Supporting information (SI)
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1 Supporting information (SI) Revisiting the Mössbauer isomer shifts of the FeMoco cluster of nitrogenase and the cofactor charge Ragnar Bjornsson,*,, Frank Neese, Serena DeBeer*,, Max Planck Institute for Chemical Energy Conversion, Stiftstr , Mülheim an der Ruhr, Germany Current affiliation: Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States Contents: 1. Fe-Fe/Mo-Fe bond length comparison of TPSSh and X-ray structure 2. Localized orbital analysis 3. Mössbauer calibration details 4. Cartesian coordinates of FeMoco and P-cluster models.
2 1. Fe-Fe/Mo-Fe bond length comparison of X-ray crystal structure and TPSSh optimized BS-DFT structure Both the FeMoco crystal structure and TPSSh-optimized structure (optimized for BS7-235) reveals notable differences in Fe-Fe bond lengths in the cofactor, suggesting the presence of delocalized pairs in both cases (although assignment is not completely obvious). In the BS7-235 spin isomer, the Fe-Fe delocalized pairs are located on Fe1-Fe4 (spin-up), Fe2-Fe3 (spindown) and Fe6-Fe7 (spin-up). Calculating a different spin isomer than BS7-235 would change the location of these delocalized pairs. X-ray structure 3U7Q Fe2 r=2.576 Å Fe6 r=2.669 Å r=2.672 Å r=2.601 Å r=2.674 Å Fe1 Fe1-Fe2: Å Fe1-Fe3: Å Fe1-Fe4: Å r=2.668 Å r=2.655 Å r=2.654 Å Fe4 Fe3 r=2.641 Å r=2.583 Å r=2.612 Å r=2.632 Å Fe5 Fe7 r=2.627 Å r=2.681 Å r=2.727 Å Mo Mo-Fe6: Å Mo-Fe7: Å Mo-Fe5: Å Fe2-Fe3: Å Fe3-Fe4: Å Fe2-Fe4: Å Fe2-Fe6: Å Fe3-Fe7: Å Fe4-Fe5: Å Fe5-Fe6: Å Fe5-Fe7: Å Fe6-Fe7: Å TPSSh Fe2 r=2.561 Å Fe6 r=2.638 Å r=2.600 Å r=2.501 Å r=2.590 Å Fe1 Fe1-Fe2: Å Fe1-Fe3: Å Fe1-Fe4: Å r=2.645 Å r=2.590 Å r=2.594 Å Fe4 Fe3 r=2.571 Å r=2.577 Å r=2.572 Å r=2.562 Å Fe5 Fe7 r=2.564 Å r=2.562 Å r=2.666 Å Mo Mo-Fe6: Å Mo-Fe7: Å Mo-Fe5: Å Fe2-Fe3: Å Fe3-Fe4: Å Fe2-Fe4: Å Fe2-Fe6: Å Fe3-Fe7: Å Fe4-Fe5: Å Fe5-Fe6: Å Fe5-Fe7: Å Fe6-Fe7: Å Figure S1. Comparison of Fe-Fe and Mo-Fe bond lengths in crystal structure (top) and TPSSh-optimized structure for the BS7-235 solution (bottom).
3 2. Localized orbital analysis Localized orbitals were calculated using the Pipek-Mezey approach on the MS=3/2 brokensymmetry solution of FeMoco with the BP86, TPSSh and B3LYP functional. Figure S2 below shows the localized orbitals for the delocalized electrons in FeMoco that were used to make the approximate oxidation state assignment. Localized orbitals for the 5 majority-spin d-electrons on Fe atoms are not shown for clarity. The isosurfaces are from the TPSSh calculation but also shown are the localized orbital populations for BP86, TPSSh and B3LYP. Fe-Fe: BP86: 51 % and 45 % TPSSh: 52 % and 43 % B3LYP: 52 % and 42 % Mo-Fe: BP86: 55 % and 43 % TPSSh: 58 % and 40 % B3LYP: 60 % and 38 % Fe-Fe: BP86: 47 % and 45 % TPSSh: 43 % and 49 % B3LYP: 41 % and 53 % S S Fe2.5+ Fe Fe2.5+ S Fe Fe Fe2.5+ S C S Fe Mo Fe S Fe2.5+ Fe2+ Mo3+ S Fe Fe Fe3+ S Fe3+ S Fe-Fe: BP86: 54 % and 47 % TPSSh: 62 % and 38 % B3LYP: 69 % and 32 % Mo-Fe: BP86: 60 % and 37 % TPSSh: 71 % and 26 % B3LYP: 76 % and 20 % Mo-Fe: BP86: 58 % and 39 % TPSSh: 68 % and 29 % B3LYP: 73 % and 24 % Figure S2. The approximate electronic structure and spin diagram from Figure 4 in the main article and the localized orbitals (TPSSh isosurfaces) for the delocalized electrons (orange arrows; denoting minory 1/2 spin) of the MS=3/2 broken-symmetry solution in FeMoco that were used to make the approximate oxidation state assignments. The large white arrows denote majority spin vectors (spin 5/2) on each Fe. Also shown are percentage contributions from each atom to the orbital for BP86, TPSSh and B3LYP.
4 3. Mössbauer calibration details 3 different calibration tests sets were used: a) test set from Römelt et al. See experimental Mössbauer references in earlier studies by Neese et al. :Neese, F. Inorg. Chim. Acta 2002, 337, 181. and Sinnecker, S.; Slep, L. D; Bill, E.; Neese, F. Inorg. Chem. 2005, 44, b) Iron-sulfur compound test set compiled from the non-nitrosyl subset from Sandala et al. and additional compounds used by Szilagyi et al. in their calibration. See table below. Sandala, G. M.; Hopmann, K. H.; Ghosh, A.; and Noodleman, L. J. Chem. Theory Comput. 2011, 7, and Harris, T. V. and Szilagyi, R. K. Inorg. Chem. 2011, 50, c) A combined test set of molecules in a) and b). XYZ files of all compounds (TPSSh-optimized geometries) are available in a compressed archive. Table S1. The compounds in the iron-sulfur molecule calibration test set. References for the experimental Mössbauer isomer shifts can be found in the study by Sandala et al. and Szilagyi et al. Cambridge ID Spin state Fe oxidation states Exp. Isomer shift [Fe(SEt 4 )] 1- CANDAW10 5/2 Fe [Fe 4 S 4 (OPh) 4 ] 2- CAPGAB 0 4*Fe [Fe 4 S 4 (SCH 2 CO 2 Et) 4 ] 2- CEQYAY 0 4*Fe [Fe 4 S 4 (SEtOH) 4 ] 2- CESSEY 0 4*Fe [Fe 4 S 4 (SPh) 2 Cl 2 ] 2- CIYKUQ 0 2*Fe 2.5+ (SPh ligand) *Fe 2.5+ (Cl ligand) 0.51 [Fe 4 S 4 (OPh) 2 Cl 2 ] 2- CIYLAX 0 2*Fe 2.5+ (OPh ligand) *Fe 2.5+ (Cl ligand) 0.52 [Fe 2 S 2 (C 4 H 4 N) 4 ] 2- CONSED10 0 2*Fe [Fe(SEt) 4 ] 2-2 Fe [Fe 4 S 4 (SPh) 4 ] 2- FEMJAI02 0 4*Fe [Fe 2 S 2 (OPh-p-CH 3 ) 4] 2- GIBCUP 0 2*Fe [Fe 4 S 4 Cl 4 ] 2- NUSROI 0 4*Fe [Fe(SPh) 4 ] 2- PTHPFE10 2 Fe [FeS 4 C 8 O 4 ] 2- PTSQFE10 2 Fe [Fe 2 S 2 ((S 2 -o-xyl) 2 ] 2- XLDTSF 0 2*Fe
5 All geometries were optimized using an ORCA example inputfile like this (spin-coupled iron-sulfur clusters were optimized on the low-spin broken-symmetry surface):! UKS TPSSh COSMO OPT ZORA RIJCOSX D3BJ def2-tzvp def2-tzvp/j TightSCF Grid5 FinalGrid6 SlowConv %method IntaccX 4.01,4.01,4.34 # Changing the 3 radial grids GridX 1,1,2 # Changing the 3 angular grids end %method SpecialGridAtoms 26 SpecialGridIntAcc 7 end *xyzfile charge mult... * All Mössbauer single-point calculations used an inputfile like below (B3LYP functional in this case):! SP UKS B3LYP NORI def2-tzvp DKH2 TightSCF Grid5 FinalGrid6 SlowConv COSMO %basis newgto Fe "CP(PPP)" end end %method SpecialGridAtoms 26 SpecialGridIntAcc 7 end *xyzfile charge mult... * %eprnmr nuclei = all 26 {rho, fgrad} end Table S2. Calibration parameters for each functional for each type of calibration used. Parameters α and β in the equation δ iso =α(ρ 0 C)+β were fitted to experimental isomer shifts and computed electron densities for molecules in 3 different test sets. Parameter C was chosen to have approximately the same value as the calculated ρ 0 values for each functional. Whole test set Römelt test set Iron-sulfur test set BP TPSSh B3LYP BP TPSSh B3LYP BP TPSSh B3LYP α α α β β β C C C
6 4. Cartesian coordinates of FeMoco and P-cluster geometries ZORA-TPSSh optimized structures: [MoFe 7 S 9 C] 3- : Fe Fe Fe Fe Fe Fe Fe Mo C S S S S S S S S S S C N C N N C C C O N C C N C C N C C C C C C C O N C
7 C O C N C O N C C O N C C O N C C O N C C C C N C N N O C C N C C N C C C C C C C O O O O O O O O O
8 O O O O O O O O O O O H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
9 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
10 H H H H H H H H H H H C C O N C C O H H H H H H H H H H H H [MoFe 7 S 9 C] 1- : Fe Fe Fe Fe Fe Fe Fe Mo C S S S S S S S S S
11 S C N C N N C C C O N C C N C C N C C C C C C C O N C C O C N C O N C C O N C C O N C C O N C C C C
12 N C N N O C C N C C N C C C C C C C O O O O O O O O O O O O O O O O O O O O H H H H H H H H H H H H
13 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
14 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H C C O N C C O H H H H H
15 H H H H H H H [MoFe 7 S 9 C] 1+ : Fe Fe Fe Fe Fe Fe Fe Mo C S S S S S S S S S S C N C N N C C C O N C C N C C N C C C C C
16 C C O N C C O C N C O N C C O N C C O N C C O N C C C C N C N N O C C N C C N C C C C C C C O O O O
17 O O O O O O O O O O O O O O O O H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
18 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
19 H H H H H H H H H H H H H H H H C C O N C C O H H H H H H H H H H H H P-cluster model (model charge -4): Fe Fe Fe Fe Fe Fe Fe Fe C S C S C
20 S C S C S C S S S S S S S S H H H H H H H H H H H H H H H H H H X-ray crystal structures: FeMoco: Fe Fe Fe Fe Fe Fe Fe Mo C S S S S
21 S S S S S S C N C N N C C C O N C C N C C N C C C C C C C O N C C O C N C O N C C O N C C O N C C O
22 N C C C C N C N N O C C N C C N C C C C C C C O O O O O O O O O O O O O O O O O O O O H H H H H H H
23 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
24 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H C C O N C C O
25 H H H H H H H H H H H H P-cluster model (model charge -4): Fe Fe Fe Fe Fe Fe Fe Fe C S C S C S C S C S C S S S S S S S S H H H H H H H
26 H H H H H H H H H H H
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