Geometry and Electronic Structure of the PCluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement
(2019) In Inorganic Chemistry 58(15). p.96729690 Abstract
We have studied the geometry and electronic structure of the Pcluster in nitrogenase in four oxidation states: P^{N}, P^{1+}, P^{2+}, and P^{3+}. We have employed combined quantum mechanical and molecular mechanical (QM/MM) calculations, using two different densityfunctional theory methods, TPSS and B3LYP. The calculations confirm that the side chain of Ser188 is most likely deprotonated in the partly oxidized P^{1+} state, thereby forming a bond to Fe6. Likewise, the backbone amide group of Cys88 is deprotonated in the doubly oxidized P^{2+} state, forming a bond to Fe5. The calculations also confirm the two conformations of the Pcluster in the atomicresolution crystal structure of... (More)
We have studied the geometry and electronic structure of the Pcluster in nitrogenase in four oxidation states: P^{N}, P^{1+}, P^{2+}, and P^{3+}. We have employed combined quantum mechanical and molecular mechanical (QM/MM) calculations, using two different densityfunctional theory methods, TPSS and B3LYP. The calculations confirm that the side chain of Ser188 is most likely deprotonated in the partly oxidized P^{1+} state, thereby forming a bond to Fe6. Likewise, the backbone amide group of Cys88 is deprotonated in the doubly oxidized P^{2+} state, forming a bond to Fe5. The calculations also confirm the two conformations of the Pcluster in the atomicresolution crystal structure of the enzyme, representing the P^{N} and P^{2+} states, but show that the finer differences between the two structures are not fully reflected in the crystal structure, because the coordinates of only two atoms differ between the two conformations. However, the recent crystal structure of the P^{1+} state seems to be of lower quality with many dubious FeFe and FeS distances. Quantum refinement of this structure indicates that it is a mixture of the P^{1+} and P^{2+} states but confirms that the side chain of Ser188 is most likely deprotonated in both states. TPSS gives structures that are appreciably closer to the crystal structures than does B3LYP. In addition, we have studied all 1648 possible brokensymmetry states of the four oxidation states of the Pcluster with DFT in the one or two observed spin states. For the reduced P^{N} state, we can settle the most likely state from the calculated energies and geometries. However, for the more oxidized states there are large differences in the predictions obtained with the two DFT methods.
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 author
 Cao, Lili ^{LU} ; Börner, Melanie C. ; Bergmann, Justin ^{LU} ; Caldararu, Octav ^{LU} and Ryde, Ulf ^{LU}
 organization
 publishing date
 20190805
 type
 Contribution to journal
 publication status
 published
 subject
 in
 Inorganic Chemistry
 volume
 58
 issue
 15
 pages
 19 pages
 publisher
 The American Chemical Society (ACS)
 external identifiers

 scopus:85070953097
 pmid:31282663
 ISSN
 00201669
 DOI
 10.1021/acs.inorgchem.9b00400
 project
 Computational Studies of Nitrogenase
 language
 English
 LU publication?
 yes
 id
 a972e49aaaad465fb5aa3b94be7f0130
 date added to LUP
 20191011 16:28:54
 date last changed
 20220511 22:12:39
@article{a972e49aaaad465fb5aa3b94be7f0130, abstract = {{<p>We have studied the geometry and electronic structure of the Pcluster in nitrogenase in four oxidation states: P<sup>N</sup>, P<sup>1+</sup>, P<sup>2+</sup>, and P<sup>3+</sup>. We have employed combined quantum mechanical and molecular mechanical (QM/MM) calculations, using two different densityfunctional theory methods, TPSS and B3LYP. The calculations confirm that the side chain of Ser188 is most likely deprotonated in the partly oxidized P<sup>1+</sup> state, thereby forming a bond to Fe6. Likewise, the backbone amide group of Cys88 is deprotonated in the doubly oxidized P<sup>2+</sup> state, forming a bond to Fe5. The calculations also confirm the two conformations of the Pcluster in the atomicresolution crystal structure of the enzyme, representing the P<sup>N</sup> and P<sup>2+</sup> states, but show that the finer differences between the two structures are not fully reflected in the crystal structure, because the coordinates of only two atoms differ between the two conformations. However, the recent crystal structure of the P<sup>1+</sup> state seems to be of lower quality with many dubious FeFe and FeS distances. Quantum refinement of this structure indicates that it is a mixture of the P<sup>1+</sup> and P<sup>2+</sup> states but confirms that the side chain of Ser188 is most likely deprotonated in both states. TPSS gives structures that are appreciably closer to the crystal structures than does B3LYP. In addition, we have studied all 1648 possible brokensymmetry states of the four oxidation states of the Pcluster with DFT in the one or two observed spin states. For the reduced P<sup>N</sup> state, we can settle the most likely state from the calculated energies and geometries. However, for the more oxidized states there are large differences in the predictions obtained with the two DFT methods.</p>}}, author = {{Cao, Lili and Börner, Melanie C. and Bergmann, Justin and Caldararu, Octav and Ryde, Ulf}}, issn = {{00201669}}, language = {{eng}}, month = {{08}}, number = {{15}}, pages = {{96729690}}, publisher = {{The American Chemical Society (ACS)}}, series = {{Inorganic Chemistry}}, title = {{Geometry and Electronic Structure of the PCluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement}}, url = {{http://dx.doi.org/10.1021/acs.inorgchem.9b00400}}, doi = {{10.1021/acs.inorgchem.9b00400}}, volume = {{58}}, year = {{2019}}, }