First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of CO2 to/from the C-Cluster

In view of the depletion of fossil fuel reserves and climatic effects of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase (Ni-CODH) enzymes have attracted increasing interest in recent years for their capability to selectively catalyze the reversible reduction of CO2 to CO (CO2 + 2H+ + 2e– CO + H2O). The possibility of converting the greenhouse gas CO2 into useful materials that can be used as synthetic building blocks or, remarkably, as carbon fuels makes Ni-CODH a very promising target for reverse-engineering studies. In this context, in order to provide insights into the chemical principles underlying the biological catalysis of CO2 activation and reduction, quantum mechanics calculations have been carried out in the framework of density functional theory (DFT) on different-sized models of the Ni-CODH active site. With the aim of uncovering which stereoelectronic properties of the active site (known as the C-cluster) are crucial for the efficient binding and release of CO2, different coordination modes of CO2 to different forms and redox states of the C-cluster have been investigated. The results obtained from this study highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. In particular, the protonation state of His93 is found to be crucial for promoting the binding or the dissociation of CO2. The oxidation state of the C-cluster is also shown to be critical. CO2 binds to Cred2 according to a dissociative mechanism (i.e., CO2 binds to the C-cluster after the release of possible ligands from Feu) when His93 is doubly protonated. CO2 can also bind noncatalytically to Cred1 according to an associative mechanism (i.e., CO2 binding is preceded by the binding of H2O to Feu). Conversely, CO2 dissociates when His93 is singly protonated and the C-cluster is oxidized at least to the Cint redox state.

O, HN (carbonyl oxygen forms an H-bond with the amidic hydrogen of Ala97, whereas HN forms an H-bond with the carbonyl oxygen atom of Gly89 in a α-helix. HN has been added at 1.02 Å from N in the C-N-Cα plane, and constrained at that position)

Ser94
N, Cα def-SVP Cα (terminal atom), HN (HN forms an H-bond with the carbonyl oxygen atom of Ala90 in a α-helix. HN has been added at 1.02 Å from N in the C-N-Cα plane, and constrained at that position)  Scheme S1 Schematic representation of all possible non-equivalent spin coupling schemes for the C-cluster, in which two pairs of Fe atoms are coupled antiferromagnetically.

Table S4
Relative energies (in kcal/mol) for all possible spin coupling schemes of all species investigated in this work, optimized at the RI-BP86/def-TZVP level in COSMO with ε=4, using the SM model in the Cred1, Cint and Cred2 redox states of the C-cluster. NBO atomic charges and Mulliken spin densities (in parenthesis) of selected atoms of the C-cluster and of the layers L1 and L2 (corresponding respectively to the blue and red layers of the BS coupling schemes shown in Scheme S1) are also indicated.
a) unbound forms of the C-cluster Table S5 Energies (in Hartree) and relative energies (in kcal/mol) for S = 0, S = 1 and S = 2 spin states of the more relevant species in the Cint redox state discussed in this work, optimized at the RI-BP86/def-TZVP-SVP level in COSMO with ε=4, using the LM H+,K+ and the LM H0,K+ models.  * During geometry optimization, a proton is transferred from His93 to the OHligand to form a H2O molecule that dissociates from the C-cluster. § During geometry optimization, a proton is transferred from Lys563 to the OHligand to form a H2O molecule. ≠ During geometry optimization, a proton is transferred from Lys5633 to the OHligand to form a H2O molecule that dissociates from the C-cluster.  Figure S1 Superimposition of the optimized geometry of a) Cred2-μCO2, b) Cred2-tCO2 and c) Cred2-CO2-OH optimized using the LM H+,K+ (red), LM H0,K+ (blue) and LM H+,K0 (white) models of the active site. S17 Table S8 RMSD values calculated for the structures of the μCO2-bound metallic cluster, the [NiFe4S4] core and the CO2 ligand extracted by the theoretical geometries, compared to the 3B52 and 4UDX crystal structures.    Table S11 NBO atomic charges and Mulliken spin densities (in parenthesis) of selected atoms of the C-cluster and of the layers L1 and L2 (corresponding respectively to the blue and red layers of the BS coupling schemes shown in Scheme S1) for the unbound form of the C-cluster and μCO2 and tCO2 adducts in the Cred2, Cint and Cred1 redox states (in the most stable spin coupling scheme) optimized using the SM, LM H+, K+      Cint-CO2-OH-LM H0,K+ and d) Cred2/Cint-CO2-OH-LM H+,K0 formation process from the naked C-cluster, CO2

SM
and H2O. The proton that is transferred from His93 and Lys563 to the OH-bound C-cluster to form a H2Oadduct, is depicted in red and blue, respectively.