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Agee A, Pace G, Yang V, Segalman R, Furst AL. Mixed Conducting Polymers Alter Electron Transfer Thermodynamics to Boost Current Generation from Electroactive Microbes. J Am Chem Soc 2024; 146:19728-19736. [PMID: 39001879 PMCID: PMC11276794 DOI: 10.1021/jacs.4c01288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024]
Abstract
Electroactive microbes that can release or take up electrons are essential components of nearly every ecological niche and are powerful tools for the development of alternative energy technologies. Small-molecule mediators are critical for this electron transfer but remain difficult to study and engineer because they perform concerted two-electron transfer in native systems but only individual, one-electron transfers in electrochemical studies. Here, we report that electrode modification with ion- and electron-conductive polymers yields biosimilar, concerted two-electron transfer from Shewanella oneidensis via flavin mediators. S. oneidensis biofilms on these polymers show significantly improved per-microbe current generation and morphologies that more closely resemble native systems, setting a new paradigm for the study and optimization of these electron transfer processes. The unprecedented concerted electron transfer was found to be due to altered mediator electron transfer thermodynamics, enabling biologically relevant studies of electroactive biofilms in the lab for the first time. These important findings pave the way for a complete understanding of the ecological role of electroactive microbes and their broad application in sustainable technologies.
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Affiliation(s)
- Alec Agee
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Gordon Pace
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Victoria Yang
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Rachel Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
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2
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Kametani Y, Ikeda K, Yoshizawa K, Shiota Y. Mechanistic Study of Reduction of Nitrite to NO by the Copper(II) Complex: Different Concerted Proton-Electron Transfer Reactivity between Nitrite and Nitro Complexes. Inorg Chem 2023; 62:13765-13774. [PMID: 37590095 DOI: 10.1021/acs.inorgchem.3c01383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The literature contains numerous reports of copper complexes for nitrite (NO2-) reduction. However, details of how protons and electrons arrive and how nitric oxide (NO) is released remain unknown. The influence of the coordination mode of nitrite on reactivity is also under debate. Kundu and co-workers have reported nitrite reduction by a copper(II) complex [J. Am. Chem. Soc. 2020, 142, 1726-1730]. In their report, the copper(II) complex reduced nitrite using a phenol derivative as a reductant, resulting in NO, a hydroxyl copper(II) complex, and the corresponding biphenol. Also, the involvement of proton-coupled electron transfer was proposed by mechanistic studies. Herein, density functional theory calculations were performed to determine a mechanism for reduction of nitrite by a copper(II) complex. As a result of geometry optimization of an initial complex, two possible structures were obtained: Cu-ONO and Cu-NO2. Two possible reaction pathways initiated from Cu-ONO or Cu-NO2 were then considered. The calculation results indicated that the Cu-ONO pathway is energetically favorable. When changes in the electronic structure were considered, both pathways were found to involve concerted proton-electron transfer (CPET). In addition, an intrinsic reaction coordinate analysis revealed that the two pathways were achieved by different types of CPET. Furthermore, an intrinsic bond orbital analysis clearly indicated that, in the Cu-ONO pathway, the chemical events involved proceeded concertedly yet asynchronously.
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Affiliation(s)
- Yohei Kametani
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kei Ikeda
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Curtolo F, Arantes GM. Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. J Chem Inf Model 2023. [PMID: 37196341 DOI: 10.1021/acs.jcim.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The interconversion between fumarate and succinate is fundamental to the energy metabolism of nearly all organisms. This redox reaction is catalyzed by a large family of enzymes, fumarate reductases and succinate dehydrogenases, using hydride and proton transfers from a flavin cofactor and a conserved Arg side-chain. These flavoenzymes also have substantial biomedical and biotechnological importance. Therefore, a detailed understanding of their catalytic mechanisms is valuable. Here, calibrated electronic structure calculations in a cluster model of the active site of the Fcc3 fumarate reductase were employed to investigate various reaction pathways and possible intermediates in the enzymatic environment and to dissect interactions that contribute to catalysis of fumarate reduction. Carbanion, covalent adduct, carbocation, and radical intermediates were examined. Significantly lower barriers were obtained for mechanisms via carbanion intermediates, with similar activation energies for hydride and proton transfers. Interestingly, the carbanion bound to the active site is best described as an enolate. Hydride transfer is stabilized by a preorganized charge dipole in the active site and by the restriction of the C1-C2 bond in a twisted conformation of the otherwise planar fumarate dianion. But, protonation of a fumarate carboxylate and quantum tunneling effects are not critical for catalysis of the hydride transfer. Calculations also suggest that the driving force for enzyme turnover is provided by regeneration of the catalytic Arg, either coupled with flavin reduction and decomposition of a proposed transient state or directly from the solvent. The detailed mechanistic description of enzymatic reduction of fumarate provided here clarifies previous contradictory views and provides new insights into catalysis by essential flavoenzyme reductases and dehydrogenases.
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Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
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Fu Y, Yang L, Zhou Z, Jia T, Shen G, Zhu X. Comparison of Thermodynamic Energies for Elementary Steps of Anionic Hydrides to Release Hydride Ions in Acetonitrile. ChemistrySelect 2022. [DOI: 10.1002/slct.202203626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yan‐Hua Fu
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 China
| | - Li‐Guo Yang
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 China
| | - Zhong‐Yuan Zhou
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 China
| | - Taixuan Jia
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 China
| | - Guang‐Bin Shen
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Xiao‐Qing Zhu
- Department of Chemistry Nankai University Tianjin 300071 China
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Highly Sensitive Electrochemical Sensor for Sunset Yellow Based on Electrochemically Activated Glassy Carbon Electrode. Molecules 2022; 27:molecules27165221. [PMID: 36014459 PMCID: PMC9412420 DOI: 10.3390/molecules27165221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
Electrochemically activated glassy carbon electrode (AGCE) was fabricated and applied for sensitive and selective detection of sunset yellow (SY). The electroanalysis of SY was investigated by square wave voltammetry (SWV). Owed to the specific oxygen-contained functional groups and the outstanding conductivity of AGCE, the proposed sensor exhibits an enhanced oxidation peak current of SY when compared with non-activated glass carbon electrode (GCE). Under the optimal analytical conditions, the oxidation peak current is linear with SY concentration in the range of 0.005–1.0 μM. The low limit of detection is 0.00167 μM (S/N = 3). This method is applied for the detection of SY in the actual samples. The recovery is between 96.19 and 103.47%, indicating that AGCE is suitable for the determination of SY in beverage sample.
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Curtolo F, Arantes GM. Molecular properties and tautomeric equilibria of isolated flavins. J Comput Chem 2022; 43:1561-1572. [PMID: 35778728 DOI: 10.1002/jcc.26957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2022] [Indexed: 11/05/2022]
Abstract
Flavins are employed as redox cofactors and chromophores in a plethora of flavoenzymes. Their versatility is an outcome of intrinsic molecular properties of the isoalloxazine ring modulated by the protein scaffold and surrounding solvent. Thus, an investigation of isolated flavins with high-level electronic-structure methods and with error assessment of the calculated properties will contribute to building better models of flavin reactivity. Here, we benchmarked ground-state properties such as electron affinity, gas-phase basicity, dipole moment, torsion energy, and tautomer stability for lumiflavins in all biologically relevant oxidation and charge states. Overall, multiconfigurational effects are small and chemical accuracy is achieved by coupled-cluster treatments of energetic properties. Augmented basis sets and extrapolations to the complete basis-set limit are necessary for consistent agreement with experimental energetics. Among DFT functionals tested, M06-2X shows the best performance for most properties, except gas-phase basicity, in which M06 and CAM-B3LYP perform better. Moreover, dipole moments of radical flavins show large deviations for all functionals studied. Tautomers with noncanonical protonation states are significantly populated at normal temperatures, adding to the complexity of modeling flavins. These results will guide future computational studies of flavoproteins and flavin chemistry by indicating the limitations of electronic-structure methodologies and the contributions of multiple tautomeric states.
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Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Scoditti S, Dabbish E, Pieslinger GE, Rezabal E, Lopez X, Sicilia E, Salassa L. Flavin-mediated photoactivation of Pt(IV) anticancer complexes: computational insights on the catalytic mechanism. Phys Chem Chem Phys 2022; 24:5323-5329. [PMID: 35188500 DOI: 10.1039/d1cp05507k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism for the photocatalytic activation of Pt(IV) anticancer prodrugs by riboflavin in the presence of NADH has been investigated by DFT. In the first step of the reaction, the oxidation kinetics of NADH to afford the catalytically active riboflavin hydroquinone is dramatically favoured by generation of the flavin triplet excited state. In the triplet, formation of a π-π stacked adduct promotes the hydride transfer from NADH to riboflavin with an almost barrierless pathway (2.7 kcal mol-1). In the singlet channel, conversely, the process is endergonic and requires overcoming a higher activation energy (19.2 kcal mol-1). In the second half of the reaction, the reduction of the studied Pt(IV) complexes by riboflavin hydroquinone occurs via an inner sphere mechanism, displaying free energy barriers smaller than 10 kcal mol-1. Pt reduction by bioreductants such as NADH and ascorbate involve instead less stabilized transition states (22.2-38.3 kcal mol-1), suggesting that riboflavin hydroquinone is an efficient reducing agent for Pt(IV) derivatives in biological settings.
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Affiliation(s)
- Stefano Scoditti
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende (CS), 87036, Italy.
| | - Eslam Dabbish
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende (CS), 87036, Italy.
| | - German E Pieslinger
- CONICET - Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina
| | - Elixabete Rezabal
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain. .,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia, 20018, Spain
| | - Xabier Lopez
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain. .,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia, 20018, Spain
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, Università della Calabria, Arcavacata di Rende (CS), 87036, Italy.
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain. .,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia, 20018, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, 48011, Spain
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Camilo SRG, Curtolo F, Galassi VV, Arantes GM. Tunneling and Nonadiabatic Effects on a Proton-Coupled Electron Transfer Model for the Q o Site in Cytochrome bc1. J Chem Inf Model 2021; 61:1840-1849. [PMID: 33793213 DOI: 10.1021/acs.jcim.1c00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytochrome bc1 is a fundamental enzyme for cellular respiration and photosynthesis. This dimeric protein complex catalyzes a proton-coupled electron transfer (PCET) from the reduced coenzyme-Q substrate (Q) to a bimetallic iron-sulfur cluster in the Qo active site. Herein, we combine molecular dynamics simulations of the complete cytochrome bc1 protein with electronic-structure calculations of truncated models and a semiclassical tunneling theory to investigate the electron-proton adiabaticity of the initial reaction catalyzed in the Qo site. After sampling possible orientations between the Q substrate and a histidine side chain that functions as hydrogen acceptor, we find that a truncated model composed by ubiquinol-methyl and imidazole-iron(III)-sulfide captures the expected changes in oxidation and spin states of the electron donor and acceptor. Diabatic electronic surfaces obtained for this model with multiconfigurational wave function calculations demonstrate that this reaction is electronic nonadiabatic, and proton tunneling is faster than mixing of electronic configurations. These results indicate the formalism that should be used to calculate vibronic couplings and kinetic parameters for the initial reaction in the Qo site of cytochrome bc1. This framework for molecular simulation may also be applied to investigate other PCET reactions in the Q-cycle or in various metalloproteins that catalyze proton translocation coupled to redox processes.
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Affiliation(s)
- Sofia R G Camilo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Vanesa V Galassi
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
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