Theoretical analysis of C-F bond cleavage mediated by cob[I]alamin-based structures

Effect of the Nucleophile's Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study

In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br^-, I^-, HS^-, and S₂O₃^-2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R² = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.

Theoretical investigation of the mechanism for the reductive dehalogenation of methyl halides mediated by the CoI-based compounds cobalamin and cobaloxime

Theoretical calculations focusing on the cleavage of the C-X bond in methyl halides (CH₃X; X = Cl, Br, I) as mediated by Co^I-based systems have been carried out using the hybrid functional ωB97-XD together with the basis set 6-311++G(2d,2p). A total of seven Co^I-based compounds were evaluated: cob[I]alamin (Co^ICbl) in its base-on form and cobaloxime (Co^ICbx) with either no ligand or different ligands (either pyridine (PYR), tributylphosphine (TBP), dimethyl sulfide (DMS), cyclohexylisocyanide (CI), or 5,6-dimethylbenzimidazole (DMB)) at the lower axial position. For the large Co^ICbl system, an ONIOM scheme was employed, where the high layer was described at the DFT level and the low layer was computed using the semi-empirical method PM6. A full DFT model was employed for the Co^ICbx cases. An S_N2-like mechanism was evaluated in all cases. The intrinsic reaction coordinate profiles suggested early transition states with activation energies of ≈ 12 kcal/mol, ≈ 10 kcal/mol, and ≈ 5 kcal/mol for C-Cl, C-Br, and C-I cleavage, respectively, which is consistent with the leaving group abilities of these halides. The evolutions of the atomic charges in and the bond orders of Co-C and C-X were computed, and the results confirmed the existence of early transition states (δB_av≈ 40%), where the polarization C^δ+-X^δ- (%E_v ≈ 43%) is the determining factor in the reaction process. Finally, a comparison of all the determined parameters showed that the reaction in the DMB-Co^ICbx system resembles the process that occurs in the larger Co^ICbl, suggesting that the former system could be a reliable model for the study of reductive dehalogenation mediated by vitamin B₁₂, which is key to the anaerobic microbiological treatment of halocarbon contaminants.