Axial and equatorial ligand effects on biomimetic cysteine dioxygenase model complexes

DFT insights into the mechanism of O2 activation catalyzed by a structural and functional model of cysteine dioxygenase with tris(2-pyridyl)methane-based ligand architecture

Cysteine dioxygenation is an important step in the metabolism of toxic L-cysteine (Cys) in the human body, carried out by cysteine dioxygenase enzyme (CDO). The disruption of this process is found to elicit neurological health issues. This work reports a computational investigation of mechanistic aspects of this reaction, using a recently reported tris(2-pyridyl)methane-based biomimetic model complex of CDO. The computed results indicate that, the initial SO2 bond formation process is the slowest step in the S-dioxygenation process, possessing an activation barrier of 12.7 kcal/mol. The remaining steps were found to be downhill requiring very small activation energies. The transition states were found to undergo spin crossover between triplet and quintet states, while the singlet surface remained unstable throughout the entire reaction. In essence, the mechanistic scheme and multistate reactivity pattern together with the relatively small computed rate-limiting activation barrier as well as the exothermic formation energy demonstrate that the model complex is an efficient biomimetic CDO model. In addition, the study also substantiates the involvement of Fe(IV)oxido intermediates in the mechanism of S-dioxygenation by the chosen model complex. The insights derived from the O₂ activation process might pave way for development of more accurate CDO model catalysts that might be capable of even more efficiently mimicking the geometric, spectroscopic and functional features of the CDO enzyme.

Chemoselectivity in the Oxidation of Cycloalkenes with a Non-Heme Iron(IV)-Oxo-Chloride Complex: Epoxidation vs. Hydroxylation Selectivity

We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]⁺, which models the active species in iron-dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways: allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze effects of the substrate, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase.

An iron-oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase

Combined spectroscopic, kinetic and computational studies provide first evidence of a short-lived intermediate in the catalytic cycle of cysteine dioxygenase.

Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm.

Synthesis, X-ray Structures, Electronic Properties, and O2/NO Reactivities of Thiol Dioxygenase Active-Site Models

Mononuclear non-heme iron complexes that serve as structural and functional mimics of the thiol dioxygenases (TDOs), cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), have been prepared and characterized with crystallographic, spectroscopic, kinetic, and computational methods. The high-spin Fe(II) complexes feature the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (^Ph2TIP) ligand that replicates the three histidine (3His) triad of the TDO active sites. Further coordination with bidentate l-cysteine ethyl ester (CysOEt) or cysteamine (CysAm) anions yielded five-coordinate (5C) complexes that resemble the substrate-bound forms of CDO and ADO, respectively. Detailed electronic-structure descriptions of the [Fe(^Ph2TIP)(L_S,N)]BPh₄ complexes, where L_S,N = CysOEt (1) or CysAm (2), were generated through a combination of spectroscopic techniques [electronic absorption, magnetic circular dichroism (MCD)] and density functional theory (DFT). Complexes 1 and 2 decompose in the presence of O₂ to yield the corresponding sulfinic acid (RSO₂H) products, thereby emulating the reactivity of the TDO enzymes and related complexes. Rate constants and activation parameters for the dioxygenation reactions were measured and interpreted with the aid of DFT calculations for O₂-bound intermediates. Treatment of the TDO models with nitric oxide (NO)-a well-established surrogate of O₂-led to a mixture of high-spin and low-spin {FeNO}⁷ species at low temperature (-70 °C), as indicated by electron paramagnetic resonance (EPR) spectroscopy. At room temperature, these Fe/NO adducts convert to a common species with EPR and infrared (IR) features typical of cationic dinitrosyl iron complexes (DNICs). To complement these results, parallel spectroscopic, computational, and O₂/NO reactivity studies were carried out using previously reported TDO models that feature an anionic hydrotris(3-phenyl-5-methyl-pyrazolyl)borate (^Ph,MeTp^-) ligand. Though the O₂ reactivities of the ^Ph2TIP- and ^Ph,MeTp-based complexes are quite similar, the supporting ligand perturbs the energies of Fe 3d-based molecular orbitals and modulates Fe-S bond covalency, suggesting possible rationales for the presence of neutral 3His coordination in CDO and ADO.

Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase

In mammals, the non-heme iron enzyme cysteine dioxygenase (CDO) helps regulate Cys levels through converting Cys to Cys sulfinic acid. Its activity is in part modulated by the formation of a Cys93-Tyr157 crosslink that increases its catalytic efficiency over 10-fold. Here, 21 high-resolution mammalian CDO structures are used to gain insight into how the Cys-Tyr crosslink promotes activity and how select competitive inhibitors bind. Crystal structures of crosslink-deficient C93A and Y157F variants reveal similar ~1.0-Å shifts in the side chain of residue 157, and both variant structures have a new chloride ion coordinating the active site iron. Cys binding is also different from wild-type CDO, and no Cys-persulfenate forms in the C93A or Y157F active sites at pH6.2 or 8.0. We conclude that the crosslink enhances activity by positioning the Tyr157 hydroxyl to enable proper Cys binding, proper oxygen binding, and optimal chemistry. In addition, structures are presented for homocysteine (Hcy), D-Cys, thiosulfate, and azide bound as competitive inhibitors. The observed binding modes of Hcy and D-Cys clarify why they are not substrates, and the binding of azide shows that in contrast to what has been proposed, it does not bind in these crystals as a superoxide mimic.

Photoinitiated Reactivity of a Thiolate-Ligated, Spin-Crossover Nonheme {FeNO}(7) Complex with Dioxygen

The nonheme iron complex, [Fe(NO)(N3PyS)]BF4, is a rare example of an {FeNO}(7) species that exhibits spin-crossover behavior. The comparison of X-ray crystallographic studies at low and high temperatures and variable-temperature magnetic susceptibility measurements show that a low-spin S = 1/2 ground state is populated at 0-150 K, while both low-spin S = 1/2 and high-spin S = 3/2 states are populated at T > 150 K. These results explain the observation of two N-O vibrational modes at 1737 and 1649 cm(-1) in CD3CN for [Fe(NO)(N3PyS)]BF4 at room temperature. This {FeNO}(7) complex reacts with dioxygen upon photoirradiation with visible light in acetonitrile to generate a thiolate-ligated, nonheme iron(III)-nitro complex, [Fe(III)(NO2)(N3PyS)](+), which was characterized by EPR, FTIR, UV-vis, and CSI-MS. Isotope labeling studies, coupled with FTIR and CSI-MS, show that one O atom from O2 is incorporated in the Fe(III)-NO2 product. The O2 reactivity of [Fe(NO)(N3PyS)]BF4 in methanol is dramatically different from CH3CN, leading exclusively to sulfur-based oxidation, as opposed to NO· oxidation. A mechanism is proposed for the NO· oxidation reaction that involves formation of both Fe(III)-superoxo and Fe(III)-peroxynitrite intermediates and takes into account the experimental observations. The stability of the Fe(III)-nitrite complex is limited, and decay of [Fe(III)(NO2)(N3PyS)](+) leads to {FeNO}(7) species and sulfur oxygenated products. This work demonstrates that a single mononuclear, thiolate-ligated nonheme {FeNO}(7) complex can exhibit reactivity related to both nitric oxide dioxygenase (NOD) and nitrite reductase (NiR) activity. The presence of the thiolate donor is critical to both pathways, and mechanistic insights into these biologically relevant processes are presented.

A trispyrazolylborato iron cysteinato complex efficiently mimics the cysteine dioxygenation process: mechanistic insights

The O2 activation process by a CDO biomimetic system has been herein investigated to gain mechanistic details on the unknown reaction mechanism. The outcomes of the DFT study show that the functional model efficiently mimics the enzymatic process, the reaction proceeding with a feasible activation barrier via multistate reactivity patterns.

Applications of density functional theory to iron-containing molecules of bioinorganic interest

The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.

Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes

In this article, we present density functional theory (DFT) calculations on the iron(IV)-oxo catalyzed methane C-H activation reactions for complexes in which the Fe(IV)═O core is surrounded by five negatively charged ligands. We found that it follows a hybrid pathway that mixes features of the classical σ- and π-pathways in quintet surfaces. These calculations show that the Fe-O-H arrangement in this hybrid pathway is bent in sharp contrast to the collinear character as observed for the classical quintet σ-pathways before. The calculations have also shown that it is the equatorial ligands that play key roles in tuning the reactivity of Fe(IV)═O complexes. The strong π-donating equatorial ligands employed in the current study cause a weak π(FeO) bond and thereby shift the electronic accepting orbitals (EAO) from the vertically orientated O pz orbital to the horizontally orientated O px. In addition, all the equatorial ligands are small in size and would therefore be expected have small steric effects upon substrate horizontal approaching. Therefore, for the small and strong π-donating equatorial ligands, the collinear Fe-O-H arrangement is not the best choice for the quintet reactivity. This study adds new element to iron(IV)-oxo catalyzed C-H bond activation reactions.

Preparation of non-heme {FeNO}7 models of cysteine dioxygenase: sulfur versus nitrogen ligation and photorelease of nitric oxide

We present the synthesis and spectroscopic characterization of [Fe(NO)(N3PyS)]BF4 (3), the first structural and electronic model of NO-bound cysteine dioxygenase. The nearly isostructural all-N-donor analogue [Fe(NO)(N4Py)](BF4)2 (4) was also prepared, and comparisons of 3 and 4 provide insight regarding the influence of S vs N ligation in {FeNO}(7) species. One key difference occurs upon photoirradiation, which causes the fully reversible release of NO from 3, but not from 4.

Synthesis and ligand non-innocence of thiolate-ligated (N4S) Iron(II) and nickel(II) bis(imino)pyridine complexes

The known iron(II) complex [Fe(II)(LN3S)(OTf)] (1) was used as starting material to prepare the new biomimetic (N4S(thiolate)) iron(II) complexes [Fe(II)(LN3S)(py)](OTf) (2) and [Fe(II)(LN3S)(DMAP)](OTf) (3), where LN3S is a tetradentate bis(imino)pyridine (BIP) derivative with a covalently tethered phenylthiolate donor. These complexes were characterized by X-ray crystallography, ultraviolet-visible (UV-vis) spectroscopic analysis, (1)H nuclear magnetic resonance (NMR), and Mössbauer spectroscopy, as well as electrochemistry. A nickel(II) analogue, [Ni(II)(LN3S)](BF4) (5), was also synthesized and characterized by structural and spectroscopic methods. Cyclic voltammetric studies showed 1-3 and 5 undergo a single reduction process with E(1/2) between -0.9 V to -1.2 V versus Fc(+)/Fc. Treatment of 3 with 0.5% Na/Hg amalgam gave the monoreduced complex [Fe(LN3S)(DMAP)](0) (4), which was characterized by X-ray crystallography, UV-vis spectroscopic analysis, electron paramagnetic resonance (EPR) spectroscopy (g = [2.155, 2.057, 2.038]), and Mössbauer (δ = 0.33 mm s(-1); ΔE(Q) = 2.04 mm s(-1)) spectroscopy. Computational methods (DFT) were employed to model complexes 3-5. The combined experimental and computational studies show that 1-3 are 5-coordinate, high-spin (S = 2) Fe(II) complexes, whereas 4 is best described as a 5-coordinate, intermediate-spin (S = 1) Fe(II) complex antiferromagnetically coupled to a ligand radical. This unique electronic configuration leads to an overall doublet spin (S(total) = 1/2) ground state. Complexes 2 and 3 are shown to react with O2 to give S-oxygenated products, as previously reported for 1. In contrast, the monoreduced 4 appears to react with O2 to give a mixture of sulfur oxygenates and iron oxygenates. The nickel(II) complex 5 does not react with O2, and even when the monoreduced nickel complex is produced, it appears to undergo only outer-sphere oxidation with O2.