201
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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202
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Kositzki R, Mebs S, Marx J, Griese JJ, Schuth N, Högbom M, Schünemann V, Haumann M. Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations. Inorg Chem 2016; 55:9869-9885. [PMID: 27610479 DOI: 10.1021/acs.inorgchem.6b01752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O2) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O2 reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal-ligand bond lengths, metal-metal distances, metal oxidation states, spin configurations, valence-level degeneracy, molecular orbital composition, nuclear quadrupole splitting energies, and vibrational normal modes for both cofactors. A protonation state with an axial water (H2O) ligand at Mn or Fe in binding site 1 and a metal-bridging hydroxo group (μOH) in a hydrogen-bonded network is assigned. Our comprehensive picture of the molecular, electronic, and dynamic properties of the cofactors highlights reorientation of the unique axis along the Mn-OH2 bond for the Mn1(III) Jahn-Teller ion but along the Fe-μOH bond for the octahedral Fe1(III). This likely corresponds to a more positive redox potential of the Mn(III)Fe(III) cofactor and higher proton affinity of its μOH group. Refined model structures for the Mn(III)Fe(III) and Fe(III)Fe(III) cofactors are presented. Implications of our findings for the site-specific metalation of R2lox and performance of the O2 reduction and cross-link formation reactions are discussed.
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Affiliation(s)
- Ramona Kositzki
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Jennifer Marx
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Nils Schuth
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden.,Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
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203
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Stasyuk AJ, Cywiński PJ, Gryko DT. Excited-state intramolecular proton transfer in 2′-(2′-hydroxyphenyl)imidazo[1,2- a ]pyridines. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2016. [DOI: 10.1016/j.jphotochemrev.2016.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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204
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Electron flow through biological molecules: does hole hopping protect proteins from oxidative damage? Q Rev Biophys 2016; 48:411-20. [PMID: 26537399 DOI: 10.1017/s0033583515000062] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biological electron transfers often occur between metal-containing cofactors that are separated by very large molecular distances. Employing photosensitizer-modified iron and copper proteins, we have shown that single-step electron tunneling can occur on nanosecond to microsecond timescales at distances between 15 and 20 Å. We also have shown that charge transport can occur over even longer distances by hole hopping (multistep tunneling) through intervening tyrosines and tryptophans. In this perspective, we advance the hypothesis that such hole hopping through Tyr/Trp chains could protect oxygenase, dioxygenase, and peroxidase enzymes from oxidative damage. In support of this view, by examining the structures of P450 (CYP102A) and 2OG-Fe (TauD) enzymes, we have identified candidate Tyr/Trp chains that could transfer holes from uncoupled high-potential intermediates to reductants in contact with protein surface sites.
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205
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Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
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Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
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206
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Markle TF, Zhang MT, Santoni MP, Johannissen LO, Hammarström L. Proton-Coupled Electron Transfer in a Series of Ruthenium-Linked Tyrosines with Internal Bases: Evaluation of a Tunneling Model for Experimental Temperature-Dependent Kinetics. J Phys Chem B 2016; 120:9308-21. [DOI: 10.1021/acs.jpcb.6b05885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Todd F. Markle
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Ming-Tian Zhang
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Marie-Pierre Santoni
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Linus O. Johannissen
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Leif Hammarström
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
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207
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Yayla HG, Wang H, Tarantino KT, Orbe HS, Knowles RR. Catalytic Ring-Opening of Cyclic Alcohols Enabled by PCET Activation of Strong O-H Bonds. J Am Chem Soc 2016; 138:10794-7. [PMID: 27515494 DOI: 10.1021/jacs.6b06517] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a new photocatalytic protocol for the redox-neutral isomerization of cyclic alcohols to linear ketones via C-C bond scission. Mechanistic studies demonstrate that key alkoxy radical intermediates in this reaction are generated via the direct homolytic activation of alcohol O-H bonds in an unusual intramolecular PCET process, wherein the electron travels to a proximal radical cation in concert with proton transfer to a weak Brønsted base. Effective bond strength considerations are shown to accurately forecast the feasibility of alkoxy radical generation with a given oxidant/base pair.
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Affiliation(s)
- Hatice G Yayla
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Huaiju Wang
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Kyle T Tarantino
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Hudson S Orbe
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Robert R Knowles
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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208
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Cannatelli MD, Ragauskas AJ. Two Decades of Laccases: Advancing Sustainability in the Chemical Industry. CHEM REC 2016; 17:122-140. [PMID: 27492131 DOI: 10.1002/tcr.201600033] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 12/30/2022]
Abstract
Given the current state of environmental affairs and that our future on this planet as we know it is in jeopardy, research and development into greener and more sustainable technologies within the chemical and forest products industries is at its peak. Given the global scale of these industries, the need for environmentally benign practices is propelling new green processes. These challenges are also impacting academic research and our reagents of interest are laccases. These enzymes are employed in a variety of biotechnological applications due to their native function as catalytic oxidants. They are about as green as it gets when it comes to chemical processes, requiring O2 as their only co-substrate and producing H2 O as the sole by-product. The following account will review our twenty year journey on the use of these enzymes within our research group, from their initial use in biobleaching of kraft pulps and for fiber modification within the pulp and paper industry, to their current application as green catalytic oxidants in the field of synthetic organic chemistry.
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Affiliation(s)
- Mark D Cannatelli
- Renewable Bioproducts Institute, School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Arthur J Ragauskas
- Renewable Bioproducts Institute, School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Chemical & Biomolecular Engineering, Department of Forestry, Wildlife & Fisheries, University of Tennessee, Knoxville, TN 37996, USA
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209
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Steidl RJ, Lampa-Pastirk S, Reguera G. Mechanistic stratification in electroactive biofilms of Geobacter sulfurreducens mediated by pilus nanowires. Nat Commun 2016; 7:12217. [PMID: 27481214 PMCID: PMC4974642 DOI: 10.1038/ncomms12217] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/09/2016] [Indexed: 01/08/2023] Open
Abstract
Electricity generation by Geobacter sulfurreducens biofilms grown on electrodes involves matrix-associated electron carriers, such as c-type cytochromes. Yet, the contribution of the biofilm's conductive pili remains uncertain, largely because pili-defective mutants also have cytochrome defects. Here we report that a pili-deficient mutant carrying an inactivating mutation in the pilus assembly motor PilB has no measurable defects in cytochrome expression, yet forms anode biofilms with reduced electroactivity and is unable to grow beyond a threshold distance (∼10 μm) from the underlying electrode. The defects are similar to those of a Tyr3 mutant, which produces poorly conductive pili. The results support a model in which the conductive pili permeate the biofilms to wire the cells to the conductive biofilm matrix and the underlying electrode, operating coordinately with cytochromes until the biofilm reaches a threshold thickness that limits the efficiency of the cytochrome pathway but not the functioning of the conductive pili network. The roles played by cytochromes and conductive filamentous appendages (pili) in the electrical conductivity of Geobacter bacterial biofilms are controversial. Here, Steidl et al. present evidence that both mechanisms cooperate in thin biofilms, while pili are important for conductivity across thicker biofilms.
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Affiliation(s)
- Rebecca J Steidl
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
| | - Sanela Lampa-Pastirk
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, Rm 6190, Biomedical and Physical Science building, East Lansing, Michigan 48824, USA
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210
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Mitome H, Ishizuka T, Kotani H, Shiota Y, Yoshizawa K, Kojima T. Mechanistic Insights into C–H Oxidations by Ruthenium(III)-Pterin Complexes: Impact of Basicity of the Pterin Ligand and Electron Acceptability of the Metal Center on the Transition States. J Am Chem Soc 2016; 138:9508-20. [DOI: 10.1021/jacs.6b03785] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroumi Mitome
- Department
of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Tomoya Ishizuka
- Department
of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroaki Kotani
- Department
of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Yoshihito Shiota
- Institute
for Materials Chemistry and Engineering, Kyushu University, Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering, Kyushu University, Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Takahiko Kojima
- Department
of Chemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
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211
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Bhagi-Damodaran A, Hosseinzadeh P, Mirts E, Reed J, Petrik ID, Lu Y. Design of Heteronuclear Metalloenzymes. Methods Enzymol 2016; 580:501-37. [PMID: 27586347 PMCID: PMC5156654 DOI: 10.1016/bs.mie.2016.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.
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Affiliation(s)
- A Bhagi-Damodaran
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Hosseinzadeh
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Mirts
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J Reed
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - I D Petrik
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Lu
- University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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212
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Miller DC, Tarantino KT, Knowles RR. Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities. Top Curr Chem (Cham) 2016; 374:30. [PMID: 27573270 PMCID: PMC5107260 DOI: 10.1007/s41061-016-0030-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.
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Affiliation(s)
- David C Miller
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle T Tarantino
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Robert R Knowles
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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213
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Nguyen LQ, Knowles RR. Catalytic C–N Bond-Forming Reactions Enabled by Proton-Coupled Electron Transfer Activation of Amide N–H Bonds. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00486] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lucas Q. Nguyen
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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214
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Vester M, Grueter A, Finkler B, Becker R, Jung G. Biexponential photon antibunching: recombination kinetics within the Förster-cycle in DMSO. Phys Chem Chem Phys 2016; 18:10281-8. [PMID: 27020473 DOI: 10.1039/c6cp00718j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Time-resolved experiments with pulsed-laser excitation are the standard approach to map the dynamic evolution of excited states, but ground-state kinetics remain hidden or require pump-dump-probe schemes. Here, we exploit the so-called photon antibunching, a purely quantum-optical effect related to single molecule detection to assess the rate constants for a chemical reaction in the electronic ground state. The measurement of the second-order correlation function g((2)), i.e. the evaluation of inter-photon arrival times, is applied to the reprotonation in a Förster-cycle. We find that the antibunching of three different photoacids in the aprotic solvent DMSO significantly differs from the behavior in water. The longer decay constant of the biexponential antibunching tl is linked to the bimolecular reprotonation kinetics of the fully separated ion-pair, independent of the acidic additives. The value of the corresponding bimolecular rate constant, kp = 4 × 10(9) M(-1) s(-1), indicates diffusion-controlled reprotonation. The analysis of tl also allows for the extraction of the separation yield of proton and the conjugated base after excitation and amounts to approximately 15%. The shorter time component ts is connected to the decay of the solvent-separated ion pair. The associated time constant for geminate reprotonation is approximately 3 ± 1 ns in agreement with independent tcspc experiments. These experiments verify that the transfer of quantum-optical experiments to problems in chemistry enables mechanistic conclusions which are hardly accessible by other methods.
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Affiliation(s)
- Michael Vester
- Biophysical Chemistry, Saarland University, 66123 Saarbrücken, Germany.
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215
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216
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Kasanmascheff M, Lee W, Nick TU, Stubbe J, Bennati M. Radical transfer in E. coli ribonucleotide reductase: a NH 2Y 731/R 411A-α mutant unmasks a new conformation of the pathway residue 731. Chem Sci 2016; 7:2170-2178. [PMID: 29899944 PMCID: PMC5968753 DOI: 10.1039/c5sc03460d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/06/2015] [Indexed: 11/21/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122˙) in subunit β2 to a cysteine (C439) in the active site of subunit α2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 Å and involves a specific pathway of redox active amino acids (Y122 ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2). The mechanisms of the PCET steps at the interface of the α2β2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731˙)-α2 trapped by incubation of NH2Y731-α2/β2/CDP(substrate)/ATP(allosteric effector) suggested that R411-α2, a residue close to the α2β2 interface, interacts with NH2Y731˙ and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-α2 with a R411A substitution. NH2Y731˙/R411A generated upon incubation of NH2Y731/R411A-α2/β2/CDP/ATP was investigated using multi-frequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron-electron double resonance (PELDOR) and electron-nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731˙/R411A relative to the NH2Y731˙ single mutant. Particularly, the inter-spin distance from NH2Y731˙/R411A in one αβ pair to Y122˙ in a second αβ pair decreases by 3 Å in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-α2 in an α2β2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731˙/R411A serves as a probe of the PCET process across the subunit interface.
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Affiliation(s)
- Müge Kasanmascheff
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - Wankyu Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Thomas U Nick
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
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217
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Jackson MN, Surendranath Y. Donor-Dependent Kinetics of Interfacial Proton-Coupled Electron Transfer. J Am Chem Soc 2016; 138:3228-34. [PMID: 26862666 DOI: 10.1021/jacs.6b00167] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The effect of the proton donor on the kinetics of interfacial concerted proton-electron transfer (CPET) to polycrystalline Au was probed indirectly by studying the rate of hydrogen evolution from trialkylammonium donors with different steric profiles, but the same pKa. Detailed kinetic studies point to a mechanism for HER catalysis that involves rate-limiting CPET from the proton donor to the electrode surface, allowing this catalytic reaction to serve as a proxy for the rate of interfacial CPET. In acetonitrile electrolyte, triethylammonium (TEAH(+)) displays up to 20-fold faster CPET kinetics than diisopropylethylammonium (DIPEAH(+)) at all measured potentials. In aqueous electrolyte, this steric constraint is largely lifted, suggesting a key role for water in mediating interfacial CPET. In acetonitrile, TEAH(+) also displays a much larger transfer coefficient (β = 0.7) than DIPEAH(+) (β = 0.4), and TEAH(+) displays a potential-dependent H/D kinetic isotope effect that is not observed for DIPEAH(+). These results demonstrate that proton donor structure strongly impacts the free energy landscape for CPET to extended solid surfaces and highlight the crucial role of the proton donor in the kinetics of electrocatalytic energy conversion reactions.
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Affiliation(s)
- Megan N Jackson
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Yogesh Surendranath
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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218
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Photoresponse of supramolecular self-assembled networks on graphene-diamond interfaces. Nat Commun 2016; 7:10700. [PMID: 26911248 PMCID: PMC4773422 DOI: 10.1038/ncomms10700] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/14/2016] [Indexed: 11/17/2022] Open
Abstract
Nature employs self-assembly to fabricate the most complex molecularly precise machinery known to man. Heteromolecular, two-dimensional self-assembled networks provide a route to spatially organize different building blocks relative to each other, enabling synthetic molecularly precise fabrication. Here we demonstrate optoelectronic function in a near-to-monolayer molecular architecture approaching atomically defined spatial disposition of all components. The active layer consists of a self-assembled terrylene-based dye, forming a bicomponent supramolecular network with melamine. The assembly at the graphene-diamond interface shows an absorption maximum at 740 nm whereby the photoresponse can be measured with a gallium counter electrode. We find photocurrents of 0.5 nA and open-circuit voltages of 270 mV employing 19 mW cm−2 irradiation intensities at 710 nm. With an ex situ calculated contact area of 9.9 × 102 μm2, an incident photon to current efficiency of 0.6% at 710 nm is estimated, opening up intriguing possibilities in bottom-up optoelectronic device fabrication with molecular resolution. Two-dimensional, self-assembled heteromolecular networks often lack functionality. Here the authors study the photoresponse of self-assembled heteromolecular networks, while controlling their positions and interfaces at an atomic level, suggesting bottom-up assembly of optoelectronics devices.
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219
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Olshansky L, Stubbe J, Nocera DG. Charge-Transfer Dynamics at the α/β Subunit Interface of a Photochemical Ribonucleotide Reductase. J Am Chem Soc 2016; 138:1196-205. [PMID: 26710997 PMCID: PMC4924928 DOI: 10.1021/jacs.5b09259] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multistep proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ∼35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask examination of the kinetics of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [Re(I)] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET), and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively "tight" subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
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220
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Khosrowabadi Kotyk JF, Ziller JW, Yang JY. Copper tetradentate N 2Py 2 complexes with pendant bases in the secondary coordination sphere: improved ligand synthesis and protonation studies. J COORD CHEM 2016. [DOI: 10.1080/00958972.2015.1130223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Joseph W. Ziller
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Jenny Y. Yang
- Department of Chemistry, University of California, Irvine, CA, USA
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221
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Najafpour MM, Renger G, Hołyńska M, Moghaddam AN, Aro EM, Carpentier R, Nishihara H, Eaton-Rye JJ, Shen JR, Allakhverdiev SI. Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures. Chem Rev 2016; 116:2886-936. [PMID: 26812090 DOI: 10.1021/acs.chemrev.5b00340] [Citation(s) in RCA: 337] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.
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Affiliation(s)
| | - Gernot Renger
- Institute of Chemistry, Max-Volmer-Laboratory of Biophysical Chemistry, Technical University Berlin , Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Małgorzata Hołyńska
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg , Hans-Meerwein-Straße, D-35032 Marburg, Germany
| | | | - Eva-Mari Aro
- Department of Biochemistry and Food Chemistry, University of Turku , 20014 Turku, Finland
| | - Robert Carpentier
- Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières , C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Hiroshi Nishihara
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1, Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Julian J Eaton-Rye
- Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Faculty of Science, Okayama University , Okayama 700-8530, Japan.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
| | - Suleyman I Allakhverdiev
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences , Botanicheskaya Street 35, Moscow 127276, Russia.,Institute of Basic Biological Problems, Russian Academy of Sciences , Pushchino, Moscow Region 142290, Russia.,Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University , Leninskie Gory 1-12, Moscow 119991, Russia
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222
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Kennedy SR, Goyal P, Kozar MN, Yennawar HP, Hammes-Schiffer S, Lear BJ. Effect of Protonation upon Electronic Coupling in the Mixed Valence and Mixed Protonated Complex, [Ni(2,3-pyrazinedithiol)2]. Inorg Chem 2016; 55:1433-45. [DOI: 10.1021/acs.inorgchem.5b02035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Steven R. Kennedy
- Department
of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Puja Goyal
- Department
of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Morgan N. Kozar
- Department
of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Hemant P. Yennawar
- Department
of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Benjamin J. Lear
- Department
of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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223
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Kenion RL, Ananth N. Direct simulation of electron transfer in the cobalt hexammine(ii/iii) self-exchange reaction. Phys Chem Chem Phys 2016; 18:26117-26124. [DOI: 10.1039/c6cp04882j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an atomistic simulation of electron transfer in a transition metal complex system using path integral methods.
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Affiliation(s)
- Rachel L. Kenion
- Robert Frederick Smith School of Chemical and Biomolecular Engineering
- Cornell University
- Ithaca
- USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
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224
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Duke JR, Ananth N. Mean field ring polymer molecular dynamics for electronically nonadiabatic reaction rates. Faraday Discuss 2016; 195:253-268. [DOI: 10.1039/c6fd00123h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a mean field ring polymer molecular dynamics method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. Our approach involves calculating a transition state theory (TST) estimate to the rate using an exact path integral in discrete electronic states and continuous Cartesian nuclear coordinates. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory. Further, we show that using a reaction coordinate based on electronic state populations allows us to capture the turnover in rates for ET in the Marcus inverted regime.
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Affiliation(s)
- Jessica Ryan Duke
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
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225
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Wilkinson LA, Vincent KB, Meijer AJHM, Patmore NJ. Mechanistic insight into proton-coupled mixed valency. Chem Commun (Camb) 2016; 52:100-3. [DOI: 10.1039/c5cc07101a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stabilisation of the mixed-valence state in [Mo2(TiPB)3(HDOP)]2+ (HTiPB = 2,4,6-triisopropylbenzoic acid, H2DOP = 3,6-dihydroxypyridazine) by electron transfer (ET) is related to the proton coordinate of the bridging ligands.
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Affiliation(s)
- Luke A. Wilkinson
- Department of Chemical Sciences
- University of Huddersfield
- Huddersfield HD1 3DH
- UK
- Department of Chemistry
| | - Kevin B. Vincent
- Department of Chemical Sciences
- University of Huddersfield
- Huddersfield HD1 3DH
- UK
| | | | - Nathan J. Patmore
- Department of Chemical Sciences
- University of Huddersfield
- Huddersfield HD1 3DH
- UK
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226
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Affiliation(s)
- Susanta K. Sen Gupta
- Department of Chemistry, Faculty of Science; Banaras Hindu University; Varanasi 221005 India
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227
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Walpita J, Yang X, Khatmullin R, Luk HL, Hadad CM, Glusac KD. Pourbaix diagrams in weakly coupled systems: a case study involving acridinol and phenanthridinol pseudobases. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Janitha Walpita
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
| | - Xin Yang
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
| | - Renat Khatmullin
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
| | - Hoi Ling Luk
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
| | - Christopher M. Hadad
- Department of Chemistry and Biochemistry; The Ohio State University; Columbus OH 43210 USA
| | - Ksenija D. Glusac
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
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228
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Magin IM, Polyakov NE, Kruppa AI, Purtov PA, Leshina TV, Kiryutin AS, Miranda MA, Nuin E, Marin ML. Low field photo-CIDNP in the intramolecular electron transfer of naproxen-pyrrolidine dyads. Phys Chem Chem Phys 2015; 18:901-7. [PMID: 26648262 DOI: 10.1039/c5cp04233j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoinduced processes with partial (exciplex) and full charge transfer in donor-acceptor systems are of interest because they are frequently used for modeling drug-protein binding. Low field photo-CIDNP (chemically induced dynamic nuclear polarization) for these processes in dyads, including the drug, (S)- and (R)-naproxen and (S)-N-methyl pyrrolidine in solutions with strong and weak permittivity have been measured. The dramatic influence of solvent permittivity on the field dependence of the N-methyl pyrrolidine (1)H CIDNP effects has been found. The field dependences of both (R,S)- and (S,S)-dyads in a polar medium are the curves with a single extremum in the area of the S-T+ terms intersection. Moreover, the CIDNP field dependences of the same protons measured in a low polar medium present curves with several extrema. The shapes of the experimental CIDNP field dependence with two extrema have been described using the Green function approach for the calculation of the CIDNP effects in the system without electron exchange interactions. The article discusses the possible causes of the differences between the CIDNP field dependence detected in a low-permittivity solvent with the strong Coulomb interactions and in a polar solvent.
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Affiliation(s)
- I M Magin
- Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya st. 3, 630090, Novosibirsk, Russia.
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229
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Wang R, Ranganathan SV, Valsangkar VA, Magliocco SM, Shen F, Chen A, Sheng J. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes. Chem Commun (Camb) 2015; 51:16389-92. [PMID: 26411524 DOI: 10.1039/c5cc06563a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-Hydroxylmethylcytosine (5hmC) has been recognized as the sixth base with important biological functions in many tissues and cell types. We present here the high-resolution crystal structures and molecular simulation studies of both A-form and B-form DNA duplexes containing 5hmC. We observed that 5hmC interacts with its 3'-neighboring bases through water-bridged hydrogen bonds and these interactions may affect the further oxidation of 5hmC.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Srivathsan V Ranganathan
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Vibhav A Valsangkar
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Stephanie M Magliocco
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Fusheng Shen
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Alan Chen
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
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230
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Miller D, Choi GJ, Orbe HS, Knowles RR. Catalytic Olefin Hydroamidation Enabled by Proton-Coupled Electron Transfer. J Am Chem Soc 2015; 137:13492-5. [PMID: 26439818 PMCID: PMC4629195 DOI: 10.1021/jacs.5b09671] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 12/24/2022]
Abstract
Here we report a ternary catalyst system for the intramolecular hydroamidation of unactivated olefins using simple N-aryl amide derivatives. Amide activation in these reactions occurs via concerted proton-coupled electron transfer (PCET) mediated by an excited state iridium complex and weak phosphate base to furnish a reactive amidyl radical that readily adds to pendant alkenes. A series of H-atom, electron, and proton transfer events with a thiophenol cocatalyst furnish the product and regenerate the active forms of the photocatalyst and base. Mechanistic studies indicate that the amide substrate can be selectively homolyzed via PCET in the presence of the thiophenol, despite a large difference in bond dissociation free energies between these functional groups.
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Affiliation(s)
- David
C. Miller
- Department of Chemistry, Princeton
University, Princeton, New Jersey 08544, United States
| | - Gilbert J. Choi
- Department of Chemistry, Princeton
University, Princeton, New Jersey 08544, United States
| | - Hudson S. Orbe
- Department of Chemistry, Princeton
University, Princeton, New Jersey 08544, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton
University, Princeton, New Jersey 08544, United States
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231
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Kretchmer JS, Miller TF. Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer. Inorg Chem 2015; 55:1022-31. [PMID: 26440812 DOI: 10.1021/acs.inorgchem.5b01821] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua S. Kretchmer
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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232
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Temperature dependence of the oxidation kinetics of TyrZ and TyrD in oxygen-evolving photosystem II complexes throughout the range from 320K to 5K. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1283-96. [DOI: 10.1016/j.bbabio.2015.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 11/21/2022]
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233
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Ru(II)-diimine functionalized metalloproteins: From electron transfer studies to light-driven biocatalysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:589-597. [PMID: 26392147 DOI: 10.1016/j.bbabio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/07/2015] [Indexed: 11/20/2022]
Abstract
The unique photochemical properties of Ru(II)-diimine complexes have helped initiate a series of seminal electron transfer studies in metalloenzymes. It has thus been possible to experimentally determine rate constants for long-range electron transfers. These studies have laid the foundation for the investigation of reactive intermediates in heme proteins and for the design of light-activated biocatalysts. Various metalloenzymes such as hydrogenase, carbon monoxide dehydrogenase, nitrogenase, laccase and cytochrome P450 BM3 have been functionalized with Ru(II)-diimine complexes. Upon visible light-excitation, these photosensitized metalloproteins are capable of sustaining photocatalytic activity to reduce small molecules such as protons, acetylene, hydrogen cyanide and carbon monoxide or activate molecular dioxygen to produce hydroxylated products. The Ru(II)-diimine photosensitizers are hence able to deliver multiple electrons to metalloenzymes buried active sites, circumventing the need for the natural redox partners. In this review, we will highlight the key achievements of the light-driven biocatalysts, which stem from the extensive electron transfer investigations. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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234
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Büldt LA, Prescimone A, Neuburger M, Wenger OS. Photoredox Properties of Homoleptic d6Metal Complexes with the Electron-Rich 4,4′,5,5′-Tetramethoxy-2,2′-bipyridine Ligand. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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235
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Welker EA, Tiley BL, Sasaran CM, Zuchero MA, Tong WS, Vettleson MJ, Richards RA, Geruntho JG, Stoll S, Wolbach JP, Rhile IJ. Conformational Change with Steric Interactions Affects the Inner Sphere Component of Concerted Proton-Electron Transfer in a Pyridyl-Appended Radical Cation System. J Org Chem 2015; 80:8705-12. [PMID: 26270193 PMCID: PMC10758225 DOI: 10.1021/acs.joc.5b01427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton-coupled electron transfer (PCET) model systems combine one-electron oxidants and bases to generate net hydrogen atom acceptors. We have generated two persistent pyridyl-appended radical cations: 10-(pyrid-2-yl)-10H-phenothiazinium (PPT•+) and 3-(pyrid-2-yl)-10-methyl-10H-phenothiazinium (MPTP•+). EPR spectra and corresponding calculations indicate phenothiazinium radical cations with minimal spin on the pyridine nitrogen. Addition of hindered phenols causes the radical cations to decay, and protonated products and the corresponding phenoxyl radicals to form. The ΔG° values for the formation of intermediates (determined through cyclic voltammetry and pKa measurements) rule out a stepwise mechanism, and kinetic isotope effects support concerted proton–electron transfer (CPET) as the mechanism. Calculations indicate that the reaction of PPT•+ + tBu3PhOH undergoes a significant conformational change with steric interactions on the diabatic surface while maintaining the hydrogen bond; in contrast, MPTP•+ + tBu3PhOH maintains its conformation throughout the reaction. This difference is reflected in both experiment and calculations with ΔG(⧧)MPTP•+ < ΔG(⧧)PPT•+ despite ΔG°MPTP•+ > ΔG°PPT•+. Experimental results with 2,6-di-tert-butyl-4-methoxyphenol are similar. Hence, despite the structural similarity between the compounds, differences in the inner sphere component for CPET affect the kinetics.
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Affiliation(s)
- Evan A. Welker
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Brittney L. Tiley
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Crina M. Sasaran
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Matthew A. Zuchero
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Wing-Sze Tong
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Melissa J. Vettleson
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Robert A. Richards
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Jonathan G. Geruntho
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, United States
| | | | - Ian J. Rhile
- Department of Chemistry and Biochemistry, Albright College, Reading, PA 19610-5234, United States
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236
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Feliciano GT, Steidl RJ, Reguera G. Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:22217-26. [PMID: 26243427 DOI: 10.1039/c5cp03432a] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geobacter sulfurreducens (GS) electronically connects with extracellular electron acceptors using conductive protein filaments or pili. To gain insights into their role as biological nanowires, we investigated the structural dynamics of the GS pilus in solution via molecular dynamics simulations. In the model, all of the pilin's aromatics clustered as a right-handed helical band along the pilus, maintaining inter-aromatic distances and dimer configurations optimal for multistep hopping. The aromatics were interspersed within the regions of highest negative potential, which influenced the type and configuration of the aromatic contacts and the rates of electron transfer. Small foci of positive potential were also present but were neutralized within uncharged regions, thus minimizing charge trapping. Consistent with the model predictions, mutant strains with reduced aromatic contacts or negative potentials had defects in pili functions such as the reduction of Fe(III) oxides and electrodes. The results therefore support the notion of a pilus fiber evolved to function as an electronic conduit between the cell and extracellular electron acceptors.
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Affiliation(s)
- G T Feliciano
- Departamento de Físico-Química, Instituto de Quimica, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Nanobionics Group, Sao Paulo, Araraquara, Brazil
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237
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Chen HB, Lambert N, Cheng YC, Chen YN, Nori F. Using non-Markovian measures to evaluate quantum master equations for photosynthesis. Sci Rep 2015; 5:12753. [PMID: 26238479 PMCID: PMC4523852 DOI: 10.1038/srep12753] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022] Open
Abstract
When dealing with system-reservoir interactions in an open quantum system, such as a photosynthetic light-harvesting complex, approximations are usually made to obtain the dynamics of the system. One question immediately arises: how good are these approximations, and in what ways can we evaluate them? Here, we propose to use entanglement and a measure of non-Markovianity as benchmarks for the deviation of approximate methods from exact results. We apply two frequently-used perturbative but non-Markovian approximations to a photosynthetic dimer model and compare their results with that of the numerically-exact hierarchy equation of motion (HEOM). This enables us to explore both entanglement and non-Markovianity measures as means to reveal how the approximations either overestimate or underestimate memory effects and quantum coherence. In addition, we show that both the approximate and exact results suggest that non-Markonivity can, counter-intuitively, increase with temperature, and with the coupling to the environment.
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Affiliation(s)
- Hong-Bin Chen
- Department of Physics and National Center for Theoretical Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | | | - Yuan-Chung Cheng
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yueh-Nan Chen
- Department of Physics and National Center for Theoretical Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Franco Nori
- 1] CEMS, RIKEN, Wako-shi, Saitama 351-0198, Japan [2] Physics Department, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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238
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Song DY, Pizano AA, Holder PG, Stubbe J, Nocera DG. Direct Interfacial Y 731 Oxidation in α 2 by a Photoβ 2 Subunit of E. coli Class Ia Ribonucleotide Reductase. Chem Sci 2015; 6:4519-4524. [PMID: 26504513 PMCID: PMC4618407 DOI: 10.1039/c5sc01125f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022] Open
Abstract
Proton-coupled electron transfer (PCET) is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalysed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair. These enzymes catalyse the conversion of nucleoside diphosphates (NDPs) to deoxynucleoside diphosphates (dNDPs). In the class Ia RNRs, NDP reduction involves a tyrosyl radical mediated oxidation occurring over 35 Å across the interface of the two required subunits (β2 and α2) involving multiple PCET steps and the conserved tyrosine triad [Y356(β2)-Y731(α2)-Y730(α2)]. We report the synthesis of an active photochemical RNR (photoRNR) complex in which a Re(I)-tricarbonyl phenanthroline ([Re]) photooxidant is attached site-specifically to the Cys in the Y356C-(β2) subunit and an ionizable, 2,3,5-trifluorotyrosine (2,3,5-F3Y) is incorporated in place of Y731 in α2. This intersubunit PCET pathway is investigated by ns laser spectroscopy on [Re356]-β2:2,3,5-F3Y731-α2 in the presence of substrate, CDP, and effector, ATP. This experiment has allowed analysis of the photoinjection of a radical into α2 from β2 in the absence of the interfacial Y356 residue. The system is competent for light-dependent substrate turnover. Time-resolved emission experiments reveal an intimate dependence of the rate of radical injection on the protonation state at position Y731(α2), which in turn highlights the importance of a well-coordinated proton exit channel involving the key residues, Y356 and Y731, at the subunit interface.
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Affiliation(s)
- David Y. Song
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Arturo A. Pizano
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Patrick G. Holder
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - JoAnne Stubbe
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139-4307 , USA .
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
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239
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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240
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Choi GJ, Knowles RR. Catalytic Alkene Carboaminations Enabled by Oxidative Proton-Coupled Electron Transfer. J Am Chem Soc 2015; 137:9226-9. [PMID: 26166022 DOI: 10.1021/jacs.5b05377] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here we describe a dual catalyst system comprised of an iridium photocatalyst and weak phosphate base that is capable of both selectively homolyzing the N-H bonds of N-arylamides (bond dissociation free energies ∼ 100 kcal/mol) via concerted proton-coupled electron transfer (PCET) and mediating efficient carboamination reactions of the resulting amidyl radicals. This manner of PCET activation, which finds its basis in numerous biological redox processes, enables the formal homolysis of a stronger amide N-H bond in the presence of weaker allylic C-H bonds, a selectivity that is uncommon in conventional molecular H atom acceptors. Moreover, this transformation affords access to a broad range of structurally complex heterocycles from simple amide starting materials. The design, synthetic scope, and mechanistic evaluation of the PCET process are described.
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Affiliation(s)
- Gilbert J Choi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert R Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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241
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Mishra A, Sahu S, Tripathi S, Krishnamoorthy G. Photoinduced intramolecular charge transfer in trans-2-[4'-(N,N-dimethylamino)styryl]imidazo[4,5-b]pyridine: effect of introducing a C[double bond, length as m-dash]C double bond. Photochem Photobiol Sci 2015; 13:1476-86. [PMID: 25103414 DOI: 10.1039/c4pp00237g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The spectral characteristics of trans-2-[4'-(N,N-dimethylamino)styryl]imidazo[4,5-b]pyridine (t-DMASIP-b) have been investigated using absorption and fluorescence techniques, and compared with 2-(4'-N,N-dimethylamino)imidazo[4,5-b]pyridine (DMAPIP-b). The study reveals that introduction of a C[double bond, length as m-dash]C double bond strongly perturbs the photophysics of the system. Unlike DMAPIP-b, t-DMASIP-b emits a single emission in aprotic and protic solvents. The emission occurs from the locally excited state in nonpolar solvents and from a planar intramolecular charge transfer (PICT) state in polar solvents. Multiple linear regression analysis suggests that among the different solvent parameters, the dipolar interaction contributes more to the stabilization of the system in both the ground and excited states. Theoretical calculations suggest that, unlike in DMAPIP-b, proton coupled twisted intramolecular charge transfer (TICT) emission does not occur in t-DMASIP-b. The higher quantum yield obtained in the viscous solvent glycerol is attributed to the restriction of the twisting of the olefinic bond. The photoirradiation of t-DMASIP-b shows that isomerization takes place in all solvents, including viscous glycerol. The theoretically simulated potential energy surface shows that isomerization occurs via a phantom state, which is a nonradiative process. The rise in temperature favors the photoisomerization, thus, the fluorescence quantum yield decreases. The prototropic study indicates that, unlike in DMAPIP-b, the protonation takes place at different places to form the monocations.
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Affiliation(s)
- Anasuya Mishra
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India.
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242
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Mitsumi M, Ezaki K, Komatsu Y, Toriumi K, Miyatou T, Mizuno M, Azuma N, Miyazaki Y, Nakano M, Kitagawa Y, Hanashima T, Kiyanagi R, Ohhara T, Nakasuji K. Proton Order-Disorder Phenomena in a Hydrogen-Bonded Rhodium-η(5)-Semiquinone Complex: A Possible Dielectric Response Mechanism. Chemistry 2015; 21:9682-96. [PMID: 26032896 DOI: 10.1002/chem.201500796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 11/06/2022]
Abstract
A newly synthesized one-dimensional (1D) hydrogen-bonded (H-bonded) rhodium(II)-η(5)-semiquinone complex, [Cp*Rh(η(5)-p-HSQ-Me4)]PF6 ([1]PF6; Cp* = 1,2,3,4,5-pentamethylcyclopentadienyl; HSQ = semiquinone) exhibits a paraelectric-antiferroelectric second-order phase transition at 237.1 K. Neutron and X-ray crystal structure analyses reveal that the H-bonded proton is disordered over two sites in the room-temperature (RT) phase. The phase transition would arise from this proton disorder together with rotation or libration of the Cp* ring and PF6(-) ion. The relative permittivity εb' along the H-bonded chains reaches relatively high values (ca., 130) in the RT phase. The temperature dependence of (13)C CP/MAS NMR spectra demonstrates that the proton is dynamically disordered in the RT phase and that the proton exchange has already occurred in the low-temperature (LT) phase. Rate constants for the proton exchange are estimated to be 10(-4)-10(-6) s in the temperature range of 240-270 K. DFT calculations predict that the protonation/deprotonation of [1](+) leads to interesting hapticity changes of the semiquinone ligand accompanied by reduction/oxidation by the π-bonded rhodium fragment, producing the stable η(6)-hydroquinone complex, [Cp*Rh(3+)(η(6)-p-H2Q-Me4)](2+) ([2](2+)), and η(4)-benzoquinone complex, [Cp*Rh(+)(η(4)-p-BQ-Me4)] ([3]), respectively. Possible mechanisms leading to the dielectric response are discussed on the basis of the migration of the protonic solitons comprising of [2](2+) and [3], which would be generated in the H-bonded chain.
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Affiliation(s)
- Minoru Mitsumi
- Department of Material Science, Graduate School of Material Science, University of Hyogo and, Research Center for New Functional Materials, Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan).
| | - Kazunari Ezaki
- Department of Material Science, Graduate School of Material Science, University of Hyogo and, Research Center for New Functional Materials, Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)
| | - Yuuki Komatsu
- Department of Material Science, Graduate School of Material Science, University of Hyogo and, Research Center for New Functional Materials, Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)
| | - Koshiro Toriumi
- Department of Material Science, Graduate School of Material Science, University of Hyogo and, Research Center for New Functional Materials, Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)
| | - Tatsuya Miyatou
- Department of Chemistry, Graduate School of Natural Science & Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192 (Japan)
| | - Motohiro Mizuno
- Department of Chemistry, Graduate School of Natural Science & Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192 (Japan).
| | - Nobuaki Azuma
- Research Center for Structural Thermodynamics, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan)
| | - Yuji Miyazaki
- Research Center for Structural Thermodynamics, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan).
| | - Motohiro Nakano
- Research Center for Structural Thermodynamics, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 (Japan)
| | - Yasutaka Kitagawa
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531 (Japan).
| | - Takayasu Hanashima
- Research Center for Neutron Science and Technology, CROSS Tokai, Ibaraki 319-1106 (Japan)
| | - Ryoji Kiyanagi
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 (Japan)
| | - Takashi Ohhara
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 (Japan).
| | - Kazuhiro Nakasuji
- School of Materials Science, Fukui University of Technology, 3-6 Gakuen, Fukui 910-8505 (Japan)
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243
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Liu Y, Liu H, Song K, Xu Y, Shi Q. Theoretical Study of Proton Coupled Electron Transfer Reactions: The Effect of Hydrogen Bond Bending Motion. J Phys Chem B 2015; 119:8104-14. [DOI: 10.1021/acs.jpcb.5b02927] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Liu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Hao Liu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Kai Song
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Yang Xu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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244
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Driscoll E, Sorenson S, Dawlaty JM. Ultrafast Intramolecular Electron and Proton Transfer in Bis(imino)isoindole Derivatives. J Phys Chem A 2015; 119:5618-25. [DOI: 10.1021/acs.jpca.5b02889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric Driscoll
- Department
of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, United States
| | - Shayne Sorenson
- Department
of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, United States
| | - Jahan M. Dawlaty
- Department
of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, United States
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245
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Zhu H, Sommerhalter M, Nguy AKL, Klinman JP. Solvent and Temperature Probes of the Long-Range Electron-Transfer Step in Tyramine β-Monooxygenase: Demonstration of a Long-Range Proton-Coupled Electron-Transfer Mechanism. J Am Chem Soc 2015; 137:5720-9. [PMID: 25919134 PMCID: PMC4970857 DOI: 10.1021/ja512388n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Tyramine
β-monooxygenase (TβM) belongs to a family
of physiologically important dinuclear copper monooxygenases that
function with a solvent-exposed active site. To accomplish each enzymatic
turnover, an electron transfer (ET) must occur between two solvent-separated
copper centers. In wild-type TβM, this event is too fast to
be rate limiting. However, we have recently shown [Osborne, R. L.;
et al. Biochemistry2013, 52, 1179] that the Tyr216Ala variant of TβM leads to rate-limiting
ET. In this study, we present a pH–rate profile study of Tyr216Ala,
together with deuterium oxide solvent kinetic isotope effects (KIEs).
A solvent KIE of 2 on kcat is found in
a region where kcat is pH/pD independent.
As a control, the variant Tyr216Trp, for which ET is not rate determining,
displays a solvent KIE of unity. We conclude, therefore, that the
observed solvent KIE arises from the rate-limiting ET step in the
Tyr216Ala variant, and show
how small solvent KIEs (ca. 2) can be fully accommodated from equilibrium effects within the Marcus equation. To gain insight into the role of the enzyme in the long-range
ET step, a temperature dependence study was also pursued. The small
enthalpic barrier of ET (Ea = 3.6 kcal/mol)
implicates a significant entropic barrier, which is attributed to
the requirement for extensive rearrangement of the inter-copper environment
during PCET catalyzed by the Tyr216Ala variant. The data lead to the
proposal of a distinct inter-domain pathway for PCET in the dinuclear
copper monooxygenases.
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Affiliation(s)
| | - Monika Sommerhalter
- #Department of Chemistry and Biochemistry, California State University, East Bay, 25800 Carlos Bee Boulevard, Hayward, California 94542, United States
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246
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Dogutan DK, Bediako DK, Graham DJ, Lemon CM, Nocera DG. Proton-coupled electron transfer chemistry of hangman macrocycles: Hydrogen and oxygen evolution reactions. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424614501016] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The splitting of water into its constituent elements is an important solar fuels conversion reaction for the storage of renewable energy. For each of the half reactions of the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), multiple protons and electrons must be coupled to avoid high-energy intermediates. To understand the mechanistic details of the PCET chemistry that underpins HER and OER, we have designed hangman porphyrin and corrole catalysts. In these hangman constructs, a pendant acid/base functionality within the secondary coordination sphere is "hung" above the macrocyclic redox platform on which substrate binds. The two critical thermodynamic properties of a PCET event, the redox potential and pKa may be tuned with the macrocycle and hanging group, respectively. This review outlines the synthesis of these catalysts, as well as the examination of the PCET kinetics of hydrogen and oxygen evolution by the hangman catalysts. The insights provided by these systems provide a guide for the design of future HER and OER catalysts that use a secondary coordination sphere to manage PCET.
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Affiliation(s)
- Dilek K. Dogutan
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - D. Kwabena Bediako
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - Daniel J. Graham
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - Christopher M. Lemon
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, 02138, United States
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247
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Greene BL, Wu CH, McTernan PM, Adams MWW, Dyer RB. Proton-coupled electron transfer dynamics in the catalytic mechanism of a [NiFe]-hydrogenase. J Am Chem Soc 2015; 137:4558-66. [PMID: 25790178 DOI: 10.1021/jacs.5b01791] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The movement of protons and electrons is common to the synthesis of all chemical fuels such as H2. Hydrogenases, which catalyze the reversible reduction of protons, necessitate transport and reactivity between protons and electrons, but a detailed mechanism has thus far been elusive. Here, we use a phototriggered chemical potential jump method to rapidly initiate the proton reduction activity of a [NiFe] hydrogenase. Coupling the photochemical initiation approach to nanosecond transient infrared and visible absorbance spectroscopy afforded direct observation of interfacial electron transfer and active site chemistry. Tuning of intramolecular proton transport by pH and isotopic substitution revealed distinct concerted and stepwise proton-coupled electron transfer mechanisms in catalysis. The observed heterogeneity in the two sequential proton-associated reduction processes suggests a highly engineered protein environment modulating catalysis and implicates three new reaction intermediates; Nia-I, Nia-D, and Nia-SR(-). The results establish an elementary mechanistic understanding of catalysis in a [NiFe] hydrogenase with implications in enzymatic proton-coupled electron transfer and biomimetic catalyst design.
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Affiliation(s)
- Brandon L Greene
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
| | - Chang-Hao Wu
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Patrick M McTernan
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael W W Adams
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R Brian Dyer
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
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248
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Bourrez M, Steinmetz R, Ott S, Gloaguen F, Hammarström L. Concerted proton-coupled electron transfer from a metal-hydride complex. Nat Chem 2015; 7:140-5. [PMID: 25615667 DOI: 10.1038/nchem.2157] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/08/2014] [Indexed: 11/09/2022]
Abstract
Metal hydrides are key intermediates in the catalytic reduction of protons and CO2 as well as in the oxidation of H2. In these reactions, electrons and protons are transferred to or from separate acceptors or donors in bidirectional protoncoupled electron transfer (PCET) steps. The mechanistic interpretation of PCET reactions of metal hydrides has focused on the stepwise transfer of electrons and protons. A concerted transfer may, however, occur with a lower reaction barrier and therefore proceed at higher catalytic rates. Here we investigate the feasibility of such a reaction by studying the oxidation–deprotonation reactions of a tungsten hydride complex. The rate dependence on the driving force for both electron transfer and proton transfer—employing different combinations of oxidants and bases—was used to establish experimentally the concerted, bidirectional PCET of a metal-hydride species. Consideration of the findings presented here in future catalyst designs may lead to more-efficient catalysts.
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Affiliation(s)
- Marc Bourrez
- UMR 6521, Centre National de la Recherche Scientifique, Université de Bretagne Occidentale, 6 Avenue Le Gorgeu, 29238 Brest, France
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249
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Abstract
An enormous variety of biological redox reactions are accompanied by changes in proton content at enzyme active sites, in their associated cofactors, in substrates and/or products, and between protein interfaces. Understanding this breadth of reactivity is an ongoing chemical challenge. A great many workers have developed and investigated biomimetic model complexes to build new ways of thinking about the mechanistic underpinnings of such complex biological proton-coupled electron transfer (PCET) reactions. Of particular importance are those model reactions that involve transfer of one proton (H(+)) and one electron (e(-)), which is equivalent to transfer of a hydrogen atom (H(•)). In this Current Topic, we review key concepts in PCET reactivity and describe important advances in biomimetic PCET chemistry, with a special emphasis on research that has enhanced efforts to understand biological PCET reactions.
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Affiliation(s)
- Jeffrey J. Warren
- Simon Fraser University, Department of Chemistry, 8888 University Drive, Burnaby BC, Canada V5A 1S6
| | - James M. Mayer
- Yale University, Department of Chemistry, P.O. Box 208107, 225 Prospect Street, New Haven, CT 06520-8107
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Chatterjee S, Sengupta K, Samanta S, Das PK, Dey A. Concerted Proton–Electron Transfer in Electrocatalytic O2 Reduction by Iron Porphyrin Complexes: Axial Ligands Tuning H/D Isotope Effect. Inorg Chem 2015; 54:2383-92. [DOI: 10.1021/ic5029959] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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