Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-9903
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Main Title: Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations
Author(s): Moubarak, Samah
Elghobashi-Meinhardt, Nadia Said
Tombolelli, Daria
Mroginski, Maria Andrea
Type: Article
Language Code: en
Abstract: The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a diamagnetic Ni2+ atom was modeled in combination with both Fe2+ and Fe3+ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe2+ and Fe3+ oxidation states may be responsible for the acquired vibrational spectra.
URI: https://depositonce.tu-berlin.de/handle/11303/11011
http://dx.doi.org/10.14279/depositonce-9903
Issue Date: 22-Jan-2020
Date Available: 24-Apr-2020
DDC Class: 540 Chemie und zugeordnete Wissenschaften
Subject(s): NiFeSe hydrogenase
quantum mechanics
QM
molecular mechanics
MM
geometry optimizations
vibrational frequency analyses
Fourier transform infrared frequencies
FTIR
Sponsor/Funder: DFG, 390540038, EXC 2008: UniSysCat
DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berlin
EC/H2020/810856/EU/Twin to Illuminate Metals in Biology and Biocatalysis through Biospectroscopy/TIMB3
License: https://creativecommons.org/licenses/by/4.0/
Journal Title: Applied Sciences
Publisher: MDPI
Publisher Place: Basel
Volume: 10
Issue: 3
Article Number: 781
Publisher DOI: 10.3390/app10030781
EISSN: 2076-3417
Appears in Collections:FG Modellierung biomolekularer Systeme » Publications

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