.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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42
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Abstract
Hydrogenases catalyze the simple yet important interconversion between H2 and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.
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43
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Uzunova EL. Pathways of selective catalytic CO2 two-step reduction on di-iron, di-cobalt and iron-cobalt disulfide carbonyls – an electronic structure study. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02203h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mixed iron–cobalt disulfide hexacarbonyl provides a selective route in the two step carbon dioxide reduction to formic acid.
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Affiliation(s)
- Ellie L. Uzunova
- Institute of General and Inorganic Chemistry
- Bulgarian Academy of Sciences
- Sofia 1113
- Bulgaria
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44
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations. Inorg Chem 2018; 58:279-293. [PMID: 30576127 DOI: 10.1021/acs.inorgchem.8b02348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The apparently simple dihydrogen formation from protons and electrons (2H+ + 2e- ⇄ H2) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H2 binding to the active site is required to convert Ni-A to the active Ni-SIa state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SIr and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SIr, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H2O and H2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.
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Tai H, Higuchi Y, Hirota S. Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases. Dalton Trans 2018. [PMID: 29532823 DOI: 10.1039/c7dt04910b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.
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Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
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Meng ZF, Gao HL, Wang JX, Shang JY, Li CG. Phenyl-functionalized diiron propanediselenolato complexes containing the chelated or bridged 1,3-bis(diphenylphosphine)propane ligand. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1485148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Zhi-Fen Meng
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, People’s Republic of China
| | - Hui-Ling Gao
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, People’s Republic of China
| | - Jiu-Xia Wang
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, People’s Republic of China
| | - Jing-Yan Shang
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, People’s Republic of China
| | - Chang-Gong Li
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, People’s Republic of China
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Slater JW, Marguet SC, Monaco HA, Shafaat HS. Going beyond Structure: Nickel-Substituted Rubredoxin as a Mechanistic Model for the [NiFe] Hydrogenases. J Am Chem Soc 2018; 140:10250-10262. [PMID: 30016865 DOI: 10.1021/jacs.8b05194] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jeffrey W. Slater
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C. Marguet
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Haleigh A. Monaco
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S. Shafaat
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Chu KT, Liu YC, Chung MW, Poerwoprajitno AR, Lee GH, Chiang MH. Energy-Efficient Hydrogen Evolution by Fe-S Electrocatalysts: Mechanistic Investigations. Inorg Chem 2018; 57:7620-7630. [PMID: 29893554 DOI: 10.1021/acs.inorgchem.8b00543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The intrinsic catalytic property of a Fe-S complex toward H2 evolution was investigated in a wide range of acids. The title complex exhibited catalytic events at -1.16 and -1.57 V (vs Fc+/Fc) in the presence of trifluoromethanesulfonic acid (HOTf) and trifluoroacetic acid (TFA), respectively. The processes corresponded to the single reduction of the Fe-hydride-S-proton and Fe-hydride species, respectively. When anilinium acid was used, the catalysis occurred at -1.16 V, identical with the working potential of the HOTf catalysis, although the employment of anilinium acid was only capable of achieving the Fe-hydride state on the basis of the spectral and calculated results. The thermodynamics and kinetics of individual steps of the catalysis were analyzed by density functional theory (DFT) calculations and electroanalytical simulations. The stepwise CCE or CE (C, chemical; E, electrochemical) mechanism was operative from the HOTf or TFA source, respectively. In contrast, the involvement of anilinium acid most likely initiated a proton-coupled electron transfer (PCET) pathway that avoided the disfavored intermediate after the initial protonation. Via the PCET pathway, the heterogeneous electron transfer rate was increased and the overpotential was decreased by 0.4 V in comparison with the stepwise pathways. The results showed that the PCET-involved catalysis exhibited substantial kinetic and thermodynamic advantages in comparison to the stepwise pathway; thus, an efficient catalytic system for proton reduction was established.
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Affiliation(s)
- Kai-Ti Chu
- Institute of Chemistry , Academia Sinica , Nankang, Taipei 115 , Taiwan
| | - Yu-Chiao Liu
- Institute of Chemistry , Academia Sinica , Nankang, Taipei 115 , Taiwan
| | - Min-Wen Chung
- Institute of Chemistry , Academia Sinica , Nankang, Taipei 115 , Taiwan
| | | | - Gene-Hsiang Lee
- Instrumentation Center , National Taiwan University , Taipei 106 , Taiwan
| | - Ming-Hsi Chiang
- Institute of Chemistry , Academia Sinica , Nankang, Taipei 115 , Taiwan
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Isegawa M, Sharma AK, Ogo S, Morokuma K. DFT Study on Fe(IV)-Peroxo Formation and H Atom Transfer Triggered O2 Activation by NiFe Complex. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku, Fukuoka 819-0385, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Akhilesh K. Sharma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku, Fukuoka 819-0385, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Stromberg CJ, Heilweil EJ. Ultrafast Photodynamics of Cyano-Functionalized [FeFe] Hydrogenase Model Compounds. J Phys Chem A 2018; 122:4023-4030. [PMID: 29652502 PMCID: PMC6051340 DOI: 10.1021/acs.jpca.8b00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[FeFe] hydrogenases are efficient enzymes that produce hydrogen gas under mild conditions. Synthetic model compounds containing all CO or mixed CO/PMe3 ligands were previously studied by us and others with ultrafast ultraviolet or visible pump-infrared probe spectroscopy in an effort to better understand the function and interactions of the active site with light. Studies of anionic species containing cyano groups, which more closely match the biological active site, have been elusive. In this work, two model compounds dissolved in room-temperature acetonitrile solution were examined: [Fe2(μ-S2C3H6)(CO)4(CN)2]2- (1) and [Fe2(μ-S2C2H4)(CO)4(CN)2]2- (2). These species exhibit long-lived transient signals consistent with loss of one CO ligand with potential isomerization of newly formed ground electronic state photoproducts, as previously observed with all-CO and CO/PMe3-containing models. We find no evidence for fast (ca. 150 ps) relaxation seen in the all-CO and CO/PMe3 compounds because of the absence of the metal-to-metal charge transfer band in the cyano-functionalized models. These results indicate that incorporation of cyano ligands may significantly alter the electronic properties and photoproducts produced immediately after photoexcitation, which may influence the catalytic activity of model compounds when attached to photosensitizers.
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Affiliation(s)
- Christopher J. Stromberg
- Department of Chemistry and Physics, Hood College, 401 Rosemont Avenue, Frederick, Maryland 21701-8524, United States
| | - Edwin J. Heilweil
- Engineering Physics Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8443 United States
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