Sulfide Oxidation by O2: Synthesis, Structure and Reactivity of Novel Sulfide-Incorporated Fe(II) Bis(imino)pyridine Complexes

Using machine learning methods to predict the diabatic bond dissociation energy of non-heme iron complexes

Bond dissociation energy (BDE) is an important property in chemical research. In the process of non-heme iron complex catalytic reactions, diabatic BDE has a significant impact on the selectivity of halogenation and hydroxylation reactions. Measuring or calculating BDE by using traditional experimental or theoretical methods is often expensive and complex, so we propose the first application of machine learning on non-heme iron complexes to predict and rationalize the diabatic BDEs of Fe-X and Fe-OH bonds in order to assist in the study of selectivity in non-heme iron complex catalytic reactions. We built a reliable and representative dataset containing over 600 types of non-heme iron complexes and used density functional theory (DFT) to calculate nearly 900 diabatic BDE for machine learning. In terms of model training, we used 2D molecular fingerprints and 3D descriptors as inputs to train the regression model. The results indicate that the ensemble algorithm combined with Morgan fingerprints can effectively predict the diabatic BDEs of non-heme iron complexes. Using the Gradient Boosting Regressor (GBR) model and Morgan fingerprints can achieve an accurate prediction of R2 = 0.791 and the mean absolute error (MAE) = 10.23 kcal mol-1. The incorporation of 3D descriptors significantly improves the predictive performance of molecular fingerprints other than Morgan fingerprints. Notably, the SOAP descriptor effectively captures key 3D molecular information, making it particularly advantageous for predicting isomers with large ΔBDE. However, when the ΔBDE of isomers in the dataset is small, Morgan fingerprints remain the more efficient choice.

Activation of Dioxygen by a Mononuclear Nonheme Iron Complex: Sequential Peroxo, Oxo, and Hydroxo Intermediates

The activation of dioxygen by Fe^II(Me₃TACN)(S₂SiMe₂) (1) is reported. Reaction of 1 with O₂ at -135 °C in 2-MeTHF generates a thiolate-ligated (peroxo)diiron complex Fe^III₂(O₂)(Me₃TACN)₂(S₂SiMe₂)₂ (2) that was characterized by UV-vis (λ_max = 300, 390, 530, 723 nm), Mössbauer (δ = 0.53, |ΔE_Q| = 0.76 mm s^-1), resonance Raman (RR) (ν(O-O) = 849 cm^-1), and X-ray absorption (XAS) spectroscopies. Complex 2 is distinct from the outer-sphere oxidation product 1^ox (UV-vis (λ_max = 435, 520, 600 nm), Mössbauer (δ = 0.45, |ΔE_Q| = 3.6 mm s^-1), and EPR (S = 5/2, g = [6.38, 5.53, 1.99])), obtained by one-electron oxidation of 1. Cleavage of the peroxo O-O bond can be initiated either photochemically or thermally to produce a new species assigned as an Fe^IV(O) complex, Fe^IV(O)(Me₃TACN)(S₂SiMe₂) (3), which was identified by UV-vis (λ_max = 385, 460, 890 nm), Mössbauer (δ = 0.21, |ΔE_Q| = 1.57 mm s^-1), RR (ν(Fe^IV═O) = 735 cm^-1), and X-ray absorption spectroscopies, as well as reactivity patterns. Reaction of 3 at low temperature with H atom donors gives a new species, Fe^III(OH)(Me₃TACN)(S₂SiMe₂) (4). Complex 4 was independently synthesized from 1 by the stoichiometric addition of a one-electron oxidant and a hydroxide source. This work provides a rare example of dioxygen activation at a mononuclear nonheme iron(II) complex that produces both Fe^III-O-O-Fe^III and Fe^IV(O) species in the same reaction with O₂. It also demonstrates the feasibility of forming Fe/O₂ intermediates with strongly donating sulfur ligands while avoiding immediate sulfur oxidation.

A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme β-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase

The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinuclear iron cluster that is reduced to the diferrous state (WTR) to initiate O2 activation. However, rapid O2 activation occurs only when WTR is bound to CmlP, the NRPS to which l-PAPA is covalently attached. Here the X-ray crystal structure of WTR is reported, which is very similar to that of the as-isolated diferric enzyme in which the irons are coordinately saturated. X-ray absorption spectroscopy is used to investigate the WTR cluster ligand structure as well as the structures of WTR in complex with a functional CmlP variant (CmlPAT) with and without l-PAPA attached. It is found that formation of the active WTR:CmlPAT-l-PAPA complex converts at least one iron of the cluster from six- to five-coordinate by changing a bidentately bound amino acid carboxylate to monodentate on Fe1. The only bidentate carboxylate in the structure of WTR is E377. The crystal structure of the CmlA variant E377D shows only monodentate carboxylate coordination. Reduced E377D reacts rapidly with O2 in the presence or absence of CmlPAT-l-PAPA, showing loss of regulation. However, this variant fails to catalyze hydroxylation, suggesting that E377 has the dual role of coupling regulation of O2 reactivity with juxtaposition of the substrate and the reactive oxygen species. The carboxylate shift in response to substrate binding represents a novel regulatory strategy for oxygen activation in diiron oxygenases.

X-ray absorption spectroscopic characterization of the diferric-peroxo intermediate of human deoxyhypusine hydroxylase in the presence of its substrate eIF5a

Human deoxyhypusine hydroxylase (hDOHH) is an enzyme that is involved in the critical post-translational modification of the eukaryotic translation initiation factor 5A (eIF5A). Following the conversion of a lysine residue on eIF5A to deoxyhypusine (Dhp) by deoxyhypusine synthase, hDOHH hydroxylates Dhp to yield the unusual amino acid residue hypusine (Hpu), a modification that is essential for eIF5A to promote peptide synthesis at the ribosome, among other functions. Purification of hDOHH overexpressed in E. coli affords enzyme that is blue in color, a feature that has been associated with the presence of a peroxo-bridged diiron(III) active site. To gain further insight into the nature of the diiron site and how it may change as hDOHH goes through the catalytic cycle, we have conducted X-ray absorption spectroscopic studies of hDOHH on five samples that represent different species along its reaction pathway. Structural analysis of each species has been carried out, starting with the reduced diferrous state, proceeding through its O2 adduct, and ending with a diferric decay product. Our results show that the Fe⋯Fe distances found for the five samples fall within a narrow range of 3.4-3.5 Å, suggesting that hDOHH has a fairly constrained active site. This pattern differs significantly from what has been associated with canonical dioxygen activating nonheme diiron enzymes, such as soluble methane monooxygenase and Class 1A ribonucleotide reductases, for which the Fe⋯Fe distance can change by as much as 1 Å during the redox cycle. These results suggest that the O2 activation mechanism for hDOHH deviates somewhat from that associated with the canonical nonheme diiron enzymes, opening the door to new mechanistic possibilities for this intriguing family of enzymes.

Oxidation of thiols to disulfides by dioxygen catalyzed by a bioinspired organocatalyst

2,3-Dihydro-2,2,2-triphenylphenanthro[9,10-d]-1,3,2-λ⁵-oxazaphosphole serves as good catalyst for the oxidation of thiophenol, cysteine and glutathione to their disulfides by molecular oxygen.

A novel iron complex containing an N,O-type bidentate oxazoline ligand: Synthesis, X-ray studies, DFT calculations and catalytic activity

A five-coordinated Fe(III) complex with the distorted trigonal bipyramidal configuration was synthesized by reactions of FeCl3⋅6H2O and 2-(2'-hydroxyphenyl)oxazoline (Hphox) as a bidentate ON donor oxazoline ligand. Complex [Fe(phox)2Cl] was fully characterized, including by single-crystal X-ray structure analysis. DFT calculations were accompanied with experimental results in order to obtain a deeper insight into the electronic structure and vibrational normal modes of complex. Oxidation of sulfides to sulfoxides in one-step was conducted by this complex as catalyst using urea hydrogen peroxide (UHP) in mixture of CH2Cl2/CH3OH (1:1) under air at room temperature. The results show that using this system in oxidation of sulfides, sulfoxides are obtained as the main products, together with variable amounts of sulfones (≤13%), depending on the nature of the substrate.