scholarly journals A Combined Probe-Molecule, Mössbauer, Nuclear Resonance Vibrational Spectroscopy, and Density Functional Theory Approach for Evaluation of Potential Iron Active Sites in an Oxygen Reduction Reaction Catalyst

2017 ◽  
Vol 121 (30) ◽  
pp. 16283-16290 ◽  
Author(s):  
Jared L. Kneebone ◽  
Stephanie L. Daifuku ◽  
Jeffrey A. Kehl ◽  
Gang Wu ◽  
Hoon T. Chung ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Reduction Reaction ◽  
Nuclear Resonance ◽  
Theory Approach ◽  
Functional Theory ◽  
Nuclear Resonance Vibrational Spectroscopy ◽  
Iron Active Sites ◽  
Oxygen Reduction Reaction Catalyst

scholarly journals Modeling nuclear resonance vibrational spectroscopic data of binuclear nonheme iron enzymes using density functional theory

2014 ◽  
Vol 92 (10) ◽  
pp. 975-978 ◽  
Author(s):  
Kiyoung Park ◽  
Edward I. Solomon
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Structural Information ◽  
Nonheme Iron ◽  
Nuclear Resonance ◽  
Functional Theory ◽  
Nonheme Iron Enzymes ◽  
Iron Enzymes ◽  
Dft Model

Nuclear resonance vibrational spectroscopy (NRVS) is a powerful technique that can provide geometric structural information on key reaction intermediates of Fe-containing systems when utilized in combination with density functional theory (DFT). However, in the case of binuclear nonheme iron enzymes, DFT-predicted NRVS spectra have been found to be sensitive to the truncation method used to model the active sites of the enzymes. Therefore, in this study various-level truncation schemes have been tested to predict the NRVS spectrum of a binuclear nonheme iron enzyme, and a reasonably sized DFT model that is suitable for employing the NRVS/DFT combined methodology to characterize binuclear nonheme iron enzymes has been developed.

scholarly journals Hydroxo-Bridged Active Site of Flavodiiron NO Reductase Revealed by Spectroscopy and Computations

2020 ◽  
Author(s):  
Filipe Folgosa ◽  
Vladimir Pelmenschikov ◽  
Matthias Keck ◽  
Christian Lorent ◽  
Yoshitaka Yoda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Density Functional Theory ◽  
Data Collection ◽  
Active Site ◽  
Density Functional ◽  
Nuclear Resonance ◽  
Structural Studies ◽  
Functional Theory ◽  
Nuclear Resonance Vibrational Spectroscopy ◽  
Ligand Interactions

<p>NO and O<sub>2</sub> are detoxified in many organisms using flavodiiron proteins (FDPs). The exact coordination of the iron centre in the active site of these enzymes remains unclear despite numerous structural studies. Here, we used <sup>57</sup>Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the iron-ligand interactions in <i>Escherichia coli</i> FDP. This data combined with density functional theory (DFT) and <sup>57</sup>Fe Mössbauer spectroscopy indicate that the oxidised form of FDP contains a dihydroxo-diferric Fe(III)–(µOH<sup>–</sup>)<sub>2</sub>–Fe(III) active site, while its reduction gives rise to a monohydroxo-diferrous Fe(II)–(µOH<sup>–</sup>)–Fe(II) site upon elimination of one bridging OH<sup>–</sup> ligand, thereby providing an open coordination site for NO binding. Prolonged NRVS data collection of the oxidised FDP resulted in photoreduction and formation of a partially reduced diiron center with two bridging hydroxyl ligands. These results have crucial implications for studying and understanding the mechanism of FDP as well as other non-haem diiron enzymes.</p>

scholarly journals Density functional theory study of active sites on nitrogen-doped graphene for oxygen reduction reaction

2021 ◽  
Vol 8 (9) ◽  
pp. 210272
Author(s):  
Ping Yan ◽  
Song Shu ◽  
Longhua Zou ◽  
Yongjun Liu ◽  
Jianjun Li ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Active Sites ◽  
Density Functional ◽  
Reduction Reaction ◽  
Functional Theory ◽  
Nitrogen Doped ◽  
Nitrogen Doped Graphene ◽  
Doped Graphene ◽  
Orr Activity

Oxygen reduction reaction (ORR) remains challenging due to its complexity and slow kinetics. In particular, Pt-based catalysts which possess outstanding ORR activity are limited in application with high cost and ease of poisoning. In recent years, nitrogen-doped graphene has been widely studied as a potential ORR catalyst for replacing Pt. However, the vague understanding of the reaction mechanism and active sites limits the potential ORR activity of nitrogen-doped graphene materials. Herein, density functional theory is used to study the reaction mechanism and active sites of nitrogen-doped graphene for ORR at the atomic level, focusing on explaining the important role of nitrogen species on ORR. The results reveal that graphitic N (GrN) doping is beneficial to improve the ORR performance of graphene, and dual-GrN-doped graphene can demonstrate the highest catalytic properties with the lowest barriers of ORR. These results provide a theoretical guide for designing catalysts with ideal ORR property, which puts forward a new approach to conceive brilliant catalysts related to energy conversion and environmental catalysis.

scholarly journals Hydroxo-Bridged Active Site of Flavodiiron NO Reductase Revealed by Spectroscopy and Computations

2020 ◽  
Author(s):  
Filipe Folgosa ◽  
Vladimir Pelmenschikov ◽  
Matthias Keck ◽  
Christian Lorent ◽  
Yoshitaka Yoda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Density Functional Theory ◽  
Data Collection ◽  
Active Site ◽  
Density Functional ◽  
Nuclear Resonance ◽  
Structural Studies ◽  
Functional Theory ◽  
Nuclear Resonance Vibrational Spectroscopy ◽  
Ligand Interactions

<p>NO and O<sub>2</sub> are detoxified in many organisms using flavodiiron proteins (FDPs). The exact coordination of the iron centre in the active site of these enzymes remains unclear despite numerous structural studies. Here, we used <sup>57</sup>Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the iron-ligand interactions in <i>Escherichia coli</i> FDP. This data combined with density functional theory (DFT) and <sup>57</sup>Fe Mössbauer spectroscopy indicate that the oxidised form of FDP contains a dihydroxo-diferric Fe(III)–(µOH<sup>–</sup>)<sub>2</sub>–Fe(III) active site, while its reduction gives rise to a monohydroxo-diferrous Fe(II)–(µOH<sup>–</sup>)–Fe(II) site upon elimination of one bridging OH<sup>–</sup> ligand, thereby providing an open coordination site for NO binding. Prolonged NRVS data collection of the oxidised FDP resulted in photoreduction and formation of a partially reduced diiron center with two bridging hydroxyl ligands. These results have crucial implications for studying and understanding the mechanism of FDP as well as other non-haem diiron enzymes.</p>

scholarly journals Study on the adsorption selection of CH$$_4$$ on CuO (110) versus (111) surfaces: a density functional theory study

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Adsorption Capacity ◽  
Active Sites ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Density Functional Theory Calculations ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Strong Adsorption ◽  
Selection Of

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.

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