scholarly journals Reaction Coordinate Leading to H2Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory

2017 ◽  
Vol 139 (46) ◽  
pp. 16894-16902 ◽  
Author(s):  
Vladimir Pelmenschikov ◽  
James A. Birrell ◽  
Cindy C. Pham ◽  
Nakul Mishra ◽  
Hongxin Wang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Vibrational Spectroscopy ◽  
Density Functional ◽  
Reaction Coordinate ◽  
Nuclear Resonance ◽  
Functional Theory ◽  
Nuclear Resonance Vibrational Spectroscopy

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 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 Structure and vibrational spectroscopy of methanesulfonic acid

2018 ◽  
Vol 5 (12) ◽  
pp. 181363 ◽  
Author(s):  
Lisha Zhong ◽  
Stewart F. Parker
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Vibrational Spectroscopy ◽  
Density Functional ◽  
Inelastic Neutron Scattering ◽  
Linear Chain ◽  
Methanesulfonic Acid ◽  
Chain Structure ◽  
Trifluoromethanesulfonic Acid ◽  
Functional Theory

In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate the structure of methanesulfonic acid (MSA) in the liquid and solid states. The spectra clearly show that the hydrogen bonding is much stronger in the solid than the liquid state. The structure of MSA is not known; however, mineral acids typically adopt a chain structure in condensed phases. A periodic density functional theory (CASTEP) calculation based on the linear chain structure found in the closely related molecule trifluoromethanesulfonic acid gave good agreement between the observed and calculated spectra, particularly with regard to the methyl and sulfonate groups. The model accounts for the large widths of the asymmetric S-O stretch modes; however, the external mode region is not well described. Together, these observations suggest that the basic model of four molecules in the primitive unit cell, linked by hydrogen bonding into chains, is correct, but that MSA crystallizes in a different space group than that of trifluoromethanesulfonic acid.

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